Serialized Form

  • Package gov.nih.mipav.model.algorithms

  • Package gov.nih.mipav.model.algorithms.filters.OpenCL.filters

  • Package gov.nih.mipav.model.dicomcomm

  • Package gov.nih.mipav.model.file

    • Class gov.nih.mipav.model.file.DTIParameters

      class DTIParameters extends Object implements Serializable

      • Serialized Fields

        • bMatrixVals
          double[][] bMatrixVals
        • bValues
          double[] bValues
        • gradients
          double[][] gradients
        • numVolumes
          int numVolumes

    • Class gov.nih.mipav.model.file.FileDicomKey

      class FileDicomKey extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -8327760986088567748L

      • Serialized Fields

        • key
          String key
          The dicom tag identifier in the format 'group,element'. 'x' is allowed in the group number for wildcards in the dicom dictionary. E.g., '0002,0010' or '50xx,00E1'.

    • Class gov.nih.mipav.model.file.FileDicomSQ

      class FileDicomSQ extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -6705966363824982534L

      • Serialized Fields

        • sequence
          Vector<FileDicomSQItem> sequence
          Sequences are composed of items (DICOM items) and store in a vector object.
        • writeAsUnknownLength
          boolean writeAsUnknownLength
          Whether the sequence should be written using an unknown length

    • Class gov.nih.mipav.model.file.FileDicomSQItem

      class FileDicomSQItem extends FileDicomTagTable implements Serializable

      • Serialized Fields

        • writeAsUnknownLength
          boolean writeAsUnknownLength
          Whether the sequence should be written using an unknown length

    • Class gov.nih.mipav.model.file.FileDicomTag

      class FileDicomTag extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -5648244595999602634L

      • Serialized Fields

        • element
          int element
          Integer element word (in hexadecimal).
        • group
          int group
          Integer group word (in hexadecimal).
        • length
          int length
          Length of the tag as defined in the input image.
        • tagInfo
          FileDicomTagInfo tagInfo
          Pointer to more information about this tag, read in and contained within the dicom dictionary.
        • value
          Object value
          Actual value of the tag (may be an array of elements).
        • valueRepresentation
          FileDicomTagInfo.VR valueRepresentation
          Value representation for this tag, if the tags in this dicom file have explicit VRs. If the dicom tags have implicit VRs, then the DicomDictionary VR is used.

    • Class gov.nih.mipav.model.file.FileDicomTagInfo

      class FileDicomTagInfo extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      3009696612758502873L

      • Serialized Fields

        • key
          FileDicomKey key
          The DICOM tag 'group,element' key indicating what tag this information pertains to.
        • keyword
          String keyword
          The tag keyword (no spaces).
        • name
          String name
          The real world DICOM tag name.
        • valueMultiplicity
          int valueMultiplicity
          Allowed value multiplicity (vm) for this tag.
        • valueRepresentation
          FileDicomTagInfo.VR valueRepresentation
          DICOM value representation (vr) for this tag.
        • version
          String version
          Version of the tag. Usually '2' or '3', although some tags get strings like 'GEM' or 'TSH' when the tag is from a private manufacturer.

    • Class gov.nih.mipav.model.file.FileDicomTagTable

      class FileDicomTagTable extends Object implements Serializable
      serialVersionUID:
      -7828203960779215940L

      • Serialized Fields

        • childTagTables
          FileDicomTagTable[] childTagTables
          A list of tag tables which point to this as their reference tag table.
        • isReferenceTagTable
          boolean isReferenceTagTable
          Whether this tag table is a reference table (meaning it contains all of the tags for a given fileInfo and does not need to refer anywhere else when retrieving values).
        • parentFileInfo
          FileInfoDicom parentFileInfo
          The dicom file info that this tag table belongs to. Used to update file info fields based on tag table changes.
        • referenceTagTable
          FileDicomTagTable referenceTagTable
          The reference table to check when a tag is not found in this table. If this table is a reference table, then the value should be this and no checking of the referenceTagTable should take place.
        • tagTable
          Hashtable<FileDicomKey,FileDicomTag> tagTable
          Tags unique to this slice, or all of the tags for this slice if this is a reference tag table.
        • vr_type
          FileInfoDicom.VRtype vr_type
          VR_type to indicate explicit/implicit nature of tags contained in tag table

    • Class gov.nih.mipav.model.file.FileImageXML.Thumbnail

      class Thumbnail extends JComponent implements Serializable
      serialVersionUID:
      6645327578121170860L

      • Serialized Fields

        • brightness
          int brightness
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • data
          int[] data
        • img
          Image img
          DOCUMENT ME!
        • imgHeight
          int imgHeight
          DOCUMENT ME!
        • imgWidth
          int imgWidth
          DOCUMENT ME!
        • memImage
          MemoryImageSource memImage
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoAfni

      class FileInfoAfni extends FileInfoBase implements Serializable
      serialVersionUID:
      5706392093050163138L

      • Serialized Fields

        • acquisitionDuration
          float acquisitionDuration
          DOCUMENT ME!
        • AFNIOrigExtents
          int[] AFNIOrigExtents
          DOCUMENT ME!
        • AFNIOrigResolutions
          float[] AFNIOrigResolutions
          DOCUMENT ME!
        • AFNITypeString
          int AFNITypeString
          DOCUMENT ME!
        • AFNIViewType
          int AFNIViewType
          DOCUMENT ME!
        • alpha
          WildMagic.LibFoundation.Mathematics.Vector3f alpha
          DOCUMENT ME!
        • alphaArray
          WildMagic.LibFoundation.Mathematics.Vector3f[] alphaArray
          arrays of 12 values used for Talairach conversions.
        • anotherPt
          WildMagic.LibFoundation.Mathematics.Vector3f anotherPt
          DOCUMENT ME!
        • anteriorPt
          WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt
          markers used for +ACPC to +tlrc transformation.
        • beta
          WildMagic.LibFoundation.Mathematics.Vector3f beta
          DOCUMENT ME!
        • betaArray
          WildMagic.LibFoundation.Mathematics.Vector3f[] betaArray
          DOCUMENT ME!
        • botX
          int[] botX
          DOCUMENT ME!
        • botY
          int[] botY
          DOCUMENT ME!
        • botZ
          int[] botZ
          DOCUMENT ME!
        • brickLabsString
          String[] brickLabsString
          Name for each sub-brick
        • brickStatAux
          float[] brickStatAux
          DOCUMENT ME!
        • datasetName
          String datasetName
          DOCUMENT ME!
        • firstPt
          WildMagic.LibFoundation.Mathematics.Vector3f firstPt
          DOCUMENT ME!
        • funcType
          int funcType
          DOCUMENT ME!
        • gamma
          WildMagic.LibFoundation.Mathematics.Vector3f gamma
          DOCUMENT ME!
        • gammaArray
          WildMagic.LibFoundation.Mathematics.Vector3f[] gammaArray
          DOCUMENT ME!
        • gapArray
          int[] gapArray
          If planeGap is not -1, then gapArray contains the values at which zero filling gaps are present.
        • highXmm
          float highXmm
          DOCUMENT ME!
        • highYmm
          float highYmm
          DOCUMENT ME!
        • highZmm
          float highZmm
          DOCUMENT ME!
        • idcodeDate
          String idcodeDate
          DOCUMENT ME!
        • idcodeString
          String idcodeString
          DOCUMENT ME!
        • inferiorEdge
          WildMagic.LibFoundation.Mathematics.Vector3f inferiorEdge
          DOCUMENT ME!
        • inferiorPt
          WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt
          DOCUMENT ME!
        • isDicom
          boolean isDicom
          DOCUMENT ME!
        • label1
          String label1
          DOCUMENT ME!
        • label2
          String label2
          DOCUMENT ME!
        • leftPt
          WildMagic.LibFoundation.Mathematics.Vector3f leftPt
          DOCUMENT ME!
        • lowXmm
          float lowXmm
          DOCUMENT ME!
        • lowYmm
          float lowYmm
          DOCUMENT ME!
        • lowZmm
          float lowZmm
          DOCUMENT ME!
        • marksFlag
          int marksFlag
          DOCUMENT ME!
        • marksFlags
          int marksFlags
          DOCUMENT ME!
        • noteDate001
          String noteDate001
          DOCUMENT ME!
        • noteDate002
          String noteDate002
          DOCUMENT ME!
        • noteDate003
          String noteDate003
          DOCUMENT ME!
        • noteDate004
          String noteDate004
          DOCUMENT ME!
        • noteDate005
          String noteDate005
          DOCUMENT ME!
        • noteNumber001
          String noteNumber001
          DOCUMENT ME!
        • noteNumber002
          String noteNumber002
          DOCUMENT ME!
        • noteNumber003
          String noteNumber003
          DOCUMENT ME!
        • noteNumber004
          String noteNumber004
          DOCUMENT ME!
        • noteNumber005
          String noteNumber005
          DOCUMENT ME!
        • origDicom
          boolean origDicom
          DOCUMENT ME!
        • OriginalPosteriorMargin
          WildMagic.LibFoundation.Mathematics.Vector3f OriginalPosteriorMargin
          DOCUMENT ME!
        • OriginalSuperiorEdge
          WildMagic.LibFoundation.Mathematics.Vector3f OriginalSuperiorEdge
          DOCUMENT ME!
        • pcie
          WildMagic.LibFoundation.Mathematics.Vector3f pcie
          The posterior commisure inferior edge. pcie is the coordinated transformed inferiorEdge
        • planeGap
          int planeGap
          Used to show a zero filling gap in functional AFNI images -1 if no gap is present, 0 = x gap, 1 = y gap, 2 = z gap Interpolation is not performed across zero filling gaps.
        • posteriorMargin
          WildMagic.LibFoundation.Mathematics.Vector3f posteriorMargin
          DOCUMENT ME!
        • posteriorPt
          WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt
          DOCUMENT ME!
        • rightPt
          WildMagic.LibFoundation.Mathematics.Vector3f rightPt
          DOCUMENT ME!
        • rr
          WildMagic.LibFoundation.Mathematics.Vector3f rr
          rr is the dicom ordered original image Talairach center location.
        • rrArray
          WildMagic.LibFoundation.Mathematics.Vector3f[] rrArray
          DOCUMENT ME!
        • slicesWithTimeOffsets
          int slicesWithTimeOffsets
          DOCUMENT ME!
        • statAux
          float[] statAux
          DOCUMENT ME!
        • subBrickNumber
          int subBrickNumber
          Specifies sub-brick that this file-info belongs to
        • superiorEdge
          WildMagic.LibFoundation.Mathematics.Vector3f superiorEdge
          markers used for +orig to +ACPC transformation.
        • superiorPt
          WildMagic.LibFoundation.Mathematics.Vector3f superiorPt
          DOCUMENT ME!
        • TalairachCenter
          WildMagic.LibFoundation.Mathematics.Vector3f TalairachCenter
          DOCUMENT ME!
        • tAxisOffsets
          float[] tAxisOffsets
          If TAXIS_NUMS[1] > 0, then this array gives the time offsets of the
        • timeOrigin
          float timeOrigin
          DOCUMENT ME!
        • timeStep
          float timeStep
          DOCUMENT ME!
        • topX
          int[] topX
          DOCUMENT ME!
        • topY
          int[] topY
          DOCUMENT ME!
        • topZ
          int[] topZ
          DOCUMENT ME!
        • translation
          WildMagic.LibFoundation.Mathematics.Vector3f translation
          DOCUMENT ME!
        • zAxisOffset
          float zAxisOffset
          DOCUMENT ME!
        • zAxisStep
          float zAxisStep
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoAnalyze

      class FileInfoAnalyze extends FileInfoBase implements Serializable
      serialVersionUID:
      7319414471012796383L

      • Serialized Fields

        • aux_file
          String aux_file
          DOCUMENT ME!
        • bitpix
          short bitpix
          Bits per pixel. Valid values include: 1, 8, 16, 32, 64, 24(rgb).
        • cal_max
          float cal_max
          Range of calibration values.
        • cal_min
          float cal_min
          Values of 0.0 for both fields imply that no calibration min and max values are used !
        • cal_units
          String cal_units
          Specifies the name of the calibration unit.
        • compressed
          float compressed
          Indicates if compression is used. Default is -1 indicating no compression
        • data_type
          String data_type
          Unknown use 10 chars.
        • datatype
          short datatype
          Stores the image data type DT_NONE = 0; DT_UNKNOWN = 0; DT_BINARY = 1; DT_UNSIGNED_CHAR = 2; DT_SIGNED_SHORT = 4; DT_UNSIGNED_SHORT = 4; DT_SIGNED_INT = 8; DT_FLOAT = 16; DT_COMPLEX = 32; DT_DOUBLE = 64; DT_RGB = 128; DT_ALL = 255;
        • db_name
          String db_name
          Name of file with a length of 18 chars.
        • descrip
          String descrip
          String with a max character length of 80 used to describe image.
        • dim_un0
          short dim_un0
          Unused.
        • exp_date
          String exp_date
          String with a max character length of 10 used to indicate the experiment date.
        • exp_time
          String exp_time
          String with a max character length of 10 used to indicate the experiment time.
        • extents
          int extents
          Should be 16384.
        • field_skip
          int field_skip
          Unknown length.
        • funused1
          float funused1
          MIPAV uses this variable to define the X-axis origin.
        • funused2
          float funused2
          MIPAV uses this variable to define the Y-axis origin.
        • funused3
          float funused3
          MIPAV uses this variable to define the Z-axis origin.
        • generated
          String generated
          Unknown use. Length of 10.
        • glmax
          int glmax
          Maximum pixel values for the entire dataset.
        • glmin
          int glmin
          Minimum pixel values for the entire database.
        • hist_un0
          String hist_un0
          Unknown use. Length of 3.
        • hkey_un0
          char hkey_un0
          Unknown use. Length of 1.
        • omax
          int omax
          Unknown use.
        • omin
          int omin
          Unknown use.
        • orient
          byte orient
          DOCUMENT ME!
        • originator
          String originator
          Unknown use. Length of 10.
        • patient_id
          String patient_id
          Patient's ID. Length of 10.
        • regular
          char regular
          I think it means data has uniform spacing (resolutions).
        • scannum
          String scannum
          Scan ID Length of 10.
        • session_error
          short session_error
          Unknown use.
        • sizeof_hdr
          int sizeof_hdr
          Always of length 348.
        • smax
          int smax
          Unknown use.
        • smin
          int smin
          Unknown use.
        • start_field
          int start_field
          Unknown use.
        • unused1
          short unused1
          MIPAV uses this variable to define the X-axis orientation.
        • unused2
          short unused2
          MIPAV uses this variable to define the Y-axis orientation.
        • unused3
          short unused3
          MIPAV uses this variable to define the Z-axis orientation.
        • verified
          float verified
          Unknown use.
        • views
          int views
          Unknown use.
        • vols_added
          int vols_added
          Unknown use.
        • vox_units
          String vox_units
          specifies the spatial units of measure for a voxel.

    • Class gov.nih.mipav.model.file.FileInfoAvi

      class FileInfoAvi extends FileInfoBase implements Serializable
      serialVersionUID:
      -5524135420342875298L

      • Serialized Fields

        • numFrames
          int numFrames
          DOCUMENT ME!
        • totalFrames
          int totalFrames
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoBase

      class FileInfoBase extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      6605143084958470864L

      • Serialized Fields

        • axisOrientation
          int[] axisOrientation
          axis orientation used to support image ordering and display for medical images. We support the right hand rule where the origin is the upper left hand of the image with the positive axis.

          x - left to right y - top to botton z - into the screen

        • cameraMake
          String cameraMake
        • cameraModel
          String cameraModel
        • compressionType
          int compressionType
          Used to indicate if the raw data was also compression (0 = no, 1 = zip).
        • dataType
          int dataType
          The data type of the data (i.e. byte, short, float ...
        • dimResolutions
          float[] dimResolutions
          Pixel or voxel resolutions for each dimension - default = 1.0. The z-dim resolution should be the spacing between the centers of adjacent slices; sometimes this will match the slice thickness, but not always.
        • dtiParams
          DTIParameters dtiParams
        • endianess
          boolean endianess
          The Endianess of the data. Intel, DEC Alpha ***** LSB first byte LITTLE_ENDIAN (false) Motorola (MAC), SPARC (SUN), SGI IRIX MSB first byte BIG_ENDIAN (true)
        • exposureTime
          double exposureTime
        • extents
          int[] extents
          Image extents as decribed by the image file format.
        • fileFormat
          int fileFormat
          File format as defined in the Filebase.
        • fileName
          String fileName
          The file name which includes the path information.
        • fileSuffix
          String fileSuffix
          File suffix (ex. "jpg")
        • FNumber
          double FNumber
        • focalLength
          double focalLength
        • focalLength35
          double focalLength35
        • imageOrientation
          int imageOrientation
          Indicates the image orientation (i.e. Axial, Coronal, ...)
        • ISOSpeedRating
          double ISOSpeedRating
        • lut
          ModelLUT lut
          ModelLUT associated with fileinfo
        • max
          double max
          Image maximum intensity for single channel image.
        • maxB
          double maxB
          Image maximum intensity for the blue channel of an RGB image.
        • maxG
          double maxG
          Image maximum intensity for the green channel of an RGB image.
        • maxR
          double maxR
          Image maximum intensity for the red channel of an RGB image.
        • min
          double min
          Image minimum intensity for single channel image.
        • minB
          double minB
          Image minimum intensity for the blue channel of an RGB image.
        • minG
          double minG
          Image minimum intensity for the green channel of an RGB image.
        • minR
          double minR
          Image minimum intensity for the red channel of an RGB image.
        • modality
          int modality
          Indicates the modality (medical image type) of the dataset.
        • multiFile
          boolean multiFile
          Flag that indicates whether or not the image is in multiple files (tiff).
        • offset
          int offset
          Number of bytes to the start the image data - ie. the header length
        • origin
          float[] origin
          The origin to support image locations (ie. DICOM, MINC ...) it is relative to the image origin. the positive axis are right hand rule.

          x - left to right y - top to botton z - into the screen

        • originalEndianess
          boolean originalEndianess
          Used for checking for endianess changes in the ModelImage.reallocate(final int type) function.
        • photometric
          short photometric
          Image minimum intensity for single channel image.
        • pixelPadValue
          Short pixelPadValue
          Some file formats have a pad value for pixels outside the acquisition domain.
        • rescaleIntercept
          double rescaleIntercept
          DICOM images have a rescale y-intercept value that we have also kept in the base.
        • rescaleSlope
          double rescaleSlope
          DICOM images have a rescale slope value that we have also kept in the base.
        • sliceThickness
          float sliceThickness
          The thickness of individual slices in the image volume. Stored in dicom tag 0018,0050 and various other places in other file formats.
        • tagDescription
          Vector<String> tagDescription
        • tagName
          Vector<String> tagName
        • unitsOfMeasure
          FileInfoBase.Unit[] unitsOfMeasure
          Describes the units of measure for the dataset.

    • Exception Class gov.nih.mipav.model.file.FileInfoBase.Unit.UnsupportedUnitConversion

      class UnsupportedUnitConversion extends Exception implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoBFLOAT

      class FileInfoBFLOAT extends FileInfoBase implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoBioRad

      class FileInfoBioRad extends FileInfoBase implements Serializable
      serialVersionUID:
      4850818161207332016L

      • Serialized Fields

        • imageDescription
          String imageDescription
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoBMP

      class FileInfoBMP extends FileInfoBase implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoBRUKER

      class FileInfoBRUKER extends FileInfoBase implements Serializable
      serialVersionUID:
      292865443840539139L

      • Serialized Fields

        • acqGradMat
          double[][][] acqGradMat
        • activeReceivers
          String[] activeReceivers
        • BValuesPerDirection
          int[] BValuesPerDirection
        • delayBetweenVolumes
          double delayBetweenVolumes
        • deriveGains
          String deriveGains
        • diffusionExperimentsPerDirection
          int diffusionExperimentsPerDirection
        • diffusionGradientAmplitude
          double[] diffusionGradientAmplitude
        • diffusionGradientDuration
          double[] diffusionGradientDuration
        • diffusionGradientSeparation
          double[] diffusionGradientSeparation
        • diffusionGradientSwitchingScheme
          String diffusionGradientSwitchingScheme
        • diffusionMeasurementMode
          String diffusionMeasurementMode
        • diffusionModuleDuration
          double diffusionModuleDuration
        • diffusionModuleEchoDelay
          double diffusionModuleEchoDelay
        • diffusionPreparation
          String diffusionPreparation
        • directScaledSwitching
          String directScaledSwitching
        • echoTime
          double echoTime
        • effectiveSpectralBandwidth
          double effectiveSpectralBandwidth
        • haveZResol
          boolean haveZResol
          Whether the z resolution is set in the acqp or reco files
        • inversionTime
          double inversionTime
          The inversion time of an MR scan.
        • maximumPossibleBValue
          double maximumPossibleBValue
        • method
          String method
        • numberOfA0Images
          int numberOfA0Images
        • numberOfAverages
          int numberOfAverages
        • numberOfDiffusionDirections
          int numberOfDiffusionDirections
        • numberOfObjects
          int numberOfObjects
        • numberOfRepetitions
          int numberOfRepetitions
        • numberOfSegments
          int numberOfSegments
        • patientPosition
          String patientPosition
        • PPIAcceleration
          int PPIAcceleration
        • recoInpSize
          int recoInpSize
        • recoSize
          int recoSize
          The size of the reconstruction
        • refocusingPulseType
          String refocusingPulseType
        • repetitionTime
          double repetitionTime
        • scanTime
          String scanTime
        • showAllParameters
          String showAllParameters
        • sliceGradient
          double sliceGradient
        • sliceGradientDuration
          double sliceGradientDuration
        • sliceGradientLimit
          double sliceGradientLimit
        • sliceSeparationMode
          String sliceSeparationMode
          The slice inversion time of the scan
        • TESliceSpoilerGradientsAmplitude
          double TESliceSpoilerGradientsAmplitude
        • TEsliceSpoilerGradientsDuration
          double TEsliceSpoilerGradientsDuration
        • TESliceSpoilerGradientsLimit
          double TESliceSpoilerGradientsLimit
        • totalNumberOfDiffusionExperiments
          int totalNumberOfDiffusionExperiments
        • usedSliceThickness
          double usedSliceThickness
        • useMultipleReceivers
          String useMultipleReceivers
        • zeroFillFactorRead
          double zeroFillFactorRead

    • Class gov.nih.mipav.model.file.FileInfoCheshire

      class FileInfoCheshire extends FileInfoBase implements Serializable
      serialVersionUID:
      4776092584175024015L

    • Class gov.nih.mipav.model.file.FileInfoCOR

      class FileInfoCOR extends FileInfoBase implements Serializable
      serialVersionUID:
      8537756143101265528L

      • Serialized Fields

        • fov
          float fov
          DOCUMENT ME!
        • te
          float te
          DOCUMENT ME!
        • ti
          float ti
          DOCUMENT ME!
        • tr
          float tr
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoCZI

      class FileInfoCZI extends FileInfoBase implements Serializable

      • Serialized Fields

        • acquisitionMode
          String[] acquisitionMode
        • acquisitionTime
          String acquisitionTime
        • address
          String address
        • author
          String author
        • channelDescription
          String[] channelDescription
        • channelID
          String[] channelID
        • channelName
          String[] channelName
        • channelsFound
          int channelsFound
        • channelWeight
          String[] channelWeight
        • city
          String city
        • color
          String[] color
        • comment
          String comment
        • condenserContrast
          String[] condenserContrast
        • contrastMethod
          String[] contrastMethod
        • country
          String country
        • creationDate
          String creationDate
        • description
          String description
        • detectionWavelength
          String[] detectionWavelength
        • detectorBinning
          String[] detectorBinning
        • detectorDigitalGain
          String[] detectorDigitalGain
        • detectorEMGain
          String[] detectorEMGain
        • detectorGain
          String[] detectorGain
        • detectorOffset
          String[] detectorOffset
        • detectorReadOutRate
          String[] detectorReadOutRate
        • detectorUseBrightnessContrastCorrection
          String[] detectorUseBrightnessContrastCorrection
        • detectorVoltage
          String[] detectorVoltage
        • dimB
          int dimB
        • dimH
          int dimH
        • dimI
          int dimI
        • dimM
          int dimM
        • dimR
          int dimR
        • dimS
          int dimS
        • dimV
          int dimV
        • displayName
          String displayName
        • dyeDatabaseID
          String[] dyeDatabaseID
        • dyeID
          String[] dyeID
        • email
          String email
        • emissionWavelength
          String[] emissionWavelength
        • excitationWavelength
          String[] excitationWavelength
        • experimenterName
          String experimenterName
        • exposureTime
          String[] exposureTime
        • fax
          String fax
        • firstName
          String firstName
        • fluor
          String[] fluor
        • focusPosition
          String focusPosition
        • gamma
          String[] gamma
        • high
          String[] high
        • ID
          String ID
        • illuminationType
          String[] illuminationType
        • illuminationWavelength
          String[] illuminationWavelength
        • imageName
          String imageName
        • institution
          String institution
        • keywords
          String keywords
        • lastName
          String lastName
        • lightSourceAttenuation
          String[] lightSourceAttenuation
        • lightSourceIntensity
          String[] lightSourceIntensity
        • lightSourceWavelength
          String[] lightSourceWavelength
        • low
          String[] low
        • microscopeSystem
          String microscopeSystem
        • microscopeType
          String microscopeType
        • middleName
          String middleName
        • mode
          String[] mode
        • NACondenser
          String[] NACondenser
        • NDFilter
          String[] NDFilter
        • originalScanData
          String originalScanData
        • phone
          String phone
        • pinholeGeometry
          String[] pinholeGeometry
        • pinholeSize
          String[] pinholeSize
        • pinholeSizeAiry
          String[] pinholeSizeAiry
        • pockelCellSetting
          String[] pockelCellSetting
        • points
          String[] points
        • rating
          String rating
        • ratio
          String[] ratio
        • reflector
          String[] reflector
        • sectionThickness
          String[] sectionThickness
        • stageXPosition
          String stageXPosition
        • stageYPosition
          String stageYPosition
        • state
          String state
        • subType
          String subType
        • thumbnail
          String thumbnail
        • timeStamps
          double[] timeStamps
        • title
          String title
        • userName
          String userName
        • validBitsPerPixel
          String validBitsPerPixel

    • Class gov.nih.mipav.model.file.FileInfoDicom

      class FileInfoDicom extends FileInfoBase implements Serializable
      serialVersionUID:
      -3072660161266896186L

      • Serialized Fields

        • bitsAllocated
          short bitsAllocated
          Bits allocated per pixel.
        • bitsStored
          short bitsStored
          Bits stored per pixel>
        • bytesPerPixel
          short bytesPerPixel
          Number of bytes per pixel.
        • containsDICM
          boolean containsDICM
          True if the DICOM file has the ID DICM at beginning at file pointer 128.
        • displayType
          int displayType
          Data type.
        • highBit
          short highBit
        • instanceNumber
          int instanceNumber
          DICOM instance number.
        • isCurrentTagSQ
          boolean isCurrentTagSQ
          Whether the tag currently being processed and read in is a sequence tag.
        • isEnhancedDicom
          boolean isEnhancedDicom
          whether it is enhanced dicom or not
        • lut
          ModelLUT lut
          LUT for pre-processing of dicom file
        • multiFrame
          boolean multiFrame
          True indicates image has multiple image planes in a single file.
        • olderVersion
          boolean olderVersion
          True is image format invalid input: '<' DICOM 3.0.
        • orientation
          String orientation
          Orientation - SAGITTAL, CORONAL, AXIAL.
        • originalDataType
          int originalDataType
        • photometricInterp
          String photometricInterp
          Type of image - color, monochrome etc.
        • pixelPaddingValue
          Short pixelPaddingValue
          Pixel Padding Value (0028, 0120). Value of pixels added to non-rectangular image to pad to rectangular format.
        • pixelRepresentation
          short pixelRepresentation
          DICOM tag (0028, 0103) -1 = undefined 0 = unsigned 1 = signed
        • planarConfig
          short planarConfig
          0 = RGB, RGB, 1 = R R R, G G G, B B B.
        • RLETAMARencapsulatedOffset
          int RLETAMARencapsulatedOffset
        • sliceLocation
          float sliceLocation
          DICOM slice location.
        • tagTable
          FileDicomTagTable tagTable
          Stores all the information about the DICOM tags.
        • vr_type
          FileInfoDicom.VRtype vr_type
          VR type can be IMPLICIT or EXPLICIT.
        • xLocation
          float xLocation
          DICOM x coordianate of the slice location.
        • yLocation
          float yLocation
          DICOM y coordianate of the slice location.
        • zLocation
          float zLocation
          DICOM z coordianate of the slice location.

    • Class gov.nih.mipav.model.file.FileInfoDM3

      class FileInfoDM3 extends FileInfoBase implements Serializable
      serialVersionUID:
      6502186871127970871L

    • Class gov.nih.mipav.model.file.FileInfoFits

      class FileInfoFits extends FileInfoBase implements Serializable
      serialVersionUID:
      8285638648507573285L

    • Class gov.nih.mipav.model.file.FileInfoGESigna4X

      class FileInfoGESigna4X extends FileInfoBase implements Serializable
      serialVersionUID:
      -6230885244735581982L

      • Serialized Fields

        • aCenter
          float aCenter
          DOCUMENT ME!
        • actualReceiveFrequency
          int actualReceiveFrequency
          DOCUMENT ME!
        • actualTransmitFrequency
          int actualTransmitFrequency
          DOCUMENT ME!
        • aNormal
          float aNormal
          DOCUMENT ME!
        • apCenter
          float apCenter
          DOCUMENT ME!
        • arrythmiaRejectionRatio
          short arrythmiaRejectionRatio
          DOCUMENT ME!
        • autoCenterFrequency
          String autoCenterFrequency
          DOCUMENT ME!
        • autoManualPrescan
          String autoManualPrescan
          DOCUMENT ME!
        • averageSAR
          float averageSAR
          DOCUMENT ME!
        • averagesNumber
          short averagesNumber
          DOCUMENT ME!
        • bitsPerPixel
          short bitsPerPixel
          DOCUMENT ME!
        • cardiacHeartRate
          short cardiacHeartRate
          DOCUMENT ME!
        • cardiacPhaseNumber
          short cardiacPhaseNumber
          DOCUMENT ME!
        • cardiacRepTime
          String cardiacRepTime
          DOCUMENT ME!
        • changedValues
          String changedValues
          DOCUMENT ME!
        • coilName
          String coilName
          DOCUMENT ME!
        • coilType
          String coilType
          DOCUMENT ME!
        • collapseImage
          String collapseImage
          DOCUMENT ME!
        • concatenatedSATSelection
          String concatenatedSATSelection
          DOCUMENT ME!
        • contiguousSlices
          String contiguousSlices
          DOCUMENT ME!
        • contrastAgent
          String contrastAgent
          DOCUMENT ME!
        • contrastAmount
          float contrastAmount
          DOCUMENT ME!
        • contrastDescription
          String contrastDescription
          DOCUMENT ME!
        • contrastUsed
          String contrastUsed
          DOCUMENT ME!
        • cPhase
          short cPhase
          DOCUMENT ME!
        • defaultLevel
          short defaultLevel
          DOCUMENT ME!
        • defaultWindow
          short defaultWindow
          DOCUMENT ME!
        • diognostician
          String diognostician
          DOCUMENT ME!
        • echoNumber
          short echoNumber
          DOCUMENT ME!
        • echoTrainLength
          int echoTrainLength
          DOCUMENT ME!
        • endX
          float endX
          DOCUMENT ME!
        • endY
          float endY
          DOCUMENT ME!
        • endZ
          float endZ
          DOCUMENT ME!
        • excitationsNumber
          float excitationsNumber
          DOCUMENT ME!
        • extremityCoil
          String extremityCoil
          DOCUMENT ME!
        • fieldOfView
          float fieldOfView
          DOCUMENT ME!
        • fieldStrength
          short fieldStrength
          DOCUMENT ME!
        • fileBlocks
          short fileBlocks
          DOCUMENT ME!
        • fileFormat
          String fileFormat
          DOCUMENT ME!
        • flipAngle
          short flipAngle
          DOCUMENT ME!
        • fractionalEffectiveEcho
          String fractionalEffectiveEcho
          DOCUMENT ME!
        • gatingType
          String gatingType
          DOCUMENT ME!
        • gatingType2
          String gatingType2
          DOCUMENT ME!
        • graphicallyPrescribed
          String graphicallyPrescribed
          DOCUMENT ME!
        • histogramPresent
          String histogramPresent
          DOCUMENT ME!
        • history
          String history
          DOCUMENT ME!
        • horizontalLandmark
          float horizontalLandmark
          DOCUMENT ME!
        • hospitalName
          String hospitalName
          DOCUMENT ME!
        • imageCreationDate
          String imageCreationDate
          DOCUMENT ME!
        • imageCreationTime
          String imageCreationTime
          DOCUMENT ME!
        • imageFieldStrength
          int imageFieldStrength
          DOCUMENT ME!
        • imageHeaderBlocks
          short imageHeaderBlocks
          DOCUMENT ME!
        • imageHeaderCreatorProcess
          String imageHeaderCreatorProcess
          DOCUMENT ME!
        • imageHeaderCreatorTask
          short imageHeaderCreatorTask
          DOCUMENT ME!
        • imageHeaderDisclaimer
          short imageHeaderDisclaimer
          DOCUMENT ME!
        • imageHeaderID
          String imageHeaderID
          DOCUMENT ME!
        • imageHeaderRevisionNumber
          String imageHeaderRevisionNumber
          DOCUMENT ME!
        • imageLocation
          float imageLocation
          DOCUMENT ME!
        • imageMatrix
          short imageMatrix
          DOCUMENT ME!
        • imageMode
          String imageMode
          DOCUMENT ME!
        • imageNumber
          String imageNumber
          DOCUMENT ME!
        • imageOffset
          short imageOffset
          DOCUMENT ME!
        • imageRawDataSystemID
          String imageRawDataSystemID
          DOCUMENT ME!
        • imagesAllocated
          short imagesAllocated
          DOCUMENT ME!
        • imageShape
          String imageShape
          DOCUMENT ME!
        • imageSpacing
          float imageSpacing
          DOCUMENT ME!
        • imagesPerCardiacCycle
          short imagesPerCardiacCycle
          DOCUMENT ME!
        • imageSystemGenerationID
          String imageSystemGenerationID
          DOCUMENT ME!
        • imageType
          String imageType
          DOCUMENT ME!
        • imgBLHC_A
          float imgBLHC_A
          DOCUMENT ME!
        • imgBLHC_R
          float imgBLHC_R
          DOCUMENT ME!
        • imgBLHC_S
          float imgBLHC_S
          DOCUMENT ME!
        • imgTLHC_A
          float imgTLHC_A
          DOCUMENT ME!
        • imgTLHC_R
          float imgTLHC_R
          DOCUMENT ME!
        • imgTLHC_S
          float imgTLHC_S
          DOCUMENT ME!
        • imgTRHC_A
          float imgTRHC_A
          DOCUMENT ME!
        • imgTRHC_R
          float imgTRHC_R
          DOCUMENT ME!
        • imgTRHC_S
          float imgTRHC_S
          DOCUMENT ME!
        • interImageDelay
          float interImageDelay
          DOCUMENT ME!
        • landmarkCounter
          int landmarkCounter
          DOCUMENT ME!
        • longitudinalAnatomicalReference
          String longitudinalAnatomicalReference
          DOCUMENT ME!
        • minimumDelay
          short minimumDelay
          DOCUMENT ME!
        • MRIProcessName
          String MRIProcessName
          DOCUMENT ME!
        • numberOfEchos
          short numberOfEchos
          DOCUMENT ME!
        • obliquePlane
          String obliquePlane
          DOCUMENT ME!
        • operator
          String operator
          DOCUMENT ME!
        • orientation
          String orientation
          DOCUMENT ME!
        • originalSeriesNumber
          String originalSeriesNumber
          DOCUMENT ME!
        • patientAge
          String patientAge
          DOCUMENT ME!
        • patientID
          String patientID
          DOCUMENT ME!
        • patientName
          String patientName
          DOCUMENT ME!
        • patientSex
          String patientSex
          DOCUMENT ME!
        • patientStatus
          String patientStatus
          DOCUMENT ME!
        • patientWeight
          int patientWeight
          DOCUMENT ME!
        • pauseInterval
          short pauseInterval
          DOCUMENT ME!
        • pauseTime
          float pauseTime
          DOCUMENT ME!
        • PCVelocityEncoding
          short PCVelocityEncoding
          DOCUMENT ME!
        • peakSAR
          float peakSAR
          DOCUMENT ME!
        • pfSwapped
          String pfSwapped
          DOCUMENT ME!
        • phaseContrastFlowAxis
          String phaseContrastFlowAxis
          DOCUMENT ME!
        • pImage2
          String pImage2
          DOCUMENT ME!
        • pixelSize
          float pixelSize
          DOCUMENT ME!
        • planeName
          String planeName
          DOCUMENT ME!
        • planeType
          String planeType
          DOCUMENT ME!
        • position
          String position
          DOCUMENT ME!
        • prescanReceiveAttenuation1
          short prescanReceiveAttenuation1
          DOCUMENT ME!
        • prescanReceiveAttenuation2
          short prescanReceiveAttenuation2
          DOCUMENT ME!
        • prescribedImageNumbers
          String prescribedImageNumbers
          DOCUMENT ME!
        • prescribedSeriesNumbers
          String prescribedSeriesNumbers
          DOCUMENT ME!
        • projectionAngle
          float projectionAngle
          DOCUMENT ME!
        • psdDay
          short psdDay
          DOCUMENT ME!
        • psdFileName
          String psdFileName
          DOCUMENT ME!
        • psdHour
          short psdHour
          DOCUMENT ME!
        • psdMinute
          short psdMinute
          DOCUMENT ME!
        • psdMonth
          short psdMonth
          DOCUMENT ME!
        • psdName
          String psdName
          DOCUMENT ME!
        • psdSeconds
          short psdSeconds
          DOCUMENT ME!
        • psdYear
          short psdYear
          DOCUMENT ME!
        • pSeries2
          String pSeries2
          DOCUMENT ME!
        • pulseSequence
          String pulseSequence
          DOCUMENT ME!
        • pulseSequenceMode
          String pulseSequenceMode
          DOCUMENT ME!
        • pulseSequenceSubtype
          String pulseSequenceSubtype
          DOCUMENT ME!
        • R1
          short R1
          DOCUMENT ME!
        • R2
          short R2
          DOCUMENT ME!
        • rawDataStudyNumber
          String rawDataStudyNumber
          DOCUMENT ME!
        • rawDataSystemID
          String rawDataSystemID
          DOCUMENT ME!
        • rCenter
          float rCenter
          DOCUMENT ME!
        • receiveAttenuatorSetting
          short receiveAttenuatorSetting
          DOCUMENT ME!
        • recommendedReceiveAttenuation
          int recommendedReceiveAttenuation
          DOCUMENT ME!
        • recommendedReceiveFrequency
          int recommendedReceiveFrequency
          DOCUMENT ME!
        • recommendedTransmitAttenuation
          int recommendedTransmitAttenuation
          DOCUMENT ME!
        • recommendedTransmitFrequency
          int recommendedTransmitFrequency
          DOCUMENT ME!
        • referringPhysician
          String referringPhysician
          DOCUMENT ME!
        • requestedNumber
          String requestedNumber
          DOCUMENT ME!
        • researchMode
          String researchMode
          DOCUMENT ME!
        • rlCenter
          float rlCenter
          DOCUMENT ME!
        • rNormal
          float rNormal
          DOCUMENT ME!
        • round
          String round
          DOCUMENT ME!
        • SARMonitored
          String SARMonitored
          DOCUMENT ME!
        • satSelections
          String satSelections
          DOCUMENT ME!
        • satXLoc1
          short satXLoc1
          DOCUMENT ME!
        • satXLoc2
          short satXLoc2
          DOCUMENT ME!
        • satXThick
          short satXThick
          DOCUMENT ME!
        • satYLoc1
          short satYLoc1
          DOCUMENT ME!
        • satYLoc2
          short satYLoc2
          DOCUMENT ME!
        • satYThick
          short satYThick
          DOCUMENT ME!
        • satZLoc1
          short satZLoc1
          DOCUMENT ME!
        • satZLoc2
          short satZLoc2
          DOCUMENT ME!
        • satZThick
          short satZThick
          DOCUMENT ME!
        • scanAcquisitionNumber
          short scanAcquisitionNumber
          DOCUMENT ME!
        • scanARRs
          int scanARRs
          DOCUMENT ME!
        • scanMatrixX
          short scanMatrixX
          DOCUMENT ME!
        • scanMatrixY
          short scanMatrixY
          DOCUMENT ME!
        • scanProtocolName
          String scanProtocolName
          DOCUMENT ME!
        • sCenter
          float sCenter
          DOCUMENT ME!
        • scIma
          String scIma
          DOCUMENT ME!
        • scSer
          String scSer
          DOCUMENT ME!
        • series
          String series
          DOCUMENT ME!
        • seriesDate
          String seriesDate
          DOCUMENT ME!
        • seriesDescription
          String seriesDescription
          DOCUMENT ME!
        • seriesHeaderBlocks
          short seriesHeaderBlocks
          DOCUMENT ME!
        • seriesHeaderID
          String seriesHeaderID
          DOCUMENT ME!
        • seriesHeaderRevisionNumber
          String seriesHeaderRevisionNumber
          DOCUMENT ME!
        • seriesNumber
          String seriesNumber
          DOCUMENT ME!
        • seriesProcessName
          String seriesProcessName
          DOCUMENT ME!
        • seriesPSDName
          String seriesPSDName
          DOCUMENT ME!
        • seriesRawDataSystemID
          String seriesRawDataSystemID
          DOCUMENT ME!
        • seriesSystemGenerationID
          String seriesSystemGenerationID
          DOCUMENT ME!
        • seriesTaskID
          short seriesTaskID
          DOCUMENT ME!
        • seriesTime
          String seriesTime
          DOCUMENT ME!
        • seriesType
          String seriesType
          DOCUMENT ME!
        • siCenter
          float siCenter
          DOCUMENT ME!
        • sliceMultiplier
          short sliceMultiplier
          DOCUMENT ME!
        • sliceQuantity
          short sliceQuantity
          DOCUMENT ME!
        • sliceThicknessDisclaimer
          String sliceThicknessDisclaimer
          DOCUMENT ME!
        • sNormal
          float sNormal
          DOCUMENT ME!
        • startX
          float startX
          DOCUMENT ME!
        • startY
          float startY
          DOCUMENT ME!
        • startZ
          float startZ
          DOCUMENT ME!
        • studyDate
          String studyDate
          DOCUMENT ME!
        • studyDescription
          String studyDescription
          DOCUMENT ME!
        • studyHeaderBlocks
          short studyHeaderBlocks
          DOCUMENT ME!
        • studyHeaderID
          String studyHeaderID
          DOCUMENT ME!
        • studyHeaderRevisionNumber
          String studyHeaderRevisionNumber
          DOCUMENT ME!
        • studyNumber
          String studyNumber
          DOCUMENT ME!
        • studyTaskID
          short studyTaskID
          DOCUMENT ME!
        • studyTime
          String studyTime
          DOCUMENT ME!
        • suppressionTechnique
          String suppressionTechnique
          DOCUMENT ME!
        • surfaceCoilIntensityCorrection
          String surfaceCoilIntensityCorrection
          DOCUMENT ME!
        • surfaceCoilsCorrectionType
          String surfaceCoilsCorrectionType
          DOCUMENT ME!
        • surfaceCoilType
          String surfaceCoilType
          DOCUMENT ME!
        • swapPF
          String swapPF
          DOCUMENT ME!
        • systemConfigHospitalName
          String systemConfigHospitalName
          DOCUMENT ME!
        • systemGenerationID
          String systemGenerationID
          DOCUMENT ME!
        • systemID
          String systemID
          Use serialVersionUID for interoperability.
        • tableLocation
          float tableLocation
          DOCUMENT ME!
        • tablePosition
          float tablePosition
          DOCUMENT ME!
        • te
          float te
          DOCUMENT ME!
        • TE2
          float TE2
          DOCUMENT ME!
        • thickness
          float thickness
          DOCUMENT ME!
        • ti
          float ti
          DOCUMENT ME!
        • totalPostTriggerDelayTime
          float totalPostTriggerDelayTime
          DOCUMENT ME!
        • tr
          float tr
          DOCUMENT ME!
        • transmitAttenuatorSetting
          short transmitAttenuatorSetting
          DOCUMENT ME!
        • ts
          float ts
          DOCUMENT ME!
        • user0
          float user0
          DOCUMENT ME!
        • user1
          float user1
          DOCUMENT ME!
        • user2
          float user2
          DOCUMENT ME!
        • user3
          float user3
          DOCUMENT ME!
        • user4
          float user4
          DOCUMENT ME!
        • user5
          float user5
          DOCUMENT ME!
        • user6
          float user6
          DOCUMENT ME!
        • user7
          float user7
          DOCUMENT ME!
        • user8
          float user8
          DOCUMENT ME!
        • user9
          float user9
          DOCUMENT ME!
        • variableBandwidth
          String variableBandwidth
          DOCUMENT ME!
        • vascularImagingFlags
          String vascularImagingFlags
          DOCUMENT ME!
        • vasMode
          String vasMode
          DOCUMENT ME!
        • vencScalingFactor
          float vencScalingFactor
          DOCUMENT ME!
        • verticalAnatomicalReference
          String verticalAnatomicalReference
          DOCUMENT ME!
        • verticalLandmark
          float verticalLandmark
          DOCUMENT ME!
        • year
          int year
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoGESigna5X

      class FileInfoGESigna5X extends FileInfoBase implements Serializable
      serialVersionUID:
      -4456298776612648834L

      • Serialized Fields

        • actualDateTime
          int actualDateTime
          18.
        • addValue
          int addValue
          112 - value to add to pixels.
        • anatomicalRef
          String anatomicalRef
          84 - 3 bytes - Anatomical Reference.
        • autoXmtFreq
          int autoXmtFreq
          282 Auto Center Frequency (0.1 Hz).
        • autoXmtGain
          short autoXmtGain
          286 Auto Transmit Gain (0.1 dB).
        • calFldStr
          int calFldStr
          388 Calibrated Field Strength (x10 uGauss).
        • cellSpace
          float cellSpace
          54 Cell spacing.
        • cenFreq
          short cenFreq
          296 Center frequency method.
        • checkSum
          int checkSum
          54 - 16 bit end around carry sum of pixels **** (read as unsigned short).
        • coilName
          String coilName
          362 17 characters.
        • coilType
          short coilType
          360.
        • compress
          short compress
          120 image compression type for allocation.
        • compression
          int compression
          20 0 as is 1 retangular 2 packed 3 compressed 4 compressed and packed.
        • contig
          short contig
          222 Continuous slices flag.
        • contrastMode
          short contrastMode
          106.
        • cPhase
          short cPhase
          260 Total cardiac phase prescribed.
        • cPhaseNum
          short cPhaseNum
          646 Cardiac phase number.
        • currentSeconds
          long currentSeconds
          DOCUMENT ME!
        • dasType
          short dasType
          68 DAS type.
        • dateTime
          int dateTime
          14 allocation date time.
        • day
          int day
          DOCUMENT ME!
        • dbdt
          float dbdt
          838 peak rate of change in gradient field, teslainvalid input: '&#47'sec.
        • dbdtPer
          float dbdtPer
          842 limit in units of percent of theoretical curve.
        • dcnDensity
          short dcnDensity
          74 Decon kernel density.
        • dcnLen
          short dcnLen
          72 Number of elements in Decon kernel.
        • dcnShiftCnt
          short dcnShiftCnt
          78 Decon kernel shift count.
        • dcnStepSize
          short dcnStepSize
          76 Decon kernel stepsize.
        • depth
          int depth
          16 - number of bits.
        • detect
          short detect
          44 detector type.
        • diagRad
          String diagRad
          245 - 33 bytes Diagnosticianinvalid input: '&#47'Radiologist.
        • diskid
          byte diskid
          6 - (internal use) Disk ID.
        • echo1Alpha
          float echo1Alpha
          240.
        • echo1Beta
          float echo1Beta
          244.
        • echo1Level
          short echo1Level
          250.
        • echo1Window
          short echo1Window
          248.
        • echo2Alpha
          float echo2Alpha
          252.
        • echo2Beta
          float echo2Beta
          256.
        • echo2Level
          short echo2Level
          262.
        • echo2Window
          short echo2Window
          260.
        • echo3Alpha
          float echo3Alpha
          264.
        • echo3Beta
          float echo3Beta
          268.
        • echo3Level
          short echo3Level
          274.
        • echo3Window
          short echo3Window
          272.
        • echo4Alpha
          float echo4Alpha
          276.
        • echo4Beta
          float echo4Beta
          280.
        • echo4Level
          short echo4Level
          286.
        • echo4Window
          short echo4Window
          284.
        • echo5Alpha
          float echo5Alpha
          288.
        • echo5Beta
          float echo5Beta
          292.
        • echo5Level
          short echo5Level
          298.
        • echo5Window
          short echo5Window
          296.
        • echo6Alpha
          float echo6Alpha
          300.
        • echo6Beta
          float echo6Beta
          304.
        • echo6Level
          short echo6Level
          310.
        • echo6Window
          short echo6Window
          308.
        • echo7Alpha
          float echo7Alpha
          312.
        • echo7Beta
          float echo7Beta
          316.
        • echo7Level
          short echo7Level
          322.
        • echo7Window
          short echo7Window
          320.
        • echo8Alpha
          float echo8Alpha
          324.
        • echo8Beta
          float echo8Beta
          328.
        • echo8Level
          short echo8Level
          334.
        • echo8Window
          short echo8Window
          332.
        • echoNum
          short echoNum
          212 echo number.
        • echoTime
          int echoTime
          202 pulse echo time (usec).
        • effEchoSpace
          short effEchoSpace
          828 effective echo spacing for EPI.
        • endLoc
          float endLoc
          128 - Last scan location (Linvalid input: '&#47'S).
        • endRAS
          String endRAS
          126 - 1 byte - RAS letter for last scan location (Linvalid input: '&#47'S).
        • entry
          int entry
          80 - Patient Entry.
        • equipmentUID
          String equipmentUID
          400 - 32 bytes.
        • estdbdtPer
          float estdbdtPer
          846 PSD estimated limit in units of percent.
        • estdbdtts
          float estdbdtts
          850 PSD estimated limit in Teslainvalid input: '&#47'sec.
        • ETL
          short ETL
          640 Echo train length.
        • exAllocKey
          String exAllocKey
          334 - 13 bytes Process that allocated this record.
        • examNum
          int examNum
          8 - Read as unsigned short.
        • examType
          String examType
          305 - 3 bytes i.e. invalid input: '&quotMR'invalid input: '&quot' or invalid input: '&quotCT'invalid input: '&quot'
        • exChecksum
          int exChecksum
          356 (internal use) Exam Record Checksum.
        • exComplete
          int exComplete
          360 (internal use) Exam complete flag.
        • exDateTime
          int exDateTime
          208 - Exam date/time stamp.
        • exDeltaCount
          int exDeltaCount
          348 (internal use) Number of updates to header.
        • exDesc
          String exDesc
          282 - 23 bytes Exam Description.
        • exDiskID
          String exDiskID
          6 - 1 byte (internal use) Disk ID for this exam.
        • exFormat
          short exFormat
          308 Exam format.
        • exLastMod
          int exLastMod
          328 Dateinvalid input: '&#47'Time of Last Change.
        • exModelCnt
          int exModelCnt
          424 (internal use) Number of 3D Models.
        • exModelNum
          int exModelNum
          420 (internal use) Last Model Number Used.
        • exModelsData
          int exModelsData
          432.
        • exModelsLen
          int exModelsLen
          428.
        • exNumArch
          int exNumArch
          368 (internal use) Number of Series Archived.
        • exNumSeries
          int exNumSeries
          372 (internal use) Number of Series Existing.
        • exNumUnSer
          int exNumUnSer
          384 (internal use) Number of Unstored series.
        • exPadding
          String exPadding
          508 - 516 bytes.
        • exProspCnt
          int exProspCnt
          408 (internal use) number of Prospinvalid input: '&#47'Scout Series.
        • exProspData
          int exProspData
          416.
        • exProspLen
          int exProspLen
          412 (internal use) Prospinvalid input: '&#47'Scout Sers Keys in Exam.
        • exSeriesCt
          int exSeriesCt
          364 (innternl use) Last Series Number Used.
        • exSeriesData
          int exSeriesData
          380.
        • exSeriesLen
          int exSeriesLen
          376 (internal use) Series keys for this exam.
        • exStat
          short exStat
          436 Patient status.
        • exSysID
          String exSysID
          318 - 9 bytes Creator suite and host.
        • exToArchCnt
          int exToArchCnt
          396 (internal use) number of Unarchived Series.
        • exToArchiveData
          int exToArchiveData
          404.
        • exToArchiveLen
          int exToArchiveLen
          400 (internal use) Unarchived series Keys in Exam.
        • exUniq
          short exUniq
          4 (internal use) The Make_Unique Flag.
        • exUnSeriesData
          int exUnSeriesData
          392.
        • exUnSeriesLen
          int exUnSeriesLen
          388 (internal use) Unstored Sers Keys in Exam.
        • exVersCre
          String exVersCre
          352 - 2 bytes Genesis Version - Created.
        • exVersCur
          String exVersCur
          354 - 2 bytes Genesis Version - Now.
        • firstAxTime
          long firstAxTime
          310 Start time(secs) of first axial in exam.
        • flax
          short flax
          574 Phase contrast flow axis.
        • forImgRev
          String forImgRev
          190 foreign image revision.
        • FOVX
          float FOVX
          34.
        • FOVY
          float FOVY
          38.
        • fracEcho
          short fracEcho
          642 Fractional echo-effective TE flag.
        • freqDir
          short freqDir
          742 Frequency Direction.
        • gOffsetX
          short gOffsetX
          818 gradient offset in x-direction.
        • gOffsetY
          short gOffsetY
          820 gradient offset in y-direction.
        • gOffsetZ
          short gOffsetZ
          822 gradient offset in z-direction.
        • gpre
          short gpre
          400 Graphically prescribed.
        • heartRate
          short heartRate
          224 cardiac heart rate (beats per minute).
        • height
          int height
          12 - height of image.
        • hist
          String hist
          134 - 61 bytes Patient history.
        • hospName
          String hospName
          10 - 33 characters hospital name.
        • hour
          int hour
          DOCUMENT ME!
        • im_alloc_key
          String im_alloc_key
          506 13 characters Process that allocated this record.
        • im_archived
          int im_archived
          544 (internal use) Image Archive Flag.
        • im_checksum
          int im_checksum
          540 (internal use) AcqRecon record checksum.
        • im_complete
          int im_complete
          548 (Internal use) Image Complete Flag.
        • im_lastmod
          int im_lastmod
          520.
        • im_pds_a
          int im_pds_a
          528 PixelData size - as stored.
        • im_pds_c
          int im_pds_c
          532 PixelData size - compressed.
        • im_pds_u
          int im_pds_u
          536 PixelData size - Uncompressed.
        • im_verscre
          String im_verscre
          524 2 characters Genesis Version - Created.
        • im_verscur
          String im_verscur
          526 2 characters Genesis Version - Now.
        • image_type
          short image_type
          584 Magnitude, Phase, Imaginary, or Real.
        • image_uid
          String image_uid
          746 32 characters Image Unique ID.
        • imageDimX
          float imageDimX
          42.
        • imageDimY
          float imageDimY
          46.
        • imageNum
          short imageNum
          12.
        • imagesData
          int imagesData
          212.
        • imagesLen
          int imagesLen
          208 - (internal use) Image keys for this Series.
        • imgBRHC_A
          float imgBRHC_A
          182 Bottom Right Hand Corner Anterior.
        • imgBRHC_R
          float imgBRHC_R
          178 Bottom Right Hand Corner Right.
        • imgBRHC_S
          float imgBRHC_S
          186 Bottom Right Hand Corner Superior.
        • imgCtrA
          float imgCtrA
          134 Anterior(i.e. X positive to anterior)
        • imgCtrR
          float imgCtrR
          130 Right (i.e. X positive to right)
        • imgCtrS
          float imgCtrS
          138 Superior(i.e. X positive to superior)
        • imgHdrExamNum
          int imgHdrExamNum
          8 - Read as unsigned short.
        • imgHdrSeriesNum
          short imgHdrSeriesNum
          10.
        • imgHdrSuiteID
          String imgHdrSuiteID
          0 - 4 bytes - suite ID.
        • imgLevel
          short imgLevel
          654 Level value.
        • imgLoc
          float imgLoc
          126.
        • imgPCycle
          short imgPCycle
          246 Images per cardiac .1 cycle.
        • imgrx
          short imgrx
          110 - image from which prescribed.
        • imgTLHC_A
          float imgTLHC_A
          158 Top Left Hand Corner Anterior.
        • imgTLHC_R
          float imgTLHC_R
          154 Top Left Hand Corner Right.
        • imgTLHC_S
          float imgTLHC_S
          162 Top Left Hand Corner Superior.
        • imgTRHC_A
          float imgTRHC_A
          170 Top Right Hand Corner Anterior.
        • imgTRHC_R
          float imgTRHC_R
          166 Top Right Hand Corner Right.
        • imgTRHC_S
          float imgTRHC_S
          174 Top Right Hand Corner Superior.
        • imgWindow
          short imgWindow
          652 Window value.
        • iMode
          short iMode
          298 Imaging mode.
        • integrity
          short integrity
          736 GE Image Integrity.
        • intr_del
          long intr_del
          402 Interimageinvalid input: '&#47'interloc delay (uSec).
        • inverTime
          int inverTime
          198 pulse inversion time (usec).
        • iOptions
          long iOptions
          300 Imaging options.
        • IVCntrstAgent
          String IVCntrstAgent
          72 - 17 bytes.
        • landmarkUID
          String landmarkUID
          368 - 32 bytes.
        • lenCmprsnHdr
          int lenCmprsnHdr
          76 - length of.
        • lenDBHdr
          int lenDBHdr
          108 - length of.
        • lenExamHdr
          int lenExamHdr
          136 - length of.
        • lenGraphics
          int lenGraphics
          100 - length of.
        • lenHistoHdr
          int lenHistoHdr
          84 - length of.
        • lenImageHdr
          int lenImageHdr
          152 - length of.
        • lenSeriesHdr
          int lenSeriesHdr
          144 - length of.
        • lenSuiteHdr
          int lenSuiteHdr
          128 - length of.
        • lenTextPlane
          int lenTextPlane
          92 - length of.
        • lenUID
          int lenUID
          60 - length of UID.
        • lenUnpackHdr
          int lenUnpackHdr
          68 - length of.
        • lenUsrDefData
          int lenUsrDefData
          120 - length of.
        • lmHor
          float lmHor
          88 - Horizontal landmark.
        • loc_ras
          String loc_ras
          124 1 byte RAS letter of image location.
        • magicNumber
          int magicNumber
          0x494d4746 or "IMGF" or 1229801286.
        • magStrength
          int magStrength
          80 Magnet strength (in gauss).
        • magWgtFlag
          short magWgtFlag
          730 Magnitude Weighting Flag.
        • matrixSizeX
          short matrixSizeX
          30.
        • matrixSizeY
          short matrixSizeY
          32.
        • minDAT
          int minDAT
          256 minimum delay after trigger (usec).
        • minute
          int minute
          DOCUMENT ME!
        • mobileLoc
          String mobileLoc
          470 - 4 bytes.
        • monSar
          short monSar
          238 Monitor SAR Flag.
        • month
          String month
          DOCUMENT ME!
        • monthIndex
          int monthIndex
          DOCUMENT ME!
        • mr_flip
          short mr_flip
          254 Flip angle for grass scans (degrees).
        • mr_padding
          String mr_padding
          990 spare space.
        • nEchoes
          short nEchoes
          210 number of echoes.
        • negScanSpacing
          float negScanSpacing
          858 Negative scan spacing for overlap slices.
        • nEPI
          short nEPI
          826 number of EPI shots.
        • NEX
          float NEX
          218 Number of excitations.
        • norm_A
          float norm_A
          146 Normal A coordinate.
        • norm_R
          float norm_R
          142 Normal R coordinate.
        • norm_S
          float norm_S
          150 Normal S coordinate.
        • nPhase
          int nPhase
          738 Number of Phases.
        • numCells
          long numCells
          46 Number of cells in det.
        • numDcnK
          short numDcnK
          70 Number of Decon kernels.
        • numUnImg
          int numUnImg
          216 - (internal use) Number of Unstored Images.
        • obliquePlane
          int obliquePlane
          270.
        • offsetFreq
          int offsetFreq
          862 offset Frequency_Mag. Transfer
        • op
          String op
          278 - 4 bytes operator.
        • OralCntrstAgent
          String OralCntrstAgent
          89 - 17 bytes.
        • panSysID
          String panSysID
          59 - 9 bytes - Archiver Suite and Host.
        • patian
          short patian
          124 Patient Age notation.
        • patientAge
          short patientAge
          122.
        • patientID
          String patientID
          84 - 13 bytes.
        • patientName
          String patientName
          97 - 25 bytes.
        • patientSex
          short patientSex
          126.
        • patWeight
          int patWeight
          128 Patient Weight.
        • pauseInterval
          short pauseInterval
          264 Pause interval (slices).
        • pauseTime
          float pauseTime
          266.
        • pixelID
          String pixelID
          58 - 14 bytes.
        • pixelResX
          float pixelResX
          50.
        • pixelResY
          float pixelResY
          54.
        • planeType
          short planeType
          114.
        • position
          int position
          76 - Patient Poisition.
        • prepPulse
          short prepPulse
          644 Prepartory pulse option.
        • prescan_r1
          short prescan_r1
          288 PreScan R1-Analog.
        • prescan_r2
          short prescan_r2
          290 PreScan R2-DIgital.
        • preScanOpts
          short preScanOpts
          816 bitmap of prescan options.
        • proj_alg
          short proj_alg
          596 Projection Algorithm.
        • proj_name
          String proj_name
          598 13 characters Projection Algorithm Name.
        • projectAngle
          float projectAngle
          498 Projection Angle.
        • protocolFlag
          short protocolFlag
          332 Non-zero indicates protocol exam.
        • prSysID
          String prSysID
          50 - 9 bytes - Primary Receiver Suite and Host.
        • ps_flag
          short ps_flag
          580 Autoinvalid input: '&#47'Manual Prescan flag.
        • ps_status
          short ps_status
          582 Bitmap of changed values.
        • psd_dateTime
          int psd_dateTime
          342 PSD Creation Date and Time.
        • psd_iname
          String psd_iname
          346 13 characters.
        • pSeq
          short pSeq
          304 Pulse sequence.
        • ptrCmprsnHdr
          int ptrCmprsnHdr
          72 - pointer to.
        • ptrDBHdr
          int ptrDBHdr
          104 - pointer to.
        • ptrExamHdr
          int ptrExamHdr
          132 - pointer to.
        • ptrGraphics
          int ptrGraphics
          96 - pointer to.
        • ptrHistoHdr
          int ptrHistoHdr
          80 - pointer to.
        • ptrImage
          int ptrImage
          4 - byte displacement to pixel data.
        • ptrImageHdr
          int ptrImageHdr
          148 - pointer to.
        • ptrSeriesHdr
          int ptrSeriesHdr
          140 - pointer to.
        • ptrSuiteHdr
          int ptrSuiteHdr
          124 - pointer to.
        • ptrTextPlane
          int ptrTextPlane
          88 - pointer to.
        • ptrUID
          int ptrUID
          56 - pointer to unique image identifier (UID).
        • ptrUnpackHdr
          int ptrUnpackHdr
          64 - pointer to.
        • ptrUsrDefData
          int ptrUsrDefData
          116 - pointer to.
        • pulseRepTime
          int pulseRepTime
          194 pulse repetition time (usec).
        • pulseSeqMode
          short pulseSeqMode
          306.
        • pulseSeqName
          String pulseSeqName
          308 33 characters.
        • rawRunNum
          int rawRunNum
          384 RawData Run Number.
        • rbpm
          short rbpm
          832 respiratory rate, breaths per minute.
        • rcvGain1
          short rcvGain1
          250 Actual receive gain analog (.1db).
        • rcvGain2
          short rcvGain2
          252 Actual receive gain digital (.1db).
        • rcvType
          short rcvType
          836 type of receiver used.
        • refImg
          String refImg
          650 Reference image field.
        • refPhy
          String refPhy
          212 - 33 bytes Referring Physician.
        • repTime
          float repTime
          242 Cardiac repertition time.
        • reqnum
          String reqnum
          195 - 13 bytes Requisition Number.
        • rtPoint
          short rtPoint
          834 repiratory trigger point as percent of max.
        • sarAvg
          float sarAvg
          230 Average SAR.
        • sarAvgHead
          float sarAvgHead
          854 Avg head SAR.
        • sarPeak
          float sarPeak
          234 Peak SAR.
        • satbits
          short satbits
          552 Bitmap of SAT selections.
        • satxloc1
          short satxloc1
          556 R-side pulse rel to lndmrk.
        • satxloc2
          short satxloc2
          558 L-side pulse rel to lndmrk.
        • satxthick
          short satxthick
          568 Thickness of X-axis SAT pulse.
        • satyloc1
          short satyloc1
          560 A-side SAT pulse rel to lndmrk.
        • satyloc2
          short satyloc2
          562 P-side SAT pulse rel to lndmrk.
        • satythick
          short satythick
          570 Thickness of Y-axis SAT pulse.
        • satzloc1
          short satzloc1
          564 S-side SAT pulse rel to lndmrk.
        • satzloc2
          short satzloc2
          566 I-side SAT pulse rel to lndmrk.
        • satzthick
          short satzthick
          572 Thickness of Z-axis SAT pulse.
        • scanAcqNum
          short scanAcqNum
          728 Scan Acquisition Number.
        • scanProtocolName
          String scanProtocolName
          92 - 25 bytes - Scan Protocol Name.
        • scanSpacing
          float scanSpacing
          116 Spacing between scans (mm?).
        • scanType
          short scanType
          74 - Scout or Axial (for CT).
        • scic
          short scic
          554 Surface Coil Intensity Correction Flag.
        • scoutType
          short scoutType
          122 Scout Type (AP or lateral).
        • screenFormat
          short screenFormat
          112 - (8invalid input: '&#4716') bits.
        • scTime
          float scTime
          22 scan duration in seconds.
        • seActualDT
          int seActualDT
          16 - Actual Series Dateinvalid input: '&#47'Time Stamp.
        • seAllocKey
          String seAllocKey
          154 - 13 bytes - Process that allocated this record.
        • seChecksum
          int seChecksum
          188 - (internal use) Series Record checksum.
        • seComplete
          int seComplete
          192 - (internal use) Series Complete Flag.
        • seconds
          int seconds
          DOCUMENT ME!
        • seContrast
          short seContrast
          118 - greater than zero if image used contrast (Linvalid input: '&#47'S).
        • seDateTime
          int seDateTime
          12 - Allocation series Dateinvalid input: '&#47'Time Stamp.
        • seDeltaCnt
          int seDeltaCnt
          168 - (internal use) number of updates to header.
        • seDesc
          String seDesc
          20 - 30 bytes - Series Description.
        • seDiskID
          byte seDiskID
          6 - Disk ID for this series - GE internal.
        • seExamNo
          short seExamNo
          8 - Exam number.
        • seImageCt
          int seImageCt
          200 - (internal use) Last Image Number Used.
        • seLandmarkCnt
          int seLandmarkCnt
          136 - Landmark counter.
        • seLastMod
          int seLastMod
          150 - Dateinvalid input: '&#47'Time of last change.
        • seNacq
          short seNacq
          140 - Number of acquisitions.
        • seNumArch
          int seNumArch
          196 - (internal use) Number of Images Archived.
        • seNumImages
          int seNumImages
          204 - (internal use) Number of Images Existing.
        • sePadding
          String sePadding
          432 - 588 bytes.
        • sePdsA
          float sePdsA
          176 - Pixel data size - as stored.
        • sePdsC
          float sePdsC
          180 - Pixel data size - Compressed.
        • sePdsU
          float sePdsU
          184 - Pixel data size - Uncompressed.
        • sePlane
          short sePlane
          72 - Most-like Plane (for Linvalid input: '&#47'S).
        • sePseq
          short sePseq
          132 - Last Pulse Sequence Used (Linvalid input: '&#47'S).
        • seriesNum
          short seriesNum
          10 - series number.
        • seriesUID
          String seriesUID
          336 - 32 bytes.
        • serrx
          short serrx
          108 - series from which prescribed.
        • serviceID
          String serviceID
          454 - 16 bytes.
        • seSortOrder
          short seSortOrder
          134 - (internal use) Image Sort Order (Linvalid input: '&#47'S).
        • seSource
          short seSource
          70 - Series from which prescribed.
        • seSuid
          String seSuid
          0 - 4 bytes - Suite ID for this Series.
        • seType
          short seType
          68 - Series Type.
        • seUniq
          short seUniq
          4 - The make-unique flag - GE internal.
        • seVersCre
          String seVersCre
          172 - 2 bytes - Genesis Version - Created.
        • seVersCur
          String seVersCur
          174 - 2 bytes - Genesis Version - Now.
        • sliceThickness
          float sliceThickness
          26 in mm.
        • slocfov
          int slocfov
          274 Slice offsets on frequency axis.
        • slop_float_1
          float slop_float_1
          676 Float Slop Field 1.
        • slop_float_2
          float slop_float_2
          680 Float Slop Field 2.
        • slop_float_3
          float slop_float_3
          684 Float Slop Field 3.
        • slop_float_4
          float slop_float_4
          688 Float Slop Field 4.
        • slop_float_5
          float slop_float_5
          692 Float Slop Field 5.
        • slop_int_1
          int slop_int_1
          656 Integer Slop Field 1.
        • slop_int_2
          int slop_int_2
          660 Integer Slop Field 2.
        • slop_int_3
          int slop_int_3
          664 Integer Slop Field 3.
        • slop_int_4
          int slop_int_4
          668 Integer Slop Field 4.
        • slop_int_5
          int slop_int_5
          672 Integer Slop Field 5.
        • slop_int_6
          int slop_int_6
          974 Integer Slop Field 6.
        • slop_int_7
          int slop_int_7
          978 Integer Slop Field 7.
        • slop_int_8
          int slop_int_8
          982 Integer Slop Field 8.
        • slop_int_9
          int slop_int_9
          986 Integer Slop Field 9.
        • slop_str_1
          String slop_str_1
          696 16 characters String Slop Field 1.
        • slop_str_2
          String slop_str_2
          712 16 characters String Slop Field 2.
        • slquant
          short slquant
          398 Number of slices in this scan group.
        • sop_uid
          String sop_uid
          778 32 characters Service Obj Clas Unique ID.
        • srcToDet
          float srcToDet
          58 Distance from source to detector.
        • srcToIso
          float srcToIso
          62 Distance from source to iso.
        • startAdjust
          int startAdjust
        • startLoc
          float startLoc
          122 - First scan location (Linvalid input: '&#47'S).
        • startRAS
          String startRAS
          120 - 1 byte - RAS letter for first scan location (Linvalid input: '&#47'S).
        • studyStatus
          short studyStatus
          506 Indicates if study has complete info (DICOMinvalid input: '&#47'genesis).
        • studyUID
          String studyUID
          474 - 32 bytes.
        • suiteID
          String suiteID
          0 - 4 bytes.
        • sumImg
          String sumImg
          651 Summary image field.
        • supp_tech
          short supp_tech
          392 SAT fatinvalid input: '&#47'waterinvalid input: '&#47'none.
        • surfaceCoilType
          short surfaceCoilType
          380.
        • surfcext
          short surfcext
          382 Extremity Coil Flag.
        • swapPF
          short swapPF
          262 Swap phase-frequency axis.
        • tableDelta
          float tableDelta
          214.
        • tDel
          int tDel
          226 Delay time after trigger (msec).
        • te2
          int te2
          206 second echo echo (usec).
        • thk_disclmr
          short thk_disclmr
          578 Slice Thickness.
        • threshMax1
          int threshMax1
          628 Upper range of pixels 1.
        • threshMax2
          int threshMax2
          636 Upper range of pixels 2.
        • threshMin1
          int threshMin1
          624 Lower range of pixels 1.
        • threshMin2
          int threshMin2
          632 Lower range of pixels 2.
        • toArchiveCnt
          int toArchiveCnt
          228 - (internal use) number of Unarchived images.
        • toArchiveData
          int toArchiveData
          236.
        • toArchiveLen
          int toArchiveLen
          232 - (internal use) Unarchived images keys in Series.
        • trauma
          short trauma
          132 Trauma Flag.
        • trgWindow
          short trgWindow
          240 Trigger window (invalid input: '&#37' of R-R interval).
        • tubeType
          short tubeType
          66.
        • unImagesData
          int unImagesData
          224.
        • unImagesLen
          int unImagesLen
          220 - (internal use) Unstored Image keys in Series.
        • uniq
          short uniq
          4 - (internal use) Make-Unique Flag.
        • uniqSysID
          String uniqSysID
          438 - 16 bytes.
        • unOriginal
          short unOriginal
          824 identifies image as original or unoriginal.
        • user_bitmap
          int user_bitmap
          292 Bitmap defining user Cvs.
        • user0
          float user0
          406 User Variable 0.
        • user1
          float user1
          410 User Variable 1.
        • user10
          float user10
          446 User Variable 10.
        • user11
          float user11
          450 User Variable 11.
        • user12
          float user12
          454 User Variable 12.
        • user13
          float user13
          458 User Variable 13.
        • user14
          float user14
          462 User Variable 14.
        • user15
          float user15
          466 User Variable 15.
        • user16
          float user16
          470 User Variable 16.
        • user17
          float user17
          474 User Variable 17.
        • user18
          float user18
          478 User Variable 18.
        • user19
          float user19
          482 User Variable 19.
        • user2
          float user2
          414 User Variable 2.
        • user20
          float user20
          486 User Variable 20.
        • user21
          float user21
          490 User Variable 21.
        • user22
          float user22
          494 User Variable 22.
        • user23n
          float user23n
          588 User Variable 23.
        • user24
          float user24
          502 Concat Sat Type Flag.
        • user24n
          float user24n
          592 User Variable 24.
        • user25
          float user25
          878 User Variable 25.
        • user26
          float user26
          882 User Variable 26.
        • user27
          float user27
          886 User Variable 27.
        • user28
          float user28
          890 User Variable 28.
        • user29
          float user29
          894 User Variable 29.
        • user3
          float user3
          418 User Variable 3.
        • user30
          float user30
          898 User Variable 30.
        • user31
          float user31
          902 User Variable 31.
        • user32
          float user32
          906 User Variable 32.
        • user33
          float user33
          910 User Variable 33.
        • user34
          float user34
          914 User Variable 34.
        • user35
          float user35
          918 User Variable 35.
        • user36
          float user36
          922 User Variable 36.
        • user37
          float user37
          926 User Variable 37.
        • user38
          float user38
          930 User Variable 38.
        • user39
          float user39
          934 User Variable 39.
        • user4
          float user4
          422 User Variable 4.
        • user40
          float user40
          938 User Variable 40.
        • user41
          float user41
          942 User Variable 41.
        • user42
          float user42
          946 User Variable 42.
        • user43
          float user43
          950 User Variable 43.
        • user44
          float user44
          954 User Variable 44.
        • user45
          float user45
          958 User Variable 45.
        • user46
          float user46
          962 User Variable 46.
        • user47
          float user47
          966 User Variable 47.
        • user48
          float user48
          970 User variable 48.
        • user5
          float user5
          426 User Variable 5.
        • user6
          float user6
          430 User Variable 6.
        • user7
          float user7
          434 User Variable 7.
        • user8
          float user8
          438 User Variable 8.
        • user9
          float user9
          442 User Variable 9.
        • userFillMapLSW
          int userFillMapLSW
          874 Describes what process fills in the user CVs, ifcc or TIR.
        • userFillMapMSW
          int userFillMapMSW
          870 Describes what process fills in the user CVs, ifcc or TIR.
        • userUsageTag
          int userUsageTag
          866 Defines how following user CVs are to be filled in.
        • valueBg
          int valueBg
          32 - background value of non image locations.
        • varEcho
          short varEcho
          648 Variable echo flag.
        • vas_collapse
          short vas_collapse
          586 Collapse image.
        • vasMode
          short vasMode
          744 Vascular Mode.
        • vbw
          float vbw
          394 Variable Bandwidth (Hz).
        • venc
          short venc
          576 Phase contrast velocity encoding (mminvalid input: '&#47'sec).
        • vencScale
          float vencScale
          732 Scale Weighting Venc (Velocity Encodinginvalid input: '&#47'PI).
        • viewsPerSeg
          short viewsPerSeg
          830 views per segment.
        • width
          int width
          8 - width of image.
        • xAxisRot
          float xAxisRot
          612 X axis rotation.
        • xBaseEnd
          short xBaseEnd
          144 - Ending number for baselines.
        • xBaseSt
          short xBaseSt
          142 - Starting number for baselines.
        • xenhEnd
          short xenhEnd
          148 - Ending number for enhanced scans.
        • xenhSt
          short xenhSt
          146 - Starting number for enhanced scans.
        • xmtFreq
          int xmtFreq
          278 Center Frequency (0.1 Hz).
        • xmtGain
          short xmtGain
          248 Actual transmit gain (.1 db).
        • yAxisRot
          float yAxisRot
          616 Yaxis rotation.
        • year
          int year
          DOCUMENT ME!
        • zAxisRot
          float zAxisRot
          620 Z axis rotation.
        • zeroCell
          float zeroCell
          50 Cell number at theta.

    • Class gov.nih.mipav.model.file.FileInfoICS

      class FileInfoICS extends FileInfoBase implements Serializable
      serialVersionUID:
      -4859517795116658689L

      • Serialized Fields

        • captureVersion
          String captureVersion
          DOCUMENT ME!
        • channels
          String[] channels
          DOCUMENT ME!
        • dataSetFileName
          String dataSetFileName
          DOCUMENT ME!
        • exPhotonCnt
          String[] exPhotonCnt
          DOCUMENT ME!
        • filterExposureTimeX
          String filterExposureTimeX
          DOCUMENT ME!
        • filterFluorophoreX
          String[] filterFluorophoreX
          DOCUMENT ME!
        • history
          String[] history
          DOCUMENT ME!
        • labels
          String[] labels
          DOCUMENT ME!
        • lambdaEm
          String[] lambdaEm
          DOCUMENT ME!
        • lambdaEx
          String[] lambdaEx
          DOCUMENT ME!
        • mapchannel
          String[] mapchannel
          DOCUMENT ME!
        • numAperture
          String[] numAperture
          DOCUMENT ME!
        • pinholeRadius
          String[] pinholeRadius
          DOCUMENT ME!
        • plateChamberID
          String plateChamberID
          DOCUMENT ME!
        • plateVesselID
          String plateVesselID
          DOCUMENT ME!
        • probe
          String[] probe
          DOCUMENT ME!
        • refrInxLensMedium
          String[] refrInxLensMedium
          DOCUMENT ME!
        • refrInxMedium
          String[] refrInxMedium
          DOCUMENT ME!
        • scilType
          String scilType
          DOCUMENT ME!
        • sensorModel
          String sensorModel
          DOCUMENT ME!
        • sensorType
          String sensorType
          DOCUMENT ME!
        • specimen
          String[] specimen
          DOCUMENT ME!
        • specimenSpecies
          String[] specimenSpecies
          DOCUMENT ME!
        • version
          String version
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoImageXML

      class FileInfoImageXML extends FileInfoXML implements Serializable
      serialVersionUID:
      -6296437302928259711L

      • Serialized Fields

        • bodyPart
          String bodyPart
          DOCUMENT ME!
        • currentPSetDesc
          String currentPSetDesc
          String for the current PSet description (for key).
        • currentSurfacePath
          String currentSurfacePath
          Used to keep track of the current surface.
        • currentVOIPath
          String currentVOIPath
          Used to keep track of the current VOI.
        • diagnosis
          String diagnosis
          DOCUMENT ME!
        • DOB
          String DOB
          DOCUMENT ME!
        • equipmentName
          String equipmentName
          Scan attributes. Optional XML tag.
        • height
          int height
          DOCUMENT ME!
        • history
          String history
          The image history. Used by the NDAR meta-information generation dialog to write out the name of the zip file where the original data files are stored.
        • invest
          boolean[] invest
          DOCUMENT ME!
        • investigators
          FileInfoImageXML.Investigator[] investigators
          Investigators (up to 3). Optional XML tag.
        • linkedImagePath
          String linkedImagePath
          linked image path (optional).
        • matrix
          TransMatrix matrix
          Transformation matrix.
        • protocol
          String protocol
          DOCUMENT ME!
        • race
          String race
          DOCUMENT ME!
        • scanDate
          String scanDate
          DOCUMENT ME!
        • scanID
          String scanID
          DOCUMENT ME!
        • scanTime
          String scanTime
          DOCUMENT ME!
        • setTable
          Hashtable<String,XMLPSet> setTable
          Hashtable for holding sets of parameters.
        • sex
          String sex
          DOCUMENT ME!
        • subjectID
          String subjectID
          DOCUMENT ME!
        • subjectName
          String subjectName
          Subject's information.
        • surfaces
          Hashtable<String,FileInfoImageXML.SurfaceLink> surfaces
          List of files which describe surfaces attached to this image.
        • VOIs
          Hashtable<String,FileInfoImageXML.VOILink> VOIs
          List of files which describe VOIs attached to this image.
        • weight
          int weight
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoImageXML.Investigator

      class Investigator extends Object implements Serializable
      serialVersionUID:
      -5267494343773142072L

      • Serialized Fields

        • affiliation
          String affiliation
          Affiliation of investigator.
        • email
          String email
          Investigator's email.
        • name
          String name
          Name of investigator.
        • phone
          String phone
          Investigator's phone number.
        • title
          String title
          Title of investigator.

    • Class gov.nih.mipav.model.file.FileInfoInterfile

      class FileInfoInterfile extends FileInfoBase implements Serializable
      serialVersionUID:
      1860672784494846816L

      • Serialized Fields

        • acquiredCardiacCycles
          String[] acquiredCardiacCycles
          DOCUMENT ME!
        • acquiredCardiacCyclesIndex
          int acquiredCardiacCyclesIndex
          DOCUMENT ME!
        • acquiredStudyDuration
          String[] acquiredStudyDuration
          DOCUMENT ME!
        • acquiredStudyDurationIndex
          int acquiredStudyDurationIndex
          DOCUMENT ME!
        • appliedCorrections
          String appliedCorrections
          DOCUMENT ME!
        • attenuationCorrection
          String attenuationCorrection
          DOCUMENT ME!
        • betaHalflife
          String[] betaHalflife
          DOCUMENT ME!
        • branchingFactor
          String[] branchingFactor
          DOCUMENT ME!
        • bytesPerPixel
          String[] bytesPerPixel
          DOCUMENT ME!
        • bytesPerPixelIndex
          int bytesPerPixelIndex
          DOCUMENT ME!
        • centerCenter
          String centerCenter
          DOCUMENT ME!
        • contactPerson
          String contactPerson
          DOCUMENT ME!
        • conversionProgram
          String conversionProgram
          DOCUMENT ME!
        • dataCompression
          String dataCompression
          DOCUMENT ME!
        • dataDescription
          String dataDescription
          DOCUMENT ME!
        • dataEncode
          String dataEncode
          DOCUMENT ME!
        • decayCorrected
          String decayCorrected
          DOCUMENT ME!
        • detectorHeadNumber
          String detectorHeadNumber
          DOCUMENT ME!
        • dimensionNumber
          String dimensionNumber
          DOCUMENT ME!
        • dynamicStudyGeneral
          boolean dynamicStudyGeneral
          DOCUMENT ME!
        • elapsedStudyDuration
          String elapsedStudyDuration
          DOCUMENT ME!
        • energyNumber
          int energyNumber
          DOCUMENT ME!
        • energyWindowName
          String[] energyWindowName
          DOCUMENT ME!
        • energyWindowsNumber
          String energyWindowsNumber
          DOCUMENT ME!
        • examType
          String examType
          DOCUMENT ME!
        • fGroupNumber
          int fGroupNumber
          DOCUMENT ME!
        • filterName
          String filterName
          DOCUMENT ME!
        • floodCorrected
          String floodCorrected
          DOCUMENT ME!
        • frameGroupImages
          String[] frameGroupImages
          DOCUMENT ME!
        • frameGroupImagesIndex
          int frameGroupImagesIndex
          DOCUMENT ME!
        • frameGroupNumber
          String frameGroupNumber
          DOCUMENT ME!
        • framingMethod
          String[] framingMethod
          DOCUMENT ME!
        • framingMethodIndex
          int framingMethodIndex
          DOCUMENT ME!
        • gammaHalflife
          String[] gammaHalflife
          DOCUMENT ME!
        • gatedFrameMode
          String[] gatedFrameMode
        • gatedFrameModeIndex
          int gatedFrameModeIndex
        • gatedStudyGeneral
          boolean gatedStudyGeneral
          DOCUMENT ME!
        • generalData
          boolean generalData
          DOCUMENT ME!
        • generalImageData
          boolean generalImageData
          DOCUMENT ME!
        • haveGated
          boolean haveGated
          DOCUMENT ME!
        • haveReconstructed
          boolean haveReconstructed
          DOCUMENT ME!
        • haveStaticStudy
          boolean haveStaticStudy
          DOCUMENT ME!
        • haveTomographic
          boolean haveTomographic
          DOCUMENT ME!
        • i
          int i
          DOCUMENT ME!
        • imageDataDescription
          boolean imageDataDescription
          DOCUMENT ME!
        • imageDuration
          String[] imageDuration
          DOCUMENT ME!
        • imageDurationIndex
          int imageDurationIndex
          DOCUMENT ME!
        • imageRelativeStartTime
          String[] imageRelativeStartTime
          DOCUMENT ME!
        • imageRelativeStartTimeIndex
          int imageRelativeStartTimeIndex
          DOCUMENT ME!
        • imagesPerEWindow
          String imagesPerEWindow
          DOCUMENT ME!
        • imageStartTime
          String[] imageStartTime
          DOCUMENT ME!
        • imageStartTimeIndex
          int imageStartTimeIndex
          DOCUMENT ME!
        • imagingModality
          String imagingModality
          DOCUMENT ME!
        • indexNestingLevel
          String indexNestingLevel
          DOCUMENT ME!
        • interfileDataType
          String interfileDataType
          DOCUMENT ME!
        • iNumber
          int iNumber
          DOCUMENT ME!
        • isoNumber
          int isoNumber
          DOCUMENT ME!
        • isotopeName
          String[] isotopeName
          DOCUMENT ME!
        • isotopeNumber
          String isotopeNumber
          DOCUMENT ME!
        • keysDate
          String keysDate
          DOCUMENT ME!
        • keysVersion
          String keysVersion
          DOCUMENT ME!
        • label
          String[] label
          DOCUMENT ME!
        • labelIndex
          int labelIndex
          DOCUMENT ME!
        • lowerLevel
          String[] lowerLevel
          DOCUMENT ME!
        • matrixSize1
          String[] matrixSize1
          DOCUMENT ME!
        • matrixSize1Index
          int matrixSize1Index
          DOCUMENT ME!
        • matrixSize2
          String[] matrixSize2
          DOCUMENT ME!
        • matrixSize2Index
          int matrixSize2Index
          DOCUMENT ME!
        • maximumPixelCount
          String[] maximumPixelCount
          DOCUMENT ME!
        • maximumPixelCountIndex
          int maximumPixelCountIndex
          DOCUMENT ME!
        • maximumPixelCountInGroup
          String[] maximumPixelCountInGroup
          DOCUMENT ME!
        • maximumPixelCountInGroupIndex
          int maximumPixelCountInGroupIndex
          DOCUMENT ME!
        • numberFormat
          String[] numberFormat
          DOCUMENT ME!
        • numberFormatIndex
          int numberFormatIndex
          DOCUMENT ME!
        • numberImages
          int numberImages
        • numberImagesPerEWindow
          int numberImagesPerEWindow
          DOCUMENT ME!
        • obliqueReconstruction
          String obliqueReconstruction
          DOCUMENT ME!
        • observedCardiacCycles
          String observedCardiacCycles
          DOCUMENT ME!
        • organ
          String organ
        • originalInstitution
          String originalInstitution
          DOCUMENT ME!
        • originatingSystem
          String originatingSystem
          DOCUMENT ME!
        • patientDOB
          String patientDOB
          DOCUMENT ME!
        • patientID
          String patientID
          DOCUMENT ME!
        • patientName
          String patientName
          DOCUMENT ME!
        • patientOrientation
          String patientOrientation
          DOCUMENT ME!
        • patientRotation
          String patientRotation
          DOCUMENT ME!
        • patientSex
          String patientSex
          DOCUMENT ME!
        • pauseBetweenFrameGroups
          String[] pauseBetweenFrameGroups
          DOCUMENT ME!
        • pauseBetweenFrameGroupsIndex
          int pauseBetweenFrameGroupsIndex
          DOCUMENT ME!
        • pauseBetweenImages
          String[] pauseBetweenImages
          DOCUMENT ME!
        • pauseBetweenImagesIndex
          int pauseBetweenImagesIndex
          DOCUMENT ME!
        • PETDataType
          String PETDataType
          DOCUMENT ME!
        • PETStudyGeneral
          boolean PETStudyGeneral
          DOCUMENT ME!
        • PETStudyImageData
          boolean PETStudyImageData
          DOCUMENT ME!
        • processStatus
          String processStatus
          DOCUMENT ME!
        • programAuthor
          String programAuthor
          DOCUMENT ME!
        • programDate
          String programDate
          DOCUMENT ME!
        • programVersion
          String programVersion
          DOCUMENT ME!
        • projectionNumber
          String projectionNumber
          DOCUMENT ME!
        • projectionTime
          String projectionTime
          DOCUMENT ME!
        • quantificationUnits
          String quantificationUnits
          DOCUMENT ME!
        • radiopharmaceutical
          String radiopharmaceutical
          DOCUMENT ME!
        • reconstructionMethod
          String reconstructionMethod
          DOCUMENT ME!
        • referenceFrameNumber
          String referenceFrameNumber
          DOCUMENT ME!
        • rotationExtent
          String rotationExtent
          DOCUMENT ME!
        • RRCycles
          String[] RRCycles
          DOCUMENT ME!
        • RRCyclesIndex
          int RRCyclesIndex
          DOCUMENT ME!
        • RRHistogram
          String[] RRHistogram
          DOCUMENT ME!
        • RRHistogramIndex
          int RRHistogramIndex
          DOCUMENT ME!
        • scalingFactor1
          String[] scalingFactor1
          DOCUMENT ME!
        • scalingFactor1Index
          int scalingFactor1Index
          DOCUMENT ME!
        • scalingFactor2
          String[] scalingFactor2
          DOCUMENT ME!
        • scalingFactor2Index
          int scalingFactor2Index
          DOCUMENT ME!
        • scannerQuantificationFactor
          String scannerQuantificationFactor
          DOCUMENT ME!
        • scatterCorrected
          String scatterCorrected
          DOCUMENT ME!
        • scatterCorrectionMethod
          String scatterCorrectionMethod
          DOCUMENT ME!
        • sliceNumber
          String sliceNumber
          DOCUMENT ME!
        • sliceOrientation
          String sliceOrientation
        • spectStudyGeneral
          boolean spectStudyGeneral
          DOCUMENT ME!
        • spectStudyReconstructedData
          boolean spectStudyReconstructedData
          DOCUMENT ME!
        • startHorizontalBedPosition
          String startHorizontalBedPosition
          DOCUMENT ME!
        • staticStudyGeneral
          boolean staticStudyGeneral
          DOCUMENT ME!
        • studyDate
          String studyDate
          DOCUMENT ME!
        • studyDuration
          String studyDuration
          DOCUMENT ME!
        • studyID
          String studyID
          DOCUMENT ME!
        • studyTime
          String studyTime
          DOCUMENT ME!
        • tFrame
          int tFrame
          DOCUMENT ME!
        • timeFrameNumber
          int timeFrameNumber
          DOCUMENT ME!
        • timeFrames
          String timeFrames
          DOCUMENT ME!
        • timeWindowImages
          String[] timeWindowImages
          DOCUMENT ME!
        • timeWindowImagesIndex
          int timeWindowImagesIndex
          DOCUMENT ME!
        • timeWindowLowerLimit
          String[] timeWindowLowerLimit
          DOCUMENT ME!
        • timeWindowLowerLimitIndex
          int timeWindowLowerLimitIndex
          DOCUMENT ME!
        • timeWindows
          String timeWindows
          DOCUMENT ME!
        • timeWindowsNumber
          int timeWindowsNumber
          DOCUMENT ME!
        • timeWindowUpperLimit
          String[] timeWindowUpperLimit
          DOCUMENT ME!
        • timeWindowUpperLimitIndex
          int timeWindowUpperLimitIndex
          DOCUMENT ME!
        • totalCounts
          String[] totalCounts
          DOCUMENT ME!
        • totalCountsIndex
          int totalCountsIndex
          DOCUMENT ME!
        • totalImageNumber
          String totalImageNumber
          DOCUMENT ME!
        • upperLevel
          String[] upperLevel
          DOCUMENT ME!
        • windowA
          String windowA
        • windowB
          String windowB
        • windowC
          String windowC
        • wNumber
          int wNumber
          DOCUMENT ME!
        • zAxisFilter
          String zAxisFilter
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoJP2

      class FileInfoJP2 extends FileInfoBase implements Serializable

      • Serialized Fields

        • imageDescription
          String imageDescription
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoJPEG_LS

      class FileInfoJPEG_LS extends FileInfoBase implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoJPEG_XL

      class FileInfoJPEG_XL extends FileInfoBase implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoJSON

      class FileInfoJSON extends FileInfoBase implements Serializable

      • Serialized Fields

        • contributor
          String contributor
        • date_created
          String date_created
        • description
          String description
          Use serialVersionUID for interoperability.
        • url
          String url
        • version
          String version
        • year
          String year

    • Class gov.nih.mipav.model.file.FileInfoLattice

      class FileInfoLattice extends FileInfoBase implements Serializable
      serialVersionUID:
      6546787758481646181L

    • Class gov.nih.mipav.model.file.FileInfoLIFF

      class FileInfoLIFF extends FileInfoBase implements Serializable

      • Serialized Fields

        • autoContrast
          double autoContrast
        • binning
          double binning
        • bitDepth
          short bitDepth
        • camera
          String camera
        • channelArray
          String[] channelArray
        • channelNumber
          int channelNumber
        • colorization
          double colorization
        • cooling
          double cooling
        • CRIRGBFilter
          double CRIRGBFilter
        • digitalGain
          double digitalGain
        • emissionFilterChangerArray
          double[] emissionFilterChangerArray
        • excitationArray
          double[] excitationArray
        • exposureArray
          double[] exposureArray
        • filterTurretArray
          double[] filterTurretArray
        • focusPosition
          double focusPosition
        • gain
          double gain
        • layerString
          String[] layerString
          Use serialVersionUID for interoperability.
        • leicaCondenserTurret
          double leicaCondenserTurret
        • leicaFilterCubeArray
          double[] leicaFilterCubeArray
        • leicaFIMArray
          double[] leicaFIMArray
        • leicaICTurret
          double leicaICTurret
        • leicaMagnificationChanger
          double leicaMagnificationChanger
        • lightMode
          double lightMode
        • ludlAuxWheel1
          double ludlAuxWheel1
        • ludlMainWheel1Array
          double[] ludlMainWheel1Array
        • microfocusPosition
          double microfocusPosition
        • microscope
          String microscope
        • objectiveName
          double objectiveName
        • objectivePosition
          double objectivePosition
        • offset
          double offset
        • sensitivityArray
          double[] sensitivityArray
        • SutterDG4Filter
          double SutterDG4Filter
        • SutterL10Filter1Array
          double[] SutterL10Filter1Array
        • SutterL10Filter2Array
          double[] SutterL10Filter2Array
        • wavelengthArray
          double[] wavelengthArray
        • xPosition
          double xPosition
        • yPosition
          double yPosition
        • zPosition
          double zPosition

    • Class gov.nih.mipav.model.file.FileInfoLSM

      class FileInfoLSM extends FileInfoBase implements Serializable
      serialVersionUID:
      4011175280016387707L

      • Serialized Fields

        • bleachedROIShape
          int bleachedROIShape
          DOCUMENT ME!
        • blueArray
          int[] blueArray
          DOCUMENT ME!
        • channelDataTypes
          int[] channelDataTypes
          DOCUMENT ME!
        • channelNames
          String[] channelNames
          DOCUMENT ME!
        • channels
          int channels
          DOCUMENT ME!
        • dimensionM
          int dimensionM
        • dimensionP
          int dimensionP
        • displayAspectTime
          double displayAspectTime
          DOCUMENT ME!
        • displayAspectX
          double displayAspectX
          DOCUMENT ME!
        • displayAspectY
          double displayAspectY
          DOCUMENT ME!
        • displayAspectZ
          double displayAspectZ
          DOCUMENT ME!
        • eventDescription
          String[] eventDescription
          DOCUMENT ME!
        • eventTime
          double[] eventTime
          DOCUMENT ME!
        • eventType
          int[] eventType
          DOCUMENT ME!
        • firstSliceAfterBleach
          int firstSliceAfterBleach
          DOCUMENT ME!
        • greenArray
          int[] greenArray
          DOCUMENT ME!
        • imageDescription
          String imageDescription
        • knotX
          double[] knotX
          DOCUMENT ME!
        • knotY
          double[] knotY
          DOCUMENT ME!
        • lastSliceBeforeBleach
          int lastSliceBeforeBleach
          DOCUMENT ME!
        • LSMDataType
          int LSMDataType
          DOCUMENT ME!
        • LSMDataType2
          int LSMDataType2
          DOCUMENT ME!
        • mono
          int mono
          DOCUMENT ME!
        • objectiveSphereCorrection
          double objectiveSphereCorrection
          DOCUMENT ME!
        • originX
          double originX
          The x-offset of the center of the image in meter relative to the optical axis. For LSM images the x-direction is the direction of the x-scanner. In releases prior to 4.0 the entry was not used and the value 0 was written instead.
        • originY
          double originY
          The y-offset of the center of the image in meter relative to the optical axis. For LSM images the y-direction is the direction of the y-scanner. In releases prior to 4.0 the entry was not used and the value 0 was written instead.
        • redArray
          int[] redArray
          DOCUMENT ME!
        • scanType
          int scanType
          DOCUMENT ME!
        • spectralScan
          int spectralScan
          DOCUMENT ME!
        • timeDifferenceX
          double timeDifferenceX
        • timeDifferenceY
          double timeDifferenceY
        • timeDifferenceZ
          double timeDifferenceZ
        • timeDim
          int timeDim
          DOCUMENT ME!
        • timeInterval
          double timeInterval
          DOCUMENT ME!
        • timeStamp
          double[] timeStamp
          DOCUMENT ME!
        • wavelengths
          double[] wavelengths
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoMagnetomVision

      class FileInfoMagnetomVision extends FileInfoBase implements Serializable
      serialVersionUID:
      -7248419259071769004L

      • Serialized Fields

        • AcquisitionDateDD
          int AcquisitionDateDD
          DOCUMENT ME!
        • AcquisitionDateMM
          int AcquisitionDateMM
          DOCUMENT ME!
        • AcquisitionDateYYYY
          int AcquisitionDateYYYY
          DOCUMENT ME!
        • AcquisitionTimeHH
          int AcquisitionTimeHH
          DOCUMENT ME!
        • AcquisitionTimeMM
          int AcquisitionTimeMM
          DOCUMENT ME!
        • AcquisitionTimeSS
          int AcquisitionTimeSS
          DOCUMENT ME!
        • Annotation
          String Annotation
          DOCUMENT ME!
        • CalibrationDateDD
          int CalibrationDateDD
          DOCUMENT ME!
        • CalibrationDateMM
          int CalibrationDateMM
          DOCUMENT ME!
        • CalibrationDateYYYY
          int CalibrationDateYYYY
          DOCUMENT ME!
        • CalibrationTimeHH
          int CalibrationTimeHH
          DOCUMENT ME!
        • CalibrationTimeMM
          int CalibrationTimeMM
          DOCUMENT ME!
        • CalibrationTimeSS
          int CalibrationTimeSS
          DOCUMENT ME!
        • CenterPointX
          double CenterPointX
          DOCUMENT ME!
        • CenterPointY
          double CenterPointY
          DOCUMENT ME!
        • CenterPointZ
          double CenterPointZ
          DOCUMENT ME!
        • ColumnVectorX
          double ColumnVectorX
          DOCUMENT ME!
        • ColumnVectorY
          double ColumnVectorY
          DOCUMENT ME!
        • ColumnVectorZ
          double ColumnVectorZ
          DOCUMENT ME!
        • DisplayMatrixSize
          int DisplayMatrixSize
          DOCUMENT ME!
        • DistanceFromIsocenter
          double DistanceFromIsocenter
          DOCUMENT ME!
        • DOBDD
          int DOBDD
          DOCUMENT ME!
        • DOBMM
          int DOBMM
          DOCUMENT ME!
        • DOBYYYY
          int DOBYYYY
          DOCUMENT ME!
        • EchoTime
          double EchoTime
          DOCUMENT ME!
        • FlipAngle
          double FlipAngle
          DOCUMENT ME!
        • FOVColumn
          double FOVColumn
          DOCUMENT ME!
        • FOVRow
          double FOVRow
          DOCUMENT ME!
        • FrequencyMHz
          double FrequencyMHz
          DOCUMENT ME!
        • ImageDateDD
          int ImageDateDD
          DOCUMENT ME!
        • ImageDateMM
          int ImageDateMM
          DOCUMENT ME!
        • ImageDateYYYY
          int ImageDateYYYY
          DOCUMENT ME!
        • ImagedNucleus
          String ImagedNucleus
          DOCUMENT ME!
        • ImageTimeHH
          int ImageTimeHH
          DOCUMENT ME!
        • ImageTimeMM
          int ImageTimeMM
          DOCUMENT ME!
        • ImageTimeSS
          int ImageTimeSS
          DOCUMENT ME!
        • InstitutionName
          String InstitutionName
          DOCUMENT ME!
        • LastMoveDateDD
          int LastMoveDateDD
          DOCUMENT ME!
        • LastMoveDateMM
          int LastMoveDateMM
          DOCUMENT ME!
        • LastMoveDateYYYY
          int LastMoveDateYYYY
          DOCUMENT ME!
        • LastMoveTimeHH
          int LastMoveTimeHH
          DOCUMENT ME!
        • LastMoveTimeMM
          int LastMoveTimeMM
          DOCUMENT ME!
        • LastMoveTimeSS
          int LastMoveTimeSS
          DOCUMENT ME!
        • MagneticFieldStrength
          double MagneticFieldStrength
          DOCUMENT ME!
        • Manufacturer
          String Manufacturer
          DOCUMENT ME!
        • ModelName
          String ModelName
          DOCUMENT ME!
        • NormalVectorX
          double NormalVectorX
          DOCUMENT ME!
        • NormalVectorY
          double NormalVectorY
          DOCUMENT ME!
        • NormalVectorZ
          double NormalVectorZ
          DOCUMENT ME!
        • OrientationSet1Back
          String OrientationSet1Back
          DOCUMENT ME!
        • OrientationSet1Left
          String OrientationSet1Left
          DOCUMENT ME!
        • OrientationSet1Top
          String OrientationSet1Top
          DOCUMENT ME!
        • OrientationSet2Down
          String OrientationSet2Down
          DOCUMENT ME!
        • OrientationSet2Front
          String OrientationSet2Front
          DOCUMENT ME!
        • OrientationSet2Right
          String OrientationSet2Right
          DOCUMENT ME!
        • PatientAge
          String PatientAge
          DOCUMENT ME!
        • PatientAgeUnits
          String PatientAgeUnits
          DOCUMENT ME!
        • PatientID
          String PatientID
          DOCUMENT ME!
        • PatientName
          String PatientName
          DOCUMENT ME!
        • ReceivingCoil
          String ReceivingCoil
          DOCUMENT ME!
        • RegistrationDateDD
          int RegistrationDateDD
          DOCUMENT ME!
        • RegistrationDateMM
          int RegistrationDateMM
          DOCUMENT ME!
        • RegistrationDateYYYY
          int RegistrationDateYYYY
          DOCUMENT ME!
        • RegistrationTimeHH
          int RegistrationTimeHH
          DOCUMENT ME!
        • RegistrationTimeMM
          int RegistrationTimeMM
          DOCUMENT ME!
        • RegistrationTimeSS
          int RegistrationTimeSS
          DOCUMENT ME!
        • RepetitionTime
          double RepetitionTime
          DOCUMENT ME!
        • RowVectorX
          double RowVectorX
          DOCUMENT ME!
        • RowVectorY
          double RowVectorY
          DOCUMENT ME!
        • RowVectorZ
          double RowVectorZ
          DOCUMENT ME!
        • SequenceAuthor
          String SequenceAuthor
          DOCUMENT ME!
        • SequenceName
          String SequenceName
          DOCUMENT ME!
        • SequencePrgName
          String SequencePrgName
          DOCUMENT ME!
        • SequenceType
          String SequenceType
          DOCUMENT ME!
        • SequenceWkcName
          String SequenceWkcName
          DOCUMENT ME!
        • SiemensStudyDateDD
          int SiemensStudyDateDD
          DOCUMENT ME!
        • SiemensStudyDateMM
          int SiemensStudyDateMM
          DOCUMENT ME!
        • SiemensStudyDateYYYY
          int SiemensStudyDateYYYY
          DOCUMENT ME!
        • SiemensStudyTimeHH
          int SiemensStudyTimeHH
          DOCUMENT ME!
        • SiemensStudyTimeMM
          int SiemensStudyTimeMM
          DOCUMENT ME!
        • SiemensStudyTimeSS
          int SiemensStudyTimeSS
          DOCUMENT ME!
        • Station
          String Station
          DOCUMENT ME!
        • TextAcquisitionMatrixFreq
          String TextAcquisitionMatrixFreq
          DOCUMENT ME!
        • TextAcquisitionMatrixFreqO
          String TextAcquisitionMatrixFreqO
          DOCUMENT ME!
        • TextAcquisitionMatrixFreqS
          String TextAcquisitionMatrixFreqS
          DOCUMENT ME!
        • TextAcquisitionMatrixPhase
          String TextAcquisitionMatrixPhase
          DOCUMENT ME!
        • TextAcquisitionMatrixPhaseAxis
          String TextAcquisitionMatrixPhaseAxis
          DOCUMENT ME!
        • TextAcquisitionTimeMM
          String TextAcquisitionTimeMM
          DOCUMENT ME!
        • TextAcquisitionTimeSS
          String TextAcquisitionTimeSS
          DOCUMENT ME!
        • TextAngle
          String TextAngle
          DOCUMENT ME!
        • TextAngleFlag1
          String TextAngleFlag1
          DOCUMENT ME!
        • TextAngleFlag2
          String TextAngleFlag2
          DOCUMENT ME!
        • TextAngleFlag3
          String TextAngleFlag3
          DOCUMENT ME!
        • TextAnnotation
          String TextAnnotation
          DOCUMENT ME!
        • TextDateDD
          String TextDateDD
          DOCUMENT ME!
        • TextDateMM
          String TextDateMM
          DOCUMENT ME!
        • TextDateYYYY
          String TextDateYYYY
          DOCUMENT ME!
        • TextDOBDD
          String TextDOBDD
          DOCUMENT ME!
        • TextDOBMM
          String TextDOBMM
          DOCUMENT ME!
        • TextDOBYYYY
          String TextDOBYYYY
          DOCUMENT ME!
        • TextEchoNumber
          String TextEchoNumber
          DOCUMENT ME!
        • TextEchoTime
          String TextEchoTime
          DOCUMENT ME!
        • TextFlipAngle
          String TextFlipAngle
          DOCUMENT ME!
        • TextFOVH
          String TextFOVH
          DOCUMENT ME!
        • TextFOVV
          String TextFOVV
          DOCUMENT ME!
        • TextImageNumber
          String TextImageNumber
          DOCUMENT ME!
        • TextImageNumber2
          String TextImageNumber2
          DOCUMENT ME!
        • TextModelName
          String TextModelName
          DOCUMENT ME!
        • TextOrganization
          String TextOrganization
          DOCUMENT ME!
        • TextPatientAge
          String TextPatientAge
          DOCUMENT ME!
        • TextPatientAgeUnits
          String TextPatientAgeUnits
          DOCUMENT ME!
        • TextPatientID
          String TextPatientID
          DOCUMENT ME!
        • TextPatientName
          String TextPatientName
          DOCUMENT ME!
        • TextPatientPosition
          String TextPatientPosition
          DOCUMENT ME!
        • TextPatientSex
          String TextPatientSex
          DOCUMENT ME!
        • TextRepetitionTime
          String TextRepetitionTime
          DOCUMENT ME!
        • TextScanNumberA
          String TextScanNumberA
          DOCUMENT ME!
        • TextScanNumberB
          String TextScanNumberB
          DOCUMENT ME!
        • TextScanStartTimeHH
          String TextScanStartTimeHH
          DOCUMENT ME!
        • TextScanStartTimeMM
          String TextScanStartTimeMM
          DOCUMENT ME!
        • TextScanStartTimeSS
          String TextScanStartTimeSS
          DOCUMENT ME!
        • TextSequence
          String TextSequence
          DOCUMENT ME!
        • TextSlicePosition
          String TextSlicePosition
          DOCUMENT ME!
        • TextSliceThickness
          String TextSliceThickness
          DOCUMENT ME!
        • TextStation
          String TextStation
          DOCUMENT ME!
        • TextStudyImageNumber3
          String TextStudyImageNumber3
          DOCUMENT ME!
        • TextStudyNumber
          String TextStudyNumber
          DOCUMENT ME!
        • TextStudyNumber2
          String TextStudyNumber2
          DOCUMENT ME!
        • TextTablePosition
          String TextTablePosition
          DOCUMENT ME!
        • TextTimeHH
          String TextTimeHH
          DOCUMENT ME!
        • TextTimeMM
          String TextTimeMM
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoMATLAB

      class FileInfoMATLAB extends FileInfoBase implements Serializable

      • Serialized Fields

        • arrayName
          String arrayName
        • fieldNames
          String[] fieldNames
        • headerTextField
          String headerTextField
          Use serialVersionUID for interoperability.
        • level5Format
          boolean level5Format
        • sourceFile
          String sourceFile
        • subsystemSpecificDataOffset
          long subsystemSpecificDataOffset
        • version
          int version

    • Class gov.nih.mipav.model.file.FileInfoMedVision

      class FileInfoMedVision extends FileInfoBase implements Serializable
      serialVersionUID:
      -88313565378572414L

      • Serialized Fields

        • cineRate
          double cineRate
          DOCUMENT ME!
        • cols
          short cols
          DOCUMENT ME!
        • dataType
          short dataType
          DOCUMENT ME!
        • dateOfBirth
          String dateOfBirth
          DOCUMENT ME!
        • eqManuf
          String eqManuf
          DOCUMENT ME!
        • eqType
          String eqType
          DOCUMENT ME!
        • fileType
          String fileType
          File header data structure format.
        • frameRefNum
          short frameRefNum
          DOCUMENT ME!
        • imageOffset
          int imageOffset
          DOCUMENT ME!
        • imageScale
          double imageScale
          DOCUMENT ME!
        • institution
          String institution
          DOCUMENT ME!
        • modality
          String modality
          DOCUMENT ME!
        • patientName
          String patientName
          Info data structure format.
        • pixelSizeH
          double pixelSizeH
          DOCUMENT ME!
        • pixelSizeV
          double pixelSizeV
          hDat dataStructure format public long version;.
        • referringPhys
          String referringPhys
          DOCUMENT ME!
        • rows
          short rows
          Slice Header data structure format.
        • sex
          String sex
          DOCUMENT ME!
        • sliceHdrSize
          short sliceHdrSize
          DOCUMENT ME!
        • slicePosition
          double slicePosition
          DOCUMENT ME!
        • sliceRefNum
          short sliceRefNum
          DOCUMENT ME!
        • sliceThickness
          double sliceThickness
          DOCUMENT ME!
        • sliceTime
          double sliceTime
          DOCUMENT ME!
        • standardCols
          short standardCols
          DOCUMENT ME!
        • standardRows
          short standardRows
          DOCUMENT ME!
        • studyDate
          String studyDate
          DOCUMENT ME!
        • studyName
          String studyName
          DOCUMENT ME!
        • studyTime
          String studyTime
          DOCUMENT ME!
        • totalSlices
          short totalSlices
          DOCUMENT ME!
        • version
          int version
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoMetaImage

      class FileInfoMetaImage extends FileInfoBase implements Serializable

      • Serialized Fields

        • centerOfRotation
          double[] centerOfRotation
          Use serialVersionUID for interoperability.

    • Class gov.nih.mipav.model.file.FileInfoMGH

      class FileInfoMGH extends FileInfoBase implements Serializable

      • Serialized Fields

        • cmdlines
          String[] cmdlines
        • dof
          int dof
        • flipAngle
          float flipAngle
        • fov
          float fov
        • leftCenter
          float leftCenter
        • matrix
          TransMatrix matrix
        • posteriorCenter
          float posteriorCenter
        • superiorCenter
          float superiorCenter
        • te
          float te
        • ti
          float ti
        • tr
          float tr
        • transformFileName
          String transformFileName
        • version
          int version
          Currently version number is 1

    • Class gov.nih.mipav.model.file.FileInfoMicroCat

      class FileInfoMicroCat extends FileInfoBase implements Serializable
      serialVersionUID:
      -388246456500624487L

      • Serialized Fields

        • autoStartCBREngine
          String autoStartCBREngine
          DOCUMENT ME!
        • baseNameforReconstructedSlices
          String baseNameforReconstructedSlices
          DOCUMENT ME!
        • CATFileName
          String CATFileName
          DOCUMENT ME!
        • CBRHostName
          String CBRHostName
          DOCUMENT ME!
        • CBRImageDirectory
          String CBRImageDirectory
          DOCUMENT ME!
        • CBRProjectionDirectory
          String CBRProjectionDirectory
          DOCUMENT ME!
        • cylinderReconstruction
          int cylinderReconstruction
          DOCUMENT ME!
        • enableStepSize
          int enableStepSize
          DOCUMENT ME!
        • filterType
          String filterType
          DOCUMENT ME!
        • imageDestinationDirectory
          String imageDestinationDirectory
          DOCUMENT ME!
        • logScale
          float logScale
          DOCUMENT ME!
        • numberOfProjections
          int numberOfProjections
          DOCUMENT ME!
        • projectionDataAlreadyOnCBR
          String projectionDataAlreadyOnCBR
          DOCUMENT ME!
        • projectionUSize
          int projectionUSize
          DOCUMENT ME!
        • projectionVSize
          int projectionVSize
          DOCUMENT ME!
        • rotationDirection
          int rotationDirection
          DOCUMENT ME!
        • RPCPortNum
          String RPCPortNum
          DOCUMENT ME!
        • startAngle
          float startAngle
          DOCUMENT ME!
        • stepSizeFile
          String stepSizeFile
          DOCUMENT ME!
        • timeoutBetweenProjectionTransfers
          int timeoutBetweenProjectionTransfers
          DOCUMENT ME!
        • UCenterOffset
          int UCenterOffset
          DOCUMENT ME!
        • VCenterOffset
          int VCenterOffset
          DOCUMENT ME!
        • volumeOriginX
          float volumeOriginX
          DOCUMENT ME!
        • volumeOriginY
          float volumeOriginY
          DOCUMENT ME!
        • volumeOriginZ
          float volumeOriginZ
          DOCUMENT ME!
        • volumeSizeX
          int volumeSizeX
          DOCUMENT ME!
        • volumeSizeY
          int volumeSizeY
          DOCUMENT ME!
        • volumeSizeZ
          int volumeSizeZ
          DOCUMENT ME!
        • voxelSizeX
          float voxelSizeX
          DOCUMENT ME!
        • voxelSizeY
          float voxelSizeY
          DOCUMENT ME!
        • voxelSizeZ
          float voxelSizeZ
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoMinc

      class FileInfoMinc extends FileInfoBase implements Serializable
      serialVersionUID:
      6804935230803731941L

      • Serialized Fields

        • dimArray
          FileMincDimElem[] dimArray
          DOCUMENT ME!
        • gattArray
          FileMincAttElem[] gattArray
          DOCUMENT ME!
        • numrecs
          int numrecs
          DOCUMENT ME!
        • varArray
          FileMincVarElem[] varArray
          DOCUMENT ME!
        • vmax
          double vmax
          Valid image maximum value. Default = -1.
        • vmin
          double vmin
          Valid image minimum value. Default = -1.

    • Class gov.nih.mipav.model.file.FileInfoMincHDF

      class FileInfoMincHDF extends FileInfoBase implements Serializable
      serialVersionUID:
      1372818551072422068L

      • Serialized Fields

        • hasImageMinMaxDimOrder
          boolean hasImageMinMaxDimOrder
        • validRange
          double[] validRange
          The valid range for image pixel values

    • Class gov.nih.mipav.model.file.FileInfoMRC

      class FileInfoMRC extends FileInfoBase implements Serializable
      serialVersionUID:
      4677697781087324517L

      • Serialized Fields

        • alpha
          float alpha
          DOCUMENT ME!
        • beta
          float beta
          DOCUMENT ME!
        • creatorID
          short creatorID
          DOCUMENT ME!
        • gamma
          float gamma
          DOCUMENT ME!
        • idType
          short idType
          DOCUMENT ME!
        • impliedFlagBytes
          int impliedFlagBytes
          DOCUMENT ME!
        • ispg
          short ispg
          DOCUMENT ME!
        • label
          String[] label
          DOCUMENT ME!
        • lens
          short lens
          DOCUMENT ME!
        • mapC
          int mapC
          DOCUMENT ME!
        • mapR
          int mapR
          DOCUMENT ME!
        • mapS
          int mapS
          DOCUMENT ME!
        • nd1
          short nd1
          DOCUMENT ME!
        • nd2
          short nd2
          DOCUMENT ME!
        • next
          int next
          DOCUMENT ME!
        • nint
          short nint
          DOCUMENT ME!
        • nreal
          short nreal
          DOCUMENT ME!
        • nSymbt
          short nSymbt
          DOCUMENT ME!
        • nwave
          short nwave
          DOCUMENT ME!
        • rms
          float rms
          DOCUMENT ME!
        • tiltAngles
          float[] tiltAngles
          DOCUMENT ME!
        • vd1
          short vd1
          DOCUMENT ME!
        • vd2
          short vd2
          DOCUMENT ME!
        • wave1
          short wave1
          DOCUMENT ME!
        • wave2
          short wave2
          DOCUMENT ME!
        • wave3
          short wave3
          DOCUMENT ME!
        • wave4
          short wave4
          DOCUMENT ME!
        • wave5
          short wave5
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoNIFTI

      class FileInfoNIFTI extends FileInfoBase implements Serializable
      serialVersionUID:
      -5506021019885109431L

      • Serialized Fields

        • accessionNumber
          String accessionNumber
        • acquisitionMatrix
          int[] acquisitionMatrix
        • AcquisitionNumber
          int[] AcquisitionNumber
        • AcquisitionTime
          double[] AcquisitionTime
        • afniGroup
          String[] afniGroup
        • angioFlag
          String angioFlag
        • asciiText
          String[] asciiText
        • aux_file
          String aux_file
          auxiliary file
        • azimuth
          float[] azimuth
        • bitpix
          short bitpix
          Bits per pixel
        • bitsAllocated
          int bitsAllocated
        • bitsStored
          int bitsStored
        • bValue
          float[] bValue
        • cal_max
          double cal_max
          The cal_min and cal_max fields (if nonzero) are used for mapping (possibly scaled) dataset values to display colors: - Minimum display intensity (black) corresponds to dataset value cal_min. - Maximum display intensity (white) corresponds to dataset value cal_max. - Dataset values below cal_min should display as black also, and values above cal_max as white. - Colors "black" and "white", of course, may refer to any scalar display scheme (e.g., a color lookup table specified via aux_file). - cal_min and cal_max only make sense when applied to scalar-valued datasets (i.e., dim[0] invalid input: '<' 5 or dim[5] = 1).
        • cal_min
          double cal_min
          values of 0.0 for both fields imply that no calibration min and max values are used !
        • caret
          String[] caret
        • columns
          int columns
        • ContentTime
          double[] ContentTime
        • coord_code
          int coord_code
          If qform_code > 0, coord_code = qform_code. If qform_code invalid input: '<'= 0 and sform_code > 0, coord_code = sform_code. coord_code has values for "Arbitrary X,Y,Z coordinate system", "Scanner based anatomical coordinates", "Coordinates aligned to another file's or to anatomical truth", "Talairach X,Y,Z coordinate system", and "MNI 152 normalized X,Y,Z coordinates".
        • coord_code2
          int coord_code2
          If qform_code > 0 and sform_code > 0, coord_code = qform_code and coord_code2 = sform_code. coord_code has values for "Arbitrary X,Y,Z coordinate system", "Scanner based anatomical coordinates", "Coordinates aligned to another file's or to anatomical truth", "Talairach X,Y,Z coordinate system", and "MNI 152 normalized X,Y,Z coordinates".
        • CsaImageAcquisitionMatrixText
          String CsaImageAcquisitionMatrixText
        • CsaImageBandwidthPerPixelPhaseEncode
          double CsaImageBandwidthPerPixelPhaseEncode
        • CsaImageEchoColumnPosition
          int CsaImageEchoColumnPosition
        • CsaImageEchoLinePosition
          int CsaImageEchoLinePosition
        • CsaImageEchoPartitionPosition
          int CsaImageEchoPartitionPosition
        • CsaImageGSWDDataType
          String CsaImageGSWDDataType
        • CsaImageICE_Dims
          String[] CsaImageICE_Dims
        • CsaImageImaAbsTablePosition
          int[] CsaImageImaAbsTablePosition
        • CsaImageImaCoilString
          String CsaImageImaCoilString
        • CsaImageImaPATModeText
          String CsaImageImaPATModeText
        • CsaImageImaRelTablePosition
          int[] CsaImageImaRelTablePosition
        • CsaImageMeasuredFourierLines
          int CsaImageMeasuredFourierLines
        • CsaImageMosaicRefAcqTimes
          double[][] CsaImageMosaicRefAcqTimes
        • CsaImageMultistepIndex
          int CsaImageMultistepIndex
        • CsaImageNonPlanarImage
          int CsaImageNonPlanarImage
        • CsaImageNumberOfImagesInMosaic
          int CsaImageNumberOfImagesInMosaic
        • CsaImagePhaseEncodingDirectionPositive
          int CsaImagePhaseEncodingDirectionPositive
        • CsaImageProtocolSliceNumber
          int CsaImageProtocolSliceNumber
        • CsaImageRealDwellTime
          int CsaImageRealDwellTime
        • CsaImageRFSWDDataType
          String CsaImageRFSWDDataType
        • CsaImageSequenceMask
          int CsaImageSequenceMask
        • CsaImageSliceMeasurementDuration
          double[] CsaImageSliceMeasurementDuration
        • CsaImageSliceNormalVector
          double[] CsaImageSliceNormalVector
        • CsaImageSlicePosition_PCS
          double[] CsaImageSlicePosition_PCS
        • CsaImageTimeAfterStart
          double[] CsaImageTimeAfterStart
        • CsaImageUsedChannelMask
          int CsaImageUsedChannelMask
        • CsaSeriesAbsTablePosition
          int CsaSeriesAbsTablePosition
        • CsaSeriesB1rms
          double[] CsaSeriesB1rms
        • CsaSeriesB1rmsSupervision
          String CsaSeriesB1rmsSupervision
        • CsaSeriesCoilForGradient
          String CsaSeriesCoilForGradient
        • CsaSeriesCoilForGradient2
          String CsaSeriesCoilForGradient2
        • CsaSeriesCoilId
          int[] CsaSeriesCoilId
        • CsaSeriesCoilString
          String CsaSeriesCoilString
        • CsaSeriesdBdt_limit
          double CsaSeriesdBdt_limit
        • CsaSeriesdBdt_max
          double CsaSeriesdBdt_max
        • CsaSeriesdBdt_thresh
          double CsaSeriesdBdt_thresh
        • CsaSeriesFlowCompensation
          String CsaSeriesFlowCompensation
        • CsaSeriesGradientDelayTime
          double[] CsaSeriesGradientDelayTime
        • CsaSeriesGradientMode
          String CsaSeriesGradientMode
        • CsaSeriesIsocentered
          int CsaSeriesIsocentered
        • CsaSeriesLongModelName
          String CsaSeriesLongModelName
        • CsaSeriesMiscSequenceParam
          int[] CsaSeriesMiscSequenceParam
        • CsaSeriesMrPhoenixProtocolacFlowComp0
          int CsaSeriesMrPhoenixProtocolacFlowComp0
        • CsaSeriesMrPhoenixProtocoladFlipAngleDegree0
          double CsaSeriesMrPhoenixProtocoladFlipAngleDegree0
        • CsaSeriesMrPhoenixProtocolalTE0
          int CsaSeriesMrPhoenixProtocolalTE0
        • CsaSeriesMrPhoenixProtocolalTR0
          int CsaSeriesMrPhoenixProtocolalTR0
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0aFFT_SCALEnbValid
          int[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0aFFT_SCALEnbValid
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0aFFT_SCALEnflFactor
          double[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0aFFT_SCALEnflFactor
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0aFFT_SCALEnlRxChannel
          int[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0aFFT_SCALEnlRxChannel
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnlElementSelected
          int[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnlElementSelected
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnlRxChannelConnected
          int[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnlRxChannelConnected
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnsCoilElementIDlCoilCopy
          int[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnsCoilElementIDlCoilCopy
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnsCoilElementIDtCoilID
          String[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnsCoilElementIDtCoilID
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnsCoilElementIDtElement
          String[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0asListnsCoilElementIDtElement
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0iUsedRFactor
          int CsaSeriesMrPhoenixProtocolasCoilSelectMeas0iUsedRFactor
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0sCOILPLUGSauiNmbrOfNibbles
          int[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0sCOILPLUGSauiNmbrOfNibbles
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0sCOILPLUGSaulPlugId
          int[] CsaSeriesMrPhoenixProtocolasCoilSelectMeas0sCOILPLUGSaulPlugId
        • CsaSeriesMrPhoenixProtocolasCoilSelectMeas0tNucleus
          String CsaSeriesMrPhoenixProtocolasCoilSelectMeas0tNucleus
        • CsaSeriesMrPhoenixProtocoldAveragesDouble
          double CsaSeriesMrPhoenixProtocoldAveragesDouble
        • CsaSeriesMrPhoenixProtocoldRefSNR
          double CsaSeriesMrPhoenixProtocoldRefSNR
        • CsaSeriesMrPhoenixProtocoldRefSNR_VOI
          double CsaSeriesMrPhoenixProtocoldRefSNR_VOI
        • CsaSeriesMrPhoenixProtocollAverages
          int CsaSeriesMrPhoenixProtocollAverages
        • CsaSeriesMrPhoenixProtocollCombinedEchoes
          int CsaSeriesMrPhoenixProtocollCombinedEchoes
        • CsaSeriesMrPhoenixProtocollContrasts
          int CsaSeriesMrPhoenixProtocollContrasts
        • CsaSeriesMrPhoenixProtocollParadigmPeriodicity
          int CsaSeriesMrPhoenixProtocollParadigmPeriodicity
        • CsaSeriesMrPhoenixProtocollProtID
          int CsaSeriesMrPhoenixProtocollProtID
        • CsaSeriesMrPhoenixProtocollRepetitions
          int CsaSeriesMrPhoenixProtocollRepetitions
        • CsaSeriesMrPhoenixProtocollScanTimeSec
          int CsaSeriesMrPhoenixProtocollScanTimeSec
        • CsaSeriesMrPhoenixProtocollTOM
          int CsaSeriesMrPhoenixProtocollTOM
        • CsaSeriesMrPhoenixProtocollTotalScanTimeSec
          int CsaSeriesMrPhoenixProtocollTotalScanTimeSec
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedInPlaneRot
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedInPlaneRot
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedPhaseFOV
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedPhaseFOV
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedReadoutFOV
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedReadoutFOV
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedThickness
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumedThickness
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesNormaldCor
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesNormaldCor
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesNormaldSag
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesNormaldSag
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesNormaldTra
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesNormaldTra
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesPositiondCor
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesPositiondCor
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesPositiondSag
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesPositiondSag
        • CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesPositiondTra
          double CsaSeriesMrPhoenixProtocolsAdjDatasAdjVolumesPositiondTra
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjFreMode
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjFreMode
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjFreProtRelated
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjFreProtRelated
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjMDSMode
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjMDSMode
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjProtID
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjProtID
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjRFMapMode
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjRFMapMode
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjShimMode
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjShimMode
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjTableTolerance
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjTableTolerance
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjVolumeValid
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjVolumeValid
        • CsaSeriesMrPhoenixProtocolsAdjDatauiAdjWatSupMode
          int CsaSeriesMrPhoenixProtocolsAdjDatauiAdjWatSupMode
        • CsaSeriesMrPhoenixProtocolsAngiolDynamicReconMode
          int CsaSeriesMrPhoenixProtocolsAngiolDynamicReconMode
        • CsaSeriesMrPhoenixProtocolsAngiolTemporalInterpolation
          int CsaSeriesMrPhoenixProtocolsAngiolTemporalInterpolation
        • CsaSeriesMrPhoenixProtocolsAngioucPCFlowMode
          int CsaSeriesMrPhoenixProtocolsAngioucPCFlowMode
        • CsaSeriesMrPhoenixProtocolsAngioucTOFInflow
          int CsaSeriesMrPhoenixProtocolsAngioucTOFInflow
        • CsaSeriesMrPhoenixProtocolsAslulMode
          int CsaSeriesMrPhoenixProtocolsAslulMode
        • CsaSeriesMrPhoenixProtocolsAutoAligndAAMatrix
          double[] CsaSeriesMrPhoenixProtocolsAutoAligndAAMatrix
        • CsaSeriesMrPhoenixProtocolsBladeParadBladeCoverage
          double CsaSeriesMrPhoenixProtocolsBladeParadBladeCoverage
        • CsaSeriesMrPhoenixProtocolsBladeParaucMotionCorr
          int CsaSeriesMrPhoenixProtocolsBladeParaucMotionCorr
        • CsaSeriesMrPhoenixProtocolsDiffusionulMode
          int CsaSeriesMrPhoenixProtocolsDiffusionulMode
        • CsaSeriesMrPhoenixProtocolsDistortionCorrFilterucMode
          int CsaSeriesMrPhoenixProtocolsDistortionCorrFilterucMode
        • CsaSeriesMrPhoenixProtocolsEFISPECbEFIDataValid
          int CsaSeriesMrPhoenixProtocolsEFISPECbEFIDataValid
        • CsaSeriesMrPhoenixProtocolsFastImaginglEchoTrainDuration
          int CsaSeriesMrPhoenixProtocolsFastImaginglEchoTrainDuration
        • CsaSeriesMrPhoenixProtocolsFastImaginglEPIFactor
          int CsaSeriesMrPhoenixProtocolsFastImaginglEPIFactor
        • CsaSeriesMrPhoenixProtocolsFastImaginglSegments
          int CsaSeriesMrPhoenixProtocolsFastImaginglSegments
        • CsaSeriesMrPhoenixProtocolsFastImaginglShots
          int CsaSeriesMrPhoenixProtocolsFastImaginglShots
        • CsaSeriesMrPhoenixProtocolsFastImaginglSliceTurboFactor
          int CsaSeriesMrPhoenixProtocolsFastImaginglSliceTurboFactor
        • CsaSeriesMrPhoenixProtocolsFastImaginglTurboFactor
          int CsaSeriesMrPhoenixProtocolsFastImaginglTurboFactor
        • CsaSeriesMrPhoenixProtocolsFastImagingucSegmentationMode
          int CsaSeriesMrPhoenixProtocolsFastImagingucSegmentationMode
        • CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent0
          int CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent0
        • CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent1
          int CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent1
        • CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent2
          int CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent2
        • CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent3
          int CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent3
        • CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent4
          int CsaSeriesMrPhoenixProtocolsGRADSPECalShimCurrent4
        • CsaSeriesMrPhoenixProtocolsGRADSPECbB0CompensationValid
          int CsaSeriesMrPhoenixProtocolsGRADSPECbB0CompensationValid
        • CsaSeriesMrPhoenixProtocolsGRADSPECbCrossTermCompensationValid
          int CsaSeriesMrPhoenixProtocolsGRADSPECbCrossTermCompensationValid
        • CsaSeriesMrPhoenixProtocolsGRADSPECbDelayValid
          int CsaSeriesMrPhoenixProtocolsGRADSPECbDelayValid
        • CsaSeriesMrPhoenixProtocolsGRADSPECbEddyCompensationValid
          int CsaSeriesMrPhoenixProtocolsGRADSPECbEddyCompensationValid
        • CsaSeriesMrPhoenixProtocolsGRADSPECbOffsetValid
          int CsaSeriesMrPhoenixProtocolsGRADSPECbOffsetValid
        • CsaSeriesMrPhoenixProtocolsGRADSPECbSensitivityValid
          int CsaSeriesMrPhoenixProtocolsGRADSPECbSensitivityValid
        • CsaSeriesMrPhoenixProtocolsGRADSPECbShimCurrentValid
          int CsaSeriesMrPhoenixProtocolsGRADSPECbShimCurrentValid
        • CsaSeriesMrPhoenixProtocolsGRADSPECflGSWDMinRiseTime
          double CsaSeriesMrPhoenixProtocolsGRADSPECflGSWDMinRiseTime
        • CsaSeriesMrPhoenixProtocolsGRADSPECflSensitivityX
          double CsaSeriesMrPhoenixProtocolsGRADSPECflSensitivityX
        • CsaSeriesMrPhoenixProtocolsGRADSPECflSensitivityY
          double CsaSeriesMrPhoenixProtocolsGRADSPECflSensitivityY
        • CsaSeriesMrPhoenixProtocolsGRADSPECflSensitivityZ
          double CsaSeriesMrPhoenixProtocolsGRADSPECflSensitivityZ
        • CsaSeriesMrPhoenixProtocolsGRADSPEClDelayX
          int CsaSeriesMrPhoenixProtocolsGRADSPEClDelayX
        • CsaSeriesMrPhoenixProtocolsGRADSPEClDelayY
          int CsaSeriesMrPhoenixProtocolsGRADSPEClDelayY
        • CsaSeriesMrPhoenixProtocolsGRADSPEClDelayZ
          int CsaSeriesMrPhoenixProtocolsGRADSPEClDelayZ
        • CsaSeriesMrPhoenixProtocolsGRADSPEClOffsetX
          int CsaSeriesMrPhoenixProtocolsGRADSPEClOffsetX
        • CsaSeriesMrPhoenixProtocolsGRADSPEClOffsetY
          int CsaSeriesMrPhoenixProtocolsGRADSPEClOffsetY
        • CsaSeriesMrPhoenixProtocolsGRADSPEClOffsetZ
          int CsaSeriesMrPhoenixProtocolsGRADSPEClOffsetZ
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflAmplitude1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflAmplitude1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflAmplitude2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflAmplitude2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflTimeConstant1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflTimeConstant1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflTimeConstant2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationXaflTimeConstant2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflAmplitude1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflAmplitude1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflAmplitude2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflAmplitude2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflTimeConstant1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflTimeConstant1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflTimeConstant2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationYaflTimeConstant2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflAmplitude1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflAmplitude1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflAmplitude2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflAmplitude2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflTimeConstant1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflTimeConstant1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflTimeConstant2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsB0CompensationZaflTimeConstant2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXYaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXYaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXYaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXYaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXZaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXZaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXZaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationXZaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYXaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYXaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYXaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYXaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYZaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYZaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYZaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationYZaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZXaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZXaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZXaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZXaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZYaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZYaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZYaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsCrossTermCompensationZYaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude3
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude3
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude4
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflAmplitude4
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant3
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant3
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant4
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationXaflTimeConstant4
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude3
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude3
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude4
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflAmplitude4
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant3
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant3
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant4
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationYaflTimeConstant4
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude3
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude3
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude4
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflAmplitude4
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant0
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant0
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant1
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant1
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant2
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant2
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant3
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant3
        • CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant4
          double CsaSeriesMrPhoenixProtocolsGRADSPECsEddyCompensationZaflTimeConstant4
        • CsaSeriesMrPhoenixProtocolsGRADSPECucMode
          int CsaSeriesMrPhoenixProtocolsGRADSPECucMode
        • CsaSeriesMrPhoenixProtocolsGroupArrayanMember
          int[] CsaSeriesMrPhoenixProtocolsGroupArrayanMember
        • CsaSeriesMrPhoenixProtocolsGroupArrayasGroup0nSize
          int CsaSeriesMrPhoenixProtocolsGroupArrayasGroup0nSize
        • CsaSeriesMrPhoenixProtocolsGroupArraylSize
          int CsaSeriesMrPhoenixProtocolsGroupArraylSize
        • CsaSeriesMrPhoenixProtocolsGroupArraysPSatdGap
          double CsaSeriesMrPhoenixProtocolsGroupArraysPSatdGap
        • CsaSeriesMrPhoenixProtocolsGroupArraysPSatdThickness
          double CsaSeriesMrPhoenixProtocolsGroupArraysPSatdThickness
        • CsaSeriesMrPhoenixProtocolsKSpacedAngioDynCentralRegionA
          double CsaSeriesMrPhoenixProtocolsKSpacedAngioDynCentralRegionA
        • CsaSeriesMrPhoenixProtocolsKSpacedAngioDynSamplingDensityB
          double CsaSeriesMrPhoenixProtocolsKSpacedAngioDynSamplingDensityB
        • CsaSeriesMrPhoenixProtocolsKSpacedPhaseResolution
          double CsaSeriesMrPhoenixProtocolsKSpacedPhaseResolution
        • CsaSeriesMrPhoenixProtocolsKSpacedSeqPhasePartialFourierForSNR
          double CsaSeriesMrPhoenixProtocolsKSpacedSeqPhasePartialFourierForSNR
        • CsaSeriesMrPhoenixProtocolsKSpacedSliceResolution
          double CsaSeriesMrPhoenixProtocolsKSpacedSliceResolution
        • CsaSeriesMrPhoenixProtocolsKSpacelBaseResolution
          int CsaSeriesMrPhoenixProtocolsKSpacelBaseResolution
        • CsaSeriesMrPhoenixProtocolsKSpacelImagesPerSlab
          int CsaSeriesMrPhoenixProtocolsKSpacelImagesPerSlab
        • CsaSeriesMrPhoenixProtocolsKSpacelLinesPerShot
          int CsaSeriesMrPhoenixProtocolsKSpacelLinesPerShot
        • CsaSeriesMrPhoenixProtocolsKSpacelPartitions
          int CsaSeriesMrPhoenixProtocolsKSpacelPartitions
        • CsaSeriesMrPhoenixProtocolsKSpacelPhaseEncodingLines
          int CsaSeriesMrPhoenixProtocolsKSpacelPhaseEncodingLines
        • CsaSeriesMrPhoenixProtocolsKSpacelRadialInterleavesPerImage
          int CsaSeriesMrPhoenixProtocolsKSpacelRadialInterleavesPerImage
        • CsaSeriesMrPhoenixProtocolsKSpacelRadialViews
          int CsaSeriesMrPhoenixProtocolsKSpacelRadialViews
        • CsaSeriesMrPhoenixProtocolsKSpaceucAsymmetricEchoMode
          int CsaSeriesMrPhoenixProtocolsKSpaceucAsymmetricEchoMode
        • CsaSeriesMrPhoenixProtocolsKSpaceucAveragingMode
          int CsaSeriesMrPhoenixProtocolsKSpaceucAveragingMode
        • CsaSeriesMrPhoenixProtocolsKSpaceucDimension
          int CsaSeriesMrPhoenixProtocolsKSpaceucDimension
        • CsaSeriesMrPhoenixProtocolsKSpaceucMultiSliceMode
          int CsaSeriesMrPhoenixProtocolsKSpaceucMultiSliceMode
        • CsaSeriesMrPhoenixProtocolsKSpaceucPhasePartialFourier
          int CsaSeriesMrPhoenixProtocolsKSpaceucPhasePartialFourier
        • CsaSeriesMrPhoenixProtocolsKSpaceucPOCS
          int CsaSeriesMrPhoenixProtocolsKSpaceucPOCS
        • CsaSeriesMrPhoenixProtocolsKSpaceucSlicePartialFourier
          int CsaSeriesMrPhoenixProtocolsKSpaceucSlicePartialFourier
        • CsaSeriesMrPhoenixProtocolsKSpaceucTrajectory
          int CsaSeriesMrPhoenixProtocolsKSpaceucTrajectory
        • CsaSeriesMrPhoenixProtocolsKSpaceucViewSharing
          int CsaSeriesMrPhoenixProtocolsKSpaceucViewSharing
        • CsaSeriesMrPhoenixProtocolsKSpaceunReordering
          int CsaSeriesMrPhoenixProtocolsKSpaceunReordering
        • CsaSeriesMrPhoenixProtocolsMDSdMdsRangeExtension
          double CsaSeriesMrPhoenixProtocolsMDSdMdsRangeExtension
        • CsaSeriesMrPhoenixProtocolsMDSlmdsLinesPerSegment
          int CsaSeriesMrPhoenixProtocolsMDSlmdsLinesPerSegment
        • CsaSeriesMrPhoenixProtocolsMDSlTableSpeedNumerator
          int CsaSeriesMrPhoenixProtocolsMDSlTableSpeedNumerator
        • CsaSeriesMrPhoenixProtocolsMDSsMdsEndPosSBCS_mmdTra
          double CsaSeriesMrPhoenixProtocolsMDSsMdsEndPosSBCS_mmdTra
        • CsaSeriesMrPhoenixProtocolsMDSulMdsModeMask
          int CsaSeriesMrPhoenixProtocolsMDSulMdsModeMask
        • CsaSeriesMrPhoenixProtocolsMDSulMdsReconMode
          int CsaSeriesMrPhoenixProtocolsMDSulMdsReconMode
        • CsaSeriesMrPhoenixProtocolsMDSulMdsVariableResolution
          int CsaSeriesMrPhoenixProtocolsMDSulMdsVariableResolution
        • CsaSeriesMrPhoenixProtocolsNavigatorParalBreathHoldMeas
          int CsaSeriesMrPhoenixProtocolsNavigatorParalBreathHoldMeas
        • CsaSeriesMrPhoenixProtocolsNavigatorParalRespComp
          int CsaSeriesMrPhoenixProtocolsNavigatorParalRespComp
        • CsaSeriesMrPhoenixProtocolsParametricMappingucParametricMap
          int CsaSeriesMrPhoenixProtocolsParametricMappingucParametricMap
        • CsaSeriesMrPhoenixProtocolsPatlAccelFact3D
          int CsaSeriesMrPhoenixProtocolsPatlAccelFact3D
        • CsaSeriesMrPhoenixProtocolsPatlAccelFactPE
          int CsaSeriesMrPhoenixProtocolsPatlAccelFactPE
        • CsaSeriesMrPhoenixProtocolsPatlRefLinesPE
          int CsaSeriesMrPhoenixProtocolsPatlRefLinesPE
        • CsaSeriesMrPhoenixProtocolsPatucPATMode
          int CsaSeriesMrPhoenixProtocolsPatucPATMode
        • CsaSeriesMrPhoenixProtocolsPatucRefScanMode
          int CsaSeriesMrPhoenixProtocolsPatucRefScanMode
        • CsaSeriesMrPhoenixProtocolsPatucTPatAverageAllFrames
          int CsaSeriesMrPhoenixProtocolsPatucTPatAverageAllFrames
        • CsaSeriesMrPhoenixProtocolsPhysioImaginglMethod1
          int CsaSeriesMrPhoenixProtocolsPhysioImaginglMethod1
        • CsaSeriesMrPhoenixProtocolsPhysioImaginglMethod2
          int CsaSeriesMrPhoenixProtocolsPhysioImaginglMethod2
        • CsaSeriesMrPhoenixProtocolsPhysioImaginglPhases
          int CsaSeriesMrPhoenixProtocolsPhysioImaginglPhases
        • CsaSeriesMrPhoenixProtocolsPhysioImaginglRetroGatedImages
          int CsaSeriesMrPhoenixProtocolsPhysioImaginglRetroGatedImages
        • CsaSeriesMrPhoenixProtocolsPhysioImaginglSignal1
          int CsaSeriesMrPhoenixProtocolsPhysioImaginglSignal1
        • CsaSeriesMrPhoenixProtocolsPhysioImaginglSignal2
          int CsaSeriesMrPhoenixProtocolsPhysioImaginglSignal2
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlArrhythmiaDetection
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlArrhythmiaDetection
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlCardiacGateOffThreshold
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlCardiacGateOffThreshold
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlCardiacGateOnThreshold
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlCardiacGateOnThreshold
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlTriggerIntervals
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlTriggerIntervals
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlTriggerPulses
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlTriggerPulses
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlTriggerWindow
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioECGlTriggerWindow
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlArrhythmiaDetection
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlArrhythmiaDetection
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlCardiacGateOffThreshold
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlCardiacGateOffThreshold
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlCardiacGateOnThreshold
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlCardiacGateOnThreshold
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlTriggerIntervals
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlTriggerIntervals
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlTriggerPulses
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlTriggerPulses
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlTriggerWindow
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioExtlTriggerWindow
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioNativeucFlowSenMode
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioNativeucFlowSenMode
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioNativeucMode
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioNativeucMode
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselArrhythmiaDetection
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselArrhythmiaDetection
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselCardiacGateOffThreshold
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselCardiacGateOffThreshold
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselCardiacGateOnThreshold
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselCardiacGateOnThreshold
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselTriggerIntervals
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselTriggerIntervals
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselTriggerPulses
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselTriggerPulses
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselTriggerWindow
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioPulselTriggerWindow
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioRespdGatingRatio
          double CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioRespdGatingRatio
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioResplRespGatePhase
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioResplRespGatePhase
        • CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioResplRespGateThreshold
          int CsaSeriesMrPhoenixProtocolsPhysioImagingsPhysioResplRespGateThreshold
        • CsaSeriesMrPhoenixProtocolsPrepPulsesdDarkBloodFlipAngle
          double CsaSeriesMrPhoenixProtocolsPrepPulsesdDarkBloodFlipAngle
        • CsaSeriesMrPhoenixProtocolsPrepPulsesdDarkBloodThickness
          double CsaSeriesMrPhoenixProtocolsPrepPulsesdDarkBloodThickness
        • CsaSeriesMrPhoenixProtocolsPrepPulsesdIRPulseThicknessFactor
          double CsaSeriesMrPhoenixProtocolsPrepPulsesdIRPulseThicknessFactor
        • CsaSeriesMrPhoenixProtocolsPrepPulsesdT2PrepDuration
          double CsaSeriesMrPhoenixProtocolsPrepPulsesdT2PrepDuration
        • CsaSeriesMrPhoenixProtocolsPrepPulsesucFatSat
          int CsaSeriesMrPhoenixProtocolsPrepPulsesucFatSat
        • CsaSeriesMrPhoenixProtocolsPrepPulsesucFatSatMode
          int CsaSeriesMrPhoenixProtocolsPrepPulsesucFatSatMode
        • CsaSeriesMrPhoenixProtocolsPrepPulsesucInversion
          int CsaSeriesMrPhoenixProtocolsPrepPulsesucInversion
        • CsaSeriesMrPhoenixProtocolsPrepPulsesucSatRecovery
          int CsaSeriesMrPhoenixProtocolsPrepPulsesucSatRecovery
        • CsaSeriesMrPhoenixProtocolsPrepPulsesucT2Prep
          int CsaSeriesMrPhoenixProtocolsPrepPulsesucT2Prep
        • CsaSeriesMrPhoenixProtocolsPrepPulsesucTIScout
          int CsaSeriesMrPhoenixProtocolsPrepPulsesucTIScout
        • CsaSeriesMrPhoenixProtocolsPrepPulsesucWaterSat
          int CsaSeriesMrPhoenixProtocolsPrepPulsesucWaterSat
        • CsaSeriesMrPhoenixProtocolsProtConsistencyInfoflGMax
          double CsaSeriesMrPhoenixProtocolsProtConsistencyInfoflGMax
        • CsaSeriesMrPhoenixProtocolsProtConsistencyInfoflNominalB0
          double CsaSeriesMrPhoenixProtocolsProtConsistencyInfoflNominalB0
        • CsaSeriesMrPhoenixProtocolsProtConsistencyInfoflRiseTime
          double CsaSeriesMrPhoenixProtocolsProtConsistencyInfoflRiseTime
        • CsaSeriesMrPhoenixProtocolsProtConsistencyInfolMaximumNofRxReceiverChannels
          int CsaSeriesMrPhoenixProtocolsProtConsistencyInfolMaximumNofRxReceiverChannels
        • CsaSeriesMrPhoenixProtocolsProtConsistencyInfotBaselineString
          String CsaSeriesMrPhoenixProtocolsProtConsistencyInfotBaselineString
        • CsaSeriesMrPhoenixProtocolsProtConsistencyInfotSystemType
          String CsaSeriesMrPhoenixProtocolsProtConsistencyInfotSystemType
        • CsaSeriesMrPhoenixProtocolsRawFilterlSlope_256
          int CsaSeriesMrPhoenixProtocolsRawFilterlSlope_256
        • CsaSeriesMrPhoenixProtocolsRawFilterucMode
          int CsaSeriesMrPhoenixProtocolsRawFilterucMode
        • CsaSeriesMrPhoenixProtocolsRawFilterucOn
          int CsaSeriesMrPhoenixProtocolsRawFilterucOn
        • CsaSeriesMrPhoenixProtocolsRSatArrayasElm0dThickness
          double CsaSeriesMrPhoenixProtocolsRSatArrayasElm0dThickness
        • CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sNormaldCor
          double CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sNormaldCor
        • CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sNormaldSag
          double CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sNormaldSag
        • CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sNormaldTra
          double CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sNormaldTra
        • CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sPositiondCor
          double CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sPositiondCor
        • CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sPositiondSag
          double CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sPositiondSag
        • CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sPositiondTra
          double CsaSeriesMrPhoenixProtocolsRSatArrayasElm0sPositiondTra
        • CsaSeriesMrPhoenixProtocolsRSatArraylSize
          int CsaSeriesMrPhoenixProtocolsRSatArraylSize
        • CsaSeriesMrPhoenixProtocolsRXSPECalDwellTime0
          int CsaSeriesMrPhoenixProtocolsRXSPECalDwellTime0
        • CsaSeriesMrPhoenixProtocolsRXSPECbGainValid
          int CsaSeriesMrPhoenixProtocolsRXSPECbGainValid
        • CsaSeriesMrPhoenixProtocolsRXSPEClGain
          int CsaSeriesMrPhoenixProtocolsRXSPEClGain
        • CsaSeriesMrPhoenixProtocolsSliceArrayanAsc
          int[] CsaSeriesMrPhoenixProtocolsSliceArrayanAsc
        • CsaSeriesMrPhoenixProtocolsSliceArrayanPos
          int[] CsaSeriesMrPhoenixProtocolsSliceArrayanPos
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdInPlaneRot
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdInPlaneRot
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdPhaseFOV
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdPhaseFOV
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdReadoutFOV
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdReadoutFOV
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdThickness
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezdThickness
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsNormaldCor
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsNormaldCor
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsNormaldSag
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsNormaldSag
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsNormaldTra
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsNormaldTra
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsPositiondCor
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsPositiondCor
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsPositiondSag
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsPositiondSag
        • CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsPositiondTra
          double[] CsaSeriesMrPhoenixProtocolsSliceArrayasSlicezsPositiondTra
        • CsaSeriesMrPhoenixProtocolsSliceArraylConc
          int CsaSeriesMrPhoenixProtocolsSliceArraylConc
        • CsaSeriesMrPhoenixProtocolsSliceArraylSize
          int CsaSeriesMrPhoenixProtocolsSliceArraylSize
        • CsaSeriesMrPhoenixProtocolsSliceArraysTSatdThickness
          double CsaSeriesMrPhoenixProtocolsSliceArraysTSatdThickness
        • CsaSeriesMrPhoenixProtocolsSliceArrayucMode
          int CsaSeriesMrPhoenixProtocolsSliceArrayucMode
        • CsaSeriesMrPhoenixProtocolsSpecParalAutoRefScanNo
          int CsaSeriesMrPhoenixProtocolsSpecParalAutoRefScanNo
        • CsaSeriesMrPhoenixProtocolsSpecParalDecouplingType
          int CsaSeriesMrPhoenixProtocolsSpecParalDecouplingType
        • CsaSeriesMrPhoenixProtocolsSpecParalExcitationType
          int CsaSeriesMrPhoenixProtocolsSpecParalExcitationType
        • CsaSeriesMrPhoenixProtocolsSpecParalNOEType
          int CsaSeriesMrPhoenixProtocolsSpecParalNOEType
        • CsaSeriesMrPhoenixProtocolsSpecParalPhaseCyclingType
          int CsaSeriesMrPhoenixProtocolsSpecParalPhaseCyclingType
        • CsaSeriesMrPhoenixProtocolsSpecParalPhaseEncodingType
          int CsaSeriesMrPhoenixProtocolsSpecParalPhaseEncodingType
        • CsaSeriesMrPhoenixProtocolsSpecParalRFExcitationBandwidth
          int CsaSeriesMrPhoenixProtocolsSpecParalRFExcitationBandwidth
        • CsaSeriesMrPhoenixProtocolsSpecParalSpecAppl
          int CsaSeriesMrPhoenixProtocolsSpecParalSpecAppl
        • CsaSeriesMrPhoenixProtocolsSpecParalSpectralSuppression
          int CsaSeriesMrPhoenixProtocolsSpecParalSpectralSuppression
        • CsaSeriesMrPhoenixProtocolsSpecParaucRemoveOversampling
          int CsaSeriesMrPhoenixProtocolsSpecParaucRemoveOversampling
        • CsaSeriesMrPhoenixProtocolsTXSPECaRFPULSEnbAmplitudeValid
          int[] CsaSeriesMrPhoenixProtocolsTXSPECaRFPULSEnbAmplitudeValid
        • CsaSeriesMrPhoenixProtocolsTXSPECaRFPULSEnflAmplitude
          double[] CsaSeriesMrPhoenixProtocolsTXSPECaRFPULSEnflAmplitude
        • CsaSeriesMrPhoenixProtocolsTXSPECaRFPULSEntName
          String[] CsaSeriesMrPhoenixProtocolsTXSPECaRFPULSEntName
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bAmplitudeCorrectionValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bAmplitudeCorrectionValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bFrequencyValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bFrequencyValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bReferenceAmplitudeValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bReferenceAmplitudeValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bRFPAIndexValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0bRFPAIndexValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0flAmplitudeCorrection
          double CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0flAmplitudeCorrection
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0flReferenceAmplitude
          double CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0flReferenceAmplitude
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0lFrequency
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0lFrequency
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0tNucleus
          String CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo0tNucleus
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bAmplitudeCorrectionValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bAmplitudeCorrectionValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bFrequencyValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bFrequencyValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bReferenceAmplitudeValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bReferenceAmplitudeValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bRFPAIndexValid
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1bRFPAIndexValid
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1flAmplitudeCorrection
          double CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1flAmplitudeCorrection
        • CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1lRFPAIndex
          int CsaSeriesMrPhoenixProtocolsTXSPECasNucleusInfo1lRFPAIndex
        • CsaSeriesMrPhoenixProtocolsTXSPECbKDynValid
          int CsaSeriesMrPhoenixProtocolsTXSPECbKDynValid
        • CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeClipHigh
          double CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeClipHigh
        • CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeClipLow
          double CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeClipLow
        • CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeMax
          double CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeMax
        • CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeMin
          double CsaSeriesMrPhoenixProtocolsTXSPECflKDynMagnitudeMin
        • CsaSeriesMrPhoenixProtocolsTXSPECflKDynPhaseClip
          double CsaSeriesMrPhoenixProtocolsTXSPECflKDynPhaseClip
        • CsaSeriesMrPhoenixProtocolsTXSPECflKDynPhaseMax
          double CsaSeriesMrPhoenixProtocolsTXSPECflKDynPhaseMax
        • CsaSeriesMrPhoenixProtocolsTXSPEClBCExcitationMode
          int CsaSeriesMrPhoenixProtocolsTXSPEClBCExcitationMode
        • CsaSeriesMrPhoenixProtocolsTXSPEClBCSeqExcitationMode
          int CsaSeriesMrPhoenixProtocolsTXSPEClBCSeqExcitationMode
        • CsaSeriesMrPhoenixProtocolsTXSPEClNoOfTraPulses
          int CsaSeriesMrPhoenixProtocolsTXSPEClNoOfTraPulses
        • CsaSeriesMrPhoenixProtocolsTXSPECucBCExcitationModeValid
          int CsaSeriesMrPhoenixProtocolsTXSPECucBCExcitationModeValid
        • CsaSeriesMrPhoenixProtocolsTXSPECucExcitMode
          int CsaSeriesMrPhoenixProtocolsTXSPECucExcitMode
        • CsaSeriesMrPhoenixProtocolsTXSPECucRFPulseType
          int CsaSeriesMrPhoenixProtocolsTXSPECucRFPulseType
        • CsaSeriesMrPhoenixProtocolsTXSPECucSimultaneousExcitation
          int CsaSeriesMrPhoenixProtocolsTXSPECucSimultaneousExcitation
        • CsaSeriesMrPhoenixProtocolsWiPMemBlockadFree
          double[] CsaSeriesMrPhoenixProtocolsWiPMemBlockadFree
        • CsaSeriesMrPhoenixProtocolsWiPMemBlockalFree
          int[] CsaSeriesMrPhoenixProtocolsWiPMemBlockalFree
        • CsaSeriesMrPhoenixProtocolsWiPMemBlocktFree
          String CsaSeriesMrPhoenixProtocolsWiPMemBlocktFree
        • CsaSeriesMrPhoenixProtocoltdefaultEVAProt
          String CsaSeriesMrPhoenixProtocoltdefaultEVAProt
        • CsaSeriesMrPhoenixProtocoltProtocolName
          String CsaSeriesMrPhoenixProtocoltProtocolName
        • CsaSeriesMrPhoenixProtocoltReferenceImage0
          String CsaSeriesMrPhoenixProtocoltReferenceImage0
        • CsaSeriesMrPhoenixProtocoltReferenceImage1
          String CsaSeriesMrPhoenixProtocoltReferenceImage1
        • CsaSeriesMrPhoenixProtocoltReferenceImage2
          String CsaSeriesMrPhoenixProtocoltReferenceImage2
        • CsaSeriesMrPhoenixProtocoltSequenceFileName
          String CsaSeriesMrPhoenixProtocoltSequenceFileName
        • CsaSeriesMrPhoenixProtocolucAAMode
          int CsaSeriesMrPhoenixProtocolucAAMode
        • CsaSeriesMrPhoenixProtocolucAARefMode
          int CsaSeriesMrPhoenixProtocolucAARefMode
        • CsaSeriesMrPhoenixProtocolucAARegionMode
          int CsaSeriesMrPhoenixProtocolucAARegionMode
        • CsaSeriesMrPhoenixProtocolucAutoAlignInit
          int CsaSeriesMrPhoenixProtocolucAutoAlignInit
        • CsaSeriesMrPhoenixProtocolucBold3dPace
          int CsaSeriesMrPhoenixProtocolucBold3dPace
        • CsaSeriesMrPhoenixProtocolucBOLDParadigmArray
          int[] CsaSeriesMrPhoenixProtocolucBOLDParadigmArray
        • CsaSeriesMrPhoenixProtocolucCineMode
          int CsaSeriesMrPhoenixProtocolucCineMode
        • CsaSeriesMrPhoenixProtocolucCoilCombineMode
          int CsaSeriesMrPhoenixProtocolucCoilCombineMode
        • CsaSeriesMrPhoenixProtocolucDisableChangeStoreImages
          int CsaSeriesMrPhoenixProtocolucDisableChangeStoreImages
        • CsaSeriesMrPhoenixProtocolucDixon
          int CsaSeriesMrPhoenixProtocolucDixon
        • CsaSeriesMrPhoenixProtocolucDixonSaveOriginal
          int CsaSeriesMrPhoenixProtocolucDixonSaveOriginal
        • CsaSeriesMrPhoenixProtocolucEnableIntro
          int CsaSeriesMrPhoenixProtocolucEnableIntro
        • CsaSeriesMrPhoenixProtocolucEnableNoiseAdjust
          int CsaSeriesMrPhoenixProtocolucEnableNoiseAdjust
        • CsaSeriesMrPhoenixProtocolucFlipAngleMode
          int CsaSeriesMrPhoenixProtocolucFlipAngleMode
        • CsaSeriesMrPhoenixProtocolucForcePositioningOnNDIS
          int CsaSeriesMrPhoenixProtocolucForcePositioningOnNDIS
        • CsaSeriesMrPhoenixProtocolucInteractiveRealtime
          int CsaSeriesMrPhoenixProtocolucInteractiveRealtime
        • CsaSeriesMrPhoenixProtocolucInternalTablePosValid
          int CsaSeriesMrPhoenixProtocolucInternalTablePosValid
        • CsaSeriesMrPhoenixProtocolucOneSeriesForAllMeas
          int CsaSeriesMrPhoenixProtocolucOneSeriesForAllMeas
        • CsaSeriesMrPhoenixProtocolucPHAPSMode
          int CsaSeriesMrPhoenixProtocolucPHAPSMode
        • CsaSeriesMrPhoenixProtocolucReadOutMode
          int CsaSeriesMrPhoenixProtocolucReadOutMode
        • CsaSeriesMrPhoenixProtocolucReconstructionMode
          int CsaSeriesMrPhoenixProtocolucReconstructionMode
        • CsaSeriesMrPhoenixProtocolucScanRegionPosValid
          int CsaSeriesMrPhoenixProtocolucScanRegionPosValid
        • CsaSeriesMrPhoenixProtocolucSequenceType
          int CsaSeriesMrPhoenixProtocolucSequenceType
        • CsaSeriesMrPhoenixProtocolucTablePositioningMode
          int CsaSeriesMrPhoenixProtocolucTablePositioningMode
        • CsaSeriesMrPhoenixProtocolucWaitForPrepareCompletion
          int CsaSeriesMrPhoenixProtocolucWaitForPrepareCompletion
        • CsaSeriesMrPhoenixProtocolulVersion
          int CsaSeriesMrPhoenixProtocolulVersion
        • CsaSeriesMrPhoenixProtocolWaitForUserStart
          int CsaSeriesMrPhoenixProtocolWaitForUserStart
        • CsaSeriesMrProtocolVersion
          int CsaSeriesMrProtocolVersion
        • CsaSeriesNumberOfPrescans
          int CsaSeriesNumberOfPrescans
        • CsaSeriesOperation_mode_flag
          int CsaSeriesOperation_mode_flag
        • CsaSeriesPATModeText
          String CsaSeriesPATModeText
        • CsaSeriesPatReinPattern
          String CsaSeriesPatReinPattern
        • CsaSeriesPhaseGradientAmplitude
          double CsaSeriesPhaseGradientAmplitude
        • CsaSeriesPositivePCSDirections
          String CsaSeriesPositivePCSDirections
        • CsaSeriesProtocolChangeHistory
          int CsaSeriesProtocolChangeHistory
        • CsaSeriesReadoutGradientAmplitude
          double CsaSeriesReadoutGradientAmplitude
        • CsaSeriesReadoutOS
          double CsaSeriesReadoutOS
        • CsaSeriesRelTablePosition
          int[] CsaSeriesRelTablePosition
        • CsaSeriesRFSWDMostCriticalAspect
          String CsaSeriesRFSWDMostCriticalAspect
        • CsaSeriesRFSWDOperationMode
          int CsaSeriesRFSWDOperationMode
        • CsaSeriesRfWatchdogMask
          int CsaSeriesRfWatchdogMask
        • CsaSeriesSARMostCriticalAspect
          double[] CsaSeriesSARMostCriticalAspect
        • CsaSeriesSed
          double[] CsaSeriesSed
        • CsaSeriesSelectionGradientAmplitude
          double CsaSeriesSelectionGradientAmplitude
        • CsaSeriesSequenceFileOwner
          String CsaSeriesSequenceFileOwner
        • CsaSeriesSliceArrayConcatenations
          int CsaSeriesSliceArrayConcatenations
        • CsaSeriesSliceResolution
          double CsaSeriesSliceResolution
        • CsaSeriesStim_faktor
          double CsaSeriesStim_faktor
        • CsaSeriesStim_lim
          double[] CsaSeriesStim_lim
        • CsaSeriesStim_max_ges_norm_online
          double CsaSeriesStim_max_ges_norm_online
        • CsaSeriesStim_max_online
          double[] CsaSeriesStim_max_online
        • CsaSeriesStim_mon_mode
          int CsaSeriesStim_mon_mode
        • CsaSeriesSW_korr_faktor
          double CsaSeriesSW_korr_faktor
        • CsaSeriest_puls_max
          double CsaSeriest_puls_max
        • CsaSeriesTablePositionOrigin
          int[] CsaSeriesTablePositionOrigin
        • CsaSeriesTalesReferencePower
          double CsaSeriesTalesReferencePower
        • CsaSeriesTransmitterCalibration
          double CsaSeriesTransmitterCalibration
        • dBdt
          double dBdt
        • dcmmeta_affine
          double[][] dcmmeta_affine
        • dcmmeta_reorient_transform
          double[][] dcmmeta_reorient_transform
        • dcmmeta_shape
          int[] dcmmeta_shape
        • dcmmeta_slice_dim
          int dcmmeta_slice_dim
        • dcmmeta_version
          double dcmmeta_version
        • degree
          int[] degree
        • descrip
          String descrip
          Any text you like
        • dtComponent
          int[][] dtComponent
        • echoNumbers
          int echoNumbers
        • echoTime
          double echoTime
        • echoTrainLength
          int echoTrainLength
        • ecode
          int[] ecode
        • esize
          int[] esize
        • flipAngle
          double flipAngle
        • freq_dim
          int freq_dim
          Bits 0 and 1 of the dim_info character contain the freq_dim information. 0 for "No frequency encoding direction is present", 1 for "Frequency encoding in the x direction", 2 for "Frequency encoding in the y direction", and 3 for "Frequency encoding in the z direction".
        • haveDcmMeta
          boolean haveDcmMeta
        • highBit
          int highBit
        • imagedNucleus
          String imagedNucleus
        • imageOrientationPatient
          double[] imageOrientationPatient
        • imagePositionPatient
          double[] imagePositionPatient
        • imageType
          String[] imageType
        • imagingFrequency
          double imagingFrequency
        • inPlanePhaseEncodingDirection
          String inPlanePhaseEncodingDirection
        • InstanceCreationTime
          double[] InstanceCreationTime
        • InstanceNumber
          int[] InstanceNumber
        • intentCode
          int intentCode
          The intent_code field can be used to indicate that the voxel data has some particular meaning. In particular, a large number of codes is given to indicate that the the voxel data should be interpreted as being drawn from a given probability distribution.
        • intentName
          String intentName
          The intent_name field provides space for a 15 character (plus 0 byte) name string for the type of data stored. Examples: - intent_code = NIFTI_INTENT_ESTIMATE; intent_name = "T1"; could be used to signify that the voxel values are estimates of the NMR parameter T1. - intent_code = NIFTI_INTENT_TTEST; intent_name = "House"; could be used to signify that the voxel values are t-statistics for the significance of activation response to a House stimulus. - intent_code = NIFTI_INTENT_DISPVECT; intent_name = "ToMNI152"; could be used to signify that the voxel values are a displacement vector that transforms each voxel (x,y,z) location to the corresponding location in the MNI152 standard brain. - intent_code = NIFTI_INTENT_SYMMATRIX; intent_name = "DTI"; could be used to signify that the voxel values comprise a diffusion tensor image.
        • intentP1
          double intentP1
          If present, first auxiliary parameter used with intentCode
        • intentP2
          double intentP2
          If present, second auxiliary parameter used with intentCode
        • intentP3
          double intentP3
          If present, third auxiliary parameter used with intentCode
        • largestImagePixelValue
          int largestImagePixelValue
        • magneticFieldStrength
          double magneticFieldStrength
        • manufacturer
          String manufacturer
        • manufacturerModelName
          String manufacturerModelName
        • matrixQ
          TransMatrix matrixQ
        • matrixS
          TransMatrix matrixS
        • mindIdent
          String[] mindIdent
        • modalityString
          String modalityString
        • MRAcquisitionType
          String MRAcquisitionType
        • numberOfAverages
          double numberOfAverages
        • numberOfPhaseEncodingSteps
          int numberOfPhaseEncodingSteps
        • order
          int[] order
        • patientOrientationString
          String patientOrientationString
        • percentPhaseFieldOfView
          double percentPhaseFieldOfView
        • percentSampling
          double percentSampling
        • performedProcedureStepStartTime
          String performedProcedureStepStartTime
        • phase_dim
          int phase_dim
          Bits 2 and 3 of the dim_info character contain the phase_dim information. 0 for "No phase encoding direction is present", 1 for "Phase encoding in the x direction", 2 for "Phase encoding in the y direction", and 3 for "Phase encoding in the z direction".
        • photometricInterpretation
          String photometricInterpretation
        • pixelBandwidth
          double pixelBandwidth
        • pixelRepresentation
          int pixelRepresentation
        • pixelSpacing
          double[] pixelSpacing
        • repetitionTime
          double repetitionTime
        • rows
          int rows
        • samplesPerPixel
          int samplesPerPixel
        • SAR
          double SAR
        • scanningSequence
          String scanningSequence
        • scanOptions
          String scanOptions
        • scl_inter
          double scl_inter
        • scl_slope
          double scl_slope
          If the scl_slope field is nonzero, then each voxel value in the dataset should be scaled as y = scl_slope * x + scl_inter where x = voxel value stored y = "true" voxel value Normally, we would expect this scaling to be used to store "true" floating values in a smaller integer datatype, but that is not required. That is, it is legal to use scaling even if the datatype is a float type (crazy, perhaps, but legal). - However, the scaling is to be ignored if datatype is DT_RGB24. - If datatype is a complex type, then the scaling is to be applied to both the real and imaginary parts.
        • sequenceName
          String sequenceName
        • sequenceVariant
          String sequenceVariant
        • seriesNumber
          int seriesNumber
        • seriesTime
          String seriesTime
        • sizeof_hdr
          int sizeof_hdr
          Should always be a length of 348.
        • slice_dim
          int slice_dim
          Bits 4 and 5 of the dim_info character contain the slice_dim information. 0 for "No slice acquisition direction is present", 1 for "Slice acquisition in the x direction", 2 for "Slice acquisition in the y direction", and 3 for "Slice acquisition in the z direction".
        • sliceCode
          byte sliceCode
          If this is nonzero, AND if slice_dim is nonzero, AND if slice_duration is positive, indicates the timing pattern of the slice acquisition. The following codes are defined: "Slice timing order is sequentially increasing", "Slice timing order is sequentially decreasing", "Slice timing order is alternately increasing", "Slice timing order is alternately decreasing", "Slice timing order is alternately increasing #2", "Slice timing order is alternately decreasing #2".
        • sliceDuration
          double sliceDuration
          Time used to acquire 1 slice.
        • sliceEnd
          long sliceEnd
          Slice timing pattern ends with slice = (sliceEnd + 1)
        • sliceLocation
          double sliceLocation
        • sliceStart
          long sliceStart
          Slice timing pattern starts with slice = (sliceStart + 1)
        • smallestImagePixelValue
          int smallestImagePixelValue
        • softwareVersions
          String softwareVersions
        • sourceBitPix
          short sourceBitPix
          Source bits per pixel : 1,8,16,32,64,128 24(rgb).
        • sourceType
          short sourceType
          Original unscaled source data type
        • spacingBetweenSlices
          double spacingBetweenSlices
        • specificCharacterSet
          String specificCharacterSet
        • studyTime
          String studyTime
        • transmitCoilName
          String transmitCoilName
        • variableFlipAngleFlag
          String variableFlipAngleFlag
        • vox_offset
          long vox_offset
          If the magic field is "n+1", then the voxel data is stored in the same file as the header. In this case, the voxel data starts at offset (int)vox_offset into the header file. Thus, vox_offset=352.0 means that the data starts immediately after the NIFTI-1 header. If vox_offset is greater than 352, the NIFTI-1 format does not say much about the contents of the dataset file between the end of the header and the start of the data. If the magic field is "ni1", then the voxel data is stored in the associated ".img" file, starting at offset 0 (i.e., vox_offset is not used in this case, and should be set to 0.0). In a .nii file, the vox_offset field value is interpreted as the start location of the image data bytes in that file. In a .hdr/.img file pair, the vox_offset field value is the start location of the image data bytes in the .img file. If vox_offset is less than 352 in a .nii file, it is equivalent to 352 (i.e., image data never starts before byte #352 in a .nii file). The default value for vox_offset in a .nii file is 352. In a .hdr file, the default value for vox_offset is 0. * vox_offset should be an integer multiple of 16; otherwise, some programs may not work properly (e.g., SPM). This is to allow memory-mapped input to be properly byte-aligned.
        • WindowCenter
          double[] WindowCenter
        • windowCenterWidthExplanation
          String windowCenterWidthExplanation
        • WindowWidth
          double[] WindowWidth
        • zenith
          float[] zenith

    • Class gov.nih.mipav.model.file.FileInfoNRRD

      class FileInfoNRRD extends FileInfoBase implements Serializable

      • Serialized Fields

        • contentString
          String contentString
          Concise textual description of the information in the array
        • DWMRI_B_VALUE
          String DWMRI_B_VALUE
          "DWMRI_b-value:=b " : This key/value pair gives the (scalar) diffusion-weighting value, in units of s/mm^2. Example: "DWMRI_b-value:=1000". The effective magnitude of diffusion-weighting for each DWI is determined with some simple calculations based on the individual per-DWI gradient directions or B-matrices.
        • dwmriGradient
          String[][] dwmriGradient
          For every index position NNNN along the DWI axis (whichever is the non-spatial axis identified by the "list" or "vector" kind field), either "DWMRI_gradient_NNNN:=x y z " or "DWMRI_B-matrix_NNNN:=xx xy xz yy yz zz " must be given (except if "DWMRI_NEX_NNNN:= M " is used).
        • encodingString
          String encodingString
          Data compression - raw, gzip
        • labelString
          String[] labelString
          Axis names such as X, Y, or Z
        • modalityString
          String modalityString
          Diffusion weighted MRI is currently the only value that has been seen for modality in our samples.
        • sliceThickness
          float sliceThickness
        • spaceString
          String spaceString
          Possible values are "right-anterior-superior", "left-anterior-superior", "left-posterior-superior", "right-anterior-superior-time", "left-anterior-superior-time", "left-posterior-superior-time", "scanner-xyz", "scanner-xyz-time", "3d-right-handed", "3d-left-handed", "3d-right-handed-time", "3d-left-handed-time"
        • versionNumber
          float versionNumber
          Version of the NRRD file format being used.

    • Class gov.nih.mipav.model.file.FileInfoOME

      class FileInfoOME extends FileInfoBase implements Serializable
      serialVersionUID:
      -4798053431303160065L

    • Class gov.nih.mipav.model.file.FileInfoPARREC

      class FileInfoPARREC extends FileInfoBase implements Serializable

      • Serialized Fields

        • cardiacFrequency
          int[] cardiacFrequency
        • cardiacPhaseNumber
          int[] cardiacPhaseNumber
        • contrastBolusAgent
          String[] contrastBolusAgent
        • contrastBolusIngredient
          String[] contrastBolusIngredient
        • contrastBolusIngredientConcentration
          float[] contrastBolusIngredientConcentration
        • contrastBolusRoute
          float[] contrastBolusRoute
        • contrastBolusStartTime
          String[] contrastBolusStartTime
        • contrastBolusTotalDose
          float[] contrastBolusTotalDose
        • contrastBolusVolume
          String[] contrastBolusVolume
        • contrastType
          String[] contrastType
        • date
          String date
          par/rec date
        • diffusion
          float[][] diffusion
        • diffusionAnisotropyType
          String[] diffusionAnisotropyType
        • diffusionBFactor
          float[] diffusionBFactor
        • diffusionBValueNumber
          int[] diffusionBValueNumber
        • dynamicScanBeginTime
          float[] dynamicScanBeginTime
        • dynamicScanNumber
          int[] dynamicScanNumber
        • echoNumber
          int[] echoNumber
        • echoTime
          float[] echoTime
        • examName
          String examName
          par/rec examName
        • firstOrientValue
          int firstOrientValue
          Slice Orientation Value (sag/cor/tra)
        • flipAngle
          float[] flipAngle
        • fmriStatusIndication
          int[] fmriStatusIndication
        • foldover
          String foldover
          par/rec PreparationDirection
        • generalInfoList
          ArrayList<String> generalInfoList
        • gradientOrientationNumber
          int[] gradientOrientationNumber
        • imageAngulation
          float[][] imageAngulation
        • imageInfoList
          ArrayList<String> imageInfoList
        • imageOffcentre
          float[][] imageOffcentre
        • imageTypeEDES
          int[] imageTypeEDES
        • imageTypeMR
          int[] imageTypeMR
        • inversionDelay
          float[] inversionDelay
        • labelType
          int[] labelType
        • maximumRRInterval
          int[] maximumRRInterval
        • minimumRRInterval
          int[] minimumRRInterval
        • numberOfAverages
          int[] numberOfAverages
        • numSlices
          int numSlices
          numSlices
        • numVolumes
          int numVolumes
          numSlices
        • offCentre
          double[] offCentre
          Off-centre translation
        • originalDataType
          int originalDataType
        • patientName
          String patientName
        • patientPosition
          String patientPosition
          par/rec patientPosition
        • protocolName
          String protocolName
          par/rec protocolName
        • repetitionTime
          String repetitionTime
        • scaleSlope
          float scaleSlope
        • scanningSequence
          int[] scanningSequence
        • scanPercentage
          int[] scanPercentage
        • sliceAng
          double[] sliceAng
          par/rec slice Angulation
        • sliceInfo
          String sliceInfo
          slice specific info
        • stringBvalueArray
          String[] stringBvalueArray
          par/rec Bvalues
        • stringGradientArray
          String[] stringGradientArray
          par/rec gradients
        • time
          String time
        • triggerTime
          float[] triggerTime
        • turboFactor
          int[] turboFactor
        • version
          String version
          par/rec version
        • windowCenter
          int[] windowCenter
        • windowWidth
          int[] windowWidth

    • Class gov.nih.mipav.model.file.FileInfoPGM

      class FileInfoPGM extends FileInfoBase implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoPPM

      class FileInfoPPM extends FileInfoBase implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoRaw

      class FileInfoRaw extends FileInfoBase implements Serializable
      serialVersionUID:
      -1470168847948086226L

    • Class gov.nih.mipav.model.file.FileInfoSiemensText

      class FileInfoSiemensText extends FileInfoBase implements Serializable
      serialVersionUID:
      7319414471012796383L

      • Serialized Fields

        • aux_file
          String aux_file
          DOCUMENT ME!
        • bitpix
          short bitpix
          Bits per pixel. Valid values include: 1, 8, 16, 32, 64, 24(rgb).
        • cal_max
          float cal_max
          Range of calibration values.
        • cal_min
          float cal_min
          Values of 0.0 for both fields imply that no calibration min and max values are used !
        • compressed
          float compressed
          Indicates if compression is used. Default is -1 indicating no compression
        • data_type
          String data_type
          Unknown use 10 chars.
        • datatype
          short datatype
          Stores the image data type DT_NONE = 0; DT_UNKNOWN = 0; DT_BINARY = 1; DT_UNSIGNED_CHAR = 2; DT_SIGNED_SHORT = 4; DT_UNSIGNED_SHORT = 4; DT_SIGNED_INT = 8; DT_FLOAT = 16; DT_COMPLEX = 32; DT_DOUBLE = 64; DT_RGB = 128; DT_ALL = 255;
        • db_name
          String db_name
          Name of file with a length of 18 chars.
        • descrip
          String descrip
          String with a max character length of 80 used to describe image.
        • dim_un0
          short dim_un0
          Unused.
        • dir
          String dir
        • exp_date
          String exp_date
          String with a max character length of 10 used to indicate the experiment date.
        • exp_time
          String exp_time
          String with a max character length of 10 used to indicate the experiment time.
        • extents
          int extents
          Should be 16384.
        • field_skip
          int field_skip
          Unknown length.
        • funused1
          float funused1
          MIPAV uses this variable to define the X-axis origin.
        • funused2
          float funused2
          MIPAV uses this variable to define the Y-axis origin.
        • funused3
          float funused3
          MIPAV uses this variable to define the Z-axis origin.
        • generated
          String generated
          Unknown use. Length of 10.
        • glmax
          int glmax
          Maximum pixel values for the entire dataset.
        • glmin
          int glmin
          Minimum pixel values for the entire database.
        • hist_un0
          String hist_un0
          Unknown use. Length of 3.
        • hkey_un0
          char hkey_un0
          Unknown use. Length of 1.
        • name
          String name
        • omax
          int omax
          Unknown use.
        • omin
          int omin
          Unknown use.
        • orient
          byte orient
          DOCUMENT ME!
        • originator
          String originator
          Unknown use. Length of 10.
        • patient_id
          String patient_id
          Patient's ID. Length of 10.
        • regular
          char regular
          I think it means data has uniform spacing (resolutions).
        • scannum
          String scannum
          Scan ID Length of 10.
        • session_error
          short session_error
          Unknown use.
        • sizeof_hdr
          int sizeof_hdr
          Always of length 348.
        • smax
          int smax
          Unknown use.
        • smin
          int smin
          Unknown use.
        • start_field
          int start_field
          Unknown use.
        • verified
          float verified
          Unknown use.
        • views
          int views
          Unknown use.
        • vols_added
          int vols_added
          Unknown use.
        • vox_units
          String vox_units
          specifies the spatial units of measure for a voxel.

    • Class gov.nih.mipav.model.file.FileInfoSPAR

      class FileInfoSPAR extends FileInfoBase implements Serializable

      • Serialized Fields

        • maskExtents
          int[] maskExtents
          Mask extents
        • offCentre
          double[] offCentre
          Off-centre translations
        • PARRECMatrix
          TransMatrix PARRECMatrix
        • sliceAng
          double[] sliceAng
          par/rec slice Angulation

    • Class gov.nih.mipav.model.file.FileInfoSPM

      class FileInfoSPM extends FileInfoBase implements Serializable
      serialVersionUID:
      -3655260345861989046L

      • Serialized Fields

        • aux_file
          String aux_file
          DOCUMENT ME!
        • bitpix
          short bitpix
          DOCUMENT ME!
        • cal_max
          float cal_max
          DOCUMENT ME!
        • cal_min
          float cal_min
          DOCUMENT ME!
        • cal_units
          String cal_units
          DOCUMENT ME!
        • compressed
          float compressed
          DOCUMENT ME!
        • data_type
          String data_type
          DOCUMENT ME!
        • datatype
          short datatype
          DOCUMENT ME!
        • db_name
          String db_name
          DOCUMENT ME!
        • descrip
          String descrip
          DOCUMENT ME!
        • dim_un0
          short dim_un0
          DOCUMENT ME!
        • exp_date
          String exp_date
          DOCUMENT ME!
        • exp_time
          String exp_time
          DOCUMENT ME!
        • extents
          int extents
          DOCUMENT ME!
        • field_skip
          int field_skip
          DOCUMENT ME!
        • generated
          String generated
          DOCUMENT ME!
        • glmax
          int glmax
          DOCUMENT ME!
        • glmin
          int glmin
          DOCUMENT ME!
        • hist_un0
          String hist_un0
          DOCUMENT ME!
        • hkey_un0
          char hkey_un0
          DOCUMENT ME!
        • omax
          int omax
          DOCUMENT ME!
        • omin
          int omin
          DOCUMENT ME!
        • orient
          byte orient
          DOCUMENT ME!
        • origin
          short[] origin
          DOCUMENT ME!
        • patient_id
          String patient_id
          DOCUMENT ME!
        • regular
          char regular
          DOCUMENT ME!
        • scale
          float scale
          a floating point scale factor used during memory mapping.
        • scannum
          String scannum
          DOCUMENT ME!
        • session_error
          short session_error
          DOCUMENT ME!
        • sizeof_hdr
          int sizeof_hdr
          DOCUMENT ME!
        • smax
          int smax
          DOCUMENT ME!
        • smin
          int smin
          DOCUMENT ME!
        • start_field
          int start_field
          DOCUMENT ME!
        • verified
          float verified
          DOCUMENT ME!
        • views
          int views
          DOCUMENT ME!
        • vols_added
          int vols_added
          DOCUMENT ME!
        • vox_offset
          float vox_offset
          public float pixdim = new float[8]; // image resolutions info mm or ms stored in FileInfoBase pixdim[0] = number of dimensions pixdim[1] = voxel width pixdim[2] = voxel height pixdim[3] = voxel thickness pixdim[4] = time.
        • vox_units
          String vox_units
          public short dim[] = new short[8]; // image dimension data stored in FileInfoBase dim[0] = number of dimensions; usally 4 dim[1] = image width dim[2] = image height dim[3] = image depth (# of slices) dim[4] = volumes in image --- must be one for 3D image.

    • Class gov.nih.mipav.model.file.FileInfoSTK

      class FileInfoSTK extends FileInfoBase implements Serializable
      serialVersionUID:
      4681901066117260212L

      • Serialized Fields

        • imageDescription
          String imageDescription
          DOCUMENT ME!
        • sameZPosition
          boolean sameZPosition
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoSurfaceRefXML

      class FileInfoSurfaceRefXML extends FileInfoXML implements Serializable
      serialVersionUID:
      6815854469776062772L

      • Serialized Fields

        • filename
          String filename
          .sur file name.
        • m_iUnique_ID
          int m_iUnique_ID
          Unique ID, for the surface:.
        • m_kLevelDetail
          int m_kLevelDetail
          surface level of detail:.
        • m_kOpacity
          float m_kOpacity
          surface opacity:.
        • m_kType
          String m_kType
          Type keyword for the surface:.

    • Class gov.nih.mipav.model.file.FileInfoSurfaceXML

      class FileInfoSurfaceXML extends FileInfoXML implements Serializable
      serialVersionUID:
      6815854469776062772L

      • Serialized Fields

        • m_iUnique_ID
          int m_iUnique_ID
          Unique ID, for the surface:.
        • m_kLevelDetail
          int m_kLevelDetail
          surface level of detail:.
        • m_kOpacity
          float m_kOpacity
          surface opacity:.
        • m_kType
          String m_kType
          Type keyword for the surface:.
        • meshIndex
          int meshIndex
          mesh index.

    • Class gov.nih.mipav.model.file.FileInfoSVS

      class FileInfoSVS extends FileInfoBase implements Serializable

      • Serialized Fields

        • imageDescription
          String imageDescription
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoTiff

      class FileInfoTiff extends FileInfoBase implements Serializable
      serialVersionUID:
      7421068113479441629L

      • Serialized Fields

        • imageDescription
          String imageDescription
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoTMG

      class FileInfoTMG extends FileInfoBase implements Serializable
      serialVersionUID:
      652378870162150500L

      • Serialized Fields

        • commentStr
          String commentStr
          DOCUMENT ME!
        • nameStr
          String nameStr
          DOCUMENT ME!
        • timeStr
          String timeStr
          DOCUMENT ME!
        • titleStr
          String titleStr
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileInfoTrackVis

      class FileInfoTrackVis extends FileInfoBase implements Serializable

      • Serialized Fields

        • hdrSize
          int hdrSize
          Size of header, should be 1000
        • invertXStr
          String invertXStr
          Internal trakcVis use
        • invertYStr
          String invertYStr
          Internal trakcVis use
        • invertZStr
          String invertZStr
          Internal trakcVis use
        • numProp
          int numProp
          Number of scalars per track point and number of properties per track
        • numScalar
          int numScalar
          Number of scalars per track point and number of properties per track
        • numTracks
          int numTracks
          Number of tracts
        • pad1
          String pad1
          Paddings
        • pad2
          String pad2
          Paddings
        • properties
          float[][] properties
          Properties per track
        • propNames
          String[] propNames
          Scalar names and property names
        • reserved
          String reserved
          Reserved for future TrackVis use
        • scalarNames
          String[] scalarNames
          Scalar names and property names
        • swapXY
          String swapXY
          Internal TrackVis use
        • swapXZ
          String swapXZ
          Internal TrackVis use
        • swapYZ
          String swapYZ
          Internal TrackVis use
        • version
          int version
          Version number, current is 2
        • voxelOrder
          String voxelOrder
          Storing order of image data

    • Class gov.nih.mipav.model.file.FileInfoVista

      class FileInfoVista extends FileInfoBase implements Serializable

    • Class gov.nih.mipav.model.file.FileInfoXML

      class FileInfoXML extends FileInfoBase implements Serializable
      serialVersionUID:
      -7709467226605763815L

      • Serialized Fields

    • Class gov.nih.mipav.model.file.FileInfoZVI

      class FileInfoZVI extends FileInfoBase implements Serializable

      • Serialized Fields

        • acquisitionBitDepth
          int acquisitionBitDepth
        • amplificationIndex
          int amplificationIndex
        • apotomeAutoShutterUsed
          int apotomeAutoShutterUsed
        • apotomeAveragingCount
          int apotomeAveragingCount
        • apotomeCamFilterHarmonics
          int apotomeCamFilterHarmonics
        • apotomeCamGenericCameraName
          String apotomeCamGenericCameraName
        • apotomeCamNormalize
          int apotomeCamNormalize
        • apotomeCamPhaseAngles
          String apotomeCamPhaseAngles
        • apotomeFilterName
          String apotomeFilterName
        • apotomeFilterStrength
          double apotomeFilterStrength
        • apotomeFullPhaseShift
          int apotomeFullPhaseShift
        • apotomeGratingPeriod
          double apotomeGratingPeriod
        • apotomeGridName
          String apotomeGridName
        • apotomeGridPosition0
          int apotomeGridPosition0
        • apotomeGridPosition1
          int apotomeGridPosition1
        • apotomeGridPosition2
          int apotomeGridPosition2
        • apotomeGridPosition3
          int apotomeGridPosition3
        • apotomeGridPositionChannel0
          int apotomeGridPositionChannel0
        • apotomeGridPositionChannel1
          int apotomeGridPositionChannel1
        • apotomeGridPositionChannel2
          int apotomeGridPositionChannel2
        • apotomeGridPositionChannel3
          int apotomeGridPositionChannel3
        • apotomeProcessingMode
          int apotomeProcessingMode
        • axioCamAnalogGainEnable
          int axioCamAnalogGainEnable
        • axioCamBlackReference
          int axioCamBlackReference
        • axioCamColorModel
          int axioCamColorModel
        • axioCamDelayTime
          int axioCamDelayTime
        • axioCamEnhanceColor
          int axioCamEnhanceColor
        • axioCamMicroScanning
          int axioCamMicroScanning
        • axioCamNIRMode
          int axioCamNIRMode
        • axioCamResolution
          int axioCamResolution
        • axioCamSaturation
          double axioCamSaturation
        • axioCamSelector
          int axioCamSelector
        • axioCamShutterControl
          int axioCamShutterControl
        • axioCamShutterSignal
          int axioCamShutterSignal
        • axioCamType
          int axioCamType
        • blackValue0
          double blackValue0
        • blackValue1
          double blackValue1
        • blackValue2
          double blackValue2
        • blackValue3
          double blackValue3
        • camera
          String camera
        • cameraAdapterMagnification
          double cameraAdapterMagnification
        • cameraBinning
          int cameraBinning
        • cameraBitDepth
          int cameraBitDepth
        • cameraFrameHeight
          int cameraFrameHeight
        • cameraFrameImageOrientation
          int cameraFrameImageOrientation
        • cameraFramePixelDistance
          double cameraFramePixelDistance
        • cameraFrameScalingFactor
          double cameraFrameScalingFactor
        • cameraFrameStartLeft
          int cameraFrameStartLeft
        • cameraFrameStartTop
          int cameraFrameStartTop
        • cameraFrameWidth
          int cameraFrameWidth
        • cameraImageAcquisitionTime0
          String cameraImageAcquisitionTime0
        • cameraImageAcquisitionTime1
          String cameraImageAcquisitionTime1
        • cameraImageAcquisitionTime2
          String cameraImageAcquisitionTime2
        • cameraImageAcquisitionTime3
          String cameraImageAcquisitionTime3
        • cameraLiveScalingFactor
          double cameraLiveScalingFactor
        • cameraShadingCorrection
          int cameraShadingCorrection
        • cameraShutterLiveEnable
          int cameraShutterLiveEnable
        • channel0
          int channel0
        • channel1
          int channel1
        • channel2
          int channel2
        • channel3
          int channel3
        • channelName0
          String channelName0
        • channelName1
          String channelName1
        • channelName2
          String channelName2
        • channelName3
          String channelName3
        • channelNameChannel0
          int channelNameChannel0
        • channelNameChannel1
          int channelNameChannel1
        • channelNameChannel2
          int channelNameChannel2
        • channelNameChannel3
          int channelNameChannel3
        • comments
          String comments
        • condenserContrast
          int condenserContrast
        • condenserNumericalAperture
          double condenserNumericalAperture
        • contrastManagerMode
          int contrastManagerMode
        • dazzleProtection
          String dazzleProtection
        • deviceScalingName
          String deviceScalingName
        • documentSubtype
          String documentSubtype
        • documentType
          String documentType
        • emissionWavelength0
          int emissionWavelength0
        • emissionWavelength1
          int emissionWavelength1
        • emissionWavelength2
          int emissionWavelength2
        • emissionWavelength3
          int emissionWavelength3
        • emissionWavelengthChannel0
          int emissionWavelengthChannel0
        • emissionWavelengthChannel1
          int emissionWavelengthChannel1
        • emissionWavelengthChannel2
          int emissionWavelengthChannel2
        • emissionWavelengthChannel3
          int emissionWavelengthChannel3
        • excitationWavelength0
          int excitationWavelength0
        • excitationWavelength1
          int excitationWavelength1
        • excitationWavelength2
          int excitationWavelength2
        • excitationWavelength3
          int excitationWavelength3
        • excitationWavelengthChannel0
          int excitationWavelengthChannel0
        • excitationWavelengthChannel1
          int excitationWavelengthChannel1
        • excitationWavelengthChannel2
          int excitationWavelengthChannel2
        • excitationWavelengthChannel3
          int excitationWavelengthChannel3
        • exposureTime0
          double exposureTime0
        • exposureTime1
          double exposureTime1
        • exposureTime2
          double exposureTime2
        • exposureTime3
          double exposureTime3
        • exposureTimeChannel0
          int exposureTimeChannel0
        • exposureTimeChannel1
          int exposureTimeChannel1
        • exposureTimeChannel2
          int exposureTimeChannel2
        • exposureTimeChannel3
          int exposureTimeChannel3
        • externalShutter1
          int externalShutter1
        • fileDate
          String fileDate
        • fileID
          String fileID
        • fileLink
          String fileLink
        • fileSize
          int fileSize
        • focusCalibrated
          String focusCalibrated
        • focusDepth
          double focusDepth
        • focusPosition
          double focusPosition
        • gammaValue
          double gammaValue
        • IDTagFileName
          String IDTagFileName
        • imageMemoryUsage
          double imageMemoryUsage
        • imageRelativeTime0
          String imageRelativeTime0
        • imageRelativeTime1
          String imageRelativeTime1
        • imageRelativeTime2
          String imageRelativeTime2
        • imageRelativeTime3
          String imageRelativeTime3
        • lastModifiedBy
          String lastModifiedBy
        • lightManagerEnabled
          String lightManagerEnabled
        • lightManagerMode
          int lightManagerMode
        • microscopeIllumination
          int microscopeIllumination
        • microscopeMagnification
          double microscopeMagnification
        • microscopeName
          String microscopeName
        • microscopePort
          int microscopePort
        • microscopeType
          int microscopeType
        • multichannelColor0
          int multichannelColor0
        • multichannelColor1
          int multichannelColor1
        • multichannelColor2
          int multichannelColor2
        • multichannelColor3
          int multichannelColor3
        • multichannelColorChannel0
          int multichannelColorChannel0
        • multichannelColorChannel1
          int multichannelColorChannel1
        • multichannelColorChannel2
          int multichannelColorChannel2
        • multichannelColorChannel3
          int multichannelColorChannel3
        • multichannelWeight
          double multichannelWeight
        • objectiveContrastMethod
          int objectiveContrastMethod
        • objectiveID
          String objectiveID
        • objectiveImmersionType
          String objectiveImmersionType
        • objectiveMagnification
          double objectiveMagnification
        • objectiveNA
          double objectiveNA
        • objectiveName
          String objectiveName
        • objectiveTurretPosition
          int objectiveTurretPosition
        • objectiveWorkingDistance
          double objectiveWorkingDistance
        • objectType
          int objectType
        • ocularTotalMagnification
          double ocularTotalMagnification
        • optovar
          double optovar
        • originalStagePositionX
          double originalStagePositionX
        • originalStagePositionY
          double originalStagePositionY
        • parfocalCorrection
          String parfocalCorrection
        • reference
          String reference
        • reflectedLightHalogenLampMode
          int reflectedLightHalogenLampMode
        • reflectedLightHalogenLampVoltage
          double reflectedLightHalogenLampVoltage
        • reflectedLightShutter
          int reflectedLightShutter
        • reflector
          String reflector
        • reflectorID
          String reflectorID
        • reflectorMagnification
          double reflectorMagnification
        • reflectorPosition0
          int reflectorPosition0
        • reflectorPosition1
          int reflectorPosition1
        • reflectorPosition2
          int reflectorPosition2
        • reflectorPosition3
          int reflectorPosition3
        • reflectorPositionChannel0
          int reflectorPositionChannel0
        • reflectorPositionChannel1
          int reflectorPositionChannel1
        • reflectorPositionChannel2
          int reflectorPositionChannel2
        • reflectorPositionChannel3
          int reflectorPositionChannel3
        • relFocusPosition1
          double relFocusPosition1
        • relFocusPosition2
          double relFocusPosition2
        • scaleHeight
          double scaleHeight
        • scaleWidth
          double scaleWidth
        • stageCalibrated
          String stageCalibrated
        • stagePositionX
          double stagePositionX
        • stagePositionY
          double stagePositionY
        • title
          String title
        • transmittedLightHalogenLampMode
          int transmittedLightHalogenLampMode
        • transmittedLightHalogenLampVoltage
          double transmittedLightHalogenLampVoltage
        • transmittedLightShutter
          int transmittedLightShutter
        • userAddress
          String userAddress
        • userCity
          String userCity
        • userCompany
          String userCompany
        • userCompanyLogo
          String userCompanyLogo
        • userCountry
          String userCountry
        • userFax
          String userFax
        • userID
          String userID
        • userName
          String userName
        • userPhone
          String userPhone
        • validBitsPerPixel
          int validBitsPerPixel
        • whiteValue0
          double whiteValue0
        • whiteValue1
          double whiteValue1
        • whiteValue2
          double whiteValue2
        • whiteValue3
          double whiteValue3

    • Class gov.nih.mipav.model.file.FileMincAttElem

      class FileMincAttElem extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -4847649204791713924L

      • Serialized Fields

        • name
          String name
          DOCUMENT ME!
        • nc_type
          int nc_type
          DOCUMENT ME!
        • nelems
          int nelems
          DOCUMENT ME!
        • values
          Object[] values
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileMincDimElem

      class FileMincDimElem extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -8677079575179802672L

      • Serialized Fields

        • length
          int length
          DOCUMENT ME!
        • name
          String name
          DOCUMENT ME!

    • Class gov.nih.mipav.model.file.FileMincHDF.HDFNode

      class HDFNode extends DefaultMutableTreeNode implements Serializable
      serialVersionUID:
      240L

    • Class gov.nih.mipav.model.file.FileMincVarElem

      class FileMincVarElem extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -3229377471887553687L

      • Serialized Fields

        • begin
          int begin
          DOCUMENT ME!
        • comments
          String comments
          DOCUMENT ME!
        • cosines
          double[] cosines
          DOCUMENT ME!
        • dimid
          int[] dimid
          DOCUMENT ME!
        • name
          String name
          DOCUMENT ME!
        • nc_type
          int nc_type
          DOCUMENT ME!
        • nelems
          int nelems
          DOCUMENT ME!
        • signtype
          String signtype
          DOCUMENT ME!
        • start
          double start
          DOCUMENT ME!
        • step
          double step
          in zspace, step == slice gap, not necessarily slice thickness
        • trueStart
          double trueStart
          DOCUMENT ME!
        • units
          String units
          DOCUMENT ME!
        • values
          Vector<Object> values
          DOCUMENT ME!
        • vattArray
          FileMincAttElem[] vattArray
          DOCUMENT ME!
        • vmax
          double vmax
          DOCUMENT ME!
        • vmin
          double vmin
          DOCUMENT ME!
        • vsize
          int vsize
          DOCUMENT ME!

    • Exception Class gov.nih.mipav.model.file.FileSVS.ModHuffmanInputStream.ModHuffmanCodingException

      class ModHuffmanCodingException extends IOException implements Serializable

    • Exception Class gov.nih.mipav.model.file.FileTiff.ModHuffmanInputStream.ModHuffmanCodingException

      class ModHuffmanCodingException extends IOException implements Serializable

    • Class gov.nih.mipav.model.file.jxlatte.CIEPrimaries

      class CIEPrimaries extends Object implements Serializable
      serialVersionUID:
      7449715919648885336L

    • Class gov.nih.mipav.model.file.jxlatte.CIEXY

      class CIEXY extends Object implements Serializable
      serialVersionUID:
      -5492629196370805350L

      • Serialized Fields

        • x
          float x
        • y
          float y

    • Exception Class gov.nih.mipav.model.file.jxlatte.InvalidBitstreamException

      class InvalidBitstreamException extends IOException implements Serializable
      serialVersionUID:
      8155236409183220281L

    • Class gov.nih.mipav.model.file.jxlatte.XorShiro

      class XorShiro extends Random implements Serializable
      serialVersionUID:
      -1587576929112523643L

      • Serialized Fields

        • batch
          int[] batch
        • batchPos
          int batchPos
        • state0
          long[] state0
        • state1
          long[] state1

    • Exception Class gov.nih.mipav.model.file.MetadataExtractor.BufferBoundsException

      class BufferBoundsException extends IOException implements Serializable
      serialVersionUID:
      2911102837808946396L

    • Exception Class gov.nih.mipav.model.file.MetadataExtractor.CompoundException

      class CompoundException extends Exception implements Serializable
      serialVersionUID:
      -9207883813472069925L

      • Serialized Fields

    • Exception Class gov.nih.mipav.model.file.MetadataExtractor.ImageProcessingException

      class ImageProcessingException extends MetadataExtractor.CompoundException implements Serializable
      serialVersionUID:
      -9115669182209912676L

    • Class gov.nih.mipav.model.file.MetadataExtractor.JpegComponent

      class JpegComponent extends Object implements Serializable
      serialVersionUID:
      61121257899091914L

      • Serialized Fields

        • _componentId
          int _componentId
        • _quantizationTableNumber
          int _quantizationTableNumber
        • _samplingFactorByte
          int _samplingFactorByte

    • Exception Class gov.nih.mipav.model.file.MetadataExtractor.JpegProcessingException

      class JpegProcessingException extends MetadataExtractor.ImageProcessingException implements Serializable
      serialVersionUID:
      -7870179776125450158L

    • Exception Class gov.nih.mipav.model.file.MetadataExtractor.MetadataException

      class MetadataException extends MetadataExtractor.CompoundException implements Serializable
      serialVersionUID:
      8612756143363919682L

    • Exception Class gov.nih.mipav.model.file.MetadataExtractor.PngProcessingException

      class PngProcessingException extends MetadataExtractor.ImageProcessingException implements Serializable
      serialVersionUID:
      -687991554932005033L

    • Class gov.nih.mipav.model.file.MetadataExtractor.Rational

      class Rational extends Number implements Serializable
      serialVersionUID:
      510688928138848770L

      • Serialized Fields

        • _denominator
          long _denominator
          Holds the denominator.
        • _numerator
          long _numerator
          Holds the numerator.

    • Exception Class gov.nih.mipav.model.file.MetadataExtractor.TiffProcessingException

      class TiffProcessingException extends MetadataExtractor.ImageProcessingException implements Serializable
      serialVersionUID:
      -1658134119488001891L

    • Class gov.nih.mipav.model.file.PrivateFileDicomKey

      class PrivateFileDicomKey extends FileDicomKey implements Serializable

      • Serialized Fields

        • publisher
          String publisher
          The publisher for this tag.

    • Class gov.nih.mipav.model.file.XMLParameter

      class XMLParameter extends Object implements Serializable
      serialVersionUID:
      4475674642754924771L

      • Serialized Fields

        • date
          String date
          Parameter date.
        • description
          String description
          Parameter description.
        • name
          String name
          Parameter name.
        • time
          String time
          Parameter time.
        • value
          String value
          Parameter value.
        • valueType
          String valueType
          Parameter value type.

    • Class gov.nih.mipav.model.file.XMLPSet

      class XMLPSet extends Object implements Serializable
      serialVersionUID:
      1087870691598758048L

      • Serialized Fields

        • currentParameterName
          String currentParameterName
          Current parameter name.
        • description
          String description
          Description of parameter.
        • parameterTable
          Hashtable<String,XMLParameter> parameterTable
          Parameter hashtable.

  • Package gov.nih.mipav.model.provenance

  • Package gov.nih.mipav.model.scripting

  • Package gov.nih.mipav.model.scripting.parameters

  • Package gov.nih.mipav.model.structures

    • Class gov.nih.mipav.model.structures.BufferBase

      class BufferBase extends Object implements Serializable
      serialVersionUID:
      -5379757071350175311L

    • Class gov.nih.mipav.model.structures.BufferBoolean

      class BufferBoolean extends BufferBase implements Serializable
      serialVersionUID:
      588861892470975804L

      • Serialized Fields

        • dataArray
          BitSet dataArray
          1D Data array of boolean stored in the BitSet object.

    • Class gov.nih.mipav.model.structures.BufferByte

      class BufferByte extends BufferBase implements Serializable
      serialVersionUID:
      -4876739041350991776L

      • Serialized Fields

        • dataArray
          byte[] dataArray
          1D Data array of bytes.

    • Class gov.nih.mipav.model.structures.BufferDouble

      class BufferDouble extends BufferBase implements Serializable
      serialVersionUID:
      3953733643360606122L

      • Serialized Fields

        • dataArray
          double[] dataArray
          1D Data array of doubles.

    • Class gov.nih.mipav.model.structures.BufferFloat

      class BufferFloat extends BufferBase implements Serializable
      serialVersionUID:
      -3011094039945269732L

      • Serialized Fields

        • dataArray
          float[] dataArray
          1D Data array of floats.

    • Class gov.nih.mipav.model.structures.BufferInt

      class BufferInt extends BufferBase implements Serializable
      serialVersionUID:
      -2929615702424425376L

      • Serialized Fields

        • dataArray
          int[] dataArray
          1D Data array of integers.

    • Class gov.nih.mipav.model.structures.BufferLong

      class BufferLong extends BufferBase implements Serializable
      serialVersionUID:
      -7762001591051273716L

      • Serialized Fields

        • dataArray
          long[] dataArray
          1D Data array of longs.

    • Class gov.nih.mipav.model.structures.BufferShort

      class BufferShort extends BufferBase implements Serializable
      serialVersionUID:
      784194545397056669L

      • Serialized Fields

        • dataArray
          short[] dataArray
          1D Data array of shorts.

    • Class gov.nih.mipav.model.structures.BufferUByte

      class BufferUByte extends BufferBase implements Serializable
      serialVersionUID:
      -3712379512280992650L

      • Serialized Fields

        • dataArray
          byte[] dataArray
          1D Data array of unsigned bytes (bytes).

    • Class gov.nih.mipav.model.structures.BufferUInt

      class BufferUInt extends BufferBase implements Serializable
      serialVersionUID:
      1794760958290773461L

      • Serialized Fields

        • dataArray
          int[] dataArray
          1D Data array of unsigned integers.

    • Class gov.nih.mipav.model.structures.BufferUShort

      class BufferUShort extends BufferBase implements Serializable
      serialVersionUID:
      -5218443296426650180L

      • Serialized Fields

        • dataArray
          short[] dataArray
          1D Data array of unsigned shorts.

    • Class gov.nih.mipav.model.structures.CustomHashtable

      class CustomHashtable extends Hashtable<String,V> implements Serializable
      serialVersionUID:
      -8592617112282655416L

    • Class gov.nih.mipav.model.structures.MatrixHolder

      class MatrixHolder extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      6886161945452841455L

      • Serialized Fields

        • compositeMatrix
          TransMatrix compositeMatrix
          The composite matrix formed by multiplying (in reverse order) all stored matrices.
        • matrixMap
          LinkedHashMap<String,TransMatrix> matrixMap
          Linked hash map that will store all of the images associated matrices.

    • Class gov.nih.mipav.model.structures.ModelHistogram

      class ModelHistogram extends ModelStorageBase implements Serializable
      serialVersionUID:
      3128722138789734543L

      • Serialized Fields

        • endRange
          int endRange
          DOCUMENT ME!
        • histogramFrameVector
          Vector<Frame> histogramFrameVector
          DOCUMENT ME!
        • maxEntropyThreshold
          int maxEntropyThreshold
          DOCUMENT ME!
        • mean
          double mean
          DOCUMENT ME!
        • mode
          int mode
          DOCUMENT ME!
        • otsuThreshold
          int otsuThreshold
          DOCUMENT ME!
        • stRange
          int stRange
          DOCUMENT ME!
        • totalPixels
          int totalPixels
          DOCUMENT ME!

    • Class gov.nih.mipav.model.structures.ModelImage

      class ModelImage extends ModelStorageBase implements Serializable
      serialVersionUID:
      1234298038008494667L

      • Serialized Fields

        • dtiParameters
          DTIParameters dtiParameters
          Reference to DWI bvalue and gradient information.
        • imageName
          String imageName
          ImageName is patient's name when using DICOM images. It is filename for any other image something other than filename must be used for DICOM because one DICOM image is made of many seperate files. ** Not necessarily the file name.
        • imageNameArray
          String[] imageNameArray
          If imageNameArray is not null, then a different image name will appear on every slice
        • imageOrder
          int imageOrder
          Indicates the image order when two images are displayed in the same frame.
        • mask
          BitSet mask
          Mask is a binary object that is true interior to a VOI and false otherwise used in algorithms to process only on VOIs if indicated by the user.
        • maskBU
          BitSet maskBU
          Backup of mask for undoing.
        • matrixHolder
          MatrixHolder matrixHolder
          Holds all of the images associated matrices.
        • talairach
          TalairachTransformInfo talairach
          Reference to talairach transform information.
        • useMask
          boolean useMask
        • voiVector
          VOIVector voiVector
          List of VOIs that are displayed with this image.

    • Class gov.nih.mipav.model.structures.ModelLUT

      class ModelLUT extends ModelStorageBase implements Serializable
      serialVersionUID:
      5061105716563814614L

      • Serialized Fields

        • alphaLine
          TransferFunction alphaLine
          Fucntion that attenuates image values.
        • blueLine
          TransferFunction blueLine
          Function that maps the blue function of the LUT.
        • greenLine
          TransferFunction greenLine
          Function that maps the green function of the LUT.
        • indexedLUT
          int[] indexedLUT
          Special int array where the LUT is packed with alpha in the most significant byte of the int, followed red, green, and blue.
        • nColors
          int nColors
          Number of colors in the LUT.
        • redLine
          TransferFunction redLine
          Function that maps the red function of the LUT.
        • remappedLUT
          int[] remappedLUT
          DOCUMENT ME!
        • transferLine
          TransferFunction transferLine
          Function that maps image values into the LUT. The x coord. ranges [image.min, image.max];
        • type
          int type
          DOCUMENT ME!
        • x
          float[] x
          The X coordinates of the transfer functions.

    • Class gov.nih.mipav.model.structures.ModelRGB

      class ModelRGB extends ModelStorageBase implements Serializable
      serialVersionUID:
      -718098067552795698L

      • Serialized Fields

        • blueLine
          TransferFunction blueLine
          Function that maps the blue function of the LUT.
        • BOn
          boolean BOn
          Flag indicating whether the blue channel should be displayed.
        • GOn
          boolean GOn
          Flag indicating whether the green channel should be displayed.
        • greenLine
          TransferFunction greenLine
          Function that maps the green function of the LUT.
        • indexedRGB
          int[] indexedRGB
          DOCUMENT ME!
        • nColors
          int nColors
          Number of colors in the LUT.
        • redLine
          TransferFunction redLine
          Function that maps the red function of the LUT.
        • ROn
          boolean ROn
          Flag indicating whether the red channel should be displayed.
        • x
          float[] x
          The X coordinates of the transfer functions.

    • Class gov.nih.mipav.model.structures.ModelSerialCloneable

      class ModelSerialCloneable extends Object implements Serializable
      serialVersionUID:
      7436115594993339188L

    • Class gov.nih.mipav.model.structures.ModelSimpleImage

      class ModelSimpleImage extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      7953112445452821048L

      • Serialized Fields

        • cMassX
          float cMassX
          X coordinate value of the center of mass for the image.
        • cMassY
          float cMassY
          Y coordinate value of the center of mass for the image.
        • cMassZ
          float cMassZ
          Z coordinate value of the center of mass for the image.
        • data
          float[] data
          Data buffer that is used to store the image.
        • dataSize
          int dataSize
          Size of the data buffer (number of pixels in image).
        • extents
          int[] extents
          The dimensionality of the dataset.
        • isColor
          boolean isColor
          Indicates whether is image is a color image or not.
        • max
          float max
          Maximum intensity values of image.
        • maxB
          float maxB
          Maximum intensity values of image.
        • maxG
          float maxG
          Maximum intensity values of image.
        • maxR
          float maxR
          Maximum intensity values of image.
        • min
          float min
          Minimum intensity values of image.
        • minB
          float minB
          Minimum intensity values of image.
        • minG
          float minG
          Minimum intensity values of image.
        • minR
          float minR
          Minimum intensity values of image.
        • name
          String name
          add simple image name for AAM model only.
        • nDims
          int nDims
          Number of dimensions of the image.
        • resolutions
          float[] resolutions
          Voxel resolutions (typically x,y,z(slice spacing),t).
        • tDim
          int tDim
          Number of volumes in the dataset. Typically t represents time.
        • tRes
          float tRes
          Resolution in the time dimension.
        • xDim
          int xDim
          Number of pixels in x dimension.
        • xRes
          float xRes
          X pixel resolution.
        • yDim
          int yDim
          Number of pixels in y dimension.
        • yRes
          float yRes
          Y pixel resolution.
        • zDim
          int zDim
          Number of pixels in z dimension.
        • zRes
          float zRes
          Z voxel resolution.

    • Class gov.nih.mipav.model.structures.ModelStorageBase

      class ModelStorageBase extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -3710345290762731636L

      • Serialized Fields

        • avgInten
          float avgInten
        • avgIntenB
          float avgIntenB
        • avgIntenG
          float avgIntenG
        • avgIntenR
          float avgIntenR
        • bufferType
          ModelStorageBase.DataType bufferType
          Type of image buffer (i.e. BOOLEAN, BYTE, UBYTE, SHORT ...)
        • data
          BufferBase data
          Storage location of image data.
        • dataSize
          int dataSize
          Total buffer length.
        • dimExtents
          int[] dimExtents
          Bounds of the image where.
          • dimExtents[0] = x dimension
          • dimExtents[1] = y dimension
          • dimExtents[2] = z dimension (typically)
          • dimExtents[3] = fourth dimension (ie time)...
        • dimOriginalExtents
          int[] dimOriginalExtents
          Bounds of the image where.
          • dimOriginalExtents[0] = x dimension
          • dimOriginalExtents[1] = y dimension
          • dimOriginalExtents[2] = z dimension (typically)
          • dimOriginalExtents[3] = fourth dimension (ie time)...
        • fileInfo
          FileInfoBase[] fileInfo
          Each image slice has a information that describes aspects of each slice of an image.
        • filterType
          int filterType
          DOCUMENT ME! - TO BE MOVED - redesigned
        • freq1
          float freq1
          DOCUMENT ME! - TO BE MOVED - redesigned
        • freq2
          float freq2
          DOCUMENT ME! - TO BE MOVED - redesigned
        • freqU
          float freqU
          5 variables used in Gabor transform. - should be removed - redesigned
        • freqV
          float freqV
          DOCUMENT ME! - TO BE MOVED - redesigned
        • haveWindowed
          boolean haveWindowed
          DOCUMENT ME! - TO BE MOVED - redesigned
        • image25D
          boolean image25D
          Boolean telling if 3D images are processed 1 slice at a time.
        • lastMax
          double lastMax
          lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.
        • lastMin
          double lastMin
          lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.
        • lockStatus
          int lockStatus
          Locking status of the image. Default = UNLOCKED
        • logMagDisp
          boolean logMagDisp
          Boolean telling if log magnitude display is used for the data buffer
        • m_bConvolve
          boolean m_bConvolve
          Set to true when the image is the product of the ffts of two images, so that on an inverse_fft this image will be centered properly. Default is false.
        • m_bRadiologicalView
          boolean m_bRadiologicalView
          When true, display the data in the Radiological View, when false display the Neurological View:.
        • m_kColorVector
          Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA> m_kColorVector
          Surface color vector. - TO BE MOVED - redesigned
        • m_kMaskColorVector
          Vector<WildMagic.LibFoundation.Mathematics.ColorRGBA[]> m_kMaskColorVector
          Surface mask color vector. - TO BE MOVED - redesigned
        • m_kMaskVector
          Vector<BitSet> m_kMaskVector
          Surface mask vector.- TO BE MOVED - redesigned.
        • max
          double max
          Minimum and maximum image intensity.
        • maxA
          double maxA
          Minimum and maximum for a color image.
        • maxB
          double maxB
          Minimum and maximum for a color image.
        • maxG
          double maxG
          Minimum and maximum for a color image.
        • maxR
          double maxR
          Minimum and maximum for a color image.
        • min
          double min
          Minimum and maximum image intensity.
        • minA
          double minA
          Minimum and maximum for a color image.
        • minB
          double minB
          Minimum and maximum for a color image.
        • minG
          double minG
          Minimum and maximum for a color image.
        • minR
          double minR
          Minimum and maximum for a color image.
        • nDims
          int nDims
          Number of dimensions of the data.
        • noLogMax
          double noLogMax
          Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED
        • noLogMin
          double noLogMin
          Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED
        • noLogMinNonZero
          double noLogMinNonZero
          Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED
        • nonZeroMax
          double nonZeroMax
          Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned
        • nonZeroMaxB
          double nonZeroMaxB
          Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
        • nonZeroMaxG
          double nonZeroMaxG
          Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
        • nonZeroMaxR
          double nonZeroMaxR
          Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
        • nonZeroMin
          double nonZeroMin
          Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned
        • nonZeroMinB
          double nonZeroMinB
          Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
        • nonZeroMinG
          double nonZeroMinG
          Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
        • nonZeroMinR
          double nonZeroMinR
          Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned
        • numPixels
          int numPixels
        • originalCropCheckbox
          boolean originalCropCheckbox
          DOCUMENT ME!- TO BE MOVED - redesigned.
        • originalDoCrop
          boolean originalDoCrop
          DOCUMENT ME! - TO BE MOVED - redesigned
        • originalEnd
          int[] originalEnd
          DOCUMENT ME!- TO BE MOVED - redesigned.
        • originalEpsilon
          double originalEpsilon
          The maximum filter ripple in Chebyshev I and II The passband ripple in decibels in Elliptic
        • originalFilterConstruction
          int originalFilterConstruction
          DOCUMENT ME! - TO BE MOVED- redesigned
        • originalFilterOrder
          int originalFilterOrder
          DOCUMENT ME!- TO BE MOVED - redesigned.
        • originalKernelDimension
          int originalKernelDimension
          This are variables used by the FFT filter algorithm. - should be removed - redesigned
        • originalRs
          double originalRs
          Decibels stopband is down in Elliptic
        • originalStart
          int[] originalStart
          DOCUMENT ME! - TO BE MOVED - redesigned
        • sigmaU
          float sigmaU
          DOCUMENT ME! - TO BE MOVED - redesigned
        • sigmaV
          float sigmaV
          DOCUMENT ME! - should be removed - redesigned
        • smallestMagnitudeNegative
          double smallestMagnitudeNegative
          smallest magnitude negative and positive.
        • smallestMagnitudeNegativeB
          double smallestMagnitudeNegativeB
          smallest magnitude negative and positive.
        • smallestMagnitudeNegativeG
          double smallestMagnitudeNegativeG
          smallest magnitude negative and positive.
        • smallestMagnitudeNegativeR
          double smallestMagnitudeNegativeR
          smallest magnitude negative and positive.
        • smallestMagnitudePositive
          double smallestMagnitudePositive
          smallest magnitude negative and positive.
        • smallestMagnitudePositiveB
          double smallestMagnitudePositiveB
          smallest magnitude negative and positive.
        • smallestMagnitudePositiveG
          double smallestMagnitudePositiveG
          smallest magnitude negative and positive.
        • smallestMagnitudePositiveR
          double smallestMagnitudePositiveR
          smallest magnitude negative and positive.
        • stdDeviation
          float stdDeviation
        • stdDeviationB
          float stdDeviationB
        • stdDeviationG
          float stdDeviationG
        • stdDeviationR
          float stdDeviationR
        • sumPixelInten
          double sumPixelInten
        • sumPixelIntenB
          double sumPixelIntenB
        • sumPixelIntenG
          double sumPixelIntenG
        • sumPixelIntenR
          double sumPixelIntenR
        • theta
          float theta
          DOCUMENT ME! - TO BE MOVED - redesigned
        • unequalDim
          boolean unequalDim
          Boolean telling if unequal dimensions are allowed in the FFT image. TO BE MOVED
        • writeLockCount
          int writeLockCount
          Locking write count.

    • Class gov.nih.mipav.model.structures.SortingTableModel

      class SortingTableModel extends DefaultTableModel implements Serializable
      serialVersionUID:
      -1782879801334035117L

    • Class gov.nih.mipav.model.structures.TableSorter

      class TableSorter extends AbstractTableModel implements Serializable
      serialVersionUID:
      3279717528747239046L

    • Class gov.nih.mipav.model.structures.TalairachTransformInfo

      class TalairachTransformInfo extends Object implements Serializable
      serialVersionUID:
      5791995578653926105L

      • Serialized Fields

        • acpcAC
          WildMagic.LibFoundation.Mathematics.Vector3f acpcAC
          Anterior Comissure in acpc space.
        • acpcDim
          int[] acpcDim
          Image dimensions.
        • acpcMax
          WildMagic.LibFoundation.Mathematics.Vector3f acpcMax
          ACPC min and max extents of the brain.
        • acpcMin
          WildMagic.LibFoundation.Mathematics.Vector3f acpcMin
          ACPC min and max extents of the brain.
        • acpcPC
          WildMagic.LibFoundation.Mathematics.Vector3f acpcPC
          Posterior Comissure in acpc space.
        • acpcRes
          float acpcRes
          Voxel resolution (cubic).
        • isAcpc
          boolean isAcpc
          True if we have the data to compute orig invalid input: '<'-> acpc.
        • isTlrc
          boolean isTlrc
          True if we ahve the data to compute acpc invalid input: '<'-> tlrc.
        • origAC
          WildMagic.LibFoundation.Mathematics.Vector3f origAC
          Anterior Comissure in original space.
        • origDim
          int[] origDim
          Original image dimensions.
        • origOrient
          float[][] origOrient
          ACPC orientation in original image.
        • origOrigin
          float[] origOrigin
          Original image origin.
        • origPC
          WildMagic.LibFoundation.Mathematics.Vector3f origPC
          Posterior Comissure in original space.
        • origRes
          float[] origRes
          Original image voxel resolutions.
        • tlrcAC
          WildMagic.LibFoundation.Mathematics.Vector3f tlrcAC
          Anterior Comissure in Talairach space.
        • tlrcDim
          int[] tlrcDim
          Image dimensions.
        • tlrcPC
          WildMagic.LibFoundation.Mathematics.Vector3f tlrcPC
          Posterior Comissure in Talairach space.
        • tlrcRes
          float[] tlrcRes
          Voxel resolutions for the sub-boxes.
        • useIncorrectAcpcXDim
          boolean useIncorrectAcpcXDim
          Whether to use the old, incorrect ACPC X dim calculation, which overcounted by one (used in backwards compatibility for Dr. Pierpaoli's group).

    • Exception Class gov.nih.mipav.model.structures.TokenizerException

      class TokenizerException extends Exception implements Serializable
      serialVersionUID:
      -5430332821046122039L

    • Class gov.nih.mipav.model.structures.TransferFunction

      class TransferFunction extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      -6859218214454354638L

      • Serialized Fields

        • capacity
          int capacity
          The total capacity of the 2D point array. Initial capacity = 10
        • endPtr
          int endPtr
          Points to the next available storage location for the point.
        • pts
          WildMagic.LibFoundation.Mathematics.Vector2f[] pts
          The array of 2D points that define the line.
        • slopes
          float[] slopes
          The array of pre-calculated slope values.

    • Class gov.nih.mipav.model.structures.TransMatrix

      class TransMatrix extends WildMagic.LibFoundation.Mathematics.Matrix4f implements Serializable
      serialVersionUID:
      5604493833934574127L

      • Serialized Fields

        • m_Is2D
          boolean m_Is2D
          Transform was constructed to transform 2D vectors, instead of 3D
        • m_IsNIFTI
          boolean m_IsNIFTI
          boolean indicating whether this matrix is associated with a NIFTI image (special case handling)
        • m_IsQform
          boolean m_IsQform
          If true, nifti matrix codes for a qform matrix If false, nifti matrix codes for a sform matrix Value has no effect if not a nifti matrix
        • m_TransformID
          int m_TransformID
          Transform ID associated with the matrix.

    • Class gov.nih.mipav.model.structures.TransMatrixd

      class TransMatrixd extends WildMagic.LibFoundation.Mathematics.Matrix4d implements Serializable

      • Serialized Fields

        • m_Is2D
          boolean m_Is2D
          Transform was constructed to transform 2D vectors, instead of 3D
        • m_IsNIFTI
          boolean m_IsNIFTI
          boolean indicating whether this matrix is associated with a NIFTI image (special case handling)
        • m_IsQform
          boolean m_IsQform
          If true, nifti matrix codes for a qform matrix If false, nifti matrix codes for a sform matrix Value has no effect if not a nifti matrix
        • m_TransformID
          int m_TransformID
          Transform ID associated with the matrix.

    • Class gov.nih.mipav.model.structures.UneditableTableModel

      class UneditableTableModel extends DefaultTableModel implements Serializable
      serialVersionUID:
      6185277710154266940L

    • Class gov.nih.mipav.model.structures.UpdateVOIEvent

      class UpdateVOIEvent extends EventObject implements Serializable
      serialVersionUID:
      8233713497226707057L

      • Serialized Fields

        • curve
          VOIBase curve
          DOCUMENT ME!
        • source
          Object source
          DOCUMENT ME!
        • usedCurve
          boolean usedCurve
          DOCUMENT ME!
        • voi
          VOI voi
          DOCUMENT ME!

    • Class gov.nih.mipav.model.structures.VOI

      class VOI extends ModelSerialCloneable implements Serializable
      serialVersionUID:
      4045424525937515770L

      • Serialized Fields

        • active
          boolean active
        • boundingBox
          boolean boundingBox
          If true the bounding box of the VOI should be displayed.
        • color
          Color color
          Indicates the color or the VOI.
        • comments
          ArrayList<String> comments
        • curves
          VOIBaseVector curves
          A vector array of curves per slice.
        • curveType
          int curveType
          Indicates the type of VOI (i.e. CONTOUR, POLYLINE, LINE, POINT, PROTRACTOR, etc. ... )
        • displayMode
          int displayMode
          Indicates if the VOI should be shown as a boundary or a solid.
        • extension
          String extension
          extension of voi file name of voi was read in through file
        • fixed
          boolean fixed
          If true the VOI cannot be moved, if false this VOI can be moved.
        • ID
          short ID
          ID of the VOI, also used when choosing the display color.
        • ignoreMax
          float ignoreMax
          Sets the maximum intensity value for operations on B invalid input: '&' W images segmented by this VOI
        • ignoreMaxB
          float ignoreMaxB
          Sets the maximum blue intensity value for operations on RGB images segmented by this VOI
        • ignoreMaxG
          float ignoreMaxG
          Sets the maximum green intensity value for operations on RGB images segmented by this VOI
        • ignoreMaxR
          float ignoreMaxR
          Sets the maximum red intensity value for operations on RGB images segmented by this VOI
        • ignoreMin
          float ignoreMin
          Sets the minimum intensity value for operations on B invalid input: '&' W images segmented by this VOI
        • ignoreMinB
          float ignoreMinB
          Sets the minimum blue intensity value for operations on RGB images segmented by this VOI
        • ignoreMinG
          float ignoreMinG
          Sets the minimum green intensity value for operations on RGB images segmented by this VOI
        • ignoreMinR
          float ignoreMinR
          Sets the minimum red intensity value for operations on RGB images segmented by this VOI
        • name
          String name
          Name of the VOI stored as a string.
        • NOT_A_POINT
          int NOT_A_POINT
          int indicating that no point was found.
        • opacity
          float opacity
          When in the solid display mode indicates how opaque the VOI should be. Zero is transparent and one is opaque.
        • polarity
          int polarity
          Indicates if the VOI should mask ones or mask as zeros.
        • process
          boolean process
          If true this flag indicates that the VOI should be included (applied) when processing the image.
        • thickness
          int thickness
          The thickness of the VOI lines
        • UID
          int UID
          Unique ID for saving invalid input: '&' retrieving.
        • visible
          boolean visible
          If true the VOI is visible.
        • watershedID
          short watershedID
          Used to objects a label or ID inconjuction with the watershed algorithm.
        • xBounds
          float[] xBounds
          The x - dimension bounds: xBounds [0] = min and xBounds[1] = max.
        • yBounds
          float[] yBounds
          The y - dimension bounds: yBounds [0] = min and yBounds[1] = max.
        • zBounds
          float[] zBounds
          The z - dimension bounds: zBounds [0] = min and zBounds[1] = max.

    • Class gov.nih.mipav.model.structures.VOIBase

      class VOIBase extends Vector<WildMagic.LibFoundation.Mathematics.Vector3f> implements Serializable
      serialVersionUID:
      -3872480526036224600L

      • Serialized Fields

        • active
          boolean active
          Flag indicating whether or not a VOI is active (selected). If the VOI is selected then the flag is true else it is false
        • autoLabel
          boolean autoLabel
          Automatically generate the label, unless it is set explicitly:
        • averagePt
          WildMagic.LibFoundation.Mathematics.Vector3f averagePt
          Stores the average of the contour of a VOI.
        • cenMassPt
          WildMagic.LibFoundation.Mathematics.Vector3f cenMassPt
          Stores the black and white center of mass of the contour of a VOI.
        • cenMassPtB
          WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtB
          Stores the blue center of mass of the contour of a VOI.
        • cenMassPtG
          WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtG
          Stores the green center of mass of the contour of a VOI.
        • cenMassPtR
          WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtR
          Stores the red center of mass of the contour of a VOI.
        • closed
          boolean closed
          True when this is a closed contour.
        • display
          boolean display
          displays the voi in the volume renderer:
        • doGeometricCenterLabel
          boolean doGeometricCenterLabel
          If doGeometricCenterLabel = true and if active == false and if closed = true, execute drawGeometricCenterLabel when in drawSelf
        • fixed
          boolean fixed
          Flag that indicates if the VOI is movable.
        • gcPt
          WildMagic.LibFoundation.Mathematics.Vector3f gcPt
          Stores the geometric center of the contour of a VOI.
        • label
          String label
          Label (Name) for this member of the VOI.
        • lastPoint
          int lastPoint
          Keeps track of the last near point value (for keyboard moving of individual pts.
        • m_akImageMinMax
          WildMagic.LibFoundation.Mathematics.Vector3f[] m_akImageMinMax
          Current contour bounding-box.
        • m_bQuickLUT
          boolean m_bQuickLUT
          True is this is a QuickLUT contour.
        • m_bReloadPoints
          boolean m_bReloadPoints
        • m_bSplit
          boolean m_bSplit
          True is this is a split-line contour.
        • m_bUpdateAverage
          boolean m_bUpdateAverage
          Set to true if the geometric center needs updating.
        • m_bUpdateBounds
          boolean m_bUpdateBounds
          Set to true if the contour bounding-box needs updating.
        • m_bUpdateGeometricCenter
          boolean m_bUpdateGeometricCenter
          Set to true if the geometric center needs updating.
        • m_bUpdateMask
          boolean m_bUpdateMask
          Set to true if the contour changes, so the mask will update when needed.
        • m_bUpdatePlane
          boolean m_bUpdatePlane
          Set to true if the contour plane needs updating.
        • m_iAnchorIndex
          int m_iAnchorIndex
          Anchor point.
        • m_iPlane
          int m_iPlane
          Current plane of this contour.
        • m_iVOIType
          int m_iVOIType
          VOI type of this contour.
        • m_kColor
          WildMagic.LibFoundation.Mathematics.ColorRGBA m_kColor
          Contour color.
        • m_kPositionSum
          WildMagic.LibFoundation.Mathematics.Vector3f m_kPositionSum
        • nearBoundPoint
          int nearBoundPoint
          Flag used to indicate if the cursor is near a point on the VOI bounding box.
        • nearPoint
          int nearPoint
          Flag used to indicate if the cursor is near a point of the VOI member.
        • numPixels
          int numPixels
          Number of pixels in the array used in graphing intensity along the boundary.
        • process
          boolean process
          If true this flag indicates that the shape should be included (applied) when processing the image. It is possible that an individual contour may not be set for processing, while a VOI may be processed.
        • subtype
          int subtype
          initialize subtype to unknown
        • voiGroup
          VOI voiGroup
          Reference to the containing VOI object.
        • volumeDisplayRange
          float volumeDisplayRange
          Used to display 3D VOIs in the three orthogonal views of the data in the volume renderer
        • xPts
          float[] xPts
        • yPts
          float[] yPts
        • zPts
          float[] zPts

    • Class gov.nih.mipav.model.structures.VOIBaseVector

      class VOIBaseVector extends Vector<VOIBase> implements Serializable
      serialVersionUID:
      8244024438846673669L

      • Serialized Fields

        • parent
          VOI parent

    • Class gov.nih.mipav.model.structures.VOIContour

      class VOIContour extends VOIBase implements Serializable
      serialVersionUID:
      -6479418081230834617L

    • Class gov.nih.mipav.model.structures.VOILine

      class VOILine extends VOIBase implements Serializable
      serialVersionUID:
      -2836164853862289329L

    • Class gov.nih.mipav.model.structures.VOIPoint

      class VOIPoint extends VOIBase implements Serializable
      serialVersionUID:
      48410548552570045L

      • Serialized Fields

        • distanceString
          String distanceString
          Distance between segments shown only for active point in polyline_slices
        • firstSlicePoint
          boolean firstSlicePoint
          True if this point is the 1st point in a slice/frame of Polyline_Slice
        • isActivePoint
          boolean isActivePoint
          True only for the active point of a polyline_slice structure (display's coordinates)
        • m_iID
          int m_iID
          ID if this VOIPoint is contained in a PolyLineSlice object.
        • m_kRotation
          TransMatrix m_kRotation
        • m_kRotationInverse
          TransMatrix m_kRotationInverse
        • totalDistanceString
          String totalDistanceString
          Distance is calculated and passed in by VOI for polyline_slices

    • Class gov.nih.mipav.model.structures.VOIPolyLineSlice

      class VOIPolyLineSlice extends VOIBase implements Serializable
      serialVersionUID:
      -7909604245705492799L

      • Serialized Fields

        • m_kPoints
          Vector<VOIPoint> m_kPoints
          List of VOIPoint that make up the polyline.

    • Class gov.nih.mipav.model.structures.VOIProtractor

      class VOIProtractor extends VOIBase implements Serializable
      serialVersionUID:
      4213485128976585397L

      • Serialized Fields

        • allSlices
          boolean allSlices
          Set to true, displays this protractor object for any z-value.

    • Class gov.nih.mipav.model.structures.VOIText

      class VOIText extends VOIBase implements Serializable
      serialVersionUID:
      -6408262409409720727L

      • Serialized Fields

        • backgroundColor
          Color backgroundColor
          The color used to draw behind the main text (so that the text will stand out)
        • comments
          ArrayList<String> comments
        • fontDescriptors
          int fontDescriptors
          The descriptors for the font which start at PLAIN and are additive (PLAIN + BOLD = bold) (BOLD+ITALIC = bold and italic) etc.
        • fontName
          String fontName
          The name (or type) of the font.
        • fontSize
          int fontSize
          The size of the font (half-sizes not allowed...int).
        • noteString
          String noteString
          The note stored in VOIText, has same font as textString
        • textColor
          Color textColor
          This must be kept separate (but parallel) to the VOI color.
        • textFont
          Font textFont
          The font is stored here so that it does not have to be reallocated on each redraw. It is only new'd at the beginning or if the fontDescriptors variable changes
        • textString
          String textString
          The String to be displayed.
        • useMarker
          boolean useMarker
          If this is set to true, a draggable arrow will be displayed

    • Class gov.nih.mipav.model.structures.VOIVector

      class VOIVector extends ViewVOIVector implements Serializable
      serialVersionUID:
      -7391734288216133947L

      • Serialized Fields

        • listenerList
          EventListenerList listenerList
          holds all interfaces listening to this vector.
        • voiUpdate
          VOIVectorEvent voiUpdate
          an instnace of the VOI update event.

  • Package gov.nih.mipav.model.structures.event

  • Package gov.nih.mipav.model.structures.jama

    • Class gov.nih.mipav.model.structures.jama.ComplexLinearEquations

      class ComplexLinearEquations extends Object implements Serializable

      • Serialized Fields

        • badc1_zlatb4
          double badc1_zlatb4
        • badc2_zlatb4
          double badc2_zlatb4
        • eps_zlatb4
          double eps_zlatb4
        • first_zlartg
          boolean first_zlartg
          Double precision machine variables found in routine zlartg.
        • first_zlatb4
          boolean first_zlatb4
          Found in routine zlatb4
        • ge
          GeneralizedEigenvalue ge
        • iparms
          int[] iparms
        • large_zlatb4
          double[] large_zlatb4
        • le
          LinearEquations le
        • safmin
          double safmin
          DOCUMENT ME!
        • safmn2
          double safmn2
          DOCUMENT ME!
        • safmx2
          double safmx2
          DOCUMENT ME!
        • small_zlatb4
          double[] small_zlatb4
        • UI
          ViewUserInterface UI

    • Class gov.nih.mipav.model.structures.jama.GeneralizedEigenvalue

      class GeneralizedEigenvalue extends Object implements Serializable
      serialVersionUID:
      3809017135250813360L

      • Serialized Fields

        • badc1_dlatb4
          double badc1_dlatb4
        • badc2_dlatb4
          double badc2_dlatb4
        • base
          double base
          DOCUMENT ME!
        • emax
          double emax
          DOCUMENT ME!
        • emin
          double emin
          DOCUMENT ME!
        • eps
          double eps
          DOCUMENT ME!
        • eps_dlatb4
          double eps_dlatb4
        • first
          boolean first
          ------------------------ Class variables ------------------------ Double precision machine parameters found in routine dlamch.
        • first_dlartg
          boolean first_dlartg
          Double precison machine variables found in routine dlartg.
        • first_dlatb4
          boolean first_dlatb4
          Found in routine dlatb4
        • iparms
          int[] iparms
          DOCUMENT ME!
        • large_dlatb4
          double[] large_dlatb4
        • prec
          double prec
          DOCUMENT ME!
        • rmax
          double rmax
          DOCUMENT ME!
        • rmin
          double rmin
          DOCUMENT ME!
        • rnd
          double rnd
          DOCUMENT ME!
        • safmin
          double safmin
          DOCUMENT ME!
        • safmn2
          double safmn2
          DOCUMENT ME!
        • safmx2
          double safmx2
          DOCUMENT ME!
        • sfmin
          double sfmin
          DOCUMENT ME!
        • small_dlatb4
          double[] small_dlatb4
        • t
          double t
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          Common variables in testing routines.

    • Class gov.nih.mipav.model.structures.jama.GeneralizedEigenvalue2

      class GeneralizedEigenvalue2 extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.GeneralizedInverse2

      class GeneralizedInverse2 extends Object implements Serializable

      • Serialized Fields

        • A
          double[][] A
        • eps
          double eps
        • ge
          GeneralizedEigenvalue ge
        • iparms
          int[] iparms
          Found in routine xlaenv
        • sfmin
          double sfmin

    • Class gov.nih.mipav.model.structures.jama.LinearEquations

      class LinearEquations extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.LinearEquations2

      class LinearEquations2 extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.LinearEquations3

      class LinearEquations3 extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.LUSOL

      class LUSOL extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.LUSOLEP

      class LUSOLEP extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.METIS

      class METIS extends Object implements Serializable

      • Serialized Fields

        • gk_cur_jbufs
          int gk_cur_jbufs
        • GK_MOPT_CORE
          int GK_MOPT_CORE
        • GK_MOPT_HEAP
          int GK_MOPT_HEAP
        • GK_MOPT_MARK
          int GK_MOPT_MARK
        • gkmcore
          METIS.gk_mcore_t gkmcore
        • KMETIS_DEFAULT_UFACTOR
          int KMETIS_DEFAULT_UFACTOR
        • MAX_JBUFS
          int MAX_JBUFS
        • MCPMETIS_DEFAULT_UFACTOR
          int MCPMETIS_DEFAULT_UFACTOR
        • OMETIS_DEFAULT_UFACTOR
          int OMETIS_DEFAULT_UFACTOR
        • PMETIS_DEFAULT_UFACTOR
          int PMETIS_DEFAULT_UFACTOR
        • seed
          long seed

    • Class gov.nih.mipav.model.structures.jama.SelectedEigenvalue

      class SelectedEigenvalue extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.SelectedEigenvalue2

      class SelectedEigenvalue2 extends Object implements Serializable

    • Class gov.nih.mipav.model.structures.jama.SparseEigenvalue

      class SparseEigenvalue extends Object implements Serializable

      • Serialized Fields

        • dgetv0_first
          boolean dgetv0_first
        • dgetv0_inits
          boolean dgetv0_inits
        • dgetv0_iseed
          int[] dgetv0_iseed
        • dgetv0_iter
          int dgetv0_iter
        • dgetv0_msglvl
          int dgetv0_msglvl
        • dgetv0_orth
          boolean dgetv0_orth
        • dgetv0_rnorm0
          double dgetv0_rnorm0
        • dsaitr_first
          boolean dsaitr_first
        • dsaitr_ierr
          int[] dsaitr_ierr
        • dsaitr_ipj
          int dsaitr_ipj
        • dsaitr_irj
          int dsaitr_irj
        • dsaitr_iter
          int dsaitr_iter
        • dsaitr_itry
          int dsaitr_itry
        • dsaitr_ivj
          int dsaitr_ivj
        • dsaitr_j
          int dsaitr_j
        • dsaitr_msglvl
          int dsaitr_msglvl
        • dsaitr_orth1
          boolean dsaitr_orth1
        • dsaitr_orth2
          boolean dsaitr_orth2
        • dsaitr_rnorm1
          double dsaitr_rnorm1
        • dsaitr_rstart
          boolean dsaitr_rstart
        • dsaitr_safmin
          double dsaitr_safmin
        • dsaitr_step3
          boolean dsaitr_step3
        • dsaitr_step4
          boolean dsaitr_step4
        • dsaitr_wnorm
          double dsaitr_wnorm
        • dsapps_epsmch
          double dsapps_epsmch
        • dsapps_first
          boolean dsapps_first
        • dsaup2_cnorm
          boolean dsaup2_cnorm
        • dsaup2_eps23
          double dsaup2_eps23
        • dsaup2_getv0
          boolean dsaup2_getv0
        • dsaup2_initv
          boolean dsaup2_initv
        • dsaup2_iter
          int dsaup2_iter
        • dsaup2_kplusp
          int dsaup2_kplusp
        • dsaup2_msglvl
          int dsaup2_msglvl
        • dsaup2_nconv
          int[] dsaup2_nconv
        • dsaup2_nev0
          int dsaup2_nev0
        • dsaup2_np0
          int dsaup2_np0
        • dsaup2_rnorm
          double[] dsaup2_rnorm
        • dsaup2_update
          boolean dsaup2_update
        • dsaup2_ushift
          boolean dsaup2_ushift
        • dsaupd_bounds
          int dsaupd_bounds
        • dsaupd_ierr
          int dsaupd_ierr
        • dsaupd_ih
          int dsaupd_ih
        • dsaupd_iq
          int dsaupd_iq
        • dsaupd_ishift
          int dsaupd_ishift
        • dsaupd_iupd
          int dsaupd_iupd
        • dsaupd_iw
          int dsaupd_iw
        • dsaupd_ldh
          int dsaupd_ldh
        • dsaupd_ldq
          int dsaupd_ldq
        • dsaupd_mode
          int dsaupd_mode
        • dsaupd_msglvl
          int dsaupd_msglvl
        • dsaupd_mxiter
          int[] dsaupd_mxiter
        • dsaupd_nb
          int dsaupd_nb
        • dsaupd_nev0
          int[] dsaupd_nev0
        • dsaupd_next
          int dsaupd_next
        • dsaupd_np
          int[] dsaupd_np
        • dsaupd_ritz
          int dsaupd_ritz
        • ge
          GeneralizedEigenvalue ge
        • le
          LinearEquations le
        • mgetv0
          int mgetv0
        • msaitr
          int msaitr
        • msapps
          int msapps
        • msaup2
          int msaup2
        • msaupd
          int msaupd
        • mseigt
          int mseigt
        • mseupd
          int mseupd
        • msgets
          int msgets
        • nbx
          int nbx
        • nf
          DecimalFormat nf
        • nitref
          int nitref
        • nopx
          int nopx
        • nrorth
          int nrorth
        • nrstrt
          int nrstrt
        • t0
          long t0
        • t1
          long t1
        • t2
          long t2
        • t3
          long t3
        • t4
          long t4
        • t5
          long t5
        • tgetv0
          double tgetv0
        • titref
          double titref
        • tmvbx
          double tmvbx
        • tmvopx
          double tmvopx
        • tsaitr
          double tsaitr
        • tsapps
          double tsapps
        • tsaup2
          double tsaup2
        • tsaupd
          double tsaupd
        • tsconv
          double tsconv
        • tseigt
          double tseigt
        • tsgets
          double tsgets
        • UI
          ViewUserInterface UI

    • Class gov.nih.mipav.model.structures.jama.SuperLU

      class SuperLU extends Object implements Serializable

      • Serialized Fields

        • ALIVE
          int ALIVE
        • COLAMD_AGGRESSIVE
          int COLAMD_AGGRESSIVE
        • colamd_debug
          int colamd_debug
        • COLAMD_DEFRAG_COUNT
          int COLAMD_DEFRAG_COUNT
        • COLAMD_DENSE_COL
          int COLAMD_DENSE_COL
        • COLAMD_DENSE_ROW
          int COLAMD_DENSE_ROW
        • COLAMD_ERROR_A_not_present
          int COLAMD_ERROR_A_not_present
        • COLAMD_ERROR_A_too_small
          int COLAMD_ERROR_A_too_small
        • COLAMD_ERROR_col_length_negative
          int COLAMD_ERROR_col_length_negative
        • COLAMD_ERROR_internal_error
          int COLAMD_ERROR_internal_error
        • COLAMD_ERROR_ncol_negative
          int COLAMD_ERROR_ncol_negative
        • COLAMD_ERROR_nnz_negative
          int COLAMD_ERROR_nnz_negative
        • COLAMD_ERROR_nrow_negative
          int COLAMD_ERROR_nrow_negative
        • COLAMD_ERROR_out_of_memory
          int COLAMD_ERROR_out_of_memory
        • COLAMD_ERROR_p_not_present
          int COLAMD_ERROR_p_not_present
        • COLAMD_ERROR_p0_nonzero
          int COLAMD_ERROR_p0_nonzero
        • COLAMD_ERROR_row_index_out_of_bounds
          int COLAMD_ERROR_row_index_out_of_bounds
        • COLAMD_INFO1
          int COLAMD_INFO1
        • COLAMD_INFO2
          int COLAMD_INFO2
        • COLAMD_INFO3
          int COLAMD_INFO3
        • COLAMD_KNOBS
          int COLAMD_KNOBS
        • COLAMD_OK
          int COLAMD_OK
        • COLAMD_OK_BUT_JUMBLED
          int COLAMD_OK_BUT_JUMBLED
        • COLAMD_STATS
          int COLAMD_STATS
        • COLAMD_STATUS
          int COLAMD_STATUS
        • DEAD
          int DEAD
        • DEAD_NON_PRINCIPAL
          int DEAD_NON_PRINCIPAL
        • DEAD_PRINCIPAL
          int DEAD_PRINCIPAL
        • DEBUGlevel
          int DEBUGlevel
        • DROP_AREA
          int DROP_AREA
        • DROP_BASIC
          int DROP_BASIC
        • DROP_COLUMN
          int DROP_COLUMN
        • DROP_DYNAMIC
          int DROP_DYNAMIC
        • DROP_INTERP
          int DROP_INTERP
        • DROP_PROWS
          int DROP_PROWS
        • DROP_SECONDARY
          int DROP_SECONDARY
        • EMPTY
          int EMPTY
        • FALSE
          int FALSE
        • GLOBAL_A
          SuperLU.SuperMatrix GLOBAL_A
        • GLOBAL_A_ORIG
          SuperLU.SuperMatrix GLOBAL_A_ORIG
        • GLOBAL_C
          double[] GLOBAL_C
        • GLOBAL_L
          SuperLU.SuperMatrix GLOBAL_L
        • GLOBAL_MEM_USAGE
          SuperLU.mem_usage_t GLOBAL_MEM_USAGE
        • GLOBAL_OPTIONS
          SuperLU.superlu_options_t GLOBAL_OPTIONS
        • GLOBAL_PERM_C
          int[] GLOBAL_PERM_C
        • GLOBAL_PERM_R
          int[] GLOBAL_PERM_R
        • GLOBAL_R
          double[] GLOBAL_R
        • GLOBAL_STAT
          SuperLU.SuperLUStat_t GLOBAL_STAT
        • GLOBAL_U
          SuperLU.SuperMatrix GLOBAL_U
        • HAVE_METIS
          boolean HAVE_METIS
        • I_DBEG
          int I_DBEG
        • I_ZBEG
          int I_ZBEG
        • IC_DBEG
          int IC_DBEG
        • IC_ZBEG
          int IC_ZBEG
        • J_ZBEG
          int J_ZBEG
        • MI_DBEG
          int MI_DBEG
        • MI_ZBEG
          int MI_ZBEG
        • MILU_ALPHA
          double MILU_ALPHA
        • MJ_ZBEG
          int MJ_ZBEG
        • NBUCKS
          int NBUCKS
        • NO_MARKER
          int NO_MARKER
        • NO_MEMTYPE
          int NO_MEMTYPE
        • NODROP
          int NODROP
        • num_dmatvec
          int num_dmatvec
        • num_zmatvec
          int num_zmatvec
        • PRNTlevel
          int PRNTlevel
        • TRUE
          int TRUE

    • Class gov.nih.mipav.model.structures.jama.SVD

      class SVD extends Object implements Serializable

  • Package gov.nih.mipav.plugins

  • Package gov.nih.mipav.util

    • Class gov.nih.mipav.util.DoubleDouble

      class DoubleDouble extends Object implements Serializable

      • Serialized Fields

        • hi
          double hi
          The high-order component of the double-double precision value.
        • lo
          double lo
          The low-order component of the double-double precision value.

  • Package gov.nih.mipav.view

    • Class gov.nih.mipav.view.AlternatingTableCellRenderer

      class AlternatingTableCellRenderer extends DefaultTableCellRenderer implements Serializable
      serialVersionUID:
      3028551564787955672L

      • Serialized Fields

        • alternateRowCount
          int alternateRowCount
          DOCUMENT ME!
        • color1
          Color color1
          DOCUMENT ME!
        • color2
          Color color2
          DOCUMENT ME!

    • Class gov.nih.mipav.view.BarMeter

      class BarMeter extends JPanel implements Serializable
      serialVersionUID:
      -560671300642650806L

      • Serialized Fields

        • amplitude
          int amplitude
          DOCUMENT ME!
        • boxHeight
          int boxHeight
          DOCUMENT ME!
        • boxWidth
          int boxWidth
          DOCUMENT ME!
        • divisions
          int divisions
          DOCUMENT ME!
        • g2d
          Graphics2D g2d
          DOCUMENT ME!
        • h
          int h
          DOCUMENT ME!
        • img
          BufferedImage img
          DOCUMENT ME!
        • unusedColor
          Color unusedColor
          DOCUMENT ME!
        • unusedRect
          Rectangle2D unusedRect
          DOCUMENT ME!
        • usedColor
          Color usedColor
          DOCUMENT ME!
        • usedRect
          Rectangle2D usedRect
          DOCUMENT ME!
        • w
          int w
          DOCUMENT ME!
        • whitespaceH
          int whitespaceH
          DOCUMENT ME!
        • whitespaceW
          int whitespaceW
          DOCUMENT ME!

    • Class gov.nih.mipav.view.BorderedButton

      class BorderedButton extends JButton implements Serializable
      serialVersionUID:
      -5566213886996905888L

      • Serialized Fields

        • borderColor
          Color borderColor
          DOCUMENT ME!
        • borderOn
          boolean borderOn
          DOCUMENT ME!

    • Class gov.nih.mipav.view.CheckTreeManager.CheckTreeCellRenderer

      class CheckTreeCellRenderer extends JPanel implements Serializable
      serialVersionUID:
      -8230844402715861092L

    • Class gov.nih.mipav.view.CheckTreeManager.CheckTreeSelectionModel

      class CheckTreeSelectionModel extends DefaultTreeSelectionModel implements Serializable
      serialVersionUID:
      8918452189008290261L

    • Class gov.nih.mipav.view.ColorIcon

      class ColorIcon extends ModelSerialCloneable implements Serializable

      • Serialized Fields

        • color
          Color color
          DOCUMENT ME!
        • h
          int h
          DOCUMENT ME!
        • w
          int w
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ColorWheel

      class ColorWheel extends Canvas implements Serializable

      • Serialized Fields

        • blueShiftColors
          float[] blueShiftColors
          array of r,g,b values after blue shifting
        • gamma
          float gamma
          gamma correction
        • greenAdjColors
          float[] greenAdjColors
          array of r,g,b values after green adj
        • offGraphics
          Graphics offGraphics
          offscreen graphics handle
        • offImage
          Image offImage
          offscreen image
        • pB
          float pB
          blue saturation
        • pC
          float pC
          color range
        • pG
          float pG
          green adj
        • pS
          float pS
          sat vs theta
        • r1
          int r1
          radii of all the circles...r6 is the outermost radius
        • r2
          int r2
          radii of all the circles...r6 is the outermost radius
        • r3
          int r3
          radii of all the circles...r6 is the outermost radius
        • r4
          int r4
          radii of all the circles...r6 is the outermost radius
        • r5
          int r5
          radii of all the circles...r6 is the outermost radius
        • r6
          int r6
          radii of all the circles...r6 is the outermost radius
        • redShiftColors
          float[] redShiftColors
          array of r,g,b values after red shifting
        • stevensBeta
          float stevensBeta
          Stevens Beta
        • type
          String type
          type of color wheel ABSVAL, NOSYMM, ROTATIONALSYMM, MIRRORSYMM

    • Class gov.nih.mipav.view.DICOMDisplayer

      class DICOMDisplayer extends JTable implements Serializable
      serialVersionUID:
      -3693967365082796271L

      • Serialized Fields

    • Class gov.nih.mipav.view.JFrameHistogram

      class JFrameHistogram extends JPanel implements Serializable
      serialVersionUID:
      6057663900661366920L

      • Serialized Fields

        • colEMFrame
          ViewJFrameColocalizationEM colEMFrame
          reference to the colocalization frame for updatng the image.
        • colRegFrame
          ViewJFrameColocalizationRegression colRegFrame
          reference to the colocalization frame for updatng the image.
        • containingFrame
          JFrame containingFrame
          frame containing the lut interface (if display in a stand-alone window)
        • containingPanel
          JPanel containingPanel
          panel containing the lut interface (used in the stand-alone frame or in an outside frame)
        • dualImage
          boolean dualImage
          set to true when the lut interface contains two images (imageA and imageB)
        • imageA
          ModelImage imageA
          source image A
        • imageB
          ModelImage imageB
          source image B
        • LUTa
          ModelStorageBase LUTa
          lut a
        • LUTb
          ModelStorageBase LUTb
          lut b
        • menuObj
          ViewMenuBuilder menuObj
          menu builder
        • panelA
          JPanelHistogram panelA
          histogram interface panels for imageA and imageB
        • panelB
          JPanelHistogram panelB
          histogram interface panels for imageA and imageB
        • parentFrame
          Frame parentFrame
          Parent frame of this dialog, usually of type ViewJFrameImage.
        • regComponent
          ViewJComponentRegistration regComponent
          false = apply algorithm only to VOI regions.
        • tabbedPane
          JTabbedPane tabbedPane
          tabbed pane, each separate tab contains the interface for imageA and imageB
        • useSeparateFrame
          boolean useSeparateFrame
          Whether this panel is contained in another frame or forms its own frame
        • voiDialog
          JDialog voiDialog
          Dialog that enables the user to choose to apply the lut to the entire image, or voi regions.
        • wholeImage
          boolean wholeImage
          true = apply algorithm to the whole image

    • Class gov.nih.mipav.view.JPanelAnonymizeImage

      class JPanelAnonymizeImage extends JPanelChecklist implements Serializable
      serialVersionUID:
      -2842282459266721252L

      • Serialized Fields

    • Class gov.nih.mipav.view.JPanelAnonymizePrivateTags

      class JPanelAnonymizePrivateTags extends JPanel implements Serializable
      serialVersionUID:
      -410753580261870012L

      • Serialized Fields

        • checkTree
          CheckTreeManager checkTree
          The checkbox tree version of the tree in the panel. Used to actually display the information.
        • elementField
          JTextField elementField
        • groupField
          JTextField groupField
        • keyList
          ArrayList<FileDicomKey> keyList
          The list of private keys in the image
        • listModel
          DefaultListModel listModel
        • nameField
          JTextField nameField
        • tagList
          ArrayList<String> tagList
          The list of private tags that map to the keys in the previous list
        • tree
          JTree tree
          The tree used to keep track of keys. Used to manipulate the selections.

    • Class gov.nih.mipav.view.JPanelAnonymizePublicTags

      class JPanelAnonymizePublicTags extends JPanel implements Serializable
      serialVersionUID:
      -4032253276365568162L

    • Class gov.nih.mipav.view.JPanelChecklist

      class JPanelChecklist extends JPanel implements Serializable
      serialVersionUID:
      -6168461302590312089L

      • Serialized Fields

        • checkboxLabels
          String[] checkboxLabels
          must be same size as listLength.
        • checkboxList
          JCheckBox[] checkboxList
          DOCUMENT ME!
        • checkboxPanel
          JPanel checkboxPanel
          DOCUMENT ME!
        • checkButton
          JButton checkButton
          DOCUMENT ME!
        • chkUnchkPanel
          JPanel chkUnchkPanel
          DOCUMENT ME!
        • enabledList
          boolean[] enabledList
          the list of the choices that can be selected.
        • listLength
          int listLength
          must be given a nonzero number on instantiation. must be of same size as checkboxLabels.
        • removeList
          boolean[] removeList
          notice that for the next two lists, ith entry on one corresponds to the ith entry on the other. the entire list of choices possible.
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • unCheckButton
          JButton unCheckButton
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEdit

      class JPanelEdit extends JPanel implements Serializable
      serialVersionUID:
      -8206200502096634672L

      • Serialized Fields

        • errorComponent
          Component errorComponent
          when necessary To CheckFields, and there is a problem with the panel such that a valid panel value cannot be made, the particular component which has a bad value will be pointed to here.
        • errorString
          String errorString
          when necessary To CheckFields, and there is a problem with the panel such that a valid panel value cannot be made, the problem will be reported in this String.
        • propertyName
          String propertyName
          A changable property name for firing PropertyChangeEvents. A panel has but one unique property associated with it, that is the file it references, but in a situation where more than one such panel may be listened to by a PropertyChangeListener, each of these panels may be given a unique name to help the Listener. Be careful when using this feature, however, because if there is more than one listener which is interested in changes in the PropertyChangeEvent, changing the property name will cause conflicts (and likely ignored events).

    • Class gov.nih.mipav.view.JPanelEditAxisOrientation

      class JPanelEditAxisOrientation extends JPanelEdit implements Serializable
      serialVersionUID:
      -6931501818687637674L

      • Serialized Fields

        • orientationBox
          JComboBox orientationBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditBoolean

      class JPanelEditBoolean extends JPanelEdit implements Serializable
      serialVersionUID:
      6795672926611666135L

      • Serialized Fields

        • booleanBox
          JComboBox booleanBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditChar

      class JPanelEditChar extends JPanelEdit implements Serializable
      serialVersionUID:
      216110617521213885L

      • Serialized Fields

        • editTextField
          JTextField editTextField
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditDate

      class JPanelEditDate extends JPanelEdit implements Serializable
      serialVersionUID:
      3504702516257604573L

      • Serialized Fields

        • dayCombobox
          JComboBox dayCombobox
          DOCUMENT ME!
        • monthCombobox
          JComboBox monthCombobox
          DOCUMENT ME!
        • noFutureDates
          boolean noFutureDates
          DOCUMENT ME!
        • noPastDates
          boolean noPastDates
          DOCUMENT ME!
        • xml
          boolean xml
          DOCUMENT ME!
        • yearTextField
          JTextField yearTextField
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditDefault

      class JPanelEditDefault extends JPanelEdit implements Serializable
      serialVersionUID:
      -2218748402204415345L

      • Serialized Fields

        • editTextField
          JTextField editTextField
          DOCUMENT ME!
        • maxLength
          int maxLength
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditImageOrientation

      class JPanelEditImageOrientation extends JPanelEdit implements Serializable
      serialVersionUID:
      155707351575492439L

      • Serialized Fields

        • orientationBox
          JComboBox orientationBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditModality

      class JPanelEditModality extends JPanelEdit implements Serializable
      serialVersionUID:
      -7456502877292143209L

      • Serialized Fields

        • modalityBox
          JComboBox modalityBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditOrientation

      class JPanelEditOrientation extends JPanelEdit implements Serializable
      serialVersionUID:
      -2127377398183049555L

      • Serialized Fields

        • orientationBox
          JComboBox orientationBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditRace

      class JPanelEditRace extends JPanelEdit implements Serializable
      serialVersionUID:
      6499425054292194113L

      • Serialized Fields

    • Class gov.nih.mipav.view.JPanelEditSetOrParam

      class JPanelEditSetOrParam extends JPanelEdit implements Serializable
      serialVersionUID:
      2261232133976028312L

      • Serialized Fields

        • editTextField
          JTextField editTextField
          DOCUMENT ME!
        • isSet
          boolean isSet
          DOCUMENT ME!
        • maxLength
          int maxLength
          DOCUMENT ME!
        • table
          Hashtable<?,?> table
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditSex

      class JPanelEditSex extends JPanelEdit implements Serializable
      serialVersionUID:
      -3767740357915707674L

      • Serialized Fields

        • sexComboBox
          JComboBox sexComboBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditTime

      class JPanelEditTime extends JPanelEdit implements Serializable
      serialVersionUID:
      -1541002811257405137L

      • Serialized Fields

        • hourCheckBox
          JCheckBox hourCheckBox
          permits whether or not to set this field.
        • hourComboBox
          JComboBox hourComboBox
          value to add to this time field.
        • minCheckBox
          JCheckBox minCheckBox
          permits whether or not to set this field.
        • minComboBox
          JComboBox minComboBox
          value to add to this time field.
        • secCheckBox
          JCheckBox secCheckBox
          permits whether or not to set this field.
        • secComboBox
          JComboBox secComboBox
          value to add to this time field.
        • secFraction
          JTextField secFraction
          DOCUMENT ME!
        • xml
          boolean xml
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelEditValueType

      class JPanelEditValueType extends JPanelEdit implements Serializable
      serialVersionUID:
      2306780604257062424L

      • Serialized Fields

        • valueTypeBox
          JComboBox valueTypeBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelFileSelection

      class JPanelFileSelection extends JPanelEdit implements Serializable
      serialVersionUID:
      5350976001384182834L

      • Serialized Fields

        • chooser
          JFileChooser chooser
          DOCUMENT ME!
        • chosenFile
          File chosenFile
          DOCUMENT ME!
        • fileBrowse
          JButton fileBrowse
          DOCUMENT ME!
        • fileTextField
          JTextField fileTextField
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelHistogram

      class JPanelHistogram extends JPanel implements Serializable
      serialVersionUID:
      2049904743460024433L

      • Serialized Fields

        • blueCheckBox
          JCheckBox blueCheckBox
          checkbox for turning on / off the blue component of the color look-up table.
        • ctDialog
          JDialogCT ctDialog
        • cursorIndex
          int cursorIndex
          Active mouse cursor index of the imageA, B and GM image A, B.
        • greenCheckBox
          JCheckBox greenCheckBox
          checkbox for turning on / off the green component of the color look-up table.
        • histogram
          ModelHistogram histogram
          red, green and blue histograms:
        • histogramB
          ModelHistogram histogramB
          red, green and blue histograms:
        • histogramG
          ModelHistogram histogramG
          red, green and blue histograms:
        • histoPanel
          ViewJPanelHistoLUT histoPanel
          histogram panel interface.
        • image
          ModelImage image
          input image
        • indexColorTextF
          JTextField indexColorTextF
          displays the selected LUT color
        • interpCheckBox
          JCheckBox interpCheckBox
          turns interpolation on/off
        • labelsTable
          Hashtable<Integer,JLabel> labelsTable
        • logCheckBox
          JCheckBox logCheckBox
          turns log display on/off
        • LUT
          ModelStorageBase LUT
          input LUT, either ModelLUT or ModelRGB
        • mouseSlider
          JSlider mouseSlider
          slider for small LUT changes
        • mouseSliderLabels
          JLabel[] mouseSliderLabels
        • nColorsTextF
          JTextField nColorsTextF
          displays the number of colors in the LUT
        • oneBasedLUTCheckBoxImage
          JCheckBox oneBasedLUTCheckBoxImage
          sets the minimum LUT value to (1,1,1)
        • outputBox
          JComboBox outputBox
          enables the user to set the image output type or LUT-based image extration
        • panelParent
          JFrameHistogram panelParent
          containing parent class.
        • rangeX
          float rangeX
          X range value of the imageA, B and GM imageA, B.
        • redCheckBox
          JCheckBox redCheckBox
          checkbox for turning on / off the red component of the color look-up table.
        • scaleRange
          int scaleRange
        • threshFillF
          JTextField threshFillF
          displays the threshold fill-value
        • threshLowerF
          JTextField threshLowerF
          displays the threshold lower-value
        • threshUpperF
          JTextField threshUpperF
          displays the threshold upper-value
        • toolBarBottom
          JToolBar toolBarBottom
          bottom tool bar
        • toolBarThreshold
          JToolBar toolBarThreshold
          threshold tool bar
        • updateCheckBox
          JCheckBox updateCheckBox
          enables the user to set updating the display in real-time or only on mouse-release
        • voxelVolumeLabel
          JLabel voxelVolumeLabel
          volume threshold vaue
        • wholeImage
          boolean wholeImage
          true = apply algorithm to the whole image
        • xRangeText
          JTextField xRangeText
        • yRangeText
          JTextField yRangeText

    • Class gov.nih.mipav.view.JPanelListController

      class JPanelListController extends JPanel implements Serializable
      serialVersionUID:
      -3060198445145485002L

      • Serialized Fields

        • deleteSelection
          JButton deleteSelection
          'X'.
        • listA
          JList listA
          upper or left-most list.
        • listB
          JList listB
          lower or right-most list.
        • listLayout
          int listLayout
          DOCUMENT ME!
        • sendAllToListA
          JButton sendAllToListA
          DOCUMENT ME!
        • sendAllToListB
          JButton sendAllToListB
          DOCUMENT ME!
        • sendSelectionToListA
          JButton sendSelectionToListA
          left arrow or up arrow.
        • sendSelectionToListB
          JButton sendSelectionToListB
          right arrow or down arrow.

    • Class gov.nih.mipav.view.JPanelProgressBar

      class JPanelProgressBar extends JPanel implements Serializable
      serialVersionUID:
      -6963733511040621440L

      • Serialized Fields

        • pBar
          JProgressBar pBar
          Actual bar which fills with color as the percentage of completion increases.

    • Class gov.nih.mipav.view.JPanelStatisticsList

      class JPanelStatisticsList extends JPanelChecklist implements Serializable
      serialVersionUID:
      -5517669600349449423L

      • Serialized Fields

        • byContour
          boolean byContour
          true if by contour or by slice and contour and show Totals is not selected
        • openContour
          boolean openContour
          Whether this list is dealing with open contours.
        • singleSlice
          boolean singleSlice
          Whether this list is dealing with lists of 2D contours.

    • Class gov.nih.mipav.view.JPanelTreeController

      class JPanelTreeController extends JPanel implements Serializable

      • Serialized Fields

        • deleteSelection
          JButton deleteSelection
          'X'.
        • sendAllToTreeA
          JButton sendAllToTreeA
          DOCUMENT ME!
        • sendAllToTreeB
          JButton sendAllToTreeB
          DOCUMENT ME!
        • sendSelectionToTreeA
          JButton sendSelectionToTreeA
          left arrow or up arrow.
        • sendSelectionToTreeB
          JButton sendSelectionToTreeB
          right arrow or down arrow.
        • treeA
          JTree treeA
          upper or left-most tree.
        • treeB
          JTree treeB
          lower or right-most tree.
        • treeLayout
          int treeLayout
          DOCUMENT ME!

    • Class gov.nih.mipav.view.JPanelVolumeOpacity

      class JPanelVolumeOpacity extends JPanel implements Serializable
      serialVersionUID:
      -5320201609864903620L

      • Serialized Fields

        • blendSlider
          JSlider blendSlider
          Opacity slider of texture 3D volume opacity changes.
        • componentOpacityA
          ViewJComponentVolOpacityBase componentOpacityA
          Reference to component opacity control A.
        • componentOpacityB
          ViewJComponentVolOpacityBase componentOpacityB
          Reference to component opacity control B.
        • componentOpacityGM_A
          ViewJComponentVolOpacityBase componentOpacityGM_A
          Reference to component opacity control A GM Rescale.
        • componentOpacityGM_B
          ViewJComponentVolOpacityBase componentOpacityGM_B
          Reference to component opacity control B GM Rescale.
        • GMCheckBox
          JCheckBox GMCheckBox
          Gradient Magnitude Check box of the grey scale image.
        • gradMagRescale_A
          ModelImage gradMagRescale_A
          Model image of the gradient magnitude of image A rescaled to have value in the range [0:255].
        • gradMagRescale_B
          ModelImage gradMagRescale_B
          Model image of the gradient magnitude of image B rescaled to have value in the range [0:255].
        • histogramA
          ModelHistogram histogramA
          Histogram reference for image A.
        • histogramB
          ModelHistogram histogramB
          Histogram reference for image B.
        • histogramGM_A
          ModelHistogram histogramGM_A
          Histogram reference for imageA GM.
        • histogramGM_B
          ModelHistogram histogramGM_B
          Histogram reference for imageB GM.
        • imageA
          ModelImage imageA
          Model image A.
        • imageB
          ModelImage imageB
          Model image B.
        • isActiveImage
          boolean isActiveImage
        • isChanging
          boolean isChanging
        • labelsTable
          Hashtable<Integer,JLabel> labelsTable
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • labelsTableB
          Hashtable<Integer,JLabel> labelsTableB
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • labelsTableGM_A
          Hashtable<Integer,JLabel> labelsTableGM_A
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • labelsTableGM_B
          Hashtable<Integer,JLabel> labelsTableGM_B
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • mainPanel
          JPanel mainPanel
          The main control.
        • middleLabelValueA
          float middleLabelValueA
          DOCUMENT ME!
        • middleLabelValueB
          float middleLabelValueB
          DOCUMENT ME!
        • middleLabelValueGM_A
          float middleLabelValueGM_A
          DOCUMENT ME!
        • middleLabelValueGM_B
          float middleLabelValueGM_B
          DOCUMENT ME!
        • mouseSlider
          JSlider mouseSlider
          DOCUMENT ME!
        • mouseSliderB
          JSlider mouseSliderB
          DOCUMENT ME!
        • mouseSliderGM_A
          JSlider mouseSliderGM_A
          DOCUMENT ME!
        • mouseSliderGM_B
          JSlider mouseSliderGM_B
          DOCUMENT ME!
        • opacitySliderLabelsA
          JLabel[] opacitySliderLabelsA
          The labels below the opacity slider.
        • opacitySliderLabelsB
          JLabel[] opacitySliderLabelsB
          The labels below the opacity slider.
        • opacitySliderLabelsGM_A
          JLabel[] opacitySliderLabelsGM_A
          DOCUMENT ME!
        • opacitySliderLabelsGM_B
          JLabel[] opacitySliderLabelsGM_B
          DOCUMENT ME!
        • panelOpacityA
          JPanel panelOpacityA
          Panels that hold the the control components (opacity maps).
        • panelOpacityB
          JPanel panelOpacityB
          DOCUMENT ME!
        • panelOpacityGM_A
          JPanel panelOpacityGM_A
          DOCUMENT ME!
        • panelOpacityGM_B
          JPanel panelOpacityGM_B
          DOCUMENT ME!
        • rangeText
          JTextField rangeText
          X range text field in the imageA, B histogram dialog.
        • rangeTextB
          JTextField rangeTextB
          X range text field in the imageA, B histogram dialog.
        • rangeTextGM_A
          JTextField rangeTextGM_A
          X range text field in the Gradient Magnitude imageA, B histogram dialog.
        • rangeTextGM_B
          JTextField rangeTextGM_B
          X range text field in the Gradient Magnitude imageA, B histogram dialog.
        • scaleRangeA
          float scaleRangeA
          Scale range value according to the image min and max.
        • scaleRangeB
          float scaleRangeB
          Scale range value according to the image min and max.
        • scaleRangeGM_A
          float scaleRangeGM_A
          Scale range value according to the image min and max.
        • scaleRangeGM_B
          float scaleRangeGM_B
          Scale range value according to the image min and max.
        • tabbedPane
          JTabbedPane tabbedPane
          Tabbed pane that contains the list of opacity functions.
        • xRangeTextA
          JTextField xRangeTextA
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • xRangeTextB
          JTextField xRangeTextB
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • xRangeTextGM_A
          JTextField xRangeTextGM_A
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • xRangeTextGM_B
          JTextField xRangeTextGM_B
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextA
          JTextField yRangeTextA
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextB
          JTextField yRangeTextB
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextGM_A
          JTextField yRangeTextGM_A
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextGM_B
          JTextField yRangeTextGM_B
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

    • Class gov.nih.mipav.view.JScrollMenu

      class JScrollMenu extends JMenu implements Serializable

      • Serialized Fields

        • popupMenu
          JPopupMenu popupMenu
          The popup menu portion of the menu.

    • Class gov.nih.mipav.view.JScrollPopupMenu

      class JScrollPopupMenu extends JPopupMenu implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.JTreeDICOM

      class JTreeDICOM extends JTree implements Serializable
      serialVersionUID:
      1L

    • Class gov.nih.mipav.view.LineMeter

      class LineMeter extends JPanel implements Serializable
      serialVersionUID:
      -7794163419733734911L

      • Serialized Fields

        • animationFrame
          int animationFrame
          DOCUMENT ME!
        • animationThread
          Thread animationThread
          monitor animation happens in its own thread.
        • aniSampleRate
          int aniSampleRate
          DOCUMENT ME!
        • chartHeight
          int chartHeight
          DOCUMENT ME!
        • chartWidth
          int chartWidth
          DOCUMENT ME!
        • chartXend
          int chartXend
          DOCUMENT ME!
        • chartXstart
          int chartXstart
          DOCUMENT ME!
        • chartYend
          int chartYend
          DOCUMENT ME!
        • chartYstart
          int chartYstart
          DOCUMENT ME!
        • counterLock
          boolean counterLock
          DOCUMENT ME!
        • countSinceLastUpdate
          int countSinceLastUpdate
          DOCUMENT ME!
        • dim
          Dimension dim
          DOCUMENT ME!
        • drawingHeight
          int drawingHeight
          DOCUMENT ME!
        • drawingWidth
          int drawingWidth
          DOCUMENT ME!
        • g2d
          Graphics2D g2d
          DOCUMENT ME!
        • insets
          Insets insets
          DOCUMENT ME!
        • lineColor
          Color lineColor
          DOCUMENT ME!
        • lineSpacing
          int lineSpacing
          DOCUMENT ME!
        • numberOfDivisions
          int numberOfDivisions
          DOCUMENT ME!
        • numberOfSamplesDisplayed
          int numberOfSamplesDisplayed
          DOCUMENT ME!
        • numberOfSamplesPerDivision
          int numberOfSamplesPerDivision
          DOCUMENT ME!
        • panelHeight
          int panelHeight
          DOCUMENT ME!
        • panelWidth
          int panelWidth
          DOCUMENT ME!
        • paperColor
          Color paperColor
          DOCUMENT ME!
        • penColor
          Color penColor
          DOCUMENT ME!
        • pixelsWidePerSample
          int pixelsWidePerSample
          DOCUMENT ME!
        • recentSamples
          float[] recentSamples
          DOCUMENT ME!
        • sampleRate
          int sampleRate
          DOCUMENT ME!
        • samplesPerUpdate
          int samplesPerUpdate
          DOCUMENT ME!
        • whitespaceH
          int whitespaceH
          DOCUMENT ME!
        • whitespaceW
          int whitespaceW
          DOCUMENT ME!
        • yLocHistory
          float[] yLocHistory
          DOCUMENT ME!

    • Class gov.nih.mipav.view.MIPAVTableCellRenderer

      class MIPAVTableCellRenderer extends DefaultTableCellRenderer implements Serializable
      serialVersionUID:
      2587142275980890594L

    • Class gov.nih.mipav.view.MipavUtil

      class MipavUtil extends JComponent implements Serializable
      serialVersionUID:
      4180127127881019813L

    • Class gov.nih.mipav.view.ProgressChangeEvent

      class ProgressChangeEvent extends ChangeEvent implements Serializable

      • Serialized Fields

        • message
          String message
          The message which will be shown with the progress bar
        • title
          String title
          The title of the progress dialog
        • value
          int value
          The value of the progress bar, the range is from 0~100

    • Class gov.nih.mipav.view.Rubberband

      class Rubberband extends Component implements Serializable
      serialVersionUID:
      7016153369248687772L

      • Serialized Fields

        • active
          boolean active
          DOCUMENT ME!
        • anchorPt
          Point anchorPt
          DOCUMENT ME!
        • component
          Component component
          DOCUMENT ME!
        • endPt
          Point endPt
          DOCUMENT ME!
        • firstStretch
          boolean firstStretch
          DOCUMENT ME!
        • lastPt
          Point lastPt
          DOCUMENT ME!
        • presetHue
          float presetHue
          DOCUMENT ME!
        • stretchedPt
          Point stretchedPt
          DOCUMENT ME!
        • usableComponent
          boolean usableComponent
          DOCUMENT ME!
        • xMax
          int xMax
          DOCUMENT ME!
        • xS
          int xS
          DOCUMENT ME!
        • yMax
          int yMax
          DOCUMENT ME!
        • yS
          int yS
          DOCUMENT ME!

    • Class gov.nih.mipav.view.RubberbandEllipse

      class RubberbandEllipse extends Rubberband implements Serializable
      serialVersionUID:
      -3765430195677943807L

      • Serialized Fields

        • endAngle
          int endAngle
          DOCUMENT ME!
        • startAngle
          int startAngle
          DOCUMENT ME!

    • Class gov.nih.mipav.view.RubberbandLine

      class RubberbandLine extends Rubberband implements Serializable
      serialVersionUID:
      6355805256478756437L

      • Serialized Fields

        • doSplit
          boolean doSplit
          boolean for if this is a VOI Splitter (not line drawer)
        • x
          int[] x
          DOCUMENT ME!
        • y
          int[] y
          DOCUMENT ME!
        • z
          int[] z
          DOCUMENT ME!

    • Class gov.nih.mipav.view.RubberbandLivewire

      class RubberbandLivewire extends Rubberband implements Serializable
      serialVersionUID:
      -2803229062633426608L

      • Serialized Fields

        • activeTree
          RubberbandLivewire.ActiveTree activeTree
          DOCUMENT ME!
        • clickPoints
          Vector<WildMagic.LibFoundation.Mathematics.Vector3f> clickPoints
          DOCUMENT ME!
        • contour
          VOIContour contour
          DOCUMENT ME!
        • costGraph
          byte[] costGraph
          DOCUMENT ME!
        • count
          int count
          DOCUMENT ME!
        • currContourCost
          float currContourCost
          DOCUMENT ME!
        • firstPoint
          boolean firstPoint
          DOCUMENT ME!
        • grad_weight
          float grad_weight
          DOCUMENT ME!
        • localCosts
          float[] localCosts
          DOCUMENT ME!
        • presetHue
          float presetHue
          DOCUMENT ME!
        • prevContourCost
          float prevContourCost
          DOCUMENT ME!
        • prevXPoints
          float[] prevXPoints
          DOCUMENT ME!
        • prevYPoints
          float[] prevYPoints
          DOCUMENT ME!
        • processedIndicies
          BitSet processedIndicies
          DOCUMENT ME!
        • progressBar
          ViewJProgressBar progressBar
          DOCUMENT ME!
        • seededCosts
          float[] seededCosts
          DOCUMENT ME!
        • seedPoint
          int seedPoint
          DOCUMENT ME!
        • selection
          int selection
          DOCUMENT ME!
        • smoothVOIFlag
          boolean smoothVOIFlag
          DOCUMENT ME!
        • tmpPt
          Point tmpPt
          DOCUMENT ME!
        • waitCursor
          Cursor waitCursor
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • xDirections
          float[] xDirections
          DOCUMENT ME!
        • xPoints
          float[] xPoints
          DOCUMENT ME!
        • xPointsDraw
          int[] xPointsDraw
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • yDirections
          float[] yDirections
          DOCUMENT ME!
        • yPoints
          float[] yPoints
          DOCUMENT ME!
        • yPointsDraw
          int[] yPointsDraw
          DOCUMENT ME!

    • Class gov.nih.mipav.view.RubberbandPolyline

      class RubberbandPolyline extends Rubberband implements Serializable
      serialVersionUID:
      -9153642132322433825L

      • Serialized Fields

        • contour
          VOIContour contour
          DOCUMENT ME!
        • firstPoint
          boolean firstPoint
          DOCUMENT ME!
        • mouseDragged
          boolean mouseDragged
          DOCUMENT ME!
        • tmpPt
          Point tmpPt
          DOCUMENT ME!

    • Class gov.nih.mipav.view.RubberbandProtractor

      class RubberbandProtractor extends Rubberband implements Serializable
      serialVersionUID:
      808272437770323870L

      • Serialized Fields

        • x
          int[] x
          DOCUMENT ME!
        • y
          int[] y
          DOCUMENT ME!
        • z
          int[] z
          DOCUMENT ME!

    • Class gov.nih.mipav.view.RubberbandRectangle

      class RubberbandRectangle extends Rubberband implements Serializable
      serialVersionUID:
      -6519290525624847778L

    • Class gov.nih.mipav.view.RubberbandRectangleVOI

      class RubberbandRectangleVOI extends RubberbandRectangle implements Serializable
      serialVersionUID:
      3071762927070207288L

    • Class gov.nih.mipav.view.ViewControlsImage

      class ViewControlsImage extends JPanel implements Serializable
      serialVersionUID:
      3317301000984234468L

      • Serialized Fields

        • alphaSlider
          JSlider alphaSlider
          DOCUMENT ME!
        • borderActiveImage
          TitledBorder borderActiveImage
          DOCUMENT ME!
        • borderImageSlider
          TitledBorder borderImageSlider
          DOCUMENT ME!
        • frame
          ViewJFrameBase frame
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • generalPanel
          JPanel generalPanel
          DOCUMENT ME!
        • group1
          ButtonGroup group1
          DOCUMENT ME!
        • imageSize
          int imageSize
          DOCUMENT ME!
        • paintToolBar
          JToolBar paintToolBar
          Paint toolbar.
        • panelActiveImage
          JPanel panelActiveImage
          DOCUMENT ME!
        • panelImageSlider
          JPanel panelImageSlider
          DOCUMENT ME!
        • panelOptionToolbars
          JPanel panelOptionToolbars
          DOCUMENT ME!
        • panelToolbars
          JPanel panelToolbars
          DOCUMENT ME!
        • radioImageA
          JRadioButton radioImageA
          DOCUMENT ME!
        • radioImageB
          JRadioButton radioImageB
          DOCUMENT ME!
        • registrationToolBar
          JToolBar registrationToolBar
          Registration toolbar.
        • scriptToolBar
          JToolBar scriptToolBar
          DOCUMENT ME!
        • tImageSlider
          ViewJSlider tImageSlider
          tImageSlider
        • toolBar
          JToolBar toolBar
          Main toolbar .
        • toolBarObj
          ViewToolBarBuilder toolBarObj
          Object builds and controls the toolbars.
        • zImageSlider
          ViewJSlider zImageSlider
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewDICOMDoubleListPanel

      class ViewDICOMDoubleListPanel extends ViewSelectableDoubleListPanel implements Serializable
      serialVersionUID:
      3583232599838861716L

    • Class gov.nih.mipav.view.ViewFileChooserSubsample

      class ViewFileChooserSubsample extends JFileChooser implements Serializable
      serialVersionUID:
      -5946259539592286508L

      • Serialized Fields

        • chkSave
          JCheckBox chkSave
          DOCUMENT ME!
        • txtResampleHeight
          JTextField txtResampleHeight
          DOCUMENT ME!
        • txtResampleWidth
          JTextField txtResampleWidth
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewFileTreeNode

      class ViewFileTreeNode extends DefaultMutableTreeNode implements Serializable
      serialVersionUID:
      2761808148905905365L

      • Serialized Fields

        • directoriesOnly
          boolean directoriesOnly
          DOCUMENT ME!
        • explored
          boolean explored
          DOCUMENT ME!
        • rootfile
          boolean rootfile
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewImageDirectory

      class ViewImageDirectory extends JFrame implements Serializable
      serialVersionUID:
      -1262294439731204344L

      • Serialized Fields

        • brightness
          int brightness
          DOCUMENT ME!
        • brightPanel
          JPanel brightPanel
          DOCUMENT ME!
        • brightSlider
          JSlider brightSlider
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • contSlider
          JSlider contSlider
          DOCUMENT ME!
        • current
          JLabel current
          DOCUMENT ME!
        • current2
          JLabel current2
          DOCUMENT ME!
        • defaultImageSize
          Dimension defaultImageSize
          DOCUMENT ME!
        • directory
          String directory
          DOCUMENT ME!
        • directoryTree
          JTree directoryTree
          DOCUMENT ME!
        • file
          File file
          DOCUMENT ME!
        • imageFilter
          ViewImageFileFilter imageFilter
          DOCUMENT ME!
        • imagePanel
          JPanel imagePanel
          DOCUMENT ME!
        • imageSliderPane
          JSplitPane imageSliderPane
          DOCUMENT ME!
        • img
          ViewJComponentPreviewImage img
          DOCUMENT ME!
        • nfc
          NumberFormat nfc
          DOCUMENT ME!
        • node
          ViewFileTreeNode node
          DOCUMENT ME!
        • openSeparate
          boolean openSeparate
          DOCUMENT ME!
        • openSeparateOption
          JCheckBoxMenuItem openSeparateOption
          DOCUMENT ME!
        • origBrightness
          int origBrightness
          DOCUMENT ME!
        • origContrast
          float origContrast
          DOCUMENT ME!
        • otherLabel
          JLabel otherLabel
          DOCUMENT ME!
        • primaryModel
          ViewTableModel primaryModel
          DOCUMENT ME!
        • primaryTable
          JTable primaryTable
          DOCUMENT ME!
        • secondaryModel
          ViewTableModel secondaryModel
          DOCUMENT ME!
        • secondaryTable
          JTable secondaryTable
          DOCUMENT ME!
        • serif12
          Font serif12
          DOCUMENT ME!
        • serif12B
          Font serif12B
          DOCUMENT ME!
        • showXMLThumbnail
          boolean showXMLThumbnail
          DOCUMENT ME!
        • sliderPanel
          JPanel sliderPanel
          DOCUMENT ME!
        • thumbnail
          FileImageXML.Thumbnail thumbnail
          DOCUMENT ME!
        • thumbnailOption
          JCheckBoxMenuItem thumbnailOption
          DOCUMENT ME!
        • treePanel
          JPanel treePanel
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJColorChooser

      class ViewJColorChooser extends JColorChooser implements Serializable
      serialVersionUID:
      -7062915703384786855L

      • Serialized Fields

        • colorDialog
          JDialog colorDialog
          Main color dialog for display

    • Class gov.nih.mipav.view.ViewJComponentAnimate

      class ViewJComponentAnimate extends ViewJComponentBase implements Serializable
      serialVersionUID:
      -2707021974594065054L

      • Serialized Fields

        • alphaBlend
          float alphaBlend
          alphaBlending values for compositing two images.
        • blue
          int blue
          Border color, red, green, and blue components:
        • brightness
          int brightness
          offset ranging from -255 to 255 add to each scaled red, green, and blue
        • contrast
          float contrast
          scale factor ranging from 0.1 to 10.0 by which to multiply each red, green, and blue
        • disposeImage
          boolean disposeImage
          whether or not to dispose of imageA and imageB true unless ViewJFrameAnimate was passed an unscaled 3D image
        • frame
          ViewJFrameBase frame
          frame - frame where the component image is displayed.
        • green
          int green
          Border color, red, green, and blue components:
        • haveFiltered
          boolean haveFiltered
          whether or not the brightness/contrast filter has been invoked
        • ignoreSlice
          boolean[] ignoreSlice
          set true if deleteSlice hit in ViewJFrameAnimate
        • imageA
          ModelImage imageA
          imageA - model for image A.
        • imageActive
          ModelImage imageActive
          Which image is currently active
        • imageB
          ModelImage imageB
          imageB - model for image B.
        • img
          Image[] img
          the image rendered in 2D graphics:
        • m_kPatientSlice
          PatientSlice m_kPatientSlice
          PatientSlice contains all the Patient Coordinate system view-specific data for rendering this component:
        • mt
          MediaTracker mt
          DOCUMENT ME!
        • nColumn
          int nColumn
          in 4D row and column numbers for z slices
        • nRow
          int nRow
          in 4D row and column numbers for z slices
        • nVOI
          int nVOI
          number of vois
        • OPACITY
          float OPACITY
          Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)
        • originalZDim
          int originalZDim
          the number of z slices in a 4D image equal to zDim before the JDialogAnimate 4D to 3D conversion
        • paintBitmap
          BitSet paintBitmap
          Buffer used to indicate if the pixel location is painted (true) or unpainted (false).
        • paintBuffer
          int[] paintBuffer
          Buffer that displays the combined paintBitmap and pixBuffer buffers.
        • paintImageBuffer
          int[] paintImageBuffer
        • red
          int red
          Border color, red, green, and blue components:
        • showNumbers
          boolean showNumbers
          whether to number each z slice for 4D
        • slice
          int slice
          current slice for 3D images:
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!
        • xDim
          int xDim
          image x, y, z dimensions in FileCoordinates
        • xLabel
          int[] xLabel
          in 4D x location of slice numbering string
        • yDim
          int yDim
          image x, y, z dimensions in FileCoordinates
        • yLabel
          int[] yLabel
          in 4D y location of slice numbering string
        • zDim
          int zDim
          image x, y, z dimensions in FileCoordinates
        • zString
          String[] zString
          string for displaying slice number

    • Class gov.nih.mipav.view.ViewJComponentAnimateClip

      class ViewJComponentAnimateClip extends ViewJComponentBase implements Serializable
      serialVersionUID:
      -3162752418756566668L

      • Serialized Fields

        • alphaBlend
          float alphaBlend
          alphaBlending values for compositing two images.
        • alphaPrime
          float alphaPrime
          DOCUMENT ME!
        • blue
          int blue
          DOCUMENT ME!
        • copy
          BufferedImage copy
          DOCUMENT ME!
        • green
          int green
          DOCUMENT ME!
        • ignoreSlice
          boolean[] ignoreSlice
          DOCUMENT ME!
        • img
          Image[] img
          DOCUMENT ME!
        • interpMode
          int interpMode
          DOCUMENT ME!
        • mode
          int mode
          mode - used to describe the cursor mode.
        • mt
          MediaTracker mt
          DOCUMENT ME!
        • nColumn
          int nColumn
          DOCUMENT ME!
        • nRow
          int nRow
          DOCUMENT ME!
        • OPACITY
          float OPACITY
          Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)
        • originalZDim
          int originalZDim
          DOCUMENT ME!
        • red
          int red
          DOCUMENT ME!
        • resX
          float resX
          DOCUMENT ME!
        • resY
          float resY
          DOCUMENT ME!
        • showNumbers
          boolean showNumbers
          DOCUMENT ME!
        • showSliceNumber
          boolean showSliceNumber
          DOCUMENT ME!
        • slice
          int slice
          DOCUMENT ME!
        • string
          String string
          DOCUMENT ME!
        • time
          long time
          DOCUMENT ME!
        • timeSlice
          int timeSlice
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • xLabel
          int[] xLabel
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • yLabel
          int[] yLabel
          DOCUMENT ME!
        • zDim
          int zDim
          DOCUMENT ME!
        • zoomX
          float zoomX
          DOCUMENT ME!
        • zoomY
          float zoomY
          DOCUMENT ME!
        • zString
          String[] zString
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentBase

      class ViewJComponentBase extends JComponent implements Serializable
      serialVersionUID:
      -1024094346997939797L

      • Serialized Fields

        • imageDim
          Dimension imageDim
          DOCUMENT ME!
        • img
          Image img
          DOCUMENT ME!
        • imgB
          Image imgB
          DOCUMENT ME!
        • interpMode
          int interpMode
          Interpolation mode for image display
        • lastMouseX
          int lastMouseX
          used by the repaintPaintBrushCursorFast method
        • lastMouseY
          int lastMouseY
          used by the repaintPaintBrushCursorFast method
        • memImageA
          MemoryImageSource memImageA
          DOCUMENT ME!
        • memImageB
          MemoryImageSource memImageB
          DOCUMENT ME!
        • OUT_OF_BOUNDS
          int OUT_OF_BOUNDS
          DOCUMENT ME!
        • resolutionX
          float resolutionX
          resolutionX and Y are used to correct difference in intra and inter plane voxel resolution These represent the aspect ratio of the image These are NOT to be confused with the pixel resolutions.
        • resolutionY
          float resolutionY
          DOCUMENT ME!
        • showSliceNumber
          boolean showSliceNumber
          DOCUMENT ME!
        • sliceString
          String sliceString
          DOCUMENT ME!
        • textColor
          Color textColor
          DOCUMENT ME!
        • zoomX
          float zoomX
          DOCUMENT ME!
        • zoomY
          float zoomY
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentColocalizationEM

      class ViewJComponentColocalizationEM extends ViewJComponentBase implements Serializable
      serialVersionUID:
      6577659651877049839L

      • Serialized Fields

        • bin2
          int bin2
          DOCUMENT ME!
        • blue
          int blue
          DOCUMENT ME!
        • bottomPad
          int bottomPad
          DOCUMENT ME!
        • brightness
          int brightness
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • destImage
          ModelImage destImage
          DOCUMENT ME!
        • frame
          ViewJFrameBase frame
          frame - frame where the component image is displayed.
        • green
          int green
          DOCUMENT ME!
        • halfMajor
          double[] halfMajor
          DOCUMENT ME!
        • halfMinor
          double[] halfMinor
          DOCUMENT ME!
        • haveFiltered
          boolean haveFiltered
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          imageA - model for image A.
        • imageB
          ModelImage imageB
          imageB - model for image B.
        • imageBufferDest
          float[] imageBufferDest
          DOCUMENT ME!
        • imgDest
          Image imgDest
          DOCUMENT ME!
        • interpMode
          int interpMode
          Creates histogram with ellipses around most prominent clusters.
        • leftPad
          int leftPad
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • lutBufferRemappedDest
          int[] lutBufferRemappedDest
          DOCUMENT ME!
        • LUTdest
          ModelLUT LUTdest
          LUTa - lookup table for destImage.
        • max1
          double max1
          DOCUMENT ME!
        • max2
          double max2
          DOCUMENT ME!
        • mean
          double[][] mean
          DOCUMENT ME!
        • memImageDest
          MemoryImageSource memImageDest
          DOCUMENT ME!
        • min1
          double min1
          DOCUMENT ME!
        • min2
          double min2
          DOCUMENT ME!
        • OPACITY
          float OPACITY
          Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)
        • paintBitmapDest
          BitSet paintBitmapDest
          Buffer used to indicate if the pixel location is painted (true) or unpainted (false).
        • paintBufferDest
          int[] paintBufferDest
          Buffer that displays the combined paintBitmap and pixBuffer buffers.
        • pixBufferDest
          int[] pixBufferDest
          Buffer used to store ARGB images of the image presently being displayed.
        • red
          int red
          DOCUMENT ME!
        • resX
          float resX
          DOCUMENT ME!
        • resY
          float resY
          DOCUMENT ME!
        • RGBTA
          ModelRGB RGBTA
          true if selected red, green, blue components present in RGB image.
        • RGBTB
          ModelRGB RGBTB
          DOCUMENT ME!
        • rightPad
          int rightPad
          DOCUMENT ME!
        • scale1
          double scale1
          DOCUMENT ME!
        • scale2
          double scale2
          DOCUMENT ME!
        • theta
          double[] theta
          DOCUMENT ME!
        • topPad
          int topPad
          DOCUMENT ME!
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • zoomX
          float zoomX
          DOCUMENT ME!
        • zoomY
          float zoomY
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentColocalizationRegression

      class ViewJComponentColocalizationRegression extends ViewJComponentBase implements Serializable
      serialVersionUID:
      -2295519432253254184L

      • Serialized Fields

        • alg
          AlgorithmColocalizationRegression alg
          DOCUMENT ME!
        • bin1
          int bin1
          DOCUMENT ME!
        • bin2
          int bin2
          DOCUMENT ME!
        • blue
          int blue
          DOCUMENT ME!
        • bottomPad
          int bottomPad
          DOCUMENT ME!
        • brightness
          int brightness
          DOCUMENT ME!
        • colocIntensity1
          float[] colocIntensity1
          DOCUMENT ME!
        • colocIntensity2
          float[] colocIntensity2
          DOCUMENT ME!
        • colocSize
          float[] colocSize
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • destImage
          ModelImage destImage
          DOCUMENT ME!
        • doSecondIteration
          boolean doSecondIteration
          DOCUMENT ME!
        • editImageFrameA
          ViewJComponentEditImage editImageFrameA
          DOCUMENT ME!
        • editImageFrameB
          ViewJComponentEditImage editImageFrameB
          DOCUMENT ME!
        • firstIndex
          float firstIndex
          DOCUMENT ME!
        • frame
          ViewJFrameBase frame
          frame - frame where the component image is displayed.
        • freeRangeColocIntensity1
          float[] freeRangeColocIntensity1
          DOCUMENT ME!
        • freeRangeColocIntensity2
          float[] freeRangeColocIntensity2
          DOCUMENT ME!
        • freeRangeColocSize
          float[] freeRangeColocSize
          DOCUMENT ME!
        • freeRangeMode
          boolean freeRangeMode
          DOCUMENT ME!
        • freeRangeRThreshold
          float[] freeRangeRThreshold
          DOCUMENT ME!
        • green
          int green
          DOCUMENT ME!
        • haveFiltered
          boolean haveFiltered
          DOCUMENT ME!
        • haveFreeRangeThreshold
          boolean[] haveFreeRangeThreshold
          DOCUMENT ME!
        • haveThreshold
          boolean[] haveThreshold
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          imageA - model for image A.
        • imageB
          ModelImage imageB
          imageB - model for image B.
        • imageBufferDest
          float[] imageBufferDest
          DOCUMENT ME!
        • imgDest
          Image imgDest
          DOCUMENT ME!
        • interpMode
          int interpMode
          DOCUMENT ME!
        • leftPad
          int leftPad
          DOCUMENT ME!
        • linearCorrelation
          float linearCorrelation
          DOCUMENT ME!
        • lineMin
          int lineMin
          DOCUMENT ME!
        • lineOffset
          double lineOffset
          DOCUMENT ME!
        • lineSlope
          double lineSlope
          DOCUMENT ME!
        • lineVOI
          VOI lineVOI
          DOCUMENT ME!
        • localizeFrame
          ViewJFrameColocalizationRegression localizeFrame
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • lutBufferRemappedDest
          int[] lutBufferRemappedDest
          DOCUMENT ME!
        • LUTdest
          ModelLUT LUTdest
          LUTa - lookup table for destImage.
        • max1
          double max1
          DOCUMENT ME!
        • max2
          double max2
          DOCUMENT ME!
        • maximumx
          double maximumx
          DOCUMENT ME!
        • memImageDest
          MemoryImageSource memImageDest
          DOCUMENT ME!
        • min1
          double min1
          DOCUMENT ME!
        • min2
          double min2
          DOCUMENT ME!
        • minimumx
          double minimumx
          DOCUMENT ME!
        • nVOI
          int nVOI
          DOCUMENT ME!
        • OPACITY
          float OPACITY
          Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)
        • originalLineOffset
          float originalLineOffset
          DOCUMENT ME!
        • originalLineSlope
          float originalLineSlope
          DOCUMENT ME!
        • paintBitmapDest
          BitSet paintBitmapDest
          Buffer used to indicate if the pixel location is painted (true) or unpainted (false).
        • paintBufferDest
          int[] paintBufferDest
          Buffer that displays the combined paintBitmap and pixBuffer buffers.
        • pixBufferDest
          int[] pixBufferDest
          Buffer used to store ARGB images of the image presently being displayed.
        • pointVOI
          VOI pointVOI
          DOCUMENT ME!
        • red
          int red
          DOCUMENT ME!
        • regionLinesDisplay
          boolean regionLinesDisplay
          DOCUMENT ME!
        • resX
          float resX
          DOCUMENT ME!
        • resY
          float resY
          DOCUMENT ME!
        • RGBTA
          ModelRGB RGBTA
          true if selected red, green, blue components present in RGB image.
        • RGBTB
          ModelRGB RGBTB
          DOCUMENT ME!
        • rightPad
          int rightPad
          DOCUMENT ME!
        • rThreshold
          float[] rThreshold
          DOCUMENT ME!
        • scale1
          double scale1
          DOCUMENT ME!
        • scale2
          double scale2
          DOCUMENT ME!
        • secondIndex
          float secondIndex
          DOCUMENT ME!
        • tDim
          int tDim
          Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
        • thresholdOn1
          boolean thresholdOn1
          DOCUMENT ME!
        • topPad
          int topPad
          DOCUMENT ME!
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!
        • xArray
          float[] xArray
          DOCUMENT ME!
        • xdiff
          double xdiff
          DOCUMENT ME!
        • xDim
          int xDim
          Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
        • yArray
          float[] yArray
          DOCUMENT ME!
        • ydiff
          double ydiff
          DOCUMENT ME!
        • yDim
          int yDim
          Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
        • zArray
          float[] zArray
          DOCUMENT ME!
        • zDim
          int zDim
          Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.
        • zoomX
          float zoomX
          DOCUMENT ME!
        • zoomY
          float zoomY
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentDTIImage

      class ViewJComponentDTIImage extends ViewJComponentEditImage implements Serializable

      • Serialized Fields

        • adjustExp
          float adjustExp
          adjust exp *
        • anisotropyBuffer
          float[] anisotropyBuffer
          anisotropy file data buffer *
        • anisotropyMax
          float anisotropyMax
          anisotropy max *
        • anisotropyMin
          float anisotropyMin
          anisotropy min *
        • blueShiftColors
          float[] blueShiftColors
          arry of r,g,b after blue shift *
        • clippedBuffer
          float[] clippedBuffer
          anisotropy file data buffer *
        • gamma
          float gamma
          gamma correction *
        • greenAdjColors
          float[] greenAdjColors
          arry of r,g,b after green adj *
        • imageA
          ModelImage imageA
          model image *
        • isMultiply
          boolean isMultiply
          boolean for truncate/multiply *
        • pB
          float pB
          blue saturation *
        • pC
          float pC
          color range *
        • pG
          float pG
          green adj *
        • piDivTwo
          float piDivTwo
          pi div two *
        • pS
          float pS
          sat vs theta *
        • redShiftColors
          float[] redShiftColors
          array of r,g,b values after red shifting *
        • stevensBeta
          float stevensBeta
          Stevens Beta *
        • truncMultColors
          float[] truncMultColors
          arry of r,g,b after scaling/truncating *
        • twoPi
          float twoPi
          two pi *
        • type
          String type
          type of color wheel ABSVAL, NOSYMM, ROTATIONALSYMM, MIRRORSYMM *

    • Class gov.nih.mipav.view.ViewJComponentEditImage

      class ViewJComponentEditImage extends ViewJComponentBase implements Serializable
      serialVersionUID:
      -3799092616373463766L

      • Serialized Fields

        • allActive
          boolean allActive
          Set to true when all contours of a VOI are active.
        • alphaBlend
          float alphaBlend
          Value used to control the display when compositing two images. Usually = 1 - alphaPrime.
        • alphaPrime
          float alphaPrime
          Value used to control the display when compositing two images. It is the amount of image A to display and is has a range of [0,1]
        • bandSpacing
          int[] bandSpacing
        • checkerDialog
          JDialogCheckerBoard checkerDialog
          Dialog used to set properties of the checkerboard display:(Image A displayed in alternating squares with Image B.
        • cleanImageB
          Image cleanImageB
          DOCUMENT ME!
        • cleanImageBufferA
          int[] cleanImageBufferA
          Buffer used to store ARGB images of the image presently being displayed.
        • cleanImageBufferB
          int[] cleanImageBufferB
          Buffer used to store ARGB images of the image presently being displayed.
        • crosshairCursor
          Cursor crosshairCursor
          Crosshair cursor that can be changed per user preference (in Mipav Options).
        • cursorMode
          int cursorMode
          Used to describe the cursor mode.
        • displayFuzzy
          boolean displayFuzzy
          DOCUMENT ME!
        • doCheckerboardAnimate
          boolean doCheckerboardAnimate
        • drawVOIs
          boolean drawVOIs
          Flag used to prohibit VOI drawing.
        • eyeTrackerRecordingMode
          int eyeTrackerRecordingMode
        • frame
          ViewJFrameBase frame
          Frame where the component image is displayed.
        • frameControls
          ViewControlsImage frameControls
          Controls having color and opacity.
        • fuzzyThreshold
          float fuzzyThreshold
          Region grow parameters fuzzyConnectedness is not used if fuzzyThreshold is less than 0. When fuzzyConnectedness is used, fuzzyThreshold ranges from 0 to 1.
        • gridColor
          Color gridColor
          color of grid.
        • gridLabelingOn
          boolean gridLabelingOn
          if number/lettering should be displayed for grid boxes.
        • gridLabelOrientation
          boolean gridLabelOrientation
          boolean to determine the orientation: true is x-axis numbered false is x-axis lettered.
        • gridOverlayOn
          boolean gridOverlayOn
          Flag to indicate if NEI grid overlay should be displayed.
        • gridSpacingX
          float gridSpacingX
          spacing of the grid (horizontal) in terms of resolution.
        • gridSpacingY
          float gridSpacingY
          spacing of the grid (vertical) in terms of resolution.
        • growDialog
          RegionGrowDialog growDialog
          Dialog used to control region growing of the paint tool.
        • imageA
          ModelImage imageA
          Model for image A.
        • imageActive
          ModelImage imageActive
          Active image.
        • imageB
          ModelImage imageB
          Model for image B.
        • imageBufferA
          float[] imageBufferA
          Buffer for image A, raw intensity.
        • imageBufferActive
          float[] imageBufferActive
          Buffer for active image.
        • imageBufferB
          float[] imageBufferB
          Buffer for image B, raw intensity.
        • imageExtents
          int[] imageExtents
          The dimensionality of the image.
        • imageStatList
          JDialogVOIStatistics imageStatList
          DOCUMENT ME!
        • intensityDropper
          float intensityDropper
          Used in paint to indicate intensity painted into the image.
        • intensityLabel
          boolean intensityLabel
          If true then the x,y location and pixel/voxel intensity should be displayed (x,y: intensity).
        • lastMouseEvent
          long lastMouseEvent
        • lastWinRegionSlice
          int lastWinRegionSlice
          Last slice the image was at when win region was ON. its necessary because otherwise, a new cleanImageB would have to be created upon every repaint. should be initialized to a negative number
        • less
          float less
          DOCUMENT ME!
        • lessB
          float lessB
          DOCUMENT ME!
        • lessG
          float lessG
          DOCUMENT ME!
        • lessR
          float lessR
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          Flag for displaying logMag.
        • LUTa
          ModelLUT LUTa
          Lookup table for image A.
        • LUTb
          ModelLUT LUTb
          Lookup table for image B.
        • m_kPatientSlice
          PatientSlice m_kPatientSlice
          PatientSlice contains all the Patient Coordinate system view-specific data for rendering this component:.
        • m_kWinLevel
          WindowLevel m_kWinLevel
          window / level mouse control:.
        • MAGR_HEIGHT
          int MAGR_HEIGHT
          Default size of magnifier window = 120 pixels.
        • MAGR_MAG
          float MAGR_MAG
          Magnification value of magnifier window -- default = 4.0.
        • MAGR_WIDTH
          int MAGR_WIDTH
          default = 120 pixels.
        • magSettings
          JDialogMagnificationControls magSettings
          Dialog used to control the magnification of the image.
        • makingCheckerboard
          boolean makingCheckerboard
        • maxDistance
          float maxDistance
          DOCUMENT ME!
        • maxExtents
          int[] maxExtents
          DOCUMENT ME!
        • modifyFlag
          boolean modifyFlag
          Used to "lock" display when an algorithm is in the calculation process.
        • more
          float more
          DOCUMENT ME!
        • moreB
          float moreB
          DOCUMENT ME!
        • moreG
          float moreG
          DOCUMENT ME!
        • moreR
          float moreR
          DOCUMENT ME!
        • mousePressIsShiftDown
          boolean mousePressIsShiftDown
          Keep track of state of shift for mouse Pressed events.
        • nColumnCheckers
          int nColumnCheckers
          The number columns when two images are displayed in the checker board mode.
        • nRowCheckers
          int nRowCheckers
          Checkerboard display parameters. The number of rows to display.
        • offscreenImage
          Image offscreenImage
          DOCUMENT ME!
        • onTop
          boolean onTop
          for the use of the user-notifier.
        • orientation
          int orientation
          orientation of the slice, may be AXIAL, CORONAL, SAGITTAL, or UNKNOWN_ORIENT.
        • overlayOn
          boolean overlayOn
          Flag to indicate if DICOM overlay should be displayed.
        • paintBitmap
          BitSet paintBitmap
          Buffer used to indicate if the pixel location is painted (true) or unpainted (false).
        • paintBitmapBU
          BitSet paintBitmapBU
          Backup of paint buffer for undo.
        • paintBitmapSwitch
          boolean paintBitmapSwitch
          if true do not getMask on a setActiveImage command so as to keep the mask from the old active image.
        • paintBrush
          BitSet paintBrush
          BitSet used for painting (brushes on/off).
        • paintBrushDim
          Dimension paintBrushDim
          Dimension of the paint.
        • paintBrushDimPrevious
          Dimension paintBrushDimPrevious
          DOCUMENT ME!
        • paintBrushPrevious
          BitSet paintBrushPrevious
          DOCUMENT ME!
        • paintBrushSize
          int paintBrushSize
          Paint brush size.
        • paintBuffer
          int[] paintBuffer
        • paintImage
          BufferedImage paintImage
          buffered image that is transparent to show the paintbrush cursor.
        • paintImageBuffer
          int[] paintImageBuffer
          This image indicates which images have been painted.
        • paintImagePrevious
          BufferedImage paintImagePrevious
          DOCUMENT ME!
        • pixBuffer
          int[] pixBuffer
          The buffer used to store the ARGB image of the image presently being displayed.
        • pixBufferB
          int[] pixBufferB
          Buffer used to store ARGB image of the windowed imageB.
        • previousPaintBrush
          int previousPaintBrush
          The previous paint brush we were using when the user temporarily changes the paint brush size using keyboard shortcuts (by pressing 1, 2, 3, 4).
        • refPtsLocation
          String refPtsLocation
        • rgbString
          String rgbString
          String representing RGB components used in applied paint
        • RGBTA
          ModelRGB RGBTA
          DOCUMENT ME!
        • RGBTB
          ModelRGB RGBTB
          DOCUMENT ME!
        • saveValue
          float saveValue
          Used with commitMask(int imagesDone), to save the value.
        • saveValueB
          float saveValueB
          DOCUMENT ME!
        • saveValueG
          float saveValueG
          DOCUMENT ME!
        • saveValueR
          float saveValueR
          DOCUMENT ME!
        • saveX
          short saveX
          Used with commitMask(int imagesDone), to save positions.
        • saveY
          short saveY
          Used with commitMask(int imagesDone), to save positions.
        • saveZ
          short saveZ
          Used with commitMask(int imagesDone), to save positions.
        • seedPaintBitmap
          BitSet seedPaintBitmap
          Buffer used to remember the area painted around the last seed point for region growing.
        • seedVal
          float seedVal
          Seed value to start the region grow.
        • seedValB
          float seedValB
          DOCUMENT ME!
        • seedValG
          float seedValG
          DOCUMENT ME!
        • seedValR
          float seedValR
          DOCUMENT ME!
        • shiftDown
          boolean shiftDown
          Flag used to indicate if the shift key is depressed. True indicates the shift key is depressed.
        • showMagIntensity
          boolean showMagIntensity
          Flag used to indicate that the intensity values of the image should be displayed in the magnified portion of the image. The intensity values can only be shown if the magnification is high enough to fit the text representation of the value in the magnified voxel/pixel.
        • sizeLimit
          int sizeLimit
          DOCUMENT ME!
        • slice
          int slice
          DOCUMENT ME!
        • stringOverride
          String stringOverride
          String used to override the slice number in the lower left corner.
        • time
          long time
          DOCUMENT ME!
        • timeSlice
          int timeSlice
          DOCUMENT ME!
        • toppedColor
          Color toppedColor
          DOCUMENT ME!
        • useBComp
          boolean useBComp
        • useGComp
          boolean useGComp
        • useRComp
          boolean useRComp
        • useVOI
          boolean useVOI
          This flag is used by the fuzzy connectedness to indicate that a VOI should be used to calculate certain values to initialize the process.
        • variableThresholds
          boolean variableThresholds
          DOCUMENT ME!
        • visRect
          Rectangle visRect
          Visible rectangle to draw topped.
        • voiManager
          VOIManager voiManager
        • wasDragging
          boolean wasDragging
          Boolean to determine if the mouse had been dragging before mouse release (for moving and setting active).
        • windowedRegionSize
          int windowedRegionSize
          The window region size of used when two images are displayed in the same frame. The size of the window indicates how much of image B is displayed.
        • winLevel
          JDialogWinLevel winLevel
        • winLevelSet
          boolean winLevelSet
          User invokes window and level adjustment with right mouse drag in DEFAULT mode.
        • xMod
          int xMod
        • xPG
          short xPG
          X coord of seed point.
        • xSep
          int xSep
        • xStart
          int[] xStart
        • yMod
          int yMod
        • yPG
          short yPG
          Y coord of seed point.
        • ySep
          int ySep
        • yStart
          int[] yStart
        • zeroToOneLUTAdj
          boolean zeroToOneLUTAdj
          flag indicating whether there is 0 to 1 LUT Adjustment *
        • zPG
          short zPG
          Z coord of seed point.

    • Class gov.nih.mipav.view.ViewJComponentFunct

      class ViewJComponentFunct extends JComponent implements Serializable
      serialVersionUID:
      -2525400551576940334L

      • Serialized Fields

        • functName
          String functName
          DOCUMENT ME!
        • lineColor
          Color lineColor
          DOCUMENT ME!
        • newX
          int[] newX
          DOCUMENT ME!
        • newXLength
          int newXLength
          DOCUMENT ME!
        • newY
          int[] newY
          DOCUMENT ME!
        • newYLength
          int newYLength
          DOCUMENT ME!
        • originalX
          float[] originalX
          DOCUMENT ME!
        • originalY
          float[] originalY
          DOCUMENT ME!
        • showFitFunction
          boolean showFitFunction
          DOCUMENT ME!
        • showFunction
          boolean showFunction
          DOCUMENT ME!
        • voi
          VOI voi
          DOCUMENT ME!
        • X
          float[] X
          DOCUMENT ME!
        • XYCoords
          int[][] XYCoords
          xy coordinates of voi boundar
        • Y
          float[] Y
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentGraph

      class ViewJComponentGraph extends JComponent implements Serializable
      serialVersionUID:
      4064300190247654824L

      • Serialized Fields

        • addSchwarzChristoffelLines
          boolean addSchwarzChristoffelLines
        • backgroundColor
          Color backgroundColor
          DOCUMENT ME!
        • bounds
          Rectangle bounds
          DOCUMENT ME!
        • crosshairCursor
          Cursor crosshairCursor
          DOCUMENT ME!
        • defaultCursor
          Cursor defaultCursor
          DOCUMENT ME!
        • defaultMaxDomain
          float defaultMaxDomain
          DOCUMENT ME!
        • defaultMaxRange
          float defaultMaxRange
          DOCUMENT ME!
        • defaultMinDomain
          float defaultMinDomain
          DOCUMENT ME!
        • defaultMinRange
          float defaultMinRange
          DOCUMENT ME!
        • doLogX
          boolean doLogX
        • doLogY
          boolean doLogY
        • fittedFunctions
          ViewJComponentFunct[] fittedFunctions
          DOCUMENT ME!
        • font10
          Font font10
          DOCUMENT ME!
        • font12
          Font font12
          DOCUMENT ME!
        • font12B
          Font font12B
          DOCUMENT ME!
        • fun2Icon
          ImageIcon fun2Icon
          DOCUMENT ME!
        • fun2PrintIcon
          ImageIcon fun2PrintIcon
          DOCUMENT ME!
        • fun3Icon
          ImageIcon fun3Icon
          DOCUMENT ME!
        • fun3PrintIcon
          ImageIcon fun3PrintIcon
          DOCUMENT ME!
        • fun4Icon
          ImageIcon fun4Icon
          DOCUMENT ME!
        • fun4PrintIcon
          ImageIcon fun4PrintIcon
          DOCUMENT ME!
        • fun5Icon
          ImageIcon fun5Icon
          DOCUMENT ME!
        • fun5PrintIcon
          ImageIcon fun5PrintIcon
          DOCUMENT ME!
        • functions
          ViewJComponentFunct[] functions
          DOCUMENT ME!
        • graphBounds
          Rectangle graphBounds
          DOCUMENT ME!
        • maxDomain
          float maxDomain
          DOCUMENT ME!
        • maxRange
          float maxRange
          DOCUMENT ME!
        • minDomain
          float minDomain
          DOCUMENT ME!
        • minRange
          float minRange
          DOCUMENT ME!
        • newX
          int[] newX
          DOCUMENT ME!
        • newY
          int[] newY
          DOCUMENT ME!
        • oldRubberband
          Rectangle oldRubberband
          DOCUMENT ME!
        • parentFrame
          JFrame parentFrame
          DOCUMENT ME!
        • rubberbandRect
          RubberbandRectangle rubberbandRect
          DOCUMENT ME!
        • showFittedFunctions
          boolean showFittedFunctions
          DOCUMENT ME!
        • showFunctions
          boolean showFunctions
          DOCUMENT ME!
        • showGridLines
          boolean showGridLines
          DOCUMENT ME!
        • showLegend
          boolean showLegend
          DOCUMENT ME!
        • showMinorTickMarks
          boolean showMinorTickMarks
          DOCUMENT ME!
        • showPointsAndLines
          int showPointsAndLines
          DOCUMENT ME!
        • title
          String title
          DOCUMENT ME!
        • userXGrid
          boolean userXGrid
        • userYGrid
          boolean userYGrid
        • x1Vector
          Vector<Double> x1Vector
        • x2Vector
          Vector<Double> x2Vector
        • xGridLines
          int xGridLines
          DOCUMENT ME!
        • xGridUserPositions
          int[] xGridUserPositions
        • xLabel
          String xLabel
          DOCUMENT ME!
        • xScale
          double xScale
          DOCUMENT ME!
        • xTick
          double xTick
          DOCUMENT ME!
        • y1Vector
          Vector<Double> y1Vector
        • y2Vector
          Vector<Double> y2Vector
        • yGridLines
          int yGridLines
          DOCUMENT ME!
        • yGridUserPositions
          int[] yGridUserPositions
        • yInvert
          int yInvert
        • yLabel
          String yLabel
          DOCUMENT ME!
        • yScale
          double yScale
          DOCUMENT ME!
        • yTick
          double yTick
          DOCUMENT ME!
        • zeroXMin
          boolean zeroXMin
        • zeroYMin
          boolean zeroYMin

    • Class gov.nih.mipav.view.ViewJComponentGraphAxes

      class ViewJComponentGraphAxes extends JComponent implements Serializable
      serialVersionUID:
      4064300190247654824L

      • Serialized Fields

        • border
          int border
        • bounds
          Rectangle bounds
          DOCUMENT ME!
        • font12B
          Font font12B
          DOCUMENT ME!
        • gridLines
          int gridLines
          DOCUMENT ME!
        • justified
          int justified
        • label
          String label
          DOCUMENT ME!
        • max
          float max
        • min
          float min
        • orientation
          int orientation

    • Class gov.nih.mipav.view.ViewJComponentHistoLUT

      class ViewJComponentHistoLUT extends ViewJComponentHLUTBase implements Serializable
      serialVersionUID:
      -1320755809299024115L

      • Serialized Fields

    • Class gov.nih.mipav.view.ViewJComponentHistoRGB

      class ViewJComponentHistoRGB extends ViewJComponentHLUTBase implements Serializable
      serialVersionUID:
      288314366500212340L

      • Serialized Fields

    • Class gov.nih.mipav.view.ViewJComponentHLUTBase

      class ViewJComponentHLUTBase extends JComponent implements Serializable
      serialVersionUID:
      3244043088343763762L

      • Serialized Fields

        • addPointFlag
          boolean addPointFlag
          DOCUMENT ME!
        • componentDim
          Dimension componentDim
          The outer dimension of the histogram component we will be drawing.
        • dim
          Dimension dim
          The histogram image dimension.
        • histogram
          ModelHistogram histogram
          The image histogram.
        • histogramBuffer
          int[] histogramBuffer
          DOCUMENT ME!
        • histogramMax
          double histogramMax
          DOCUMENT ME!
        • histogramMaxLog
          double histogramMaxLog
          DOCUMENT ME!
        • histogramParent
          HistoLUTParent histogramParent
          The container of this histogram component.
        • image
          ModelImage image
          The image whose histo lut we are displaying.
        • img
          Image img
          DOCUMENT ME!
        • index
          int index
          DOCUMENT ME!
        • logFlag
          boolean logFlag
          Whether to transform the histogram data by log10.
        • lutIndexBuffer
          int[] lutIndexBuffer
          DOCUMENT ME!
        • mode
          int mode
          The current mode of the histogram component.
        • offsetX
          int offsetX
          DOCUMENT ME!
        • offsetY
          int offsetY
          DOCUMENT ME!
        • pixBuffer
          int[] pixBuffer
          DOCUMENT ME!
        • range
          int range
          DOCUMENT ME!
        • stRange
          int stRange
          DOCUMENT ME!
        • thresholdMode
          int thresholdMode
          The current threshold mode (dual or dual inverse) or NO_THRESHOLD if not in theshold mode.
        • x
          float[] x
          DOCUMENT ME!
        • xN
          int[] xN
          DOCUMENT ME!
        • y
          float[] y
          DOCUMENT ME!
        • yN
          int[] yN
          DOCUMENT ME!
        • z
          float[] z
          DOCUMENT ME!
        • zN
          int[] zN
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentLUT

      class ViewJComponentLUT extends ViewJComponentBase implements Serializable
      serialVersionUID:
      5027534629757769708L

      • Serialized Fields

        • LUT
          ModelLUT LUT
          DOCUMENT ME!
        • LUTDims
          Dimension LUTDims
          DOCUMENT ME!
        • LUTIndexBuffer
          int[] LUTIndexBuffer
          DOCUMENT ME!
        • orientation
          int orientation
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentLUTTable

      class ViewJComponentLUTTable extends ViewJComponentBase implements Serializable
      serialVersionUID:
      4862175635665317557L

      • Serialized Fields

        • image
          ModelImage image
          DOCUMENT ME!
        • LUT
          ModelLUT LUT
          DOCUMENT ME!
        • LUTDims
          Dimension LUTDims
          DOCUMENT ME!
        • LUTIndexBuffer
          int[] LUTIndexBuffer
          DOCUMENT ME!
        • offsetX
          int offsetX
          Offset to draw the tick mark and value label.
        • offsetY
          int offsetY
          DOCUMENT ME!
        • orientation
          int orientation
          DOCUMENT ME!
        • x
          float[] x
          control points coordinate of LUT transfer function .
        • xN
          int[] xN
          DOCUMENT ME!
        • y
          float[] y
          DOCUMENT ME!
        • yN
          int[] yN
          DOCUMENT ME!
        • z
          float[] z
          DOCUMENT ME!
        • zN
          int[] zN
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentPedsAtlasIconImage

      class ViewJComponentPedsAtlasIconImage extends ViewJComponentEditImage implements Serializable

      • Serialized Fields

        • iconHeight
          int iconHeight
        • iconWidth
          int iconWidth
        • linePosition
          int linePosition
        • selectedOrientation
          String selectedOrientation
          selected orientation
        • thisOrientation
          String thisOrientation

    • Class gov.nih.mipav.view.ViewJComponentPreviewImage

      class ViewJComponentPreviewImage extends ViewJComponentBase implements Serializable
      serialVersionUID:
      5183033960229966439L

      • Serialized Fields

        • brightness
          int brightness
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • image
          ModelImage image
          The model image this preview image is derived from.
        • imageSize
          int imageSize
          DOCUMENT ME!
        • imgHeight
          int imgHeight
          DOCUMENT ME!
        • imgWidth
          int imgWidth
          DOCUMENT ME!
        • m_kPatientSlice
          PatientSlice m_kPatientSlice
          PatientSlice interfaces with the ModelImage class to render the image w/LUT changes for this component. Slices are rendered in FileCoordinates.
        • memImage
          MemoryImageSource memImage
          DOCUMENT ME!
        • overlayText
          String overlayText
          Overlay text to show on the image.
        • paintBuffer
          int[] paintBuffer
          DOCUMENT ME!
        • panelHeight
          int panelHeight
          DOCUMENT ME!
        • panelWidth
          int panelWidth
          DOCUMENT ME!
        • parent
          PreviewImageContainer parent
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJComponentRegistration

      class ViewJComponentRegistration extends ViewJComponentEditImage implements Serializable
      serialVersionUID:
      4961820290271772572L

      • Serialized Fields

        • addPointCursor
          Cursor addPointCursor
          DOCUMENT ME!
        • adjMark
          int adjMark
          number of VOIs for adjustable slice
        • anchorPt
          Point anchorPt
          DOCUMENT ME!
        • blue
          int blue
          DOCUMENT ME!
        • centerid
          short centerid
          id of rotation center
        • centerVOI
          VOI centerVOI
          center rotation VOI
        • defaultCursor
          Cursor defaultCursor
          DOCUMENT ME!
        • doAdjMark
          boolean doAdjMark
          DOCUMENT ME!
        • doCenter
          boolean doCenter
          DOCUMENT ME!
        • doDrag
          boolean doDrag
          no adjusted slice movements with mouseDrag
        • doRefMark
          boolean doRefMark
          DOCUMENT ME!
        • green
          int green
          DOCUMENT ME!
        • hue
          float hue
          DOCUMENT ME!
        • id
          short id
          DOCUMENT ME!
        • magRegionCursor
          Cursor magRegionCursor
          Custom cursor: magnify region.
        • markerType
          int[] markerType
          DOCUMENT ME!
        • memCount
          int memCount
          DOCUMENT ME!
        • moveCursor
          Cursor moveCursor
          DOCUMENT ME!
        • newVOI
          VOI newVOI
          DOCUMENT ME!
        • newX
          int newX
          adjustable slice VOI.
        • newY
          int newY
          adjustable slice VOI.
        • oldFrame
          boolean oldFrame
          Used to set old or new mode of registration.
        • OPACITY
          float OPACITY
          Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)
        • pointCursor
          Cursor pointCursor
          DOCUMENT ME!
        • ptCoord
          float[] ptCoord
          DOCUMENT ME!
        • rectCursor
          Cursor rectCursor
          DOCUMENT ME!
        • red
          int red
          DOCUMENT ME!
        • refMark
          int refMark
          number of VOIs for reference slice
        • removePointCursor
          Cursor removePointCursor
          DOCUMENT ME!
        • rotCenterMark
          int rotCenterMark
          number of VOIs for rotation center
        • toolFrame
          ViewJFrameRegistrationTool toolFrame
          Frame where component image is displayed (only for new RegistrationTool).
        • waitCursor
          Cursor waitCursor
          DOCUMENT ME!
        • wandCursor
          Cursor wandCursor
          DOCUMENT ME!
        • xFinish
          float xFinish
          values obtained when mouseReleased
        • xOrg
          int[] xOrg
          DOCUMENT ME!
        • xPres
          int[] xPres
          DOCUMENT ME!
        • xRotation
          float xRotation
          DOCUMENT ME!
        • xStart
          float xStart
          values obtained when mousePressed
        • yFinish
          float yFinish
          values obtained when mouseReleased
        • yOrg
          int[] yOrg
          DOCUMENT ME!
        • yPres
          int[] yPres
          DOCUMENT ME!
        • yRotation
          float yRotation
          DOCUMENT ME!
        • yStart
          float yStart
          values obtained when mousePressed

    • Class gov.nih.mipav.view.ViewJComponentSingleRegistration

      class ViewJComponentSingleRegistration extends ViewJComponentEditImage implements Serializable
      serialVersionUID:
      -6751136899996457162L

      • Serialized Fields

        • centerPtLocation
          int centerPtLocation
          location of the center pt VOI (for registration rotation).
        • isReference
          boolean isReference
          if the image is in a registration window, is the image the reference (and not the adjusted).
        • ptCoord
          float[] ptCoord
          Temporary buffer used when extracting points from a VOI. Save reallocating memory often.
        • xCoords
          int[] xCoords
          Buffers used to save the X coordinates for the points that make up a VOI.
        • yCoords
          int[] yCoords
          Buffers used to save the Y coordinates for the points that make up a VOI.

    • Class gov.nih.mipav.view.ViewJComponentTriImage

      class ViewJComponentTriImage extends ViewJComponentEditImage implements Serializable
      serialVersionUID:
      -389214941507734031L

      • Serialized Fields

        • axisLabels
          String[][] axisLabels
          Labels for the axes:.
        • axisOrientation
          int[] axisOrientation
        • cornerCropPt
          WildMagic.LibFoundation.Mathematics.Vector3f[] cornerCropPt
          Crop Bounding Box Corners in Screen Coordinates:.
        • cropColor
          Color[] cropColor
          Crop Bounding Box Colors:.
        • cropPoints
          WildMagic.LibFoundation.Mathematics.Vector2f[] cropPoints
          Crop Bounding Box in Screen Coordinates:.
        • crosshairPixelGap
          int crosshairPixelGap
          the gap (in one direction) between the center of the crosshair and the actual crosshair line
        • crosshairPt
          WildMagic.LibFoundation.Mathematics.Vector3f crosshairPt
          The x and y coordinate of the cursor position in screen space of this component.
        • doCenter
          boolean doCenter
          Whether to show the center of rotation point in the volume and allow the user to change it. doCenter is set true by center command and set false by DEFAULT and CUBE_BOUNDS modes.
        • dragBBpt
          int dragBBpt
          DOCUMENT ME!
        • dragCenterPt
          boolean dragCenterPt
          DOCUMENT ME!
        • hasOrientation
          boolean hasOrientation
          true if the imageActive has an orientation, false if imageActive is of FileInfoBase.UNKNOWN_ORIENT.
        • horizontalTalGridPts
          int[] horizontalTalGridPts
          DOCUMENT ME!
        • localImageExtents
          int[] localImageExtents
          imageActive extents in the local (Patient) coordinate system:.
        • m_kLocalCropLower
          WildMagic.LibFoundation.Mathematics.Vector3f m_kLocalCropLower
          Lower Crop Bounding Box in Patient Coordinates:.
        • m_kLocalCropUpper
          WildMagic.LibFoundation.Mathematics.Vector3f m_kLocalCropUpper
          Upper Crop Bounding Box in Patient Coordinates:.
        • m_kVolumePoint
          WildMagic.LibFoundation.Mathematics.Vector3f m_kVolumePoint
          Cursor 3D point in FileCoordinates.
        • res
          float[] res
          Reordered resolutions according to orientation. See ModelStorageBase.getResolutions( int index, int orientation ). The orientation parameter may be either: FileInfoBase.AXIAL, FileInfoBase.CORONAL, FileInfoBase.SAGITTAL for oriented slices, or FileInfoBase.UNKNOWN_ORIENT for the default slice orientation.
        • showAxes
          boolean showAxes
          If true, show XY, XZ, or ZY orientation axes in a corner of the component.
        • showBoundingRect
          boolean showBoundingRect
          Specifies whether the user wants to show the cropping / paint bounds rectangle.
        • showCrosshairs
          boolean showCrosshairs
          If true, show crosshairs indicating the currently position within the component.
        • showTalairachGrid
          boolean showTalairachGrid
          Whether to show the talairach grid on the component.
        • showTalairachGridmarkers
          boolean showTalairachGridmarkers
          Whether to show the talairach gridmarkers on the component.
        • talairachMajorLineColor
          Color talairachMajorLineColor
          DOCUMENT ME!
        • talairachMinorLineColor
          Color talairachMinorLineColor
          DOCUMENT ME!
        • triImageFrame
          ViewJFrameTriImage triImageFrame
          The tri image frame of which this object is a component.
        • verticalTalGridPts
          int[] verticalTalGridPts
          DOCUMENT ME!
        • voiProtractor
          VOIProtractor voiProtractor
          The protractor VOI.
        • xColor
          Color[] xColor
          color of the crosshairs.
        • xCursorAdjustment
          int xCursorAdjustment
        • yColor
          Color[] yColor
          DOCUMENT ME!
        • yCursorAdjustment
          int yCursorAdjustment
        • zColor
          Color[] zColor
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameAnimate

      class ViewJFrameAnimate extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -2372670418729121051L

      • Serialized Fields

        • actualPerSecond
          float actualPerSecond
          DOCUMENT ME!
        • alphaBlend
          float alphaBlend
          DOCUMENT ME!
        • aps
          String aps
          set to give 2 digits to the right of the decimal.
        • backForthButton
          JToggleButton backForthButton
          DOCUMENT ME!
        • bfRun
          boolean bfRun
          DOCUMENT ME!
        • borderCol
          Color borderCol
          z slice.
        • buttonArray
          JButton[] buttonArray
          DOCUMENT ME!
        • cForwardButton
          JToggleButton cForwardButton
          DOCUMENT ME!
        • cfRun
          boolean cfRun
          DOCUMENT ME!
        • componentImage
          ViewJComponentAnimate componentImage
          with complex images.
        • componentY
          int componentY
          DOCUMENT ME!
        • controlFrame
          ViewJFrameBase controlFrame
          DOCUMENT ME!
        • controlPanel
          JPanel controlPanel
          DOCUMENT ME!
        • controls
          ViewControlsImage controls
          DOCUMENT ME!
        • cpGBC
          GridBagConstraints cpGBC
          DOCUMENT ME!
        • cpGBL
          GridBagLayout cpGBL
          DOCUMENT ME!
        • cReverseButton
          JToggleButton cReverseButton
          DOCUMENT ME!
        • crRun
          boolean crRun
          DOCUMENT ME!
        • cycleTime
          long cycleTime
          DOCUMENT ME!
        • deleteButton
          JButton deleteButton
          DOCUMENT ME!
        • disposeImage
          boolean disposeImage
          DOCUMENT ME!
        • etchedBorder
          Border etchedBorder
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • forwardButton
          JToggleButton forwardButton
          DOCUMENT ME!
        • fpsSlider
          JSlider fpsSlider
          DOCUMENT ME!
        • framesPerSecond
          float framesPerSecond
          DOCUMENT ME!
        • fRun
          boolean fRun
          DOCUMENT ME!
        • gbcTP
          GridBagConstraints gbcTP
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • imageB
          ModelImage imageB
          DOCUMENT ME!
        • imageBufferA
          float[] imageBufferA
          DOCUMENT ME!
        • imageBufferB
          float[] imageBufferB
          DOCUMENT ME!
        • innerPanel
          JPanel innerPanel
          DOCUMENT ME!
        • labelAnimationFrame
          JLabel labelAnimationFrame
          DOCUMENT ME!
        • labelFramesPerSecond
          JLabel labelFramesPerSecond
          DOCUMENT ME!
        • labelTable
          Hashtable<Integer,JLabel> labelTable
          DOCUMENT ME!
        • localTime
          long localTime
          newmsWait = msWait - msElapsed is passed to the sleep function.
        • localTime2
          long localTime2
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • LUTa
          ModelLUT LUTa
          DOCUMENT ME!
        • LUTb
          ModelLUT LUTb
          DOCUMENT ME!
        • menuObj
          ViewMenuBuilder menuObj
          DOCUMENT ME!
        • minimumHeight
          int minimumHeight
          DOCUMENT ME!
        • minimumToolBarWidth
          int minimumToolBarWidth
          DOCUMENT ME!
        • mjpegQuality
          float mjpegQuality
          DOCUMENT ME!
        • msElapsed
          long msElapsed
          DOCUMENT ME!
        • msWait
          long msWait
          DOCUMENT ME!
        • nColumn
          int nColumn
          DOCUMENT ME!
        • newmsWait
          long newmsWait
          DOCUMENT ME!
        • nf
          NumberFormat nf
          DOCUMENT ME!
        • nImage
          int nImage
          DOCUMENT ME!
        • nRow
          int nRow
          DOCUMENT ME!
        • openingMenuBar
          JMenuBar openingMenuBar
          DOCUMENT ME!
        • origBrightness
          int origBrightness
          DOCUMENT ME!
        • origContrast
          float origContrast
          red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.
        • originalZDim
          int originalZDim
          for 4D originalXDim and originalYDim are xDim and yDim before 4D to 3D conversion.
        • paintBuffer
          int[] paintBuffer
          DOCUMENT ME!
        • pause
          boolean pause
          DOCUMENT ME!
        • pauseButton
          JToggleButton pauseButton
          DOCUMENT ME!
        • pixBuffer
          int[] pixBuffer
          DOCUMENT ME!
        • pressedBorder
          Border pressedBorder
          DOCUMENT ME!
        • progressBar
          ViewJProgressBar progressBar
          currently running.
        • recordButton
          JButton recordButton
          DOCUMENT ME!
        • reverseButton
          JToggleButton reverseButton
          DOCUMENT ME!
        • RGBTA
          ModelRGB RGBTA
          DOCUMENT ME!
        • RGBTB
          ModelRGB RGBTB
          DOCUMENT ME!
        • rRun
          boolean rRun
          currently running.
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • scrollPaneSize
          int scrollPaneSize
          DOCUMENT ME!
        • showFrameBorder
          boolean showFrameBorder
          DOCUMENT ME!
        • showNumbers
          boolean showNumbers
          equals zDim of original 4D before 4D to 3D conversion.
        • sliceOldNumber
          int[] sliceOldNumber
          red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.
        • slider
          JSlider slider
          DOCUMENT ME!
        • startTime
          long startTime
          = localTime2 - localTime.
        • stop
          boolean stop
          containing only 5 msec. sleep commands.
        • stopButton
          JToggleButton stopButton
          DOCUMENT ME!
        • stopTime
          long stopTime
          = localTime2 - localTime.
        • structureY
          int structureY
          DOCUMENT ME!
        • textActualPerSecond
          JTextField textActualPerSecond
          DOCUMENT ME!
        • textAnimationFrame
          JTextField textAnimationFrame
          Note that an attempt to have DocumentListener for textAnimationFrame set the slider value was unsuccessful.
        • textFramesPerSecond
          JTextField textFramesPerSecond
          DOCUMENT ME!
        • toggleArray
          JToggleButton[] toggleArray
          DOCUMENT ME!
        • toolBar
          JToolBar toolBar
          DOCUMENT ME!
        • topPanel
          JPanel topPanel
          and innerPanel placed in scrollPane.
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!
        • zoom
          float zoom
          DOCUMENT ME!
        • zShow
          int zShow
          DOCUMENT ME!
        • zSlice
          int zSlice
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameAnimateClip

      class ViewJFrameAnimateClip extends ViewJFrameBase implements Serializable
      serialVersionUID:
      8057377898754491817L

      • Serialized Fields

        • actualPerSecond
          float actualPerSecond
          DOCUMENT ME!
        • aps
          String aps
          set to give 2 digits to the right of the decimal.
        • backForthButton
          JToggleButton backForthButton
          DOCUMENT ME!
        • bfRun
          boolean bfRun
          DOCUMENT ME!
        • buttonArray
          JButton[] buttonArray
          DOCUMENT ME!
        • cForwardButton
          JToggleButton cForwardButton
          DOCUMENT ME!
        • cfRun
          boolean cfRun
          DOCUMENT ME!
        • componentImage
          ViewJComponentAnimateClip componentImage
          with complex images.
        • componentY
          int componentY
          DOCUMENT ME!
        • controlPanel
          JPanel controlPanel
          DOCUMENT ME!
        • controls
          ViewControlsImage controls
          DOCUMENT ME!
        • cpGBC
          GridBagConstraints cpGBC
          DOCUMENT ME!
        • cpGBL
          GridBagLayout cpGBL
          DOCUMENT ME!
        • cReverseButton
          JToggleButton cReverseButton
          DOCUMENT ME!
        • crRun
          boolean crRun
          DOCUMENT ME!
        • cycleTime
          long cycleTime
          DOCUMENT ME!
        • deleteButton
          JButton deleteButton
          DOCUMENT ME!
        • dir
          String dir
          DOCUMENT ME!
        • etchedBorder
          Border etchedBorder
          DOCUMENT ME!
        • forwardButton
          JToggleButton forwardButton
          DOCUMENT ME!
        • fpsSlider
          JSlider fpsSlider
          DOCUMENT ME!
        • framesPerSecond
          float framesPerSecond
          DOCUMENT ME!
        • fRun
          boolean fRun
          DOCUMENT ME!
        • gbcTP
          GridBagConstraints gbcTP
          DOCUMENT ME!
        • innerPanel
          JPanel innerPanel
          DOCUMENT ME!
        • labelAnimationFrame
          JLabel labelAnimationFrame
          DOCUMENT ME!
        • labelFramesPerSecond
          JLabel labelFramesPerSecond
          DOCUMENT ME!
        • labelTable
          Hashtable<Integer,JLabel> labelTable
          DOCUMENT ME!
        • localTime
          long localTime
          newmsWait = msWait - msElapsed is passed to the sleep function.
        • localTime2
          long localTime2
          DOCUMENT ME!
        • menuObj
          ViewMenuBuilder menuObj
          DOCUMENT ME!
        • minimumHeight
          int minimumHeight
          DOCUMENT ME!
        • minimumToolBarWidth
          int minimumToolBarWidth
          DOCUMENT ME!
        • msElapsed
          long msElapsed
          DOCUMENT ME!
        • msWait
          long msWait
          DOCUMENT ME!
        • nColumn
          int nColumn
          DOCUMENT ME!
        • newmsWait
          long newmsWait
          DOCUMENT ME!
        • nf
          NumberFormat nf
          DOCUMENT ME!
        • nImage
          int nImage
          DOCUMENT ME!
        • nRow
          int nRow
          DOCUMENT ME!
        • openingMenuBar
          JMenuBar openingMenuBar
          DOCUMENT ME!
        • pause
          boolean pause
          DOCUMENT ME!
        • pauseButton
          JToggleButton pauseButton
          DOCUMENT ME!
        • pressedBorder
          Border pressedBorder
          DOCUMENT ME!
        • progressBar
          ViewJProgressBar progressBar
          currently running.
        • recordButton
          JButton recordButton
          DOCUMENT ME!
        • reverseButton
          JToggleButton reverseButton
          DOCUMENT ME!
        • rRun
          boolean rRun
          currently running.
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • scrollPaneSize
          int scrollPaneSize
          DOCUMENT ME!
        • showNumbers
          boolean showNumbers
          equals zDim of original 4D before 4D to 3D conversion.
        • sliceOldNumber
          int[] sliceOldNumber
          DOCUMENT ME!
        • slider
          JSlider slider
          DOCUMENT ME!
        • startTime
          long startTime
          = localTime2 - localTime.
        • stop
          boolean stop
          containing only 5 msec. sleep commands.
        • stopButton
          JToggleButton stopButton
          DOCUMENT ME!
        • stopTime
          long stopTime
          = localTime2 - localTime.
        • structureY
          int structureY
          DOCUMENT ME!
        • textActualPerSecond
          JTextField textActualPerSecond
          DOCUMENT ME!
        • textAnimationFrame
          JTextField textAnimationFrame
          Note that an attempt to have DocumentListener for textAnimationFrame set the slider value was unsuccessful.
        • textFramesPerSecond
          JTextField textFramesPerSecond
          DOCUMENT ME!
        • toggleArray
          JToggleButton[] toggleArray
          DOCUMENT ME!
        • toolBar
          JToolBar toolBar
          DOCUMENT ME!
        • topPanel
          JPanel topPanel
          and innerPanel placed in scrollPane.
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!
        • zoom
          float zoom
          DOCUMENT ME!
        • zShow
          int zShow
          DOCUMENT ME!
        • zSlice
          int zSlice
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameBase

      class ViewJFrameBase extends JFrame implements Serializable
      serialVersionUID:
      -3040123414501128141L

      • Serialized Fields

        • absoluteGoToButton
          JButton absoluteGoToButton
        • absoluteGoToPanel
          JPanel absoluteGoToPanel
        • absoluteLabel
          JLabel absoluteLabel
          Labels for the current absolute position:.
        • absoluteLabelVals
          JLabel[] absoluteLabelVals
          Labels for the current absolute position values:.
        • absolutePanel
          JPanel absolutePanel
          JPanel containing the absoulte position labels:.
        • absoluteXLabel
          JLabel absoluteXLabel
          voxel absolute goto components*
        • absoluteXTextField
          JTextField absoluteXTextField
        • absoluteYLabel
          JLabel absoluteYLabel
          voxel absolute goto components*
        • absoluteYTextField
          JTextField absoluteYTextField
        • absoluteZLabel
          JLabel absoluteZLabel
          voxel absolute goto components*
        • absoluteZTextField
          JTextField absoluteZTextField
        • alphaBlend
          float alphaBlend
          Indicates the amount of blending when two images are loaded in the image frame.
        • blue
          int blue
          Blue channel value of the paint color.
        • defaultLUTa
          ModelLUT defaultLUTa
          Reference to LUT for image A and to the default LUT for image A.
        • defaultLUTb
          ModelLUT defaultLUTb
          Reference to LUT for image B and to the default LUT for image B.
        • displayMode
          int displayMode
          Indicates which image is to be acted upon when two images are displayed.
        • enableCloseImageB
          boolean enableCloseImageB
          Tells whether the ViewMenuBuilder should allow Close Image(B) after loading image B.
        • green
          int green
          Green channel value of the paint color.
        • imageA
          ModelImage imageA
          Reference to the image A of this frame.
        • imageB
          ModelImage imageB
          Reference to the image B of this frame.
        • isClosing
          boolean isClosing
          Whether the frame's close() method is being called.
        • lastState
          int lastState
          Save if last state was iconified or normal.
        • linkedScrolling
          boolean linkedScrolling
          Variable indicating if images of like dimensions should be scrolled simult.
        • linkFrame
          ViewJFrameImage linkFrame
          Holds a reference (link) to another frame so that it be updated with this frame.
        • linkTriFrame
          ViewJFrameTriImage linkTriFrame
          Holds a reference (link) to another frame so that it can be updated with this frame.
        • LUTa
          ModelLUT LUTa
          Reference to LUT for image A and to the default LUT for image A.
        • LUTb
          ModelLUT LUTb
          Reference to LUT for image B and to the default LUT for image B.
        • newFrameCreated
          boolean newFrameCreated
        • opacity
          float opacity
          Opacity value of the paint color.
        • paintBitmap
          BitSet paintBitmap
          Reference to the BitSet map used in painting the image.
        • progressBar
          ViewJProgressBar progressBar
          Reference to progress bar.
        • red
          int red
          Red channel value of the paint color.
        • scannerLPS_APLabel
          JLabel scannerLPS_APLabel
          scanner lps goto components*
        • scannerLPS_APTextField
          JTextField scannerLPS_APTextField
        • scannerLPS_GoToButton
          JButton scannerLPS_GoToButton
        • scannerLPS_GoToPanel
          JPanel scannerLPS_GoToPanel
        • scannerLPS_ISLabel
          JLabel scannerLPS_ISLabel
          scanner lps goto components*
        • scannerLPS_ISTextField
          JTextField scannerLPS_ISTextField
        • scannerLPS_RLLabel
          JLabel scannerLPS_RLLabel
          scanner lps goto components*
        • scannerLPS_RLTextField
          JTextField scannerLPS_RLTextField
        • scannerLPSLabel
          JLabel scannerLPSLabel
          Labels for the current scanner position:.
        • scannerLPSLabelVals
          JLabel[] scannerLPSLabelVals
          Labels for the current scanner position values:.
        • scannerLPSPanel
          JPanel scannerLPSPanel
          JPanel containing the scanner position labels:.
        • scannerRAS_APLabel
          JLabel scannerRAS_APLabel
          scanner ras goto components*
        • scannerRAS_APTextField
          JTextField scannerRAS_APTextField
        • scannerRAS_GoToButton
          JButton scannerRAS_GoToButton
        • scannerRAS_GoToPanel
          JPanel scannerRAS_GoToPanel
        • scannerRAS_ISLabel
          JLabel scannerRAS_ISLabel
          scanner ras goto components*
        • scannerRAS_ISTextField
          JTextField scannerRAS_ISTextField
        • scannerRAS_RLLabel
          JLabel scannerRAS_RLLabel
          scanner ras goto components*
        • scannerRAS_RLTextField
          JTextField scannerRAS_RLTextField
        • scannerRASLabel
          JLabel scannerRASLabel
          Labels for the current scanner position:.
        • scannerRASLabelVals
          JLabel[] scannerRASLabelVals
          Labels for the current scanner position values:.
        • scannerRASPanel
          JPanel scannerRASPanel
          JPanel containing the scanner position labels:.
        • scannerTabbedPane
          JTabbedPane scannerTabbedPane
          The tabbed pane to hold teh LPS, RAS and absolution coordinate panels.
        • tabbedPane
          JTabbedPane tabbedPane
          The main tabbed pane in the volume view frame.
        • talGoToButton
          JButton talGoToButton
        • talGoToPanel
          JPanel talGoToPanel
        • talXLabel
          JLabel talXLabel
          talairach goto components*
        • talXTextField
          JTextField talXTextField
        • talYLabel
          JLabel talYLabel
          talairach goto components*
        • talYTextField
          JTextField talYTextField
        • talZLabel
          JLabel talZLabel
          talairach goto components*
        • talZTextField
          JTextField talZTextField
        • userInterface
          ViewUserInterface userInterface
          Reference to the user interface.
        • voiSavedFileName
          String voiSavedFileName
          DOCUMENT ME!
        • zoomMode
          int zoomMode
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameColocalizationEM

      class ViewJFrameColocalizationEM extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -7006573111870808134L

      • Serialized Fields

        • bottomPad
          int bottomPad
          DOCUMENT ME!
        • componentImage
          ViewJComponentColocalizationEM componentImage
          DOCUMENT ME!
        • componentY
          int componentY
          DOCUMENT ME!
        • controlFrame
          ViewJFrameBase controlFrame
          DOCUMENT ME!
        • controls
          ViewControlsImage controls
          DOCUMENT ME!
        • destImage
          ModelImage destImage
          The image containing the 2D histogram.
        • etchedBorder
          Border etchedBorder
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • gbcTP
          GridBagConstraints gbcTP
          DOCUMENT ME!
        • halfMajor
          double[] halfMajor
          DOCUMENT ME!
        • halfMinor
          double[] halfMinor
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • imageB
          ModelImage imageB
          DOCUMENT ME!
        • imageBufferDest
          float[] imageBufferDest
          DOCUMENT ME!
        • innerPanel
          JPanel innerPanel
          DOCUMENT ME!
        • leftPad
          int leftPad
          The spaces around the histogram bin area.
        • logDisplayButton
          JToggleButton logDisplayButton
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • LUTa
          ModelLUT LUTa
          DOCUMENT ME!
        • LUTdest
          ModelLUT LUTdest
          The LUT for the 2D histogram.
        • max1
          double max1
          Minimum and maximum buffer and secondBuffer areas.
        • max2
          double max2
          Minimum and maximum buffer and secondBuffer areas.
        • mean
          double[][] mean
          red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.
        • menuObj
          ViewMenuBuilder menuObj
          DOCUMENT ME!
        • min1
          double min1
          Minimum and maximum buffer and secondBuffer areas.
        • min2
          double min2
          Minimum and maximum buffer and secondBuffer areas.
        • minimumHeight
          int minimumHeight
          DOCUMENT ME!
        • minimumToolBarWidth
          int minimumToolBarWidth
          DOCUMENT ME!
        • openingMenuBar
          JMenuBar openingMenuBar
          DOCUMENT ME!
        • origBrightness
          int origBrightness
          DOCUMENT ME!
        • origContrast
          float origContrast
          red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.
        • paintBufferDest
          int[] paintBufferDest
          DOCUMENT ME!
        • pixBufferDest
          int[] pixBufferDest
          DOCUMENT ME!
        • pressedBorder
          Border pressedBorder
          DOCUMENT ME!
        • raisedBorder
          Border raisedBorder
          DOCUMENT ME!
        • RGBTA
          ModelRGB RGBTA
          DOCUMENT ME!
        • rightPad
          int rightPad
          DOCUMENT ME!
        • scale1
          double scale1
          bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).
        • scale2
          double scale2
          bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • scrollPaneSize
          int scrollPaneSize
          DOCUMENT ME!
        • structureY
          int structureY
          DOCUMENT ME!
        • theta
          double[] theta
          DOCUMENT ME!
        • toolBar
          JToolBar toolBar
          DOCUMENT ME!
        • topPad
          int topPad
          DOCUMENT ME!
        • topPanel
          JPanel topPanel
          and innerPanel placed in scrollPane.
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!
        • zoom
          float zoom
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameColocalizationRegression

      class ViewJFrameColocalizationRegression extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -2084669389930362925L

      • Serialized Fields

        • alg
          AlgorithmColocalizationRegression alg
          DOCUMENT ME!
        • bottomPad
          int bottomPad
          DOCUMENT ME!
        • colocIntensity1
          float[] colocIntensity1
          DOCUMENT ME!
        • colocIntensity2
          float[] colocIntensity2
          DOCUMENT ME!
        • colocSize
          float[] colocSize
          DOCUMENT ME!
        • componentImage
          ViewJComponentColocalizationRegression componentImage
          DOCUMENT ME!
        • componentY
          int componentY
          DOCUMENT ME!
        • controlFrame
          ViewJFrameBase controlFrame
          DOCUMENT ME!
        • controls
          ViewControlsImage controls
          DOCUMENT ME!
        • cpGBC
          GridBagConstraints cpGBC
          DOCUMENT ME!
        • cpGBL
          GridBagLayout cpGBL
          DOCUMENT ME!
        • dataLine1
          String dataLine1
          DOCUMENT ME!
        • dataLine2
          String dataLine2
          DOCUMENT ME!
        • destImage
          ModelImage destImage
          The image containing the 2D histogram.
        • doSecondIteration
          boolean doSecondIteration
          DOCUMENT ME!
        • etchedBorder
          Border etchedBorder
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • freeRangeButton
          JToggleButton freeRangeButton
          DOCUMENT ME!
        • freeRangeMode
          boolean freeRangeMode
          DOCUMENT ME!
        • gbcTP
          GridBagConstraints gbcTP
          DOCUMENT ME!
        • haveFreeRangeThreshold
          boolean[] haveFreeRangeThreshold
          true for pixels with calculated freeRangeRThreshold values.
        • haveThreshold
          boolean[] haveThreshold
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • imageB
          ModelImage imageB
          DOCUMENT ME!
        • imageBufferDest
          float[] imageBufferDest
          DOCUMENT ME!
        • innerPanel
          JPanel innerPanel
          DOCUMENT ME!
        • labelCurrent
          JLabel labelCurrent
          DOCUMENT ME!
        • labelCurrentColoc
          JLabel labelCurrentColoc
          private JLabel labelLineFunction;.
        • labelCurrentIntensity1
          JLabel labelCurrentIntensity1
          DOCUMENT ME!
        • labelCurrentIntensity2
          JLabel labelCurrentIntensity2
          DOCUMENT ME!
        • labelLinearCorrelation
          JLabel labelLinearCorrelation
          DOCUMENT ME!
        • labelPValue
          JLabel labelPValue
          DOCUMENT ME!
        • leftPad
          int leftPad
          The spaces around the histogram bin area.
        • linearCorrelation
          float linearCorrelation
          The linear correlation coefficient for all points with either buffer[i] >= threshold1 or secondBuffer[i] >= threshold2.
        • lineMax1
          double lineMax1
          The endpoints of the line segment in (buffer,secondBuffer) values.
        • lineMax2
          double lineMax2
          The endpoints of the line segment in (buffer,secondBuffer) values.
        • lineMin1
          double lineMin1
          The endpoints of the line segment in (buffer,secondBuffer) values.
        • lineMin2
          double lineMin2
          The endpoints of the line segment in (buffer,secondBuffer) values.
        • logDisplayButton
          JToggleButton logDisplayButton
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • LUTa
          ModelLUT LUTa
          DOCUMENT ME!
        • LUTdest
          ModelLUT LUTdest
          The LUT for the 2D histogram.
        • max1
          double max1
          Minimum and maximum buffer and secondBuffer areas.
        • max2
          double max2
          Minimum and maximum buffer and secondBuffer areas.
        • menuObj
          ViewMenuBuilder menuObj
          DOCUMENT ME!
        • min1
          double min1
          Minimum and maximum buffer and secondBuffer areas.
        • min2
          double min2
          Minimum and maximum buffer and secondBuffer areas.
        • minimumHeight
          int minimumHeight
          DOCUMENT ME!
        • minimumToolBarWidth
          int minimumToolBarWidth
          DOCUMENT ME!
        • nf
          NumberFormat nf
          DOCUMENT ME!
        • nVOI
          int nVOI
          DOCUMENT ME!
        • offset
          float offset
          DOCUMENT ME!
        • openingMenuBar
          JMenuBar openingMenuBar
          DOCUMENT ME!
        • origBrightness
          int origBrightness
          DOCUMENT ME!
        • origContrast
          float origContrast
          red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.
        • originalX
          int originalX
          DOCUMENT ME!
        • originalY
          int originalY
          DOCUMENT ME!
        • paintBufferDest
          int[] paintBufferDest
          DOCUMENT ME!
        • pixBufferDest
          int[] pixBufferDest
          DOCUMENT ME!
        • pointCalculation
          boolean pointCalculation
          DOCUMENT ME!
        • pointVOI
          VOI pointVOI
          DOCUMENT ME!
        • pressedBorder
          Border pressedBorder
          DOCUMENT ME!
        • PValue
          float PValue
          statistic giving the portion of images generated with randomly scrambled blocks of pixels having a linear correlation coefficient less than that of the actual image.
        • raisedBorder
          Border raisedBorder
          DOCUMENT ME!
        • regionLinesDisplay
          boolean regionLinesDisplay
          DOCUMENT ME!
        • regionLinesDisplayButton
          JToggleButton regionLinesDisplayButton
          DOCUMENT ME!
        • RGBTA
          ModelRGB RGBTA
          set to give 6 digits to the right of the decimal.
        • rightPad
          int rightPad
          DOCUMENT ME!
        • rThreshold
          float[] rThreshold
          The linear correlation coefficients for all pixels with values either below color1 for buffer or below a*color1 + b for secondBuffer.
        • scale1
          double scale1
          bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).
        • scale2
          double scale2
          bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • scrollPaneSize
          int scrollPaneSize
          DOCUMENT ME!
        • slope
          float slope
          The slope and offset of the total least squares line.
        • statusPanel
          JPanel statusPanel
          DOCUMENT ME!
        • structureY
          int structureY
          DOCUMENT ME!
        • thresholdOn1
          boolean thresholdOn1
          If true, the matrix of linear correlation coefficients is taken along color 1 at unity spacings. If false, along color 2.
        • toolBar
          JToolBar toolBar
          DOCUMENT ME!
        • topPad
          int topPad
          DOCUMENT ME!
        • topPanel
          JPanel topPanel
          and innerPanel placed in scrollPane.
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!
        • zoom
          float zoom
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameCreatePaint

      class ViewJFrameCreatePaint extends JFrame implements Serializable

      • Serialized Fields

        • blackImage
          ImageIcon blackImage
          used to create the "selected" state of the buttons
        • buttonGrid
          JToggleButton[][] buttonGrid
          Array of toggle buttons used to create the grid
        • buttonSize
          Dimension buttonSize
          Make sure the button size is always this dimension
        • gridDialog
          ViewJFrameCreatePaint.JDialogGridSize gridDialog
          The grid resize dialog
        • gridHeight
          int gridHeight
          grid's height
        • gridPanel
          JPanel gridPanel
          Panel that holds the grid (stored as private variable so as to remove/rebuild the grid as needed
        • gridWidth
          int gridWidth
          grid's width
        • loadName
          String loadName
          the name of the loaded brush (used with the above wasLoaded parameter)
        • openItem
          JMenu openItem
          Menu item that holds the list of paintbrushes to open (for editing)
        • wasLoaded
          boolean wasLoaded
          switch that tells the save-dialog that this brush was opened from disk, so brush will be re-written on save
        • whiteImage
          ImageIcon whiteImage
          used to create the "unselected" state of the buttons

    • Class gov.nih.mipav.view.ViewJFrameDICOMParser

      class ViewJFrameDICOMParser extends ViewImageDirectory implements Serializable
      serialVersionUID:
      1085995416072088026L

      • Serialized Fields

        • brightness
          int brightness
          DOCUMENT ME!
        • brightnessContrastPanel
          JPanel brightnessContrastPanel
          DOCUMENT ME!
        • brightnessSlider
          JSlider brightnessSlider
          DOCUMENT ME!
        • columnKeyTable
          Hashtable columnKeyTable
          DOCUMENT ME!
        • componentImageDicom
          ViewJComponentPreviewImage componentImageDicom
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • contrastSlider
          JSlider contrastSlider
          DOCUMENT ME!
        • current
          JLabel current
          DOCUMENT ME!
        • current2
          JLabel current2
          DOCUMENT ME!
        • fileInfoVector
          Vector<FileInfoDicom> fileInfoVector
          fileInfoVector represents images in image table but imageTableVector was needed also becasue this handles multiple series in the same dir. fileInfoVector is all the images in the dir but imageTableVector represents all the images that are in the image table at a particular instance or series
        • imageTable
          JTable imageTable
          DOCUMENT ME!
        • imageTableModel
          SortingTableModel imageTableModel
          DOCUMENT ME!
        • imageTableSorter
          TableSorter imageTableSorter
          DOCUMENT ME!
        • imageTableVector
          Vector<FileInfoDicom> imageTableVector
        • nfc
          NumberFormat nfc
          DOCUMENT ME!
        • origBrightness
          int origBrightness
          DOCUMENT ME!
        • origContrast
          float origContrast
          DOCUMENT ME!
        • rightPane
          JSplitPane rightPane
          DOCUMENT ME!
        • seriesNumberCounters
          HashMap<String,Integer> seriesNumberCounters
          This is a hashmasp of series numbers and corresponding counter for the number of images in each series.*
        • seriesOptionBox
          JCheckBoxMenuItem seriesOptionBox
          DOCUMENT ME!
        • seriesTable
          JTable seriesTable
          DOCUMENT ME!
        • seriesTableModel
          SortingTableModel seriesTableModel
          DOCUMENT ME!
        • seriesTableSorter
          TableSorter seriesTableSorter
          DOCUMENT ME!
        • studyTable
          JTable studyTable
          DOCUMENT ME!
        • studyTableModel
          SortingTableModel studyTableModel
          DOCUMENT ME!
        • studyTableSorter
          TableSorter studyTableSorter
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameDICOMQuery

      class ViewJFrameDICOMQuery extends JFrame implements Serializable
      serialVersionUID:
      3899062842723888728L

      • Serialized Fields

        • aboutPanel
          JPanel aboutPanel
        • activateStore
          JButton activateStore
          Buttons used for the host tab
        • browseButton
          JButton browseButton
          DOCUMENT ME!
        • cancel
          JButton cancel
          Buttons used for the host tab
        • cancelQ
          JButton cancelQ
          DOCUMENT ME!
        • create
          JButton create
          DOCUMENT ME!
        • createStore
          JButton createStore
          Buttons used for the host tab
        • currentDateL
          JLabel currentDateL
          DOCUMENT ME!
        • delete
          JButton delete
          DOCUMENT ME!
        • deleteStore
          JButton deleteStore
          Buttons used for the host tab
        • dicomQuery
          DICOM_Query dicomQuery
          DOCUMENT ME!
        • down
          JButton down
          DOCUMENT ME!
        • edit
          JButton edit
          DOCUMENT ME!
        • editStore
          JButton editStore
          Buttons used for the host tab
        • endCalendar
          Calendar endCalendar
          DOCUMENT ME!
        • endDayBox
          JComboBox endDayBox
          DOCUMENT ME!
        • endMonthBox
          JComboBox endMonthBox
          DOCUMENT ME!
        • endYearBox
          JComboBox endYearBox
          DOCUMENT ME!
        • help1
          JButton help1
          Buttons used for the host tab
        • help2
          JButton help2
          Buttons used for the host tab
        • help3
          JButton help3
          Buttons used for the host tab
        • help4
          JButton help4
          Buttons used for the host tab
        • listPanel
          JPanel listPanel
          DOCUMENT ME!
        • messageTable
          DICOMDisplayer messageTable
          DOCUMENT ME!
        • move
          JButton move
          DOCUMENT ME!
        • moveRequestHash
          Hashtable<String,ViewJFrameDICOMQuery.MoveRequestInfo> moveRequestHash
          DOCUMENT ME!
        • physText
          JTextField physText
          DOCUMENT ME!
        • ptIDText
          JTextField ptIDText
          DOCUMENT ME!
        • ptNameText
          JTextField ptNameText
          DOCUMENT ME!
        • queryLev
          JLabel queryLev
          DOCUMENT ME!
        • queryLevel
          int queryLevel
          DOCUMENT ME!
        • queryMsgID
          int queryMsgID
          DOCUMENT ME!
        • queryPDU
          DICOM_PDUService queryPDU
          DOCUMENT ME!
        • queryResultTable
          JTable queryResultTable
          DOCUMENT ME!
        • queryTableModel
          ViewTableModel queryTableModel
          DOCUMENT ME!
        • refreshButton
          JButton refreshButton
          DOCUMENT ME!
        • rootQueryPanel
          JPanel rootQueryPanel
          DOCUMENT ME!
        • send
          JButton send
          DOCUMENT ME!
        • sendButton
          JButton sendButton
          DOCUMENT ME!
        • sendDestCBox
          JComboBox sendDestCBox
          DOCUMENT ME!
        • sendModel
          ViewTableModel sendModel
          DOCUMENT ME!
        • sendPanel
          JPanel sendPanel
        • sendQueryThread
          Thread sendQueryThread
          DOCUMENT ME!
        • sendStatusClearButton
          JButton sendStatusClearButton
          DOCUMENT ME!
        • sendStatusTArea
          JTextArea sendStatusTArea
          DOCUMENT ME!
        • sendTable
          JTable sendTable
          DOCUMENT ME!
        • seriesInstanceUID
          String seriesInstanceUID
          DOCUMENT ME!
        • serverModel
          ViewTableModel serverModel
          DOCUMENT ME!
        • serverTable
          JTable serverTable
          DOCUMENT ME!
        • set
          JButton set
          Buttons used for the host tab
        • setStore
          JButton setStore
          Buttons used for the host tab
        • SOPInstanceUID
          String SOPInstanceUID
          DOCUMENT ME!
        • sourceTextF
          JTextField sourceTextF
          DOCUMENT ME!
        • startCalendar
          Calendar startCalendar
          DOCUMENT ME!
        • startDayBox
          JComboBox startDayBox
          DOCUMENT ME!
        • startMonthBox
          JComboBox startMonthBox
          DOCUMENT ME!
        • startYearBox
          JComboBox startYearBox
          DOCUMENT ME!
        • storageModel
          ViewTableModel storageModel
          DOCUMENT ME!
        • storageTable
          JTable storageTable
          DOCUMENT ME!
        • studyInstanceUID
          String studyInstanceUID
          DOCUMENT ME!
        • studyNOText
          JTextField studyNOText
          DOCUMENT ME!
        • subQueryPanel
          JPanel subQueryPanel
          DOCUMENT ME!
        • tabbedPane
          JTabbedPane tabbedPane
          DOCUMENT ME!
        • testButton
          JButton testButton
          DOCUMENT ME!
        • textArea
          JTextArea textArea
          DOCUMENT ME!
        • todayCalendar
          Calendar todayCalendar
          DOCUMENT ME!
        • uids
          DICOM_UID[] uids
          DOCUMENT ME!
        • up
          JButton up
          DOCUMENT ME!
        • upDirButton
          JButton upDirButton
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameFastMarching2

      class ViewJFrameFastMarching2 extends ViewJFrameImage implements Serializable
      serialVersionUID:
      -949160895087175876L

      • Serialized Fields

        • m_bIterate
          boolean m_bIterate
          DOCUMENT ME!
        • m_bNext
          boolean m_bNext
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameFastMarching3

      class ViewJFrameFastMarching3 extends ViewJFrameImage implements Serializable
      serialVersionUID:
      7827645314485923857L

      • Serialized Fields

        • m_bIterate
          boolean m_bIterate
          DOCUMENT ME!
        • m_bNext
          boolean m_bNext
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameGraph

      class ViewJFrameGraph extends JFrame implements Serializable
      serialVersionUID:
      5127841803361813975L

      • Serialized Fields

        • autoShrinkDomain
          boolean autoShrinkDomain
        • autoShrinkDomainCheckbox
          JCheckBox autoShrinkDomainCheckbox
        • autoShrinkRange
          boolean autoShrinkRange
          DOCUMENT ME!
        • autoShrinkRangeCheckbox
          JCheckBox autoShrinkRangeCheckbox
          DOCUMENT ME!
        • axisPanel
          JPanel axisPanel
          DOCUMENT ME!
        • backgroundButton
          JButton backgroundButton
          DOCUMENT ME!
        • backgroundLabel
          JLabel backgroundLabel
          DOCUMENT ME!
        • backgroundPanel
          JPanel backgroundPanel
          DOCUMENT ME!
        • binsField
          JTextField binsField
        • colorChooser
          ViewJColorChooser colorChooser
          DOCUMENT ME!
        • colorDialog
          JDialog colorDialog
          DOCUMENT ME!
        • copyMenu
          JMenu copyMenu
          DOCUMENT ME!
        • defaultDirectory
          String defaultDirectory
          DOCUMENT ME!
        • deleteMenu
          JMenu deleteMenu
          DOCUMENT ME!
        • doLogX
          boolean doLogX
        • doLogY
          boolean doLogY
        • domainPanel
          JPanel domainPanel
        • editMenu
          JMenu editMenu
          DOCUMENT ME!
        • entireImage
          boolean entireImage
        • fileMenu
          JMenu fileMenu
          DOCUMENT ME!
        • fitFunctPanel
          JPanel fitFunctPanel
          DOCUMENT ME!
        • fitFunctTypePanel
          JPanel fitFunctTypePanel
          DOCUMENT ME!
        • fitFunctVisibleCheckbox
          JCheckBox[] fitFunctVisibleCheckbox
          DOCUMENT ME!
        • fitFunctVisiblePanel
          JPanel fitFunctVisiblePanel
          DOCUMENT ME!
        • fitMode
          ViewJFrameGraph.FitMode fitMode
          Current mode for fitting functions
        • fitType
          JComboBox fitType
          Combo box for selecting the fitting function type
        • frameGraphVOI
          VOI frameGraphVOI
          DOCUMENT ME!
        • functionIndex
          int functionIndex
          DOCUMENT ME!
        • functionLabel
          JLabel[] functionLabel
          DOCUMENT ME!
        • functionPropPanel
          JPanel functionPropPanel
          DOCUMENT ME!
        • functLineColorButton
          JButton[] functLineColorButton
          DOCUMENT ME!
        • functVisibleCheckbox
          JCheckBox[] functVisibleCheckbox
          the slope changes.
        • graph
          ViewJComponentGraph graph
          DOCUMENT ME!
        • gridlinesCheckbox
          JCheckBox gridlinesCheckbox
          DOCUMENT ME!
        • gridPanel
          JPanel gridPanel
          DOCUMENT ME!
        • histogramPanel
          JPanel histogramPanel
        • image
          ModelImage image
        • imageMax
          double imageMax
        • imageMin
          double imageMin
        • initialSummaryBins
          int initialSummaryBins
        • initialUserMax
          double initialUserMax
        • initialUserMin
          double initialUserMin
        • itemClose
          JMenuItem itemClose
          DOCUMENT ME!
        • itemModifyGraph
          JMenuItem itemModifyGraph
          DOCUMENT ME!
        • itemNormalize
          JMenuItem itemNormalize
          DOCUMENT ME!
        • itemOpenNewGraph
          JMenuItem itemOpenNewGraph
        • itemOpenSameGraph
          JMenuItem itemOpenSameGraph
          DOCUMENT ME!
        • itemPasteFunct
          JMenuItem itemPasteFunct
          DOCUMENT ME!
        • itemPrintGraph
          JMenuItem itemPrintGraph
          DOCUMENT ME!
        • itemResetDomain
          JMenuItem itemResetDomain
        • itemResetGraph
          JMenuItem itemResetGraph
          DOCUMENT ME!
        • itemResetRange
          JMenuItem itemResetRange
          DOCUMENT ME!
        • itemSaveGraph
          JMenuItem itemSaveGraph
          DOCUMENT ME!
        • itemTableOutput
          JMenuItem itemTableOutput
        • lastUnits
          String lastUnits
          DOCUMENT ME!
        • legendCheckbox
          JCheckBox legendCheckbox
          DOCUMENT ME!
        • legendPanel
          JPanel legendPanel
          DOCUMENT ME!
        • linesOnlyButton
          JRadioButton linesOnlyButton
          DOCUMENT ME!
        • logScaleCheckboxX
          JCheckBox logScaleCheckboxX
        • logScaleCheckboxY
          JCheckBox logScaleCheckboxY
        • mainPanel
          JPanel mainPanel
          DOCUMENT ME!
        • maxBins
          int maxBins
        • maxDomainField
          JTextField maxDomainField
        • maxDomainLabel
          JLabel maxDomainLabel
        • maxField
          JTextField maxField
        • maxRangeField
          JTextField maxRangeField
          DOCUMENT ME!
        • maxRangeLabel
          JLabel maxRangeLabel
          DOCUMENT ME!
        • minDomainField
          JTextField minDomainField
        • minDomainLabel
          JLabel minDomainLabel
        • minField
          JTextField minField
        • minorTickMarksCheckbox
          JCheckBox minorTickMarksCheckbox
          DOCUMENT ME!
        • minRangeField
          JTextField minRangeField
          DOCUMENT ME!
        • minRangeLabel
          JLabel minRangeLabel
          DOCUMENT ME!
        • modifyDialog
          JDialog modifyDialog
          DOCUMENT ME!
        • modifyGraphPanel
          JPanel modifyGraphPanel
          DOCUMENT ME!
        • nameField
          JTextField[] nameField
          DOCUMENT ME!
        • numVariables
          int numVariables
        • numVariablesField
          JTextField numVariablesField
        • numVariablesLabel
          JLabel numVariablesLabel
        • openingMenuBar
          JMenuBar openingMenuBar
          DOCUMENT ME!
        • pointsAndLinesButton
          JRadioButton pointsAndLinesButton
        • pointsAndLinesGroup
          ButtonGroup pointsAndLinesGroup
        • pointsOnlyButton
          JRadioButton pointsOnlyButton
        • pointsVisiblePanel
          JPanel pointsVisiblePanel
          DOCUMENT ME!
        • rangePanel
          JPanel rangePanel
          DOCUMENT ME!
        • resetDomainButton
          JButton resetDomainButton
        • resetRangeButton
          JButton resetRangeButton
          DOCUMENT ME!
        • RGBOffset
          int RGBOffset
        • showPanel
          JPanel showPanel
          DOCUMENT ME!
        • summaryBins
          int summaryBins
        • tabbedPane
          JTabbedPane tabbedPane
          DOCUMENT ME!
        • titleField
          JTextField titleField
          DOCUMENT ME!
        • titleLabel
          JLabel titleLabel
          DOCUMENT ME!
        • units
          String units
          DOCUMENT ME!
        • updateRGBIndex
          int updateRGBIndex
          DOCUMENT ME!
        • userMax
          double userMax
        • userMin
          double userMin
        • vectorCopyFunct
          Vector<JMenuItem> vectorCopyFunct
          DOCUMENT ME!
        • vectorDeleteFunct
          Vector<JMenuItem> vectorDeleteFunct
          DOCUMENT ME!
        • viewMenu
          JMenu viewMenu
          DOCUMENT ME!
        • voi
          VOI voi
          DOCUMENT ME!
        • xAxisLabel
          JLabel xAxisLabel
          DOCUMENT ME!
        • xAxisLabelField
          JTextField xAxisLabelField
          DOCUMENT ME!
        • xGridButtonGroup
          ButtonGroup xGridButtonGroup
        • xGridCheckBoxList
          JCheckBox[] xGridCheckBoxList
        • xGridCheckBoxPanel
          JPanel xGridCheckBoxPanel
        • xGridEvenSpacedButton
          JRadioButton xGridEvenSpacedButton
        • xGridLineField
          JTextField xGridLineField
          DOCUMENT ME!
        • xGridLineLabel
          JLabel xGridLineLabel
          DOCUMENT ME!
        • xGridScrollPane
          JScrollPane xGridScrollPane
        • xGridUserSpacedButton
          JRadioButton xGridUserSpacedButton
        • xyCoords
          int[][] xyCoords
          this is a list of the x,y coords of the voi's boundary
        • yAxisLabel
          JLabel yAxisLabel
          DOCUMENT ME!
        • yAxisLabelField
          JTextField yAxisLabelField
          DOCUMENT ME!
        • yGridButtonGroup
          ButtonGroup yGridButtonGroup
        • yGridCheckBoxList
          JCheckBox[] yGridCheckBoxList
        • yGridCheckBoxPanel
          JPanel yGridCheckBoxPanel
        • yGridEvenSpacedButton
          JRadioButton yGridEvenSpacedButton
        • yGridLineField
          JTextField yGridLineField
          DOCUMENT ME!
        • yGridLineLabel
          JLabel yGridLineLabel
          DOCUMENT ME!
        • yGridScrollPane
          JScrollPane yGridScrollPane
        • yGridUserSpacedButton
          JRadioButton yGridUserSpacedButton

    • Class gov.nih.mipav.view.ViewJFrameHistoLUT

      class ViewJFrameHistoLUT extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -5323312688163424096L

    • Class gov.nih.mipav.view.ViewJFrameHistoRGB

      class ViewJFrameHistoRGB extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -4685406207107911894L

      • Serialized Fields

        • allRGBButton
          JToggleButton allRGBButton
          Deprecated.
          DOCUMENT ME!
        • blueCheckBoxA
          JCheckBox blueCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • blueCheckBoxB
          JCheckBox blueCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • blueRGBButton
          JToggleButton blueRGBButton
          Deprecated.
          DOCUMENT ME!
        • calcThresholdVolume
          boolean calcThresholdVolume
          Deprecated.
          DOCUMENT ME!
        • entireFlag
          boolean entireFlag
          Deprecated.
          DOCUMENT ME!
        • fillValuesA
          float[] fillValuesA
          Deprecated.
          DOCUMENT ME!
        • fillValuesB
          float[] fillValuesB
          Deprecated.
          DOCUMENT ME!
        • greenCheckBoxA
          JCheckBox greenCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • greenCheckBoxB
          JCheckBox greenCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • greenRGBButton
          JToggleButton greenRGBButton
          Deprecated.
          DOCUMENT ME!
        • histogramABlue
          ModelHistogram histogramABlue
          Deprecated.
          DOCUMENT ME!
        • histogramAGreen
          ModelHistogram histogramAGreen
          Deprecated.
          DOCUMENT ME!
        • histogramARed
          ModelHistogram histogramARed
          Deprecated.
          DOCUMENT ME!
        • histogramBBlue
          ModelHistogram histogramBBlue
          Deprecated.
          DOCUMENT ME!
        • histogramBGreen
          ModelHistogram histogramBGreen
          Deprecated.
          DOCUMENT ME!
        • histogramBRed
          ModelHistogram histogramBRed
          Deprecated.
          DOCUMENT ME!
        • histoPanelA
          ViewJPanelHistoLUT histoPanelA
          Deprecated.
          DOCUMENT ME!
        • histoPanelB
          ViewJPanelHistoLUT histoPanelB
          Deprecated.
          DOCUMENT ME!
        • logCheckBoxA
          JCheckBox logCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • logCheckBoxB
          JCheckBox logCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • lutAdjustCheckboxB
          JCheckBox lutAdjustCheckboxB
          Deprecated.
          DOCUMENT ME
        • menuObj
          ViewMenuBuilder menuObj
          Deprecated.
          DOCUMENT ME!
        • panelA
          JPanel panelA
          Deprecated.
          DOCUMENT ME!
        • panelB
          JPanel panelB
          Deprecated.
          DOCUMENT ME!
        • redCheckBoxA
          JCheckBox redCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • redCheckBoxB
          JCheckBox redCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • redRGBButton
          JToggleButton redRGBButton
          Deprecated.
          DOCUMENT ME!
        • regComponent
          ViewJComponentRegistration regComponent
          Deprecated.
          DOCUMENT ME!
        • RGBExtents
          int[] RGBExtents
          Deprecated.
          DOCUMENT ME!
        • RGBTA
          ModelRGB RGBTA
          Deprecated.
          DOCUMENT ME!
        • RGBTB
          ModelRGB RGBTB
          Deprecated.
          DOCUMENT ME!
        • tabbedPane
          JTabbedPane tabbedPane
          Deprecated.
          DOCUMENT ME!
        • threshFillBF
          JTextField threshFillBF
          Deprecated.
          DOCUMENT ME!
        • threshFillF
          JTextField threshFillF
          Deprecated.
          threshold related.
        • threshLowerBF
          JTextField threshLowerBF
          Deprecated.
          DOCUMENT ME!
        • threshLowerF
          JTextField threshLowerF
          Deprecated.
          threshold related.
        • threshUpperBF
          JTextField threshUpperBF
          Deprecated.
          DOCUMENT ME!
        • threshUpperF
          JTextField threshUpperF
          Deprecated.
          threshold related.
        • toolBar
          JToolBar toolBar
          Deprecated.
          DOCUMENT ME!
        • toolBarObj
          ViewToolBarBuilder toolBarObj
          Deprecated.
          Object which generates the toolbar.
        • updateCheckBoxA
          JCheckBox updateCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • updateCheckBoxB
          JCheckBox updateCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • useThresholdChannelA
          boolean[] useThresholdChannelA
          Deprecated.
          DOCUMENT ME!
        • useThresholdChannelB
          boolean[] useThresholdChannelB
          Deprecated.
          DOCUMENT ME!
        • voxelVolumeLabel
          JLabel voxelVolumeLabel
          Deprecated.
          DOCUMENT ME!
        • voxelVolumeLabelB
          JLabel voxelVolumeLabelB
          Deprecated.
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameImage

      class ViewJFrameImage extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -5990635548319625443L

      • Serialized Fields

        • colorChooser
          ViewJColorChooser colorChooser
          Reference to the color chooser.
        • componentImage
          ViewJComponentEditImage componentImage
          Object where DICOM image, ... is converted and displayed as a Java image
        • controls
          ViewControlsImage controls
          Reference to the toolbars located in the controls object.
        • doOrients
          boolean doOrients
          DOCUMENT ME!
        • doOrigins
          boolean doOrigins
          When loading an image into B slot, should origins and orients be matched?
        • dpDialog
          JDialogDataProvenance dpDialog
          Data provenance dialog
        • gridOptions
          JDialogGridOptions gridOptions
          Only want one gridoptions dialog per jframeimage.
        • heightResFactor
          float heightResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • imageBufferA
          float[] imageBufferA
          Buffer used to store image intensities the presently viewed slice of image A.
        • imageBufferB
          float[] imageBufferB
          Buffer used to store image intensities the presently viewed slice of image B.
        • infoDialogA
          JDialogImageInfo infoDialogA
          reference to the JDialogImageInfo for updating slice/resolutions.
        • infoDialogB
          JDialogImageInfo infoDialogB
          DOCUMENT ME!
        • isShiftDown
          boolean isShiftDown
          boolean indicating if shift button is down.
        • logMagDisplay
          boolean logMagDisplay
          Flag indicating whether or not that the image should be displayed in Log scale. Used primarily for displaying the FFT of an image.
        • menuBar
          JMenuBar menuBar
          Reference to the frame's menu bar.
        • menuBarMaker
          ViewMenuBar menuBarMaker
          Constructs the image menu bar.
        • menuBuilder
          ViewMenuBuilder menuBuilder
          This object contains a number of useful functions for building a menu and querying the state of menu items.
        • multipaintDialog
          JDialogMultiPaint multipaintDialog
          reference to the JDialogMultiPaint for shortcuts
        • nImage
          int nImage
          Number of slices in a 3D dataset.
        • nTImage
          int nTImage
          Number of time sequences in a 4D dataset.
        • paintBrushLocked
          boolean paintBrushLocked
          used in conjuction with the above variable, stating that the paint brush has been changed but will change back to previous.
        • pixBuffer
          int[] pixBuffer
          Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageA intensities as a index into a LUT.
        • pixBufferB
          int[] pixBufferB
          Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageB intensities as a index into a LUT.
        • prostateAAMClassification
          JDialogAAMClassification prostateAAMClassification
        • prostateML
          JDialogAAMplusSVM prostateML
        • quickPaintBrushIndex
          int quickPaintBrushIndex
          DOCUMENT ME!
        • resols
          float[] resols
          Storage of the image voxel resolutions. One resolution value per dimension.
        • scrollPane
          JScrollPane scrollPane
          The scrollPane where the image is displayed.
        • units
          int[] units
          Storage of the resolution units of measure. For example, mm, cm, inches ...
        • VOIGroup
          ButtonGroup VOIGroup
        • voiManager
          VOIManagerInterface voiManager
        • voiMenu
          JMenu voiMenu
        • widthResFactor
          float widthResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • windowLevel
          JDialogWinLevel[] windowLevel
          Reference to the two window and level dialogs where [0] is for imageA, [1] for imageB.
        • zoom
          float zoom
          Defaults magnification of image to 1.
        • zoomDialog
          JDialogZoom zoomDialog
          Reference to the magnification tool.

    • Class gov.nih.mipav.view.ViewJFrameLightBox

      class ViewJFrameLightBox extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -4014825600247045462L

      • Serialized Fields

        • activeSliceButton
          JButton activeSliceButton
          DOCUMENT ME!
        • borderColor
          Color borderColor
          Color for the line border surrounding each image in the light-box.
        • borderSize
          int borderSize
          Spacing for the line border surrounding each image in the light-box.
        • componentImage
          ViewJComponentEditImage[] componentImage
          DOCUMENT ME!
        • controls
          ViewControlsImage controls
          DOCUMENT ME!
        • currentPage
          int currentPage
          Page information.
        • currentSelectedSlice
          int currentSelectedSlice
          DOCUMENT ME!
        • currentSlice
          int currentSlice
          Current info -- this slice info refers to the *real* slice number, not the page index for a slice on a page.
        • currentTSlice
          int currentTSlice
          DOCUMENT ME!
        • deleteButton
          JButton deleteButton
          DOCUMENT ME!
        • deleteSelection
          JMenuItem deleteSelection
          DOCUMENT ME!
        • extractButton
          JButton extractButton
          DOCUMENT ME!
        • extractSelection
          JMenuItem extractSelection
          DOCUMENT ME!
        • firstPageButton
          JButton firstPageButton
          DOCUMENT ME!
        • firstPageMenuItem
          JMenuItem firstPageMenuItem
          DOCUMENT ME!
        • frameHeight
          int frameHeight
          DOCUMENT ME!
        • frameWidth
          int frameWidth
          Frame information.
        • goToSliceText
          JTextField goToSliceText
          DOCUMENT ME!
        • gridColor
          Color gridColor
          Color for the region in-between the images in the light-box.
        • gridColumn
          int gridColumn
          DOCUMENT ME!
        • gridRow
          int gridRow
          Value for the number of rows (number of images along the y-axis) and columns (number of images along the x-axis) in the light-box.

          Note that both row and column set to 1 cannot make sense, but that one or the other will be the 'dependent variable' as defined by the row_dependent boolean var.

          A value of 0 means that the dependent variable will automatically be sized to its maximum size that can fit nicely on the screen.

        • gridSpacing
          int gridSpacing
          Spacing between images in the light-box.
        • group
          ButtonGroup group
          DOCUMENT ME!
        • imageBorder
          CompoundBorder[] imageBorder
          DOCUMENT ME!
        • imageBufferA
          float[] imageBufferA
          DOCUMENT ME!
        • imageBufferB
          float[] imageBufferB
          DOCUMENT ME!
        • imageFrame
          ViewJFrameImage imageFrame
          DOCUMENT ME!
        • imageHeight
          int imageHeight
          DOCUMENT ME!
        • imagePanel
          JPanel[] imagePanel
          DOCUMENT ME!
        • imagePanelSizeX
          int imagePanelSizeX
          Per num visible images information.
        • imagePanelSizeY
          int imagePanelSizeY
          Per num visible images information.
        • imageWidth
          int imageWidth
          DOCUMENT ME!
        • increment
          int increment
        • interpolateShapesButton
          JButton interpolateShapesButton
          DOCUMENT ME!
        • lastPageButton
          JButton lastPageButton
          DOCUMENT ME!
        • lastPageMenuItem
          JMenuItem lastPageMenuItem
          DOCUMENT ME!
        • lastSelectedSlice
          int lastSelectedSlice
          DOCUMENT ME!
        • lightBoxOptions
          JDialogLightBox lightBoxOptions
          DOCUMENT ME!
        • LUTa
          ModelLUT LUTa
          DOCUMENT ME!
        • LUTb
          ModelLUT LUTb
          DOCUMENT ME!
        • magMax
          float magMax
          DOCUMENT ME!
        • magMin
          float magMin
          DOCUMENT ME!
        • magnification
          float magnification
          Magnification of images in the light-box (mag is a percentage).
        • maxPagePanelSizeX
          int maxPagePanelSizeX
          DOCUMENT ME!
        • maxPagePanelSizeY
          int maxPagePanelSizeY
          DOCUMENT ME!
        • menuBar
          JMenuBar menuBar
          Variables for the menubar.
        • nextPageButton
          JButton nextPageButton
          elements of paging toolbar.
        • nextPageMenuItem
          JMenuItem nextPageMenuItem
          DOCUMENT ME!
        • numPages
          int numPages
          DOCUMENT ME!
        • numTotalSlices
          int numTotalSlices
          DOCUMENT ME!
        • numTSlices
          int numTSlices
          DOCUMENT ME!
        • numVisibleSlices
          int numVisibleSlices
          DOCUMENT ME!
        • pagePanel
          JPanel pagePanel
          DOCUMENT ME!
        • pagePanelSizeX
          int pagePanelSizeX
          DOCUMENT ME!
        • pagePanelSizeY
          int pagePanelSizeY
          DOCUMENT ME!
        • pagingTBar
          JToolBar pagingTBar
          DOCUMENT ME!
        • pixBuffer
          int[] pixBuffer
          DOCUMENT ME!
        • pixBufferB
          int[] pixBufferB
          DOCUMENT ME!
        • prevPageButton
          JButton prevPageButton
          DOCUMENT ME!
        • prevPageMenuItem
          JMenuItem prevPageMenuItem
          DOCUMENT ME!
        • repaintButton
          JButton repaintButton
          DOCUMENT ME!
        • resolutionX
          float resolutionX
          DOCUMENT ME!
        • resolutionY
          float resolutionY
          DOCUMENT ME!
        • row_dependent
          boolean row_dependent
          Indicates which--row or column--should be dependent on the other.

          the default is the number of rows is the dependent variable, and is dependent apon the total number of images and the number of columns. Don't confuse the reading to be "This display is (t/f) dependent on the row." It -could- be read as "The display is a column-independent (t/f) matrix".

        • selectedBorderColor
          Color selectedBorderColor
          Color for the line border surrounding each selected image in the light-box.
        • selectedBorderSize
          int selectedBorderSize
          Spacing for the selected line border surrounding each image in the light-box.
        • selectedImages
          Vector<String> selectedImages
          The selectedImages contains the *real* slice numbers -- not the index of a slice on a page. So the maximum number in the vector will be numTotalSlices - 1.
        • selectedTimeSlices
          Vector<String> selectedTimeSlices
          The selected Time Slices vector contains the real slice number and time slice number in the format (slice #).(time slice #) the maximum number in the vector will be numTotalSlices * t.
        • selectIndividualTSlices
          JCheckBoxMenuItem selectIndividualTSlices
          DOCUMENT ME!
        • singleTSlice
          boolean singleTSlice
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          DOCUMENT ME!
        • tBar
          JToolBar tBar
          DOCUMENT ME!
        • toolbarPanel
          JPanel toolbarPanel
          Variables for the toolbar.
        • unselectedBorderColor
          Color unselectedBorderColor
          DOCUMENT ME!
        • updatePaint
          JCheckBoxMenuItem updatePaint
          DOCUMENT ME!
        • voiManager
          VOIManagerInterface voiManager
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameMemory

      class ViewJFrameMemory extends JFrame implements Serializable
      serialVersionUID:
      -8863264033308071151L

    • Class gov.nih.mipav.view.ViewJFrameMessage

      class ViewJFrameMessage extends JFrame implements Serializable
      serialVersionUID:
      -1198653323631787447L

      • Serialized Fields

        • delTabButton
          JButton delTabButton
          DOCUMENT ME!
        • frameInsets
          Insets frameInsets
          DOCUMENT ME!
        • lastState
          int lastState
          Indicates last state of frame - NORMAL or ICONIFIED.
        • menu
          JMenuBar menu
          DOCUMENT ME!
        • removeCurrentTab
          JMenuItem removeCurrentTab
          DOCUMENT ME!
        • tabbedPane
          JTabbedPane tabbedPane
          DOCUMENT ME!
        • tBar
          JToolBar tBar
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameMessage.ScrollTextArea

      class ScrollTextArea extends JScrollPane implements Serializable
      serialVersionUID:
      3869765356771292936L

    • Class gov.nih.mipav.view.ViewJFrameMessageGraph

      class ViewJFrameMessageGraph extends JFrame implements Serializable
      serialVersionUID:
      -3229727417859189823L

      • Serialized Fields

        • debugArea
          JTextArea debugArea
          DOCUMENT ME!
        • debugSPane
          JScrollPane debugSPane
          DOCUMENT ME!
        • font12
          Font font12
          DOCUMENT ME!
        • font12B
          Font font12B
          DOCUMENT ME!
        • frameInsets
          Insets frameInsets
          DOCUMENT ME!
        • menu
          JMenuBar menu
          DOCUMENT ME!
        • tBar
          JToolBar tBar
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameMultimodalitySingleViewer

      class ViewJFrameMultimodalitySingleViewer extends ViewJFrameTriImage implements Serializable

    • Class gov.nih.mipav.view.ViewJFrameMultimodalityViewer

      class ViewJFrameMultimodalityViewer extends ViewJFrameTriImage implements Serializable

    • Class gov.nih.mipav.view.ViewJFramePaintVasculature

      class ViewJFramePaintVasculature extends ViewJFrameBase implements Serializable
      serialVersionUID:
      1332576394417707204L

      • Serialized Fields

        • componentImage
          ViewJComponentEditImage componentImage
          Display of the MIP image.
        • fudgeFactor
          int fudgeFactor
          Frame adjustment to keep the frame from being just small enough for the ScrollPane to display the scroll bars. Windows seems to find an inset value needing a fudge factor of 3, but Mac OS 10 (X), doesn't, and needs a fudge factor of 7 to not require scroll bars. Either way, insets + fudge-factor must equal 7.
        • heightResFactor
          float heightResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • imageBuffer
          float[] imageBuffer
          Buffer used to store image intensities the presently viewed slice of image.
        • logMagDisplay
          boolean logMagDisplay
          Flag indicating whether or not that the image should be displayed in Log scale. Used primarily for displaying the FFT of an image.
        • mipBuffer
          float[] mipBuffer
          Buffer to store the MIP image that results from the raytrace.
        • mipExtents
          int[] mipExtents
          The dimensions of the MIP image.
        • mipImage
          ModelImage mipImage
          MIP image generated from the volume.
        • mipZTable
          Hashtable<Integer,Float> mipZTable
          Table which holds the z coordinate on the 3D volume for a point (x,y) on the 2D MIP image.
        • paintDialog
          JDialogPaintVasculature paintDialog
          Dialog to facilitate vasculature painting.
        • parent
          ViewJFrameBase parent
          Parent frame of this frame.
        • pixBuffer
          int[] pixBuffer
          Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the mipImage intensities as a index into a LUT.
        • resols
          float[] resols
          Storage of the image voxel resolutions. One resolution value per dimension.
        • scrollPane
          JScrollPane scrollPane
          The scrollPane where the image is displayed.
        • seedPoints
          VOI seedPoints
          VOI containing the possible seed points.
        • units
          int[] units
          Storage of the resolution units of measure. For example, mm, cm, inches ...
        • widthResFactor
          float widthResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • xScreen
          int xScreen
          Width of the display screen.
        • yScreen
          int yScreen
          Height of the display screen.
        • zoom
          float zoom
          Defaults magnification of image to 1.

    • Class gov.nih.mipav.view.ViewJFrameRegisteredImages

      class ViewJFrameRegisteredImages extends JFrame implements Serializable
      serialVersionUID:
      -4417297294466318211L

      • Serialized Fields

        • callFrameDeleteAllButton
          JButton callFrameDeleteAllButton
          Buttons for dealing with frame deletion.
        • callFrameDeleteButton
          JButton callFrameDeleteButton
          Buttons for dealing with frame deletion.
        • callFrameToFrontButton
          JButton callFrameToFrontButton
          Button for bringing frame to front
        • callGCButton
          JButton callGCButton
          Button for dealing with garbage collection
        • callImageDeleteAllButton
          JButton callImageDeleteAllButton
          Buttons for dealing with image deletions
        • callImageDeleteButton
          JButton callImageDeleteButton
          Buttons for dealing with image deletions
        • imageList
          JList imageList
          The list of images and frames
        • pauseButton
          JButton pauseButton
          Button for pausing updating of currently registered images
        • paused
          boolean paused
          Whether currently registered images list is updating
        • sampleRate
          JTextField sampleRate
          The rate at which to update imageList
        • scrollPane
          JScrollPane scrollPane
          The scroll pane containing the image list
        • surf
          ImageRegistryMonitor surf
          thread to watch image registry.
        • UI
          ViewUserInterface UI
          The current user interface

    • Class gov.nih.mipav.view.ViewJFrameRegistration

      class ViewJFrameRegistration extends ViewJFrameBase implements Serializable
      serialVersionUID:
      229266911029610324L

      • Serialized Fields

        • adjMark
          int adjMark
          DOCUMENT ME!
        • adjMarkButton
          JToggleButton adjMarkButton
          DOCUMENT ME!
        • adjMarkMinusButton
          JButton adjMarkMinusButton
          DOCUMENT ME!
        • algoCost
          AlgorithmCostFunctions2D algoCost
        • alphaSlider
          JSlider alphaSlider
          DOCUMENT ME!
        • bufferFactor
          int bufferFactor
          DOCUMENT ME!
        • bufferSize
          int bufferSize
          DOCUMENT ME!
        • buttonArray
          JButton[] buttonArray
          DOCUMENT ME!
        • calculateCostButton
          JButton calculateCostButton
        • ccwButton
          JButton ccwButton
          DOCUMENT ME!
        • componentImage
          ViewJComponentRegistration componentImage
          DOCUMENT ME!
        • componentY
          int componentY
          DOCUMENT ME!
        • controlPanel
          JPanel controlPanel
          DOCUMENT ME!
        • controls
          ViewControlsImage controls
          DOCUMENT ME!
        • costFunctionScrollPane
          JScrollPane costFunctionScrollPane
          Scroll Pane for the Text Area
        • costFunctionTextArea
          JTextArea costFunctionTextArea
        • cpGBC
          GridBagConstraints cpGBC
          DOCUMENT ME!
        • cpGBL
          GridBagLayout cpGBL
          DOCUMENT ME!
        • curAdjMark
          int curAdjMark
          DOCUMENT ME!
        • curRefMark
          int curRefMark
          DOCUMENT ME!
        • cwButton
          JButton cwButton
          DOCUMENT ME!
        • defaultModeButton
          JToggleButton defaultModeButton
          DOCUMENT ME!
        • degreeIncrement
          float degreeIncrement
          DOCUMENT ME!
        • degreeIncrementButton
          JButton degreeIncrementButton
          DOCUMENT ME!
        • doDrag
          boolean doDrag
          DOCUMENT ME!
        • doneLeastSquares
          boolean doneLeastSquares
          DOCUMENT ME!
        • doRegionB
          boolean doRegionB
          DOCUMENT ME!
        • downButton
          JButton downButton
          DOCUMENT ME!
        • dragButton
          JToggleButton dragButton
          DOCUMENT ME!
        • etchedBorder
          Border etchedBorder
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • fileMenu
          JMenu fileMenu
          DOCUMENT ME!
        • font12
          Font font12
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • haveVOIPoints
          boolean haveVOIPoints
          DOCUMENT ME!
        • helpMenu
          JMenu helpMenu
          DOCUMENT ME!
        • i
          int i
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageBufferA
          float[] imageBufferA
          DOCUMENT ME!
        • imageBufferB
          float[] imageBufferB
          DOCUMENT ME!
        • imageBufferOriginalB
          float[] imageBufferOriginalB
          DOCUMENT ME!
        • imageSize
          int imageSize
          DOCUMENT ME!
        • itemClose
          JMenuItem itemClose
          DOCUMENT ME!
        • itemHelp
          JMenuItem itemHelp
          DOCUMENT ME!
        • j
          int j
          DOCUMENT ME!
        • labelAdjustedSlice
          JLabel labelAdjustedSlice
          DOCUMENT ME!
        • labelReferenceSlice
          JLabel labelReferenceSlice
          DOCUMENT ME!
        • labelTable
          Hashtable<Integer,JLabel> labelTable
          DOCUMENT ME!
        • labelTable2
          Hashtable<Integer,JLabel> labelTable2
          DOCUMENT ME!
        • leftButton
          JButton leftButton
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • markerType
          int[] markerType
          DOCUMENT ME!
        • minimumToolBarWidth
          int minimumToolBarWidth
          DOCUMENT ME!
        • mode
          int mode
          DOCUMENT ME!
        • movementGroup
          ButtonGroup movementGroup
          DOCUMENT ME!
        • n
          int n
          DOCUMENT ME!
        • newAlphaBlend
          int newAlphaBlend
          DOCUMENT ME!
        • newExtents
          int[] newExtents
          DOCUMENT ME!
        • nImage
          int nImage
          DOCUMENT ME!
        • nVOI
          int nVOI
          DOCUMENT ME!
        • openingMenuBar
          JMenuBar openingMenuBar
          DOCUMENT ME!
        • pixBuffer
          int[] pixBuffer
          DOCUMENT ME!
        • pixBufferB
          int[] pixBufferB
          DOCUMENT ME!
        • pixelIncrement
          float pixelIncrement
          DOCUMENT ME!
        • pixelIncrementButton
          JButton pixelIncrementButton
          DOCUMENT ME!
        • pointSetA
          double[][] pointSetA
          DOCUMENT ME!
        • pointSetB
          double[][] pointSetB
          DOCUMENT ME!
        • refMark
          int refMark
          DOCUMENT ME!
        • refMarkButton
          JToggleButton refMarkButton
          DOCUMENT ME!
        • refMarkMinusButton
          JButton refMarkMinusButton
          DOCUMENT ME!
        • rightButton
          JButton rightButton
          DOCUMENT ME!
        • rotateButton
          JToggleButton rotateButton
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • scrollPaneSize
          int scrollPaneSize
          DOCUMENT ME!
        • secondImage
          ModelImage secondImage
          DOCUMENT ME!
        • serif12
          Font serif12
          DOCUMENT ME!
        • simpleImg1
          ModelSimpleImage simpleImg1
          Holds extents, other info about firstImage and SecondImage
        • simpleImg2
          ModelSimpleImage simpleImg2
          Holds extents, other info about firstImage and SecondImage
        • slider
          JSlider slider
          DOCUMENT ME!
        • slider2
          JSlider slider2
          DOCUMENT ME!
        • textAdjustedSlice
          JTextField textAdjustedSlice
          DOCUMENT ME!
        • textReferenceSlice
          JTextField textReferenceSlice
          DOCUMENT ME!
        • tMatrix
          TransMatrix tMatrix
          Identity matrix for testing cost
        • toggleArray
          JToggleButton[] toggleArray
          DOCUMENT ME!
        • toolBar
          JToolBar toolBar
          DOCUMENT ME!
        • toolBar2
          JToolBar toolBar2
          DOCUMENT ME!
        • topPanel
          JPanel topPanel
          DOCUMENT ME!
        • translateButton
          JToggleButton translateButton
          DOCUMENT ME!
        • upButton
          JButton upButton
          DOCUMENT ME!
        • voi
          VOI voi
          DOCUMENT ME!
        • voiManager
          VOIManagerInterface voiManager
        • VOIPoints
          Vector<WildMagic.LibFoundation.Mathematics.Vector3f> VOIPoints
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • xfrm
          TransMatrix xfrm
          DOCUMENT ME!
        • xfrmBA
          TransMatrix xfrmBA
          DOCUMENT ME!
        • xfrmD
          TransMatrix xfrmD
          DOCUMENT ME!
        • xfrmH
          TransMatrix xfrmH
          DOCUMENT ME!
        • xOrg
          int[] xOrg
          DOCUMENT ME!
        • xPres
          int[] xPres
          DOCUMENT ME!
        • xRes
          float xRes
          DOCUMENT ME!
        • xRotation
          float xRotation
          DOCUMENT ME!
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • yOrg
          int[] yOrg
          DOCUMENT ME!
        • yPres
          int[] yPres
          DOCUMENT ME!
        • yRes
          float yRes
          DOCUMENT ME!
        • yRotation
          float yRotation
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!
        • zLastSlice
          int zLastSlice
          DOCUMENT ME!
        • zLastSlice2
          int zLastSlice2
          DOCUMENT ME!
        • zoom
          float zoom
          DOCUMENT ME!
        • zSlice
          int zSlice
          DOCUMENT ME!
        • zSlice2
          int zSlice2
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameRegistrationTool

      class ViewJFrameRegistrationTool extends ViewJFrameBase implements Serializable
      serialVersionUID:
      5476210706978180244L

      • Serialized Fields

        • adjMark
          int adjMark
          DOCUMENT ME!
        • adjMarkButton
          JToggleButton adjMarkButton
          DOCUMENT ME!
        • adjMarkMinusButton
          JButton adjMarkMinusButton
          DOCUMENT ME!
        • algoCost
          AlgorithmCostFunctions2D algoCost
        • alphaSlider
          JSlider alphaSlider
          DOCUMENT ME!
        • bothPanel
          JPanel bothPanel
          DOCUMENT ME!
        • bufferFactor
          int bufferFactor
          DOCUMENT ME!
        • bufferSize
          int bufferSize
          DOCUMENT ME!
        • buttonArray
          JButton[] buttonArray
          DOCUMENT ME!
        • calculateCostButton
          JButton calculateCostButton
        • ccwButton
          JButton ccwButton
          DOCUMENT ME!
        • componentImage
          ViewJComponentRegistration componentImage
          for both images displayed together.
        • componentImageA
          ViewJComponentSingleRegistration componentImageA
          for images to be displayed separately.
        • componentImageB
          ViewJComponentSingleRegistration componentImageB
          DOCUMENT ME!
        • controlPanel
          JPanel controlPanel
          DOCUMENT ME!
        • controls
          ViewControlsImage controls
          DOCUMENT ME!
        • copyAdjToRefButton
          JButton copyAdjToRefButton
          DOCUMENT ME!
        • copyRefToAdjButton
          JButton copyRefToAdjButton
          DOCUMENT ME!
        • costFunctionScrollPane
          JScrollPane costFunctionScrollPane
          Scroll Pane for the Text Area
        • costFunctionTextArea
          JTextArea costFunctionTextArea
        • cpGBC
          GridBagConstraints cpGBC
          DOCUMENT ME!
        • cpGBL
          GridBagLayout cpGBL
          DOCUMENT ME!
        • curAdjMark
          int curAdjMark
          DOCUMENT ME!
        • curRefMark
          int curRefMark
          DOCUMENT ME!
        • cwButton
          JButton cwButton
          DOCUMENT ME!
        • defaultModeButton
          JToggleButton defaultModeButton
          DOCUMENT ME!
        • degreeIncrement
          float degreeIncrement
          DOCUMENT ME!
        • degreeIncrementButton
          JButton degreeIncrementButton
          DOCUMENT ME!
        • doDrag
          boolean doDrag
          DOCUMENT ME!
        • doneLeastSquares
          boolean doneLeastSquares
          DOCUMENT ME!
        • doRegionB
          boolean doRegionB
          DOCUMENT ME!
        • downButton
          JButton downButton
          DOCUMENT ME!
        • etchedBorder
          Border etchedBorder
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • fileMenu
          JMenu fileMenu
          DOCUMENT ME!
        • firstDraw
          boolean firstDraw
          DOCUMENT ME!
        • font12
          Font font12
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • helpMenu
          JMenu helpMenu
          DOCUMENT ME!
        • i
          int i
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageBufferA
          float[] imageBufferA
          DOCUMENT ME!
        • imageBufferB
          float[] imageBufferB
          DOCUMENT ME!
        • imageBufferOriginalB
          float[] imageBufferOriginalB
          DOCUMENT ME!
        • imageSize
          int imageSize
          DOCUMENT ME!
        • itemClose
          JMenuItem itemClose
          DOCUMENT ME!
        • itemHelp
          JMenuItem itemHelp
          DOCUMENT ME!
        • j
          int j
          DOCUMENT ME!
        • leftButton
          JButton leftButton
          DOCUMENT ME!
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • lsPerformed
          boolean lsPerformed
          DOCUMENT ME!
        • mode
          int mode
          DOCUMENT ME!
        • movementGroup
          ButtonGroup movementGroup
          DOCUMENT ME!
        • n
          int n
          DOCUMENT ME!
        • newAlphaBlend
          int newAlphaBlend
          DOCUMENT ME!
        • newExtents
          int[] newExtents
          DOCUMENT ME!
        • openingMenuBar
          JMenuBar openingMenuBar
          DOCUMENT ME!
        • pixBuffer
          int[] pixBuffer
          DOCUMENT ME!
        • pixBufferB
          int[] pixBufferB
          DOCUMENT ME!
        • pixBufferCompA
          int[] pixBufferCompA
          DOCUMENT ME!
        • pixBufferCompB
          int[] pixBufferCompB
          DOCUMENT ME!
        • pixelIncrement
          float pixelIncrement
          DOCUMENT ME!
        • pixelIncrementButton
          JButton pixelIncrementButton
          DOCUMENT ME!
        • pointSetA
          double[][] pointSetA
          DOCUMENT ME!
        • pointSetB
          double[][] pointSetB
          DOCUMENT ME!
        • pointSetBT
          double[][] pointSetBT
          DOCUMENT ME!
        • refMark
          int refMark
          DOCUMENT ME!
        • refMarkButton
          JToggleButton refMarkButton
          DOCUMENT ME!
        • refMarkMinusButton
          JButton refMarkMinusButton
          DOCUMENT ME!
        • regButton
          JToggleButton regButton
          DOCUMENT ME!
        • RGBa
          ModelRGB RGBa
          DOCUMENT ME!
        • RGBb
          ModelRGB RGBb
          DOCUMENT ME!
        • rightButton
          JButton rightButton
          DOCUMENT ME!
        • rotateButton
          JToggleButton rotateButton
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • scrollPaneSeparateA
          JScrollPane scrollPaneSeparateA
          DOCUMENT ME!
        • scrollPaneSeparateB
          JScrollPane scrollPaneSeparateB
          DOCUMENT ME!
        • scrollPaneSize
          int scrollPaneSize
          DOCUMENT ME!
        • secondImage
          ModelImage secondImage
          DOCUMENT ME!
        • separatePanel
          JPanel separatePanel
          DOCUMENT ME!
        • serif12
          Font serif12
          DOCUMENT ME!
        • showVOIs
          JCheckBoxMenuItem showVOIs
          DOCUMENT ME!
        • simpleImg1
          ModelSimpleImage simpleImg1
          Holds extents, other info about firstImage and SecondImage
        • simpleImg2
          ModelSimpleImage simpleImg2
          Holds extents, other info about firstImage and SecondImage
        • tabbedPane
          JTabbedPane tabbedPane
          DOCUMENT ME!
        • tMatrix
          TransMatrix tMatrix
          Identity matrix for testing cost
        • toggleArray
          JToggleButton[] toggleArray
          DOCUMENT ME!
        • toolBar
          JToolBar toolBar
          DOCUMENT ME!
        • toolBar2
          JToolBar toolBar2
          DOCUMENT ME!
        • toolBarSep
          JToolBar toolBarSep
          DOCUMENT ME!
        • topPanel
          JPanel topPanel
          DOCUMENT ME!
        • translateButton
          JToggleButton translateButton
          DOCUMENT ME!
        • upButton
          JButton upButton
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • voiManager
          VOIManagerInterface voiManager
        • xCoords
          int[] xCoords
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • xfrm
          TransMatrix xfrm
          DOCUMENT ME!
        • xfrmBA
          TransMatrix xfrmBA
          DOCUMENT ME!
        • xfrmD
          TransMatrix xfrmD
          DOCUMENT ME!
        • xfrmH
          TransMatrix xfrmH
          DOCUMENT ME!
        • xOrg
          int[] xOrg
          DOCUMENT ME!
        • xRes
          float xRes
          DOCUMENT ME!
        • xRotation
          float xRotation
          DOCUMENT ME!
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yCoords
          int[] yCoords
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • yOrg
          int[] yOrg
          DOCUMENT ME!
        • yRes
          float yRes
          DOCUMENT ME!
        • yRotation
          float yRotation
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!
        • zoom
          float zoom
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJFrameTriImage

      class ViewJFrameTriImage extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -7588617549055746009L

      • Serialized Fields

        • addPointToggleButton
          JToggleButton addPointToggleButton
          Toggle buttons for voi/points
        • bogusBorderPaintButton
          JToggleButton bogusBorderPaintButton
        • borderPaintButton
          JToggleButton borderPaintButton
        • btnInvisible
          JToggleButton[] btnInvisible
          DOCUMENT ME!
        • bufferFactor
          int bufferFactor
          1 for black and white, 4 for color.
        • centerButtonSelected
          boolean centerButtonSelected
          DOCUMENT ME!
        • chkShowTalairachGrid
          JCheckBox chkShowTalairachGrid
          "Show talairach grid" checkbox.
        • chkShowTalairachGridMarkers
          JCheckBox chkShowTalairachGridMarkers
          "Show talairach gridmarkers" checkbox.
        • color
          Color color
          Color of the paint.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser to use when selecting paint color.
        • colorPaintButton
          JButton colorPaintButton
          Button for changing the color of the paint.
        • controls
          ViewControlsImage controls
          Used to obtain initial paint opacity and color.
        • coordinateListeners
          Vector<CoordinateChangeListener> coordinateListeners
          A list of CoordinateChangeListeners who want to know about changes to the coordinate currently pointed to by the tri-image frame's crosshairs.
        • crosshairSpinner
          JSpinner crosshairSpinner
          Spinner component for the crosshair gap size.
        • currentAbsolutePositionLabels
          Point3D currentAbsolutePositionLabels
          The current values of the absolute position labels.
        • currentOrientation
          int currentOrientation
        • defaultPreferredHeight
          int defaultPreferredHeight
          The default hight of the window, if it cannot be calculated.
        • dropperPaintToggleButton
          JToggleButton dropperPaintToggleButton
          Toggle buttons for voi/points
        • extents
          int[] extents
          Extents of image.
        • imageAlignToolBar
          JToolBar imageAlignToolBar
        • imageToolBar
          JToolBar imageToolBar
          Image control toolbar.
        • indivMagButton
          JToggleButton indivMagButton
          refs to indiviadual frame zooming in and out buttons.
        • indivMinButton
          JToggleButton indivMinButton
          refs to indiviadual frame zooming in and out buttons.
        • intensitySpinner
          JSpinner intensitySpinner
          Spinner component for the paint intensity.
        • iTalLabel
          JLabel iTalLabel
          talaraich intensity label*
        • labelXTal
          JTextField labelXTal
          Label the Talairach position x value in the image volume.
        • labelYTal
          JTextField labelYTal
          Label the Talairach position y value in the image volume.
        • labelZTal
          JTextField labelZTal
          Label the Talairach position z value in the image volume.
        • leastSquaresButton
          JButton leastSquaresButton
          DOCUMENT ME!
        • magButton
          JButton magButton
          refs to the magnify and minimize button.*
        • menuObj
          ViewMenuBuilder menuObj
          Menu items storage.
        • minButton
          JButton minButton
          refs to the magnify and minimize button.*
        • oldLayout
          boolean oldLayout
          DOCUMENT ME!
        • OPACITY
          float OPACITY
          Opacity of paint.
        • paintBox
          JComboBox paintBox
          Box holding the list of available paint brushes.
        • paintBrushLocked
          boolean paintBrushLocked
          used with the above to say the paint brush has been changed, waiting to change back.
        • paintBrushNames
          String[] paintBrushNames
          List of built-in and user-defined paint brushes.
        • paintCanToggleButton
          JToggleButton paintCanToggleButton
          Toggle buttons for voi/points
        • paintToolBar
          JToolBar paintToolBar
          Paint tool bar.
        • panelActiveImage
          JPanel panelActiveImage
          Panel for deciding which image is active; appears when 2 images are loaded.
        • panelToolbar
          JPanel panelToolbar
          Panel that holds the toolbars.
        • panelToolBarGBC
          GridBagConstraints panelToolBarGBC
        • parentFrame
          ViewJFrameImage parentFrame
          Reference to the parent window.
        • pluginPanel
          Component pluginPanel
          Reference to the plug-in panel in the 2x2 (old) layout.
        • quickPaintBrushIndex
          int quickPaintBrushIndex
          int used for quick-key painting for speedier paint brush access.
        • radioImageA
          JRadioButton radioImageA
          Radio button for selecting image A as active.
        • radioImageB
          JRadioButton radioImageB
          Radio button for selecting image B as active.
        • radioImageBoth
          JRadioButton radioImageBoth
          Radio button for selecting both images as active.
        • resols
          float[] resols
          Resolutions of image.
        • RGBTa
          ModelRGB RGBTa
          RGB tables for imageA and imageB
        • RGBTb
          ModelRGB RGBTb
          RGB tables for imageA and imageB
        • scrollButton
          JCheckBox scrollButton
          The button that indicates whether this triframe is linked with tri-frames of similar dimensionality.
        • scrollOriginalCrosshair
          boolean scrollOriginalCrosshair
          Flag telling the crosshair movement to update slice in original image frame.
        • scrollPane
          JScrollPane[] scrollPane
          DOCUMENT ME!
        • showTalairachGrid
          boolean showTalairachGrid
          Flag for showing the Talairach grid on the component images.
        • showTalairachPosition
          boolean showTalairachPosition
          Flag for showing the Talairach position on the component images.
        • spinnerDefaultValue
          double spinnerDefaultValue
          Used to setup the paint spinner.
        • spinnerMax
          double spinnerMax
          Used to setup the paint spinner.
        • spinnerMin
          double spinnerMin
          Used to setup the paint spinner.
        • spinnerStep
          double spinnerStep
          Used to setup the paint spinner.
        • talairachPanel
          JPanel talairachPanel
          Panel for Talairach position display.
        • tDim
          int tDim
          Time dimension of the original image.
        • tImageSlider
          JSlider tImageSlider
          Slider for 4D images, time dimension.
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          Toolbar builder reference.
        • tpSplineButton
          JButton tpSplineButton
          DOCUMENT ME!
        • traverseButton
          JToggleButton traverseButton
          Button for traversing the images.
        • triImage
          ViewJComponentTriImage[] triImage
          DOCUMENT ME!
        • triImagePanel
          JPanel[] triImagePanel
          DOCUMENT ME!
        • tSlice
          int tSlice
          Time slice that this image is on.
        • tTalVoxLabel
          JLabel tTalVoxLabel
          talairach voxel label *
        • units
          int[] units
          Units of image - mm, inches, etc.
        • useInfNew
          boolean useInfNew
          if true use cerebellum-adjusted static variable.
        • viewPanel
          JPanel viewPanel
          Panel for switching between radiological and neurological viewing conventions.
        • VOIGroup
          ButtonGroup VOIGroup
        • voiManager
          VOIManagerInterface voiManager
          The VOI managers for each triComponent
        • voiMenu
          JMenu voiMenu
          Menu displaying VOI options
        • volumeBounds
          CubeBounds volumeBounds
          Volume Boundary may be changed for cropping the volume.
        • volumeCenter
          int[] volumeCenter
          The point to become center of transformed image.
        • volumePositionFrame
          VolumePositionFrame volumePositionFrame
          Reference to the volume coordinate frame.
        • volumePositionPanel
          JPanel volumePositionPanel
          Reference to the volume coordinate panel when it is in the plug-in position.
        • xTalLabel
          JLabel xTalLabel
        • yTalLabel
          JLabel yTalLabel
        • zoom
          float zoom
          Magnification for image.
        • zTalLabel
          JLabel zTalLabel

    • Class gov.nih.mipav.view.ViewJPanelHistoLUT

      class ViewJPanelHistoLUT extends JPanel implements Serializable
      serialVersionUID:
      -3873204112932340987L

      • Serialized Fields

        • colorChooser
          ViewJColorChooser colorChooser
          The LUT color chooser.
        • componentHistogram
          ViewJComponentHLUTBase componentHistogram
          The histogram LUT of the image. The square one.
        • componentLUT
          ViewJComponentLUT componentLUT
          Lookup table of image. The narrow rectangular one.
        • histogram
          ModelHistogram histogram
          Model histogram.
        • histoLUTType
          int histoLUTType
          The type of histogram component to show.
        • image
          ModelImage image
          The image.
        • lut
          ModelLUT lut
          The grayscale lookup table for the image.
        • LUTIndex
          int LUTIndex
          The LUT index used when chaning the LUT color by clicking on the ViewJComponentLUT.
        • lutRecorder
          JDialogRecordLUT lutRecorder
          LUT recorder.
        • parent
          HistoLUTParent parent
          The component containing this panel.
        • RGBT
          ModelRGB RGBT
          The RGB lookup table.

    • Class gov.nih.mipav.view.ViewJPanelLUT

      class ViewJPanelLUT extends JPanel implements Serializable
      serialVersionUID:
      -1769974472965867218L

      • Serialized Fields

        • ctDialogA
          JDialogCT ctDialogA
          Deprecated.
          DOCUMENT ME!
        • ctDialogB
          JDialogCT ctDialogB
          Deprecated.
          DOCUMENT ME!
        • cursorIndex
          int cursorIndex
          Deprecated.
          Active mouse cursor index of the imageA, B and GM image A, B.
        • cursorIndexB
          int cursorIndexB
          Deprecated.
          Active mouse cursor index of the imageA, B and GM image A, B.
        • entireFlag
          boolean entireFlag
          Deprecated.
          DOCUMENT ME!
        • histogramA
          ModelHistogram histogramA
          Deprecated.
          DOCUMENT ME!
        • histogramB
          ModelHistogram histogramB
          Deprecated.
          DOCUMENT ME!
        • histoPanelA
          ViewJPanelHistoLUT histoPanelA
          Deprecated.
          DOCUMENT ME!
        • histoPanelB
          ViewJPanelHistoLUT histoPanelB
          Deprecated.
          DOCUMENT ME!
        • indexColorATextF
          JTextField indexColorATextF
          Deprecated.
          DOCUMENT ME!
        • indexColorBTextF
          JTextField indexColorBTextF
          Deprecated.
          DOCUMENT ME!
        • interpCheckBoxA
          JCheckBox interpCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • interpCheckBoxB
          JCheckBox interpCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • labelsTable
          Hashtable<Integer,JLabel> labelsTable
          Deprecated.
          Histogram dialog slider labels of the imageA, B and GM imageA, B.
        • labelsTableB
          Hashtable<Integer,JLabel> labelsTableB
          Deprecated.
          Histogram dialog slider labels of the imageA, B and GM imageA, B.
        • logCheckBoxA
          JCheckBox logCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • logCheckBoxB
          JCheckBox logCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • mouseLabel
          JLabel mouseLabel
          Deprecated.
          The opacity slider label.
        • mouseLabelB
          JLabel mouseLabelB
          Deprecated.
          The opacity slider label.
        • mouseSlider
          JSlider mouseSlider
          Deprecated.
          Opacity X scale sliders.
        • mouseSliderB
          JSlider mouseSliderB
          Deprecated.
          Opacity X scale sliders.
        • mouseSliderLabels
          JLabel[] mouseSliderLabels
          Deprecated.
          The labels below the opacity slider.
        • mouseSliderLabelsB
          JLabel[] mouseSliderLabelsB
          Deprecated.
          The labels below the opacity slider.
        • nColorsATextF
          JTextField nColorsATextF
          Deprecated.
          DOCUMENT ME!
        • nColorsBTextF
          JTextField nColorsBTextF
          Deprecated.
          DOCUMENT ME!
        • oneBasedLUTCheckBoxImageB
          JCheckBox oneBasedLUTCheckBoxImageB
          Deprecated.
          DOCUMENT ME!
        • outputBox
          JComboBox outputBox
          Deprecated.
          DOCUMENT ME!
        • outputBoxB
          JComboBox outputBoxB
          Deprecated.
          DOCUMENT ME!
        • panelA
          JPanel panelA
          Deprecated.
          DOCUMENT ME!
        • panelB
          JPanel panelB
          Deprecated.
          DOCUMENT ME!
        • panelParent
          ViewJFrameHistoLUT panelParent
          Deprecated.
          DOCUMENT ME!
        • rangeText
          JTextField rangeText
          Deprecated.
          X range text field in the imageA, B histogram dialog.
        • rangeTextB
          JTextField rangeTextB
          Deprecated.
          X range text field in the imageA, B histogram dialog.
        • rangeX
          float rangeX
          Deprecated.
          X range value of the imageA, B and GM imageA, B.
        • rangeXB
          float rangeXB
          Deprecated.
          X range value of the imageA, B and GM imageA, B.
        • scaleRangeA
          int scaleRangeA
          Deprecated.
          Scale range value according to the image min and max.
        • scaleRangeB
          int scaleRangeB
          Deprecated.
          Scale range value according to the image min and max.
        • tabbedPane
          JTabbedPane tabbedPane
          Deprecated.
          DOCUMENT ME!
        • threshFillBF
          JTextField threshFillBF
          Deprecated.
          DOCUMENT ME!
        • threshFillF
          JTextField threshFillF
          Deprecated.
          threshold related.
        • threshLowerBF
          JTextField threshLowerBF
          Deprecated.
          DOCUMENT ME!
        • threshLowerF
          JTextField threshLowerF
          Deprecated.
          threshold related.
        • threshUpperBF
          JTextField threshUpperBF
          Deprecated.
          DOCUMENT ME!
        • threshUpperF
          JTextField threshUpperF
          Deprecated.
          threshold related.
        • toolBarBottom
          JToolBar toolBarBottom
          Deprecated.
          DOCUMENT ME!
        • toolBarCenter
          JToolBar toolBarCenter
          Deprecated.
          center toolbar
        • toolBarObj
          ViewToolBarBuilder toolBarObj
          Deprecated.
          DOCUMENT ME!
        • toolBarThreshold
          JToolBar toolBarThreshold
          Deprecated.
          DOCUMENT ME!
        • toolBarTop
          JToolBar toolBarTop
          Deprecated.
          DOCUMENT ME!
        • updateCheckBoxA
          JCheckBox updateCheckBoxA
          Deprecated.
          DOCUMENT ME!
        • updateCheckBoxB
          JCheckBox updateCheckBoxB
          Deprecated.
          DOCUMENT ME!
        • voxelVolumeLabel
          JLabel voxelVolumeLabel
          Deprecated.
          Used to display the volume or area of the voxels/pixels between the upper and lower bounds.
        • xRangeTextA
          JTextField xRangeTextA
          Deprecated.
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • xRangeTextB
          JTextField xRangeTextB
          Deprecated.
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextA
          JTextField yRangeTextA
          Deprecated.
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextB
          JTextField yRangeTextB
          Deprecated.
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

    • Class gov.nih.mipav.view.ViewJPopupPlugin

      class ViewJPopupPlugin extends JPanel implements Serializable

      • Serialized Fields

        • itemProps
          JMenuItem itemProps
          The uninstall menu item
        • pluginName
          String pluginName
          String text of the button representing the plugin to be uninstalled.
        • popup
          JPopupMenu popup
          The stored popup menu

    • Class gov.nih.mipav.view.ViewJPopupPt

      class ViewJPopupPt extends JPanel implements Serializable
      serialVersionUID:
      393929198484576018L

      • Serialized Fields

    • Class gov.nih.mipav.view.ViewJPopupVOI

      class ViewJPopupVOI extends JPanel implements Serializable
      serialVersionUID:
      -7134535981914560813L

      • Serialized Fields

        • contourOrderSubMenu
          JMenu contourOrderSubMenu
          DOCUMENT ME!
        • editCircleDiameter
          JMenuItem editCircleDiameter
        • editSquareLength
          JMenuItem editSquareLength
        • editSubMenu
          JMenu editSubMenu
          DOCUMENT ME!
        • flipSubMenu
          JMenu flipSubMenu
          DOCUMENT ME!
        • graphSubMenu
          JMenu graphSubMenu
          DOCUMENT ME!
        • itemClose
          JMenuItem itemClose
          DOCUMENT ME!
        • itemCrop
          JMenuItem itemCrop
          DOCUMENT ME!
        • itemOutputDistance
          JMenuItem itemOutputDistance
          DOCUMENT ME!
        • itemProps
          JMenuItem itemProps
          DOCUMENT ME!
        • itemTrim
          JMenuItem itemTrim
        • orderSubMenu
          JMenu orderSubMenu
          DOCUMENT ME!
        • popup
          JPopupMenu popup
          DOCUMENT ME!
        • propSubMenu
          JMenu propSubMenu
          DOCUMENT ME!
        • selectedVOI
          VOIBase selectedVOI
        • selectionMenu
          JMenu selectionMenu
          DOCUMENT ME!
        • voiHandler
          VOIHandlerInterface voiHandler
          DOCUMENT ME!

    • Class gov.nih.mipav.view.ViewJProgressBar

      class ViewJProgressBar extends JFrame implements Serializable
      serialVersionUID:
      -4893646677987678693L

      • Serialized Fields

        • cancelButton
          JButton cancelButton
          Cancel button, if applicable.
        • messageLocked
          boolean messageLocked
          indicates if the message string (in the progress bar) is locked so that it wont be updated
        • messagePBar
          JLabel messagePBar
          Label directly above the bar that is updated during operation if necessary.
        • pBar
          JProgressBar pBar
          Actual bar which fills with color as the percentage of completion increases.
        • percentage
          JLabel percentage
          Percentage label, puts a number next to the bar with the actual percent completed.
        • readyToDispose
          boolean readyToDispose
          For users wanting to override the automatic closing option when progress reaches 100.
        • separateThread
          boolean separateThread
          DOCUMENT ME!
        • title
          String title
          Title of the frame for the progress bar.

    • Class gov.nih.mipav.view.ViewJProgressBarMulti

      class ViewJProgressBarMulti extends ViewJProgressBar implements Serializable
      serialVersionUID:
      1298459723854411415L

      • Serialized Fields

        • actionListener
          ActionListener actionListener
        • algCont
          ArrayList<ViewJProgressBarMulti.AlgoContainer> algCont
          List of containers that hold all the information to correctly draw each progress bar
        • algList
          ArrayList<Runnable> algList
          List containing which runnables are registered to this listener
        • barPanel
          JPanel barPanel
          Panel containing all the progress bars as well as relevent text labels
        • cancelButton
          JButton cancelButton
        • cancelFlag
          boolean cancelFlag
        • closeList
          ArrayList<JLabel> closeList
          List to determine which progress bar to close
        • emptyDisplayed
          boolean emptyDisplayed
          Whether or not emptyLabel is currently displayed
        • emptyLabel
          JLabel emptyLabel
          Label to display when there are no runnables to display or listen for.
        • gbc
          GridBagConstraints gbc
        • hideList
          ArrayList<JLabel> hideList
          List to determine which progress bar to hide/show
        • messageLocked
          boolean messageLocked
        • windowListener
          WindowListener windowListener

    • Class gov.nih.mipav.view.ViewJSlider

      class ViewJSlider extends JSlider implements Serializable

      • Serialized Fields

        • dim
          Dimension dim
          Holds the old dimension to minimize redrawing of slider table
        • minAllowableMajorTickSpacing
          double minAllowableMajorTickSpacing
        • minAllowableMinorTickSpacing
          double minAllowableMinorTickSpacing
          The closest number of pixels that major/minor ticks may be next to each other. Used to set GUI and create labels.
        • type
          ViewJSlider.SliderType type
          Refers to the type of slider being used by MIPAV

    • Class gov.nih.mipav.view.ViewMenuBuilder.QuickList

      class QuickList extends JComponent implements Serializable
      serialVersionUID:
      -4787325627153954566L

    • Class gov.nih.mipav.view.ViewOpenImageSequence

      class ViewOpenImageSequence extends JFrame implements Serializable
      serialVersionUID:
      5007701357886039L

      • Serialized Fields

        • brightnessSlider
          JSlider brightnessSlider
          DOCUMENT ME!
        • cellRenderer
          AlternatingTableCellRenderer cellRenderer
          DOCUMENT ME!
        • channelMap
          int[] channelMap
          DOCUMENT ME!
        • chkForceUBYTE
          JCheckBox chkForceUBYTE
          DOCUMENT ME!
        • cmbFilter
          JComboBox cmbFilter
          DOCUMENT ME!
        • contrastSlider
          JSlider contrastSlider
          DOCUMENT ME!
        • CTZ
          int CTZ
          Int denoting CTZ sequence
        • currentPath
          File currentPath
          DOCUMENT ME!
        • CZT
          int CZT
          Int denoting CZT sequence
        • enableCheckbox
          JCheckBox enableCheckbox
          DOCUMENT ME!
        • fileListData
          File[] fileListData
          DOCUMENT ME!
        • filenameTable
          JTable filenameTable
          DOCUMENT ME!
        • filenameTableModel
          SortingTableModel filenameTableModel
          DOCUMENT ME!
        • filenameTableSorter
          TableSorter filenameTableSorter
          DOCUMENT ME!
        • lblOrigDim
          JLabel lblOrigDim
          DOCUMENT ME!
        • previewFilename
          String previewFilename
          DOCUMENT ME!
        • previewPanel
          JPanel previewPanel
          DOCUMENT ME!
        • radCTZ
          JRadioButton radCTZ
          Radio button for CTZ sequence
        • radCZT
          JRadioButton radCZT
          Radio button for CZT sequence
        • radTCZ
          JRadioButton radTCZ
          Radio button for TCZ sequence
        • radTZC
          JRadioButton radTZC
          Radio button for TZC sequence
        • radZCT
          JRadioButton radZCT
          Radio button for ZCT sequence
        • radZTC
          JRadioButton radZTC
          Radio button for ZTC sequence
        • table
          JTable table
          DOCUMENT ME!
        • tableModel
          UneditableTableModel tableModel
          DOCUMENT ME!
        • TCZ
          int TCZ
          Int denoting TCZ sequence
        • txtChannels
          JTextField txtChannels
          DOCUMENT ME!
        • txtDirectory
          JTextField txtDirectory
          DOCUMENT ME!
        • txtHeight
          JTextField txtHeight
          DOCUMENT ME!
        • txtSlices
          JTextField txtSlices
          DOCUMENT ME!
        • txtTimePoints
          JTextField txtTimePoints
          DOCUMENT ME!
        • txtWidth
          JTextField txtWidth
          DOCUMENT ME!
        • TZC
          int TZC
          Int denoting TZC sequence
        • ZCT
          int ZCT
          Int denoting ZCT sequence
        • ZTC
          int ZTC
          Int denoting ZTC sequence

    • Class gov.nih.mipav.view.ViewSelectableDoubleListPanel

      class ViewSelectableDoubleListPanel extends JPanel implements Serializable
      serialVersionUID:
      -7066171606587907360L

    • Class gov.nih.mipav.view.ViewSplashScreen

      class ViewSplashScreen extends JFrame implements Serializable
      serialVersionUID:
      924235664168779459L

      • Serialized Fields

        • image
          Image image
          The splash screen image.
        • loadOK
          boolean loadOK
          Whether the splash screen was loaded from disk successfully.

    • Class gov.nih.mipav.view.ViewTableModel

      class ViewTableModel extends DefaultTableModel implements Serializable
      serialVersionUID:
      487484434950231158L

    • Class gov.nih.mipav.view.ViewToolBarBuilder

      class ViewToolBarBuilder extends Object implements Serializable

      • Serialized Fields

        • bgVector
          Vector<ButtonGroup> bgVector
          Vector to hold all toggle groups for VOI toggle (and custom toggle configurations)
        • bogusBorderPaintButton
          JToggleButton bogusBorderPaintButton
          The button used to toggle borders around painted areas.
        • borderPaintButton
          JToggleButton borderPaintButton
          The button used to toggle borders around painted areas.
        • checkerBoardButton
          JButton checkerBoardButton
          The button used to enable checker board display of two images.
        • colorPaintButton
          JButton colorPaintButton
          The button used to select the color of the paint used.
        • ctButton
          JButton ctButton
          The button for presets used only for CT images.
        • currentScriptComboBox
          JComboBox currentScriptComboBox
          The combo box containing the possible choices for the current script in the script toolbar. Filled with entries from the currently selected "Scripting directory".
        • currentSelectedScript
          String currentSelectedScript
          The script currently selected in the scripting toolbar (null if no script is selected).
        • intensitySpinner
          JSpinner intensitySpinner
          The spinner for indicating the intensity to fill the image with when commiting paint in an image.
        • intensityStep
          double intensityStep
          The amount to change the value in the intensity spinner by when the user clicks it.
        • intensityValue
          double intensityValue
          The current value chosen in the intensity spinner.
        • maxIntensity
          double maxIntensity
          The maximum value which can be chosen in the intensity spinner.
        • minIntensity
          double minIntensity
          The minimum value which can be chosen in the intensity spinner.
        • opacity
          float opacity
          The opacity of the paint, between 0 (transparent) and 1 (opaque). Set from the opacity dialog.
        • paintBox
          JComboBox paintBox
          Combo box to hold all of the paint brushes.
        • paintBrushButton
          JToggleButton paintBrushButton
          DOCUMENT ME!
        • paintBrushNames
          String[] paintBrushNames
          DOCUMENT ME!
        • paintColor
          Color paintColor
          The paint color to be used when the user paints in the image.
        • pointerVOIButton
          JToggleButton pointerVOIButton
          The button for the "default" mode of the mouse, where clicking in the image shows the intensity of that voxel.
        • popup
          JPopupMenu popup
          DOCUMENT ME!
        • popupListener
          ViewToolBarBuilder.PopupListener popupListener
          DOCUMENT ME!
        • regButton
          JToggleButton regButton
          The button used to enable the showing of a small portion of image b near the mouse cursor.
        • scriptTable
          Hashtable<String,String> scriptTable
          DOCUMENT ME!
        • scrollButton
          JCheckBox scrollButton
        • syncImagesIcon
          JButton syncImagesIcon
        • UI
          Object UI
          The class which wants to listen to changes made to this components of the toolbars. May have to be a ActionListener, MouseListener, ChangeListener, or ViewJFrameBase depending on which toolbars are being used in a particular dialog or frame.
        • voiColorButton
          ViewToolBarBuilder.VOIColorButton voiColorButton
        • VOIGroup
          ButtonGroup VOIGroup
          A button group for all toggle buttons which change the effect of mouse usage in the image.
        • voiRedoButton
          JButton voiRedoButton
        • voiUndoButton
          JButton voiUndoButton

    • Class gov.nih.mipav.view.ViewToolBarBuilder.JScriptToolBar

      class JScriptToolBar extends JToolBar implements Serializable
      serialVersionUID:
      6205577015710803423L

      • Serialized Fields

        • recordScriptButton
          JButton recordScriptButton
          The recording button.

    • Class gov.nih.mipav.view.ViewToolBarBuilder.VOIColorButton

      class VOIColorButton extends JButton implements Serializable

    • Class gov.nih.mipav.view.ViewVOIVector

      class ViewVOIVector extends Vector<VOI> implements Serializable
      serialVersionUID:
      6003086288473157573L

    • Class gov.nih.mipav.view.VOIContourNode

      class VOIContourNode extends DefaultMutableTreeNode implements Serializable
      serialVersionUID:
      -1101994985217434811L

    • Class gov.nih.mipav.view.VOIFrameNode

      class VOIFrameNode extends DefaultMutableTreeNode implements Serializable
      serialVersionUID:
      -6795049606234900885L

      • Serialized Fields

        • frameNumber
          int frameNumber
          The slice number of the VOI component

    • Class gov.nih.mipav.view.VOIGroupNode

      class VOIGroupNode extends DefaultMutableTreeNode implements Serializable
      serialVersionUID:
      2278502889235734935L

      • Serialized Fields

        • extents
          int[] extents

    • Class gov.nih.mipav.view.VOIGroupTree

      class VOIGroupTree extends JTree implements Serializable
      serialVersionUID:
      -6853661393602487962L

    • Class gov.nih.mipav.view.VOIOrientationNode

      class VOIOrientationNode extends DefaultMutableTreeNode implements Serializable
      serialVersionUID:
      -6795049606234900885L

      • Serialized Fields

        • orientation
          String orientation
        • voiName
          String voiName
          Name of parent voi

    • Class gov.nih.mipav.view.VolumePositionFrame

      class VolumePositionFrame extends JFrame implements Serializable
      serialVersionUID:
      3115465399315063208L

      • Serialized Fields

        • parentFrame
          ViewJFrameTriImage parentFrame
          Reference to the parentFrame, to notify when this window closes:.

  • Package gov.nih.mipav.view.components

  • Package gov.nih.mipav.view.dialogs

    • Class gov.nih.mipav.view.dialogs.DialogDTIColorDisplay

      class DialogDTIColorDisplay extends ViewJFrameBase implements Serializable
      serialVersionUID:
      7511908857729035381L

      • Serialized Fields

        • adjustExp
          float adjustExp
          adjust exp *
        • adjustExpPanel
          JPanel adjustExpPanel
          panels *
        • adjustExpSlider
          JSlider adjustExpSlider
          various sliders in dialog *
        • adjustExpTextField
          JTextField adjustExpTextField
          textfields *
        • alg
          AlgorithmDTIColorDisplay alg
          handle to the algorithm *
        • anisotropyFilename
          String anisotropyFilename
          names of eigenvector and anisotropy files*
        • anisotropyImage
          ModelImage anisotropyImage
          anisotropy src image *
        • anisotropyMax
          float anisotropyMax
          anisotropy max *
        • anisotropyMaxPanel
          JPanel anisotropyMaxPanel
          panels *
        • anisotropyMaxSlider
          JSlider anisotropyMaxSlider
          various sliders in dialog *
        • anisotropyMaxTextField
          JTextField anisotropyMaxTextField
          textfields *
        • anisotropyMin
          float anisotropyMin
          anisotropy min *
        • anisotropyMinPanel
          JPanel anisotropyMinPanel
          panels *
        • anisotropyMinSlider
          JSlider anisotropyMinSlider
          various sliders in dialog *
        • anisotropyMinTextField
          JTextField anisotropyMinTextField
          textfields *
        • bottomPanel
          JPanel bottomPanel
          panels *
        • captureImageButton
          JButton captureImageButton
          buttons *
        • colorPanel
          JPanel colorPanel
          panels *
        • colorRangePanel
          JPanel colorRangePanel
          panels *
        • colorRangeSlider
          JSlider colorRangeSlider
          various sliders in dialog *
        • colorRangeTextField
          JTextField colorRangeTextField
          textfields *
        • colorWheel
          ColorWheel colorWheel
          Color Wheels *
        • colorWheelChoicesPanel
          JPanel colorWheelChoicesPanel
          panels *
        • colorWheelComboBox
          JComboBox colorWheelComboBox
          color wheel choices combo box *
        • colorWheelPanel
          JPanel colorWheelPanel
          panels *
        • componentImage
          ViewJComponentDTIImage componentImage
          ViewJComponentDTIImage *
        • currentColorWheelType
          String currentColorWheelType
          String indicating current color wheel type *
        • currentRectangle
          Rectangle currentRectangle
          rectangle for screen capture*
        • currentResultImageSlicesLabel
          JLabel currentResultImageSlicesLabel
          labels *
        • dimGreenPanel
          JPanel dimGreenPanel
          panels *
        • dimGreenSlider
          JSlider dimGreenSlider
          various sliders in dialog *
        • dimGreenTextField
          JTextField dimGreenTextField
          textfields *
        • eigvecFilename
          String eigvecFilename
          names of eigenvector and anisotropy files*
        • eigvecSrcImage
          ModelImage eigvecSrcImage
          eigenvector src image *
        • flag
          boolean flag
          flag needed when performing restore defaults *
        • gamma
          float gamma
          gamma correction *
        • gammaPanel
          JPanel gammaPanel
          panels *
        • gammaSlider
          JSlider gammaSlider
          various sliders in dialog *
        • gammaTextField
          JTextField gammaTextField
          textfields *
        • gbc
          GridBagConstraints gbc
          GridbagConstraints *
        • gbl
          GridBagLayout gbl
          GridBagLayout *
        • heightResFactor
          float heightResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • heuristicParametersPanel
          JPanel heuristicParametersPanel
          panels *
        • imageBufferA
          float[] imageBufferA
          Buffer used to store image intensities the presently viewed slice of image A.
        • in
          BufferedReader in
          Buffered Reader for loading params *
        • isMultiply
          boolean isMultiply
          boolean for truncate/multiply *
        • loadButton
          JButton loadButton
          buttons *
        • m_afScreenResolutions
          float[] m_afScreenResolutions
          Sets the correct resolutions for the image that is created by captureImage.
        • m_fSliceThickness
          float m_fSliceThickness
          Sets the correct slice thickness
        • magButton
          JButton magButton
          buttons *
        • magLabel
          JLabel magLabel
          labels *
        • mainPanel
          JPanel mainPanel
          panels *
        • maxAdjustExp
          float maxAdjustExp
          mins and maxes for heuristic parameters*
        • maxAdjustExpLabel
          JLabel maxAdjustExpLabel
          labels *
        • maxAnisotropyMax
          float maxAnisotropyMax
          mins and maxes for heuristic parameters*
        • maxAnisotropyMaxLabel
          JLabel maxAnisotropyMaxLabel
          labels *
        • maxAnisotropyMin
          float maxAnisotropyMin
          mins and maxes for heuristic parameters*
        • maxAnisotropyMinLabel
          JLabel maxAnisotropyMinLabel
          labels *
        • maxColorRange
          float maxColorRange
          mins and maxes for heuristic parameters*
        • maxColorRangeLabel
          JLabel maxColorRangeLabel
          labels *
        • maxDimGreen
          float maxDimGreen
          mins and maxes for heuristic parameters*
        • maxDimGreenLabel
          JLabel maxDimGreenLabel
          labels *
        • maxGamma
          float maxGamma
          mins and maxes for heuristic parameters*
        • maxGammaLabel
          JLabel maxGammaLabel
          labels *
        • maxResultImageSlicesLabel
          JLabel maxResultImageSlicesLabel
          labels *
        • maxSatBlue
          float maxSatBlue
          mins and maxes for heuristic parameters*
        • maxSatBlueLabel
          JLabel maxSatBlueLabel
          labels *
        • maxSatVsTheta
          float maxSatVsTheta
          mins and maxes for heuristic parameters*
        • maxSatVsThetaLabel
          JLabel maxSatVsThetaLabel
          labels *
        • maxStevensBeta
          float maxStevensBeta
          mins and maxes for heuristic parameters*
        • maxStevensBetaLabel
          JLabel maxStevensBetaLabel
          labels *
        • minAdjustExp
          float minAdjustExp
          mins and maxes for heuristic parameters*
        • minAdjustExpLabel
          JLabel minAdjustExpLabel
          labels *
        • minAnisotropyMax
          float minAnisotropyMax
          mins and maxes for heuristic parameters*
        • minAnisotropyMaxLabel
          JLabel minAnisotropyMaxLabel
          labels *
        • minAnisotropyMin
          float minAnisotropyMin
          mins and maxes for heuristic parameters*
        • minAnisotropyMinLabel
          JLabel minAnisotropyMinLabel
          labels *
        • minColorRange
          float minColorRange
          mins and maxes for heuristic parameters*
        • minColorRangeLabel
          JLabel minColorRangeLabel
          labels *
        • minDimGreen
          float minDimGreen
          mins and maxes for heuristic parameters*
        • minDimGreenLabel
          JLabel minDimGreenLabel
          labels *
        • minGamma
          float minGamma
          mins and maxes for heuristic parameters*
        • minGammaLabel
          JLabel minGammaLabel
          labels *
        • minResultImageSlicesLabel
          JLabel minResultImageSlicesLabel
          labels *
        • minSatBlue
          float minSatBlue
          mins and maxes for heuristic parameters*
        • minSatBlueLabel
          JLabel minSatBlueLabel
          labels *
        • minSatVsTheta
          float minSatVsTheta
          mins and maxes for heuristic parameters*
        • minSatVsThetaLabel
          JLabel minSatVsThetaLabel
          labels *
        • minStevensBeta
          float minStevensBeta
          mins and maxes for heuristic parameters*
        • minStevensBetaLabel
          JLabel minStevensBetaLabel
          labels *
        • multRadio
          JRadioButton multRadio
          radio buttons for truncate/multiply *
        • nImage
          int nImage
          Number of slices in a 3D dataset.
        • nTImage
          int nTImage
          Number of time sequences in a 4D dataset.
        • numSlices
          int numSlices
          num slices for result image *
        • optionsPanel
          JPanel optionsPanel
          panels *
        • out
          BufferedWriter out
          Buffered Writer for saving params *
        • pB
          float pB
          blue saturation *
        • pC
          float pC
          color range *
        • pG
          float pG
          green saturation *
        • pixBuffer
          int[] pixBuffer
          Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageA intensities as a index into a LUT.
        • pS
          float pS
          saturation vs theta *
        • refLabel1
          JLabel refLabel1
          labels *
        • refLabel2
          JLabel refLabel2
          labels *
        • refLabel3
          JLabel refLabel3
          labels *
        • refPanel
          JPanel refPanel
          panels *
        • resols
          float[] resols
          Storage of the image voxel resolutions. One resolution value per dimension.
        • restoreDefaultsButton
          JButton restoreDefaultsButton
          buttons *
        • restoreDefaultsPanel
          JPanel restoreDefaultsPanel
          panels *
        • resultImage
          ModelImage resultImage
          result image *
        • resultImagePanel
          JPanel resultImagePanel
          panels *
        • resultImageSlider
          JSlider resultImageSlider
          various sliders in dialog *
        • resultImageSliderPanel
          JPanel resultImageSliderPanel
          panels *
        • resultPanel
          JPanel resultPanel
          panels *
        • resultScrollPanel
          JScrollPane resultScrollPanel
          scroll pane for result image *
        • satBluePanel
          JPanel satBluePanel
          panels *
        • satBlueSlider
          JSlider satBlueSlider
          various sliders in dialog *
        • satBlueTextField
          JTextField satBlueTextField
          textfields *
        • satVsThetaPanel
          JPanel satVsThetaPanel
          panels *
        • satVsThetaSlider
          JSlider satVsThetaSlider
          various sliders in dialog *
        • satVsThetaTextField
          JTextField satVsThetaTextField
          textfields *
        • saveButton
          JButton saveButton
          buttons *
        • saveLoadPanel
          JPanel saveLoadPanel
          panels *
        • stevensBeta
          float stevensBeta
          steven's beta *
        • stevensBetaPanel
          JPanel stevensBetaPanel
          panels *
        • stevensBetaSlider
          JSlider stevensBetaSlider
          various sliders in dialog *
        • stevensBetaTextField
          JTextField stevensBetaTextField
          textfields *
        • tempPanel
          JPanel tempPanel
          panels *
        • title
          String title
          dialog title and version *
        • titledBorder
          TitledBorder titledBorder
          titled border for certain components *
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          ViewToolBarBuilder *
        • toolbarPanel
          JPanel toolbarPanel
          panels *
        • truncMultPanel
          JPanel truncMultPanel
          panels *
        • truncMultRadioGroup
          ButtonGroup truncMultRadioGroup
          radio group for truncate/multiply *
        • truncRadio
          JRadioButton truncRadio
          radio buttons for truncate/multiply *
        • tSlice
          int tSlice
          Image time sequence number of image that is displayed. Zero indexed based.
        • type
          String type
          type of color wheel ABSVAL, NOSYMM, ROTATIONALSYMM, MIRRORSYMM *
        • units
          int[] units
          Storage of the resolution units of measure. For example, mm, cm, inches ...
        • unMagButton
          JButton unMagButton
          buttons *
        • widthResFactor
          float widthResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • zoom
          float zoom
          current zoom for result image *
        • zoomOneButton
          JButton zoomOneButton
          buttons *
        • zSlice
          int zSlice
          current z slice *

    • Class gov.nih.mipav.view.dialogs.JDialog3DMosaicTo4DSlices

      class JDialog3DMosaicTo4DSlices extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialog4DImageCalculator

      class JDialog4DImageCalculator extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogACPC

      class JDialogACPC extends JDialogBase implements Serializable

      • Serialized Fields

        • ACPCGroup
          ButtonGroup ACPCGroup
        • ACPCImage
          ModelImage ACPCImage
        • anotherMidSagPt
          WildMagic.LibFoundation.Mathematics.Vector3f anotherMidSagPt
        • anotherPt
          JRadioButton anotherPt
        • applyACPCButton
          JButton applyACPCButton
        • cancelACPCButton
          JButton cancelACPCButton
        • clearACPCButton
          JButton clearACPCButton
        • comboBoxOrientX
          JComboBox comboBoxOrientX
        • comboBoxOrientY
          JComboBox comboBoxOrientY
        • comboBoxOrientZ
          JComboBox comboBoxOrientZ
        • firstMidSagPt
          WildMagic.LibFoundation.Mathematics.Vector3f firstMidSagPt
        • firstPt
          JRadioButton firstPt
        • frame
          ViewJFrameTriImage frame
        • haveAnotherPt
          boolean haveAnotherPt
        • haveFirstPt
          boolean haveFirstPt
        • haveInferiorEdge
          boolean haveInferiorEdge
        • havePosteriorMargin
          boolean havePosteriorMargin
        • haveSuperiorEdge
          boolean haveSuperiorEdge
        • image
          ModelImage image
        • inferiorEdge
          JRadioButton inferiorEdge
        • inferiorEdgePt
          WildMagic.LibFoundation.Mathematics.Vector3f inferiorEdgePt
        • interpolation
          int interpolation
        • orient
          int[] orient
        • posteriorMargin
          JRadioButton posteriorMargin
        • posteriorMarginPt
          WildMagic.LibFoundation.Mathematics.Vector3f posteriorMarginPt
        • setACPCButton
          JButton setACPCButton
        • setOrientationButton
          JButton setOrientationButton
        • superiorEdge
          JRadioButton superiorEdge
        • superiorEdgePt
          WildMagic.LibFoundation.Mathematics.Vector3f superiorEdgePt
        • textVoxelLength
          JTextField textVoxelLength
        • transform
          TalairachTransformInfo transform
        • useIncorrectAcpcXDim
          boolean useIncorrectAcpcXDim
          Flag used to force acpc x dim to old (incorrect) value of 192 instead of fixed value calculation (which results in x dim of 191).
        • voxelLength
          float voxelLength

    • Class gov.nih.mipav.view.dialogs.JDialogActiveContoursWithoutEdges

      class JDialogActiveContoursWithoutEdges extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogAdaptiveKuwaharaFilter

      class JDialogAdaptiveKuwaharaFilter extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogAddMargins

      class JDialogAddMargins extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8624253753510650511L

      • Serialized Fields

        • backInput
          JTextField backInput
          DOCUMENT ME!
        • blueValue
          double blueValue
          DOCUMENT ME!
        • bottomInput
          JTextField bottomInput
          DOCUMENT ME!
        • colorFactor
          int colorFactor
          DOCUMENT ME!
        • defaultBlueInput
          JTextField defaultBlueInput
          DOCUMENT ME!
        • defaultGreenInput
          JTextField defaultGreenInput
          DOCUMENT ME!
        • defaultImaginaryInput
          JTextField defaultImaginaryInput
        • defaultRealInput
          JTextField defaultRealInput
        • defaultRedInput
          JTextField defaultRedInput
          DOCUMENT ME!
        • defaultValue
          double defaultValue
          DOCUMENT ME!
        • defaultValueInput
          JTextField defaultValueInput
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • frontInput
          JTextField frontInput
          DOCUMENT ME!
        • greenValue
          double greenValue
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageMarginsAlgo
          AlgorithmAddMargins imageMarginsAlgo
          DOCUMENT ME!
        • imaginaryValue
          double imaginaryValue
        • leftSideInput
          JTextField leftSideInput
          DOCUMENT ME!
        • marginX
          int[] marginX
          DOCUMENT ME!
        • marginY
          int[] marginY
        • marginZ
          int[] marginZ
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • realValue
          double realValue
        • redValue
          double redValue
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rightSideInput
          JTextField rightSideInput
          DOCUMENT ME!
        • topInput
          JTextField topInput
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAGCIE

      class JDialogAGCIE extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogAGVF

      class JDialogAGVF extends JDialogBase implements Serializable
      serialVersionUID:
      -3328779751424483654L

      • Serialized Fields

        • agvfAlgo
          AlgorithmAGVF agvfAlgo
          DOCUMENT ME!
        • boundaryIterations
          int boundaryIterations
          DOCUMENT ME!
        • checkboxDisplay
          JCheckBox checkboxDisplay
          DOCUMENT ME!
        • dilation
          float dilation
          default dilation:.
        • do25D
          boolean do25D
          DOCUMENT ME!
        • do25DCheckBox
          JCheckBox do25DCheckBox
          DOCUMENT ME!
        • doCellTracking
          boolean doCellTracking
          When true, do a Cell-tracking version of Active GVF Contours:.
        • doCellTrackingCheckBox
          JCheckBox doCellTrackingCheckBox
          Checkbox to turn cell-tracking on/off:.
        • doDilate
          boolean doDilate
          When true, dilate the cell radius before finding the next contour:.
        • doDilateCheckBox
          JCheckBox doDilateCheckBox
          Checkbox to turn cell-tracking on/off:.
        • groupNum
          int groupNum
          DOCUMENT ME!
        • gvfIterations
          int gvfIterations
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • kValue
          float kValue
          DOCUMENT ME!
        • labelDilation
          JLabel labelDilation
          user-interface for setting the cell-radius dilation (multiple of cell expected radius).
        • labelGaussZ
          JLabel labelGaussZ
          DOCUMENT ME!
        • labelRadius
          JLabel labelRadius
          user-interface for setting the estimated cell-radius (pixels).
        • labelResampling
          JLabel labelResampling
          user-interface for setting the uniform-resampling constraint contribution:.
        • labelShape
          JLabel labelShape
          user-interface for setting the shape constraint contribution:.
        • labelSize
          JLabel labelSize
          user-interface for setting the size constraint contribution:.
        • labelVelocity
          JLabel labelVelocity
          user-interface for setting the initial cell velocity:.
        • propagate
          JRadioButton propagate
          DOCUMENT ME!
        • propagationFlag
          boolean propagationFlag
          DOCUMENT ME!
        • radiusConstraint
          float radiusConstraint
          Default cell radius (pixels).
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • resamplingConstraint
          float resamplingConstraint
          default sampling constraint contribution:.
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • scaleZ
          float scaleZ
          DOCUMENT ME!
        • shapeConstraint
          float shapeConstraint
          default shape constraint contribution:.
        • sigmas
          float[] sigmas
          DOCUMENT ME!
        • singleSlice
          JRadioButton singleSlice
          DOCUMENT ME!
        • sizeConstraint
          float sizeConstraint
          default size constraint contribution:.
        • smoothness
          float smoothness
          DOCUMENT ME!
        • srcVOI
          VOI srcVOI
          DOCUMENT ME!
        • textBoundaryIterations
          JTextField textBoundaryIterations
          DOCUMENT ME!
        • textDilation
          JTextField textDilation
          DOCUMENT ME!
        • textDx
          JTextField textDx
          DOCUMENT ME!
        • textDy
          JTextField textDy
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textGaussZ
          JTextField textGaussZ
          DOCUMENT ME!
        • textGVFIterations
          JTextField textGVFIterations
          DOCUMENT ME!
        • textK
          JTextField textK
          DOCUMENT ME!
        • textRadius
          JTextField textRadius
          DOCUMENT ME!
        • textResampling
          JTextField textResampling
          DOCUMENT ME!
        • textShape
          JTextField textShape
          DOCUMENT ME!
        • textSize
          JTextField textSize
          DOCUMENT ME!
        • textSmoothness
          JTextField textSmoothness
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • velocityDx
          float velocityDx
          default initial velocity (dx):.
        • velocityDy
          float velocityDy
          default initial velocity (dx):.
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAHE

      class JDialogAHE extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -6408786765504411315L

      • Serialized Fields

        • aheAlgo
          AlgorithmAHE aheAlgo
          DOCUMENT ME!
        • blueBox
          JCheckBox blueBox
        • CIELabButton
          JRadioButton CIELabButton
        • clamp
          boolean clamp
          DOCUMENT ME!
        • clampImage
          JCheckBox clampImage
          DOCUMENT ME!
        • clampingValue
          JTextField clampingValue
          DOCUMENT ME!
        • clampValue
          int clampValue
          DOCUMENT ME!
        • clampValueLabel
          JLabel clampValueLabel
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
        • comboBoxHeightDiv
          JComboBox comboBoxHeightDiv
          DOCUMENT ME!
        • comboBoxWidthDiv
          JComboBox comboBoxWidthDiv
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          or if the source image is to be replaced.
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • greenBox
          JCheckBox greenBox
        • heightDivisions
          int heightDivisions
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • redBox
          JCheckBox redBox
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • RGBButton
          JRadioButton RGBButton
        • titles
          String[] titles
          DOCUMENT ME!
        • useBlue
          boolean useBlue
        • useCIELab
          boolean useCIELab
        • useGreen
          boolean useGreen
        • useRed
          boolean useRed
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • widthDivisions
          int widthDivisions
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAHElocal

      class JDialogAHElocal extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -6607139120847474768L

      • Serialized Fields

        • aheAlgo
          AlgorithmAHElocal aheAlgo
          DOCUMENT ME!
        • blueBox
          JCheckBox blueBox
        • CIELabButton
          JRadioButton CIELabButton
        • clamp
          boolean clamp
          DOCUMENT ME!
        • clampCheckBox
          JCheckBox clampCheckBox
          DOCUMENT ME!
        • clampLabel
          JLabel clampLabel
          DOCUMENT ME!
        • clampValue
          int clampValue
          DOCUMENT ME!
        • clampValueText
          JTextField clampValueText
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
        • colorPanel
          JPanelColorChannels colorPanel
          DOCUMENT ME!
        • comboBoxKernelShape
          JComboBox comboBoxKernelShape
          DOCUMENT ME!
        • comboBoxKernelSize
          JComboBox comboBoxKernelSize
          DOCUMENT ME!
        • comboBoxScaleMax
          JComboBox comboBoxScaleMax
          DOCUMENT ME!
        • greenBox
          JCheckBox greenBox
        • image
          ModelImage image
          DOCUMENT ME!
        • kernelShape
          int kernelShape
          DOCUMENT ME!
        • kernelSize
          int kernelSize
          DOCUMENT ME!
        • Lmax
          float[] Lmax
        • Lmin
          float[] Lmin
        • minThresholdLabel
          JLabel minThresholdLabel
          DOCUMENT ME!
        • minThresholdText
          JTextField minThresholdText
          DOCUMENT ME!
        • minThresholdValue
          float minThresholdValue
          DOCUMENT ME!
        • minThresholdValueL
          float minThresholdValueL
        • minThresholdValueRGB
          float minThresholdValueRGB
        • outputPanel
          JPanelAlgorithmOutputOptions outputPanel
          DOCUMENT ME!
        • redBox
          JCheckBox redBox
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • RGBButton
          JRadioButton RGBButton
        • scaleMaxValue
          int scaleMaxValue
          DOCUMENT ME!
        • threshold
          boolean threshold
          DOCUMENT ME!
        • thresholdCheckBox
          JCheckBox thresholdCheckBox
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • useBlue
          boolean useBlue
        • useCIELab
          boolean useCIELab
        • useGreen
          boolean useGreen
        • useRed
          boolean useRed
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAINDANE

      class JDialogAINDANE extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogAnalyzeNIFTIChoice

      class JDialogAnalyzeNIFTIChoice extends JDialogBase implements Serializable
      serialVersionUID:
      4588130080855618027L

      • Serialized Fields

        • analyzeFile
          JRadioButton analyzeFile
          Radio button to indicate that an analyze img file should be written out.
        • comboBoxSaveMethod
          JComboBox comboBoxSaveMethod
          Whether to save as selected by dialog or always as analyze, interfile, or nifti.
        • interfileFile
          JRadioButton interfileFile
          Radio button to indicate that an Interfile img file should be written out.
        • niftiFile
          JRadioButton niftiFile
          Radio button to indicate that a nifti img file should be written out.
        • okayPressed
          boolean okayPressed
          Whether the window was closed through the user clicking the OK button (and not just killing the dialog).
        • zeroCheckBox
          JCheckBox zeroCheckBox
          Checkbox to zero funused fields at 112, 116, and 120. Default is not selected.

    • Class gov.nih.mipav.view.dialogs.JDialogAnimate

      class JDialogAnimate extends JDialogBase implements Serializable
      serialVersionUID:
      3763989468823480229L

      • Serialized Fields

        • algoTrans
          AlgorithmTransform algoTrans
          DOCUMENT ME!
        • algoTransB
          AlgorithmTransform algoTransB
          DOCUMENT ME!
        • borderB
          JButton borderB
          false if column radio button selected.
        • borderCol
          Color borderCol
          DOCUMENT ME!
        • colorChooser
          ViewJColorChooser colorChooser
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • controlFrame
          ViewJFrameBase controlFrame
          DOCUMENT ME!
        • DIM
          int DIM
          DOCUMENT ME!
        • frameAnimate
          ViewJFrameAnimate frameAnimate
          DOCUMENT ME!
        • frameBorderCheckBox
          JCheckBox frameBorderCheckBox
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • imageB
          ModelImage imageB
          DOCUMENT ME!
        • isVisible
          boolean isVisible
          Is dialog visible or not.
        • LUTa
          ModelLUT LUTa
          DOCUMENT ME!
        • LUTb
          ModelLUT LUTb
          DOCUMENT ME!
        • radioColumn
          JRadioButton radioColumn
          DOCUMENT ME!
        • radioRow
          JRadioButton radioRow
          DOCUMENT ME!
        • rcText
          JTextField rcText
          DOCUMENT ME!
        • resultImageA
          ModelImage resultImageA
          DOCUMENT ME!
        • resultImageB
          ModelImage resultImageB
          DOCUMENT ME!
        • RGBTA
          ModelRGB RGBTA
          DOCUMENT ME!
        • RGBTB
          ModelRGB RGBTB
          DOCUMENT ME!
        • rowBFlag
          boolean rowBFlag
          each z slice in 4D images.
        • scaleText
          JTextField scaleText
          DOCUMENT ME!
        • showFrameBorder
          boolean showFrameBorder
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAnisotropicDiffusion

      class JDialogAnisotropicDiffusion extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7624088316240843823L

    • Class gov.nih.mipav.view.dialogs.JDialogAnnotation

      class JDialogAnnotation extends JDialogBase implements Serializable
      serialVersionUID:
      2171038314100102783L

      • Serialized Fields

        • activeImage
          ModelImage activeImage
          The image that contains the VOI text.
        • backgroundColorButton
          JButton backgroundColorButton
          button to bring up the background color chooser.
        • boldBox
          JCheckBox boldBox
          checkbox for bold style.
        • buttonPanel
          JPanel buttonPanel
          Panel to contain the okay/cancel/help buttons.
        • colorButton
          JButton colorButton
          button to bring up color chooser.
        • colorChooser
          ViewJColorChooser colorChooser
          color chooser to select text color.
        • element
          int element
          the VOIText element in the VOI to modify
        • fontDescriptors
          int fontDescriptors
          descriptors for font (BOLD, PLAIN, ITALIC).
        • fontName
          String fontName
          name/style of the font.
        • fontSize
          int fontSize
          size of font (int).
        • fontSizeField
          JTextField fontSizeField
          textfield for font size (int only).
        • fontTypeBox
          JComboBox fontTypeBox
          combobox to hold the names of all available fonts.
        • isBackground
          boolean isBackground
          toggle between background and text color changing.
        • isRegistered
          boolean isRegistered
          whether this is an existing or new VOIText (isRegistered = existing).
        • italicBox
          JCheckBox italicBox
          checkbox for italic style.
        • nameField
          JTextField nameField
          NameField that will contain the string to be displayed.
        • noteField
          JTextArea noteField
          NoteField for providing a note about this marker. Note only displayed when clicked.
        • textEditable
          boolean textEditable
        • textVOI
          VOI textVOI
          the VOI that contains the VOIText.
        • useMarkerBox
          JCheckBox useMarkerBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAnnotation.UpdateTextAction

      class UpdateTextAction extends AbstractAction implements Serializable
      serialVersionUID:
      -7210907002611412247L

    • Class gov.nih.mipav.view.dialogs.JDialogAnonymizeDirectory

      class JDialogAnonymizeDirectory extends JDialogBase implements Serializable
      serialVersionUID:
      -6606891655523582196L

      • Serialized Fields

        • actOnPath
          TreePath[] actOnPath
          for the files selected ...
        • anonymizer
          Thread anonymizer
          Access to the running thread which is anonymising directories.
        • changeFilenameBox
          JCheckBox changeFilenameBox
          DOCUMENT ME!
        • checkBoxPanel
          JPanelAnonymizeImage checkBoxPanel
          DOCUMENT ME!
        • directoryTree
          JTree directoryTree
          Actual things we can see...
        • everything
          JTabbedPane everything
          Onscreen objects.
        • filePanel
          JPanel filePanel
          Logical construct to reuild a source tree...
        • genericImageName
          String genericImageName
          Used as part of the image name; used in all processed image-sets.
        • grouping
          ButtonGroup grouping
          DOCUMENT ME!
        • imageDestBrowse
          JButton imageDestBrowse
          DOCUMENT ME!
        • imageDestDirectory
          File imageDestDirectory
          private File srcDirectory; // Defined by the.
        • imageDestDirText
          JTextField imageDestDirText
          DOCUMENT ME!
        • imageNameText
          JTextField imageNameText
          DOCUMENT ME!
        • keyLog
          String keyLog
          Translation key, stored in "patient.key.doc".
        • logPane
          JTextArea logPane
          holds output log; updated as processed.
        • noisyProcess
          boolean noisyProcess
          Noisy means notifying the user of stupid errors.
        • noRandButton
          JRadioButton noRandButton
          DOCUMENT ME!
        • outputLog
          String outputLog
          String to hold all file checks, changes and ignores.
        • privateTagsPanel
          JPanelAnonymizePrivateTags privateTagsPanel
        • publicTagsPanel
          JPanelAnonymizePublicTags publicTagsPanel
        • rand
          Random rand
          To generate wierd, unrecoverable names for anon images.
        • randChildButton
          JRadioButton randChildButton
          DOCUMENT ME!
        • randTopButton
          JRadioButton randTopButton
          DOCUMENT ME!
        • recursiveCheckBox
          JCheckBox recursiveCheckBox
          private JButton srcBrowse;.
        • removeBox
          JCheckBox removeBox
        • selectedList
          JTextArea selectedList
          All directory-tree selected directories are listed for user-consumption in this whitespace.
        • sequenceStart
          int sequenceStart
          Used as part of the image name; represents beginning of sequence for all processed image sets.
        • sequenceText
          JTextField sequenceText
          DOCUMENT ME!
        • sourcePanel
          JPanel sourcePanel
          DOCUMENT ME!
        • stopButton
          JButton stopButton
          stops the thread from continuing its processing. on same panel as OK and Cancel.
        • toplevelOnly
          int toplevelOnly
          DOCUMENT ME!
        • xlatDestBrowse
          JButton xlatDestBrowse
          DOCUMENT ME!
        • xlatDestDirectory
          File xlatDestDirectory
          DOCUMENT ME!
        • xlatDestDirText
          JTextField xlatDestDirText
          DOCUMENT ME!
        • xlatDestinationUsage
          int xlatDestinationUsage
          Defines options for WRITE, OVERWRITE, APPEND for the xlat file.

    • Class gov.nih.mipav.view.dialogs.JDialogAnonymizeImage

      class JDialogAnonymizeImage extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5845185607194185354L

    • Class gov.nih.mipav.view.dialogs.JDialogAnonymizePresets

      class JDialogAnonymizePresets extends JDialogBase implements Serializable
      serialVersionUID:
      1564864947768799239L

    • Class gov.nih.mipav.view.dialogs.JDialogAntigradient2

      class JDialogAntigradient2 extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • antigradient2Algo
          AlgorithmAntigradient2 antigradient2Algo
          DOCUMENT ME!
        • entireImage
          boolean entireImage
        • image
          ModelImage image
          DOCUMENT ME!
        • iters
          int iters
          DOCUMENT ME!
        • labelDestinationMean
          JLabel labelDestinationMean
          DOCUMENT ME!
        • mean
          double mean
          DOCUMENT ME!
        • radioEntireImage
          JRadioButton radioEntireImage
        • radioVOIRegion
          JRadioButton radioVOIRegion
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textDestinationMean
          JTextField textDestinationMean
          DOCUMENT ME!
        • textNIter
          JTextField textNIter
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAnyTwoImagesSNR

      class JDialogAnyTwoImagesSNR extends JDialogBase implements Serializable

      • Serialized Fields

        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • cost
          int cost
          DOCUMENT ME!
        • createRegCheckBox
          JCheckBox createRegCheckBox
          DOCUMENT ME!
        • createRegImage
          boolean createRegImage
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image2
          ModelImage image2
          DOCUMENT ME!
        • imageComboBox
          JComboBox imageComboBox
          DOCUMENT ME!
        • labelCost
          JLabel labelCost
          DOCUMENT ME!
        • regCheckBox
          JCheckBox regCheckBox
          DOCUMENT ME!
        • register
          boolean register
          DOCUMENT ME!
        • scale
          boolean scale
        • scaleCheckBox
          JCheckBox scaleCheckBox
        • snrAlgo
          AlgorithmAnyTwoImagesSNR snrAlgo
          DOCUMENT ME!
        • UI
          ViewUserInterface UI

    • Class gov.nih.mipav.view.dialogs.JDialogAutoCorrelation

      class JDialogAutoCorrelation extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      5909303016264063087L

      • Serialized Fields

        • algoAutoCorrelation
          AlgorithmAutoCorrelation algoAutoCorrelation
          DOCUMENT ME!
        • haveBlue
          boolean haveBlue
          DOCUMENT ME!
        • haveGreen
          boolean haveGreen
          DOCUMENT ME!
        • haveRed
          boolean haveRed
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • maxB
          double maxB
          DOCUMENT ME!
        • maxG
          double maxG
          DOCUMENT ME!
        • maxR
          double maxR
          DOCUMENT ME!
        • minB
          double minB
          DOCUMENT ME!
        • minG
          double minG
          DOCUMENT ME!
        • minR
          double minR
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • resultImageB
          ModelImage resultImageB
          DOCUMENT ME!
        • resultImageG
          ModelImage resultImageG
          DOCUMENT ME!
        • resultImageR
          ModelImage resultImageR
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAutoCovariance

      class JDialogAutoCovariance extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      5044633994224797404L

      • Serialized Fields

        • algoAutoCovariance
          AlgorithmAutoCovariance algoAutoCovariance
          DOCUMENT ME!
        • haveBlue
          boolean haveBlue
          DOCUMENT ME!
        • haveGreen
          boolean haveGreen
          DOCUMENT ME!
        • haveRed
          boolean haveRed
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • maxB
          double maxB
          DOCUMENT ME!
        • maxG
          double maxG
          DOCUMENT ME!
        • maxR
          double maxR
          DOCUMENT ME!
        • minB
          double minB
          DOCUMENT ME!
        • minG
          double minG
          DOCUMENT ME!
        • minR
          double minR
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • resultImageB
          ModelImage resultImageB
          DOCUMENT ME!
        • resultImageG
          ModelImage resultImageG
          DOCUMENT ME!
        • resultImageR
          ModelImage resultImageR
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogAutoSeedWatershed

      class JDialogAutoSeedWatershed extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogAVIChoice

      class JDialogAVIChoice extends JDialogBase implements Serializable
      serialVersionUID:
      4858762290060675316L

      • Serialized Fields

        • compressionBox
          JComboBox compressionBox
          Combo box to select compression.
        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • operating_system
          int operating_system
          DOCUMENT ME!
        • qualityField
          JTextField qualityField
          Text Field for M-JPEG quality.

    • Class gov.nih.mipav.view.dialogs.JDialogBarrelDistortion

      class JDialogBarrelDistortion extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogBase

      class JDialogBase extends JDialog implements Serializable
      serialVersionUID:
      -6802105487936807310L

      • Serialized Fields

        • applyButton
          JButton applyButton
          Apply button is used to apply the setting of the dialog.
        • bar
          JMenuBar bar
          JMenuBar for loading/saving defaults
        • cancelButton
          JButton cancelButton
          Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • cancelFlag
          boolean cancelFlag
          Flag indicating if the dialog had been cancelled or not.
        • closeButton
          JButton closeButton
          Close button is used to close the dialog.
        • helpButton
          JButton helpButton
          Help button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • mainDialogPanel
          JPanel mainDialogPanel
          The main panel of the dialog. To be filled by inheriting classes. Defaults to BorderLayout since that's what the contentPane defaults to (makes it easier to change over to using mainDialogPanel without messing up the layout).
        • OKButton
          JButton OKButton
          OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • parentFrame
          Frame parentFrame
          Parent frame of this dialog, usually of type ViewJFrameImage.
        • profiles
          ArrayList<String> profiles
          List of existing default profiles for this dialog
        • progressBar
          ViewJProgressBar progressBar
          Progress bar that will listen to a dialog's algorithm (and reflect current progress)
        • runInSeparateThread
          boolean runInSeparateThread
          Flag indicating if the algorithm should run in a separate thread. Default is true.
        • runningScriptFlag
          boolean runningScriptFlag
          Whether we are using this dialog as part of a script.
        • runQuiet
          boolean runQuiet
          Whether algorithm is running in quiet mode (such as part of a script, in headless environment, within other algorithm )
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • voiManager
          VOIManagerInterface voiManager

    • Class gov.nih.mipav.view.dialogs.JDialogBase.CancelAction

      class CancelAction extends AbstractAction implements Serializable
      serialVersionUID:
      8763437075181255552L

    • Class gov.nih.mipav.view.dialogs.JDialogBase.HelpAction

      class HelpAction extends AbstractAction implements Serializable
      serialVersionUID:
      -1362974760098666480L

    • Class gov.nih.mipav.view.dialogs.JDialogBase.OKAction

      class OKAction extends AbstractAction implements Serializable
      serialVersionUID:
      -7409235372458546982L

    • Class gov.nih.mipav.view.dialogs.JDialogBGAndFGDistanceMap

      class JDialogBGAndFGDistanceMap extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogBGDistanceMap

      class JDialogBGDistanceMap extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8286579547782268746L

    • Class gov.nih.mipav.view.dialogs.JDialogBilateralFilter

      class JDialogBilateralFilter extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • bilateralFilterAlgo
          AlgorithmBilateralFilter bilateralFilterAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          Source image.
        • image25D
          boolean image25D
          Flag indicating if slices should be blurred independently.
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • intensityFraction
          float intensityFraction
        • intensityLabel
          JLabel intensityLabel
        • intensityPanel
          JPanel intensityPanel
        • intensityText
          JTextField intensityText
        • outputOptionsPanel
          JPanelAlgorithmOutputOptions outputOptionsPanel
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          Result image.
        • sigmaPanel
          JPanelSigmas sigmaPanel
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • useProgressBar
          boolean useProgressBar
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogBiorthogonalWavelets

      class JDialogBiorthogonalWavelets extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • bwAlgo
          BiorthogonalWavelets bwAlgo
        • CDF_type
          int CDF_type
          Use serialVersionUID for interoperability.
        • CDFButton
          JRadioButton CDFButton
        • compressedTransformImage
          ModelImage compressedTransformImage
        • compressionFactor
          double compressionFactor
        • compressionText
          JTextField compressionText
        • convolution_method
          int convolution_method
        • convolutionButton
          JRadioButton convolutionButton
        • display
          boolean display
        • displayCheckBox
          JCheckBox displayCheckBox
        • iterations
          int iterations
        • iterationsText
          JTextField iterationsText
        • len
          int len
        • lent
          int lent
        • lenText
          JTextField lenText
        • lentText
          JTextField lentText
        • method
          int method
        • methodGroup
          ButtonGroup methodGroup
        • reconstructedImage
          ModelImage reconstructedImage
        • spline_type
          int spline_type
        • splineButton
          JRadioButton splineButton
        • srcImage
          ModelImage srcImage
        • transformImage
          ModelImage transformImage
        • type
          int type
        • typeGroup
          ButtonGroup typeGroup
        • waveletMatrix_method
          int waveletMatrix_method
        • waveletMatrixButton
          JRadioButton waveletMatrixButton

    • Class gov.nih.mipav.view.dialogs.JDialogBlankImage

      class JDialogBlankImage extends JDialogBase implements Serializable
      serialVersionUID:
      8301756369819912860L

      • Serialized Fields

        • dataType
          ModelStorageBase.DataType dataType
          The ModelStorageBase.DataType of the blank image.
        • group1
          ButtonGroup group1
          The composed group of radio buttons.
        • image
          ModelImage image
          The blank image to be created.
        • radioTypes
          JRadioButton[] radioTypes
          The Radio buttons for selecting the new data type of the image

    • Class gov.nih.mipav.view.dialogs.JDialogBM3D

      class JDialogBM3D extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • bm3dAlgo
          BM3D bm3dAlgo
        • checkBoxHardSDWeighting
          JCheckBox checkBoxHardSDWeighting
        • checkBoxWienerSDWeighting
          JCheckBox checkBoxWienerSDWeighting
        • destImage
          ModelImage[] destImage
        • estimateNoiseCheckBox
          JCheckBox estimateNoiseCheckBox
        • estimateNoiseStandardDeviation
          boolean estimateNoiseStandardDeviation
        • filterPanel
          JPanel filterPanel
        • hardBIORButton
          JRadioButton hardBIORButton
        • hardDCTButton
          JRadioButton hardDCTButton
        • hardTransformGroup
          ButtonGroup hardTransformGroup
        • image
          ModelImage image
          Use serialVersionUID for interoperability.
        • labelHardCoefficient
          JLabel labelHardCoefficient
        • labelHardSearchSize
          JLabel labelHardSearchSize
        • labelHardSimilar
          JLabel labelHardSimilar
        • labelHardStep
          JLabel labelHardStep
        • labelHardTransform
          JLabel labelHardTransform
        • labelSigma
          JLabel labelSigma
        • labelWienerSearchSize
          JLabel labelWienerSearchSize
        • labelWienerSimilar
          JLabel labelWienerSimilar
        • labelWienerStep
          JLabel labelWienerStep
        • labelWienerTransform
          JLabel labelWienerTransform
        • lambda3D_H
          double lambda3D_H
        • n_H
          int n_H
        • N_H
          int N_H
        • n_W
          int n_W
        • N_W
          int N_W
        • p_H
          int p_H
        • p_W
          int p_W
        • sigma
          double sigma
        • tau_2D_H
          String tau_2D_H
        • tau_2D_W
          String tau_2D_W
        • textHardCoefficient
          JTextField textHardCoefficient
        • textHardSearchSize
          JTextField textHardSearchSize
        • textHardSimilar
          JTextField textHardSimilar
        • textHardStep
          JTextField textHardStep
        • textSigma
          JTextField textSigma
        • textWienerSearchSize
          JTextField textWienerSearchSize
        • textWienerSimilar
          JTextField textWienerSimilar
        • textWienerStep
          JTextField textWienerStep
        • useSD_H
          boolean useSD_H
        • useSD_W
          boolean useSD_W
        • WienerBIORButton
          JRadioButton WienerBIORButton
        • WienerDCTButton
          JRadioButton WienerDCTButton
        • WienerTransformGroup
          ButtonGroup WienerTransformGroup

    • Class gov.nih.mipav.view.dialogs.JDialogBorderClearing

      class JDialogBorderClearing extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogBottomHat

      class JDialogBottomHat extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogBoundaryAttenuation

      class JDialogBoundaryAttenuation extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7736447447170989384L

      • Serialized Fields

        • attenuationAlgo
          AlgorithmBoundaryAttenuation attenuationAlgo
          The attenuation algorithm.
        • destImage
          ModelImage destImage
          The attenuated image.
        • maxAttenuation
          float maxAttenuation
          The maximum amount of attenuation to apply to the image (0 = no attenuation, 1 = full attenuation).
        • maxAttenuationTF
          JTextField maxAttenuationTF
          Maximum attenuation text field.
        • numErosions
          int numErosions
          The number of levels of attenuation to perform (done through morphological erosion).
        • numErosionsTF
          JTextField numErosionsTF
          Number of erosions text field.
        • srcImage
          ModelImage srcImage
          The image to attenuate.
        • userInterface
          ViewUserInterface userInterface
          The MIPAV user interface.

    • Class gov.nih.mipav.view.dialogs.JDialogBoundingVOIs

      class JDialogBoundingVOIs extends JDialogBase implements Serializable

      • Serialized Fields

        • doInner
          boolean doInner
        • doOuter
          boolean doOuter
        • groupNum
          int groupNum
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • innerCurveCheckBox
          JCheckBox innerCurveCheckBox
        • innerDistance
          float innerDistance
        • innerDistanceLabel
          JLabel innerDistanceLabel
        • innerDistanceText
          JTextField innerDistanceText
        • maxDistance
          float maxDistance
        • outerCurveCheckBox
          JCheckBox outerCurveCheckBox
        • outerDistance
          float outerDistance
        • outerDistanceLabel
          JLabel outerDistanceLabel
        • outerDistanceText
          JTextField outerDistanceText
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • sideLabel
          JLabel sideLabel
        • sidePointsForTangent
          int sidePointsForTangent
          Maximum number of points to take from each side of a point on a curve in determining a tangent
        • sideText
          JTextField sideText
        • srcVOI
          VOI srcVOI
          DOCUMENT ME!
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogBoxCount

      class JDialogBoxCount extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogBrainSurfaceExtractor

      class JDialogBrainSurfaceExtractor extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4594568089644651497L

      • Serialized Fields

        • closeKernelSize
          float closeKernelSize
          Size of the kernel used in the closing operations.
        • closeKernelSizeTF
          JTextField closeKernelSizeTF
          Text field used to enter the number of closings to perform.
        • edgeKernelSize
          float edgeKernelSize
          Edge detection kernel size (.6 in Shattuck paper).
        • edgeKernelSizeTF
          JTextField edgeKernelSizeTF
          Text field used to enter the edge detection kernel size.
        • erosion25D
          boolean erosion25D
          Whether to process the slices of the 3D image separately while performing the erosion / dilation.
        • erosion25DCB
          JCheckBox erosion25DCB
          Check box for indicating whether erosion / dilation should process slices independently.
        • erosionIterations
          int erosionIterations
          Number of erosion / dilation operations to perform (2 in Shattuck paper).
        • erosionIterationsTF
          JTextField erosionIterationsTF
          Text field used to enter the number of erosions / dilations.
        • extractBrainAlgo
          AlgorithmBrainSurfaceExtractor extractBrainAlgo
          Reference to the algorithm we will be running.
        • extractPaint
          boolean extractPaint
          Whether to extract the brain to paint instead of removing image data.
        • extractPaintCheckBox
          JCheckBox extractPaintCheckBox
          Checkbox to extract the brain to paint instead of removing image data.
        • fillHoles
          boolean fillHoles
          Whether to fill in all internal holes in the extracted brain.
        • fillHolesCB
          JCheckBox fillHolesCB
          Checkbox for indicating whether to close all of the interior holes in the extracted brain.
        • filterGaussianStdDev
          float filterGaussianStdDev
          Standard deviation of the filter's gaussian kernel.
        • filterGaussianStdDevTF
          JTextField filterGaussianStdDevTF
          Text field used to enter the standard deviation of the filter's gaussian kernel.
        • filterIterations
          int filterIterations
          Number of filter iterations.
        • filterIterationsTF
          JTextField filterIterationsTF
          Text field used to enter the number of filter iterations.
        • image
          ModelImage image
          The source image.
        • imageCopy
          ModelImage imageCopy
          A copy of the source image to run the algorithm on.
        • imgName
          String imgName
          The original image name.
        • resultImage
          ModelImage resultImage
          The result image.
        • showIntermediateImages
          boolean showIntermediateImages
          Whether to show images from intermediate steps of the BSE algorithm.
        • showIntermediateImagesCB
          JCheckBox showIntermediateImagesCB
          Checkbox to show images which can help in paramater tweaking.
        • userInterface
          ViewUserInterface userInterface
          Reference to the main user interface.
        • useSeparable
          boolean useSeparable
          Whether to use a separable convolver during edge detection.
        • useSeparableCB
          JCheckBox useSeparableCB
          Checkbox to elect to use the separable convolver in the edge detection algorithm.

    • Class gov.nih.mipav.view.dialogs.JDialogBrightness

      class JDialogBrightness extends JDialogBase implements Serializable
      serialVersionUID:
      -1222614304368736757L

    • Class gov.nih.mipav.view.dialogs.JDialogBRISK

      class JDialogBRISK extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • bAlgo
          AlgorithmBRISK bAlgo
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
        • destImage
          ModelImage destImage
          DOCUMENT ME!
        • dMax
          double dMax
        • dMin
          double dMin
        • HammingDistanceThreshold
          int HammingDistanceThreshold
        • image
          ModelImage image
          DOCUMENT ME!
        • imageVOIGroup
          ButtonGroup imageVOIGroup
        • imageVOIPanel
          JPanel imageVOIPanel
        • indexChange
          Vector<Integer> indexChange
        • labelHammingDistanceThreshold
          JLabel labelHammingDistanceThreshold
        • labelOctaves
          JLabel labelOctaves
        • labelThreshold
          JLabel labelThreshold
        • numberList
          Vector<Integer> numberList
        • octaves
          int octaves
        • paramPanel
          JPanel paramPanel
        • patternScale
          double patternScale
        • radiusList
          Vector<Double> radiusList
        • rotationCheckBox
          JCheckBox rotationCheckBox
        • rotationInvariant
          boolean rotationInvariant
        • scaleCheckBox
          JCheckBox scaleCheckBox
        • scaleInvariant
          boolean scaleInvariant
        • textHammingDistanceThreshold
          JTextField textHammingDistanceThreshold
        • textOctaves
          JTextField textOctaves
        • textThreshold
          JTextField textThreshold
        • threshold
          int threshold
        • userInterface
          ViewUserInterface userInterface
        • VOIRegions
          JRadioButton VOIRegions
        • wholeImage
          JRadioButton wholeImage
        • wholeImageFlag
          boolean wholeImageFlag

    • Class gov.nih.mipav.view.dialogs.JDialogBSmooth

      class JDialogBSmooth extends JDialogBase implements Serializable
      serialVersionUID:
      -2582311598077394632L

      • Serialized Fields

        • BSplineButton
          JRadioButton BSplineButton
        • defaultPts
          int defaultPts
          DOCUMENT ME!
        • doEllipticFourierDescription
          boolean doEllipticFourierDescription
        • doMinimumPerimeterPolygon
          boolean doMinimumPerimeterPolygon
        • elementNum
          int elementNum
          DOCUMENT ME!
        • ellipticAlgo
          AlgorithmEllipticFourierDescriptors ellipticAlgo
        • ellipticButton
          JRadioButton ellipticButton
        • groupNum
          int groupNum
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelInterpNPts
          JLabel labelInterpNPts
        • minimumPerimeterPolygonButton
          JRadioButton minimumPerimeterPolygonButton
        • mppAlgo
          AlgorithmMinimumPerimeterPolygon mppAlgo
        • nPoints
          int nPoints
        • nPts
          int nPts
          DOCUMENT ME!
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • smoothAlgo
          AlgorithmBSmooth smoothAlgo
          DOCUMENT ME!
        • smoothGroup
          ButtonGroup smoothGroup
        • textInterpNPts
          JTextField textInterpNPts
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • trim
          boolean trim
          DOCUMENT ME!
        • trimCheckBox
          JCheckBox trimCheckBox
          DOCUMENT ME!
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • voiManager
          VOIManagerInterface voiManager
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogBSnake

      class JDialogBSnake extends JDialogBase implements Serializable
      serialVersionUID:
      6813632326437983422L

      • Serialized Fields

        • boundaryIterations
          int boundaryIterations
          DOCUMENT ME!
        • groupNum
          int groupNum
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelCorrected
          JLabel labelCorrected
          DOCUMENT ME!
        • normFactor
          float normFactor
          DOCUMENT ME!
        • propagate
          JRadioButton propagate
          DOCUMENT ME!
        • propagationType
          int propagationType
          DOCUMENT ME!
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • resolutionCheckbox
          JCheckBox resolutionCheckbox
          difference between x,y resolutions (in plane) and z resolution (between planes).
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • scaleZ
          float scaleZ
          DOCUMENT ME!
        • singleSlice
          JRadioButton singleSlice
          DOCUMENT ME!
        • snakeAlgo
          AlgorithmBSnake snakeAlgo
          DOCUMENT ME!
        • srcVOI
          VOI srcVOI
          DOCUMENT ME!
        • textBoundaryIterations
          JTextField textBoundaryIterations
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textGaussZ
          JTextField textGaussZ
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogBulkImageCalculator

      class JDialogBulkImageCalculator extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • addImageBrowseButton
          JButton addImageBrowseButton
          browse button
        • additionalImagesLabel
          JLabel additionalImagesLabel
          label for browsing for additional images
        • additionalImagesList
          ArrayList<ModelImage> additionalImagesList
          list of any additional images browsed to
        • alg
          AlgorithmImageCalculator alg
          handle to algorithm
        • clipMode
          int clipMode
          clip mode
        • comboBoxOperator
          JComboBox comboBoxOperator
          operator combo box
        • displayLoc
          int displayLoc
          result image in new frame
        • imageA
          ModelImage imageA
          source image.
        • isColor
          boolean isColor
          is color boolean
        • isMultifile
          boolean isMultifile
          boolean isMultifile
        • opType
          int opType
          operation type....for now set to ADD
        • removeSelectedButton
          JButton removeSelectedButton
          remove button
        • removeSelectedImagesLabel
          JLabel removeSelectedImagesLabel
          label for removing selected images
        • resultImage
          ModelImage resultImage
          result image
        • selectedRows
          int[] selectedRows
          indices of selcted rows to remove
        • srcImagesList
          ArrayList<ModelImage> srcImagesList
          list of images to send to algorithm
        • srcImagesTable
          JTable srcImagesTable
          table to display the src image names.
        • srcTableModel
          ViewTableModel srcTableModel
          table model for the srcimages.

    • Class gov.nih.mipav.view.dialogs.JDialogCannyEdgeDetection

      class JDialogCannyEdgeDetection extends JDialogScriptableBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogCaptureScreen

      class JDialogCaptureScreen extends JDialogBase implements Serializable
      serialVersionUID:
      -2364847865242983737L

      • Serialized Fields

        • activeFrame
          ViewJFrameImage activeFrame
          Active frame
        • copy
          boolean copy
          Flag that indicates whether to copy capture to clipboard
        • copyCheck
          JRadioButton copyCheck
          Button for selecting copy to clipboard.
        • currentRectangle
          Rectangle currentRectangle
          The rectangle that will be captured from the screen to save to a file.
        • display
          boolean display
          Flag that indicates whether to put capture in a new frame on screen.
        • displayCheck
          JRadioButton displayCheck
          Button for selecting display in window.
        • fileField
          JTextField fileField
          JTextField for the name of the file being attached
        • fileName
          String fileName
          String to house the user inputed file name
        • imageAttacher
          boolean imageAttacher
          Boolean indicating if JDialogCaptureScreen has been initialized through ReportBugBuilder
        • imagePix
          Image imagePix
          The image selected by the user
        • insert
          boolean insert
          Boolean indicating if the Insert button has been pressed
        • insertButton
          JButton insertButton
          Button for inserting the image into the body of a bug report
        • instructions
          JLabel instructions
          Instructions on how to use screen capture, line 1.
        • instructions2
          JLabel instructions2
          Instructions on how to use screen capture, line 2.
        • instructions3
          JLabel instructions3
          Instructions on how to use screen capture, line 3.
        • mode
          JDialogCaptureScreen.WindowProperties mode
          Mode - region or window
        • myGlassPanes
          JDialogCaptureScreen.MyGlassPane[] myGlassPanes
          Special glass panes for all the valid frames in the GUI so that the user can draw rectangles on top of objects in the GUI.
        • ok
          boolean ok
          Boolean indicating if the OK button has been pressed when JDialogCaptureScreen is launched through the report bug form
        • oldFrames
          JFrame[] oldFrames
          All the valid JFrames in the GUI.
        • oldPanes
          Component[] oldPanes
          Old glass panes to reset to after drawing is done.
        • regionButton
          JRadioButton regionButton
          Button for selecting region mode.
        • save
          boolean save
          Flag that indicates whether to save capture as file.
        • saveCheck
          JRadioButton saveCheck
          Button for selecting save to computer.
        • userInterface
          ViewUserInterface userInterface
          Pointer to the user interface.
        • windowButton
          JRadioButton windowButton
          Button for selecting window mode.

    • Class gov.nih.mipav.view.dialogs.JDialogCaptureScreens

      class JDialogCaptureScreens extends JDialogBase implements Serializable
      serialVersionUID:
      5133757391495903883L

      • Serialized Fields

        • currentRectangle
          Rectangle currentRectangle
          The rectangle that will be captured from the screen to save to a file.
        • currentSlice
          int currentSlice
        • imageFrame
          ViewJFrameImage imageFrame
          The parent image frame.
        • numSlices
          int numSlices
          Number of slices in the image.

    • Class gov.nih.mipav.view.dialogs.JDialogCenterOfMass

      class JDialogCenterOfMass extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • comAlgo
          AlgorithmCenterOfMass comAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelThres2
          JLabel labelThres2
          DOCUMENT ME!
        • max
          float max
          DOCUMENT ME!
        • min
          float min
          DOCUMENT ME!
        • regionFlag
          boolean regionFlag
          or if the source image is to be replaced.
        • textThres1
          JTextField textThres1
          DOCUMENT ME!
        • textThres2
          JTextField textThres2
          DOCUMENT ME!
        • thres1
          float thres1
          DOCUMENT ME!
        • thres2
          float thres2
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCenterOfMass.CheckValueAction

      class CheckValueAction extends AbstractAction implements Serializable
      serialVersionUID:
      -1531686009578681460L

    • Class gov.nih.mipav.view.dialogs.JDialogCenterOfMassRGB

      class JDialogCenterOfMassRGB extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • applyToAllBox
          JCheckBox applyToAllBox
          false = apply algorithm only to VOI regions apply same threshold to all.
        • comAlgoRGB
          AlgorithmCenterOfMassRGB comAlgoRGB
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • maxs
          float[] maxs
          DOCUMENT ME!
        • mins
          float[] mins
          Minimum and maximum values for red/gree/blue.
        • regionFlag
          boolean regionFlag
          or if the source image is to be replaced.
        • textThreshold1
          JTextField[] textThreshold1
          Text fields for lower invalid input: '&' upper thresholds and fill values.
        • textThreshold2
          JTextField[] textThreshold2
          DOCUMENT ME!
        • thresholdB
          float[] thresholdB
          DOCUMENT ME!
        • thresholdG
          float[] thresholdG
          DOCUMENT ME!
        • thresholdLabels1
          JLabel[] thresholdLabels1
          DOCUMENT ME!
        • thresholdLabels2
          JLabel[] thresholdLabels2
          DOCUMENT ME!
        • thresholdR
          float[] thresholdR
          lower [0] and upper [1] thresholds for RGB.
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCentroidThreshold

      class JDialogCentroidThreshold extends JDialogBase implements Serializable
      serialVersionUID:
      5102272946311012581L

      • Serialized Fields

        • centroids
          float[] centroids
          DOCUMENT ME!
        • defaultValueInput
          JTextField[] defaultValueInput
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • gbl
          GridBagLayout gbl
          DOCUMENT ME!
        • i
          int i
          DOCUMENT ME!
        • imageName
          String imageName
          DOCUMENT ME!
        • maximum
          float maximum
          DOCUMENT ME!
        • minimum
          float minimum
          DOCUMENT ME!
        • nClasses
          int nClasses
          DOCUMENT ME!
        • threshold
          float threshold
          DOCUMENT ME!
        • thresholdValueInput
          JTextField thresholdValueInput
          DOCUMENT ME!
        • tmpStr
          String tmpStr
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogChangeMaskNumber

      class JDialogChangeMaskNumber extends JDialogBase implements Serializable

      • Serialized Fields

        • btArrayList
          ArrayList<Integer> btArrayList
          this is the array list of the texts on the buttons
        • changeButton
          JButton changeButton
          this is the action button to change
        • changeLabel
          JLabel changeLabel
          this is the text in the Dialog
        • color
          Color[] color
          re f to Color array
        • correspButton
          JButton correspButton
          this is a ref to the corresponding button becasue they need to be in sync
        • currentMaskNumberIndex
          int currentMaskNumberIndex
          this represents the current index of the btArrayList
        • image
          ModelImage image
          ref to image
        • intensityLockVector
          Vector<Integer> intensityLockVector
          ref to IntensityLockVector
        • lutB
          ModelLUT lutB
          lutB
        • numberField
          JTextField numberField
          this is the input for the user to enter what number they want to change to
        • srcButton
          JButton srcButton
          this is a ref to the source button so that the text on the button can be changed
        • srcValue
          int srcValue
          src button text number

    • Class gov.nih.mipav.view.dialogs.JDialogCheckerBoard

      class JDialogCheckerBoard extends JDialogBase implements Serializable
      serialVersionUID:
      4180573157937289440L

      • Serialized Fields

        • animateButton
          JButton animateButton
        • animateThread
          Thread animateThread
        • animateTime
          long animateTime
        • animating
          boolean animating
        • bandSpacingCounter
          int bandSpacingCounter
        • cc
          int cc
        • checkerboardApplied
          boolean checkerboardApplied
        • checkerboardTypesCB
          JComboBox checkerboardTypesCB
          DOCUMENT ME!
        • checkerboardTypesLabel
          JLabel checkerboardTypesLabel
        • cleanImageBufferB
          int[] cleanImageBufferB
        • closeButton
          JButton closeButton
          DOCUMENT ME!
        • columnNumber
          int columnNumber
        • compImage
          ViewJComponentEditImage compImage
          DOCUMENT ME!
        • doReg
          boolean doReg
          DOCUMENT ME!
        • isStopped
          boolean isStopped
        • labelColumnNumber
          JLabel labelColumnNumber
          DOCUMENT ME!
        • labelRowNumber
          JLabel labelRowNumber
          DOCUMENT ME!
        • labelTable
          Hashtable<Integer,JLabel> labelTable
          DOCUMENT ME!
        • labelTable2
          Hashtable<Integer,JLabel> labelTable2
          DOCUMENT ME!
        • maxColumn
          int maxColumn
          DOCUMENT ME!
        • maxExtents
          int[] maxExtents
        • maxRow
          int maxRow
          DOCUMENT ME!
        • negativeSpeed
          boolean negativeSpeed
        • pixBufferB
          int[] pixBufferB
        • pressedStart
          int pressedStart
        • regImage
          ViewJComponentRegistration regImage
          DOCUMENT ME!
        • rowNumber
          int rowNumber
        • slider
          JSlider slider
          DOCUMENT ME!
        • slider2
          JSlider slider2
          DOCUMENT ME!
        • speedLabel
          JLabel speedLabel
          DOCUMENT ME!
        • speedLabelTable
          Hashtable<Integer,JLabel> speedLabelTable
          DOCUMENT ME!
        • speedSlider
          JSlider speedSlider
          DOCUMENT ME!
        • textColumnNumber
          JTextField textColumnNumber
          DOCUMENT ME!
        • textRowNumber
          JTextField textRowNumber
          DOCUMENT ME!
        • xMod
          int xMod
        • xSep
          int xSep
        • yMod
          int yMod
        • ySep
          int ySep

    • Class gov.nih.mipav.view.dialogs.JDialogCircleGeneration

      class JDialogCircleGeneration extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • aggregatedButton
          JRadioButton aggregatedButton
        • aggregatedCirclesDifferentSizesButton
          JRadioButton aggregatedCirclesDifferentSizesButton
        • aggregatedEllipseButton
          JRadioButton aggregatedEllipseButton
        • aggregatedEllipseRandomOrientationButton
          JRadioButton aggregatedEllipseRandomOrientationButton
        • aggregatedEllipseRandomOrientationDifferentSizes
          JRadioButton aggregatedEllipseRandomOrientationDifferentSizes
        • cAlgo
          AlgorithmCircleGeneration cAlgo
          DOCUMENT ME!
        • constrainedButton
          JRadioButton constrainedButton
        • extents
          int[] extents
        • highestForbiddenLabel
          JLabel highestForbiddenLabel
        • highestForbiddenNNDistance
          double highestForbiddenNNDistance
        • highestForbiddenText
          JTextField highestForbiddenText
        • highestRegenerationLabel
          JLabel highestRegenerationLabel
        • highestRegenerationNNDistance
          double highestRegenerationNNDistance
        • highestRegenerationText
          JTextField highestRegenerationText
        • initialCirclesLabel
          JLabel initialCirclesLabel
        • initialCirclesText
          JTextField initialCirclesText
        • initialRandomCircles
          int initialRandomCircles
        • lowestForbiddenLabel
          JLabel lowestForbiddenLabel
        • lowestForbiddenNNDistance
          double lowestForbiddenNNDistance
        • lowestForbiddenText
          JTextField lowestForbiddenText
        • maximumDistanceLabel
          JLabel maximumDistanceLabel
        • maximumDistanceText
          JTextField maximumDistanceText
        • maximumNearestNeighborDistance
          double maximumNearestNeighborDistance
        • minimumDistanceLabel
          JLabel minimumDistanceLabel
        • minimumDistanceText
          JTextField minimumDistanceText
        • minimumNearestNeighborDistance
          double minimumNearestNeighborDistance
        • numCircles
          int numCircles
        • numCirclesText
          JTextField numCirclesText
        • pattern
          int pattern
        • patternGroup
          ButtonGroup patternGroup
        • phi
          double phi
        • phiLabel
          JLabel phiLabel
        • phiText
          JTextField phiText
        • radius
          int radius
        • radiusText
          JTextField radiusText
          DOCUMENT ME!
        • randomButton
          JRadioButton randomButton
        • ratioLabel
          JLabel ratioLabel
        • ratioText
          JTextField ratioText
        • regularButton
          JRadioButton regularButton
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • semiMajorAxis
          double semiMajorAxis
        • semiMajorAxisLabel
          JLabel semiMajorAxisLabel
        • semiMajorAxisText
          JTextField semiMajorAxisText
        • semiMinorAxis
          double semiMinorAxis
        • semiMinorAxisLabel
          JLabel semiMinorAxisLabel
        • semiMinorAxisText
          JTextField semiMinorAxisText
        • smallestToLargestAxisRatio
          double smallestToLargestAxisRatio
        • xDim
          int xDim
          DOCUMENT ME!
        • xDimText
          JTextField xDimText
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • yDimText
          JTextField yDimText

    • Class gov.nih.mipav.view.dialogs.JDialogCircleToRectangle

      class JDialogCircleToRectangle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • cAlgo
          AlgorithmCircleToRectangle cAlgo
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • xSource
          double[] xSource
          DOCUMENT ME!
        • xText
          JTextField xText
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • ySource
          double[] ySource
          DOCUMENT ME!
        • yText
          JTextField yText
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCircularSectorToRectangle

      class JDialogCircularSectorToRectangle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • cAlgo
          AlgorithmCircularSectorToRectangle cAlgo
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • xSource
          double[] xSource
          DOCUMENT ME!
        • xText
          JTextField xText
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • ySource
          double[] ySource
          DOCUMENT ME!
        • yText
          JTextField yText
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogClose

      class JDialogClose extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -8489706932459076773L

    • Class gov.nih.mipav.view.dialogs.JDialogCoherenceEnhancingDiffusion

      class JDialogCoherenceEnhancingDiffusion extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      1141466038513737001L

      • Serialized Fields

        • checkBox25D
          JCheckBox checkBox25D
          DOCUMENT ME!
        • coherenceEnhancingDiffusionAlgo
          AlgorithmCoherenceEnhancingDiffusion coherenceEnhancingDiffusionAlgo
          DOCUMENT ME!
        • derivativeScale
          float derivativeScale
          DOCUMENT ME!
        • diffusitivityDenom
          float diffusitivityDenom
          DOCUMENT ME!
        • do25D
          boolean do25D
          DOCUMENT ME!
        • entireImage
          boolean entireImage
          DOCUMENT ME!
        • gaussianScale
          float gaussianScale
          DOCUMENT ME!
        • numIterations
          int numIterations
          DOCUMENT ME!
        • radioEntireImage
          JRadioButton radioEntireImage
          DOCUMENT ME!
        • radioVOIRegion
          JRadioButton radioVOIRegion
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          DOCUMENT ME!
        • textDerivative
          JTextField textDerivative
          DOCUMENT ME!
        • textDiffusitivity
          JTextField textDiffusitivity
          DOCUMENT ME!
        • textGaussian
          JTextField textGaussian
          DOCUMENT ME!
        • textNumberIterations
          JTextField textNumberIterations
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogColocalizationEM

      class JDialogColocalizationEM extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2241466976779150747L

      • Serialized Fields

        • andButton
          JRadioButton andButton
          DOCUMENT ME!
        • bin1
          int bin1
          DOCUMENT ME!
        • bin1Label
          JLabel bin1Label
          DOCUMENT ME!
        • bin1Text
          JTextField bin1Text
          DOCUMENT ME!
        • bin2
          int bin2
          DOCUMENT ME!
        • bin2Label
          JLabel bin2Label
          DOCUMENT ME!
        • bin2Text
          JTextField bin2Text
          DOCUMENT ME!
        • blueCheckBox
          JCheckBox blueCheckBox
          DOCUMENT ME!
        • bottomPad
          int bottomPad
          DOCUMENT ME!
        • buffer
          float[] buffer
          DOCUMENT ME!
        • colocalizationAlgo
          AlgorithmColocalizationEM colocalizationAlgo
          DOCUMENT ME!
        • colorsPresent
          int colorsPresent
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • cost
          int cost
          DOCUMENT ME!
        • doOr
          boolean doOr
          DOCUMENT ME!
        • entireImage
          boolean entireImage
          DOCUMENT ME!
        • firstImage
          ModelImage firstImage
          DOCUMENT ME!
        • gaussianLabel
          JLabel gaussianLabel
          DOCUMENT ME!
        • gaussians
          int gaussians
          DOCUMENT ME!
        • gaussianText
          JTextField gaussianText
          DOCUMENT ME!
        • greenCheckBox
          JCheckBox greenCheckBox
          DOCUMENT ME!
        • imageComboBox
          JComboBox imageComboBox
          DOCUMENT ME!
        • imageLength
          int imageLength
          DOCUMENT ME!
        • iterationLabel
          JLabel iterationLabel
          DOCUMENT ME!
        • iterations
          int iterations
          DOCUMENT ME!
        • iterationText
          JTextField iterationText
          DOCUMENT ME!
        • labelCost
          JLabel labelCost
          DOCUMENT ME!
        • labelImage
          JLabel labelImage
          DOCUMENT ME!
        • leftPad
          int leftPad
          DOCUMENT ME!
        • mask
          BitSet mask
          DOCUMENT ME!
        • maxB
          double maxB
          DOCUMENT ME!
        • maxBV
          double maxBV
          DOCUMENT ME!
        • maxG
          double maxG
          DOCUMENT ME!
        • maxGV
          double maxGV
          DOCUMENT ME!
        • maxR
          double maxR
          DOCUMENT ME!
        • maxRV
          double maxRV
          DOCUMENT ME!
        • maxV
          double maxV
          DOCUMENT ME!
        • minB
          double minB
          DOCUMENT ME!
        • minBV
          double minBV
          DOCUMENT ME!
        • minG
          double minG
          DOCUMENT ME!
        • minGV
          double minGV
          DOCUMENT ME!
        • minR
          double minR
          DOCUMENT ME!
        • minRV
          double minRV
          DOCUMENT ME!
        • minV
          double minV
          DOCUMENT ME!
        • nBoundingVOIs
          int nBoundingVOIs
          DOCUMENT ME!
        • orButton
          JRadioButton orButton
          DOCUMENT ME!
        • possibleInt2Values
          double possibleInt2Values
          DOCUMENT ME!
        • possibleIntValues
          double possibleIntValues
          DOCUMENT ME!
        • redCheckBox
          JCheckBox redCheckBox
          DOCUMENT ME!
        • regCheckBox
          JCheckBox regCheckBox
          DOCUMENT ME!
        • register
          boolean register
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rightPad
          int rightPad
          DOCUMENT ME!
        • secondImage
          ModelImage secondImage
          DOCUMENT ME!
        • secondMaxV
          double secondMaxV
          DOCUMENT ME!
        • secondMinV
          double secondMinV
          DOCUMENT ME!
        • secondName
          String secondName
          DOCUMENT ME!
        • segImage
          ModelImage segImage
          Class segmentation shown.
        • threshold1
          float threshold1
          DOCUMENT ME!
        • threshold1Label
          JLabel threshold1Label
          DOCUMENT ME!
        • threshold1Text
          JTextField threshold1Text
          DOCUMENT ME!
        • threshold2
          float threshold2
          DOCUMENT ME!
        • threshold2Label
          JLabel threshold2Label
          DOCUMENT ME!
        • threshold2Text
          JTextField threshold2Text
          DOCUMENT ME!
        • topPad
          int topPad
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • zDim
          int zDim
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogColocalizationRegression

      class JDialogColocalizationRegression extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      2982353729666791012L

      • Serialized Fields

        • background1
          float background1
          DOCUMENT ME!
        • background2
          float background2
          DOCUMENT ME!
        • bin1
          int bin1
          DOCUMENT ME!
        • bin1Label
          JLabel bin1Label
          DOCUMENT ME!
        • bin1Text
          JTextField bin1Text
          DOCUMENT ME!
        • bin2
          int bin2
          DOCUMENT ME!
        • bin2Label
          JLabel bin2Label
          DOCUMENT ME!
        • bin2Text
          JTextField bin2Text
          DOCUMENT ME!
        • blueCheckBox
          JCheckBox blueCheckBox
          DOCUMENT ME!
        • bottomPad
          int bottomPad
          DOCUMENT ME!
        • buffer
          float[] buffer
          DOCUMENT ME!
        • colocalizationAlgo
          AlgorithmColocalizationRegression colocalizationAlgo
          DOCUMENT ME!
        • colocCheckBox
          JCheckBox colocCheckBox
          DOCUMENT ME!
        • colorsPresent
          int colorsPresent
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • componentImage1
          ViewJComponentEditImage componentImage1
          DOCUMENT ME!
        • componentImage2
          ViewJComponentEditImage componentImage2
          DOCUMENT ME!
        • cost
          int cost
          DOCUMENT ME!
        • doColocWithThresholds
          boolean doColocWithThresholds
          DOCUMENT ME!
        • doSecondIteration
          boolean doSecondIteration
          DOCUMENT ME!
        • doVOISubtraction
          boolean doVOISubtraction
          DOCUMENT ME!
        • entireImage
          boolean entireImage
          DOCUMENT ME!
        • firstImage
          ModelImage firstImage
          DOCUMENT ME!
        • firstName
          String firstName
          DOCUMENT ME!
        • greenCheckBox
          JCheckBox greenCheckBox
          DOCUMENT ME!
        • imageComboBox
          JComboBox imageComboBox
          DOCUMENT ME!
        • imageLength
          int imageLength
          DOCUMENT ME!
        • labelCost
          JLabel labelCost
          DOCUMENT ME!
        • labelImage
          JLabel labelImage
          DOCUMENT ME!
        • leftPad
          int leftPad
          DOCUMENT ME!
        • mask
          BitSet mask
          DOCUMENT ME!
        • maskButton
          JButton maskButton
          DOCUMENT ME!
        • maskFileDir
          String maskFileDir
          DOCUMENT ME!
        • maskFileName
          String maskFileName
          DOCUMENT ME!
        • maskImage
          ModelImage maskImage
          DOCUMENT ME!
        • maskRadio
          JRadioButton maskRadio
          DOCUMENT ME!
        • maskText
          JTextField maskText
          DOCUMENT ME!
        • maxB
          double maxB
          DOCUMENT ME!
        • maxG
          double maxG
          DOCUMENT ME!
        • maxR
          double maxR
          DOCUMENT ME!
        • minB
          double minB
          DOCUMENT ME!
        • minG
          double minG
          DOCUMENT ME!
        • minR
          double minR
          DOCUMENT ME!
        • nBoundingVOIs
          int nBoundingVOIs
          DOCUMENT ME!
        • point1
          float point1
          DOCUMENT ME!
        • point1Label
          JLabel point1Label
          DOCUMENT ME!
        • point1Text
          JTextField point1Text
          DOCUMENT ME!
        • point2
          float point2
          DOCUMENT ME!
        • point2Label
          JLabel point2Label
          DOCUMENT ME!
        • point2Text
          JTextField point2Text
          DOCUMENT ME!
        • pointCalculation
          boolean pointCalculation
          DOCUMENT ME!
        • pointCheckBox
          JCheckBox pointCheckBox
          DOCUMENT ME!
        • possibleInt2Values
          double possibleInt2Values
          DOCUMENT ME!
        • possibleIntValues
          double possibleIntValues
          DOCUMENT ME!
        • redCheckBox
          JCheckBox redCheckBox
          DOCUMENT ME!
        • regCheckBox
          JCheckBox regCheckBox
          DOCUMENT ME!
        • register
          boolean register
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rightPad
          int rightPad
          DOCUMENT ME!
        • secondImage
          ModelImage secondImage
          DOCUMENT ME!
        • secondIterationCheckBox
          JCheckBox secondIterationCheckBox
          DOCUMENT ME!
        • secondName
          String secondName
          DOCUMENT ME!
        • topPad
          int topPad
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • VOICheckBox
          JCheckBox VOICheckBox
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!
        • xDim
          int xDim
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • zDim
          int zDim
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogColorEdge

      class JDialogColorEdge extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5364017650931720063L

      • Serialized Fields

        • algoColorEdge
          AlgorithmColorEdge algoColorEdge
          DOCUMENT ME!
        • blue1
          long blue1
          DOCUMENT ME!
        • blue1Text
          JTextField blue1Text
          DOCUMENT ME!
        • blue2
          long blue2
          DOCUMENT ME!
        • blue2Text
          JTextField blue2Text
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • green1
          long green1
          DOCUMENT ME!
        • green1Text
          JTextField green1Text
          DOCUMENT ME!
        • green2
          long green2
          DOCUMENT ME!
        • green2Text
          JTextField green2Text
          DOCUMENT ME!
        • red1
          long red1
          DOCUMENT ME!
        • red1Text
          JTextField red1Text
          DOCUMENT ME!
        • red2
          long red2
          DOCUMENT ME!
        • red2Text
          JTextField red2Text
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sourceImage
          ModelImage sourceImage
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogColorSaturation

      class JDialogColorSaturation extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogConcat

      class JDialogConcat extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3284724231720657011L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogConcatMult2Dto3D

      class JDialogConcatMult2Dto3D extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • additionalImagesToConcat
          ArrayList<ModelImage> additionalImagesToConcat
          additional images to concat...the ones you add later on
        • alg
          AlgorithmConcatMult2Dto3D alg
          algorithm
        • availableImagesToConcat
          ArrayList<ModelImage> availableImagesToConcat
          available images to concat...the ones that are open in mipav
        • copyAllInfo
          boolean copyAllInfo
          Whether all info in the image's FileInfo is copied
        • copyAllInfoBox
          JCheckBox copyAllInfoBox
          Checkbox for representing whether FileInfo is copied
        • destImage
          ModelImage destImage
          destination image
        • destImagesTable
          JTable destImagesTable
          table
        • destTableModel
          ViewTableModel destTableModel
          table model
        • imagesToConcat
          ArrayList<ModelImage> imagesToConcat
          images to concat
        • selectedRow
          int selectedRow
          indices of selcted rows to remove
        • srcImagesTable
          JTable srcImagesTable
          table
        • srcTableModel
          ViewTableModel srcTableModel
          table model

    • Class gov.nih.mipav.view.dialogs.JDialogConcatMult3Dto3D

      class JDialogConcatMult3Dto3D extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • additionalImagesToConcat
          ArrayList<ModelImage> additionalImagesToConcat
          additional images to concat...the ones you add later on
        • alg
          AlgorithmConcatMult3Dto3D alg
          algorithm
        • availableImagesToConcat
          ArrayList<ModelImage> availableImagesToConcat
          available images to concat...the ones that are open in mipav
        • copyAllInfo
          boolean copyAllInfo
          Whether all info in the image's FileInfo is copied
        • copyAllInfoBox
          JCheckBox copyAllInfoBox
          Checkbox for representing whether FileInfo is copied
        • destImage
          ModelImage destImage
          destination image
        • destImagesTable
          JTable destImagesTable
          table
        • destTableModel
          ViewTableModel destTableModel
          table model
        • imagesToConcat
          ArrayList<ModelImage> imagesToConcat
          images to concat
        • selectedRow
          int selectedRow
          indices of selcted rows to remove
        • srcImagesTable
          JTable srcImagesTable
          table
        • srcTableModel
          ViewTableModel srcTableModel
          table model

    • Class gov.nih.mipav.view.dialogs.JDialogConcatMult3Dto4D

      class JDialogConcatMult3Dto4D extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • additionalImagesToConcat
          ArrayList<ModelImage> additionalImagesToConcat
          additional images to concat...the ones you add later on
        • alg
          AlgorithmConcatMult3Dto4D alg
          algorithm
        • availableImagesToConcat
          ArrayList<ModelImage> availableImagesToConcat
          available images to concat...the ones that are open in mipav
        • copyAllInfo
          boolean copyAllInfo
          Whether all info in the image's FileInfo is copied
        • copyAllInfoBox
          JCheckBox copyAllInfoBox
          Checkbox for representing whether FileInfo is copied
        • destImage
          ModelImage destImage
          destination image
        • destImagesTable
          JTable destImagesTable
          table
        • destTableModel
          ViewTableModel destTableModel
          table model
        • imagesToConcat
          ArrayList<ModelImage> imagesToConcat
          images to concat
        • selectedRow
          int selectedRow
          indices of selcted rows to remove
        • srcImagesTable
          JTable srcImagesTable
          table
        • srcTableModel
          ViewTableModel srcTableModel
          table model

    • Class gov.nih.mipav.view.dialogs.JDialogConstrainedOAR3D

      class JDialogConstrainedOAR3D extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5867077647353095805L

      • Serialized Fields

        • advancedDialog
          JDialog advancedDialog
          Variables for Advanced Settings dialog.
        • bracketBound
          int bracketBound
          DOCUMENT ME!
        • bracketBound_def
          int bracketBound_def
          DOCUMENT ME!
        • bracketBoundText
          JTextField bracketBoundText
          DOCUMENT ME!
        • buttonWeightInput
          JButton buttonWeightInput
          DOCUMENT ME!
        • buttonWeightRef
          JButton buttonWeightRef
          DOCUMENT ME!
        • calcCOG
          boolean calcCOG
          DOCUMENT ME!
        • calcCOGCheckbox
          JCheckBox calcCOGCheckbox
          DOCUMENT ME!
        • coarsePanelX
          JPanel coarsePanelX
          DOCUMENT ME!
        • coarsePanelY
          JPanel coarsePanelY
          DOCUMENT ME!
        • coarsePanelZ
          JPanel coarsePanelZ
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • comboBoxDOF
          JComboBox comboBoxDOF
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • comboBoxInterp2
          JComboBox comboBoxInterp2
          DOCUMENT ME!
        • comboBoxSearchAlgo
          JComboBox comboBoxSearchAlgo
        • cost
          int cost
          DOCUMENT ME!
        • costName
          String costName
          DOCUMENT ME!
        • dataType
          int dataType
        • directoryWInput
          String directoryWInput
          DOCUMENT ME!
        • directoryWRef
          String directoryWRef
          DOCUMENT ME!
        • displayTransform
          boolean displayTransform
          DOCUMENT ME!
        • doColor
          boolean doColor
          DOCUMENT ME!
        • DOF
          int DOF
          DOCUMENT ME!
        • doSubsample
          boolean doSubsample
          DOCUMENT ME!
        • fastMode
          boolean fastMode
          DOCUMENT ME!
        • fastModeCheckbox
          JCheckBox fastModeCheckbox
          DOCUMENT ME!
        • fileNameWInput
          String fileNameWInput
          DOCUMENT ME!
        • fileNameWRef
          String fileNameWRef
          DOCUMENT ME!
        • fillValue
          float fillValue
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • imageMax
          double imageMax
        • imageMin
          double imageMin
        • inputWeightImage
          ModelImage inputWeightImage
          DOCUMENT ME!
        • interp
          int interp
          DOCUMENT ME!
        • interp2
          int interp2
          DOCUMENT ME!
        • labelInterp2
          JLabel labelInterp2
          DOCUMENT ME!
        • labelTranslateRangeX
          JLabel labelTranslateRangeX
          DOCUMENT ME!
        • labelTranslateRangeY
          JLabel labelTranslateRangeY
          DOCUMENT ME!
        • labelTranslateRangeZ
          JLabel labelTranslateRangeZ
          DOCUMENT ME!
        • limitTranslation
          boolean limitTranslation
          DOCUMENT ME!
        • limitTranslationCheckbox
          JCheckBox limitTranslationCheckbox
          DOCUMENT ME!
        • matchImage
          ModelImage matchImage
          DOCUMENT ME!
        • matrixComboBox
          JComboBox matrixComboBox
        • matrixDirectory
          String matrixDirectory
        • matrixLabel
          JLabel matrixLabel
        • maxIterations
          int maxIterations
          DOCUMENT ME!
        • maxIterations_def
          int maxIterations_def
          DOCUMENT ME!
        • maxIterationsText
          JTextField maxIterationsText
          DOCUMENT ME!
        • maxLimits
          float[][] maxLimits
          when done debugging: private boolean limitTranslation = false, oneTransLimit = false;.
        • maxOfMinResol
          boolean maxOfMinResol
          DOCUMENT ME!
        • maxTransTextX
          JTextField maxTransTextX
          DOCUMENT ME!
        • maxTransTextY
          JTextField maxTransTextY
          DOCUMENT ME!
        • maxTransTextZ
          JTextField maxTransTextZ
          DOCUMENT ME!
        • minMaxCheckbox
          JCheckBox minMaxCheckbox
          DOCUMENT ME!
        • minTransTextX
          JTextField minTransTextX
          DOCUMENT ME!
        • minTransTextY
          JTextField minTransTextY
          DOCUMENT ME!
        • minTransTextZ
          JTextField minTransTextZ
          DOCUMENT ME!
        • mmLabelX
          JLabel mmLabelX
          DOCUMENT ME!
        • mmLabelY
          JLabel mmLabelY
          DOCUMENT ME!
        • mmLabelZ
          JLabel mmLabelZ
          DOCUMENT ME!
        • noneRadio
          JRadioButton noneRadio
          DOCUMENT ME!
        • numberCoarseTextX
          JTextField numberCoarseTextX
          DOCUMENT ME!
        • numberCoarseTextY
          JTextField numberCoarseTextY
          DOCUMENT ME!
        • numberCoarseTextZ
          JTextField numberCoarseTextZ
          DOCUMENT ME!
        • numCoarseX
          int numCoarseX
          DOCUMENT ME!
        • numCoarseY
          int numCoarseY
          DOCUMENT ME!
        • numCoarseZ
          int numCoarseZ
          DOCUMENT ME!
        • numMinima
          int numMinima
          DOCUMENT ME!
        • numMinima_def
          int numMinima_def
          DOCUMENT ME!
        • numMinText
          JTextField numMinText
          DOCUMENT ME!
        • oneTransLimit
          boolean oneTransLimit
          DOCUMENT ME!
        • outOfBoundsComboBox
          JComboBox outOfBoundsComboBox
        • outOfBoundsIndex
          int outOfBoundsIndex
          Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum
        • outOfBoundsLabel
          JLabel outOfBoundsLabel
        • refImage
          ModelImage refImage
          DOCUMENT ME!
        • refWeightImage
          ModelImage refWeightImage
          DOCUMENT ME!
        • reg3
          AlgorithmConstrainedOAR3D reg3
        • reg3E
          AlgorithmConstrainedELSUNCOAR3D reg3E
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rotateBeginTextX
          JTextField rotateBeginTextX
          DOCUMENT ME!
        • rotateBeginTextY
          JTextField rotateBeginTextY
          DOCUMENT ME!
        • rotateBeginTextZ
          JTextField rotateBeginTextZ
          DOCUMENT ME!
        • rotateBeginX
          float rotateBeginX
          private JTextField fineRateTextX, fineRateTextY, fineRateTextZ;.
        • rotateBeginY
          float rotateBeginY
          DOCUMENT ME!
        • rotateBeginZ
          float rotateBeginZ
          DOCUMENT ME!
        • rotateEndTextX
          JTextField rotateEndTextX
          DOCUMENT ME!
        • rotateEndTextY
          JTextField rotateEndTextY
          DOCUMENT ME!
        • rotateEndTextZ
          JTextField rotateEndTextZ
          DOCUMENT ME!
        • rotateEndX
          float rotateEndX
          private JTextField fineRateTextX, fineRateTextY, fineRateTextZ;.
        • rotateEndY
          float rotateEndY
          DOCUMENT ME!
        • rotateEndZ
          float rotateEndZ
          DOCUMENT ME!
        • rotatePanel
          JPanel rotatePanel
          Variables for Rotation and Translation bounds.
        • rotateRangePanelX
          JPanel rotateRangePanelX
          DOCUMENT ME!
        • rotateRangePanelY
          JPanel rotateRangePanelY
          DOCUMENT ME!
        • rotateRangePanelZ
          JPanel rotateRangePanelZ
          DOCUMENT ME!
        • rotateRangeX
          float rotateRangeX
          private JTextField fineRateTextX, fineRateTextY, fineRateTextZ;.
        • rotateRangeY
          float rotateRangeY
          DOCUMENT ME!
        • rotateRangeZ
          float rotateRangeZ
          DOCUMENT ME!
        • sampleCheckbox
          JCheckBox sampleCheckbox
          DOCUMENT ME!
        • textInput
          JTextField textInput
          DOCUMENT ME!
        • textRef
          JTextField textRef
          DOCUMENT ME!
        • toLabelX
          JLabel toLabelX
          DOCUMENT ME!
        • toLabelY
          JLabel toLabelY
          DOCUMENT ME!
        • toLabelZ
          JLabel toLabelZ
          DOCUMENT ME!
        • transformCheckbox
          JCheckBox transformCheckbox
          DOCUMENT ME!
        • translatePanel
          JPanel translatePanel
          DOCUMENT ME!
        • translateRangePanelX
          JPanel translateRangePanelX
          private JPanel finePanelX, finePanelY, finePanelZ;.
        • translateRangePanelY
          JPanel translateRangePanelY
          private JPanel finePanelX, finePanelY, finePanelZ;.
        • translateRangePanelZ
          JPanel translateRangePanelZ
          private JPanel finePanelX, finePanelY, finePanelZ;.
        • transLimits
          float[][] transLimits
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • universalRotationCheckbox
          JCheckBox universalRotationCheckbox
          DOCUMENT ME!
        • universalTranslationCheckbox
          JCheckBox universalTranslationCheckbox
          DOCUMENT ME!
        • useELSUNC
          boolean useELSUNC
        • userDirectoryLabel
          JLabel userDirectoryLabel
        • userDirectoryText
          JTextField userDirectoryText
        • valueLabel
          JLabel valueLabel
        • valueText
          JTextField valueText
        • voiRadio
          JRadioButton voiRadio
          DOCUMENT ME!
        • voisOnly
          boolean voisOnly
          DOCUMENT ME!
        • weighted
          boolean weighted
          DOCUMENT ME!
        • weightRadio
          JRadioButton weightRadio
          DOCUMENT ME!
        • xRRadio
          JRadioButton xRRadio
          DOCUMENT ME!
        • xRSelected
          boolean xRSelected
          DOCUMENT ME!
        • yRRadio
          JRadioButton yRRadio
          DOCUMENT ME!
        • yRSelected
          boolean yRSelected
          DOCUMENT ME!
        • zRRadio
          JRadioButton zRRadio
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogContrastEnhancementUsingExposureFusion

      class JDialogContrastEnhancementUsingExposureFusion extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogConvergenceField

      class JDialogConvergenceField extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogConvert3Dto4D

      class JDialogConvert3Dto4D extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      5353653644655035651L

      • Serialized Fields

        • comboBoxUnitOfMeasure3
          JComboBox comboBoxUnitOfMeasure3
          DOCUMENT ME!
        • comboBoxUnitOfMeasure4
          JComboBox comboBoxUnitOfMeasure4
          DOCUMENT ME!
        • convert3Dto4DAlgo
          AlgorithmConvert3Dto4D convert3Dto4DAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageName
          String imageName
          DOCUMENT ME!
        • labelVolumeLength
          JLabel labelVolumeLength
          DOCUMENT ME!
        • measure3
          int measure3
          DOCUMENT ME!
        • measure4
          int measure4
          DOCUMENT ME!
        • res3
          float res3
          DOCUMENT ME!
        • res4
          float res4
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textRes3
          JTextField textRes3
          DOCUMENT ME!
        • textRes4
          JTextField textRes4
          DOCUMENT ME!
        • textVolumeLength
          JTextField textVolumeLength
          DOCUMENT ME!
        • volumeLength
          int volumeLength
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogConvert4Dto3D

      class JDialogConvert4Dto3D extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4079283618961189766L

      • Serialized Fields

        • convert4Dto3DAlgo
          AlgorithmConvert4Dto3D convert4Dto3DAlgo
          DOCUMENT ME!
        • copyAllInfo
          boolean copyAllInfo
          Whether all info in the image's FileInfo is copied
        • copyAllInfoBox
          JCheckBox copyAllInfoBox
          Checkbox for representing whether to copy all file info
        • image
          ModelImage image
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogConvert4DtoMultiple3D

      class JDialogConvert4DtoMultiple3D extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogConvert4DtoRGB

      class JDialogConvert4DtoRGB extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • blank
          ModelImage blank
          blank image
        • channelColorsComboBoxes
          JComboBox[] channelColorsComboBoxes
          corresponding dropdown for each channel image
        • channelImages
          ModelImage[] channelImages
          extraced 3D Model Images from src image
        • colorGroup
          ButtonGroup colorGroup
        • commonMapping
          boolean commonMapping
        • copyAllInfo
          boolean copyAllInfo
          Whether all info in the image's FileInfo is copied
        • copyAllInfoBox
          JCheckBox copyAllInfoBox
          Checkbox for representing whether to copy all file info
        • dataType
          int dataType
          ARGB, ARGB_USHORT, ARGB_UINTEGER, or ARGB_FLOAT for color image
        • destExtents
          int[] destExtents
          extents for extracted 3D subset
        • image
          ModelImage image
          src image
        • imageB
          ModelImage imageB
          blue channel image
        • imageG
          ModelImage imageG
          green channel image
        • imageR
          ModelImage imageR
          red channel image
        • inputPanel
          JPanel inputPanel
          input panel of dialog
        • mainPanel
          JPanel mainPanel
          main panel of dialog
        • mathAlgo
          AlgorithmRGBConcat mathAlgo
          ref to AlgorithmRGBConcat
        • OKCancelPanel
          JPanel OKCancelPanel
          ok/cancel panel of dialog
        • radioARGB
          JRadioButton radioARGB
        • radioARGB_FLOAT
          JRadioButton radioARGB_FLOAT
          DOCUMENT ME!
        • radioARGB_UINTEGER
          JRadioButton radioARGB_UINTEGER
        • radioARGB_USHORT
          JRadioButton radioARGB_USHORT
          DOCUMENT ME!
        • radioCommon
          JRadioButton radioCommon
        • radioSeparate
          JRadioButton radioSeparate
        • remapCheckBox
          JCheckBox remapCheckBox
          re-map checkbox
        • remapGroup
          ButtonGroup remapGroup
        • remapHighestValue
          float remapHighestValue
        • remapMode
          boolean remapMode
          boolean for remap
        • resultImage
          ModelImage resultImage
          result image
        • subsetAlgo
          AlgorithmSubset subsetAlgo
          ref to AlgorithmSubset
        • textRemap
          JTextField textRemap
        • vol1Channel
          String vol1Channel
          vol 1 channel for scripting
        • vol2Channel
          String vol2Channel
          vol 2 channel for scripting
        • vol3Channel
          String vol3Channel
          vol 3 channel for scriptin
        • xSlices
          int xSlices
          num x slices of src image
        • ySlices
          int ySlices
          num y slices of src image
        • zSlices
          int zSlices
          num z slices for src image

    • Class gov.nih.mipav.view.dialogs.JDialogConvertType

      class JDialogConvertType extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -6815107682654273857L

      • Serialized Fields

        • bigEnd
          JRadioButton bigEnd
          DOCUMENT ME!
        • changeTypeAlgo
          AlgorithmChangeType changeTypeAlgo
          DOCUMENT ME!
        • dataType
          int dataType
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • endianess
          boolean endianess
          DOCUMENT ME!
        • fullRangeRadio
          JRadioButton fullRangeRadio
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • inEnd
          JLabel inEnd
          DOCUMENT ME!
        • inMax
          double inMax
          DOCUMENT ME!
        • inMin
          double inMin
          DOCUMENT ME!
        • inputRangeGroup
          ButtonGroup inputRangeGroup
          DOCUMENT ME!
        • inStart
          JLabel inStart
          DOCUMENT ME!
        • inTempMax
          double inTempMax
          DOCUMENT ME!
        • inTempMin
          double inTempMin
          DOCUMENT ME!
        • littleEnd
          JRadioButton littleEnd
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • outEnd
          JLabel outEnd
          DOCUMENT ME!
        • outMax
          double outMax
          DOCUMENT ME!
        • outMin
          double outMin
          DOCUMENT ME!
        • outStart
          JLabel outStart
          DOCUMENT ME!
        • outTempMax
          double outTempMax
          DOCUMENT ME!
        • outTempMin
          double outTempMin
          DOCUMENT ME!
        • processIndep
          boolean processIndep
          DOCUMENT ME!
        • processIndepBox
          JCheckBox processIndepBox
          DOCUMENT ME!
        • radioARGB
          JRadioButton radioARGB
          DOCUMENT ME!
        • radioARGB_FLOAT
          JRadioButton radioARGB_FLOAT
          DOCUMENT ME!
        • radioARGB_UINTEGER
          JRadioButton radioARGB_UINTEGER
        • radioARGB_USHORT
          JRadioButton radioARGB_USHORT
          DOCUMENT ME!
        • radioBool
          JRadioButton radioBool
          DOCUMENT ME!
        • radioByte
          JRadioButton radioByte
          DOCUMENT ME!
        • radioComplex
          JRadioButton radioComplex
        • radioDComplex
          JRadioButton radioDComplex
        • radioDouble
          JRadioButton radioDouble
          DOCUMENT ME!
        • radioFloat
          JRadioButton radioFloat
          DOCUMENT ME!
        • radioInt
          JRadioButton radioInt
          DOCUMENT ME!
        • radioLong
          JRadioButton radioLong
          DOCUMENT ME!
        • radioShort
          JRadioButton radioShort
          DOCUMENT ME!
        • radioUByte
          JRadioButton radioUByte
          DOCUMENT ME!
        • radioUInt
          JRadioButton radioUInt
          DOCUMENT ME!
        • radioUShort
          JRadioButton radioUShort
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textInEnd
          JTextField textInEnd
          DOCUMENT ME!
        • textInStart
          JTextField textInStart
          DOCUMENT ME!
        • textOutEnd
          JTextField textOutEnd
          DOCUMENT ME!
        • textOutStart
          JTextField textOutStart
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • useDefaultRanges
          boolean useDefaultRanges
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • userRangeRadio
          JRadioButton userRangeRadio
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogConvexHull2D

      class JDialogConvexHull2D extends JDialogBase implements Serializable

      • Serialized Fields

        • defaultPts
          int defaultPts
          DOCUMENT ME!
        • elementNum
          int elementNum
        • groupNum
          int groupNum
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • nPts
          int nPts
          DOCUMENT ME!
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • smoothAlgo
          AlgorithmBSmooth smoothAlgo
          DOCUMENT ME!
        • textInterpNPts
          JTextField textInterpNPts
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • trim
          boolean trim
          DOCUMENT ME!
        • trimCheckBox
          JCheckBox trimCheckBox
          DOCUMENT ME!
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • voiManager
          VOIManagerInterface voiManager
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCorrectSpacing

      class JDialogCorrectSpacing extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      6267255098982835652L

      • Serialized Fields

        • correctSpaceAlgo
          AlgorithmCorrectSpacing correctSpaceAlgo
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • fileInfoBuffer
          FileInfoBase fileInfoBuffer
          DOCUMENT ME!
        • gap
          float gap
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • newNumIm
          int newNumIm
          DOCUMENT ME!
        • newThick
          float newThick
          DOCUMENT ME!
        • newZStart
          float newZStart
          DOCUMENT ME!
        • numBlank
          int numBlank
          DOCUMENT ME!
        • numIm
          int numIm
          DOCUMENT ME!
        • numRepIm
          int numRepIm
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • space
          float space
          DOCUMENT ME!
        • thick
          float thick
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • zStart
          float zStart
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCrop

      class JDialogCrop extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      9000755868801202116L

      • Serialized Fields

        • borderSize
          int borderSize
          DOCUMENT ME!
        • cropAlgo
          AlgorithmAddMargins cropAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imgRes
          float[] imgRes
          DOCUMENT ME!
        • lowXmm
          float lowXmm
          DOCUMENT ME!
        • lowYmm
          float lowYmm
          DOCUMENT ME!
        • lowZmm
          float lowZmm
          DOCUMENT ME!
        • nDims
          int nDims
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • resXUnit
          int resXUnit
          DOCUMENT ME!
        • resYUnit
          int resYUnit
          DOCUMENT ME!
        • startPos
          float[] startPos
          DOCUMENT ME!
        • textBorderSize
          JTextField textBorderSize
          DOCUMENT ME!
        • textDepth
          JTextField textDepth
          DOCUMENT ME!
        • textHeight
          JTextField textHeight
          DOCUMENT ME!
        • textLowerXmm
          JTextField textLowerXmm
          DOCUMENT ME!
        • textLowerYmm
          JTextField textLowerYmm
          DOCUMENT ME!
        • textLowerZmm
          JTextField textLowerZmm
          DOCUMENT ME!
        • textWidth
          JTextField textWidth
          DOCUMENT ME!
        • textXmin
          JTextField textXmin
          DOCUMENT ME!
        • textYmin
          JTextField textYmin
          DOCUMENT ME!
        • textZmin
          JTextField textZmin
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • xBounds
          int[] xBounds
          DOCUMENT ME!
        • yBounds
          int[] yBounds
          DOCUMENT ME!
        • zBounds
          int[] zBounds
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCropBoundaryParam

      class JDialogCropBoundaryParam extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2434000521271688512L

      • Serialized Fields

        • back
          int back
          DOCUMENT ME!
        • backInput
          JTextField backInput
          DOCUMENT ME!
        • bottomInput
          JTextField bottomInput
          DOCUMENT ME!
        • bottomSide
          int bottomSide
          DOCUMENT ME!
        • cropAlgo
          AlgorithmAddMargins cropAlgo
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • front
          int front
          DOCUMENT ME!
        • frontInput
          JTextField frontInput
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • leftSide
          int leftSide
          DOCUMENT ME!
        • leftSideInput
          JTextField leftSideInput
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rightSide
          int rightSide
          DOCUMENT ME!
        • rightSideInput
          JTextField rightSideInput
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • topInput
          JTextField topInput
          DOCUMENT ME!
        • topSide
          int topSide
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • xBounds
          int[] xBounds
          DOCUMENT ME!
        • yBounds
          int[] yBounds
          DOCUMENT ME!
        • zBounds
          int[] zBounds
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCropPointParam

      class JDialogCropPointParam extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • back
          int back
          DOCUMENT ME!
        • backInput
          JTextField backInput
          DOCUMENT ME!
        • bottomInput
          JTextField bottomInput
          DOCUMENT ME!
        • bottomSide
          int bottomSide
          DOCUMENT ME!
        • cropAlgo
          AlgorithmAddMargins cropAlgo
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • front
          int front
          DOCUMENT ME!
        • frontInput
          JTextField frontInput
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • leftSide
          int leftSide
          DOCUMENT ME!
        • leftSideInput
          JTextField leftSideInput
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rightSide
          int rightSide
          DOCUMENT ME!
        • rightSideInput
          JTextField rightSideInput
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • topInput
          JTextField topInput
          DOCUMENT ME!
        • topSide
          int topSide
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • xBounds
          int[] xBounds
          DOCUMENT ME!
        • xPoint
          int xPoint
        • xPointInput
          JTextField xPointInput
        • yBounds
          int[] yBounds
          DOCUMENT ME!
        • yPoint
          int yPoint
        • yPointInput
          JTextField yPointInput
        • zBounds
          int[] zBounds
          DOCUMENT ME!
        • zPoint
          int zPoint
        • zPointInput
          JTextField zPointInput

    • Class gov.nih.mipav.view.dialogs.JDialogCropTiltedCuboid

      class JDialogCropTiltedCuboid extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • cropAlgo
          AlgorithmCropTilted cropAlgo
        • image
          ModelImage image
          DOCUMENT ME!
        • MASK_METHOD
          int MASK_METHOD
        • maskButton
          JRadioButton maskButton
        • method
          int method
        • methodGroup
          ButtonGroup methodGroup
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • VERTICES_METHOD
          int VERTICES_METHOD
        • verticesButton
          JRadioButton verticesButton
        • VOI_METHOD
          int VOI_METHOD
        • x1
          double x1
        • x2
          double x2
        • x3
          double x3
        • x4
          double x4
        • x5
          double x5
        • x6
          double x6
        • x7
          double x7
        • x8
          double x8
        • y1
          double y1
        • y2
          double y2
        • y3
          double y3
        • y4
          double y4
        • y5
          double y5
        • y6
          double y6
        • y7
          double y7
        • y8
          double y8
        • z1
          double z1
        • z2
          double z2
        • z3
          double z3
        • z4
          double z4
        • z5
          double z5
        • z6
          double z6
        • z7
          double z7
        • z8
          double z8

    • Class gov.nih.mipav.view.dialogs.JDialogCropTiltedRectangle

      class JDialogCropTiltedRectangle extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • cropAlgo
          AlgorithmCropTilted cropAlgo
        • image
          ModelImage image
          DOCUMENT ME!
        • MASK_METHOD
          int MASK_METHOD
        • maskButton
          JRadioButton maskButton
        • method
          int method
        • methodGroup
          ButtonGroup methodGroup
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • VERTICES_METHOD
          int VERTICES_METHOD
        • verticesButton
          JRadioButton verticesButton
        • VOI_METHOD
          int VOI_METHOD
        • VOIButton
          JRadioButton VOIButton
        • x1
          double x1
        • x2
          double x2
        • x3
          double x3
        • x4
          double x4
        • y1
          double y1
        • y2
          double y2
        • y3
          double y3
        • y4
          double y4

    • Class gov.nih.mipav.view.dialogs.JDialogCT

      class JDialogCT extends JDialogBase implements Serializable
      serialVersionUID:
      8061222665925432857L

      • Serialized Fields

        • abdomenLabel
          JLabel abdomenLabel
          Preset labels.
        • abdomenMax
          int abdomenMax
          Preset min, max values. Min presents the min window value. Max presents the max window value.
        • abdomenMin
          int abdomenMin
          Preset min, max values. Min presents the min window value. Max presents the max window value.
        • headLabel
          JLabel headLabel
          DOCUMENT ME!
        • headMax
          int headMax
          DOCUMENT ME!
        • headMin
          int headMin
          DOCUMENT ME!
        • histoPanel
          ViewJPanelHistoLUT histoPanel
        • lungLabel
          JLabel lungLabel
          DOCUMENT ME!
        • lungMax
          int lungMax
          DOCUMENT ME!
        • lungMin
          int lungMin
          DOCUMENT ME!
        • LUT
          ModelLUT LUT
        • maxLabel
          JLabel maxLabel
          DOCUMENT ME!
        • maxText
          JTextField maxText
          Min, max text fields.
        • mediastinumLabel
          JLabel mediastinumLabel
          DOCUMENT ME!
        • mediastinumMax
          int mediastinumMax
          DOCUMENT ME!
        • mediastinumMin
          int mediastinumMin
          DOCUMENT ME!
        • minLabel
          JLabel minLabel
          DOCUMENT ME!
        • minText
          JTextField minText
          Min, max text fields.
        • origNPts
          int origNPts
          Single Transfer Line size.
        • origX
          float[] origX
          x, y, z arrays of the LUT transfer function.
        • origY
          float[] origY
          x, y, z arrays of the LUT transfer function.
        • radioAbdomen
          JRadioButton radioAbdomen
          Preset radio buttons.
        • radioHead
          JRadioButton radioHead
          DOCUMENT ME!
        • radioLung
          JRadioButton radioLung
          DOCUMENT ME!
        • radioMediastinum
          JRadioButton radioMediastinum
          DOCUMENT ME!
        • radioSpine
          JRadioButton radioSpine
          DOCUMENT ME!
        • radioVertebrae
          JRadioButton radioVertebrae
          DOCUMENT ME!
        • resetButton
          JButton resetButton
          Reset button to reset the default preset values.
        • setButton
          JButton setButton
          When user change the window, level values, setButton sets the min, max of the window values.
        • spineLabel
          JLabel spineLabel
          DOCUMENT ME!
        • spineMax
          int spineMax
          DOCUMENT ME!
        • spineMin
          int spineMin
          DOCUMENT ME!
        • vertebraeLabel
          JLabel vertebraeLabel
          DOCUMENT ME!
        • vertebraeMax
          int vertebraeMax
          DOCUMENT ME!
        • vertebraeMin
          int vertebraeMin
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCTHistoLUT

      class JDialogCTHistoLUT extends JDialogBase implements Serializable
      serialVersionUID:
      8061222665925432857L

      • Serialized Fields

        • abdomenLabel
          JLabel abdomenLabel
          Preset labels.
        • abdomenMax
          int abdomenMax
          Preset min, max values. Min presents the min window value. Max presents the max window value.
        • abdomenMin
          int abdomenMin
          Preset min, max values. Min presents the min window value. Max presents the max window value.
        • componentHistogram
          ViewJComponentHistoLUT componentHistogram
          Histogram component reference inside the JPanelHistoLUT.
        • headLabel
          JLabel headLabel
          DOCUMENT ME!
        • headMax
          int headMax
          DOCUMENT ME!
        • headMin
          int headMin
          DOCUMENT ME!
        • lungLabel
          JLabel lungLabel
          DOCUMENT ME!
        • lungMax
          int lungMax
          DOCUMENT ME!
        • lungMin
          int lungMin
          DOCUMENT ME!
        • maxLabel
          JLabel maxLabel
          DOCUMENT ME!
        • maxText
          JTextField maxText
          Min, max text fields.
        • mediastinumLabel
          JLabel mediastinumLabel
          DOCUMENT ME!
        • mediastinumMax
          int mediastinumMax
          DOCUMENT ME!
        • mediastinumMin
          int mediastinumMin
          DOCUMENT ME!
        • minLabel
          JLabel minLabel
          DOCUMENT ME!
        • minText
          JTextField minText
          Min, max text fields.
        • origNPts
          int origNPts
          Single Transfer Line size.
        • origX
          float[] origX
          x, y, z arrays of the LUT transfer function.
        • origY
          float[] origY
          x, y, z arrays of the LUT transfer function.
        • radioAbdomen
          JRadioButton radioAbdomen
          Preset radio buttons.
        • radioHead
          JRadioButton radioHead
          DOCUMENT ME!
        • radioLung
          JRadioButton radioLung
          DOCUMENT ME!
        • radioMediastinum
          JRadioButton radioMediastinum
          DOCUMENT ME!
        • radioSpine
          JRadioButton radioSpine
          DOCUMENT ME!
        • radioVertebrae
          JRadioButton radioVertebrae
          DOCUMENT ME!
        • resetButton
          JButton resetButton
          Reset button to reset the default preset values.
        • setButton
          JButton setButton
          When user change the window, level values, setButton sets the min, max of the window values.
        • spineLabel
          JLabel spineLabel
          DOCUMENT ME!
        • spineMax
          int spineMax
          DOCUMENT ME!
        • spineMin
          int spineMin
          DOCUMENT ME!
        • vertebraeLabel
          JLabel vertebraeLabel
          DOCUMENT ME!
        • vertebraeMax
          int vertebraeMax
          DOCUMENT ME!
        • vertebraeMin
          int vertebraeMin
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCTPreset

      class JDialogCTPreset extends JDialogBase implements Serializable
      serialVersionUID:
      3709628941183114805L

      • Serialized Fields

        • abdomenLabel
          JLabel abdomenLabel
          Preset labels.
        • abdomenMax
          int abdomenMax
          Preset min, max values. Min presents the min window value. Max presents the max window value.
        • abdomenMin
          int abdomenMin
          Preset min, max values. Min presents the min window value. Max presents the max window value.
        • dataSlice
          float[] dataSlice
          Reference to the image data of the slice presently displayed. Needed to calculate the max/min of the slice used to adjust the transfer function.
        • dim
          Dimension dim
          DOCUMENT ME!
        • headLabel
          JLabel headLabel
          DOCUMENT ME!
        • headMax
          int headMax
          DOCUMENT ME!
        • headMin
          int headMin
          DOCUMENT ME!
        • image
          ModelImage image
          Reference to the image that will be affected by the adjust of the window and level.
        • lungLabel
          JLabel lungLabel
          DOCUMENT ME!
        • lungMax
          int lungMax
          DOCUMENT ME!
        • lungMin
          int lungMin
          DOCUMENT ME!
        • LUT
          ModelLUT LUT
          Reference to the LUT used to display the image.
        • maxImage
          float maxImage
          Image's maximum intensity.
        • maxLabel
          JLabel maxLabel
          DOCUMENT ME!
        • maxText
          JTextField maxText
          Min, max text fields.
        • mediastinumLabel
          JLabel mediastinumLabel
          DOCUMENT ME!
        • mediastinumMax
          int mediastinumMax
          DOCUMENT ME!
        • mediastinumMin
          int mediastinumMin
          DOCUMENT ME!
        • minImage
          float minImage
          Image's minimum intensity.
        • minLabel
          JLabel minLabel
          DOCUMENT ME!
        • minText
          JTextField minText
          Min, max text fields.
        • radioAbdomen
          JRadioButton radioAbdomen
          Preset radio buttons.
        • radioHead
          JRadioButton radioHead
          DOCUMENT ME!
        • radioLung
          JRadioButton radioLung
          DOCUMENT ME!
        • radioMediastinum
          JRadioButton radioMediastinum
          DOCUMENT ME!
        • radioSpine
          JRadioButton radioSpine
          DOCUMENT ME!
        • radioVertebrae
          JRadioButton radioVertebrae
          DOCUMENT ME!
        • resetButton
          JButton resetButton
          Reset button to reset the default preset values.
        • setButton
          JButton setButton
          When user change the window, level values, setButton sets the min, max of the window values.
        • spineLabel
          JLabel spineLabel
          DOCUMENT ME!
        • spineMax
          int spineMax
          DOCUMENT ME!
        • spineMin
          int spineMin
          DOCUMENT ME!
        • vertebraeLabel
          JLabel vertebraeLabel
          DOCUMENT ME!
        • vertebraeMax
          int vertebraeMax
          DOCUMENT ME!
        • vertebraeMin
          int vertebraeMin
          DOCUMENT ME!
        • x
          float[] x
          Three arrays to save the coordinates of the LUT's transfer fucntion. z[] not used.
        • y
          float[] y
          DOCUMENT ME!
        • z
          float[] z
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogCumulativeHistogram

      class JDialogCumulativeHistogram extends JDialogBase implements Serializable
      serialVersionUID:
      -2835835380784019616L

      • Serialized Fields

        • hist
          ModelHistogram hist
          MoelHistogram object.*
        • histoBuffer
          int[] histoBuffer
          int array of histogram values.
        • image
          ModelImage image
          Source Image.
        • RGBValue
          int RGBValue
          int vlaue indicating RGB channel.

    • Class gov.nih.mipav.view.dialogs.JDialogCyclicPermutation

      class JDialogCyclicPermutation extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • cpAlgo
          AlgorithmCyclicPermutation cpAlgo
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • shiftT
          int shiftT
          DOCUMENT ME!
        • shiftTInput
          JTextField shiftTInput
          DOCUMENT ME!
        • shiftX
          int shiftX
          DOCUMENT ME!
        • shiftXInput
          JTextField shiftXInput
          DOCUMENT ME!
        • shiftY
          int shiftY
          DOCUMENT ME!
        • shiftYInput
          JTextField shiftYInput
          DOCUMENT ME!
        • shiftZ
          int shiftZ
          DOCUMENT ME!
        • shiftZInput
          JTextField shiftZInput
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogDataProvenance

      class JDialogDataProvenance extends JDialogBase implements Serializable
      serialVersionUID:
      3861014709972568409L

      • Serialized Fields

        • buttonPanel
          JPanel buttonPanel
          DOCUMENT ME!
        • DEFAULT_SIZE
          Dimension DEFAULT_SIZE
          Describes the initial size of the textual display area when the dialog is created. The value is given in pixel size rather than the number of characters since the display area has no characters to display.
        • dpModel
          ViewTableModel dpModel
          The table model
        • isSystem
          boolean isSystem
          boolean determining if this is the system's data provenance, or an open image's
        • path
          String path
          The path to the provenance file
        • pHolder
          ProvenanceHolder pHolder
          The provenance holder to display (or inject provenance data for "open provenance")
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • textArea
          JTextArea textArea
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogDBSCANClusteringSegment

      class JDialogDBSCANClusteringSegment extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogDeconvolution

      class JDialogDeconvolution extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5074546334694615886L

      • Serialized Fields

        • colorChannelPanel
          JPanelColorChannels colorChannelPanel
          for processing color images
        • conversionFactorCheckbox
          JCheckBox conversionFactorCheckbox
          sigma conversion factor is by 1.0 / (2*Math.sqrt(2*Math.log(2)))
        • image
          ModelImage image
          Source image.
        • imageB
          ModelImage imageB
          Source image.
        • method
          int method
        • outputOptionsPanel
          JPanelAlgorithmOutputOptions outputOptionsPanel
          output to a new image or overwite the current image
        • resultImage
          ModelImage resultImage
          Result image.
        • textGaussX
          JTextField[] textGaussX
          gui, sigma value
        • textGaussY
          JTextField[] textGaussY
          gui, sigma value
        • textGaussZ
          JTextField[] textGaussZ
          gui, sigma value
        • textIterations
          JTextField textIterations
        • titles
          String[] titles
          locks the frame title
        • userInterface
          ViewUserInterface userInterface
          locking the image

    • Class gov.nih.mipav.view.dialogs.JDialogDeleteObjects

      class JDialogDeleteObjects extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5905410727732570098L

    • Class gov.nih.mipav.view.dialogs.JDialogDemonsLite

      class JDialogDemonsLite extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogDEMRI3

      class JDialogDEMRI3 extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • bloodGroup
          ButtonGroup bloodGroup
        • buttonMpFile
          JButton buttonMpFile
        • buttonTissueFile
          JButton buttonTissueFile
        • CONSTANT_TISSUE
          int CONSTANT_TISSUE
        • constantTissueRadioButton
          JRadioButton constantTissueRadioButton
        • demri3Algo
          AlgorithmDEMRI3 demri3Algo
          DOCUMENT ME!
        • directoryMp
          String directoryMp
        • directoryTissue
          String directoryTissue
        • fileNameMp
          String fileNameMp
        • fileNameTissue
          String fileNameTissue
        • FIRST_VOLUME_TISSUE
          int FIRST_VOLUME_TISSUE
        • firstVolumeTissueRadioButton
          JRadioButton firstVolumeTissueRadioButton
        • image
          ModelImage image
          DOCUMENT ME!
        • kepButton
          JRadioButton kepButton
        • labelBloodIntrinsicRelaxivityRate
          JLabel labelBloodIntrinsicRelaxivityRate
        • labelBloodIntrinsicRelaxivityRate2
          JLabel labelBloodIntrinsicRelaxivityRate2
        • labelContrastRelaxivityRate
          JLabel labelContrastRelaxivityRate
          DOCUMENT ME!
        • labelFlipAngle
          JLabel labelFlipAngle
        • labelMaxConstr0
          JLabel labelMaxConstr0
        • labelMaxConstr1
          JLabel labelMaxConstr1
        • labelMaxConstr2
          JLabel labelMaxConstr2
        • labelMinConstr0
          JLabel labelMinConstr0
        • labelMinConstr1
          JLabel labelMinConstr1
        • labelMinConstr2
          JLabel labelMinConstr2
        • labelMp
          JLabel labelMp
        • labelNFirst
          JLabel labelNFirst
        • labelParamsToFit
          JLabel labelParamsToFit
          Use serialVersionUID for interoperability.
        • labelTimeBetweenShots
          JLabel labelTimeBetweenShots
        • labelTissueIntrinsicRelaxivityRate
          JLabel labelTissueIntrinsicRelaxivityRate
        • labelTissueIntrinsicRelaxivityRate2
          JLabel labelTissueIntrinsicRelaxivityRate2
        • max_constr
          double[] max_constr
        • min_constr
          double[] min_constr
        • minuteButton
          JRadioButton minuteButton
        • nFirst
          int nFirst
        • nFirstMax
          int nFirstMax
        • nFirstMin
          int nFirstMin
        • perMin
          boolean perMin
        • r1
          double r1
        • r1i
          double[] r1i
        • r1Max
          double r1Max
        • r1Min
          double r1Min
        • rateGroup
          ButtonGroup rateGroup
        • resultImage
          ModelImage resultImage
        • rib
          double rib
        • ribMax
          double ribMax
        • ribMin
          double ribMin
        • rit
          double rit
        • ritMax
          double ritMax
        • ritMin
          double ritMin
        • secondButton
          JRadioButton secondButton
        • secondParamGroup
          ButtonGroup secondParamGroup
        • SEPARATE_VOLUME_TISSUE
          int SEPARATE_VOLUME_TISSUE
        • separateVolumeTissueRadioButton
          JRadioButton separateVolumeTissueRadioButton
        • textBloodIntrinsicRelaxivityRate
          JTextField textBloodIntrinsicRelaxivityRate
        • textContrastRelaxivityRate
          JTextField textContrastRelaxivityRate
        • textFlipAngle
          JTextField textFlipAngle
        • textMaxConstr0
          JTextField textMaxConstr0
        • textMaxConstr1
          JTextField textMaxConstr1
        • textMaxConstr2
          JTextField textMaxConstr2
        • textMinConstr0
          JTextField textMinConstr0
        • textMinConstr1
          JTextField textMinConstr1
        • textMinConstr2
          JTextField textMinConstr2
        • textNFirst
          JTextField textNFirst
        • textTimeBetweenShots
          JTextField textTimeBetweenShots
        • textTissueFile
          JTextField textTissueFile
        • textTissueIntrinsicRelaxivityRate
          JTextField textTissueIntrinsicRelaxivityRate
        • theta
          double theta
        • thetaMax
          double thetaMax
        • thetaMin
          double thetaMin
        • tissueGroup
          ButtonGroup tissueGroup
        • tissueImage
          ModelImage tissueImage
        • tissueSource
          int tissueSource
        • tr
          double tr
        • trMax
          double trMax
        • trMin
          double trMin
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • userBloodRadioButton
          JRadioButton userBloodRadioButton
        • userSpecifiedBlood
          boolean userSpecifiedBlood
        • useVe
          boolean useVe
        • veButton
          JRadioButton veButton
        • voiBloodRadioButton
          JRadioButton voiBloodRadioButton
        • VOIs
          ViewVOIVector VOIs

    • Class gov.nih.mipav.view.dialogs.JDialogDicom2XMLSelection

      class JDialogDicom2XMLSelection extends JDialogListSaveSelection implements Serializable
      serialVersionUID:
      -1864581773877529737L

      • Serialized Fields

        • destFormatStr
          String destFormatStr
        • sourceInfo
          FileInfoDicom sourceInfo
          FileInfoDicom for source image
        • wasOkay
          boolean wasOkay
          Boolean that determines if the window was closed (hitting the X) wasOkay = true means the [x] was not clicked.

    • Class gov.nih.mipav.view.dialogs.JDialogDICOMDeleteTagEditor

      class JDialogDICOMDeleteTagEditor extends JDialogBase implements Serializable

      • Serialized Fields

        • applyToAllSlicesCheckBox
          JCheckBox applyToAllSlicesCheckBox
          DOCUMENT ME!
        • mainBox
          Box mainBox
          The main panel that is accessed.
        • originalTextField
          JTextField originalTextField
          DOCUMENT ME!
        • struckOkayButton
          boolean struckOkayButton
          DOCUMENT ME!
        • tagKey
          String tagKey
          DOCUMENT ME!
        • tagTable
          FileDicomTagTable tagTable
          A reference to the tag table containing the tag we will be editing.

    • Class gov.nih.mipav.view.dialogs.JDialogDicomDir

      class JDialogDicomDir extends JDialogBase implements Serializable
      serialVersionUID:
      3861014709972568409L

      • Serialized Fields

        • base
          DefaultMutableTreeNode base
        • brightness
          int brightness
          DOCUMENT ME!
        • brightPanel
          JPanel brightPanel
          DOCUMENT ME!
        • brightSlider
          JSlider brightSlider
          DOCUMENT ME!
        • buttonPanel
          JPanel buttonPanel
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • contSlider
          JSlider contSlider
          DOCUMENT ME!
        • current
          JLabel current
          DOCUMENT ME!
        • current2
          JLabel current2
          DOCUMENT ME!
        • DEFAULT_SIZE
          Dimension DEFAULT_SIZE
          Describes the initial size of the textual display area when the dialog is created. The value is given in pixel size rather than the number of characters since the display area has no characters to display.
        • defaultImageSize
          Dimension defaultImageSize
          DOCUMENT ME!
        • dicomInfo
          FileInfoDicom dicomInfo
        • dirInfo
          FileDicomSQ dirInfo
        • file
          File file
        • ifSuccess
          boolean ifSuccess
        • imagePanel
          JPanel imagePanel
        • imageSliderPane
          JSplitPane imageSliderPane
          DOCUMENT ME!
        • img
          ViewJComponentPreviewImage img
        • nfc
          NumberFormat nfc
          DOCUMENT ME!
        • opener
          FileDicom opener
        • origBrightness
          int origBrightness
          DOCUMENT ME!
        • origContrast
          float origContrast
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • serif12
          Font serif12
          DOCUMENT ME!
        • serif12B
          Font serif12B
          DOCUMENT ME!
        • sliderPanel
          JPanel sliderPanel
          DOCUMENT ME!
        • tagViewer
          ViewTableModel tagViewer
          The table model
        • thumbnail
          FileImageXML.Thumbnail thumbnail
          DOCUMENT ME!
        • tree
          JTreeDICOM tree

    • Class gov.nih.mipav.view.dialogs.JDialogDICOMNewTagEditor

      class JDialogDICOMNewTagEditor extends JDialogBase implements Serializable

      • Serialized Fields

        • applyToAllSlicesCheckBox
          JCheckBox applyToAllSlicesCheckBox
          DOCUMENT ME!
        • elementString
          String elementString
        • groupString
          String groupString
        • struckOkayButton
          boolean struckOkayButton
          DOCUMENT ME!
        • tagKey
          String tagKey
          DOCUMENT ME!
        • tagName
          String tagName
        • tagTable
          FileDicomTagTable tagTable
          A reference to the tag table containing the tag we will be editing.
        • tagValue
          String tagValue
        • textTagElement
          JTextField textTagElement
        • textTagGroup
          JTextField textTagGroup
          DOCUMENT ME!
        • textTagName
          JTextField textTagName
        • textTagValue
          JTextField textTagValue

    • Class gov.nih.mipav.view.dialogs.JDialogDICOMTagEditor

      class JDialogDICOMTagEditor extends JDialogBase implements Serializable
      serialVersionUID:
      8765963102638731411L

      • Serialized Fields

        • applyToAllSlicesCheckBox
          JCheckBox applyToAllSlicesCheckBox
          DOCUMENT ME!
        • mainBox
          Box mainBox
          The main panel that is accessed.
        • newInputPanel
          JPanelEdit[] newInputPanel
          DOCUMENT ME!
        • originalTextField
          JTextField originalTextField
          DOCUMENT ME!
        • struckOkayButton
          boolean struckOkayButton
          DOCUMENT ME!
        • tagKey
          String tagKey
          DOCUMENT ME!
        • tagTable
          FileDicomTagTable tagTable
          A reference to the tag table containing the tag we will be editing.

    • Class gov.nih.mipav.view.dialogs.JDialogDicomTagMultiEditor

      class JDialogDicomTagMultiEditor extends JDialogDicomTagSelector implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogDicomTagSelector

      class JDialogDicomTagSelector extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • addButton
          JButton addButton
          Buttons used by this dialog
        • addButtonSeq
          JButton addButtonSeq
          Buttons used by this dialog
        • addListener
          FocusListener addListener
        • clearButton
          JButton clearButton
          Buttons used by this dialog
        • closeButton
          JButton closeButton
          Buttons used by this dialog
        • elementCombo
          JComboBox elementCombo
          Combo boxes used for sequence tags
        • elementFocus
          JComponent elementFocus
        • elementList
          JList elementList
          Lists used to display available DICOM tags
        • elementSeqText
          JTextField elementSeqText
          Text fields for displaying/entering a group/element tag
        • elementText
          JTextField elementText
          Text fields for displaying/entering a group/element tag
        • embeddedPanel
          JPanel embeddedPanel
          When this object exists as an embedded panel, this variable contains all necessary data elements.
        • groupCombo
          JComboBox groupCombo
          Combo boxes used for sequence tags
        • groupList
          JList groupList
          Lists used to display available DICOM tags
        • groupSeqText
          JTextField groupSeqText
          Text fields for displaying/entering a group/element tag
        • groupText
          JTextField groupText
          Text fields for displaying/entering a group/element tag
        • groupToElement
          TreeMap<String,ArrayList<String>> groupToElement
          List of all file's elements for each group of a FileDicomKey set
        • groupToElementSeq
          TreeMap<String,ArrayList<String>> groupToElementSeq
          List of all file's elements for each group of a FileDicomKey set
        • isStandalone
          boolean isStandalone
        • k1
          JDialogDicomTagSelector.TagInputListener k1
        • k2
          JDialogDicomTagSelector.TagInputListener k2
        • keyToName
          TreeMap<String,String> keyToName
          FileDicomTag to its name in the Dicom dictionary
        • keyToNameSeq
          TreeMap<String,String> keyToNameSeq
          FileDicomTag to its name in the Dicom dictionary
        • keyToValue
          TreeMap<String,String> keyToValue
          FileDicomTag to its value in the file
        • keyToValueSeq
          TreeMap<String,String> keyToValueSeq
          FileDicomTag to its value in the file
        • nameValue
          JLabel nameValue
          Name and property labels that describe a DICOM tag for a particular file
        • nameValueSeq
          JLabel nameValueSeq
          Name and property labels that describe a DICOM tag for a particular file
        • parentDialog
          DicomTagSelectorImpl parentDialog
          The parent dialog which receives text from this dicom tag editor
        • propertyLabel
          JLabel propertyLabel
          When a tag value exists, this label displays the text "Tag value:"
        • propertyValue
          JTextField propertyValue
        • propertyValueSeq
          JLabel propertyValueSeq
          Name and property labels that describe a DICOM tag for a particular file
        • propPane
          JScrollPane propPane
          When a tag value exists, this panel displays the value
        • SCROLL_PANE_SIZE
          Dimension SCROLL_PANE_SIZE
          Min/max size of all text boxes contained in scroll panes.
        • sequenceInformationPanel
          JPanel sequenceInformationPanel
          Panels used by this dialog box
        • tablePanel
          JPanel tablePanel
          Panel contains JTable for storing dicom tags.
        • tagInformationPanel
          JPanel tagInformationPanel
          Panels used by this dialog box
        • tagList
          Hashtable<FileDicomKey,FileDicomTag> tagList
          Original list of available DICOM tags
        • tagSelectorPanel
          JPanel tagSelectorPanel
          Panels used by this dialog box
        • tagsTable
          JTable tagsTable
          Option table where dicom tags are reported to.

    • Class gov.nih.mipav.view.dialogs.JDialogDicomTagSelector.DicomTableModel

      class DicomTableModel extends DefaultTableModel implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogDICOMtoAVI

      class JDialogDICOMtoAVI extends JDialogBase implements Serializable
      serialVersionUID:
      4954811111242576089L

      • Serialized Fields

        • aviField
          JTextField aviField
          DOCUMENT ME!
        • browseButton
          JButton browseButton
          DOCUMENT ME!
        • browseOutputButton
          JButton browseOutputButton
          DOCUMENT ME!
        • compression
          int compression
          DOCUMENT ME!
        • compressionBox
          JComboBox compressionBox
          DOCUMENT ME!
        • dirField
          JTextField dirField
          DOCUMENT ME!
        • qualityField
          JTextField qualityField
          DOCUMENT ME!
        • qualityLabel
          JLabel qualityLabel
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogDilate

      class JDialogDilate extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2780388883449887106L

    • Class gov.nih.mipav.view.dialogs.JDialogDirectResample

      class JDialogDirectResample extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      2885627426314170051L

      • Serialized Fields

        • algoTransform
          AlgorithmTransform algoTransform
          The algorithm.
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • dim
          int dim
          Number of available dimension.
        • enableVolRender
          boolean enableVolRender
          Boolean flag to enable volume render button.
        • extents
          int[] extents
          Original dimensions extents value array.
        • extXInput
          JTextField extXInput
          Original X, Y, Z dimension extents values.
        • extXOutput
          JTextField extXOutput
          Power of 2 X, Y, Z dimension extents values.
        • extYInput
          JTextField extYInput
          Original X, Y, Z dimension extents values.
        • extYOutput
          JTextField extYOutput
          Power of 2 X, Y, Z dimension extents values.
        • extZInput
          JTextField extZInput
          Original X, Y, Z dimension extents values.
        • extZOutput
          JTextField extZOutput
          Power of 2 X, Y, Z dimension extents values.
        • forceResample
          boolean forceResample
          Boolean flag to do resample images.
        • image
          ModelImage image
          Model images A and B.
        • imageB
          ModelImage imageB
          Model images A and B.
        • interp
          int interp
          DOCUMENT ME!
        • leftPanel
          JPanel leftPanel
          Left panel and right panels corresponding to original and expected extents.
        • newRes
          float[] newRes
          Resample resolutioin corresponding to Power of 2.
        • originalVolPowerOfTwo
          boolean originalVolPowerOfTwo
          Boolean flag to indicate the original image is in Power of 2.
        • res
          float[] res
          Original resolutioin arrray.
        • resampledImageFrame
          ViewJFrameImage resampledImageFrame
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          Temp Model image.
        • resultImageB
          ModelImage resultImageB
          DOCUMENT ME!
        • rightPanel
          JPanel rightPanel
          Left panel and right panels corresponding to original and expected extents.
        • userInterface
          ViewUserInterface userInterface
          Parent ui.
        • volExtents
          int[] volExtents
          Resampled dimension value in Power of 2.
        • volSize
          int volSize
          Volume size X*Y*Z.

    • Class gov.nih.mipav.view.dialogs.JDialogDiscreteCosineTransform

      class JDialogDiscreteCosineTransform extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogDiscreteSineTransform

      class JDialogDiscreteSineTransform extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogDistanceMap

      class JDialogDistanceMap extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5952815004874741476L

    • Class gov.nih.mipav.view.dialogs.JDialogDoublyConnectedSC

      class JDialogDoublyConnectedSC extends JDialogBase implements Serializable
      serialVersionUID:
      0L

    • Class gov.nih.mipav.view.dialogs.JDialogDSC_MRI_toolbox

      class JDialogDSC_MRI_toolbox extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • aif_nSlice
          int aif_nSlice
        • aif_nSliceLabel
          JLabel aif_nSliceLabel
        • aif_nSliceText
          JTextField aif_nSliceText
        • csvdCheckBox
          JCheckBox csvdCheckBox
        • deconv_method
          String[] deconv_method
        • do_csvd
          boolean do_csvd
        • do_osvd
          boolean do_osvd
        • do_svd
          boolean do_svd
        • dsc
          DSC_MRI_toolbox dsc
          DOCUMENT ME!
        • image
          ModelImage image
          Source image.
        • nS
          int nS
        • osvdCheckBox
          JCheckBox osvdCheckBox
        • outputFileDirectory
          String outputFileDirectory
        • outputFileDirectoryText
          JTextField outputFileDirectoryText
        • svdCheckBox
          JCheckBox svdCheckBox
        • svdLabel
          JLabel svdLabel
        • svdMethodsSelected
          int svdMethodsSelected
        • te
          double te
        • teLabel
          JLabel teLabel
        • TEString
          String TEString
        • teText
          JTextField teText
        • tr
          double tr
        • trLabel
          JLabel trLabel
        • TRString
          String TRString
        • trText
          JTextField trText
        • userInterface
          ViewUserInterface userInterface

    • Class gov.nih.mipav.view.dialogs.JDialogDTICreateListFile

      class JDialogDTICreateListFile extends JDialogBase implements Serializable

      • Serialized Fields

        • alg
          AlgorithmDTICreateListFile alg
          handle to the algorithm
        • bmatrixPath
          String bmatrixPath
          bmatrix path
        • bmtxtFileBrowseButton
          JButton bmtxtFileBrowseButton
          browse button
        • bmtxtFilePathTextField
          JTextField bmtxtFilePathTextField
          path to bmatrix file
        • bmtxtFileRadio
          JRadioButton bmtxtFileRadio
          b-matrix file option
        • currDir
          String currDir
          current directory
        • dicomB0VolumeBrowseButton
          JButton dicomB0VolumeBrowseButton
          browse button to locate the dicom b0 volume if doing registration
        • dicomB0VolumeLabel
          JLabel dicomB0VolumeLabel
          label for dicom b0 volume if doing registration
        • dicomB0VolumePath
          String dicomB0VolumePath
        • dicomB0VolumeTextField
          JTextField dicomB0VolumeTextField
          path to dicom b0 volume if doing registration
        • dwiLabel
          JLabel dwiLabel
          dwi data label
        • dwiPathBrowseButton
          JButton dwiPathBrowseButton
          browse button for dwi file/folder
        • dwiPathTextField
          JTextField dwiPathTextField
          path to dwi file/dir
        • gradFileRadio
          JRadioButton gradFileRadio
          gradient file option
        • gradientFileBrowseButton
          JButton gradientFileBrowseButton
          browse button
        • gradientFilePathTextField
          JTextField gradientFilePathTextField
          path to gradient file
        • gradientPath
          String gradientPath
          gradient path
        • isDICOM
          boolean isDICOM
          boolean indicating if we are dealing with dicom or par/rec
        • isInterleaved
          boolean isInterleaved
          boolean if interleaved
        • optionsGroup
          ButtonGroup optionsGroup
          button group for radio buttons
        • outputTextArea
          JTextArea outputTextArea
          output text area
        • performRegistrationCheckbox
          JCheckBox performRegistrationCheckbox
          checkbox for performing registration
        • prFileDir
          String prFileDir
          par/rec file directory
        • prFileName
          String prFileName
          par/rec file name
        • registrationSettingsButton
          JButton registrationSettingsButton
          button to launch the registration settings
        • regOptions
          JDialogDTICreateListFileRegOAR35DOptions regOptions
          handle to JDialogDTICreateListFileRegOAR35DOptions
        • scrollPane
          JScrollPane scrollPane
          Scroll Pane for the Text Area
        • studyName
          String studyName
          study name string
        • studyPath
          String studyPath
          study path

    • Class gov.nih.mipav.view.dialogs.JDialogDTICreateListFileRegOAR35DOptions

      class JDialogDTICreateListFileRegOAR35DOptions extends JDialogBase implements Serializable
      serialVersionUID:
      -4309868934393418962L

      • Serialized Fields

        • advancedDialog
          JDialog advancedDialog
          Variables for Advanced Settings dialog.
        • bracketBound
          int bracketBound
          DOCUMENT ME!
        • bracketBound_def
          int bracketBound_def
          DOCUMENT ME!
        • bracketBoundText
          JTextField bracketBoundText
          DOCUMENT ME!
        • coarsePanelX
          JPanel coarsePanelX
          DOCUMENT ME!
        • coarsePanelY
          JPanel coarsePanelY
          DOCUMENT ME!
        • coarsePanelZ
          JPanel coarsePanelZ
          DOCUMENT ME!
        • coarseRate
          float coarseRate
          DOCUMENT ME!
        • coarseRateText
          JTextField coarseRateText
          DOCUMENT ME!
        • coarseRateTextX
          JTextField coarseRateTextX
          DOCUMENT ME!
        • coarseRateTextY
          JTextField coarseRateTextY
          DOCUMENT ME!
        • coarseRateTextZ
          JTextField coarseRateTextZ
          DOCUMENT ME!
        • coarseRateX
          float coarseRateX
          DOCUMENT ME!
        • coarseRateY
          float coarseRateY
          DOCUMENT ME!
        • coarseRateZ
          float coarseRateZ
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • comboBoxDOF
          JComboBox comboBoxDOF
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • comboBoxInterp2
          JComboBox comboBoxInterp2
          DOCUMENT ME!
        • cost
          int cost
          DOCUMENT ME!
        • DOF
          int DOF
          DOCUMENT ME!
        • doMultiThread
          boolean doMultiThread
        • doSubsample
          boolean doSubsample
          DOCUMENT ME!
        • fastMode
          boolean fastMode
          DOCUMENT ME!
        • fastModeCheckbox
          JCheckBox fastModeCheckbox
          DOCUMENT ME!
        • finePanelX
          JPanel finePanelX
          DOCUMENT ME!
        • finePanelY
          JPanel finePanelY
          DOCUMENT ME!
        • finePanelZ
          JPanel finePanelZ
          DOCUMENT ME!
        • fineRate
          float fineRate
          DOCUMENT ME!
        • fineRateText
          JTextField fineRateText
          DOCUMENT ME!
        • fineRateTextX
          JTextField fineRateTextX
          DOCUMENT ME!
        • fineRateTextY
          JTextField fineRateTextY
          DOCUMENT ME!
        • fineRateTextZ
          JTextField fineRateTextZ
          DOCUMENT ME!
        • fineRateX
          float fineRateX
          DOCUMENT ME!
        • fineRateY
          float fineRateY
          DOCUMENT ME!
        • fineRateZ
          float fineRateZ
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • interp
          int interp
          DOCUMENT ME!
        • interp2
          int interp2
          DOCUMENT ME!
        • isDICOM
          boolean isDICOM
        • labelInterp2
          JLabel labelInterp2
          DOCUMENT ME!
        • maxIterations
          int maxIterations
          DOCUMENT ME!
        • maxIterations_def
          int maxIterations_def
          DOCUMENT ME!
        • maxIterationsText
          JTextField maxIterationsText
          DOCUMENT ME!
        • maxOfMinResol
          boolean maxOfMinResol
          DOCUMENT ME!
        • minMaxCheckbox
          JCheckBox minMaxCheckbox
          DOCUMENT ME!
        • multiThreadCheckBox
          JCheckBox multiThreadCheckBox
        • numMinima
          int numMinima
          DOCUMENT ME!
        • numMinima_def
          int numMinima_def
          DOCUMENT ME!
        • numMinText
          JTextField numMinText
          DOCUMENT ME!
        • registerTo
          int registerTo
        • rotateBegin
          float rotateBegin
          DOCUMENT ME!
        • rotateBeginText
          JTextField rotateBeginText
          DOCUMENT ME!
        • rotateBeginTextX
          JTextField rotateBeginTextX
          DOCUMENT ME!
        • rotateBeginTextY
          JTextField rotateBeginTextY
          DOCUMENT ME!
        • rotateBeginTextZ
          JTextField rotateBeginTextZ
          DOCUMENT ME!
        • rotateBeginX
          float rotateBeginX
          DOCUMENT ME!
        • rotateBeginY
          float rotateBeginY
          DOCUMENT ME!
        • rotateBeginZ
          float rotateBeginZ
          DOCUMENT ME!
        • rotateEnd
          float rotateEnd
          DOCUMENT ME!
        • rotateEndText
          JTextField rotateEndText
          DOCUMENT ME!
        • rotateEndTextX
          JTextField rotateEndTextX
          DOCUMENT ME!
        • rotateEndTextY
          JTextField rotateEndTextY
          DOCUMENT ME!
        • rotateEndTextZ
          JTextField rotateEndTextZ
          DOCUMENT ME!
        • rotateEndX
          float rotateEndX
          DOCUMENT ME!
        • rotateEndY
          float rotateEndY
          DOCUMENT ME!
        • rotateEndZ
          float rotateEndZ
          DOCUMENT ME!
        • rotatePanel
          JPanel rotatePanel
        • rotateRangePanelX
          JPanel rotateRangePanelX
          DOCUMENT ME!
        • rotateRangePanelY
          JPanel rotateRangePanelY
          DOCUMENT ME!
        • rotateRangePanelZ
          JPanel rotateRangePanelZ
          DOCUMENT ME!
        • sampleCheckBox
          JCheckBox sampleCheckBox
          DOCUMENT ME!
        • universalCheckbox
          JCheckBox universalCheckbox
          DOCUMENT ME!
        • xRadio
          JRadioButton xRadio
          DOCUMENT ME!
        • xSelected
          boolean xSelected
          DOCUMENT ME!
        • yRadio
          JRadioButton yRadio
          DOCUMENT ME!
        • ySelected
          boolean ySelected
          DOCUMENT ME!
        • zRadio
          JRadioButton zRadio
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogDTIEstimateTensor

      class JDialogDTIEstimateTensor extends JDialogBase implements Serializable

      • Serialized Fields

        • bValueTextField
          JTextField bValueTextField
          textfields *
        • currDir
          String currDir
          current directory *
        • DTI
          ModelImage DTI
          Diffusion Tensor image.
        • formatTextField
          JTextField formatTextField
          textfields *
        • gapTextField
          JTextField gapTextField
          textfields *
        • gbc
          GridBagConstraints gbc
          grid bag constraints *
        • gbc2
          GridBagConstraints gbc2
          grid bag constraints *
        • gbc3
          GridBagConstraints gbc3
          grid bag constraints *
        • hFOVTextField
          JTextField hFOVTextField
          textfields *
        • imagePlaneTextField
          JTextField imagePlaneTextField
          textfields *
        • kAlgorithm
          AlgorithmDWI2DTI kAlgorithm
          handle to algorithm *
        • listFile
          File listFile
          list file *
        • loadMaskButton
          JButton loadMaskButton
          button *
        • m_aakDWIList
          String[][] m_aakDWIList
          List of file names for the Diffusion Weighted Images, from the .path *
        • m_aiMatrixEntries
          int[] m_aiMatrixEntries
          keeps track of unique entries in the BMatrix
        • m_fMeanNoise
          float m_fMeanNoise
          Mean noise vale read from the .list file
        • m_fResX
          float m_fResX
          Slice thickness read from .list file
        • m_fResY
          float m_fResY
          Slice thickness read from .list file
        • m_fResZ
          float m_fResZ
          Slice thickness read from .list file
        • m_iBOrig
          int m_iBOrig
          Number of different BMatrix rows:
        • m_iDimX
          int m_iDimX
          X-dimensions for Diffusion Weighted Images.
        • m_iDimY
          int m_iDimY
          Y-dimensions for Diffusion Weighted Images.
        • m_iSlices
          int m_iSlices
          Number of slices in the Diffusion Weighted Images series.
        • m_iWeights
          int m_iWeights
          Number of weights in the Diffusion Weighted Images series.
        • m_kBMatrix
          WildMagic.LibFoundation.Mathematics.GMatrixd m_kBMatrix
          General matrix storing BMatrix values.
        • m_kParentDir
          String m_kParentDir
          paren tdir *
        • m_kRawFormat
          String m_kRawFormat
          raw image format read from the .list file:
        • mainPanel
          JPanel mainPanel
          main panel *
        • maskImage
          ModelImage maskImage
          mask Image *
        • maskImageTextField
          JTextField maskImageTextField
          textfields *
        • numSlicesTextField
          JTextField numSlicesTextField
          textfields *
        • numVolumesTextField
          JTextField numVolumesTextField
          textfields *
        • outputDirTextField
          JTextField outputDirTextField
          textfields *
        • phaseEncodingTextField
          JTextField phaseEncodingTextField
          textfields *
        • slicesVector
          Vector<ArrayList<String>> slicesVector
          slices *
        • sliceThicknessTextField
          JTextField sliceThicknessTextField
          textfields *
        • srcImage
          ModelImage srcImage
          src image *
        • srcImagesTable
          JTable srcImagesTable
          table to display the src image names.
        • srcTableModel
          DefaultTableModel srcTableModel
          table model for the srcimages.
        • vFOVTextField
          JTextField vFOVTextField
          textfields *
        • xdimTextField
          JTextField xdimTextField
          textfields *
        • ydimTextField
          JTextField ydimTextField
          textfields *

    • Class gov.nih.mipav.view.dialogs.JDialogDualContourSearch

      class JDialogDualContourSearch extends JDialogBase implements Serializable

      • Serialized Fields

        • componentImage
          ViewJComponentEditImage componentImage
          DOCUMENT ME!
        • contourPoints
          int contourPoints
        • dualAlgo
          AlgorithmDualContourSearch dualAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • innerButton
          JRadioButton innerButton
          DOCUMENT ME!
        • innerIndex
          int innerIndex
          DOCUMENT ME!
        • linePoints
          int linePoints
        • outerButton
          JRadioButton outerButton
          DOCUMENT ME!
        • outerIndex
          int outerIndex
          DOCUMENT ME!
        • pixelsContract
          int pixelsContract
        • pixelsExpand
          int pixelsExpand
        • regularization
          double regularization
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • sigmas
          double[] sigmas
        • textContourPoints
          JTextField textContourPoints
        • textContract
          JTextField textContract
        • textExpand
          JTextField textExpand
        • textGaussX
          JTextField textGaussX
        • textGaussY
          JTextField textGaussY
        • textLinePoints
          JTextField textLinePoints
        • textRegularization
          JTextField textRegularization
        • titles
          String[] titles
        • VOIGroup
          ButtonGroup VOIGroup
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogEdgeDetection3D

      class JDialogEdgeDetection3D extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogEdgeLaplacian

      class JDialogEdgeLaplacian extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4875093981299828397L

    • Class gov.nih.mipav.view.dialogs.JDialogEdgeNMSuppression

      class JDialogEdgeNMSuppression extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7682705151759726551L

    • Class gov.nih.mipav.view.dialogs.JDialogEdgePreservingSmoothing

      class JDialogEdgePreservingSmoothing extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogEditCircleDiameter

      class JDialogEditCircleDiameter extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogEditor

      class JDialogEditor extends JDialogBase implements Serializable
      serialVersionUID:
      1979336171963042575L

      • Serialized Fields

        • closedOkay
          boolean closedOkay
          DOCUMENT ME!
        • imageFileName
          String imageFileName
          DOCUMENT ME!
        • key
          Object key
          the representative key of this object; must be unique.
        • newValue
          JPanelEdit[] newValue
          DOCUMENT ME!
        • oldValue
          JTextField oldValue
          DOCUMENT ME!
        • psetDesc
          String psetDesc
          DOCUMENT ME!
        • row
          int row
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogEditSquareLength

      class JDialogEditSquareLength extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogEditUserDefinedFileTypes

      class JDialogEditUserDefinedFileTypes extends JDialogBase implements Serializable

      • Serialized Fields

        • applyClosePanel
          JPanel applyClosePanel
          The panels that make up this Dialog
        • checkBoxArrList
          ArrayList<JCheckBox> checkBoxArrList
          This is the ArrayList of JCheckBoxes
        • checkboxNames
          ArrayList<String> checkboxNames
          This is a list of the checkbox names that is used for validation of user input to make sure there are no duplicates
        • checkedFileTypes
          ArrayList<String> checkedFileTypes
          This a list is the list of checked check boxes that is populated when user hits apply
        • displayPanel
          JPanel displayPanel
          The panels that make up this Dialog
        • fileExtensionsTS
          TreeSet<String> fileExtensionsTS
          This is the alphabetically sorted collection of supported file extension names
        • preferencesFileTypes
          String[] preferencesFileTypes
          This array is the list of file extensions that is pulled from the Preferences. We need this in order to check the appropriate check boxes and the user input text field when the user opens up this dialog initailly
        • userInput
          JTextField userInput
          This is the user input for additional file extensions
        • userInputFileTypes
          String[] userInputFileTypes
          This array is the list of additional file extensions that user typed in that is populated when user hits apply

    • Class gov.nih.mipav.view.dialogs.JDialogEfficientWatershed

      class JDialogEfficientWatershed extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogEllipseGeneration

      class JDialogEllipseGeneration extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • aggregatedButton
          JRadioButton aggregatedButton
        • constrainedButton
          JRadioButton constrainedButton
        • eAlgo
          AlgorithmEllipseGeneration eAlgo
          DOCUMENT ME!
        • extents
          int[] extents
        • highestForbiddenLabel
          JLabel highestForbiddenLabel
        • highestForbiddenNNDistance
          double highestForbiddenNNDistance
        • highestForbiddenText
          JTextField highestForbiddenText
        • highestRegenerationLabel
          JLabel highestRegenerationLabel
        • highestRegenerationNNDistance
          double highestRegenerationNNDistance
        • highestRegenerationText
          JTextField highestRegenerationText
        • initialEllipsesLabel
          JLabel initialEllipsesLabel
        • initialEllipsesText
          JTextField initialEllipsesText
        • initialRandomEllipses
          int initialRandomEllipses
        • lowestForbiddenLabel
          JLabel lowestForbiddenLabel
        • lowestForbiddenNNDistance
          double lowestForbiddenNNDistance
        • lowestForbiddenText
          JTextField lowestForbiddenText
        • maximumDistanceLabel
          JLabel maximumDistanceLabel
        • maximumDistanceText
          JTextField maximumDistanceText
        • maximumNearestNeighborDistance
          double maximumNearestNeighborDistance
        • minimumDistanceLabel
          JLabel minimumDistanceLabel
        • minimumDistanceText
          JTextField minimumDistanceText
        • minimumNearestNeighborDistance
          double minimumNearestNeighborDistance
        • numEllipses
          int numEllipses
        • numEllipsesText
          JTextField numEllipsesText
        • pattern
          int pattern
        • patternGroup
          ButtonGroup patternGroup
        • phi
          double phi
        • phiText
          JTextField phiText
        • randomButton
          JRadioButton randomButton
        • regularButton
          JRadioButton regularButton
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • semiMajorAxis
          int semiMajorAxis
        • semiMajorAxisText
          JTextField semiMajorAxisText
          DOCUMENT ME!
        • semiMinorAxis
          int semiMinorAxis
        • semiMinorAxisText
          JTextField semiMinorAxisText
        • xDim
          int xDim
          DOCUMENT ME!
        • xDimText
          JTextField xDimText
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • yDimText
          JTextField yDimText

    • Class gov.nih.mipav.view.dialogs.JDialogEllipseToCircle

      class JDialogEllipseToCircle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

    • Class gov.nih.mipav.view.dialogs.JDialogEllipseToRectangle

      class JDialogEllipseToRectangle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

    • Class gov.nih.mipav.view.dialogs.JDialogEmbeddedConfidenceEdgeDetection

      class JDialogEmbeddedConfidenceEdgeDetection extends JDialogScriptableBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogEnhancedDicomChoice

      class JDialogEnhancedDicomChoice extends JDialogBase implements Serializable

      • Serialized Fields

        • enhancedCT
          JRadioButton enhancedCT
          Radio button to indicate that an enhanced CT file should be written out.
        • enhancedMR
          JRadioButton enhancedMR
          Radio button to indicate that an enhanced MR file should be written out.
        • enhancedOther
          JRadioButton enhancedOther
        • enhancedXA
          JRadioButton enhancedXA
          Radio button to indicate that an enhanced XA file should be written out.
        • okayPressed
          boolean okayPressed
          Whether the window was closed through the user clicking the OK button (and not just killing the dialog).

    • Class gov.nih.mipav.view.dialogs.JDialogEntropicEdgeDetection

      class JDialogEntropicEdgeDetection extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogEntropyMinimization

      class JDialogEntropyMinimization extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -417774372547972740L

      • Serialized Fields

        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • emAlgo
          AlgorithmEntropyMinimization emAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • m2Button
          JRadioButton m2Button
          DOCUMENT ME!
        • m3Button
          JRadioButton m3Button
          DOCUMENT ME!
        • ma2Button
          JRadioButton ma2Button
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • noiseGroup
          ButtonGroup noiseGroup
          DOCUMENT ME!
        • noiseType
          int noiseType
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • subsample
          boolean subsample
          DOCUMENT ME!
        • subsampleCheckbox
          JCheckBox subsampleCheckbox
          DOCUMENT ME!
        • thresholdCheckbox
          JCheckBox thresholdCheckbox
          DOCUMENT ME!
        • thresholdLabel
          JLabel thresholdLabel
          DOCUMENT ME!
        • thresholdLevel
          float thresholdLevel
          DOCUMENT ME!
        • thresholdSelected
          boolean thresholdSelected
          DOCUMENT ME!
        • thresholdText
          JTextField thresholdText
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogErode

      class JDialogErode extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -3069882376396094338L

    • Class gov.nih.mipav.view.dialogs.JDialogEvaluateMaskSegmentation

      class JDialogEvaluateMaskSegmentation extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -1381945839499712050L

    • Class gov.nih.mipav.view.dialogs.JDialogEvaluateSegmentation

      class JDialogEvaluateSegmentation extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -6446476110592386369L

      • Serialized Fields

        • comboBoxImage
          JComboBox comboBoxImage
          Combo box with image names for choosing test image.
        • evalSeg
          AlgorithmEvaluateSegmentation evalSeg
          Algorithm to run from this dialog.
        • imagesFound
          int imagesFound
          DOCUMENT ME!
        • testImage
          ModelImage testImage
          DOCUMENT ME!
        • titles
          String[] titles
          Used to lock and unlock images.
        • trueBoundingVOIs
          int trueBoundingVOIs
          DOCUMENT ME!
        • trueID
          int[] trueID
          DOCUMENT ME!
        • trueImage
          ModelImage trueImage
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          Reference to userface.

    • Class gov.nih.mipav.view.dialogs.JDialogEvolveBoundaryManual

      class JDialogEvolveBoundaryManual extends JDialogBase implements Serializable
      serialVersionUID:
      -2170631279185094655L

      • Serialized Fields

        • boundaryDir
          int boundaryDir
          DOCUMENT ME!
        • boundaryDirBox
          JComboBox boundaryDirBox
          DOCUMENT ME!
        • groupNum
          int groupNum
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • srcVOI
          VOI srcVOI
          DOCUMENT ME!
        • textChangeX
          JTextField textChangeX
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogExtractBrain

      class JDialogExtractBrain extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7723410343739118755L

      • Serialized Fields

        • aboveMedian
          float aboveMedian
          The factor above which second stage edge erosion occurs.
        • centerOfMass
          WildMagic.LibFoundation.Mathematics.Vector3f centerOfMass
          The volume's center of mass computed from computeCenter(ModelImage, int, boolean)
        • depth
          int depth
          The maximum depth within the brain's surface to sample image intensities, by default set to 5.
        • depthTF
          JTextField depthTF
          Field for entering the maximum depth. The dialog box suggests a value between 3 - 19 and requires a value from 3 - 33.
        • erosionLabel
          JLabel erosionLabel
          Label for the percentage entered for second stage edge erosion.
        • erosionTF
          JTextField erosionTF
          Defines the allowable percentage for edge intensity values ub second stage edge erosion, default is 50 percent.
        • extractBrainAlgo
          AlgorithmBrainExtractor extractBrainAlgo
          Algorithm used for brain extraction.
        • extractToPaint
          boolean extractToPaint
          When true, mask of extracted brain is painted over the source image.
        • extractToPaintCheckBox
          JCheckBox extractToPaintCheckBox
          When checked, mask of extracted brain is painted over the source image.
        • image
          ModelImage image
          Source image for extracting brain, default image is null.
        • imageRatio
          float imageRatio
          Image influence ratio for controlling the sampling depth used to calculate intensity extrema, by default set to .1.
        • imageRatioTF
          JTextField imageRatioTF
          Field for entering the image influence ratio. The dialog box requires that a value from .01 - .51 be entered.
        • initCenterPoint
          WildMagic.LibFoundation.Mathematics.Vector3f initCenterPoint
          Either the volume's center of mass or a user indicated point depending on the value of useCenterOfMass.
        • initCenterX
          float initCenterX
          Used to denote the brain's center of mass y-coordinate. By default set to zero.
        • initCenterXLabel
          JLabel initCenterXLabel
          Label for the x-coordinate of the user-defined center.
        • initCenterXTF
          JTextField initCenterXTF
          An optional field for denoting a desired initial x-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false
        • initCenterY
          float initCenterY
          Used to denote the brain's center of mass y-coordinate. By default set to zero.
        • initCenterYLabel
          JLabel initCenterYLabel
          Label for the y-coordinate of the user-defined center.
        • initCenterYTF
          JTextField initCenterYTF
          An optional field for denoting a desired initial y-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false
        • initCenterZ
          float initCenterZ
          Used to denote the brain's center of mass y-coordinate. By default set to zero.
        • initCenterZLabel
          JLabel initCenterZLabel
          Label for the z-coordinate of the user-defined center.
        • initCenterZTF
          JTextField initCenterZTF
          An optional field for denoting a desired initial z-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false
        • justEllipse
          boolean justEllipse
          When true, image mask is set to the initial ellipsoid approximation of the brain calculated from the volume's center of mass.
        • justInitEllipsoidCheckbox
          JCheckBox justInitEllipsoidCheckbox
          When checked, justEllipse is set to true.
        • nIterations
          int nIterations
          Number of surface evolutions to perform, by default set to 500.
        • nIterationsTF
          JTextField nIterationsTF
          Field for inputting the number of surface evolutions to perform. This requests, but does not require, a value from 100 - 2000
        • orientation
          int orientation
          Orientation value corresponding to not the value of AlgorithmBrainExtractor.SAT_COR
        • orientCheckbox
          JCheckBox orientCheckbox
          When checked, denotes that the images orientation does not correspond to AlgorithmBrainExtractor.SAT_COR
        • secondStageCheckBox
          JCheckBox secondStageCheckBox
          Initially unchecked, determined whether this algorithm performs secondStageErosion
        • secondStageErosion
          boolean secondStageErosion
          When true, sets edge values which are greater than the median intensity by a user-defined factor of aboveMedian to zero.
        • stiffness
          float stiffness
          Allows for variable motion of the mesh in the surface normal direction, default value of .15
        • stiffnessTF
          JTextField stiffnessTF
          Field for specifing stiffness of the mesh. The dialog box suggests, but does not require that a value between .01 and .5 entered.
        • titles
          String[] titles
          DOCUMENT ME!
        • useCenterOfMass
          boolean useCenterOfMass
          By default true, parameter indicates that the center position of the brain should be calculated using JDialogExtractBrain.computeCenter(ModelImage, int, boolean)
        • useCenterOfMassCheckBox
          JCheckBox useCenterOfMassCheckBox
          By default checked, yields a true value for useCenterOfMass
        • userInterface
          ViewUserInterface userInterface
          The user interface for this dialog box.
        • useSphere
          boolean useSphere
          When true estimates that boundary of the VOI by a sphere.
        • useSphereCheckbox
          JCheckBox useSphereCheckbox
          Initially not checked, estimates the boundary by a sphere rather than an ellipse.

    • Class gov.nih.mipav.view.dialogs.JDialogExtractObject

      class JDialogExtractObject extends JDialogBase implements Serializable
      serialVersionUID:
      -4587834627195392398L

      • Serialized Fields

        • chooserButton
          JButton chooserButton
          DOCUMENT ME!
        • chooserButton2
          JButton chooserButton2
          DOCUMENT ME!
        • extractObjectAlgo
          AlgorithmObjectExtractor extractObjectAlgo
          DOCUMENT ME!
        • groupNum
          int groupNum
          DOCUMENT ME!
        • gvfImage
          ModelImage[] gvfImage
          DOCUMENT ME!
        • gvfModel
          DefaultListModel gvfModel
          DOCUMENT ME!
        • gvfName
          String gvfName
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • justInit
          boolean justInit
          DOCUMENT ME!
        • justInitCheckbox
          JCheckBox justInitCheckbox
          DOCUMENT ME!
        • model
          DefaultListModel model
          DOCUMENT ME!
        • removeButton
          JButton removeButton
          DOCUMENT ME!
        • removeButton2
          JButton removeButton2
          DOCUMENT ME!
        • saveGVF
          boolean saveGVF
          DOCUMENT ME!
        • saveGVFCheckBox
          JCheckBox saveGVFCheckBox
          DOCUMENT ME!
        • srcVOI
          VOI srcVOI
          DOCUMENT ME!
        • surName
          String surName
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • triMesh
          WildMagic.LibGraphics.SceneGraph.TriMesh triMesh
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogExtractSlices

      class JDialogExtractSlices extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      5258936423490848172L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogExtractSlicesVolumes

      class JDialogExtractSlicesVolumes extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2217089541745539442L

      • Serialized Fields

        • checkboxList
          JCheckBox[] checkboxList
          DOCUMENT ME!
        • checkboxPanel
          JPanel checkboxPanel
          DOCUMENT ME!
        • checkButton
          JButton checkButton
          DOCUMENT ME!
        • checkEvenButton
          JButton checkEvenButton
          DOCUMENT ME!
        • checkListExtract
          boolean[] checkListExtract
          DOCUMENT ME!
        • checkOddButton
          JButton checkOddButton
          DOCUMENT ME!
        • exampleLabel
          JLabel exampleLabel
          DOCUMENT ME!
        • exampleLabel2
          JLabel exampleLabel2
          DOCUMENT ME!
        • extractedImages
          ModelImage[] extractedImages
          DOCUMENT ME!
        • extractSlicesAlgo
          AlgorithmExtractSlicesVolumes extractSlicesAlgo
          DOCUMENT ME!
        • nSlices
          int nSlices
          DOCUMENT ME!
        • numChecked
          int numChecked
          DOCUMENT ME!
        • rangeField
          JTextField rangeField
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          DOCUMENT ME!
        • unCheckButton
          JButton unCheckButton
          DOCUMENT ME!
        • useRange
          JCheckBox useRange
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogExtractSurfaceCubes

      class JDialogExtractSurfaceCubes extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7919553320035488503L

      • Serialized Fields

        • blurCheck
          JCheckBox blurCheck
          DOCUMENT ME!
        • blurFlag
          boolean blurFlag
          DOCUMENT ME!
        • blurTF
          JTextField blurTF
          DOCUMENT ME!
        • blurValue
          float blurValue
          DOCUMENT ME!
        • decimateFlag
          boolean decimateFlag
          DOCUMENT ME!
        • decimateSurfaceCB
          JCheckBox decimateSurfaceCB
          DOCUMENT ME!
        • disposeImage
          boolean disposeImage
          Flag indicates if this object should dispose the input image.
        • extractSurAlgo
          AlgorithmExtractSurfaceCubes extractSurAlgo
          DOCUMENT ME!
        • fileButton
          JButton fileButton
          DOCUMENT ME!
        • fileName
          String fileName
          DOCUMENT ME!
        • fileTF
          JTextField fileTF
          DOCUMENT ME!
        • fileTypeList
          JComboBox fileTypeList
          surface file format list.
        • fileTypes
          String[] fileTypes
          surface file formats.
        • image
          ModelImage image
          DOCUMENT ME!
        • intensityLevelRB
          JRadioButton intensityLevelRB
          DOCUMENT ME!
        • intensityTF
          JTextField intensityTF
          DOCUMENT ME!
        • level
          int level
          DOCUMENT ME!
        • maskImageRB
          JRadioButton maskImageRB
          DOCUMENT ME!
        • mode
          int mode
          DOCUMENT ME!
        • useOCL
          boolean useOCL
          DOCUMENT ME!
        • useOCLCheckbox
          JCheckBox useOCLCheckbox
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIRegionsRB
          JRadioButton VOIRegionsRB
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFaceAnonymize

      class JDialogFaceAnonymize extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      4849596386051779471L

      • Serialized Fields

        • atlasImage
          ModelImage atlasImage
        • blur
          boolean blur
        • blurAllRadio
          JRadioButton blurAllRadio
          Button for blurring the face / skull.
        • blurFaceRadio
          JRadioButton blurFaceRadio
          Button for blurring just the face.
        • defaceAlgo
          AlgorithmSkullRemoval defaceAlgo
          The algorithm corresponding to this dialog box.
        • extraBrainPaddingField
          JTextField extraBrainPaddingField
          Text field corresponding to brain padding parameter.
        • extraMMsToPad
          int extraMMsToPad
          FaceAnonymizer parameter. Guarantees that the extracted brain will be avoided by the specified number of millimeters. Initially set to 20.
        • face
          boolean face
        • faceOrientation
          int faceOrientation
          Indicates face orientation of the image.
        • facingDownRadio
          JRadioButton facingDownRadio
          Button for facing down image.
        • facingIntoRadio
          JRadioButton facingIntoRadio
          Button for facing into the screen image.
        • facingLeftRadio
          JRadioButton facingLeftRadio
          Button for facing left image.
        • facingOutRadio
          JRadioButton facingOutRadio
          Button for facing out image.
        • facingRightRadio
          JRadioButton facingRightRadio
          Button for facing right image.
        • facingUpRadio
          JRadioButton facingUpRadio
          Button for facing up image.
        • imageTextField
          JTextField imageTextField
        • remove
          boolean remove
        • removeAllRadio
          JRadioButton removeAllRadio
          Button for removing the face / skull.
        • removeFaceRadio
          JRadioButton removeFaceRadio
          Button for removing just the face.
        • showAllSegmentationRadio
          JRadioButton showAllSegmentationRadio
          Button for displaying the full segmentation.
        • showFaceSegmentation
          boolean showFaceSegmentation
        • showFaceSegmentationRadio
          JRadioButton showFaceSegmentationRadio
          Button for displaying the face segmentation.
        • showSkullSegmentation
          boolean showSkullSegmentation
        • srcImage
          ModelImage srcImage
          The image that face anonymization will be performed on.

    • Class gov.nih.mipav.view.dialogs.JDialogFaceAnonymizerBET

      class JDialogFaceAnonymizerBET extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -1027127665518969757L

      • Serialized Fields

        • defaceAlgo
          AlgorithmFaceAnonymizerBET defaceAlgo
          The algorithm corresponding to this dialog box.
        • estimateWithSphereBET
          boolean estimateWithSphereBET
          Flag indicates BET should approximate initial brain by sphere. Initially set to false.
        • estimateWithSphereCheckbox
          JCheckBox estimateWithSphereCheckbox
          Check box corresponding to estimateSphereBET.
        • extraBrainPaddingField
          JTextField extraBrainPaddingField
          Text field corresponding to brain padding parameter.
        • extraMMsToPad
          int extraMMsToPad
          FaceAnonymizer parameter. Guarantees that the extracted brain will be avoided by the specified number of millimeters. Initially set to 20.
        • faceOrientation
          int faceOrientation
          Indicates face orientation of the image.
        • facingDownRadio
          JRadioButton facingDownRadio
          Button for facing down image.
        • facingIntoRadio
          JRadioButton facingIntoRadio
          Button for facing into the screen image.
        • facingLeftRadio
          JRadioButton facingLeftRadio
          Button for facing left image.
        • facingOutRadio
          JRadioButton facingOutRadio
          Button for facing out image.
        • facingRightRadio
          JRadioButton facingRightRadio
          Button for facing right image.
        • facingUpRadio
          JRadioButton facingUpRadio
          Button for facing up image.
        • imageInfluenceBET
          float imageInfluenceBET
          the depth to calculate in approximating brain maximum and minimum intensities. Initially set to .1
        • imageInfluenceField
          JTextField imageInfluenceField
          The text field corresponding to imageInfluenceField.
        • srcImage
          ModelImage srcImage
          The image that face anonymization will be performed on.
        • stiffnessBET
          float stiffnessBET
          Controls the stiffness of the brain approximation mesh. Initially set to 0.15.
        • stiffnessField
          JTextField stiffnessField
          The text field corresponding to stiffnessBET.

    • Class gov.nih.mipav.view.dialogs.JDialogFacetModel

      class JDialogFacetModel extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogFastMarching

      class JDialogFastMarching extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2307387171411648198L

      • Serialized Fields

        • image
          ModelImage image
          Source Image
        • image25DCheckbox
          JCheckBox image25DCheckbox
          Process each slice independently, or as a 3D image.
        • m_bImage25D
          boolean m_bImage25D
        • m_fAdvectionWeight
          float m_fAdvectionWeight
        • m_fCurvatureWeight
          float m_fCurvatureWeight
        • m_fGMScale
          float m_fGMScale
        • m_fLaplacianWeight
          float m_fLaplacianWeight
        • m_fMaxDistance
          float m_fMaxDistance
        • m_fPropagationWeight
          float m_fPropagationWeight
        • m_fSAlpha
          float m_fSAlpha
        • m_fSBeta
          float m_fSBeta
        • m_fSMax
          float m_fSMax
        • m_fSMin
          float m_fSMin
        • m_iCoarseMax
          int m_iCoarseMax
        • m_iEvolveMax
          int m_iEvolveMax
        • m_iFilterType
          int m_iFilterType
        • m_iIters
          int m_iIters
        • textAdvectionWeight
          JTextField textAdvectionWeight
          Advection weight parameter
        • textCoarseMax
          JTextField textCoarseMax
          Max coarse iterations.
        • textCurvatureWeight
          JTextField textCurvatureWeight
          Curvature weight parameter
        • textGMScale
          JTextField textGMScale
          Gradient Magnitude Scale factor
        • textIters
          JTextField textIters
          Number of Iterations
        • textLaplacianWeight
          JTextField textLaplacianWeight
          Laplacian weight parameter
        • textMaxDistance
          JTextField textMaxDistance
          Max Distance parameter
        • textMaxEvolution
          JTextField textMaxEvolution
          Maximum Evolution steps
        • textPropagationWeight
          JTextField textPropagationWeight
          Propagation weight parameter
        • textSigmoiBeta
          JTextField textSigmoiBeta
          Sigmoid Beta parameter
        • textSigmoidAlpha
          JTextField textSigmoidAlpha
          Sigmoid Alpha parameter
        • textSigmoidMax
          JTextField textSigmoidMax
          Sigmoid Max parameter
        • textSigmoidMin
          JTextField textSigmoidMin
          Sigmoid Min parameter

    • Class gov.nih.mipav.view.dialogs.JDialogFFT

      class JDialogFFT extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7969114857894881595L

      • Serialized Fields

        • bandPass
          JRadioButton bandPass
          DOCUMENT ME!
        • bandStop
          JRadioButton bandStop
          DOCUMENT ME!
        • butterworthFilter
          JRadioButton butterworthFilter
          DOCUMENT ME!
        • buttonPanel
          JPanel buttonPanel
          DOCUMENT ME!
        • chebyshevIFilter
          JRadioButton chebyshevIFilter
        • chebyshevIIFilter
          JRadioButton chebyshevIIFilter
        • complexInverse
          boolean complexInverse
          Whether a complex inverse FFT should be computed
        • complexInverseCheckbox
          JCheckBox complexInverseCheckbox
          Whether the inverse FFT should return a complex image (appropriate when only when source image is complex)
        • constructionGroup
          ButtonGroup constructionGroup
          DOCUMENT ME!
        • constructionMethod
          int constructionMethod
          DOCUMENT ME!
        • constructionPanel
          JPanel constructionPanel
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • directionGroup
          ButtonGroup directionGroup
          DOCUMENT ME!
        • directionPanel
          JPanel directionPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • ellipticFilter
          JRadioButton ellipticFilter
        • epsilon
          double epsilon
        • FFTAlgo
          AlgorithmFFT FFTAlgo
          Float precision default, openCL enabled FFT algorithm
        • FFTAlgo2
          AlgorithmFFT2 FFTAlgo2
          Double precision, openCL enabled FFT algroithm
        • filterOrder
          int filterOrder
          DOCUMENT ME!
        • filterPanel
          JPanel filterPanel
          DOCUMENT ME!
        • filterType
          int filterType
          DOCUMENT ME!
        • filterTypeGroup
          ButtonGroup filterTypeGroup
          DOCUMENT ME!
        • fltFmt
          DecimalFormat fltFmt
        • forwardFFT
          JRadioButton forwardFFT
          User selects to indicate forward FFT processing should occur, resulting in frequency image
        • freq1
          double freq1
          DOCUMENT ME!
        • freq2
          double freq2
          DOCUMENT ME!
        • frequencyFilter
          JRadioButton frequencyFilter
          DOCUMENT ME!
        • FrequencyFilterAlgo
          AlgorithmFrequencyFilter FrequencyFilterAlgo
        • gaussianFilter
          JRadioButton gaussianFilter
          DOCUMENT ME!
        • highPass
          JRadioButton highPass
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          Whether algorithm should run seperately on each slice of a 3D image
        • image25DCheckbox
          JCheckBox image25DCheckbox
          User can indicate whether the FFT of each slice of a 3D image is computed seperately
        • imageCrop
          boolean imageCrop
          DOCUMENT ME!
        • imageCropCheckbox
          JCheckBox imageCropCheckbox
          DOCUMENT ME!
        • inverseFFT
          JRadioButton inverseFFT
          DOCUMENT ME!
        • kernelDiameter
          int kernelDiameter
          DOCUMENT ME!
        • labelEpsilon
          JLabel labelEpsilon
        • labelF1
          JLabel labelF1
          DOCUMENT ME!
        • labelF2
          JLabel labelF2
          DOCUMENT ME!
        • labelKernelDiameter
          JLabel labelKernelDiameter
          DOCUMENT ME!
        • labelOrder
          JLabel labelOrder
          DOCUMENT ME!
        • labelRs
          JLabel labelRs
        • logDisplayCheckbox
          JCheckBox logDisplayCheckbox
          private JPanel optionsPanel;.
        • logMagDisplay
          boolean logMagDisplay
          DOCUMENT ME!
        • lowPass
          JRadioButton lowPass
          DOCUMENT ME!
        • mainPanel
          JPanel mainPanel
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • onlyFrequencyFilter
          boolean onlyFrequencyFilter
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rs
          double rs
        • testDouble
          boolean testDouble
          True when double precision testing should be performed, default is float.
        • textEpsilon
          JTextField textEpsilon
        • textF1
          JTextField textF1
          DOCUMENT ME!
        • textF2
          JTextField textF2
          DOCUMENT ME!
        • textKernelDiameter
          JTextField textKernelDiameter
          DOCUMENT ME!
        • textOrder
          JTextField textOrder
          DOCUMENT ME!
        • textRs
          JTextField textRs
        • titles
          String[] titles
          DOCUMENT ME!
        • transformDir
          int transformDir
          DOCUMENT ME!
        • unequalDim
          boolean unequalDim
          Whether FFT algorithm can return non-equal x,y dimensions
        • unequalDimCheckbox
          JCheckBox unequalDimCheckbox
          Indicates whether user wants FFT to return non-equal x,y dimensions
        • useOCL
          boolean useOCL
          Flag indicating whether to use OpenCL processing.
        • useOCLCheckbox
          JCheckBox useOCLCheckbox
          Indicates whether user wants openCL for processing.
        • windowFilter
          JRadioButton windowFilter
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFileInfo

      class JDialogFileInfo extends JDialogBase implements Serializable
      serialVersionUID:
      1629395651992086059L

    • Class gov.nih.mipav.view.dialogs.JDialogFileInfoDICOM

      class JDialogFileInfoDICOM extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7337962386655472087L

      • Serialized Fields

        • anchorPane
          JScrollPane anchorPane
          DOCUMENT ME!
        • anonymizeButton
          JButton anonymizeButton
          buttons for toolbar *
        • bogusShowPrivateButton
          JToggleButton bogusShowPrivateButton
        • breakDownArea
          JTextArea breakDownArea
        • checkAllButton
          JButton checkAllButton
          buttons for toolbar *
        • columnNames
          ArrayList<String> columnNames
        • deleteTagButton
          JButton deleteTagButton
          buttons for toolbar *
        • DicomInfo
          FileInfoDicom DicomInfo
          DOCUMENT ME!
        • directory
          String directory
          directory of where dicom tags are save to *
        • editorDeleteTag
          JDialogDICOMDeleteTagEditor editorDeleteTag
        • editorDialogDicom
          JDialogDICOMTagEditor editorDialogDicom
          DOCUMENT ME!
        • editorDialogDicomList
          Vector<JDialogDICOMTagEditor> editorDialogDicomList
          DOCUMENT ME!
        • editorNewTag
          JDialogDICOMNewTagEditor editorNewTag
        • editTagButton
          JButton editTagButton
          buttons for toolbar *
        • fileName
          String fileName
          fileName of where dicom tags are save to *
        • groupColorMap
          TreeMap<String,Color> groupColorMap
          Maps the group word to a displayed color, private tags are not specified. *
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • isAppend
          boolean isAppend
          DOCUMENT ME!
        • launchFileChooser
          boolean launchFileChooser
        • listSelectorDicom
          ListSelectionModel listSelectorDicom
          DOCUMENT ME!
        • newTagButton
          JButton newTagButton
          Button for inserting new tags
        • overlayButton
          JButton overlayButton
          buttons for toolbar *
        • saveCheckedAppendButton
          JButton saveCheckedAppendButton
          buttons for toolbar *
        • saveCheckedButton
          JButton saveCheckedButton
          buttons for toolbar *
        • selectedRowDicom
          int selectedRowDicom
          DOCUMENT ME!
        • showPrivate
          boolean showPrivate
          DOCUMENT ME!
        • showPrivateButton
          JToggleButton showPrivateButton
        • sliceIndex
          int sliceIndex
          slice index for which fileInfo is saved *
        • splitPane
          JSplitPane splitPane
        • tablePane
          JScrollPane tablePane
          DOCUMENT ME!
        • tagsModel
          ViewTableModel tagsModel
          DOCUMENT ME!
        • tagsTable
          JTable tagsTable
          DOCUMENT ME!
        • toolBar
          JToolBar toolBar
          tool bar *
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          DOCUMENT ME !
        • toolbarPanel
          JPanel toolbarPanel
          DOCUMENT ME!
        • uncheckAllButton
          JButton uncheckAllButton
          buttons for toolbar *

    • Class gov.nih.mipav.view.dialogs.JDialogFileInfoMinc

      class JDialogFileInfoMinc extends JDialogText implements Serializable
      serialVersionUID:
      -966963254580510543L

    • Class gov.nih.mipav.view.dialogs.JDialogFileInfoMincHDF

      class JDialogFileInfoMincHDF extends JDialogBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogFileInfoXML

      class JDialogFileInfoXML extends JDialogBase implements Serializable
      serialVersionUID:
      -8790820691884630599L

    • Class gov.nih.mipav.view.dialogs.JDialogFillObjects

      class JDialogFillObjects extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3464349858386521845L

      • Serialized Fields

        • destinationGroup
          ButtonGroup destinationGroup
          use later.
        • destinationPanel
          JPanel destinationPanel
          panel that hold the new image radio button.
        • displayLoc
          int displayLoc
          Flag indicating if a new image is to be generated.
        • do25D
          boolean do25D
          DOCUMENT ME!
        • idObjectsAlgo25D
          AlgorithmMorphology25D idObjectsAlgo25D
          Morphology25D algorithm reference.
        • idObjectsAlgo2D
          AlgorithmMorphology2D idObjectsAlgo2D
          Morphology2D algorithm reference.
        • idObjectsAlgo3D
          AlgorithmMorphology3D idObjectsAlgo3D
          Morphology3D algorithm reference.
        • image
          ModelImage image
          source image.
        • image25D
          JCheckBox image25D
          DOCUMENT ME!
        • imageVOIGroup
          ButtonGroup imageVOIGroup
          DOCUMENT ME!
        • imageVOIPanel
          JPanel imageVOIPanel
          used later.
        • newImage
          JRadioButton newImage
          new image radio button.
        • regionFlag
          boolean regionFlag
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          use later.
        • titles
          String[] titles
          DOCUMENT ME!
        • ubyteImage
          ModelImage ubyteImage
          Usigned byte image, the actual image to do the morphology calculation.
        • userInterface
          ViewUserInterface userInterface
          user interface renference.
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFilterChoice

      class JDialogFilterChoice extends JDialogBase implements Serializable
      serialVersionUID:
      3198970819287117617L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogFindEdges

      class JDialogFindEdges extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8141787725573550699L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogFIREEdgeExtraction

      class JDialogFIREEdgeExtraction extends JDialogScriptableBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogFlip

      class JDialogFlip extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5672670158596197276L

      • Serialized Fields

        • changeOrientationOrigin
          boolean changeOrientationOrigin
        • flipAlgo
          AlgorithmFlip flipAlgo
          Algorithm used by the dialog.
        • flipAxis
          int flipAxis
          Axis to flip around.
        • flipAxisXRadioButton
          JRadioButton flipAxisXRadioButton
          Image is flipped vertically when selected
        • flipAxisYRadioButton
          JRadioButton flipAxisYRadioButton
          Image is flipped horizontally when selected
        • flipAxisZRadioButton
          JRadioButton flipAxisZRadioButton
          Image is flipped by depth when selected
        • flipObject
          int flipObject
          The object to be flipped
        • flipVoiCheckbox
          JCheckBox flipVoiCheckbox
          When checked, VOIs are flipped when image is flipped.
        • image
          ModelImage image
          Source image.
        • loadAxisDefaults
          boolean loadAxisDefaults
        • optionsPanel
          JPanel optionsPanel
        • orientationOriginCheckBox
          JCheckBox orientationOriginCheckBox
          When checked, change orientation and origin upon flipping. When unchecked, orienation and origin remain the same.
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFrameLinker

      class JDialogFrameLinker extends JDialogBase implements Serializable
      serialVersionUID:
      8115834657630127291L

    • Class gov.nih.mipav.view.dialogs.JDialogFRAP

      class JDialogFRAP extends JDialogBase implements Serializable
      serialVersionUID:
      6390017817188485094L

      • Serialized Fields

        • analysisGroup
          ButtonGroup analysisGroup
          DOCUMENT ME!
        • backgroundButton
          JRadioButton backgroundButton
          DOCUMENT ME!
        • backgroundIndex
          int backgroundIndex
          DOCUMENT ME!
        • bandButton
          JRadioButton bandButton
          DOCUMENT ME!
        • bleachedROIShape
          int bleachedROIShape
          DOCUMENT ME!
        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • circleButton
          JRadioButton circleButton
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorsPresent
          int colorsPresent
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • componentImage
          ViewJComponentEditImage componentImage
          DOCUMENT ME!
        • cost
          int cost
          DOCUMENT ME!
        • createRegCheckBox
          JCheckBox createRegCheckBox
          DOCUMENT ME!
        • createRegImage
          boolean createRegImage
          DOCUMENT ME!
        • diffusion
          double diffusion
          DOCUMENT ME!
        • fileInfo
          FileInfoLSM fileInfo
          DOCUMENT ME!
        • fileInfoImageXML
          FileInfoImageXML fileInfoImageXML
          DOCUMENT ME!
        • findDiffusion
          boolean findDiffusion
        • findDiffusionCheckBox
          JCheckBox findDiffusionCheckBox
        • firstSliceAfterBleach
          int firstSliceAfterBleach
          DOCUMENT ME!
        • firstSliceNum
          int firstSliceNum
          DOCUMENT ME!
        • firstSliceNumText
          JTextField firstSliceNumText
          DOCUMENT ME!
        • frapAlgo
          AlgorithmFRAP frapAlgo
          DOCUMENT ME!
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • knotX
          double[] knotX
          DOCUMENT ME!
        • labelCost
          JLabel labelCost
          DOCUMENT ME!
        • labelDiffusion
          JLabel labelDiffusion
          DOCUMENT ME!
        • labelFirstSlice
          JLabel labelFirstSlice
          DOCUMENT ME!
        • labelImage
          JLabel labelImage
          DOCUMENT ME!
        • labelRef
          JLabel labelRef
          DOCUMENT ME!
        • labelShape
          JLabel labelShape
          DOCUMENT ME!
        • maxB
          double maxB
          DOCUMENT ME!
        • maxG
          double maxG
          DOCUMENT ME!
        • maxR
          double maxR
          DOCUMENT ME!
        • minB
          double minB
          DOCUMENT ME!
        • minG
          double minG
          DOCUMENT ME!
        • minR
          double minR
          DOCUMENT ME!
        • model
          int model
          DOCUMENT ME!
        • nBoundingVOIs
          int nBoundingVOIs
          DOCUMENT ME!
        • oneDButton
          JRadioButton oneDButton
          DOCUMENT ME!
        • paramVary
          boolean paramVary
          DOCUMENT ME!
        • paramVaryCheckBox
          JCheckBox paramVaryCheckBox
          DOCUMENT ME!
        • photoBleachedButton
          JRadioButton photoBleachedButton
          DOCUMENT ME!
        • photoBleachedIndex
          int photoBleachedIndex
          DOCUMENT ME!
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • regCheckBox
          JCheckBox regCheckBox
          DOCUMENT ME!
        • register
          boolean register
          DOCUMENT ME!
        • singleExpButton
          JRadioButton singleExpButton
          DOCUMENT ME!
        • textDiffusion
          JTextField textDiffusion
          DOCUMENT ME!
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • VOIGroup
          ButtonGroup VOIGroup
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!
        • wholeOrganButton
          JRadioButton wholeOrganButton
          DOCUMENT ME!
        • wholeOrganCheckBox
          JCheckBox wholeOrganCheckBox
          DOCUMENT ME!
        • wholeOrganIndex
          int wholeOrganIndex
          DOCUMENT ME!
        • wholeOrganNormalize
          boolean wholeOrganNormalize
          DOCUMENT ME!
        • xPos
          int xPos
          DOCUMENT ME!
        • yPos
          int yPos
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFrequencyFilter

      class JDialogFrequencyFilter extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      4979580288393418858L

      • Serialized Fields

        • bandPass
          JRadioButton bandPass
          DOCUMENT ME!
        • bandStop
          JRadioButton bandStop
          DOCUMENT ME!
        • butterworthFilter
          JRadioButton butterworthFilter
          DOCUMENT ME!
        • chebyshevIFilter
          JRadioButton chebyshevIFilter
        • chebyshevIIFilter
          JRadioButton chebyshevIIFilter
        • constructionGroup
          ButtonGroup constructionGroup
          DOCUMENT ME!
        • constructionMethod
          int constructionMethod
          DOCUMENT ME!
        • constructionPanel
          JPanel constructionPanel
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • ellipticFilter
          JRadioButton ellipticFilter
        • epsilon
          double epsilon
        • filterOrder
          int filterOrder
          DOCUMENT ME!
        • filterPanel
          JPanel filterPanel
          DOCUMENT ME!
        • filterType
          int filterType
          DOCUMENT ME!
        • filterTypeGroup
          ButtonGroup filterTypeGroup
          DOCUMENT ME!
        • fltFmt
          DecimalFormat fltFmt
        • freq1
          double freq1
          DOCUMENT ME!
        • freq2
          double freq2
          DOCUMENT ME!
        • FrequencyFilterAlgo
          AlgorithmFrequencyFilter FrequencyFilterAlgo
          DOCUMENT ME!
        • FrequencyFilterColorAlgo
          AlgorithmFrequencyFilterColor FrequencyFilterColorAlgo
        • gaussianFilter
          JRadioButton gaussianFilter
          DOCUMENT ME!
        • highPass
          JRadioButton highPass
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          DOCUMENT ME!
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • imageCrop
          boolean imageCrop
          DOCUMENT ME!
        • imageCropCheckbox
          JCheckBox imageCropCheckbox
          DOCUMENT ME!
        • kernelDiameter
          int kernelDiameter
          DOCUMENT ME!
        • labelEpsilon
          JLabel labelEpsilon
        • labelF1
          JLabel labelF1
          DOCUMENT ME!
        • labelF2
          JLabel labelF2
          DOCUMENT ME!
        • labelKernelDiameter
          JLabel labelKernelDiameter
          DOCUMENT ME!
        • labelOrder
          JLabel labelOrder
          DOCUMENT ME!
        • labelRs
          JLabel labelRs
        • lowPass
          JRadioButton lowPass
          DOCUMENT ME!
        • mainPanel
          JPanel mainPanel
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • onlyFrequencyFilter
          boolean onlyFrequencyFilter
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rs
          double rs
        • textEpsilon
          JTextField textEpsilon
        • textF1
          JTextField textF1
          DOCUMENT ME!
        • textF2
          JTextField textF2
          DOCUMENT ME!
        • textKernelDiameter
          JTextField textKernelDiameter
          DOCUMENT ME!
        • textOrder
          JTextField textOrder
          DOCUMENT ME!
        • textRs
          JTextField textRs
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • windowFilter
          JRadioButton windowFilter
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFRET

      class JDialogFRET extends JDialogBase implements Serializable
      serialVersionUID:
      1026032715678640392L

      • Serialized Fields

        • backgroundButton
          JRadioButton backgroundButton
          DOCUMENT ME!
        • backgroundIndex
          int backgroundIndex
          DOCUMENT ME!
        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorsPresent
          int colorsPresent
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • componentImage
          ViewJComponentEditImage componentImage
          DOCUMENT ME!
        • componentPostImage
          ViewJComponentEditImage componentPostImage
          DOCUMENT ME!
        • cost
          int cost
          DOCUMENT ME!
        • createRegCheckBox
          JCheckBox createRegCheckBox
          DOCUMENT ME!
        • createRegImage
          boolean createRegImage
          DOCUMENT ME!
        • donorButton
          JRadioButton donorButton
          DOCUMENT ME!
        • donorIndex
          int donorIndex
          DOCUMENT ME!
        • fretAlgo
          AlgorithmFRETAcceptorPhotobleach fretAlgo
          DOCUMENT ME!
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageComboBox
          JComboBox imageComboBox
          DOCUMENT ME!
        • labelCost
          JLabel labelCost
          DOCUMENT ME!
        • maxB
          double maxB
          DOCUMENT ME!
        • maxG
          double maxG
          DOCUMENT ME!
        • maxR
          double maxR
          DOCUMENT ME!
        • minB
          double minB
          DOCUMENT ME!
        • minG
          double minG
          DOCUMENT ME!
        • minR
          double minR
          DOCUMENT ME!
        • nBoundingVOIs
          int nBoundingVOIs
          DOCUMENT ME!
        • postImage
          ModelImage postImage
          DOCUMENT ME!
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • regCheckBox
          JCheckBox regCheckBox
          DOCUMENT ME!
        • register
          boolean register
          DOCUMENT ME!
        • signalButton
          JRadioButton signalButton
          DOCUMENT ME!
        • signalIndex
          int signalIndex
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • VOIGroup
          ButtonGroup VOIGroup
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!
        • yPos
          int yPos
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFRETBleedThrough

      class JDialogFRETBleedThrough extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8726771970079234501L

      • Serialized Fields

        • acceptorButton
          JRadioButton acceptorButton
          DOCUMENT ME!
        • acceptorRun
          boolean acceptorRun
          DOCUMENT ME!
        • activeButton
          JRadioButton activeButton
          DOCUMENT ME!
        • activeIndex
          int activeIndex
          DOCUMENT ME!
        • backgroundButton
          JRadioButton backgroundButton
          DOCUMENT ME!
        • backgroundIndex
          int backgroundIndex
          DOCUMENT ME!
        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • chooserButton
          JButton chooserButton
          DOCUMENT ME!
        • chooserButton2
          JButton chooserButton2
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorPanel
          JPanel colorPanel
          DOCUMENT ME!
        • componentImage
          ViewJComponentEditImage componentImage
          DOCUMENT ME!
        • doColor
          boolean doColor
          DOCUMENT ME!
        • donorButton
          JRadioButton donorButton
          DOCUMENT ME!
        • dyeGroup
          ButtonGroup dyeGroup
          DOCUMENT ME!
        • fbtAlgo
          AlgorithmFRETBleedThrough fbtAlgo
          DOCUMENT ME!
        • FP2Image
          ModelImage FP2Image
          DOCUMENT ME!
        • FRETImage
          ModelImage FRETImage
          DOCUMENT ME!
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • imageList
          JList imageList
          DOCUMENT ME!
        • imageList2
          JList imageList2
          DOCUMENT ME!
        • imagePanel
          JPanel imagePanel
          DOCUMENT ME!
        • imagePanel2
          JPanel imagePanel2
          DOCUMENT ME!
        • model
          DefaultListModel model
          DOCUMENT ME!
        • model2
          DefaultListModel model2
          DOCUMENT ME!
        • nBoundingVOIs
          int nBoundingVOIs
          DOCUMENT ME!
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • removeButton
          JButton removeButton
          DOCUMENT ME!
        • removeButton2
          JButton removeButton2
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          The source image must be either an image with donor dye only taken with a donor fluorescent peak filter or an image with acceptor dye only taken with a acceptor fluorescent peak filter.
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIGroup
          ButtonGroup VOIGroup
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFRETEfficiency

      class JDialogFRETEfficiency extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      156910291527442369L

      • Serialized Fields

        • acceptorImage
          ModelImage acceptorImage
          DOCUMENT ME!
        • activeButton
          JRadioButton activeButton
          DOCUMENT ME!
        • activeIndex
          int activeIndex
          DOCUMENT ME!
        • AFPintoDFP
          float AFPintoDFP
          DOCUMENT ME!
        • AFPintoFRET
          float AFPintoFRET
          DOCUMENT ME!
        • backgroundButton
          JRadioButton backgroundButton
          DOCUMENT ME!
        • backgroundIndex
          int backgroundIndex
          DOCUMENT ME!
        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • chooserButton
          JButton chooserButton
          DOCUMENT ME!
        • chooserButton2
          JButton chooserButton2
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorPanel
          JPanel colorPanel
          DOCUMENT ME!
        • componentImage
          ViewJComponentEditImage componentImage
          DOCUMENT ME!
        • createEfficiencyImage
          boolean createEfficiencyImage
          DOCUMENT ME!
        • createFDivAImage
          boolean createFDivAImage
          DOCUMENT ME!
        • createFDivDImage
          boolean createFDivDImage
          DOCUMENT ME!
        • DFPintoAFP
          float DFPintoAFP
          DOCUMENT ME!
        • DFPintoFRET
          float DFPintoFRET
          DOCUMENT ME!
        • doColor
          boolean doColor
          DOCUMENT ME!
        • efficiencyImage
          ModelImage efficiencyImage
          DOCUMENT ME!
        • effImageCheckBox
          JCheckBox effImageCheckBox
          DOCUMENT ME!
        • fDivACheckBox
          JCheckBox fDivACheckBox
          DOCUMENT ME!
        • fDivAImage
          ModelImage fDivAImage
          DOCUMENT ME!
        • fDivDCheckBox
          JCheckBox fDivDCheckBox
          DOCUMENT ME!
        • fDivDImage
          ModelImage fDivDImage
          DOCUMENT ME!
        • feffAlgo
          AlgorithmFRETEfficiency feffAlgo
          DOCUMENT ME!
        • FRETImage
          ModelImage FRETImage
          DOCUMENT ME!
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • imageList
          JList imageList
          DOCUMENT ME!
        • imageList2
          JList imageList2
          DOCUMENT ME!
        • imagePanel
          JPanel imagePanel
          DOCUMENT ME!
        • imagePanel2
          JPanel imagePanel2
          DOCUMENT ME!
        • model
          DefaultListModel model
          DOCUMENT ME!
        • model2
          DefaultListModel model2
          DOCUMENT ME!
        • nBoundingVOIs
          int nBoundingVOIs
          DOCUMENT ME!
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • removeButton
          JButton removeButton
          DOCUMENT ME!
        • removeButton2
          JButton removeButton2
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          The source image must be the image taken with the donor fluorescent peak filter.
        • textAFPintoDFP
          JTextField textAFPintoDFP
          DOCUMENT ME!
        • textAFPintoFRET
          JTextField textAFPintoFRET
          DOCUMENT ME!
        • textDFPintoAFP
          JTextField textDFPintoAFP
          DOCUMENT ME!
        • textDFPintoFRET
          JTextField textDFPintoFRET
          DOCUMENT ME!
        • useBlue
          boolean useBlue
          DOCUMENT ME!
        • useGreen
          boolean useGreen
          DOCUMENT ME!
        • useRed
          boolean useRed
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIGroup
          ButtonGroup VOIGroup
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFuzzMinDeAndChatterji

      class JDialogFuzzMinDeAndChatterji extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • autoCheckBox
          JCheckBox autoCheckBox
        • autoThreshold
          boolean autoThreshold
          If true, ignore srcThreshold input and calculate best value
        • crossVal
          double crossVal
        • enhancedThreshold
          double enhancedThreshold
          Enhanced image threshold
        • fuzzMinAlgo
          AlgorithmFuzzMinDeAndChatterji fuzzMinAlgo
        • gmax
          double gmax
        • gmin
          double gmin
        • image
          ModelImage image
          DOCUMENT ME!
        • labelEnhancedThreshold
          JLabel labelEnhancedThreshold
        • labelgmax
          JLabel labelgmax
        • labelgmin
          JLabel labelgmin
        • labelP1
          JLabel labelP1
        • labelP2
          JLabel labelP2
        • labelSrcThreshold
          JLabel labelSrcThreshold
        • labelTheta1
          JLabel labelTheta1
        • labelTheta2
          JLabel labelTheta2
        • maxVal
          double maxVal
        • minVal
          double minVal
        • outputPanel
          JPanelAlgorithmOutputOptions outputPanel
          DOCUMENT ME!
        • p1
          double p1
          Black region exponent, 0 invalid input: '<'= p1 invalid input: '<'= 1.0
        • p2
          double p2
          White region exponent, 0 invalid input: '<'= p2 invalid input: '<'= 1.0
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • srcThreshold
          double srcThreshold
          Original image threshold
        • textEnhancedThreshold
          JTextField textEnhancedThreshold
        • textgmax
          JTextField textgmax
        • textgmin
          JTextField textgmin
        • textP1
          JTextField textP1
        • textP2
          JTextField textP2
        • textSrcThreshold
          JTextField textSrcThreshold
        • textTheta1
          JTextField textTheta1
        • textTheta2
          JTextField textTheta2
        • theta1
          double theta1
          Angular equivalence of black band, 0 invalid input: '<'= theta1 invalid input: '<'= PI/2
        • theta2
          double theta2
          Angular equivalence of white band, 0 invalid input: '<'= theta2 invalid input: '<'= PI/2
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFuzzyCMeans

      class JDialogFuzzyCMeans extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7191124209694457297L

      • Serialized Fields

        • centroids
          float[] centroids
          DOCUMENT ME!
        • cropBackground
          boolean cropBackground
          DOCUMENT ME!
        • cropCheckbox
          JCheckBox cropCheckbox
          DOCUMENT ME!
        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • endTol
          float endTol
          DOCUMENT ME!
        • fcmAlgo
          AlgorithmFuzzyCMeans fcmAlgo
          DOCUMENT ME!
        • fuzzyOnly
          JRadioButton fuzzyOnly
          DOCUMENT ME!
        • hardFuzzyBoth
          JRadioButton hardFuzzyBoth
          DOCUMENT ME!
        • hardOnly
          JRadioButton hardOnly
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageVOIGroup
          ButtonGroup imageVOIGroup
          DOCUMENT ME!
        • imageVOIPanel
          JPanel imageVOIPanel
          DOCUMENT ME!
        • labelEndTol
          JLabel labelEndTol
          DOCUMENT ME!
        • labelExpo
          JLabel labelExpo
          DOCUMENT ME!
        • labelMaxIter
          JLabel labelMaxIter
          DOCUMENT ME!
        • labelNClasses
          JLabel labelNClasses
          DOCUMENT ME!
        • labelSignal
          JLabel labelSignal
          DOCUMENT ME!
        • maxIter
          int maxIter
          DOCUMENT ME!
        • nClasses
          int nClasses
          DOCUMENT ME!
        • nPyramid
          int nPyramid
          DOCUMENT ME!
        • oneJacobiIter
          int oneJacobiIter
          DOCUMENT ME!
        • oneSmooth
          float oneSmooth
          DOCUMENT ME!
        • outputGainField
          boolean outputGainField
          private JCheckBox calcGainFieldCheckbox;.
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • presentNumber
          int presentNumber
          DOCUMENT ME!
        • q
          float q
          DOCUMENT ME!
        • regionFlag
          boolean regionFlag
          DOCUMENT ME!
        • resultImage
          ModelImage[] resultImage
          DOCUMENT ME!
        • resultNumber
          int resultNumber
          DOCUMENT ME!
        • segmentation
          int segmentation
          DOCUMENT ME!
        • segmentationGroup
          ButtonGroup segmentationGroup
          DOCUMENT ME!
        • segmentationPanel
          JPanel segmentationPanel
          DOCUMENT ME!
        • textEndTol
          JTextField textEndTol
          DOCUMENT ME!
        • textExpo
          JTextField textExpo
          DOCUMENT ME!
        • textMaxIter
          JTextField textMaxIter
          DOCUMENT ME!
        • textNClasses
          JTextField textNClasses
          DOCUMENT ME!
        • textSignal
          JTextField textSignal
          DOCUMENT ME!
        • threshold
          float threshold
          DOCUMENT ME!
        • twoJacobiIter
          int twoJacobiIter
          DOCUMENT ME!
        • twoSmooth
          float twoSmooth
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogFuzzyConnectednessSegmentation

      class JDialogFuzzyConnectednessSegmentation extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogFuzzyMinimization

      class JDialogFuzzyMinimization extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogGaborFilter

      class JDialogGaborFilter extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7693130193527088045L

      • Serialized Fields

        • createGabor
          boolean createGabor
          DOCUMENT ME!
        • createGaborCheckBox
          JCheckBox createGaborCheckBox
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • filterPanel
          JPanel filterPanel
          DOCUMENT ME!
        • freqU
          float freqU
          DOCUMENT ME!
        • FrequencyFilterAlgo
          AlgorithmFrequencyFilter FrequencyFilterAlgo
          DOCUMENT ME!
        • FrequencyFilterColorAlgo
          AlgorithmFrequencyFilterColor FrequencyFilterColorAlgo
        • freqV
          float freqV
          DOCUMENT ME!
        • gaborImage
          ModelImage gaborImage
        • image
          ModelImage image
          DOCUMENT ME!
        • labelFU
          JLabel labelFU
          DOCUMENT ME!
        • labelFV
          JLabel labelFV
          DOCUMENT ME!
        • labelSU
          JLabel labelSU
          DOCUMENT ME!
        • labelSV
          JLabel labelSV
          DOCUMENT ME!
        • labelTheta
          JLabel labelTheta
          DOCUMENT ME!
        • mainPanel
          JPanel mainPanel
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sigmaU
          float sigmaU
          DOCUMENT ME!
        • sigmaV
          float sigmaV
          DOCUMENT ME!
        • textFU
          JTextField textFU
          DOCUMENT ME!
        • textFV
          JTextField textFV
          DOCUMENT ME!
        • textSU
          JTextField textSU
          DOCUMENT ME!
        • textSV
          JTextField textSV
          DOCUMENT ME!
        • textTheta
          JTextField textTheta
          DOCUMENT ME!
        • theta
          float theta
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogGaussianBlur

      class JDialogGaussianBlur extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5074546334694615886L

      • Serialized Fields

        • colorChannelPanel
          JPanelColorChannels colorChannelPanel
          DOCUMENT ME!
        • gaussianBlurAlgo
          AlgorithmGaussianBlur gaussianBlurAlgo
          DOCUMENT ME!
        • gaussianBlurSepAlgo
          AlgorithmGaussianBlurSep gaussianBlurSepAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          Source image.
        • image25D
          boolean image25D
          Flag indicating if slices should be blurred independently.
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • outputOptionsPanel
          JPanelAlgorithmOutputOptions outputOptionsPanel
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          Result image.
        • separable
          boolean separable
          DOCUMENT ME!
        • sepCheckbox
          JCheckBox sepCheckbox
          DOCUMENT ME!
        • sigmaPanel
          JPanelSigmas sigmaPanel
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • useOCL
          boolean useOCL
          Flag indicating whether to use OpenCL processing.
        • useOCLCheckbox
          JCheckBox useOCLCheckbox
          Indicates whether user wants openCL for processing.
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogGenerateGrid

      class JDialogGenerateGrid extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • colorChooser
          ViewJColorChooser colorChooser
        • componentImage
          ViewJComponentEditImage componentImage
        • gridColor
          Color gridColor
        • gridColorButton
          JButton gridColorButton
        • height
          float height
        • heightField
          JTextField heightField
        • horizontalSpacing
          int horizontalSpacing
        • image
          ModelImage image
        • intensity
          float intensity
        • intensityB
          float intensityB
        • intensityField
          JTextField intensityField
        • intensityG
          float intensityG
        • intensityR
          float intensityR
        • isColor
          boolean isColor
        • newImage
          ModelImage newImage
        • numHorizontal
          float numHorizontal
        • numVertical
          float numVertical
        • resX
          float resX
        • resY
          float resY
        • type
          int type
        • unitsStr
          String unitsStr
        • verticalSpacing
          int verticalSpacing
        • width
          float width
        • widthField
          JTextField widthField
        • xDim
          int xDim
        • yDim
          int yDim
        • zDim
          int zDim

    • Class gov.nih.mipav.view.dialogs.JDialogGenerateIsolines

      class JDialogGenerateIsolines extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • colorButton
          JButton colorButton
        • colorChooser
          ViewJColorChooser colorChooser
        • contourColor
          Color contourColor
        • defaultThreshold
          double defaultThreshold
        • image
          ModelImage image
          DOCUMENT ME!
        • imageMax
          double imageMax
        • imageMin
          double imageMin
        • intensityB
          float intensityB
        • intensityG
          float intensityG
        • intensityR
          float intensityR
        • isoAlgo
          AlgorithmGenerateIsolines isoAlgo
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textThreshold
          JTextField textThreshold
        • threshold
          double threshold

    • Class gov.nih.mipav.view.dialogs.JDialogGradientInverseWeightedSmoothing

      class JDialogGradientInverseWeightedSmoothing extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogGradientMagnitude

      class JDialogGradientMagnitude extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      2890654165880748219L

      • Serialized Fields

        • colorChannelPanel
          JPanelColorChannels colorChannelPanel
          DOCUMENT ME!
        • displayProgressBar
          boolean displayProgressBar
          display progress bar or not.
        • gradientMagAlgo
          AlgorithmGradientMagnitude gradientMagAlgo
          DOCUMENT ME!
        • gradientMagSepAlgo
          AlgorithmGradientMagnitudeSep gradientMagSepAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          DOCUMENT ME!
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • outputImageType
          int outputImageType
        • outputOptionsPanel
          JPanelAlgorithmOutputOptions outputOptionsPanel
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • separable
          boolean separable
          DOCUMENT ME!
        • sepCheckbox
          JCheckBox sepCheckbox
          DOCUMENT ME!
        • sigmaPanel
          JPanelSigmas sigmaPanel
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • useOCL
          boolean useOCL
          Flag indicating whether to use OpenCL processing.
        • useOCLCheckbox
          JCheckBox useOCLCheckbox
          Indicates whether user wants openCL for processing.
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogGraphBasedSegmentation

      class JDialogGraphBasedSegmentation extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogGridOptions

      class JDialogGridOptions extends JDialogBase implements Serializable
      serialVersionUID:
      1869680780124245552L

    • Class gov.nih.mipav.view.dialogs.JDialogGUIDClient

      class JDialogGUIDClient extends JDialog implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogGuidedFilter

      class JDialogGuidedFilter extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogGVF

      class JDialogGVF extends JDialogBase implements Serializable
      serialVersionUID:
      -7812609363025907144L

      • Serialized Fields

        • boundaryIterations
          int boundaryIterations
          DOCUMENT ME!
        • checkboxDisplay
          JCheckBox checkboxDisplay
          DOCUMENT ME!
        • do25D
          boolean do25D
          DOCUMENT ME!
        • do25DCheckBox
          JCheckBox do25DCheckBox
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • groupNum
          int groupNum
          DOCUMENT ME!
        • gvfAlgo
          AlgorithmGVF gvfAlgo
          DOCUMENT ME!
        • gvfIterations
          int gvfIterations
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • kValue
          float kValue
          DOCUMENT ME!
        • labelGaussZ
          JLabel labelGaussZ
          DOCUMENT ME!
        • propagate
          JRadioButton propagate
          DOCUMENT ME!
        • propagationFlag
          boolean propagationFlag
          DOCUMENT ME!
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • scaleZ
          float scaleZ
          DOCUMENT ME!
        • singleSlice
          JRadioButton singleSlice
          DOCUMENT ME!
        • srcVOI
          VOI srcVOI
          DOCUMENT ME!
        • textBoundaryIterations
          JTextField textBoundaryIterations
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textGaussZ
          JTextField textGaussZ
          DOCUMENT ME!
        • textGVFIterations
          JTextField textGVFIterations
          DOCUMENT ME!
        • textK
          JTextField textK
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogHaarTransform

      class JDialogHaarTransform extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • comboBoxFilterType
          JComboBox<String> comboBoxFilterType
        • FILTER_GREATER
          int FILTER_GREATER
        • FILTER_HARD
          int FILTER_HARD
        • FILTER_LESS
          int FILTER_LESS
        • FILTER_NN_GARROTE
          int FILTER_NN_GARROTE
        • FILTER_NONE
          int FILTER_NONE
        • FILTER_SOFT
          int FILTER_SOFT
        • FILTER_THRESHOLD_FIRM
          int FILTER_THRESHOLD_FIRM
        • filterType
          int filterType
        • filterVal1
          double filterVal1
        • filterVal2
          double filterVal2
        • htAlgo
          HaarTransform htAlgo
        • inverseImage
          ModelImage inverseImage
        • labelVal1
          JLabel labelVal1
        • labelVal2
          JLabel labelVal2
        • srcImage
          ModelImage srcImage
          Use serialVersionUID for interoperability.
        • textVal1
          JTextField textVal1
        • textVal2
          JTextField textVal2
        • transformImage
          ModelImage transformImage

    • Class gov.nih.mipav.view.dialogs.JDialogHaralickTexture

      class JDialogHaralickTexture extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      2408406330754526954L

      • Serialized Fields

        • asm
          boolean asm
          DOCUMENT ME!
        • asmCheckBox
          JCheckBox asmCheckBox
          DOCUMENT ME!
        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorPanel
          JPanel colorPanel
          DOCUMENT ME!
        • concatenate
          boolean concatenate
          If true, only one result image with the original source concatenated with the calculated features.
        • concatenateCheckBox
          JCheckBox concatenateCheckBox
        • contrast
          boolean contrast
          DOCUMENT ME!
        • contrastCheckBox
          JCheckBox contrastCheckBox
          DOCUMENT ME!
        • correlation
          boolean correlation
          DOCUMENT ME!
        • correlationCheckBox
          JCheckBox correlationCheckBox
          DOCUMENT ME!
        • dissimilarity
          boolean dissimilarity
          DOCUMENT ME!
        • dissimilarityCheckBox
          JCheckBox dissimilarityCheckBox
          DOCUMENT ME!
        • energy
          boolean energy
          DOCUMENT ME!
        • energyCheckBox
          JCheckBox energyCheckBox
          DOCUMENT ME!
        • entropy
          boolean entropy
          DOCUMENT ME!
        • entropyCheckBox
          JCheckBox entropyCheckBox
          DOCUMENT ME!
        • ew
          boolean ew
          DOCUMENT ME!
        • ewCheckBox
          JCheckBox ewCheckBox
          DOCUMENT ME!
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • greyLevels
          int greyLevels
          Number of grey levels used if data must be rescaled
        • homogeneity
          boolean homogeneity
          DOCUMENT ME!
        • homogeneityCheckBox
          JCheckBox homogeneityCheckBox
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • invariantCheckBox
          JCheckBox invariantCheckBox
          DOCUMENT ME!
        • invariantDir
          boolean invariantDir
          DOCUMENT ME!
        • inverseOrder1
          boolean inverseOrder1
          DOCUMENT ME!
        • inverseOrder1CheckBox
          JCheckBox inverseOrder1CheckBox
          DOCUMENT ME!
        • labelOffsetDistance
          JLabel labelOffsetDistance
          DOCUMENT ME!
        • labelRescaling
          JLabel labelRescaling
        • labelWindowSize
          JLabel labelWindowSize
          DOCUMENT ME!
        • maxProbability
          boolean maxProbability
          DOCUMENT ME!
        • maxProbabilityCheckBox
          JCheckBox maxProbabilityCheckBox
          DOCUMENT ME!
        • mean
          boolean mean
          DOCUMENT ME!
        • meanCheckBox
          JCheckBox meanCheckBox
          DOCUMENT ME!
        • nesw
          boolean nesw
          DOCUMENT ME!
        • neswCheckBox
          JCheckBox neswCheckBox
          DOCUMENT ME!
        • ns
          boolean ns
          DOCUMENT ME!
        • nsCheckBox
          JCheckBox nsCheckBox
          DOCUMENT ME!
        • numDirections
          int numDirections
          DOCUMENT ME!
        • numOperators
          int numOperators
          DOCUMENT ME!
        • offsetDistance
          int offsetDistance
          DOCUMENT ME!
        • promenance
          boolean promenance
        • promenanceCheckBox
          JCheckBox promenanceCheckBox
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • resultImage
          ModelImage[] resultImage
          DOCUMENT ME!
        • resultNumber
          int resultNumber
          DOCUMENT ME!
        • RGBOffset
          int RGBOffset
          DOCUMENT ME!
        • scalePanel
          JPanel scalePanel
          DOCUMENT ME!
        • senw
          boolean senw
          DOCUMENT ME!
        • senwCheckBox
          JCheckBox senwCheckBox
          DOCUMENT ME!
        • shade
          boolean shade
        • shadeCheckBox
          JCheckBox shadeCheckBox
        • standardDeviation
          boolean standardDeviation
          DOCUMENT ME!
        • standardDeviationCheckBox
          JCheckBox standardDeviationCheckBox
          DOCUMENT ME!
        • textOffsetDistance
          JTextField textOffsetDistance
          DOCUMENT ME!
        • textRescaling
          JTextField textRescaling
        • textureAlgo
          AlgorithmHaralickTexture textureAlgo
          DOCUMENT ME!
        • textWindowSize
          JTextField textWindowSize
          DOCUMENT ME!
        • variance
          boolean variance
          DOCUMENT ME!
        • varianceCheckBox
          JCheckBox varianceCheckBox
          DOCUMENT ME!
        • windowSize
          int windowSize
          DOCUMENT ME!
        • zscore
          boolean zscore
          If true, produce z score = (value - mean)/(standard deviation) output of Haralick features
        • zscoreCheckBox
          JCheckBox zscoreCheckBox

    • Class gov.nih.mipav.view.dialogs.JDialogHarrisCornerDetector

      class JDialogHarrisCornerDetector extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogHarrisLaplace

      class JDialogHarrisLaplace extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogHartleyTransform

      class JDialogHartleyTransform extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogHessian

      class JDialogHessian extends JDialogBase implements Serializable
      serialVersionUID:
      -8129223463637379259L

      • Serialized Fields

        • eigenSystemAlgo
          WildMagic.LibFoundation.NumericalAnalysis.Eigenf eigenSystemAlgo
          DOCUMENT ME!
        • gaussianScale
          float gaussianScale
          DOCUMENT ME!
        • hess00
          JLabel hess00
          DOCUMENT ME!
        • hess01
          JLabel hess01
          DOCUMENT ME!
        • hess02
          JLabel hess02
          DOCUMENT ME!
        • hess10
          JLabel hess10
          DOCUMENT ME!
        • hess11
          JLabel hess11
          DOCUMENT ME!
        • hess12
          JLabel hess12
          DOCUMENT ME!
        • hess20
          JLabel hess20
          DOCUMENT ME!
        • hess21
          JLabel hess21
          DOCUMENT ME!
        • hess22
          JLabel hess22
          DOCUMENT ME!
        • hessianAlgo
          AlgorithmHessian hessianAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imgHessianAlgor
          AlgorithmImageHessian imgHessianAlgor
          DOCUMENT ME!
        • locationX
          int locationX
          DOCUMENT ME!
        • locationY
          int locationY
          DOCUMENT ME!
        • locationZ
          int locationZ
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • runBatchButton
          JButton runBatchButton
          DOCUMENT ME!
        • runItAllButton
          JButton runItAllButton
          DOCUMENT ME!
        • runItButton
          JButton runItButton
          DOCUMENT ME!
        • runMethod
          int runMethod
          DOCUMENT ME!
        • textGaussScale
          JTextField textGaussScale
          DOCUMENT ME!
        • textLocX
          JTextField textLocX
          DOCUMENT ME!
        • textLocY
          JTextField textLocY
          DOCUMENT ME!
        • textLocZ
          JTextField textLocZ
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogHillClimbingWatershed

      class JDialogHillClimbingWatershed extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogHistogram2Dim

      class JDialogHistogram2Dim extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2641827384253148080L

      • Serialized Fields

        • bin1
          int bin1
          Number of bins for first image.
        • bin1Default
          boolean bin1Default
          Default number of bins for first image. Default is 256.
        • bin1Label
          JLabel bin1Label
          Label description for bin1.
        • bin1Text
          JTextField bin1Text
          Textfield for bin1.
        • bin2
          int bin2
          Number of bins for second image.
        • bin2Default
          boolean bin2Default
          Default number of bins for first image. Default is 256.
        • bin2Label
          JLabel bin2Label
          Label description for bin1.
        • bin2Text
          JTextField bin2Text
          Textfield for bin2.
        • blueCheckBox
          JCheckBox blueCheckBox
          Checkbox to select blue image.
        • colorsPresent
          int colorsPresent
          Number of colors present.
        • doLinearRescale
          boolean doLinearRescale
          If true, the range of second image is same as the range of the first image.
        • doLogResult
          boolean doLogResult
          If true, calculates the log of the result image for better visualization.
        • firstImage
          ModelImage firstImage
          First image (Source image).
        • greenCheckBox
          JCheckBox greenCheckBox
          Checkbox to select green image.
        • histogram2DimAlgo
          AlgorithmHistogram2Dim histogram2DimAlgo
          Instance of AlgorithmHistogram2Dim.
        • imageComboBox
          JComboBox imageComboBox
          Combobox to select the second image.
        • labelImage
          JLabel labelImage
          Image label.
        • linearCheckbox
          JCheckBox linearCheckbox
          Checkbox to select linear rescaling of second image.
        • maxB
          double maxB
          Max intensity values in Red, Green and Blue images respectively.
        • maxG
          double maxG
          Max intensity values in Red, Green and Blue images respectively.
        • maxR
          double maxR
          Max intensity values in Red, Green and Blue images respectively.
        • minB
          double minB
          Min. intensity values in Red, Green and Blue images respectively
        • minG
          double minG
          Min. intensity values in Red, Green and Blue images respectively
        • minR
          double minR
          Min. intensity values in Red, Green and Blue images respectively
        • possibleInt2Values
          double possibleInt2Values
          Possible intensity values for second image.
        • possibleIntValues
          double possibleIntValues
          Possible intensity values for first image.
        • redCheckBox
          JCheckBox redCheckBox
          Checkbox to select Red image.
        • resultCheckbox
          JCheckBox resultCheckbox
          Checkbox to display the log of result image.
        • resultImage
          ModelImage resultImage
          Image where the result is stored.
        • secondImage
          ModelImage secondImage
          Second image (Base image).
        • titles
          String[] titles
          String titles for the new windows.
        • useBlue
          boolean useBlue
          If true, blue image is selected as of the two images for calculating histogram.
        • useGreen
          boolean useGreen
          If true, green image is selected as of the two images for calculating histogram.
        • useRed
          boolean useRed
          If true, red image is selected as of the two images for calculating histogram.
        • userInterface
          ViewUserInterface userInterface
          Keeps record of the present structure of the application.

    • Class gov.nih.mipav.view.dialogs.JDialogHistogramLUT

      class JDialogHistogramLUT extends JDialogBase implements Serializable
      serialVersionUID:
      1863683975229524849L

      • Serialized Fields

        • colocalizationEMFrame
          boolean colocalizationEMFrame
          Deprecated.
          DOCUMENT ME!
        • colocalizationRegFrame
          boolean colocalizationRegFrame
          Deprecated.
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          Deprecated.
          DOCUMENT ME!
        • imageB
          ModelImage imageB
          Deprecated.
          DOCUMENT ME!
        • LUTa
          ModelLUT LUTa
          Deprecated.
          DOCUMENT ME!
        • LUTb
          ModelLUT LUTb
          Deprecated.
          DOCUMENT ME!
        • regComponent
          ViewJComponentRegistration regComponent
          Deprecated.
          false = apply algorithm only to VOI regions.
        • regionFlag
          boolean regionFlag
          Deprecated.
          DOCUMENT ME!
        • RGBa
          ModelRGB RGBa
          Deprecated.
          DOCUMENT ME!
        • RGBb
          ModelRGB RGBb
          Deprecated.
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          Deprecated.
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          Deprecated.
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogHistogramMatch

      class JDialogHistogramMatch extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4835888925289199854L

    • Class gov.nih.mipav.view.dialogs.JDialogHistogramSliceMatch

      class JDialogHistogramSliceMatch extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • matchHistogramSliceAlgo
          AlgorithmHistogramSliceMatch matchHistogramSliceAlgo
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • nSlices
          int nSlices
        • referenceSlice
          int referenceSlice
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          DOCUMENT ME!
        • textSlice
          JTextField textSlice
        • titles
          String[] titles
          or if the source image is to be replaced.
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogHistogramSummary

      class JDialogHistogramSummary extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -1570864449910121911L

      • Serialized Fields

        • bins
          int bins
          DOCUMENT ME!
        • binText
          JTextField binText
          DOCUMENT ME!
        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorPanel
          JPanel colorPanel
          DOCUMENT ME!
        • displayGraph
          boolean displayGraph
        • error
          String error
          DOCUMENT ME!
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • histAlgo
          AlgorithmHistogram histAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageMax
          double imageMax
          DOCUMENT ME!
        • imageMin
          double imageMin
          DOCUMENT ME!
        • processMode
          int processMode
        • radSeparateVOIs
          JRadioButton radSeparateVOIs
        • radTotalVOIs
          JRadioButton radTotalVOIs
          DOCUMENT ME!
        • radWholeImage
          JRadioButton radWholeImage
          DOCUMENT ME!
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • RGBOffset
          int RGBOffset
          DOCUMENT ME!
        • userLimits
          boolean userLimits
        • userLimitsCheckBox
          JCheckBox userLimitsCheckBox
        • userMax
          float userMax
        • userMaxLabel
          JLabel userMaxLabel
        • userMaxText
          JTextField userMaxText
        • userMin
          float userMin
        • userMinLabel
          JLabel userMinLabel
        • userMinText
          JTextField userMinText

    • Class gov.nih.mipav.view.dialogs.JDialogHMRF_EM

      class JDialogHMRF_EM extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • alg
          AlgorithmHMRF_EM alg
        • colorWeighting
          int colorWeighting
        • equalButton
          JRadioButton equalButton
        • fileNameBase
          String fileNameBase
        • gaussianSigma
          float gaussianSigma
        • graphicsButton
          JRadioButton graphicsButton
        • image
          ModelImage image
          Source image.
        • maxEMIterations
          int maxEMIterations
        • maxMAPIterations
          int maxMAPIterations
        • numberClusters
          int numberClusters
        • resultImage
          ModelImage resultImage
          result image
        • resultsFileName
          String resultsFileName
        • resultsFileNameLabel
          JLabel resultsFileNameLabel
        • resultsFileNameText
          JTextField resultsFileNameText
        • showMAPplot
          boolean showMAPplot
        • showMAPplotCheckBox
          JCheckBox showMAPplotCheckBox
        • textClusters
          JTextField textClusters
        • textGauss
          JTextField textGauss
        • textMaxEMIterations
          JTextField textMaxEMIterations
        • textMaxMAPIterations
          JTextField textMaxMAPIterations

    • Class gov.nih.mipav.view.dialogs.JDialogHomomorphicFilter

      class JDialogHomomorphicFilter extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      1061706659841470806L

      • Serialized Fields

        • butterworthOrder
          int butterworthOrder
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • filterPanel
          JPanel filterPanel
          DOCUMENT ME!
        • freq1
          float freq1
          DOCUMENT ME!
        • FrequencyFilterAlgo
          AlgorithmFrequencyFilter FrequencyFilterAlgo
          DOCUMENT ME!
        • highGain
          float highGain
          DOCUMENT ME!
        • highTruncated
          float highTruncated
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          DOCUMENT ME!
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • labelF1
          JLabel labelF1
          DOCUMENT ME!
        • labelHighGain
          JLabel labelHighGain
          DOCUMENT ME!
        • labelHighTruncated
          JLabel labelHighTruncated
          DOCUMENT ME!
        • labelLowGain
          JLabel labelLowGain
          DOCUMENT ME!
        • labelLowTruncated
          JLabel labelLowTruncated
          DOCUMENT ME!
        • labelOrder
          JLabel labelOrder
          DOCUMENT ME!
        • lowGain
          float lowGain
          DOCUMENT ME!
        • lowTruncated
          float lowTruncated
          DOCUMENT ME!
        • mainPanel
          JPanel mainPanel
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • nf
          DecimalFormat nf
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textF1
          JTextField textF1
          DOCUMENT ME!
        • textHighGain
          JTextField textHighGain
          DOCUMENT ME!
        • textHighTruncated
          JTextField textHighTruncated
          DOCUMENT ME!
        • textLowGain
          JTextField textLowGain
          DOCUMENT ME!
        • textLowTruncated
          JTextField textLowTruncated
          DOCUMENT ME!
        • textOrder
          JTextField textOrder
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogHoughCardioid

      class JDialogHoughCardioid extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • a0Num
          int a0Num
        • aText
          JTextField aText
          DOCUMENT ME!
        • hAlgo
          AlgorithmHoughCardioid hAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • numCardioids
          int numCardioids
        • numCardioidsText
          JTextField numCardioidsText
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sidePointsForCurvature
          int sidePointsForCurvature
          Maximum number of points to take from each side of a point on a curve in determining a curvature
        • sideText
          JTextField sideText
        • theta0Num
          int theta0Num
          DOCUMENT ME!
        • theta0Text
          JTextField theta0Text
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogHoughCardioidChoice

      class JDialogHoughCardioidChoice extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • a0Array
          double[] a0Array
        • countArray
          int[] countArray
        • maxA
          double maxA
        • numCardioidsFound
          int numCardioidsFound
        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • selectedArray
          JCheckBox[] selectedArray
        • selectedCardioid
          boolean[] selectedCardioid
        • theta0Array
          double[] theta0Array
        • x0Array
          double[] x0Array
        • xDim
          int xDim
        • y0Array
          double[] y0Array
        • yDim
          int yDim

    • Class gov.nih.mipav.view.dialogs.JDialogHoughCircle

      class JDialogHoughCircle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

    • Class gov.nih.mipav.view.dialogs.JDialogHoughCircleChoice

      class JDialogHoughCircleChoice extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • countArray
          int[] countArray
        • maxRad
          double maxRad
        • numCirclesFound
          int numCirclesFound
        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • radArray
          double[] radArray
        • selectedArray
          JCheckBox[] selectedArray
        • selectedCircle
          boolean[] selectedCircle
        • x0Array
          double[] x0Array
        • xDimSource
          int xDimSource
        • y0Array
          double[] y0Array
        • yDimSource
          int yDimSource

    • Class gov.nih.mipav.view.dialogs.JDialogHoughEllipse

      class JDialogHoughEllipse extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • countText
          JTextField countText
        • countThreshold
          int countThreshold
          Number of counts required to find an ellipse
        • degreesWidthText
          JTextField degreesWidthText
        • ellipseRangeTolerance
          double ellipseRangeTolerance
          Maximum percent by which perimiter pixels can deviate from the ellipse equation
        • hAlgo
          AlgorithmHoughEllipse hAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • maxBufferSize
          int maxBufferSize
          The maximum Hough transform size in megabytes - default is currently 256
        • maxBufferText
          JTextField maxBufferText
        • maxCyclesText
          JTextField maxCyclesText
        • maxDegreesBinWidth
          double maxDegreesBinWidth
          For theta must have bin width invalid input: '<'= maxDegreesBinWidth
        • maxEllipseFindCycles
          int maxEllipseFindCycles
          Maximum number of pointSetsRequired triplet point acqusitions that is allowed to occur
        • maxPixelBinWidth
          double maxPixelBinWidth
          For xCenter, yCenter, r1, and r2 must bin width invalid input: '<'= maxPixelBinWidth
        • maxPointDistance
          double maxPointDistance
          Largest allowable distance between 2 of 3 picked points
        • maxPointText
          JTextField maxPointText
        • minCoverage
          double minCoverage
          Minimum percentage of the perimiter of a found ellipse that must be covered by points for it to be valid.
        • minCoverageText
          JTextField minCoverageText
          DOCUMENT ME!
        • minPointDistance
          double minPointDistance
          Smallest allowable distance between 2 of 3 picked points
        • minPointText
          JTextField minPointText
        • numEllipses
          int numEllipses
          number of ellipses to be found
        • numEllipsesText
          JTextField numEllipsesText
        • pixelWidthText
          JTextField pixelWidthText
        • pointSetsRequired
          int pointSetsRequired
          Number of point triplets required before each ellipse find is performed
        • pointSetsText
          JTextField pointSetsText
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sidePointsForTangent
          int sidePointsForTangent
          Maximum number of points to take from each side of a point on a curve in determining a tangent
        • sideText
          JTextField sideText
        • toleranceText
          JTextField toleranceText

    • Class gov.nih.mipav.view.dialogs.JDialogHoughEllipseChoice

      class JDialogHoughEllipseChoice extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • count
          short[] count
        • maxR1
          double maxR1
        • maxR2
          double maxR2
        • minR1
          double minR1
        • minR2
          double minR2
        • numEllipsesFound
          int numEllipsesFound
        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • r1
          float[] r1
        • r2
          float[] r2
        • selectedArray
          JCheckBox[] selectedArray
        • selectedEllipse
          boolean[] selectedEllipse
        • theta
          float[] theta
        • xCenter
          float[] xCenter
        • xDimSource
          int xDimSource
        • yCenter
          float[] yCenter
        • yDimSource
          int yDimSource

    • Class gov.nih.mipav.view.dialogs.JDialogHoughHyperbola

      class JDialogHoughHyperbola extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • countText
          JTextField countText
        • countThreshold
          int countThreshold
          Number of counts required to find a hyperbola
        • degreesWidthText
          JTextField degreesWidthText
        • hAlgo
          AlgorithmHoughHyperbola hAlgo
          DOCUMENT ME!
        • hyperbolaRangeTolerance
          double hyperbolaRangeTolerance
          Maximum percent by which perimiter pixels can deviate from the hyperbola equation
        • image
          ModelImage image
          DOCUMENT ME!
        • maxBufferSize
          int maxBufferSize
          The maximum Hough transform size in megabytes - default is currently 256
        • maxBufferText
          JTextField maxBufferText
        • maxCyclesText
          JTextField maxCyclesText
        • maxDegreesBinWidth
          double maxDegreesBinWidth
          For theta must have bin width invalid input: '<'= maxDegreesBinWidth
        • maxHyperbolaFindCycles
          int maxHyperbolaFindCycles
          Maximum number of pointSetsRequired triplet point acquisitions that is allowed to occur
        • maxPixelBinWidth
          double maxPixelBinWidth
          For xCenter, yCenter, r1, and r2 must bin width invalid input: '<'= maxPixelBinWidth
        • maxPointDistance
          double maxPointDistance
          Largest allowable distance between 2 of 3 picked points
        • maxPointText
          JTextField maxPointText
        • minPixels
          int minPixels
          Minimum number of points found on a hyperbola for it to be valid.
        • minPixelsText
          JTextField minPixelsText
          DOCUMENT ME!
        • minPointDistance
          double minPointDistance
          Smallest allowable distance between 2 of 3 picked points
        • minPointText
          JTextField minPointText
        • numHyperbolas
          int numHyperbolas
          number of hyperbolas to be found
        • numHyperbolasText
          JTextField numHyperbolasText
        • pixelWidthText
          JTextField pixelWidthText
        • pointSetsRequired
          int pointSetsRequired
          Number of point triplets required before each hyperbola find is performed
        • pointSetsText
          JTextField pointSetsText
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sidePointsForTangent
          int sidePointsForTangent
          Maximum number of points to take from each side of a point on a curve in determining a tangent
        • sideText
          JTextField sideText
        • toleranceText
          JTextField toleranceText

    • Class gov.nih.mipav.view.dialogs.JDialogHoughHyperbolaChoice

      class JDialogHoughHyperbolaChoice extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • count
          short[] count
        • maxR1
          double maxR1
        • maxR2
          double maxR2
        • minR1
          double minR1
        • minR2
          double minR2
        • numHyperbolasFound
          int numHyperbolasFound
        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • r1
          float[] r1
        • r2
          float[] r2
        • selectedArray
          JCheckBox[] selectedArray
        • selectedHyperbola
          boolean[] selectedHyperbola
        • theta
          float[] theta
        • xCenter
          float[] xCenter
        • xDimSource
          int xDimSource
        • yCenter
          float[] yCenter
        • yDimSource
          int yDimSource

    • Class gov.nih.mipav.view.dialogs.JDialogHoughLine

      class JDialogHoughLine extends JDialogBase implements Serializable
      serialVersionUID:
      0L

    • Class gov.nih.mipav.view.dialogs.JDialogHoughLineChoice

      class JDialogHoughLineChoice extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • countArray
          int[] countArray
        • distanceArray
          JTextField[] distanceArray
        • maxDistance
          float[] maxDistance
        • n1
          int n1
        • n2
          int n2
        • numLinesFound
          int numLinesFound
        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • rhoArray
          int[] rhoArray
        • selectedArray
          JCheckBox[] selectedArray
        • selectedLine
          boolean[] selectedLine
        • thetaArray
          int[] thetaArray

    • Class gov.nih.mipav.view.dialogs.JDialogHoughParabola

      class JDialogHoughParabola extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • hAlgo
          AlgorithmHoughParabola hAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • maxBufferSize
          int maxBufferSize
          The maximum Hough transform size in megabytes - default is currently 256
        • maxBufferText
          JTextField maxBufferText
        • numParabolas
          int numParabolas
        • numParabolasText
          JTextField numParabolasText
        • pBins
          int pBins
        • phiBins
          int phiBins
        • phiConstant
          double phiConstant
        • phiConstantText
          JTextField phiConstantText
        • phiText
          JTextField phiText
          DOCUMENT ME!
        • pMax
          float pMax
        • pMaxText
          JTextField pMaxText
        • pMin
          float pMin
        • pMinText
          JTextField pMinText
        • pText
          JTextField pText
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sidePointsForTangent
          int sidePointsForTangent
          Maximum number of points to take from each side of a point on a curve in determining a tangent
        • sideText
          JTextField sideText
        • xvBins
          int xvBins
          DOCUMENT ME!
        • xvText
          JTextField xvText
          DOCUMENT ME!
        • yvBins
          int yvBins
          DOCUMENT ME!
        • yvText
          JTextField yvText

    • Class gov.nih.mipav.view.dialogs.JDialogHoughParabolaChoice

      class JDialogHoughParabolaChoice extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • countTable
          int[] countTable
        • numParabolasFound
          int numParabolasFound
        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • phiBins
          int phiBins
        • phiTable
          double[] phiTable
        • pMax
          float pMax
        • pMin
          float pMin
        • pTable
          float[] pTable
        • selectedArray
          JCheckBox[] selectedArray
        • selectedParabola
          boolean[] selectedParabola
        • xDim
          int xDim
        • xvTable
          float[] xvTable
        • yDim
          int yDim
        • yvTable
          float[] yvTable

    • Class gov.nih.mipav.view.dialogs.JDialogHurstIndex

      class JDialogHurstIndex extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorPanel
          JPanel colorPanel
          DOCUMENT ME!
        • distancePanel
          JPanel distancePanel
          DOCUMENT ME!
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • grouping
          int grouping
        • hurstAlgo
          AlgorithmHurstIndex hurstAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • integerDistanceRound
          boolean integerDistanceRound
          If true, take rounding of Euclidean distance as distance If false, take Euclidean distance as distance
        • integerDistanceRoundCheckBox
          JCheckBox integerDistanceRoundCheckBox
        • labelDimensionality
          JLabel labelDimensionality
        • labelMaxDistance
          JLabel labelMaxDistance
        • labelMinDistance
          JLabel labelMinDistance
        • maxDistance
          double maxDistance
        • minDistance
          double minDistance
        • pixelButton
          JRadioButton pixelButton
        • pixelOrVOIGroup
          ButtonGroup pixelOrVOIGroup
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
        • RGBOffset
          int RGBOffset
          DOCUMENT ME!
        • sliceButton
          JRadioButton sliceButton
        • textMaxDistance
          JTextField textMaxDistance
        • textMinDistance
          JTextField textMinDistance
        • voiButton
          JRadioButton voiButton

    • Class gov.nih.mipav.view.dialogs.JDialogIAGCWD

      class JDialogIAGCWD extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • alphaBright
          double alphaBright
        • alphaDim
          double alphaDim
        • expectedFmt
          DecimalFormat expectedFmt
        • iagcwdAlgo
          AlgorithmIAGCWD iagcwdAlgo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • Tau
          double Tau
        • Taut
          double Taut
        • textAlphaBright
          JTextField textAlphaBright
        • textAlphaDim
          JTextField textAlphaDim
        • textcdfTruncation
          JTextField textcdfTruncation
        • textDistortionThreshold
          JTextField textDistortionThreshold
          DOCUMENT ME!
        • textExpected
          JTextField textExpected
        • Tt
          double Tt

    • Class gov.nih.mipav.view.dialogs.JDialogIDObjects

      class JDialogIDObjects extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -6478138973143988561L

    • Class gov.nih.mipav.view.dialogs.JDialogIHN3Correction

      class JDialogIHN3Correction extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      9210373092056571003L

      • Serialized Fields

        • autoThreshold
          boolean autoThreshold
          DOCUMENT ME!
        • autoThresholdCheckbox
          JCheckBox autoThresholdCheckbox
          DOCUMENT ME!
        • convertTomm
          float convertTomm
          DOCUMENT ME!
        • createField
          boolean createField
          DOCUMENT ME!
        • createFieldCheckbox
          JCheckBox createFieldCheckbox
          DOCUMENT ME!
        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • endTol
          float endTol
          DOCUMENT ME!
        • fieldDistance
          float fieldDistance
          DOCUMENT ME!
        • fieldImage
          ModelImage fieldImage
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • kernelfwhm
          float kernelfwhm
          DOCUMENT ME!
        • labelDistance
          JLabel labelDistance
          DOCUMENT ME!
        • labelEndTol
          JLabel labelEndTol
          DOCUMENT ME!
        • labelKernel
          JLabel labelKernel
          DOCUMENT ME!
        • labelMaxIter
          JLabel labelMaxIter
          DOCUMENT ME!
        • labelNoise
          JLabel labelNoise
          DOCUMENT ME!
        • labelShrink
          JLabel labelShrink
          DOCUMENT ME!
        • labelSignal
          JLabel labelSignal
          DOCUMENT ME!
        • maxIter
          int maxIter
          DOCUMENT ME!
        • N3Algo
          AlgorithmIHN3Correction N3Algo
          DOCUMENT ME!
        • noise
          float noise
          DOCUMENT ME!
        • orgResol
          float[] orgResol
          DOCUMENT ME!
        • regionFlag
          boolean regionFlag
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • resXUnit
          int resXUnit
          DOCUMENT ME!
        • resYUnit
          int resYUnit
          DOCUMENT ME!
        • resZUnit
          int resZUnit
          DOCUMENT ME!
        • shrink
          float shrink
          DOCUMENT ME!
        • textDistance
          JTextField textDistance
          DOCUMENT ME!
        • textEndTol
          JTextField textEndTol
          DOCUMENT ME!
        • textKernel
          JTextField textKernel
          DOCUMENT ME!
        • textMaxIter
          JTextField textMaxIter
          DOCUMENT ME!
        • textNoise
          JTextField textNoise
          DOCUMENT ME!
        • textShrink
          JTextField textShrink
          DOCUMENT ME!
        • textSignal
          JTextField textSignal
          DOCUMENT ME!
        • threshold
          float threshold
          DOCUMENT ME!
        • useScript
          boolean useScript
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogImageCalculator

      class JDialogImageCalculator extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7373755862535613674L

      • Serialized Fields

        • adOpString
          String adOpString
          Advanced function string.
        • advancedButton
          JButton advancedButton
          DOCUMENT ME!
        • clipMode
          int clipMode
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
          DOCUMENT ME!
        • comboBoxOperator
          JComboBox comboBoxOperator
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          source image.
        • imageB
          ModelImage imageB
          DOCUMENT ME!
        • isColor
          boolean isColor
          DOCUMENT ME!
        • mathAlgo
          AlgorithmImageCalculator mathAlgo
          DOCUMENT ME!
        • opType
          int opType
          DOCUMENT ME!
        • radioClip
          JRadioButton radioClip
          DOCUMENT ME!
        • radioNew
          JRadioButton radioNew
          DOCUMENT ME!
        • radioPromote
          JRadioButton radioPromote
          DOCUMENT ME!
        • radioReplace
          JRadioButton radioReplace
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          result image.
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogImageInfo

      class JDialogImageInfo extends JDialogBase implements Serializable
      serialVersionUID:
      -3239665202530115877L

      • Serialized Fields

        • acpcACFields
          JTextField[] acpcACFields
          DOCUMENT ME!
        • acpcDimFields
          JTextField[] acpcDimFields
          DOCUMENT ME!
        • acpcMaxFields
          JTextField[] acpcMaxFields
          DOCUMENT ME!
        • acpcMinFields
          JTextField[] acpcMinFields
          TLRC Specific info.
        • acpcPCFields
          JTextField[] acpcPCFields
          DOCUMENT ME!
        • acpcResField
          JTextField acpcResField
          DOCUMENT ME!
        • addReplaceMatrix
          JButton addReplaceMatrix
          Add as New/Replace button (depending on selected matrix type).
        • applyButton
          JButton applyButton
          DOCUMENT ME!
        • bigEnd
          JRadioButton bigEnd
          Radio button to denote image is big endian.
        • buttonPanel
          JPanel buttonPanel
          DOCUMENT ME!
        • changeTypeAlgo
          AlgorithmChangeType changeTypeAlgo
          DOCUMENT ME!!
        • comboBoxUnitOfMeasure1
          JComboBox comboBoxUnitOfMeasure1
          DOCUMENT ME!
        • comboBoxUnitOfMeasure3
          JComboBox comboBoxUnitOfMeasure3
          DOCUMENT ME!
        • comboBoxUnitOfMeasure4
          JComboBox comboBoxUnitOfMeasure4
          DOCUMENT ME!
        • comboBoxUnitOfMeasure5
          JComboBox comboBoxUnitOfMeasure5
          DOCUMENT ME!
        • DIM
          int DIM
          DOCUMENT ME!
        • endianess
          boolean endianess
          Indicates the endianess of the image.
        • fileTransMatrix
          TransMatrix fileTransMatrix
          DOCUMENT ME!
        • font12B
          Font font12B
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • isTLRCBox
          JCheckBox isTLRCBox
          DOCUMENT ME!
        • leftHandSystem
          boolean leftHandSystem
          If true change matrix to the left-hand coordinate system.
        • linkedImageButton
          JButton linkedImageButton
          DOCUMENT ME!
        • linkedImageField
          JTextField linkedImageField
          DOCUMENT ME!
        • littleEnd
          JRadioButton littleEnd
          Radio button to denote image is little endian.
        • loadButton
          JButton loadButton
          DOCUMENT ME!
        • matrix
          double[][] matrix
          DOCUMENT ME!
        • matrixBox
          JComboBox matrixBox
          Box to hold the matrices parsed from the MatrixHolder.
        • matrixFile
          String matrixFile
          DOCUMENT ME!
        • measure1
          int measure1
          DOCUMENT ME!
        • measure3
          int measure3
          DOCUMENT ME!
        • measure4
          int measure4
          DOCUMENT ME!
        • measure5
          int measure5
          DOCUMENT ME!
        • modality
          int modality
          DOCUMENT ME!
        • modalityBox
          JComboBox modalityBox
          DOCUMENT ME!
        • modalityStr
          String[] modalityStr
          DOCUMENT ME!
        • nameText
          JTextField nameText
          DOCUMENT ME!
        • newImageName
          String newImageName
          DOCUMENT ME!
        • orient
          int orient
          DOCUMENT ME!
        • orientationBox1
          JComboBox orientationBox1
          DOCUMENT ME!
        • orientationBox2
          JComboBox orientationBox2
          DOCUMENT ME!
        • orientationBox3
          JComboBox orientationBox3
          DOCUMENT ME!
        • orientAxis
          int[] orientAxis
          DOCUMENT ME!
        • orientBox
          JComboBox orientBox
          DOCUMENT ME!
        • orientFields
          JTextField[] orientFields
          DOCUMENT ME!
        • origACFields
          JTextField[] origACFields
          ACPC Specific info.
        • origDimFields
          JTextField[] origDimFields
          DOCUMENT ME!
        • origin
          float[] origin
          DOCUMENT ME!
        • origOriginFields
          JTextField[] origOriginFields
        • origPCFields
          JTextField[] origPCFields
          DOCUMENT ME!
        • origResFields
          JTextField[] origResFields
          DOCUMENT ME!
        • resampleImage
          ModelImage resampleImage
          DOCUMENT ME!
        • resIndex
          int resIndex
          DOCUMENT ME!
        • resizeOnClose
          boolean resizeOnClose
        • resolutionBox
          JCheckBox resolutionBox
          DOCUMENT ME!
        • resolutions
          float[] resolutions
          DOCUMENT ME!
        • saveButton
          JButton saveButton
          DOCUMENT ME!
        • sliceThickness
          float sliceThickness
          DOCUMENT ME!
        • tabbedPane
          JTabbedPane tabbedPane
          DOCUMENT ME!
        • textMatrix
          JTextField[][] textMatrix
          DOCUMENT ME!
        • textRes1
          JTextField textRes1
          DOCUMENT ME!
        • textRes2
          JTextField textRes2
          DOCUMENT ME!
        • textRes3
          JTextField textRes3
          DOCUMENT ME!
        • textRes4
          JTextField textRes4
          DOCUMENT ME!
        • textRes5
          JTextField textRes5
          DOCUMENT ME!
        • textSliceThickness
          JTextField textSliceThickness
          DOCUMENT ME!
        • textSt1
          JTextField textSt1
          DOCUMENT ME!
        • textSt2
          JTextField textSt2
          DOCUMENT ME!
        • textSt3
          JTextField textSt3
          DOCUMENT ME!
        • textSt4
          JTextField textSt4
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • tlrcACFields
          JTextField[] tlrcACFields
          DOCUMENT ME!
        • tlrcDimFields
          JTextField[] tlrcDimFields
          DOCUMENT ME!
        • tlrcPCFields
          JTextField[] tlrcPCFields
          DOCUMENT ME!
        • tlrcResFields
          JTextField[] tlrcResFields
          DOCUMENT ME!
        • transformIDBox
          JComboBox transformIDBox
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • wcSystem
          boolean wcSystem
          If true change matrix to the world coordinate system.

    • Class gov.nih.mipav.view.dialogs.JDialogImageMath

      class JDialogImageMath extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2720105824431405427L

      • Serialized Fields

        • blueValue
          double blueValue
        • clipMode
          int clipMode
          DOCUMENT ME!
        • comboBoxOperator
          JComboBox comboBoxOperator
          DOCUMENT ME!
        • group
          ButtonGroup group
          DOCUMENT ME!
        • image
          ModelImage image
          source image.
        • imaginaryValue
          double imaginaryValue
          Used as both imaginary value and blue value
        • inputPanel
          JPanel inputPanel
          DOCUMENT ME!
        • labelOperator
          JLabel labelOperator
          DOCUMENT ME!
        • labelValue
          JLabel labelValue
          Used for single value, real part of complex, and red part of color
        • labelValueB
          JLabel labelValueB
          Used for blue part of color
        • labelValueI
          JLabel labelValueI
          Used for imaginary part of complex and green part of color
        • mathAlgo
          AlgorithmImageMath mathAlgo
          DOCUMENT ME!
        • opType
          AlgorithmImageMath.Operator opType
          DOCUMENT ME!
        • outputPanel
          JPanelAlgorithmOutputOptions outputPanel
          DOCUMENT ME!
        • radioClip
          JRadioButton radioClip
          DOCUMENT ME!
        • radioFloat
          JRadioButton radioFloat
          DOCUMENT ME!
        • radioPromote
          JRadioButton radioPromote
          DOCUMENT ME!
        • realValue
          double realValue
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          result image.
        • textValue
          JTextField textValue
          Used for single value, real part of complex, and red part of color
        • textValueB
          JTextField textValueB
          Used for blue part of color
        • textValueI
          JTextField textValueI
          Use for imaginary part of complex and green part of color
        • titles
          String[] titles
          DOCUMENT ME!
        • useComplex
          boolean useComplex
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogImRegPOC

      class JDialogImRegPOC extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogIndependentComponents

      class JDialogIndependentComponents extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • a1
          double a1
        • aicAlgo
          AlgorithmIndependentComponents aicAlgo
          DOCUMENT ME!
        • changeRemoveIndex
          boolean changeRemoveIndex
          DOCUMENT ME!
        • chooserButton
          JButton chooserButton
          DOCUMENT ME!
        • colorPanel
          JPanelColorChannels colorPanel
          DOCUMENT ME!
        • cubicButton
          JRadioButton cubicButton
        • deflationaryOrthogonalization
          JRadioButton deflationaryOrthogonalization
          DOCUMENT ME!
        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • endTol
          double endTol
          DOCUMENT ME!
        • expButton
          JRadioButton expButton
        • icAlgorithm
          int icAlgorithm
          DOCUMENT ME!
        • icAlgorithmGroup
          ButtonGroup icAlgorithmGroup
          DOCUMENT ME!
        • icAlgorithmPanel
          JPanel icAlgorithmPanel
          DOCUMENT ME!
        • icNumber
          int icNumber
          Number of independent components
        • imageList
          JList imageList
          DOCUMENT ME!
        • imagePanel
          JPanel imagePanel
          DOCUMENT ME!
        • labela1
          JLabel labela1
        • labelEndTol
          JLabel labelEndTol
          DOCUMENT ME!
        • labelICNumber
          JLabel labelICNumber
          DOCUMENT ME!
        • labelMaxIter
          JLabel labelMaxIter
          DOCUMENT ME!
        • maximumLikelihoodEstimation
          JRadioButton maximumLikelihoodEstimation
          DOCUMENT ME!
        • maxIter
          int maxIter
          DOCUMENT ME!
        • model
          DefaultListModel model
          DOCUMENT ME!
        • nonlinearFunction
          int nonlinearFunction
        • nonlinearFunctionGroup
          ButtonGroup nonlinearFunctionGroup
          DOCUMENT ME!
        • nonlinearFunctionPanel
          JPanel nonlinearFunctionPanel
          DOCUMENT ME!
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • removeButton
          JButton removeButton
          DOCUMENT ME!
        • removeIndex
          int removeIndex
          DOCUMENT ME!
        • resultImage
          ModelImage[] resultImage
          DOCUMENT ME!
        • srcImage
          ModelImage[] srcImage
          DOCUMENT ME!
        • srcNumber
          int srcNumber
          DOCUMENT ME!
        • symmetricOrthogonalization
          JRadioButton symmetricOrthogonalization
          DOCUMENT ME!
        • tanhButton
          JRadioButton tanhButton
        • tempImage
          ModelImage[] tempImage
          DOCUMENT ME!
        • texta1
          JTextField texta1
        • textEndTol
          JTextField textEndTol
          DOCUMENT ME!
        • textICNumber
          JTextField textICNumber
          DOCUMENT ME!
        • textMaxIter
          JTextField textMaxIter
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogInitialCentroids

      class JDialogInitialCentroids extends JDialogBase implements Serializable
      serialVersionUID:
      -7070007899490674843L

      • Serialized Fields

        • centroids
          float[] centroids
          DOCUMENT ME!
        • defaultValueInput
          JTextField[] defaultValueInput
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • gbl
          GridBagLayout gbl
          DOCUMENT ME!
        • i
          int i
          DOCUMENT ME!
        • maximum
          float maximum
          DOCUMENT ME!
        • minimum
          float minimum
          DOCUMENT ME!
        • nClasses
          int nClasses
          DOCUMENT ME!
        • tmpStr
          String tmpStr
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogInsertMissingSlices

      class JDialogInsertMissingSlices extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5205189127854148892L

      • Serialized Fields

        • allPresent
          boolean allPresent
          true if no slices are missing.
        • average
          JRadioButton average
          Radio button selected if inserted slices are a weighted average of surrounding slices.
        • blank
          JRadioButton blank
          Radio button selected if inserted slices are blank.
        • checkListInsert
          boolean[] checkListInsert
          Array of length totalSlices, false where slice is already present, true where slice must be inserted.
        • destFlag
          boolean destFlag
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          Flag indicating if a new image is to be generated.
        • image
          ModelImage image
          source image.
        • insertBlank
          boolean insertBlank
          If true insert blank slices, if false insert weighted average slices.
        • missingNumberArray
          int[] missingNumberArray
          DOCUMENT ME!
        • missingPositions
          int missingPositions
          DOCUMENT ME!
        • missingSliceArray
          int[] missingSliceArray
          DOCUMENT ME!
        • missingSlices
          int missingSlices
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • nSlices
          int nSlices
          Number of slices in original 3D image.
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          image create if new image button is selected.
        • rSliceAlgo
          AlgorithmReplaceRemovedSlices rSliceAlgo
          DOCUMENT ME!
        • totalSlices
          int totalSlices
          Number of slices that will be present in the 3D image after the missing slices have been inserted.

    • Class gov.nih.mipav.view.dialogs.JDialogInsertSlice

      class JDialogInsertSlice extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7157371462824445245L

    • Class gov.nih.mipav.view.dialogs.JDialogInsertVolume

      class JDialogInsertVolume extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7157371462824445245L

      • Serialized Fields

        • average
          JRadioButton average
          DOCUMENT ME!
        • blank
          JRadioButton blank
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • insertedImage
          ModelImage insertedImage
          DOCUMENT ME!
        • insertedImgButton
          JRadioButton insertedImgButton
          DOCUMENT ME!
        • insertVolume
          int insertVolume
          DOCUMENT ME!
        • insertVolumeAlgo
          AlgorithmInsertVolume insertVolumeAlgo
          DOCUMENT ME!
        • nVolumes
          int nVolumes
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textVolume
          JTextField textVolume
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • volumeType
          int volumeType
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogInstallPlugin

      class JDialogInstallPlugin extends JDialogBase implements Serializable
      serialVersionUID:
      -8736744495208652866L

      • Serialized Fields

        • checkShow
          JCheckBox checkShow
          Check box for whether to display files that are not likely sources of MIPAV plugins.*
        • checkUnpack
          JCheckBox checkUnpack
          Check box for unpacking container files
        • files
          Vector<File> files
          The class, zip, jar etc files that were selected before they were unzipped
        • filesColor
          Vector<Color> filesColor
          The results of working with the files in a temporary class environment
        • selectorPanel
          JDialogInstallPlugin.ClassSelectorPanel selectorPanel
          The sub-gui *
        • ui
          ViewUserInterface ui
          The default user interface

    • Class gov.nih.mipav.view.dialogs.JDialogInstallPlugin.JFileTreePanel

      class JFileTreePanel extends JPanel implements Serializable

      • Serialized Fields

        • tree
          JTree tree
          The file tree.

    • Class gov.nih.mipav.view.dialogs.JDialogIntensityHistogram

      class JDialogIntensityHistogram extends JDialogBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogIntensityPaint

      class JDialogIntensityPaint extends JDialogBase implements Serializable
      serialVersionUID:
      -736880761566398344L

      • Serialized Fields

        • inputLabel
          JLabel inputLabel
          DOCUMENT ME!
        • inputText
          JTextField inputText
          DOCUMENT ME!
        • intensityDouble
          double intensityDouble
          DOCUMENT ME!
        • intensityStringValue
          String intensityStringValue
          DOCUMENT ME!
        • outMax
          double outMax
          DOCUMENT ME!
        • outMin
          double outMin
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogIntensityThreshold

      class JDialogIntensityThreshold extends JDialogBase implements Serializable
      serialVersionUID:
      988706874933899996L

    • Class gov.nih.mipav.view.dialogs.JDialogInvert

      class JDialogInvert extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      6770504320836953902L

      • Serialized Fields

        • changeTypeAlgo
          AlgorithmChangeType changeTypeAlgo
          DOCUMENT ME!
        • dataType
          int dataType
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • endianess
          boolean endianess
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageMathAlgo
          AlgorithmImageMath imageMathAlgo
        • inTempMax
          double inTempMax
          DOCUMENT ME!
        • inTempMin
          double inTempMin
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • outTempMax
          double outTempMax
          DOCUMENT ME!
        • outTempMin
          double outTempMin
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogIsophoteCurvature

      class JDialogIsophoteCurvature extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogKernelRegression

      class JDialogKernelRegression extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • alpha
          float alpha
          Structure sensitive parameter
        • classicStepSize
          float classicStepSize
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • equalCheckBox
          JCheckBox equalCheckBox
        • equalValue
          double equalValue
        • greaterEqualCheckBox
          JCheckBox greaterEqualCheckBox
        • greaterEqualValue
          double greaterEqualValue
        • hasEqual
          boolean hasEqual
        • hasGreaterEqual
          boolean hasGreaterEqual
        • hasInfinity
          boolean hasInfinity
        • hasLesserEqual
          boolean hasLesserEqual
        • hasNaN
          boolean hasNaN
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          DOCUMENT ME!
        • image25DCheckBox
          JCheckBox image25DCheckBox
          DOCUMENT ME!
        • infinityCheckBox
          JCheckBox infinityCheckBox
        • initialGlobalSmoothing
          float initialGlobalSmoothing
          0.8 for STEERING_KERNEL_SECOND_ORDER_L1_NORM
        • initialKernelSize
          int initialKernelSize
        • iterations
          int iterations
          Total number of iterations
        • iterations2
          int iterations2
          Iterations in skr2L1_regular for steepest descent method in L1 steering kernel regression in STEERING_KERNEL_SECOND_ORDER_L1_NORM.
        • iterativeGlobalSmoothing
          float iterativeGlobalSmoothing
          1.5 for STEERING_KERNEL_SECOND_ORDER_L1_NORM
        • iterativeGlobalSmoothing2
          float iterativeGlobalSmoothing2
        • iterativeKernelSize
          int iterativeKernelSize
        • iterIrregular
          JRadioButton iterIrregular
        • iterSteering2
          JRadioButton iterSteering2
        • kernelRegressionAlgo
          AlgorithmKernelRegression kernelRegressionAlgo
          DOCUMENT ME!
        • labelAlpha
          JLabel labelAlpha
        • labelClassicStep
          JLabel labelClassicStep
        • labelInitialGlobal
          JLabel labelInitialGlobal
        • labelInitialKernel
          JLabel labelInitialKernel
        • labelIterations
          JLabel labelIterations
        • labelIterations2
          JLabel labelIterations2
        • labelIterativeGlobal
          JLabel labelIterativeGlobal
        • labelIterativeGlobal2
          JLabel labelIterativeGlobal2
        • labelIterativeKernel
          JLabel labelIterativeKernel
        • labelLambda
          JLabel labelLambda
        • labelSteeringStep
          JLabel labelSteeringStep
        • labelUpscale
          JLabel labelUpscale
        • labelWindowSize
          JLabel labelWindowSize
        • lambda
          float lambda
          Regularization for the elongation parameter
        • lesserEqualCheckBox
          JCheckBox lesserEqualCheckBox
        • lesserEqualValue
          double lesserEqualValue
        • method
          int method
        • methodGroup
          ButtonGroup methodGroup
        • NaNCheckBox
          JCheckBox NaNCheckBox
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • regSampled2Classic
          JRadioButton regSampled2Classic
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • steering2L1Norm
          JRadioButton steering2L1Norm
        • steeringStepSize
          float steeringStepSize
        • textAlpha
          JTextField textAlpha
        • textClassicStep
          JTextField textClassicStep
        • textEqual
          JTextField textEqual
        • textGreaterEqual
          JTextField textGreaterEqual
        • textInitialGlobal
          JTextField textInitialGlobal
        • textInitialKernel
          JTextField textInitialKernel
        • textIterations
          JTextField textIterations
        • textIterations2
          JTextField textIterations2
        • textIterativeGlobal
          JTextField textIterativeGlobal
        • textIterativeGlobal2
          JTextField textIterativeGlobal2
        • textIterativeKernel
          JTextField textIterativeKernel
        • textLambda
          JTextField textLambda
        • textLesserEqual
          JTextField textLesserEqual
        • textSteeringStep
          JTextField textSteeringStep
        • textUpscale
          JTextField textUpscale
        • textWindowSize
          JTextField textWindowSize
        • titles
          String[] titles
          DOCUMENT ME!
        • upscale
          int upscale
          Upscaling factor
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • windowSize
          int windowSize
          Size of local orientation analysis window

    • Class gov.nih.mipav.view.dialogs.JDialogKMeans

      class JDialogKMeans extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • alg
          AlgorithmKMeans alg
          handle to algorithm
        • algorithmGroup
          ButtonGroup algorithmGroup
        • algoSelection
          int algoSelection
        • axesRatio
          double[] axesRatio
        • axesRatioLabel
          JLabel axesRatioLabel
        • axesRatioText
          JTextField axesRatioText
        • blueBuffer
          float[] blueBuffer
        • br
          BufferedReader br
        • BradleyInit
          JRadioButton BradleyInit
        • buttonImage
          JButton buttonImage
        • buttonPointsFile
          JButton buttonPointsFile
        • bwImageGroup
          ButtonGroup bwImageGroup
        • bwSegmentedImage
          boolean bwSegmentedImage
        • centroidPos
          double[][] centroidPos
        • CIELABSpace
          JRadioButton CIELABSpace
        • cityBlock
          JRadioButton cityBlock
        • clusterImage
          JRadioButton clusterImage
        • colorHistogramBox
          JCheckBox colorHistogramBox
        • colorSegmentInRGB
          boolean colorSegmentInRGB
        • colorSpaceGroup
          ButtonGroup colorSpaceGroup
        • differentSpheresButton
          JRadioButton differentSpheresButton
        • directoryPoints
          String directoryPoints
        • distanceGroup
          ButtonGroup distanceGroup
        • distanceMeasure
          int distanceMeasure
        • doubleBuffer
          double[] doubleBuffer
        • euclideanSquared
          JRadioButton euclideanSquared
        • extents
          int[] extents
        • fastGlobalAlgo
          JRadioButton fastGlobalAlgo
        • fileNamePoints
          String fileNamePoints
        • filePoints
          File filePoints
        • followBatchBox
          JCheckBox followBatchBox
        • followBatchWithIncremental
          boolean followBatchWithIncremental
        • globalAlgo
          JRadioButton globalAlgo
        • greenBuffer
          float[] greenBuffer
        • groupNum
          int[] groupNum
        • havePoints
          boolean havePoints
        • hierarchicalInit
          JRadioButton hierarchicalInit
        • image
          ModelImage image
          source image.
        • imageList
          JComboBox imageList
        • initGroup
          ButtonGroup initGroup
        • initLabel
          JLabel initLabel
        • initSelection
          int initSelection
        • isMultifile
          boolean isMultifile
          boolean isMultifile
        • kMeansAlgo
          JRadioButton kMeansAlgo
        • mahalanobis
          JRadioButton mahalanobis
        • maxMinInit
          JRadioButton maxMinInit
        • nDims
          int nDims
        • nPoints
          int nPoints
        • numberClusters
          int numberClusters
        • pos
          double[][] pos
        • randomInit
          JRadioButton randomInit
        • redBuffer
          float[] redBuffer
        • resultImage
          ModelImage resultImage
          result image
        • resultsFileName
          String resultsFileName
        • resultsFileNameLabel
          JLabel resultsFileNameLabel
        • resultsFileNameText
          JTextField resultsFileNameText
        • RGBSpace
          JRadioButton RGBSpace
        • SButton
          JRadioButton SButton
        • scale
          double[] scale
        • scaleMax
          double scaleMax
        • scaleVariablesToUnitVariance
          boolean scaleVariablesToUnitVariance
        • segmentedImage
          JRadioButton segmentedImage
        • showSegmentedImage
          boolean showSegmentedImage
        • textClusters
          JTextField textClusters
        • textImage
          JTextField textImage
        • textPointsFile
          JTextField textPointsFile
        • unitVarianceCheckBox
          JCheckBox unitVarianceCheckBox
        • useColorHistogram
          boolean useColorHistogram
        • weight
          double[] weight

    • Class gov.nih.mipav.view.dialogs.JDialogLaplacian

      class JDialogLaplacian extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      2631054897246586311L

      • Serialized Fields

        • ampFactor
          float ampFactor
          DOCUMENT ME!
        • comboBoxKernelSize
          JComboBox comboBoxKernelSize
        • displayProgressBar
          boolean displayProgressBar
          display progress bar or not.
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          DOCUMENT ME!
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • kernelSize
          int kernelSize
        • labelAmpFact
          JLabel labelAmpFact
          DOCUMENT ME!
        • labelKernelSize
          JLabel labelKernelSize
        • laplacianAlgo
          AlgorithmLaplacian laplacianAlgo
          DOCUMENT ME!
        • nonLinear
          boolean nonLinear
        • nonLinearCheckBox
          JCheckBox nonLinearCheckBox
        • outputPanel
          JPanelAlgorithmOutputOptions outputPanel
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • separable
          boolean separable
          DOCUMENT ME!
        • sepCheckbox
          JCheckBox sepCheckbox
          DOCUMENT ME!
        • sigmasPanel
          JPanelSigmas sigmasPanel
          DOCUMENT ME!
        • textAmpFact
          JTextField textAmpFact
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • useOCL
          boolean useOCL
          Flag indicating whether to use OpenCL processing.
        • useOCLCheckbox
          JCheckBox useOCLCheckbox
          Indicates whether user wants openCL for processing.
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLargestCircle

      class JDialogLargestCircle extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogLawsTexture

      class JDialogLawsTexture extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogLevelSet

      class JDialogLevelSet extends JDialogBase implements Serializable
      serialVersionUID:
      -1593443884995027289L

      • Serialized Fields

        • contractButton
          JRadioButton contractButton
          DOCUMENT ME!
        • deltaT
          float deltaT
          DOCUMENT ME!
        • edgeAttract
          float edgeAttract
          DOCUMENT ME!
        • epsilon
          float epsilon
          DOCUMENT ME!
        • expandButton
          JRadioButton expandButton
          DOCUMENT ME!
        • expandContractButton
          JRadioButton expandContractButton
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          Flag indicating if slices should be blurred independently.
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • iters
          int iters
          DOCUMENT ME!
        • itersCheckBox
          JCheckBox itersCheckBox
          DOCUMENT ME!
        • label3D
          JLabel label3D
          difference between x,y resolutions (in plane) and z resolution (between planes).
        • labelCorrected
          JLabel labelCorrected
          DOCUMENT ME!
        • labelDeltaT
          JLabel labelDeltaT
          DOCUMENT ME!
        • labelEdgeAttract
          JLabel labelEdgeAttract
          DOCUMENT ME!
        • labelEpsilon
          JLabel labelEpsilon
          DOCUMENT ME!
        • labelGaussX
          JLabel labelGaussX
          DOCUMENT ME!
        • labelGaussY
          JLabel labelGaussY
          DOCUMENT ME!
        • labelGaussZ
          JLabel labelGaussZ
          DOCUMENT ME!
        • labelIters
          JLabel labelIters
          DOCUMENT ME!
        • labelTestIters
          JLabel labelTestIters
          DOCUMENT ME!
        • levelSetAlgo
          AlgorithmLevelSet levelSetAlgo
          DOCUMENT ME!
        • movement
          int movement
          DOCUMENT ME!
        • movementGroup
          ButtonGroup movementGroup
          DOCUMENT ME!
        • normFactor
          float normFactor
          DOCUMENT ME!
        • paintMask
          BitSet paintMask
          DOCUMENT ME!
        • resolutionCheckbox
          JCheckBox resolutionCheckbox
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • scaleZ
          float scaleZ
          DOCUMENT ME!
        • testIters
          int testIters
          DOCUMENT ME!
        • textDeltaT
          JTextField textDeltaT
          DOCUMENT ME!
        • textEdgeAttract
          JTextField textEdgeAttract
          DOCUMENT ME!
        • textEpsilon
          JTextField textEpsilon
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textGaussZ
          JTextField textGaussZ
          DOCUMENT ME!
        • textIters
          JTextField textIters
          DOCUMENT ME!
        • textTestIters
          JTextField textTestIters
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLevelSetDiffusion

      class JDialogLevelSetDiffusion extends JDialogBase implements Serializable
      serialVersionUID:
      -6530047904436344937L

      • Serialized Fields

        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          Flag indicating if slices should be blurred independently.
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • iters
          int iters
          DOCUMENT ME!
        • kValue
          float kValue
          DOCUMENT ME!
        • labelCorrected
          JLabel labelCorrected
          DOCUMENT ME!
        • labelGaussX
          JLabel labelGaussX
          DOCUMENT ME!
        • labelGaussY
          JLabel labelGaussY
          DOCUMENT ME!
        • labelGaussZ
          JLabel labelGaussZ
          DOCUMENT ME!
        • labelIters
          JLabel labelIters
          DOCUMENT ME!
        • labelK
          JLabel labelK
          DOCUMENT ME!
        • levelSetAlgo
          AlgorithmLevelSetDiffusion levelSetAlgo
          DOCUMENT ME!
        • normFactor
          float normFactor
          DOCUMENT ME!
        • paintMask
          BitSet paintMask
          DOCUMENT ME!
        • resolutionCheckbox
          JCheckBox resolutionCheckbox
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • scaleZ
          float scaleZ
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textGaussZ
          JTextField textGaussZ
          DOCUMENT ME!
        • textIters
          JTextField textIters
          difference between x,y resolutions (in plane) and z resolution (between planes).
        • textK
          JTextField textK
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLightBox

      class JDialogLightBox extends JDialogBase implements Serializable
      serialVersionUID:
      -4983517621211045288L

      • Serialized Fields

        • backgroundB
          JButton backgroundB
          DOCUMENT ME!
        • bgColor
          Color bgColor
          DOCUMENT ME!
        • borderB
          JButton borderB
          DOCUMENT ME!
        • borderColor
          Color borderColor
          DOCUMENT ME!
        • borderSize
          int borderSize
          DOCUMENT ME!
        • bordersizeL
          JLabel bordersizeL
          DOCUMENT ME!
        • bordersizeText
          JTextField bordersizeText
          DOCUMENT ME!
        • col
          int col
          DOCUMENT ME!
        • colLabel
          JLabel colLabel
          DOCUMENT ME!
        • colorChooser
          ViewJColorChooser colorChooser
          DOCUMENT ME!
        • colorPanel
          JPanel colorPanel
          DOCUMENT ME!
        • colPanel
          JPanel colPanel
          DOCUMENT ME!
        • colText
          JTextField colText
          DOCUMENT ME!
        • font12
          Font font12
          DOCUMENT ME!
        • font12B
          Font font12B
          DOCUMENT ME!
        • frame
          ViewJFrameLightBox frame
          DOCUMENT ME!
        • gridSize
          int gridSize
          DOCUMENT ME!
        • gridsizeL
          JLabel gridsizeL
          DOCUMENT ME!
        • gridsizeText
          JTextField gridsizeText
          DOCUMENT ME!
        • increment
          int increment
        • incrementLabel
          JLabel incrementLabel
        • incrementText
          JTextField incrementText
        • lastBorderSize
          int lastBorderSize
          DOCUMENT ME!
        • lastCol
          int lastCol
          DOCUMENT ME!
        • lastGridSize
          int lastGridSize
          DOCUMENT ME!
        • lastIncrement
          int lastIncrement
        • lastRow
          int lastRow
          DOCUMENT ME!
        • lastRowBFlag
          boolean lastRowBFlag
          DOCUMENT ME!
        • magnification
          float magnification
          DOCUMENT ME!
        • magniWindow
          JWindow magniWindow
          DOCUMENT ME!
        • magSlider
          JSlider magSlider
          DOCUMENT ME!
        • magSliderDictionary
          Hashtable<Integer,JLabel> magSliderDictionary
          DOCUMENT ME!
        • magSliderPanel
          JPanel magSliderPanel
          DOCUMENT ME!
        • panelRowColumn
          JPanel panelRowColumn
          DOCUMENT ME!
        • radioColumn
          JRadioButton radioColumn
          DOCUMENT ME!
        • radioRow
          JRadioButton radioRow
          DOCUMENT ME!
        • resetButton
          JButton resetButton
          DOCUMENT ME!
        • row
          int row
          DOCUMENT ME!
        • row_dependent
          boolean row_dependent
          DOCUMENT ME!
        • rowBFlag
          boolean rowBFlag
          values obtained from settings.
        • rowLabel
          JLabel rowLabel
          DOCUMENT ME!
        • rowPanel
          JPanel rowPanel
          DOCUMENT ME!
        • rowText
          JTextField rowText
          DOCUMENT ME!
        • toolTip
          JLabel toolTip
          DOCUMENT ME!
        • tSlider
          JSlider tSlider
          DOCUMENT ME!
        • tSliderDictionary
          Hashtable<Integer,JLabel> tSliderDictionary
          DOCUMENT ME!
        • tSliderPanel
          JPanel tSliderPanel
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLightboxGen

      class JDialogLightboxGen extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4508090288311270016L

    • Class gov.nih.mipav.view.dialogs.JDialogListSaveSelection

      class JDialogListSaveSelection extends JDialogBase implements Serializable
      serialVersionUID:
      -5740263457469223226L

      • Serialized Fields

        • selectedList
          JList selectedList
          List of selected VOIs.
        • selectFileA
          JPanelFileSelection selectFileA
          Indicates the source file for list A. The Default property name given to this file selector is "SelectFileA"
        • selectFileB
          JPanelFileSelection selectFileB
          Indicates the source file for list B. The Default property name given to this file selector is "SelectFileB"
        • selector
          JDialogListSaveSelection.JPanelListSelection selector
          Allows the user to modify listB based on either the file provided in selectFileA or selectFileB.
        • sourceList
          JList sourceList
          List of available VOIs.

    • Class gov.nih.mipav.view.dialogs.JDialogListSaveSelection.JPanelListSelection

      class JPanelListSelection extends JPanelListController implements Serializable
      serialVersionUID:
      -4660560256657187754L

    • Class gov.nih.mipav.view.dialogs.JDialogLivewire

      class JDialogLivewire extends JDialogBase implements Serializable
      serialVersionUID:
      -5986380794955471822L

      • Serialized Fields

        • radioGradient
          JRadioButton radioGradient
          Radio button for Gradient magnitude and direction
        • radioGradientAll
          JRadioButton radioGradientAll
          Radio button for Gradient, Medialness and Intensity
        • radioGradientInt
          JRadioButton radioGradientInt
          Radio button for Gradient and Intensity
        • radioGradientMed
          JRadioButton radioGradientMed
          Radio button for Gradient and Medialness
        • radioIntensity
          JRadioButton radioIntensity
          Radio button for Intensity
        • radioMedial
          JRadioButton radioMedial
          Radio button for Laplacian medialness
        • selection
          int selection
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLLE

      class JDialogLLE extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • destImage
          ModelImage destImage
          DOCUMENT ME!
        • embeddedDimensions
          int embeddedDimensions
          Use serialVersionUID for interoperability.
        • image
          ModelImage image
          DOCUMENT ME!
        • lleAlgo
          AlgorithmLLE lleAlgo
          DOCUMENT ME!
        • numberOfNeighbors
          int numberOfNeighbors
        • textEmbeddedDimensions
          JTextField textEmbeddedDimensions
          DOCUMENT ME!
        • textNeighbors
          JTextField textNeighbors
        • textTol
          JTextField textTol
        • tol
          double tol

    • Class gov.nih.mipav.view.dialogs.JDialogLoadImage

      class JDialogLoadImage extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -8455082719816268161L

      • Serialized Fields

        • browseButton
          JButton browseButton
          DOCUMENT ME!
        • dataType
          int dataType
          If blank image is to be loaded...need the type (for non-color images).
        • defaultBlueInput
          JTextField defaultBlueInput
          DOCUMENT ME!
        • defaultGreenInput
          JTextField defaultGreenInput
          DOCUMENT ME!
        • defaultRedInput
          JTextField defaultRedInput
          DOCUMENT ME!
        • doOrients
          boolean doOrients
          DOCUMENT ME!
        • doOrigins
          boolean doOrigins
          DOCUMENT ME!
        • image
          ModelImage image
          Source image.
        • imageChooser
          JComboBox imageChooser
          DOCUMENT ME!
        • importImage
          ModelImage importImage
          image taken from the frame to be imported:.
        • importLUT
          ModelLUT importLUT
        • importRGB
          ModelRGB importRGB
        • loadType
          int loadType
          are we loading from frame, file, or blank.
        • matchOrients
          JCheckBox matchOrients
          DOCUMENT ME!
        • matchOrigins
          JCheckBox matchOrigins
          DOCUMENT ME!
        • picListingPanel
          JPanel picListingPanel
          DOCUMENT ME!
        • radioBool
          JRadioButton radioBool
          DOCUMENT ME!
        • radioByte
          JRadioButton radioByte
          DOCUMENT ME!
        • radioDouble
          JRadioButton radioDouble
          DOCUMENT ME!
        • radioFloat
          JRadioButton radioFloat
          DOCUMENT ME!
        • radioInt
          JRadioButton radioInt
          DOCUMENT ME!
        • radioLong
          JRadioButton radioLong
          DOCUMENT ME!
        • radioShort
          JRadioButton radioShort
          DOCUMENT ME!
        • radioUByte
          JRadioButton radioUByte
          DOCUMENT ME!
        • radioUInt
          JRadioButton radioUInt
          DOCUMENT ME!
        • radioUShort
          JRadioButton radioUShort
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          a cloned version of importImage that will be inserted into the source images's B slot.
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLoadImageForRegistration

      class JDialogLoadImageForRegistration extends JDialogBase implements Serializable
      serialVersionUID:
      3843075015237096037L

      • Serialized Fields

        • browseButton
          JButton browseButton
          DOCUMENT ME!
        • directory
          String directory
          DOCUMENT ME!
        • fileButton
          JRadioButton fileButton
          DOCUMENT ME!
        • fileName
          String fileName
          DOCUMENT ME!
        • fileTFld
          JTextField fileTFld
          DOCUMENT ME!
        • frameButton
          JRadioButton frameButton
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • imageChooser
          JComboBox imageChooser
          DOCUMENT ME!
        • importImage
          ModelImage importImage
          image taken from the frame to be imported:.
        • isFrame
          boolean isFrame
          DOCUMENT ME!
        • LUTb
          ModelLUT LUTb
          DOCUMENT ME!
        • masterImage
          ViewJFrameImage masterImage
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLoadLeica

      class JDialogLoadLeica extends JDialogBase implements Serializable
      serialVersionUID:
      5662541302525039992L

      • Serialized Fields

        • headerFile
          File headerFile
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • seriesList
          JList seriesList
          DOCUMENT ME!
        • successful
          boolean successful
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLoadLeica.LeicaSeries

      class LeicaSeries extends JComponent implements Serializable
      serialVersionUID:
      1101169071873919736L

      • Serialized Fields

        • channels
          int[] channels
          DOCUMENT ME!
        • description
          String description
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • fileNames
          Vector<String> fileNames
          DOCUMENT ME!
        • numImages
          int numImages
          DOCUMENT ME!
        • resolutions
          float[] resolutions
          DOCUMENT ME!
        • seriesName
          String seriesName
          DOCUMENT ME!
        • units
          int[] units
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLocalNormalization

      class JDialogLocalNormalization extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      4460969182116331919L

      • Serialized Fields

        • algoLocal
          AlgorithmLocalNormalization algoLocal
          DOCUMENT ME!
        • blurringDiameter
          int blurringDiameter
          DOCUMENT ME!
        • blurringDiameterText
          JTextField blurringDiameterText
          DOCUMENT ME!
        • blurringFreq
          float blurringFreq
          user-selectable variables used in the FFT-blurring operation used as interim variables in starting the algorithm op.
        • blurringFreqText
          JTextField blurringFreqText
          DOCUMENT ME!
        • colorPanel
          JPanelColorChannels colorPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • errorComponent
          JTextField errorComponent
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sourceImage
          ModelImage sourceImage
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • unsharp
          float[] unsharp
          user-selectable variables used in the unsharping operation. used as interim variables in starting the algorithm op.
        • unsharpWeight
          double unsharpWeight
          DOCUMENT ME!
        • unsharpWeightText
          JTextField unsharpWeightText
          DOCUMENT ME!
        • unsharpXtext
          JTextField unsharpXtext
          DOCUMENT ME!
        • unsharpYtext
          JTextField unsharpYtext
          DOCUMENT ME!
        • unsharpZtext
          JTextField unsharpZtext
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogLocalVariance

      class JDialogLocalVariance extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogLogSlopeMapping

      class JDialogLogSlopeMapping extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • addImageBrowseButton
          JButton addImageBrowseButton
          browse button
        • additionalImagesLabel
          JLabel additionalImagesLabel
          label for browsing for additional images
        • alg
          AlgorithmLogSlopeMapping alg
          handle to algorithm
        • displayLoc
          int displayLoc
          result image in new frame
        • imageA
          ModelImage imageA
          source image.
        • imagesAdded
          int imagesAdded
        • isColor
          boolean isColor
          is color boolean
        • isMultifile
          boolean isMultifile
          boolean isMultifile
        • removeSelectedButton
          JButton removeSelectedButton
          remove button
        • removeSelectedImagesLabel
          JLabel removeSelectedImagesLabel
          label for removing selected images
        • resultImage
          ModelImage resultImage
          result image
        • selectedRows
          int[] selectedRows
          indices of selcted rows to remove
        • srcImagesList
          ArrayList<ModelImage> srcImagesList
          list of images to send to algorithm
        • srcImagesTable
          JTable srcImagesTable
          table to display the src image names.
        • srcTableModel
          ViewTableModel srcTableModel
          table model for the srcimages.
        • xValue
          double xValue
        • xValueButton
          JButton xValueButton
        • xValuesAdded
          int xValuesAdded
        • xValuesList
          ArrayList<Double> xValuesList
          list of x values to send to algorithm
        • xValueText
          JTextField xValueText

    • Class gov.nih.mipav.view.dialogs.JDialogLowerCompletion

      class JDialogLowerCompletion extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogLuminanceAdaptation

      class JDialogLuminanceAdaptation extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMagnificationControls

      class JDialogMagnificationControls extends JDialogZoom implements Serializable
      serialVersionUID:
      2838490243455666340L

      • Serialized Fields

        • boxHeight
          int boxHeight
          Width and height of zoom box
        • boxWidth
          int boxWidth
          Width and height of zoom box
        • circleButton
          JRadioButton circleButton
          Buttons for selecting magnifying shape.
        • heightButton
          JButton heightButton
          Buttons for width, height values
        • heightText
          JTextField heightText
          Text fields for zoom box
        • radius
          int radius
          Radius of zoom circle
        • radiusButton
          JButton radiusButton
          Button for setting radius value.
        • radiusText
          JTextField radiusText
          Text fields for zoom circle.
        • squareButton
          JRadioButton squareButton
          Buttons for selecting magnifying shape.
        • widthButton
          JButton widthButton
          Buttons for width, height values
        • widthText
          JTextField widthText
          Text fields for zoom box

    • Class gov.nih.mipav.view.dialogs.JDialogMarkovSegment

      class JDialogMarkovSegment extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • class_number
          int class_number
          Use serialVersionUID for interoperability.
        • image
          ModelImage image
          DOCUMENT ME!
        • iterations
          int iterations
        • labelClassNumber
          JLabel labelClassNumber
          DOCUMENT ME!
        • labelIterations
          JLabel labelIterations
        • labelPotential
          JLabel labelPotential
          DOCUMENT ME!
        • msAlgo
          AlgorithmMarkovSegment msAlgo
          DOCUMENT ME!
        • optionsPanel
          JPanel optionsPanel
          DOCUMENT ME!
        • potential
          double potential
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textClassNumber
          JTextField textClassNumber
          DOCUMENT ME!
        • textIterations
          JTextField textIterations
        • textPotential
          JTextField textPotential

    • Class gov.nih.mipav.view.dialogs.JDialogMarkovSmooth

      class JDialogMarkovSmooth extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • covariance
          double covariance
          The known covariance of the Gaussian noise
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • iterations
          int iterations
          The number of iterations to perform
        • labelCovariance
          JLabel labelCovariance
          DOCUMENT ME!
        • labelIterations
          JLabel labelIterations
        • labelMaxDiff
          JLabel labelMaxDiff
          DOCUMENT ME!
        • labelWeightDiff
          JLabel labelWeightDiff
        • max_diff
          double max_diff
          The maximum contribution to the potential of the difference between two neighboring pixel values.
        • msAlgo
          AlgorithmMarkovSmooth msAlgo
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • optionsPanel
          JPanel optionsPanel
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textCovariance
          JTextField textCovariance
          DOCUMENT ME!
        • textIterations
          JTextField textIterations
        • textMaxDiff
          JTextField textMaxDiff
        • textWeightDiff
          JTextField textWeightDiff
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • weight_diff
          double weight_diff
          The weighting attached to the component of the potential due to the difference between two neighboring pixel values.

    • Class gov.nih.mipav.view.dialogs.JDialogMask

      class JDialogMask extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7339956453691640420L

      • Serialized Fields

        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • exteriorFill
          JRadioButton exteriorFill
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • interiorFill
          JRadioButton interiorFill
          DOCUMENT ME!
        • maskAlgo
          AlgorithmMask maskAlgo
          DOCUMENT ME!
        • max
          double max
          DOCUMENT ME!
        • min
          double min
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • polarity
          boolean polarity
          or if the source image is to be replaced.
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textValue
          JTextField textValue
          DOCUMENT ME!
        • textValueB
          JTextField textValueB
          DOCUMENT ME!
        • textValueG
          JTextField textValueG
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • useVOI
          boolean useVOI
        • value
          float value
          DOCUMENT ME!
        • valueB
          float valueB
          DOCUMENT ME!
        • valueG
          float valueG
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMask3D4D

      class JDialogMask3D4D extends JDialogBase implements Serializable
      serialVersionUID:
      7339956453691640420L

      • Serialized Fields

        • fourD
          JRadioButton fourD
          Radio button indicating that the image should be masked in 4D
        • saveMasksAs4D
          boolean saveMasksAs4D
        • threeD
          JRadioButton threeD
          Radio button indicating that the image should only be masked in 3D

    • Class gov.nih.mipav.view.dialogs.JDialogMatchImages

      class JDialogMatchImages extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4508090288311270016L

      • Serialized Fields

        • checkDimensions
          JCheckBox checkDimensions
          DOCUMENT ME!
        • checkOrigins
          JCheckBox checkOrigins
          DOCUMENT ME!
        • comboBoxImageA
          JComboBox comboBoxImageA
          DOCUMENT ME!
        • comboBoxImageB
          JComboBox comboBoxImageB
          DOCUMENT ME!
        • doDimensions
          boolean doDimensions
          DOCUMENT ME!
        • doOrigins
          boolean doOrigins
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • imageB
          ModelImage imageB
          DOCUMENT ME!
        • matchAlgo
          AlgorithmMatchImages matchAlgo
          DOCUMENT ME!
        • padValTxt
          JTextField padValTxt
          DOCUMENT ME!
        • padValue
          int padValue
          DOCUMENT ME!
        • resultImageA
          ModelImage resultImageA
          DOCUMENT ME!
        • resultImageB
          ModelImage resultImageB
          DOCUMENT ME!
        • selectedNameA
          String selectedNameA
          DOCUMENT ME!
        • selectedNameB
          String selectedNameB
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMaximumIntensityProjection

      class JDialogMaximumIntensityProjection extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -586175799570928868L

      • Serialized Fields

        • cachedTab
          int cachedTab
          Cached value of selected tab
        • cFactor
          int cFactor
          Used for construction of the preview.
        • dim
          int dim
          Used for construction of the preview.
        • doPreview
          boolean doPreview
          Whether preview mode is turned on.
        • endSlice
          int[] endSlice
          Value of the end slice for the calculation (X,Y,Z).
        • extents
          int[] extents
          Image extents.
        • image
          ModelImage image
          Source Image.
        • index
          int index
          Used for construction of the preview.
        • maximum
          boolean[] maximum
          When true, calculate the maximum (X,Y,Z) slices.
        • maximumCheck
          JCheckBox[] maximumCheck
          CheckBox turns on/off calculating the maximum projection.
        • maxInput
          JTextField[] maxInput
          JTextfield for maximum value of threshold.
        • maxInputB
          JTextField[] maxInputB
          JTextfield for maximum Blue value of threshold.
        • maxInputG
          JTextField[] maxInputG
          JTextfield for maximum Green value of threshold.
        • maxInputR
          JTextField[] maxInputR
          JTextfield for maximum Red value of threshold.
        • maxIntensity
          float[] maxIntensity
          Maximum intensity threshold.
        • maxIntensityB
          float[] maxIntensityB
          Maximum Blue intensity threshold.
        • maxIntensityG
          float[] maxIntensityG
          Maximum Green intensity threshold.
        • maxIntensityR
          float[] maxIntensityR
          Maximum Red intensity threshold.
        • maxSlicePreview
          ModelImage maxSlicePreview
          Single slice preview images
        • maxSliceWindow
          ViewJFrameImage maxSliceWindow
          Windows containing preview images
        • minimum
          boolean[] minimum
          When true, calculate the minimum (X,Y,Z) slices.
        • minimumCheck
          JCheckBox[] minimumCheck
          CheckBox turns on/off calculating the minimum projection.
        • minInput
          JTextField[] minInput
          JTextfield for minimum value of threshold.
        • minInputB
          JTextField[] minInputB
          JTextfield for minimum Blue value of threshold.
        • minInputG
          JTextField[] minInputG
          JTextfield for minimum Green value of threshold.
        • minInputR
          JTextField[] minInputR
          JTextfield for minimum Red value of threshold.
        • minIntensity
          float[] minIntensity
          Minimum intensity threshold.
        • minIntensityB
          float[] minIntensityB
          Minimum Blue intensity threshold.
        • minIntensityG
          float[] minIntensityG
          Minimum Green intensity threshold.
        • minIntensityR
          float[] minIntensityR
          Minimum Red intensity threshold.
        • minSlicePreview
          ModelImage minSlicePreview
          Single slice preview images
        • minSliceWindow
          ViewJFrameImage minSliceWindow
          Windows containing preview images
        • nDims
          int nDims
          Image dimension, must be 3.
        • projection
          boolean[] projection
          When true output the X,Y,Z projections.
        • slice
          int slice
          Current slice of image
        • sliceLoc
          int sliceLoc
          Used for construction of the preview.
        • sliceSize
          int sliceSize
          Used for construction of the preview.
        • startInput
          JTextField[] startInput
          JTextfield for start slice of the computation.
        • startSlice
          int[] startSlice
          Value of the start slice for the calculation (X,Y,Z).
        • stopInput
          JTextField[] stopInput
          JTextfield for end slice of the computation.
        • tabbedPane
          JTabbedPane tabbedPane
          The tabbed pane that holds each dimension
        • window
          int[] window
          Value of the window size for the calculation (X,Y,Z).
        • windowLabel
          JLabel[] windowLabel
          Label displays the number of slices in the sliding window.
        • windowSlider
          ViewJSlider[] windowSlider
          Slider enables user to change the size of the sliding window.

    • Class gov.nih.mipav.view.dialogs.JDialogMaximumLikelihoodIteratedBlindDeconvolution

      class JDialogMaximumLikelihoodIteratedBlindDeconvolution extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7390265931793649147L

      • Serialized Fields

        • dim
          int dim
          Number of dimensions in an image e.g 2D, 3D
        • doResample
          boolean doResample
          The boolean value to determine whether to resample the original image or not.
        • extents
          int[] extents
          The extents of original image
        • ibdAlgor
          AlgorithmMaximumLikelihoodIteratedBlindDeconvolution ibdAlgor
          The MaximumLikelihood Blind Deconvolution algorithm:
        • newExtents
          int[] newExtents
          The extents of transformed (to the power of 2) image
        • numberIterations
          int numberIterations
          The number of iterations for calculating the deconvolution:
        • objectiveNumericalAperature
          float objectiveNumericalAperature
          The object numerical aperature, a property of the lens used to image the sample:
        • originalImage
          ModelImage originalImage
          The original data image to be reconstructed:
        • refractiveIndex
          float refractiveIndex
          The index of refraction of the sample:
        • showProgress
          int showProgress
          Display the deconvolved image every X images to show progress:
        • textExpectedExtentX
          JTextField textExpectedExtentX
          User-Interface for entering the expected extent X
        • textExpectedExtentY
          JTextField textExpectedExtentY
          User-Interface for entering the expected extent Y
        • textExpectedExtentZ
          JTextField textExpectedExtentZ
          User-Interface for entering the expected extent Z
        • textNumberIterations
          JTextField textNumberIterations
          User-Interface for entering the number of deconvolution iterations:
        • textObjectiveNumericalAperature
          JTextField textObjectiveNumericalAperature
          User-Interface for entering the objective numerical aperature:
        • textOriginalExtentX
          JTextField textOriginalExtentX
          User-Interface for displaying the original extent X
        • textOriginalExtentY
          JTextField textOriginalExtentY
          User-Interface for displaying the original extent Y
        • textOriginalExtentZ
          JTextField textOriginalExtentZ
          User-Interface for displaying the original extent Z
        • textRefractiveIndex
          JTextField textRefractiveIndex
          User-Interface for entering the index of refraction:
        • textShowProgress
          JTextField textShowProgress
          User-Interface for entering the number of intermediate images to show:
        • textWavelength
          JTextField textWavelength
          User-Interface for entering the sample wavelength:
        • useMicroscopeSettings
          boolean useMicroscopeSettings
          When true the lens NA, wavelength, and refractive index are used in the deconvolution process
        • wavelength
          float wavelength
          The reflected or fluorescence wavelength of the sample:

    • Class gov.nih.mipav.view.dialogs.JDialogMean

      class JDialogMean extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5373013772234532691L

      • Serialized Fields

        • adaptiveVectorButton
          JRadioButton adaptiveVectorButton
          DOCUMENT ME!
        • blue
          boolean blue
          DOCUMENT ME!
        • blueChannel
          JCheckBox blueChannel
          DOCUMENT ME!
        • blueLabel
          JLabel blueLabel
          DOCUMENT ME!
        • blueText
          JTextField blueText
          DOCUMENT ME!
        • blueVector
          long blueVector
          DOCUMENT ME!
        • bySlice
          JRadioButton bySlice
          DOCUMENT ME!
        • comboBoxKernelSize
          JComboBox comboBoxKernelSize
          DOCUMENT ME!
        • filterType
          int filterType
          DOCUMENT ME!
        • green
          boolean green
          DOCUMENT ME!
        • greenChannel
          JCheckBox greenChannel
          DOCUMENT ME!
        • greenLabel
          JLabel greenLabel
          DOCUMENT ME!
        • greenText
          JTextField greenText
          DOCUMENT ME!
        • greenVector
          long greenVector
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          false = apply algorithm only to VOI regions.
        • kernelSize
          int kernelSize
          DOCUMENT ME!
        • meanAlgo
          AlgorithmMean meanAlgo
          DOCUMENT ME!
        • outputPanel
          JPanelAlgorithmOutputOptions outputPanel
          DOCUMENT ME!
        • parallelVectorButton
          JRadioButton parallelVectorButton
          DOCUMENT ME!
        • red
          boolean red
          DOCUMENT ME!
        • redChannel
          JCheckBox redChannel
          DOCUMENT ME!
        • redLabel
          JLabel redLabel
          DOCUMENT ME!
        • redText
          JTextField redText
          DOCUMENT ME!
        • redVector
          long redVector
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • separateButton
          JRadioButton separateButton
          DOCUMENT ME!
        • separateVectorGroup
          ButtonGroup separateVectorGroup
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • wholeVolume
          JRadioButton wholeVolume
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMeanShiftClustering

      class JDialogMeanShiftClustering extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMeanShiftSegmentation

      class JDialogMeanShiftSegmentation extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMedian

      class JDialogMedian extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7749097890204237664L

      • Serialized Fields

        • adaptiveButton
          JRadioButton adaptiveButton
        • ATVMFButton
          JRadioButton ATVMFButton
        • blue
          boolean blue
          DOCUMENT ME!
        • blueChannel
          JCheckBox blueChannel
          DOCUMENT ME!
        • bySlice
          JRadioButton bySlice
          DOCUMENT ME!
        • colorFilterType
          int colorFilterType
          DOCUMENT ME!
        • comboBoxKernelShape
          JComboBox comboBoxKernelShape
          DOCUMENT ME!
        • comboBoxKernelSize
          JComboBox comboBoxKernelSize
          DOCUMENT ME!
        • comboBoxMaximumSize
          JComboBox comboBoxMaximumSize
          DOCUMENT ME!
        • componentButton
          JRadioButton componentButton
          DOCUMENT ME!
        • delta
          float delta
        • filterType
          int filterType
        • fuzzyTruncatedButton
          JRadioButton fuzzyTruncatedButton
        • green
          boolean green
          DOCUMENT ME!
        • greenChannel
          JCheckBox greenChannel
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          false = apply algorithm only to VOI regions.
        • iters
          int iters
          DOCUMENT ME!
        • kernelShape
          int kernelShape
          DOCUMENT ME!
        • kernelSize
          int kernelSize
          DOCUMENT ME!
        • labelDelta
          JLabel labelDelta
        • labelMaximumSize
          JLabel labelMaximumSize
          DOCUMENT ME!
        • labelSTDDeviation
          JLabel labelSTDDeviation
          DOCUMENT ME!
        • maximumSize
          int maximumSize
          DOCUMENT ME!
        • medianAlgo
          AlgorithmMedian medianAlgo
          DOCUMENT ME!
        • outputPanel
          JPanelAlgorithmOutputOptions outputPanel
          DOCUMENT ME!
        • red
          boolean red
          DOCUMENT ME!
        • redChannel
          JCheckBox redChannel
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • standardButton
          JRadioButton standardButton
        • stdDev
          float stdDev
          DOCUMENT ME!
        • textDelta
          JTextField textDelta
        • textNIter
          JTextField textNIter
          DOCUMENT ME!
        • textSTDDeviation
          JTextField textSTDDeviation
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • truncatedButton
          JRadioButton truncatedButton
        • typeGroup
          ButtonGroup typeGroup
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • vectorDirectionButton
          JRadioButton vectorDirectionButton
          DOCUMENT ME!
        • vectorGroup
          ButtonGroup vectorGroup
          DOCUMENT ME!
        • vectorMagnitudeButton
          JRadioButton vectorMagnitudeButton
          DOCUMENT ME!
        • wholeVolume
          JRadioButton wholeVolume
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMemoryAllocation

      class JDialogMemoryAllocation extends JDialogBase implements Serializable
      serialVersionUID:
      -1470759041555523857L

      • Serialized Fields

        • maxHeapText
          JTextField maxHeapText
          DOCUMENT ME!
        • startupFile
          File startupFile
          Contains all java properties of the MIPAV app (used at least when loading!)
        • usePreferencesButton
          JButton usePreferencesButton
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMetaImageChoice

      class JDialogMetaImageChoice extends JDialogBase implements Serializable

      • Serialized Fields

        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • oneFile
          JRadioButton oneFile
          DOCUMENT ME!
        • twoFiles
          JRadioButton twoFiles
          DOCUMENT ME!
        • writeGroup
          ButtonGroup writeGroup
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMidsagittal

      class JDialogMidsagittal extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2594860465921132823L

    • Class gov.nih.mipav.view.dialogs.JDialogMipavOptions

      class JDialogMipavOptions extends JDialogBase implements Serializable
      serialVersionUID:
      6756915900242085699L

      • Serialized Fields

        • absoluteWindowLevelButton
          JRadioButton absoluteWindowLevelButton
        • activeColor
          JButton activeColor
          DOCUMENT ME!
        • activeImageColorBorderSize
          JComboBox activeImageColorBorderSize
          border size for active image color
        • checkOnFrameClose
          JCheckBox checkOnFrameClose
          DOCUMENT ME!
        • colorChooser
          JColorChooser colorChooser
          DOCUMENT ME!
        • comboBoxSaveImgMethod
          JComboBox comboBoxSaveImgMethod
          Whether to save .img files as selected by dialog or always as analyze, interfile, or nifti.
        • comboBoxSaveMncMethod
          JComboBox comboBoxSaveMncMethod
          Whether to save .mnc files as selected by dialog or always as minc1 or minc2.
        • complexDisplayChoices
          JComboBox complexDisplayChoices
          The available choices for displaying the numerical values of complex data
        • continuousVOIBox
          JCheckBox continuousVOIBox
        • crosshairChoices
          JComboBox crosshairChoices
          DOCUMENT ME!
        • crosshairNames
          String[] crosshairNames
          DOCUMENT ME!
        • debugAlgorithmBox
          JComboBox debugAlgorithmBox
          Box to select logging level for Algorithm category
        • debugCommsBox
          JComboBox debugCommsBox
          Box to select logging level for Comms category
        • debugFileIOBox
          JComboBox debugFileIOBox
          Box to select logging level for FileIO category
        • debugMinorBox
          JComboBox debugMinorBox
          Box to select logging level for Minor category
        • debugScriptingBox
          JComboBox debugScriptingBox
          Box to select logging level for Scripting category
        • defaultDisplayChoices
          JComboBox defaultDisplayChoices
          Available choices for displaying brightness/color display correlations for pixel values.
        • dicomCatcher
          JCheckBox dicomCatcher
          DOCUMENT ME!
        • dicomReceiverOnStart
          JCheckBox dicomReceiverOnStart
          Dicom Receiver check box
        • displayColorPanel
          JPanel displayColorPanel
          DOCUMENT ME!
        • displayHistogram
          JCheckBox displayHistogram
          Whether images are updated in real-time based on histogram changes.
        • displayImagePanel
          JPanel displayImagePanel
          Gives user choices for displaying complex images.
        • displayLogMag
          JCheckBox displayLogMag
          The check box to indicate whether images are displayed using the log of their magnitude
        • displayLUT
          JCheckBox displayLUT
          Whether to auto-display lut associated with file.
        • displayPanel
          JPanel displayPanel
          MIPAV global options private JPanel globalChangesPanel;.
        • displaySplash
          JCheckBox displaySplash
          DOCUMENT ME!
        • displayUserInterfacePanel
          JPanel displayUserInterfacePanel
          DOCUMENT ME!
        • doIntensityOnLeftBox
          JCheckBox doIntensityOnLeftBox
          Check boxes for whether right and left mouse clicks produce default actions.
        • doWinLevOnRightBox
          JCheckBox doWinLevOnRightBox
          Check boxes for whether right and left mouse clicks produce default actions.
        • editUserDefButton
          JButton editUserDefButton
          Button to lasunch the Edit User Defined File Types Dialog
        • enableLoggingBox
          JCheckBox enableLoggingBox
          DOCUMENT ME!
        • fileFilter
          int fileFilter
          DOCUMENT ME!
        • fileMiscPanel
          JPanel fileMiscPanel
          DOCUMENT ME!
        • filePanel
          JPanel filePanel
          DOCUMENT ME!
        • fileSavePanel
          JPanel fileSavePanel
          DOCUMENT ME!
        • fileTempDirBrowseButton
          JButton fileTempDirBrowseButton
        • fileTempDirField
          JTextField fileTempDirField
        • filterButton
          JButton filterButton
          DOCUMENT ME!
        • flipNIFTIReadCheckBox
          JCheckBox flipNIFTIReadCheckBox
        • fontChooser
          JComboBox fontChooser
          DOCUMENT ME!
        • fontNames
          String[] fontNames
          DOCUMENT ME!
        • fontSizeField
          JTextField fontSizeField
          DOCUMENT ME!
        • frameRateField
          JTextField frameRateField
          DOCUMENT ME!
        • gpuCompEnabledCheckBox
          JCheckBox gpuCompEnabledCheckBox
          GPU computing enabled check box
        • gpuInfoButton
          JButton gpuInfoButton
          DOCUMENT ME!
        • histoForceUBYTE
          JCheckBox histoForceUBYTE
        • imageChooser
          JComboBox imageChooser
          DOCUMENT ME!
        • intensityLabelBackgroundButton
          JButton intensityLabelBackgroundButton
          DOCUMENT ME!
        • intensityLabelBackgroundColor
          Color intensityLabelBackgroundColor
          DOCUMENT ME!
        • intensityLabelColor
          Color intensityLabelColor
          DOCUMENT ME!
        • intensityLabelColorButton
          JButton intensityLabelColorButton
          DOCUMENT ME!
        • interpolateDisplayChoices
          JComboBox interpolateDisplayChoices
          Available options for image interpolation
        • labels
          JLabel[] labels
          DOCUMENT ME!
        • lfDisplayChoices
          JComboBox lfDisplayChoices
          Look and feel choices.
        • logFileButton
          JButton logFileButton
          DOCUMENT ME!
        • logFilename
          String logFilename
          DOCUMENT ME!
        • maxDebugLineField
          JTextField maxDebugLineField
        • multiThreadingEnabledCheckBox
          JCheckBox multiThreadingEnabledCheckBox
          Multi-Threading Enabled Check Box
        • openImagesInTiledFormatBox
          JCheckBox openImagesInTiledFormatBox
          opens images in tiled format
        • otherPanel
          JPanel otherPanel
          DOCUMENT ME!
        • performHeapMaxCheck
          JCheckBox performHeapMaxCheck
          DOCUMENT ME!
        • pointVOIChoices
          JComboBox pointVOIChoices
          DOCUMENT ME!
        • preferredActiveColor
          Color preferredActiveColor
          DOCUMENT ME!
        • preferredCrosshair
          String preferredCrosshair
          DOCUMENT ME!
        • provenanceCheckBox
          JCheckBox provenanceCheckBox
          DOCUMENT ME!
        • provenanceFileButton
          JButton provenanceFileButton
        • provenanceFilename
          String provenanceFilename
        • provenanceImageCheckBox
          JCheckBox provenanceImageCheckBox
        • quickListLevel
          JComboBox quickListLevel
          DOCUMENT ME!
        • relativeWindowLevelButton
          JRadioButton relativeWindowLevelButton
        • resetButton
          JButton resetButton
          Button used to reset all preferences to default state.
        • saveAllCheckBox
          JCheckBox saveAllCheckBox
          DOCUMENT ME!
        • saveDefaultsCheckBox
          JCheckBox saveDefaultsCheckBox
          DOCUMENT ME!
        • saveLabel
          JLabel saveLabel
          Label before comboBoxSaveMethod
        • savePromptOverwriteBox
          JCheckBox savePromptOverwriteBox
          DOCUMENT ME!
        • saveThumbnailCheckBox
          JCheckBox saveThumbnailCheckBox
          DOCUMENT ME!
        • saveVOILPSButton
          JRadioButton saveVOILPSButton
        • saveVOIVoxelButton
          JRadioButton saveVOIVoxelButton
        • showLineVOIAngleBox
          JCheckBox showLineVOIAngleBox
          DOCUMENT ME!
        • showOutputWindow
          JCheckBox showOutputWindow
          DOCUMENT ME!
        • tabbedPane
          JTabbedPane tabbedPane
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          ui must be set to access the list of images to set image-specfic options (ie,. log mode)
        • voiColorChoices
          JComboBox voiColorChoices
          DOCUMENT ME!
        • voiColorNames
          String[] voiColorNames
          DOCUMENT ME!
        • voiColors
          Color[] voiColors
          DOCUMENT ME!
        • voiDrawButton
          JButton voiDrawButton
          DOCUMENT ME!
        • voiDrawColor
          Color voiDrawColor
          DOCUMENT ME!
        • VOIGroup
          ButtonGroup VOIGroup
        • WindowLevelGroup
          ButtonGroup WindowLevelGroup

    • Class gov.nih.mipav.view.dialogs.JDialogMode

      class JDialogMode extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      4183545541629455949L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogMorphologicalFilter

      class JDialogMorphologicalFilter extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -523142924576794921L

    • Class gov.nih.mipav.view.dialogs.JDialogMorphologicalGradient

      class JDialogMorphologicalGradient extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMorphologicalLaplacian

      class JDialogMorphologicalLaplacian extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMorphologicalReconstruction

      class JDialogMorphologicalReconstruction extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMosaicToSlices

      class JDialogMosaicToSlices extends JDialogScriptableBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogMotionDetection

      class JDialogMotionDetection extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMRIShadingCorrection

      class JDialogMRIShadingCorrection extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      2132712619224805730L

      • Serialized Fields

        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • iters
          int iters
          DOCUMENT ME!
        • labelGaussX
          JLabel labelGaussX
          DOCUMENT ME!
        • labelGaussY
          JLabel labelGaussY
          DOCUMENT ME!
        • labelIters
          JLabel labelIters
          DOCUMENT ME!
        • labelNorm
          JLabel labelNorm
          DOCUMENT ME!
        • mAlgo
          AlgorithmMRIShadingCorrection mAlgo
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • norm
          float norm
          DOCUMENT ME!
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textIters
          JTextField textIters
          DOCUMENT ME!
        • textNorm
          JTextField textNorm
          DOCUMENT ME!
        • thresholdCheckbox
          JCheckBox thresholdCheckbox
          DOCUMENT ME!
        • thresholdLabel
          JLabel thresholdLabel
          DOCUMENT ME!
        • thresholdLevel
          float thresholdLevel
          DOCUMENT ME!
        • thresholdSelected
          boolean thresholdSelected
          DOCUMENT ME!
        • thresholdText
          JTextField thresholdText
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMSER

      class JDialogMSER extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • bright_on_dark
          boolean bright_on_dark
        • brightOnDarkCheckBox
          JCheckBox brightOnDarkCheckBox
        • dark_on_bright
          boolean dark_on_bright
        • darkOnBrightCheckBox
          JCheckBox darkOnBrightCheckBox
        • delta
          double delta
        • ellipsesOnly
          JRadioButton ellipsesOnly
        • image
          ModelImage image
          DOCUMENT ME!
        • imageVOIGroup
          ButtonGroup imageVOIGroup
        • imageVOIPanel
          JPanel imageVOIPanel
        • labelDelta
          JLabel labelDelta
        • labelMaxArea
          JLabel labelMaxArea
        • labelMaxVariation
          JLabel labelMaxVariation
        • labelMinArea
          JLabel labelMinArea
        • labelMinDiversity
          JLabel labelMinDiversity
        • max_area
          double max_area
        • max_variation
          double max_variation
        • min_area
          double min_area
        • min_diversity
          double min_diversity
        • mserAlgo
          AlgorithmMSER mserAlgo
          DOCUMENT ME!
        • outputVOIType
          int outputVOIType
        • paramPanel
          JPanel paramPanel
        • pointsAndEllipses
          JRadioButton pointsAndEllipses
        • pointsOnly
          JRadioButton pointsOnly
        • textDelta
          JTextField textDelta
        • textMaxArea
          JTextField textMaxArea
        • textMaxVariation
          JTextField textMaxVariation
        • textMinArea
          JTextField textMinArea
        • textMinDiversity
          JTextField textMinDiversity

    • Class gov.nih.mipav.view.dialogs.JDialogMSFuzzyCMeans

      class JDialogMSFuzzyCMeans extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      5469772983205216898L

      • Serialized Fields

        • afcmAlgo
          AlgorithmMSpectralFuzzyCMeans afcmAlgo
          DOCUMENT ME!
        • centroids
          float[] centroids
          DOCUMENT ME!
        • changeRemoveIndex
          boolean changeRemoveIndex
          DOCUMENT ME!
        • chooserButton
          JButton chooserButton
          DOCUMENT ME!
        • colorPanel
          JPanelColorChannels colorPanel
          DOCUMENT ME!
        • cropBackground
          boolean cropBackground
          DOCUMENT ME!
        • cropCheckbox
          JCheckBox cropCheckbox
          DOCUMENT ME!
        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • endTol
          float endTol
          DOCUMENT ME!
        • fuzzyOnly
          JRadioButton fuzzyOnly
          DOCUMENT ME!
        • hardFuzzyBoth
          JRadioButton hardFuzzyBoth
          DOCUMENT ME!
        • hardOnly
          JRadioButton hardOnly
          DOCUMENT ME!
        • imageList
          JList imageList
          DOCUMENT ME!
        • imagePanel
          JPanel imagePanel
          DOCUMENT ME!
        • imageVOIGroup
          ButtonGroup imageVOIGroup
          DOCUMENT ME!
        • imageVOIPanel
          JPanel imageVOIPanel
          DOCUMENT ME!
        • labelEndTol
          JLabel labelEndTol
          DOCUMENT ME!
        • labelExpo
          JLabel labelExpo
          DOCUMENT ME!
        • labelMaxIter
          JLabel labelMaxIter
          DOCUMENT ME!
        • labelNClasses
          JLabel labelNClasses
          DOCUMENT ME!
        • maxIter
          int maxIter
          DOCUMENT ME!
        • model
          DefaultListModel model
          DOCUMENT ME!
        • nClasses
          int nClasses
          DOCUMENT ME!
        • nPyramid
          int nPyramid
          DOCUMENT ME!
        • oneJacobiIter
          int oneJacobiIter
          DOCUMENT ME!
        • oneSmooth
          float oneSmooth
          DOCUMENT ME!
        • outputGainField
          boolean outputGainField
          private JCheckBox calcGainFieldCheckbox;.
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • presentNumber
          int presentNumber
          DOCUMENT ME!
        • q
          float q
          DOCUMENT ME!
        • regionFlag
          boolean regionFlag
          DOCUMENT ME!
        • removeButton
          JButton removeButton
          DOCUMENT ME!
        • removeIndex
          int removeIndex
          DOCUMENT ME!
        • resultImage
          ModelImage[] resultImage
          DOCUMENT ME!
        • resultNumber
          int resultNumber
          DOCUMENT ME!
        • segmentation
          int segmentation
          DOCUMENT ME!
        • segmentationGroup
          ButtonGroup segmentationGroup
          DOCUMENT ME!
        • segmentationPanel
          JPanel segmentationPanel
          DOCUMENT ME!
        • srcImage
          ModelImage[] srcImage
          DOCUMENT ME!
        • srcNumber
          int srcNumber
          DOCUMENT ME!
        • tempImage
          ModelImage[] tempImage
          DOCUMENT ME!
        • textEndTol
          JTextField textEndTol
          DOCUMENT ME!
        • textExpo
          JTextField textExpo
          DOCUMENT ME!
        • textMaxIter
          JTextField textMaxIter
          DOCUMENT ME!
        • textNClasses
          JTextField textNClasses
          DOCUMENT ME!
        • threshold
          float[] threshold
          DOCUMENT ME!
        • twoJacobiIter
          int twoJacobiIter
          DOCUMENT ME!
        • twoSmooth
          float twoSmooth
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogMultiPaint

      class JDialogMultiPaint extends JDialogBase implements Serializable
      serialVersionUID:
      -7497259210728078264L

      • Serialized Fields

        • alphaBlend
          int alphaBlend
          DOCUMENT ME!
        • bottomPanel
          JPanel bottomPanel
          DOCUMENT ME!
        • buttonShortkeys
          JToggleButton buttonShortkeys
          DOCUMENT ME!
        • buttonTextArrayList
          ArrayList<Integer> buttonTextArrayList
          this is the array list of texts for the mask number buttons.
        • changeMaskNumberDialog
          JDialogChangeMaskNumber changeMaskNumberDialog
          Ref to JDialogChangeMaskNumber.*
        • checkAutosave
          JToggleButton checkAutosave
        • closePanel
          JPanel closePanel
          DOCUMENT ME!
        • collapseButton
          JButton collapseButton
          Button that allows user to collapse masks/paint to single value.*
        • color
          Color[] color
          array of colors to use for the labels.
        • currentOpacity
          float currentOpacity
          saved opacity parameter when hiding the paint
        • displayMasksButton
          JToggleButton displayMasksButton
          display masks toggle button.
        • displayModeButton
          JToggleButton displayModeButton
          DOCUMENT ME!
        • displayPaintButton
          JToggleButton displayPaintButton
          DOCUMENT ME!
        • editBox
          JCheckBox editBox
          DOCUMENT ME!
        • exportVoiButton
          JButton exportVoiButton
          button VOI export.
        • image
          ModelImage image
          source image.
        • imgBSize
          int imgBSize
          The size, in voxels, of the mask.
        • importVoiButton
          JButton importVoiButton
          button VOI import.
        • indeterminateProgressBar
          JProgressBar indeterminateProgressBar
          DOCUMENT ME!
        • intensityLockVector
          Vector<Integer> intensityLockVector
          DOCUMENT ME!
        • isCompactDisplay
          boolean isCompactDisplay
        • isVisibleMask
          boolean isVisibleMask
        • isVisiblePaint
          boolean isVisiblePaint
        • label
          String[] label
          labels for the painted objects.
        • labelField
          JTextField[] labelField
          DOCUMENT ME!
        • leftPanel
          JPanel leftPanel
          DOCUMENT ME!
        • leftRightPanel
          JPanel leftRightPanel
          DOCUMENT ME!
        • listButton
          BorderedButton[] listButton
          DOCUMENT ME!
        • listPanel
          JPanel listPanel
          DOCUMENT ME!
        • loadDialog
          JFileChooser loadDialog
          DOCUMENT ME!
        • loadLabelsButton
          JButton loadLabelsButton
          DOCUMENT ME!
        • loadMaskButton
          JButton loadMaskButton
          DOCUMENT ME!
        • lockAllButton
          JButton lockAllButton
          lock all masks checkbox *
        • lockPanel
          JPanel lockPanel
          lock panel
        • mainPanel
          JPanel mainPanel
          dialog elements.
        • multiButton
          BorderedButton[] multiButton
          DOCUMENT ME!
        • multiPanel
          JPanel multiPanel
          DOCUMENT ME!
        • nbx
          int nbx
          number of paint masks initially.
        • nby
          int nby
          number of paint masks initially.
        • newSelection
          int newSelection
          This represents the button the user selects to..initally at 1.*
        • numberLabel
          JLabel numberLabel
          DOCUMENT ME!
        • numberPanel
          JPanel numberPanel
          DOCUMENT ME!
        • numberXField
          JTextField numberXField
          resize x value.
        • numberYField
          JTextField numberYField
          resize y value.
        • optionPanel
          JPanel optionPanel
          DOCUMENT ME!
        • preserveBox
          JCheckBox[] preserveBox
          DOCUMENT ME!
        • preserved
          boolean[] preserved
          check whether the mask can be affected by new paint or not.
        • radioGroup
          ButtonGroup radioGroup
          button group for radio buttons
        • resizeButton
          JButton resizeButton
          resize button.
        • rightPanel
          JPanel rightPanel
          DOCUMENT ME!
        • save
          MultiPaintAutoSave save
          DOCUMENT ME!
        • saveAs3DMaskRadio
          JRadioButton saveAs3DMaskRadio
          radio buttons for commmiting masks as 3d or 4d if image is 4d
        • saveAs4DMaskRadio
          JRadioButton saveAs4DMaskRadio
          radio buttons for commmiting masks as 3d or 4d if image is 4d
        • saveDialog
          JFileChooser saveDialog
          DOCUMENT ME!
        • saveLabelsButton
          JButton saveLabelsButton
          save labels button.
        • saveMaskButton
          JButton saveMaskButton
          save mask button.
        • saveMasksAs4D
          boolean saveMasksAs4D
          this boolean is needed for commiting masks for a 4d image
        • saver
          Timer saver
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          This is the scroll pane for the label list panel.*
        • selected
          int selected
          id for the selected paint mask.
        • threads
          ThreadGroup threads
        • triPlanarAlphaBlend
          int triPlanarAlphaBlend
          DOCUMENT ME!
        • unlockAllButton
          JButton unlockAllButton
          unlock all masks checkbox *
        • userInterface
          ViewUserInterface userInterface
          private int destExtents[];.

    • Class gov.nih.mipav.view.dialogs.JDialogMultiResolutionBilateralFilter

      class JDialogMultiResolutionBilateralFilter extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMultiResolutionGuidedFilter

      class JDialogMultiResolutionGuidedFilter extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogMultiScaleHornSchunk

      class JDialogMultiScaleHornSchunk extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogN4MRIBiasFieldCorrection

      class JDialogN4MRIBiasFieldCorrection extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • autoThreshold
          boolean autoThreshold
          DOCUMENT ME!
        • autoThresholdCheckbox
          JCheckBox autoThresholdCheckbox
          DOCUMENT ME!
        • confidenceImage
          ModelImage confidenceImage
        • controlPoints
          int controlPoints
        • convertTomm
          float convertTomm
          DOCUMENT ME!
        • createField
          boolean createField
          DOCUMENT ME!
        • createFieldCheckbox
          JCheckBox createFieldCheckbox
          DOCUMENT ME!
        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • endTol
          double endTol
          DOCUMENT ME!
        • fieldDistance
          float fieldDistance
          DOCUMENT ME!
        • fieldImage
          ModelImage fieldImage
          DOCUMENT ME!
        • fittingLevels
          int fittingLevels
        • image
          ModelImage image
          DOCUMENT ME!
        • kernelfwhm
          double kernelfwhm
          DOCUMENT ME!
        • labelControlPoints
          JLabel labelControlPoints
        • labelDistance
          JLabel labelDistance
          DOCUMENT ME!
        • labelEndTol
          JLabel labelEndTol
          DOCUMENT ME!
        • labelFittingLevels
          JLabel labelFittingLevels
        • labelKernel
          JLabel labelKernel
          DOCUMENT ME!
        • labelMaxIter
          JLabel labelMaxIter
          DOCUMENT ME!
        • labelNoise
          JLabel labelNoise
          DOCUMENT ME!
        • labelShrink
          JLabel labelShrink
          DOCUMENT ME!
        • labelSignal
          JLabel labelSignal
          DOCUMENT ME!
        • maxIter
          int maxIter
          DOCUMENT ME!
        • N4Algo
          AlgorithmN4MRIBiasFieldCorrectionFilter N4Algo
          DOCUMENT ME!
        • noise
          double noise
          DOCUMENT ME!
        • orgResol
          float[] orgResol
          DOCUMENT ME!
        • regionFlag
          boolean regionFlag
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • resXUnit
          int resXUnit
          DOCUMENT ME!
        • resYUnit
          int resYUnit
          DOCUMENT ME!
        • resZUnit
          int resZUnit
          DOCUMENT ME!
        • shrink
          float shrink
          DOCUMENT ME!
        • textControlPoints
          JTextField textControlPoints
        • textDistance
          JTextField textDistance
          DOCUMENT ME!
        • textEndTol
          JTextField textEndTol
          DOCUMENT ME!
        • textFittingLevels
          JTextField textFittingLevels
        • textKernel
          JTextField textKernel
          DOCUMENT ME!
        • textMaxIter
          JTextField textMaxIter
          DOCUMENT ME!
        • textNoise
          JTextField textNoise
          DOCUMENT ME!
        • textShrink
          JTextField textShrink
          DOCUMENT ME!
        • textSignal
          JTextField textSignal
          DOCUMENT ME!
        • threshold
          float threshold
          DOCUMENT ME!
        • useScript
          boolean useScript
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogNColors

      class JDialogNColors extends JDialogBase implements Serializable
      serialVersionUID:
      -2280005601447558064L

      • Serialized Fields

        • field
          JTextField field
          DOCUMENT ME!
        • nColors
          int nColors
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogNearlyCircleToCircle

      class JDialogNearlyCircleToCircle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

    • Class gov.nih.mipav.view.dialogs.JDialogNIFTIChoice

      class JDialogNIFTIChoice extends JDialogBase implements Serializable
      serialVersionUID:
      5469246588202892297L

      • Serialized Fields

        • okayPressed
          boolean okayPressed
          DOCUMENT ME!
        • oneFile
          JRadioButton oneFile
          DOCUMENT ME!
        • twoFiles
          JRadioButton twoFiles
          DOCUMENT ME!
        • writeGroup
          ButtonGroup writeGroup
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogNLMeans_filt2D

      class JDialogNLMeans_filt2D extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • filterPanel
          JPanel filterPanel
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • ksize
          int ksize
          Neighbor window size
        • labelKSize
          JLabel labelKSize
          DOCUMENT ME!
        • labelNoise
          JLabel labelNoise
          DOCUMENT ME!
        • labelSigmaX
          JLabel labelSigmaX
          DOCUMENT ME!
        • labelSigmaY
          JLabel labelSigmaY
          DOCUMENT ME!
        • labelSSize
          JLabel labelSSize
          DOCUMENT ME!
        • mainPanel
          JPanel mainPanel
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • NLMeansAlgo
          NLMeans_filt2D NLMeansAlgo
          DOCUMENT ME!
        • noise_std
          double noise_std
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sigmaX
          double sigmaX
          DOCUMENT ME!
        • sigmaY
          double sigmaY
          DOCUMENT ME!
        • ssize
          int ssize
          DOCUMENT ME!
        • textKSize
          JTextField textKSize
          DOCUMENT ME!
        • textNoise
          JTextField textNoise
          DOCUMENT ME!
        • textSigmaX
          JTextField textSigmaX
          DOCUMENT ME!
        • textSigmaY
          JTextField textSigmaY
          DOCUMENT ME!
        • textSSize
          JTextField textSSize
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogNLNoiseReduction

      class JDialogNLNoiseReduction extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -6988226818561396907L

      • Serialized Fields

        • bt
          double bt
          DOCUMENT ME!
        • defaultThreshold
          long defaultThreshold
          DOCUMENT ME!
        • defaultThresholdDouble
          double defaultThresholdDouble
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          DOCUMENT ME!
        • image25DCheckbox
          JCheckBox image25DCheckbox
          of similar brightness voxels is empty, a local median filter is used. This allows the correction of impulse ("salt-and-pepper") noise. If false, when no neighborhood is found, the original intensity of the voxel of interest remains unchanged.
        • labelMaskSD
          JLabel labelMaskSD
          DOCUMENT ME!
        • labelThreshold
          JLabel labelThreshold
          DOCUMENT ME!
        • maskSD
          float maskSD
          DOCUMENT ME!
        • maximumThreshold
          long maximumThreshold
          DOCUMENT ME!
        • maximumThresholdDouble
          double maximumThresholdDouble
          DOCUMENT ME!
        • medianCheckbox
          JCheckBox medianCheckbox
          The mask is basically Gaussian with standard deviation in image units - e.g. mm set by the user. However, for a small, fast, flat response with a 3x3 or 3x3x3 voxel mask, set maskSD to 0.
        • minimumThreshold
          long minimumThreshold
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • nlnrAlgo
          AlgorithmNLNoiseReduction nlnrAlgo
          DOCUMENT ME!
        • optionsPanel
          JPanel optionsPanel
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textMaskSD
          JTextField textMaskSD
          discriminate between noise and the underlying image. Ideally, the value should be set greater than the noise level and less than the contrast of the underlying image. Edges of contrast smaller than this threshold will tend to be blurred whereas those of greater contrast will not be.
        • textThreshold
          JTextField textThreshold
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • useMedian
          boolean useMedian
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogNMSuppression

      class JDialogNMSuppression extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3261350233947714913L

    • Class gov.nih.mipav.view.dialogs.JDialogNoise

      class JDialogNoise extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3214808660601346651L

      • Serialized Fields

        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • gain
          double gain
        • gainText
          JTextField gainText
        • group1
          ButtonGroup group1
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageRangeLabel
          JLabel imageRangeLabel
          DOCUMENT ME!
        • max
          double max
          DOCUMENT ME!
        • maximumNoise
          double maximumNoise
          DOCUMENT ME!
        • maxNoiseLabel
          JLabel maxNoiseLabel
          DOCUMENT ME!
        • maxNoiseLabel2
          JLabel maxNoiseLabel2
        • mean
          double mean
        • meanText
          JTextField meanText
        • min
          double min
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • noiseType
          int noiseType
          DOCUMENT ME!
        • offset
          double offset
        • offsetText
          JTextField offsetText
        • panelGU
          JPanel panelGU
          DOCUMENT ME!
        • panelImageType
          JPanel panelImageType
          DOCUMENT ME!
        • panelPO
          JPanel panelPO
        • panelRayleigh
          JPanel panelRayleigh
        • panelRician
          JPanel panelRician
        • radioGaussian
          JRadioButton radioGaussian
          DOCUMENT ME!
        • radioPoisson
          JRadioButton radioPoisson
        • radioRayleigh
          JRadioButton radioRayleigh
        • radioRician
          JRadioButton radioRician
        • radioUniform
          JRadioButton radioUniform
          DOCUMENT ME!
        • randomAlgo
          AlgorithmNoise randomAlgo
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sigma
          double sigma
        • sigmaText
          JTextField sigmaText
        • textMaxNoise
          JTextField textMaxNoise
          DOCUMENT ME!
        • textMaxNoise2
          JTextField textMaxNoise2
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogNoiseLevel

      class JDialogNoiseLevel extends JDialogScriptableBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogNonlocalMeansFilter

      class JDialogNonlocalMeansFilter extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • BayesCheckBox
          JCheckBox BayesCheckBox
        • degreeOfFiltering
          float degreeOfFiltering
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • doBayesShrinkThresholdComputation
          boolean doBayesShrinkThresholdComputation
        • doRician
          boolean doRician
        • doRicianCheckBox
          JCheckBox doRicianCheckBox
        • estimateNoiseCheckBox
          JCheckBox estimateNoiseCheckBox
        • estimateNoiseStandardDeviation
          boolean estimateNoiseStandardDeviation
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          DOCUMENT ME!
        • image25DCheckBox
          JCheckBox image25DCheckBox
          DOCUMENT ME!
        • labelDegree
          JLabel labelDegree
        • labelNoiseStandardDeviation
          JLabel labelNoiseStandardDeviation
          DOCUMENT ME!
        • labelSearchWindowSide
          JLabel labelSearchWindowSide
          DOCUMENT ME!
        • labelSimilarityWindowSide
          JLabel labelSimilarityWindowSide
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • nlMeansFilterAlgo
          AlgorithmNonlocalMeansFilter nlMeansFilterAlgo
          DOCUMENT ME!
        • noiseStandardDeviation
          float noiseStandardDeviation
          Should be set equal to the noise standard deviation
        • paramPanel
          JPanel paramPanel
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • searchWindowSide
          int searchWindowSide
          DOCUMENT ME!
        • similarityWindowSide
          int similarityWindowSide
          DOCUMENT ME!
        • textDegree
          JTextField textDegree
        • textNoiseStandardDeviation
          JTextField textNoiseStandardDeviation
          DOCUMENT ME!
        • textSearchWindowSide
          JTextField textSearchWindowSide
          DOCUMENT ME!
        • textSimilarityWindowSide
          JTextField textSimilarityWindowSide
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogOpacityControls

      class JDialogOpacityControls extends JDialogBase implements Serializable
      serialVersionUID:
      844490628214011726L

      • Serialized Fields

        • controls
          ViewControlsImage controls
          Controls affected by opacity changes.
        • current
          JLabel current
          Label that gives current value of slider.
        • opacity
          float opacity
          Opacity number.
        • opacitySlider
          JSlider opacitySlider
          Opacity slider.
        • surfacePaint
          SurfacePaint surfacePaint
          SurfacePaint reference
        • surfacePaint_WM
          SurfacePaint_WM surfacePaint_WM
          SurfacePaint reference
        • voiManager
          VOIManagerInterface voiManager

    • Class gov.nih.mipav.view.dialogs.JDialogOpen

      class JDialogOpen extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -9116067564431404676L

    • Class gov.nih.mipav.view.dialogs.JDialogOrder

      class JDialogOrder extends JDialogBase implements Serializable
      serialVersionUID:
      670499188247272869L

      • Serialized Fields

        • datasetOrder
          JRadioButton datasetOrder
          Load image using dataset-specific ordering
        • dicomOrder
          JRadioButton dicomOrder
          Load image using dicom ordering (R-L, A-P, I-S)
        • dontAskAgain
          JCheckBox dontAskAgain
          Whether to ask user next time choice is available for AFNI ordering.

    • Class gov.nih.mipav.view.dialogs.JDialogOrientMatrix

      class JDialogOrientMatrix extends JDialogBase implements Serializable
      serialVersionUID:
      -5386555201530113228L

      • Serialized Fields

        • leftHandRuleCheckbox
          JCheckBox leftHandRuleCheckbox
          DOCUMENT ME!
        • matrix
          TransMatrix matrix
          DOCUMENT ME!
        • panelAxisMode
          JPanel panelAxisMode
          DOCUMENT ME!
        • pFrame
          JDialogBase pFrame
          DOCUMENT ME!
        • worldCoordCheckbox
          JCheckBox worldCoordCheckbox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogOverlay

      class JDialogOverlay extends JDialogBase implements Serializable
      serialVersionUID:
      -2470981064995748425L

    • Class gov.nih.mipav.view.dialogs.JDialogPadImages

      class JDialogPadImages extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      4451162492289524768L

      • Serialized Fields

        • displayLoc
          int displayLoc
          Flag indicating if a new image is to be generated or if the source image is to be replaced
        • image
          ModelImage image
          source image
        • newImage
          JRadioButton newImage
          generate new image
        • nSlices
          int nSlices
          number of slices in image
        • paddedSlices
          int paddedSlices
          number of slices in padded image
        • padMode
          int padMode
          Padding mode, defaults to front.
        • padSlicesAlgo
          AlgorithmAddMargins padSlicesAlgo
          Algorithm that adds slices to front/back of image.
        • padToBack
          JRadioButton padToBack
          Select padding to the back:
        • padToFront
          JRadioButton padToFront
          Select padding to the front:
        • padToHalf
          JRadioButton padToHalf
          Select padding to the front and back:
        • replaceImage
          JRadioButton replaceImage
          Select replacing the current image
        • resultImage
          ModelImage resultImage
          result image
        • userInterface
          ViewUserInterface userInterface
          Reference to the main user interface

    • Class gov.nih.mipav.view.dialogs.JDialogPaintGrow

      class JDialogPaintGrow extends JDialogBase implements Serializable
      serialVersionUID:
      -165750503127683051L

      • Serialized Fields

        • constrainBoundsCheckbox
          JCheckBox constrainBoundsCheckbox
          DOCUMENT ME!
        • currentFuzzy
          JLabel currentFuzzy
          DOCUMENT ME!
        • disableSliders
          boolean disableSliders
          DOCUMENT ME!
        • disableSlidersB
          boolean disableSlidersB
          DOCUMENT ME!
        • disableSlidersG
          boolean disableSlidersG
          DOCUMENT ME!
        • disableSlidersR
          boolean disableSlidersR
          DOCUMENT ME!
        • displayFuzzy
          boolean displayFuzzy
          DOCUMENT ME!
        • distanceCheckbox
          JCheckBox distanceCheckbox
          DOCUMENT ME!
        • enableVariableCheckbox
          boolean enableVariableCheckbox
          DOCUMENT ME!
        • font12B
          Font font12B
          DOCUMENT ME!
        • frame
          Frame frame
          DOCUMENT ME!
        • fuzzyCheckbox
          JCheckBox fuzzyCheckbox
          DOCUMENT ME!
        • fuzzyImageCheckbox
          JCheckBox fuzzyImageCheckbox
          DOCUMENT ME!
        • fuzzySlider
          JSlider fuzzySlider
          DOCUMENT ME!
        • fuzzyThreshold
          float fuzzyThreshold
          DOCUMENT ME!
        • haveBlue
          boolean haveBlue
          DOCUMENT ME!
        • haveColor
          boolean haveColor
          DOCUMENT ME!
        • haveGreen
          boolean haveGreen
          DOCUMENT ME!
        • haveRed
          boolean haveRed
          DOCUMENT ME!
        • imageType
          int imageType
          DOCUMENT ME!
        • initialDelta
          int initialDelta
          DOCUMENT ME!
        • initialDeltaB
          int initialDeltaB
          DOCUMENT ME!
        • initialDeltaG
          int initialDeltaG
          DOCUMENT ME!
        • initialDeltaR
          int initialDeltaR
          DOCUMENT ME!
        • leadString
          String leadString
          DOCUMENT ME!
        • less
          float less
          DOCUMENT ME!
        • lowerMid
          JLabel lowerMid
          DOCUMENT ME!
        • lowerMidB
          JLabel lowerMidB
          DOCUMENT ME!
        • lowerMidG
          JLabel lowerMidG
          DOCUMENT ME!
        • lowerMidR
          JLabel lowerMidR
          DOCUMENT ME!
        • lowSetFromField
          boolean lowSetFromField
          DOCUMENT ME!
        • lowSetFromFieldB
          boolean lowSetFromFieldB
          DOCUMENT ME!
        • lowSetFromFieldG
          boolean lowSetFromFieldG
          DOCUMENT ME!
        • lowSetFromFieldR
          boolean lowSetFromFieldR
          DOCUMENT ME!
        • lowSlider
          JSlider lowSlider
          DOCUMENT ME!
        • lowSliderB
          JSlider lowSliderB
          DOCUMENT ME!
        • lowSliderField
          JTextField lowSliderField
          DOCUMENT ME!
        • lowSliderFieldB
          JTextField lowSliderFieldB
          DOCUMENT ME!
        • lowSliderFieldG
          JTextField lowSliderFieldG
          DOCUMENT ME!
        • lowSliderFieldR
          JTextField lowSliderFieldR
          DOCUMENT ME!
        • lowSliderG
          JSlider lowSliderG
          DOCUMENT ME!
        • lowSliderR
          JSlider lowSliderR
          DOCUMENT ME!
        • max
          float max
          DOCUMENT ME!
        • maxB
          float maxB
          DOCUMENT ME!
        • maxDistLabel
          JLabel maxDistLabel
          DOCUMENT ME!
        • maxDistTextF
          JTextField maxDistTextF
          DOCUMENT ME!
        • maxG
          float maxG
          DOCUMENT ME!
        • maximumFuzzy
          JLabel maximumFuzzy
          DOCUMENT ME!
        • maximumL
          JLabel maximumL
          DOCUMENT ME!
        • maximumLB
          JLabel maximumLB
          DOCUMENT ME!
        • maximumLG
          JLabel maximumLG
          DOCUMENT ME!
        • maximumLR
          JLabel maximumLR
          DOCUMENT ME!
        • maximumU
          JLabel maximumU
          DOCUMENT ME!
        • maximumUB
          JLabel maximumUB
          DOCUMENT ME!
        • maximumUG
          JLabel maximumUG
          DOCUMENT ME!
        • maximumUR
          JLabel maximumUR
          DOCUMENT ME!
        • maximumValue
          double maximumValue
          DOCUMENT ME!
        • maximumValueButton
          JButton maximumValueButton
          DOCUMENT ME!
        • maximumValueField
          JTextField maximumValueField
          DOCUMENT ME!
        • maxR
          float maxR
          DOCUMENT ME!
        • maxSizeLabel
          JLabel maxSizeLabel
          DOCUMENT ME!
        • maxSizeTextF
          JTextField maxSizeTextF
          DOCUMENT ME!
        • maxValue
          double maxValue
          DOCUMENT ME!
        • maxValueB
          double maxValueB
          DOCUMENT ME!
        • maxValueG
          double maxValueG
          DOCUMENT ME!
        • maxValueR
          double maxValueR
          DOCUMENT ME!
        • min
          float min
          DOCUMENT ME!
        • minB
          float minB
          DOCUMENT ME!
        • minG
          float minG
          DOCUMENT ME!
        • minimumFuzzy
          JLabel minimumFuzzy
          DOCUMENT ME!
        • minimumL
          JLabel minimumL
          DOCUMENT ME!
        • minimumLB
          JLabel minimumLB
          DOCUMENT ME!
        • minimumLG
          JLabel minimumLG
          DOCUMENT ME!
        • minimumLR
          JLabel minimumLR
          DOCUMENT ME!
        • minimumU
          JLabel minimumU
          DOCUMENT ME!
        • minimumUB
          JLabel minimumUB
          DOCUMENT ME!
        • minimumUG
          JLabel minimumUG
          DOCUMENT ME!
        • minimumUR
          JLabel minimumUR
          DOCUMENT ME!
        • minR
          float minR
          DOCUMENT ME!
        • minValue
          double minValue
          DOCUMENT ME!
        • minValueB
          double minValueB
          DOCUMENT ME!
        • minValueG
          double minValueG
          DOCUMENT ME!
        • minValueR
          double minValueR
          DOCUMENT ME!
        • more
          float more
          DOCUMENT ME!
        • paintGrowListeners
          Vector<PaintGrowListener> paintGrowListeners
          DOCUMENT ME!
        • posTextF
          JTextField posTextF
          DOCUMENT ME!
        • range
          double range
          DOCUMENT ME!
        • rangeB
          double rangeB
          DOCUMENT ME!
        • rangeG
          double rangeG
          DOCUMENT ME!
        • rangeR
          double rangeR
          DOCUMENT ME!
        • regionGrowAlgo
          AlgorithmRegionGrow regionGrowAlgo
          DOCUMENT ME!
        • setRadioBoth
          boolean setRadioBoth
          DOCUMENT ME!
        • sizeCheckbox
          JCheckBox sizeCheckbox
          DOCUMENT ME!
        • surfacePaint
          SurfacePaint surfacePaint
          SurfacePaint reference
        • surfacePaint_WM
          SurfacePaint_WM surfacePaint_WM
          SurfacePaint reference
        • tabbedPane
          JTabbedPane tabbedPane
          DOCUMENT ME!
        • upperMid
          JLabel upperMid
          DOCUMENT ME!
        • upperMidB
          JLabel upperMidB
          DOCUMENT ME!
        • upperMidG
          JLabel upperMidG
          DOCUMENT ME!
        • upperMidR
          JLabel upperMidR
          DOCUMENT ME!
        • upSetFromField
          boolean upSetFromField
          DOCUMENT ME!
        • upSetFromFieldB
          boolean upSetFromFieldB
          DOCUMENT ME!
        • upSetFromFieldG
          boolean upSetFromFieldG
          DOCUMENT ME!
        • upSetFromFieldR
          boolean upSetFromFieldR
          DOCUMENT ME!
        • upSlider
          JSlider upSlider
          DOCUMENT ME!
        • upSliderB
          JSlider upSliderB
          DOCUMENT ME!
        • upSliderField
          JTextField upSliderField
          DOCUMENT ME!
        • upSliderFieldB
          JTextField upSliderFieldB
          DOCUMENT ME!
        • upSliderFieldG
          JTextField upSliderFieldG
          DOCUMENT ME!
        • upSliderFieldR
          JTextField upSliderFieldR
          DOCUMENT ME!
        • upSliderG
          JSlider upSliderG
          DOCUMENT ME!
        • upSliderR
          JSlider upSliderR
          DOCUMENT ME!
        • useVOI
          boolean useVOI
          DOCUMENT ME!
        • variableDeltasCheckbox
          JCheckBox variableDeltasCheckbox
          DOCUMENT ME!
        • variableThresholds
          boolean variableThresholds
          DOCUMENT ME!
        • voiCheckbox
          JCheckBox voiCheckbox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogPaintRGBComponents

      class JDialogPaintRGBComponents extends JDialogBase implements Serializable
      serialVersionUID:
      844490628214011726L

    • Class gov.nih.mipav.view.dialogs.JDialogPaintVasculature

      class JDialogPaintVasculature extends JDialogBase implements Serializable
      serialVersionUID:
      -7746172110383193434L

      • Serialized Fields

        • deltaSetFromField
          boolean deltaSetFromField
          Boolean which indicates that the seed point intensity bounds were changed from one of the text fields and not from one of the sliders.
        • doneButton
          JButton doneButton
          Button to indicate that the painting is finished and the dialog and attached image frame should be closed.
        • growButton
          JButton growButton
          Button which indicates that a region grow has been initiated / is being adjusted.
        • intensityTF
          JTextField intensityTF
          Text field containing the seed value intensity.
        • intensityValue
          int intensityValue
          The value of seed points to use.
        • isCloseOkay
          boolean isCloseOkay
          Indicates that we are done with the current grow, and can close the MIP when the done button is next clicked.
        • lowerDeltaSlider
          JSlider lowerDeltaSlider
          Slider which adjusts the lower bound of the region grow.
        • lowerDeltaTF
          JTextField lowerDeltaTF
          Text field containing the lower bound of the region grow.
        • maxDelta
          int maxDelta
          The most we can get away from the initial seed point intensity value (151).
        • mouseIntensityLabel
          JLabel mouseIntensityLabel
          The intensity of the current mouse position within the mip.
        • mouseXLabel
          JLabel mouseXLabel
          The x position of the current mouse position within the mip.
        • mouseYLabel
          JLabel mouseYLabel
          The y position of the current mouse position within the mip.
        • mouseZLabel
          JLabel mouseZLabel
          The z position of the current mouse position within the mip (the z position of the volume voxel put into the mip).
        • oldSeedIntensity
          int oldSeedIntensity
          The intensity value to use to recalculate the possible seed points when switching from CLICK_POINT mode back to AUTO_MODE.
        • paintGrowListeners
          Vector<ViewJComponentEditImage> paintGrowListeners
          List of frames that want to know about paint updates.
        • paintGrowMode
          int paintGrowMode
          The point selection mode.
        • rfastFrame
          ViewJFrameImage rfastFrame
          The main RFAST frame.
        • seedPoints
          Vector<WildMagic.LibFoundation.Mathematics.Vector3f> seedPoints
          List of points where we have grown a region from.
        • toolbarPanel
          JPanel toolbarPanel
          The dialog's toolbar panel.
        • undoButton
          JButton undoButton
          Button to undo the last region grow change (either a click of the grow button, or an adjustment of the threshold sliders).
        • upperDeltaSlider
          JSlider upperDeltaSlider
          Slider which adjusts the upper bound of the region grow.
        • upperDeltaTF
          JTextField upperDeltaTF
          Text field containing the upper bound of the region grow.

    • Class gov.nih.mipav.view.dialogs.JDialogParticleAnalysisNew

      class JDialogParticleAnalysisNew extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7849492525308767787L

      • Serialized Fields

        • comboBoxKernelClose
          JComboBox comboBoxKernelClose
          DOCUMENT ME!
        • comboBoxKernelOpen
          JComboBox comboBoxKernelOpen
          DOCUMENT ME!
        • do25D
          boolean do25D
          DOCUMENT ME!
        • erodePanel
          JPanel erodePanel
          Erode panel.
        • image
          ModelImage image
          DOCUMENT ME!
        • itersClose
          int itersClose
        • itersErode
          int itersErode
        • itersOpen
          int itersOpen
        • kernelClose
          int kernelClose
          DOCUMENT ME!
        • kernelOpen
          int kernelOpen
          DOCUMENT ME!
        • kernelSizeClose
          float kernelSizeClose
          DOCUMENT ME!
        • kernelSizeOpen
          float kernelSizeOpen
          DOCUMENT ME!
        • labelKernelClose
          JLabel labelKernelClose
          DOCUMENT ME!
        • labelKernelOpen
          JLabel labelKernelOpen
          DOCUMENT ME!
        • labelKernelSizeClose
          JLabel labelKernelSizeClose
          DOCUMENT ME!
        • labelKernelSizeOpen
          JLabel labelKernelSizeOpen
          DOCUMENT ME!
        • labelNIterClose
          JLabel labelNIterClose
          DOCUMENT ME!
        • labelNIterErode
          JLabel labelNIterErode
          DOCUMENT ME!
        • labelNIterOpen
          JLabel labelNIterOpen
          DOCUMENT ME!
        • maskPanelClose
          JPanel maskPanelClose
          Close declearation.
        • maskPanelOpen
          JPanel maskPanelOpen
          DOCUMENT ME!
        • outputPanel
          JPanelAlgorithmOutputOptions outputPanel
        • particleAlgo25D
          AlgorithmMorphology25D particleAlgo25D
          DOCUMENT ME!
        • particleAlgo2D
          AlgorithmMorphology2D particleAlgo2D
          DOCUMENT ME!
        • particleAlgo3D
          AlgorithmMorphology3D particleAlgo3D
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • showFrame
          boolean showFrame
          DOCUMENT ME!
        • showResultCB
          JCheckBox showResultCB
          DOCUMENT ME!
        • textErode
          JTextField textErode
          DOCUMENT ME!
        • textKernelSizeClose
          JTextField textKernelSizeClose
          DOCUMENT ME!
        • textKernelSizeOpen
          JTextField textKernelSizeOpen
          DOCUMENT ME!
        • textNIterClose
          JTextField textNIterClose
          DOCUMENT ME!
        • textNIterOpen
          JTextField textNIterOpen
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogPbBoundaryDetection

      class JDialogPbBoundaryDetection extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogPhaseCongruency

      class JDialogPhaseCongruency extends JDialogBase implements Serializable
      serialVersionUID:
      5977927697947830216L

    • Class gov.nih.mipav.view.dialogs.JDialogPhasePreservingDenoising

      class JDialogPhasePreservingDenoising extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogPointArea

      class JDialogPointArea extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2157089114762708039L

      • Serialized Fields

        • averageIntensities
          float[] averageIntensities
          DOCUMENT ME!
        • constrainBox
          JCheckBox constrainBox
          DOCUMENT ME!
        • leftPad
          boolean leftPad
          DOCUMENT ME!
        • leftPadBox
          JCheckBox leftPadBox
          DOCUMENT ME!
        • locationField
          JTextField locationField
          DOCUMENT ME!
        • pointAlgo
          AlgorithmPointArea pointAlgo
          DOCUMENT ME!
        • rgbAverageIntensities
          float[][] rgbAverageIntensities
          DOCUMENT ME!
        • showGraph
          boolean showGraph
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          DOCUMENT ME!
        • threshold
          float threshold
          DOCUMENT ME!
        • thresholdBox
          JCheckBox thresholdBox
          DOCUMENT ME!
        • thresholdField
          JTextField thresholdField
          DOCUMENT ME!
        • topPad
          boolean topPad
          DOCUMENT ME!
        • topPadBox
          JCheckBox topPadBox
          DOCUMENT ME!
        • useThreshold
          boolean useThreshold
          DOCUMENT ME!
        • xLoc
          int xLoc
          DOCUMENT ME!
        • xSpaceField
          JTextField xSpaceField
          DOCUMENT ME!
        • xSpacing
          int xSpacing
          DOCUMENT ME!
        • yLoc
          int yLoc
          DOCUMENT ME!
        • ySpaceField
          JTextField ySpaceField
          DOCUMENT ME!
        • ySpacing
          int ySpacing
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogPointArea.JTextFieldFilter

      class JTextFieldFilter extends PlainDocument implements Serializable
      serialVersionUID:
      -4552252563901427164L

      • Serialized Fields

        • acceptedChars
          String acceptedChars
          DOCUMENT ME!
        • box
          JCheckBox box
          DOCUMENT ME!
        • negativeAccepted
          boolean negativeAccepted
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogPointArea.UpdateYSpaceAction

      class UpdateYSpaceAction extends AbstractAction implements Serializable
      serialVersionUID:
      578406985180315919L

    • Class gov.nih.mipav.view.dialogs.JDialogPolygonToCircle

      class JDialogPolygonToCircle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • algorithm
          int algorithm
        • CROSSRATIO_POLYGON_TO_CIRCLE
          int CROSSRATIO_POLYGON_TO_CIRCLE
        • crossRatioCheckBox
          JCheckBox crossRatioCheckBox
        • extents
          int[] extents
          DOCUMENT ME!
        • exteriorCheckBox
          JCheckBox exteriorCheckBox
        • image
          ModelImage image
          DOCUMENT ME!
        • POLYGON_EXTERIOR_TO_CIRCLE
          int POLYGON_EXTERIOR_TO_CIRCLE
        • POLYGON_TO_CIRCLE
          int POLYGON_TO_CIRCLE
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sAlgo
          SchwarzChristoffelMapping sAlgo
          DOCUMENT ME!
        • setCenter
          boolean setCenter
        • setCenterCheckBox
          JCheckBox setCenterCheckBox
        • xCenter
          double xCenter
        • xCenterLabel
          JLabel xCenterLabel
        • xCenterText
          JTextField xCenterText
        • xDim
          int xDim
          DOCUMENT ME!
        • xSource
          double[] xSource
          DOCUMENT ME!
        • xText
          JTextField xText
          DOCUMENT ME!
        • yCenter
          double yCenter
        • yCenterLabel
          JLabel yCenterLabel
        • yCenterText
          JTextField yCenterText
        • ySource
          double[] ySource
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogPolygonToRectangle

      class JDialogPolygonToRectangle extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • algorithm
          int algorithm
        • corners
          int[] corners
        • CROSSRATIO_POLYGON_TO_RECTANGLE
          int CROSSRATIO_POLYGON_TO_RECTANGLE
        • crossRatioCheckBox
          JCheckBox crossRatioCheckBox
        • extents
          int[] extents
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • POLYGON_TO_RECTANGLE
          int POLYGON_TO_RECTANGLE
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sAlgo
          SchwarzChristoffelMapping sAlgo
          DOCUMENT ME!
        • v0Text
          JTextField v0Text
        • v1Text
          JTextField v1Text
        • v2Text
          JTextField v2Text
        • v3Text
          JTextField v3Text
        • xDim
          int xDim
          DOCUMENT ME!
        • xSource
          double[] xSource
          DOCUMENT ME!
        • xText
          JTextField xText
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • ySource
          double[] ySource
          DOCUMENT ME!
        • yText
          JTextField yText
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogPowerPaint

      class JDialogPowerPaint extends JDialogBase implements Serializable
      serialVersionUID:
      6175130808453006120L

      • Serialized Fields

        • backgroundDim
          int backgroundDim
          DOCUMENT ME!
        • backgroundsDim
          int backgroundsDim
          DOCUMENT ME!
        • botPanel
          JPanel botPanel
          DOCUMENT ME!
        • buttonDilate
          JButton buttonDilate
          DOCUMENT ME!
        • buttonErode
          JButton buttonErode
          DOCUMENT ME!
        • buttonExportToMask
          JButton buttonExportToMask
          DOCUMENT ME!
        • buttonExportToVOI
          JButton buttonExportToVOI
          DOCUMENT ME!
        • buttonFillBackground
          JButton buttonFillBackground
          DOCUMENT ME!
        • buttonFillBackgrounds
          JButton buttonFillBackgrounds
          DOCUMENT ME!
        • buttonGrowRegion
          JButton buttonGrowRegion
          DOCUMENT ME!
        • buttonImportFromMask
          JButton buttonImportFromMask
          DOCUMENT ME!
        • buttonImportFromVOI
          JButton buttonImportFromVOI
          DOCUMENT ME!
        • buttonRevert
          JButton buttonRevert
          DOCUMENT ME!
        • buttonRmObject
          JButton buttonRmObject
          DOCUMENT ME!
        • buttonRmObjects
          JButton buttonRmObjects
          DOCUMENT ME!
        • buttonShortkeys
          JToggleButton buttonShortkeys
          DOCUMENT ME!
        • c2x
          int c2x
          DOCUMENT ME!
        • c2y
          int c2y
          DOCUMENT ME!
        • c2z
          int c2z
          DOCUMENT ME!
        • c3x
          int c3x
          DOCUMENT ME!
        • c3y
          int c3y
          DOCUMENT ME!
        • c3z
          int c3z
          DOCUMENT ME!
        • checkSave
          JCheckBox checkSave
          DOCUMENT ME!
        • checkThreshold
          JCheckBox checkThreshold
          handling of intensity threshold.
        • comboConnectType
          JComboBox comboConnectType
          DOCUMENT ME!
        • comboDilateDimType
          JComboBox comboDilateDimType
          DOCUMENT ME!
        • comboErodeDimType
          JComboBox comboErodeDimType
          DOCUMENT ME!
        • comboStructureType
          JComboBox comboStructureType
          DOCUMENT ME!
        • connectType
          String connectType
          DOCUMENT ME!
        • connectTypes
          String[] connectTypes
          DOCUMENT ME!
        • dilateDimType
          String dilateDimType
          DOCUMENT ME!
        • dimTypes
          String[] dimTypes
          DOCUMENT ME!
        • erodeDimType
          String erodeDimType
          DOCUMENT ME!
        • exportPanel
          JPanel exportPanel
          DOCUMENT ME!
        • getMouseInput
          int getMouseInput
          DOCUMENT ME!
        • groupBackground
          ButtonGroup groupBackground
          DOCUMENT ME!
        • groupBackgrounds
          ButtonGroup groupBackgrounds
          DOCUMENT ME!
        • groupGrowRegion
          ButtonGroup groupGrowRegion
          DOCUMENT ME!
        • groupObject
          ButtonGroup groupObject
          DOCUMENT ME!
        • groupObjects
          ButtonGroup groupObjects
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelConnectType
          JLabel labelConnectType
          DOCUMENT ME!
        • labelO2D
          JLabel labelO2D
          DOCUMENT ME!
        • labelO3D
          JLabel labelO3D
          DOCUMENT ME!
        • labelStructureType
          JLabel labelStructureType
          DOCUMENT ME!
        • labelStructuring
          JLabel labelStructuring
          DOCUMENT ME!
        • lowerThreshold
          float lowerThreshold
          handling of intensity threshold.
        • mainPanel
          JPanel mainPanel
          dialog elements.
        • morphoPanel
          JPanel morphoPanel
          DOCUMENT ME!
        • movePanel
          JPanel movePanel
          DOCUMENT ME!
        • nx
          int nx
          DOCUMENT ME!
        • ny
          int ny
          DOCUMENT ME!
        • nz
          int nz
          DOCUMENT ME!
        • objectPanel
          JPanel objectPanel
          DOCUMENT ME!
        • panelThreshold
          JPanel panelThreshold
          DOCUMENT ME!
        • previous
          BitSet previous
          internal objects.
        • radioBackground2D
          JRadioButton radioBackground2D
          DOCUMENT ME!
        • radioBackground3D
          JRadioButton radioBackground3D
          DOCUMENT ME!
        • radioBackgrounds2D
          JRadioButton radioBackgrounds2D
          DOCUMENT ME!
        • radioBackgrounds3D
          JRadioButton radioBackgrounds3D
          DOCUMENT ME!
        • radioGrowRegion2D
          JRadioButton radioGrowRegion2D
          DOCUMENT ME!
        • radioGrowRegion3D
          JRadioButton radioGrowRegion3D
          DOCUMENT ME!
        • radioObject2D
          JRadioButton radioObject2D
          DOCUMENT ME!
        • radioObject3D
          JRadioButton radioObject3D
          DOCUMENT ME!
        • radioObjects2D
          JRadioButton radioObjects2D
          DOCUMENT ME!
        • radioObjects3D
          JRadioButton radioObjects3D
          DOCUMENT ME!
        • regionGrowDim
          int regionGrowDim
          parameters.
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rmObjDim
          int rmObjDim
          DOCUMENT ME!
        • rmObjsDim
          int rmObjsDim
          DOCUMENT ME!
        • save
          PaintAutoSave save
          DOCUMENT ME!
        • saver
          Timer saver
          DOCUMENT ME!
        • se2xy
          BitSet se2xy
          DOCUMENT ME!
        • se2xz
          BitSet se2xz
          DOCUMENT ME!
        • se2yz
          BitSet se2yz
          DOCUMENT ME!
        • se3
          BitSet se3
          DOCUMENT ME!
        • spinLower
          JSpinner spinLower
          handling of intensity threshold.
        • spinUpper
          JSpinner spinUpper
          DOCUMENT ME!
        • structureSize
          float structureSize
          DOCUMENT ME!
        • structureType
          String structureType
          DOCUMENT ME!
        • structureTypes
          String[] structureTypes
          DOCUMENT ME!
        • textSave
          JTextField textSave
          DOCUMENT ME!
        • textStructuring
          JTextField textStructuring
          DOCUMENT ME!
        • upperThreshold
          float upperThreshold
          handling of intensity threshold.

    • Class gov.nih.mipav.view.dialogs.JDialogPowerWatershed

      class JDialogPowerWatershed extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogPrincipalComponents

      class JDialogPrincipalComponents extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7032654276398964355L

      • Serialized Fields

        • averagedImageCheckbox
          JCheckBox averagedImageCheckbox
          DOCUMENT ME!
        • buttonMatchFile
          JButton buttonMatchFile
        • directoryMatch
          String directoryMatch
        • displayAndAsk
          boolean displayAndAsk
          DOCUMENT ME!
        • displayPCheckbox
          JCheckBox displayPCheckbox
          DOCUMENT ME!
        • distanceGroup
          ButtonGroup distanceGroup
        • doAveraging
          boolean doAveraging
          DOCUMENT ME!
        • doFilter
          boolean doFilter
          DOCUMENT ME!
        • doMahalanobisDistance
          boolean doMahalanobisDistance
        • EuclideanButton
          JRadioButton EuclideanButton
        • fileNameMatch
          String fileNameMatch
        • filteredImageCheckbox
          JCheckBox filteredImageCheckbox
          DOCUMENT ME!
        • imageFrame
          ViewJFrameImage[] imageFrame
          DOCUMENT ME!
        • imageNumber
          int imageNumber
          DOCUMENT ME!
        • imageType
          int imageType
          DOCUMENT ME!
        • iNumber
          int iNumber
          DOCUMENT ME!
        • labelNumber
          JLabel labelNumber
          DOCUMENT ME!
        • MahalanobisButton
          JRadioButton MahalanobisButton
        • matchImage
          ModelImage matchImage
        • nPlanes
          int nPlanes
          DOCUMENT ME!
        • pComponentAlgo
          AlgorithmPrincipalComponents pComponentAlgo
          DOCUMENT ME!
        • pNumber
          int pNumber
          DOCUMENT ME!
        • resultImage
          ModelImage[] resultImage
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          DOCUMENT ME!
        • textMatchFile
          JTextField textMatchFile
        • textNumber
          JTextField textNumber
          DOCUMENT ME!
        • UI
          ViewUserInterface UI

    • Class gov.nih.mipav.view.dialogs.JDialogPyWavelets

      class JDialogPyWavelets extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • axes
          int[] axes
        • BayesCheckBox
          JCheckBox BayesCheckBox
        • comboBoxFilterType
          JComboBox<String>[] comboBoxFilterType
        • comboBoxLevels
          JComboBox<String> comboBoxLevels
        • comboBoxModeX
          JComboBox<String> comboBoxModeX
        • comboBoxModeY
          JComboBox<String> comboBoxModeY
        • comboBoxModeZ
          JComboBox<String> comboBoxModeZ
        • comboBoxNameX
          JComboBox<String> comboBoxNameX
        • comboBoxNameY
          JComboBox<String> comboBoxNameY
        • comboBoxNameZ
          JComboBox<String> comboBoxNameZ
        • comboBoxOrderX
          JComboBox<String> comboBoxOrderX
        • comboBoxOrderY
          JComboBox<String> comboBoxOrderY
        • comboBoxOrderZ
          JComboBox<String> comboBoxOrderZ
        • comboBoxStartLevel
          JComboBox<String> comboBoxStartLevel
        • doBayesShrinkThresholdComputation
          boolean doBayesShrinkThresholdComputation
        • doX
          boolean doX
        • doY
          boolean doY
        • doZ
          boolean doZ
        • FILTER_GREATER
          int FILTER_GREATER
        • FILTER_HARD
          int FILTER_HARD
        • FILTER_LESS
          int FILTER_LESS
        • FILTER_NN_GARROTE
          int FILTER_NN_GARROTE
        • FILTER_NONE
          int FILTER_NONE
        • FILTER_SOFT
          int FILTER_SOFT
        • FILTER_THRESHOLD_FIRM
          int FILTER_THRESHOLD_FIRM
        • filteredCheckBox
          JCheckBox filteredCheckBox
        • filterType
          int[] filterType
        • filterVal1
          double[] filterVal1
        • filterVal2
          double[] filterVal2
        • gbc
          GridBagConstraints gbc
        • image
          ModelImage image
          Source image.
        • labelComponents
          JLabel[] labelComponents
        • labelLevels
          JLabel labelLevels
        • labelModeX
          JLabel labelModeX
        • labelModeY
          JLabel labelModeY
        • labelModeZ
          JLabel labelModeZ
        • labelNameX
          JLabel labelNameX
        • labelNameY
          JLabel labelNameY
        • labelNameZ
          JLabel labelNameZ
        • labelOrderX
          JLabel labelOrderX
        • labelOrderY
          JLabel labelOrderY
        • labelOrderZ
          JLabel labelOrderZ
        • labelStartLevel
          JLabel labelStartLevel
        • labelVal1
          JLabel[] labelVal1
        • labelVal2
          JLabel[] labelVal2
        • lastNameStringX
          String lastNameStringX
        • lastNameStringY
          String lastNameStringY
        • lastNameStringZ
          String lastNameStringZ
        • levels
          int levels
        • modes
          PyWavelets.MODE[] modes
        • MULTILEVEL_DWT
          int MULTILEVEL_DWT
        • multiLevelDWTButton
          JRadioButton multiLevelDWTButton
        • names
          PyWavelets.WAVELET_NAME[] names
        • numComponents
          int numComponents
        • orders
          int[] orders
        • resultImage
          ModelImage resultImage
          Result image.
        • showFilteredTransform
          boolean showFilteredTransform
        • showTransform
          boolean showTransform
        • SINGLE_LEVEL_DWT
          int SINGLE_LEVEL_DWT
        • singleLevelDWTButton
          JRadioButton singleLevelDWTButton
        • start_level
          int start_level
        • SWT
          int SWT
        • SWTButton
          JRadioButton SWTButton
        • tabbedPane
          JTabbedPane tabbedPane
          Tabbed pane
        • textVal1
          JTextField[] textVal1
        • textVal2
          JTextField[] textVal2
        • transformCheckBox
          JCheckBox transformCheckBox
        • transformTypeGroup
          ButtonGroup transformTypeGroup
        • tType
          int tType
        • waveletAlgo
          PyWavelets waveletAlgo
          Use serialVersionUID for interoperability.
        • waveletPanel
          JPanel waveletPanel
        • xAxisCheckBox
          JCheckBox xAxisCheckBox
        • yAxisCheckBox
          JCheckBox yAxisCheckBox
        • zAxisCheckBox
          JCheckBox zAxisCheckBox

    • Class gov.nih.mipav.view.dialogs.JDialogQuantify

      class JDialogQuantify extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      412669652447327059L

    • Class gov.nih.mipav.view.dialogs.JDialogQuantifyMask

      class JDialogQuantifyMask extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogRandomizeSliceOrder

      class JDialogRandomizeSliceOrder extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8562091054505687054L

    • Class gov.nih.mipav.view.dialogs.JDialogRawIO

      class JDialogRawIO extends JDialogBase implements Serializable
      serialVersionUID:
      -1588091095156376702L

      • Serialized Fields

        • checkboxEnd
          JCheckBox checkboxEnd
          DOCUMENT ME!
        • comboBoxUnitOfMeasure1
          JComboBox comboBoxUnitOfMeasure1
          DOCUMENT ME!
        • comboBoxUnitOfMeasure2
          JComboBox comboBoxUnitOfMeasure2
          DOCUMENT ME!
        • comboBoxUnitOfMeasure3
          JComboBox comboBoxUnitOfMeasure3
          DOCUMENT ME!
        • comboBoxUnitOfMeasure4
          JComboBox comboBoxUnitOfMeasure4
          DOCUMENT ME!
        • comboBoxUnitOfMeasure5
          JComboBox comboBoxUnitOfMeasure5
          DOCUMENT ME!
        • dataType
          int dataType
          DOCUMENT ME!
        • dimExtents
          int[] dimExtents
          DOCUMENT ME!
        • endianess
          boolean endianess
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • labelOffset
          JLabel labelOffset
          DOCUMENT ME!
        • offset
          int offset
          DOCUMENT ME!
        • radioARGB
          JRadioButton radioARGB
          DOCUMENT ME!
        • radioARGB_FLOAT
          JRadioButton radioARGB_FLOAT
        • radioARGB_UINTEGER
          JRadioButton radioARGB_UINTEGER
        • radioARGB_USHORT
          JRadioButton radioARGB_USHORT
          DOCUMENT ME!
        • radioBool
          JRadioButton radioBool
          DOCUMENT ME!
        • radioByte
          JRadioButton radioByte
          DOCUMENT ME!
        • radioDouble
          JRadioButton radioDouble
          DOCUMENT ME!
        • radioFloat
          JRadioButton radioFloat
          DOCUMENT ME!
        • radioInt
          JRadioButton radioInt
          DOCUMENT ME!
        • radioLong
          JRadioButton radioLong
          DOCUMENT ME!
        • radioShort
          JRadioButton radioShort
          DOCUMENT ME!
        • radioUByte
          JRadioButton radioUByte
          DOCUMENT ME!
        • radioUInt
          JRadioButton radioUInt
          DOCUMENT ME!
        • radioUShort
          JRadioButton radioUShort
          DOCUMENT ME!
        • resolutions
          float[] resolutions
          DOCUMENT ME!
        • textDim1
          JTextField textDim1
          DOCUMENT ME!
        • textDim2
          JTextField textDim2
          DOCUMENT ME!
        • textDim3
          JTextField textDim3
          DOCUMENT ME!
        • textDim4
          JTextField textDim4
          DOCUMENT ME!
        • textDim5
          JTextField textDim5
          DOCUMENT ME!
        • textOffset
          JTextField textOffset
          DOCUMENT ME!
        • textRes1
          JTextField textRes1
          DOCUMENT ME!
        • textRes2
          JTextField textRes2
          DOCUMENT ME!
        • textRes3
          JTextField textRes3
          DOCUMENT ME!
        • textRes4
          JTextField textRes4
          DOCUMENT ME!
        • textRes5
          JTextField textRes5
          DOCUMENT ME!
        • unitsOfMeasure
          int[] unitsOfMeasure
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRecordLUT

      class JDialogRecordLUT extends JDialogBase implements Serializable
      serialVersionUID:
      2240336763327716473L

      • Serialized Fields

        • compLUT
          ViewJComponentLUTTable compLUT
          Lookup table of image. The rectangular LUT table.
        • image
          ModelImage image
          ModelImage reference.
        • lut
          ModelLUT lut
          LUT table renference.
        • lutTablePanel
          JPanel lutTablePanel
          LUT table panel.
        • offsetX
          int offsetX
          Offset to draw the tick mark and value label.
        • offsetY
          int offsetY
          DOCUMENT ME!
        • tBarPanel
          JPanel tBarPanel
          Panel to hold the toolbar.
        • toolBar
          JToolBar toolBar
          Toolbar.
        • x
          float[] x
          control points coordinate of LUT transfer function .
        • xN
          int[] xN
          DOCUMENT ME!
        • y
          float[] y
          DOCUMENT ME!
        • yN
          int[] yN
          DOCUMENT ME!
        • z
          float[] z
          DOCUMENT ME!
        • zN
          int[] zN
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRegionMergingViaBoundaryMelting

      class JDialogRegionMergingViaBoundaryMelting extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogRegionsFromPartialBorders

      class JDialogRegionsFromPartialBorders extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationBSpline

      class JDialogRegistrationBSpline extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8193864043052368084L

      • Serialized Fields

        • kStringDimension
          String kStringDimension
          DOCUMENT ME.*
        • m_akNamesCompatibleTargetImages
          String[] m_akNamesCompatibleTargetImages
          Contains names of compatible target images that can be registered to the input source image for 2D/3D registration. Null reference for 2.5D registration.
        • m_bCreateDeformationImage
          boolean m_bCreateDeformationImage
          Flag set if the deformation computation is to be performed. Reflects the state of the associated check box in the dialog.
        • m_iTargetSlice
          int m_iTargetSlice
          Index of the slice from the source image to use for 2.5 registration. The index may be -1 to indicate registration is with adjacent slice. Reflects the state of the target slice radio buttons and the combo box if a particular reference slice is to be used.
        • m_kAlgorithmReg
          AlgorithmRegBSpline m_kAlgorithmReg
          Flag set if the deformation computation is to be performed.
        • m_kCheckCreateDeformationImage
          JCheckBox m_kCheckCreateDeformationImage
          DOCUMENT ME!
        • m_kCheckMultiPass
          JCheckBox m_kCheckMultiPass
          DOCUMENT ME!
        • m_kComboBoxCostFunction
          JComboBox m_kComboBoxCostFunction
          DOCUMENT ME!
        • m_kComboBoxTargetImage
          JComboBox m_kComboBoxTargetImage
          Controls displayed in the dialog box. All of these controls are always displayed unless otherwise noted.
        • m_kComboBoxTargetSlice
          JComboBox m_kComboBoxTargetSlice
          DOCUMENT ME!
        • m_kControlsPass1
          JDialogRegistrationBSpline.Controls m_kControlsPass1
          Container for controls to select the parameters for the first pass of registration. These controls are always displayed.
        • m_kControlsPass2
          JDialogRegistrationBSpline.Controls m_kControlsPass2
          Container for controls to select the parameters for the optional second pass of registration. These controls are created but are only displayed when the check box is selected for two-pass registration.
        • m_kImageDef
          ModelImage m_kImageDef
          Reference to new image creatd with computed deformation resulting from registration. Null reference is deformation computation is not selected.
        • m_kImageReg
          ModelImage m_kImageReg
          Reference to new image created with result of registration of source image. Cannot be null.
        • m_kImageSrc
          ModelImage m_kImageSrc
          Reference to the input source image. Cannot be null.
        • m_kImageTrg
          ModelImage m_kImageTrg
          Reference to the selected target image. Null reference for 2.5D registration.
        • m_kLabelIterationsPass1
          JLabel m_kLabelIterationsPass1
          DOCUMENT ME!
        • m_kLabelIterationsPass2
          JLabel m_kLabelIterationsPass2
          DOCUMENT ME!
        • m_kLabelOptionsPass1
          JLabel m_kLabelOptionsPass1
          DOCUMENT ME!
        • m_kLabelOptionsPass2
          JLabel m_kLabelOptionsPass2
          DOCUMENT ME!
        • m_kOptionsPass1
          AlgorithmRegBSpline.Options m_kOptionsPass1
          Reference to parameters to use for first pass of registration. Cannot be null.
        • m_kOptionsPass2
          AlgorithmRegBSpline.Options m_kOptionsPass2
          Reference to parameters to use for optional second pass of registration. Null reference if only a single pass of registration is to be performed.
        • m_kRadioSliceAdjacent
          JRadioButton m_kRadioSliceAdjacent
          DOCUMENT ME!
        • m_kRadioSliceReference
          JRadioButton m_kRadioSliceReference
          DOCUMENT ME!
        • m_kRegMeasure
          RegistrationMeasure m_kRegMeasure
          Reference to concrete implementation of the RegistrationMeasure abstract class which defines the particular measure to use during registration. Cannot be null. Reflects the selection in the associated combo box in the dialog.
        • m_kUI
          ViewUserInterface m_kUI
          Used for scripting and to access the currently registered images.

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationChamfer

      class JDialogRegistrationChamfer extends JDialogBase implements Serializable
      serialVersionUID:
      8391544557885381489L

      • Serialized Fields

        • baseImage
          ModelImage baseImage
          Register match image to base image.
        • chamfer
          AlgorithmRegChamfer chamfer
          Algorithm this dialog will call.
        • comboBox2or3D
          JComboBox comboBox2or3D
          GUI components.
        • comboBoxEdge
          JComboBox comboBoxEdge
          DOCUMENT ME!
        • comboBoxOriginal
          JComboBox comboBoxOriginal
          DOCUMENT ME!
        • edge
          JLabel edge
          DOCUMENT ME!
        • image25D
          boolean image25D
          true means do each slice individually, false means do them all together.
        • matchImage
          ModelImage matchImage
          Register match image to base image.
        • original
          JLabel original
          DOCUMENT ME!
        • regionFlag
          boolean regionFlag
          true means apply algorithm to whole image, false means to just the VOI.
        • register25D
          JRadioButton register25D
          DOCUMENT ME!
        • register2Dor3D
          JRadioButton register2Dor3D
          DOCUMENT ME!
        • titles
          String[] titles
          Used for setting image to locked and unlocked.
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • voiRegions
          JRadioButton voiRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationLeastSquares

      class JDialogRegistrationLeastSquares extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -2171665599919057675L

      • Serialized Fields

        • baseImage
          ModelImage baseImage
          Base image - register match image to base image.
        • comboBoxImage
          JComboBox comboBoxImage
          Combo box with image names for choosing base image.
        • dataType
          int dataType
        • DIM
          int DIM
          Number of dimensions in match image.
        • fillValue
          float fillValue
        • fromOAR3D
          boolean fromOAR3D
          DOCUMENT ME!
        • haveNonPointVOI
          boolean haveNonPointVOI
        • imageMax
          double imageMax
        • imageMin
          double imageMin
        • lsCompleted
          boolean lsCompleted
          DOCUMENT ME!
        • LSMatch
          AlgorithmRegLeastSquares LSMatch
          Algorithm to run from this dialog.
        • matchImage
          ModelImage matchImage
          Match image - register match image to base image.
        • matrixComboBox
          JComboBox matrixComboBox
        • matrixDirectory
          String matrixDirectory
        • matrixLabel
          JLabel matrixLabel
        • outOfBoundsComboBox
          JComboBox outOfBoundsComboBox
        • outOfBoundsIndex
          int outOfBoundsIndex
          Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum
        • outOfBoundsLabel
          JLabel outOfBoundsLabel
        • resultImage
          ModelImage resultImage
          Result image - image returned from registration algorithm.
        • resultMatrix
          TransMatrix resultMatrix
          DOCUMENT ME!
        • titles
          String[] titles
          Used to lock and unlock images.
        • userDirectoryLabel
          JLabel userDirectoryLabel
        • userDirectoryText
          JTextField userDirectoryText
        • userInterface
          ViewUserInterface userInterface
          Reference to userface.
        • valueLabel
          JLabel valueLabel
        • valueText
          JTextField valueText
        • xdimA
          int xdimA
          Dimensions of match image and base image.
        • xresA
          float xresA
          Resolutions of match image and base image.
        • xresB
          float xresB
          Resolutions of match image and base image.
        • ydimA
          int ydimA
          Dimensions of match image and base image.
        • yresA
          float yresA
          Resolutions of match image and base image.
        • yresB
          float yresB
          Resolutions of match image and base image.
        • zdimA
          int zdimA
          Dimensions of match image and base image.
        • zresA
          float zresA
          Resolutions of match image and base image.
        • zresB
          float zresB
          Resolutions of match image and base image.

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR25D

      class JDialogRegistrationOAR25D extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -8324270868997072706L

      • Serialized Fields

        • adjacentImageRButton
          JRadioButton adjacentImageRButton
          DOCUMENT ME!
        • advancedDialog
          JDialog advancedDialog
          Variables for Advanced Settings dialog.
        • buttonWeightInput
          JButton buttonWeightInput
          DOCUMENT ME!
        • coarseRate
          float coarseRate
          DOCUMENT ME!
        • coarseRateText
          JTextField coarseRateText
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • comboBoxDOF
          JComboBox comboBoxDOF
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • comboBoxInterp2
          JComboBox comboBoxInterp2
          DOCUMENT ME!
        • comboBoxSearchAlgo
          JComboBox comboBoxSearchAlgo
        • cost
          int cost
          DOCUMENT ME!
        • directoryWInput
          String directoryWInput
          DOCUMENT ME!
        • doAdjacent
          boolean doAdjacent
          DOCUMENT ME!
        • doColor
          boolean doColor
          DOCUMENT ME!
        • DOF
          int DOF
          DOCUMENT ME!
        • doGraph
          boolean doGraph
          DOCUMENT ME!
        • doSubsample
          boolean doSubsample
          DOCUMENT ME!
        • ELSUNC
          int ELSUNC
        • fileNameWInput
          String fileNameWInput
          DOCUMENT ME!
        • fineRate
          float fineRate
          DOCUMENT ME!
        • fineRateText
          JTextField fineRateText
          DOCUMENT ME!
        • graphCheckBox
          JCheckBox graphCheckBox
          DOCUMENT ME!
        • inputWeightImage
          ModelImage inputWeightImage
          DOCUMENT ME!
        • interp
          int interp
          DOCUMENT ME!
        • interp2
          int interp2
          DOCUMENT ME!
        • labelCoarse
          JLabel labelCoarse
          DOCUMENT ME!
        • labelCoarseDegrees
          JLabel labelCoarseDegrees
          DOCUMENT ME!
        • labelFine
          JLabel labelFine
          DOCUMENT ME!
        • labelFineDegrees
          JLabel labelFineDegrees
          DOCUMENT ME!
        • labelInterp2
          JLabel labelInterp2
          DOCUMENT ME!
        • labelRotateDegrees
          JLabel labelRotateDegrees
          DOCUMENT ME!
        • labelRotateRange
          JLabel labelRotateRange
          DOCUMENT ME!
        • labelRotateRangeTo
          JLabel labelRotateRangeTo
          DOCUMENT ME!
        • LEVENBERG_MARQUARDT
          int LEVENBERG_MARQUARDT
        • matchImage
          ModelImage matchImage
          DOCUMENT ME!
        • maxIterations
          int maxIterations
          DOCUMENT ME!
        • maxIterations_def
          int maxIterations_def
          DOCUMENT ME!
        • maxIterationsText
          JTextField maxIterationsText
          DOCUMENT ME!
        • NL2SOL
          int NL2SOL
        • noneRadio
          JRadioButton noneRadio
          DOCUMENT ME!
        • numMinima
          int numMinima
          DOCUMENT ME!
        • numMinima_def
          int numMinima_def
          DOCUMENT ME!
        • numMinText
          JTextField numMinText
          DOCUMENT ME!
        • POWELL
          int POWELL
        • refImageNum
          int refImageNum
          DOCUMENT ME!
        • refImageNumText
          JTextField refImageNumText
          DOCUMENT ME!
        • refImageRButton
          JRadioButton refImageRButton
          DOCUMENT ME!
        • refSlice
          ModelImage refSlice
          DOCUMENT ME!
        • reg25
          AlgorithmRegOAR25D2 reg25
          DOCUMENT ME!
        • reg25E
          AlgorithmRegELSUNCOAR25D reg25E
        • rotateBegin
          float rotateBegin
          DOCUMENT ME!
        • rotateBeginText
          JTextField rotateBeginText
          DOCUMENT ME!
        • rotateEnd
          float rotateEnd
          DOCUMENT ME!
        • rotateEndText
          JTextField rotateEndText
          DOCUMENT ME!
        • sampleCheckBox
          JCheckBox sampleCheckBox
          DOCUMENT ME!
        • searchAlgorithm
          int searchAlgorithm
        • textInput
          JTextField textInput
          DOCUMENT ME!
        • transformVOIs
          boolean transformVOIs
          DOCUMENT ME!
        • transformVOIsBox
          JCheckBox transformVOIsBox
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • useOutsideReferenceSlice
          boolean useOutsideReferenceSlice
          DOCUMENT ME!
        • voiRadio
          JRadioButton voiRadio
          DOCUMENT ME!
        • voisOnly
          boolean voisOnly
          DOCUMENT ME!
        • weighted
          boolean weighted
          DOCUMENT ME!
        • weightRadio
          JRadioButton weightRadio
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR2D

      class JDialogRegistrationOAR2D extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -688716905705879638L

      • Serialized Fields

        • advancedDialog
          JDialog advancedDialog
          Variables for Advanced Settings dialog.
        • bruteForceCheckBox
          JCheckBox bruteForceCheckBox
          CheckBox to turn brute-force registration on or off:.
        • bruteForceDialog
          JDialog bruteForceDialog
          Dialog to set the brute-force registration parameters:.
        • buttonWeightInput
          JButton buttonWeightInput
          DOCUMENT ME!
        • buttonWeightRef
          JButton buttonWeightRef
          DOCUMENT ME!
        • coarseRate
          float coarseRate
          DOCUMENT ME!
        • coarseRateText
          JTextField coarseRateText
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • comboBoxDOF
          JComboBox comboBoxDOF
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • comboBoxInterp2
          JComboBox comboBoxInterp2
          DOCUMENT ME!
        • comboBoxSearchAlgo
          JComboBox comboBoxSearchAlgo
        • cost
          int cost
          DOCUMENT ME!
        • dataType
          int dataType
        • directoryWInput
          String directoryWInput
          DOCUMENT ME!
        • directoryWRef
          String directoryWRef
          DOCUMENT ME!
        • displayTransform
          boolean displayTransform
          DOCUMENT ME!
        • doColor
          boolean doColor
          DOCUMENT ME!
        • doColorCheckBox
          JCheckBox doColorCheckBox
          CheckBox to turn color registration on or off:.
        • DOF
          int DOF
          DOCUMENT ME!
        • doJTEM
          boolean doJTEM
        • doMultiThread
          boolean doMultiThread
        • doSubsample
          boolean doSubsample
          DOCUMENT ME!
        • ELSUNC
          int ELSUNC
        • fileNameWInput
          String fileNameWInput
          DOCUMENT ME!
        • fileNameWRef
          String fileNameWRef
          DOCUMENT ME!
        • fillValue
          float fillValue
        • fineRate
          float fineRate
          DOCUMENT ME!
        • fineRateText
          JTextField fineRateText
          DOCUMENT ME!
        • imageMax
          double imageMax
        • imageMin
          double imageMin
        • inputWeightImage
          ModelImage inputWeightImage
          DOCUMENT ME!
        • interp
          int interp
          DOCUMENT ME!
        • interp2
          int interp2
          DOCUMENT ME!
        • jtemCheckBox
          JCheckBox jtemCheckBox
          DOCUMENT ME!
        • labelCoarse
          JLabel labelCoarse
          DOCUMENT ME!
        • labelCoarseDegrees
          JLabel labelCoarseDegrees
          DOCUMENT ME!
        • labelFine
          JLabel labelFine
          DOCUMENT ME!
        • labelFineDegrees
          JLabel labelFineDegrees
          DOCUMENT ME!
        • labelInterp2
          JLabel labelInterp2
          DOCUMENT ME!
        • labelRotateDegrees
          JLabel labelRotateDegrees
          DOCUMENT ME!
        • labelRotateRange
          JLabel labelRotateRange
          DOCUMENT ME!
        • labelRotateRangeTo
          JLabel labelRotateRangeTo
          DOCUMENT ME!
        • LEVENBERG_MARQUARDT
          int LEVENBERG_MARQUARDT
        • m_bSubsetDialog
          boolean m_bSubsetDialog
          If true the dialog for this instance of JDialogRegistrationOAR2D will not activate the AlgorithmRegOAR2D:.
        • matchImage
          ModelImage matchImage
          DOCUMENT ME!
        • matrixComboBox
          JComboBox matrixComboBox
        • matrixDirectory
          String matrixDirectory
        • matrixLabel
          JLabel matrixLabel
        • maxIterations
          int maxIterations
          DOCUMENT ME!
        • maxIterations_def
          int maxIterations_def
          DOCUMENT ME!
        • maxIterationsText
          JTextField maxIterationsText
          DOCUMENT ME!
        • multiThreadCheckBox
          JCheckBox multiThreadCheckBox
        • NL2SOL
          int NL2SOL
        • noneRadio
          JRadioButton noneRadio
          DOCUMENT ME!
        • numMinima
          int numMinima
          DOCUMENT ME!
        • numMinima_def
          int numMinima_def
          DOCUMENT ME!
        • numMinText
          JTextField numMinText
          DOCUMENT ME!
        • outOfBoundsComboBox
          JComboBox outOfBoundsComboBox
        • outOfBoundsIndex
          int outOfBoundsIndex
          Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum
        • outOfBoundsLabel
          JLabel outOfBoundsLabel
        • POWELL
          int POWELL
        • refImage
          ModelImage refImage
          DOCUMENT ME!
        • refWeightImage
          ModelImage refWeightImage
          DOCUMENT ME!
        • reg2
          AlgorithmRegOAR2D reg2
          DOCUMENT ME!
        • reg2E
          AlgorithmRegELSUNCOAR2D reg2E
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rotateBegin
          float rotateBegin
          DOCUMENT ME!
        • rotateBeginText
          JTextField rotateBeginText
          DOCUMENT ME!
        • rotateEnd
          float rotateEnd
          DOCUMENT ME!
        • rotateEndText
          JTextField rotateEndText
          DOCUMENT ME!
        • rotationBF
          float rotationBF
          DOCUMENT ME!
        • rotationText
          JTextField rotationText
          Brute-force registration parameters:.
        • sampleCheckBox
          JCheckBox sampleCheckBox
          DOCUMENT ME!
        • scaleStepsBF
          int scaleStepsBF
          DOCUMENT ME!
        • scaleStepsText
          JTextField scaleStepsText
          Brute-force registration parameters:.
        • searchAlgorithm
          int searchAlgorithm
        • textInput
          JTextField textInput
          DOCUMENT ME!
        • textRef
          JTextField textRef
          DOCUMENT ME!
        • transformCheckbox
          JCheckBox transformCheckbox
          DOCUMENT ME!
        • translationBF
          int translationBF
          DOCUMENT ME!
        • translationText
          JTextField translationText
          Brute-force registration parameters:.
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • userDirectoryLabel
          JLabel userDirectoryLabel
        • userDirectoryText
          JTextField userDirectoryText
        • valueLabel
          JLabel valueLabel
        • valueText
          JTextField valueText
        • voiRadio
          JRadioButton voiRadio
          DOCUMENT ME!
        • voisOnly
          boolean voisOnly
          DOCUMENT ME!
        • weighted
          boolean weighted
          DOCUMENT ME!
        • weightRadio
          JRadioButton weightRadio
          DOCUMENT ME!
        • xscaleBF
          float xscaleBF
          DOCUMENT ME!
        • xscaleText
          JTextField xscaleText
          Brute-force registration parameters:.
        • yscaleBF
          float yscaleBF
          DOCUMENT ME!
        • yscaleText
          JTextField yscaleText
          Brute-force registration parameters:.

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR35D

      class JDialogRegistrationOAR35D extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4309868934393418962L

      • Serialized Fields

        • adjacentImageRButton
          JRadioButton adjacentImageRButton
          DOCUMENT ME!
        • advancedDialog
          JDialog advancedDialog
          Variables for Advanced Settings dialog.
        • averageImageRButton
          JRadioButton averageImageRButton
          DOCUMENT ME!
        • buttonWeightInput
          JButton buttonWeightInput
          DOCUMENT ME!
        • coarseRate
          float coarseRate
          DOCUMENT ME!
        • coarseRateText
          JTextField coarseRateText
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • comboBoxDOF
          JComboBox comboBoxDOF
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • comboBoxInterp2
          JComboBox comboBoxInterp2
          DOCUMENT ME!
        • comboBoxSearchAlgo
          JComboBox comboBoxSearchAlgo
        • cost
          int cost
          DOCUMENT ME!
        • directoryWInput
          String directoryWInput
          DOCUMENT ME!
        • doColor
          boolean doColor
          DOCUMENT ME!
        • DOF
          int DOF
          DOCUMENT ME!
        • doGraph
          boolean doGraph
          DOCUMENT ME!
        • doJTEM
          boolean doJTEM
          When true, the full version of JTEM Powell search is used in the registration algorithm.
        • doSubsample
          boolean doSubsample
          DOCUMENT ME!
        • ELSUNC
          int ELSUNC
        • fastMode
          boolean fastMode
          DOCUMENT ME!
        • fastModeCheckbox
          JCheckBox fastModeCheckbox
          DOCUMENT ME!
        • fileNameWInput
          String fileNameWInput
          DOCUMENT ME!
        • fineRate
          float fineRate
          DOCUMENT ME!
        • fineRateText
          JTextField fineRateText
          DOCUMENT ME!
        • graphCheckBox
          JCheckBox graphCheckBox
          DOCUMENT ME!
        • inputWeightImage
          ModelImage inputWeightImage
          DOCUMENT ME!
        • interp
          int interp
          DOCUMENT ME!
        • interp2
          int interp2
          DOCUMENT ME!
        • jtemCheckbox
          JCheckBox jtemCheckbox
          Turns on the JTEM full version of Powell's algorithm on or off
        • labelInterp2
          JLabel labelInterp2
          DOCUMENT ME!
        • LEVENBERG_MARQUARDT
          int LEVENBERG_MARQUARDT
        • matchImage
          ModelImage matchImage
          DOCUMENT ME!
        • maxIterations
          int maxIterations
          DOCUMENT ME!
        • maxIterations_def
          int maxIterations_def
          DOCUMENT ME!
        • maxIterationsText
          JTextField maxIterationsText
          DOCUMENT ME!
        • NL2SOL
          int NL2SOL
        • noneRadio
          JRadioButton noneRadio
          DOCUMENT ME!
        • numMinima
          int numMinima
          DOCUMENT ME!
        • numMinima_def
          int numMinima_def
          DOCUMENT ME!
        • numMinText
          JTextField numMinText
          DOCUMENT ME!
        • POWELL
          int POWELL
        • refImageNum
          int refImageNum
          DOCUMENT ME!
        • refImageNumText
          JTextField refImageNumText
          DOCUMENT ME!
        • refImageRButton
          JRadioButton refImageRButton
          DOCUMENT ME!
        • refVolume
          ModelImage refVolume
          DOCUMENT ME!
        • reg35
          AlgorithmRegOAR35D reg35
          DOCUMENT ME!
        • reg35E
          AlgorithmRegELSUNCOAR35D reg35E
        • registerTo
          int registerTo
          DOCUMENT ME!
        • rotateBegin
          float rotateBegin
          DOCUMENT ME!
        • rotateBeginText
          JTextField rotateBeginText
          DOCUMENT ME!
        • rotateEnd
          float rotateEnd
          DOCUMENT ME!
        • rotateEndText
          JTextField rotateEndText
          DOCUMENT ME!
        • sampleCheckBox
          JCheckBox sampleCheckBox
          DOCUMENT ME!
        • searchAlgorithm
          int searchAlgorithm
        • textInput
          JTextField textInput
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • useOutsideReferenceVolume
          boolean useOutsideReferenceVolume
          DOCUMENT ME!
        • voiRadio
          JRadioButton voiRadio
          DOCUMENT ME!
        • voisOnly
          boolean voisOnly
          DOCUMENT ME!
        • weighted
          boolean weighted
          DOCUMENT ME!
        • weightRadio
          JRadioButton weightRadio
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR3D

      class JDialogRegistrationOAR3D extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -1461819906844299206L

      • Serialized Fields

        • advancedDialog
          JDialog advancedDialog
          Variables for Advanced Settings dialog.
        • buttonWeightInput
          JButton buttonWeightInput
          DOCUMENT ME!
        • buttonWeightRef
          JButton buttonWeightRef
          DOCUMENT ME!
        • calcCOG
          boolean calcCOG
          DOCUMENT ME!
        • calcCOGCheckbox
          JCheckBox calcCOGCheckbox
          DOCUMENT ME!
        • calcLSBox
          JCheckBox calcLSBox
          DOCUMENT ME!
        • coarsePanelX
          JPanel coarsePanelX
          DOCUMENT ME!
        • coarsePanelY
          JPanel coarsePanelY
          DOCUMENT ME!
        • coarsePanelZ
          JPanel coarsePanelZ
          DOCUMENT ME!
        • coarseRateTextX
          JTextField coarseRateTextX
          DOCUMENT ME!
        • coarseRateTextY
          JTextField coarseRateTextY
          DOCUMENT ME!
        • coarseRateTextZ
          JTextField coarseRateTextZ
          DOCUMENT ME!
        • coarseRateX
          float coarseRateX
          DOCUMENT ME!
        • coarseRateY
          float coarseRateY
          DOCUMENT ME!
        • coarseRateZ
          float coarseRateZ
          DOCUMENT ME!
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • comboBoxDOF
          JComboBox comboBoxDOF
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • comboBoxInterp2
          JComboBox comboBoxInterp2
          DOCUMENT ME!
        • comboBoxSearchAlgo
          JComboBox comboBoxSearchAlgo
        • cost
          int cost
          DOCUMENT ME!
        • costName
          String costName
          DOCUMENT ME!
        • dataType
          int dataType
        • directoryWInput
          String directoryWInput
          DOCUMENT ME!
        • directoryWRef
          String directoryWRef
          DOCUMENT ME!
        • displayTransform
          boolean displayTransform
          DOCUMENT ME!
        • doColor
          boolean doColor
          DOCUMENT ME!
        • DOF
          int DOF
          DOCUMENT ME!
        • doJTEM
          boolean doJTEM
          When true, the full version of JTEM Powell search is used in the registration algorithm.
        • doLS
          boolean doLS
          DOCUMENT ME!
        • doMultiThread
          boolean doMultiThread
        • doSubsample
          boolean doSubsample
          DOCUMENT ME!
        • ELSUNC
          int ELSUNC
        • fastMode
          boolean fastMode
          DOCUMENT ME!
        • fastModeCheckbox
          JCheckBox fastModeCheckbox
          DOCUMENT ME!
        • fileNameWInput
          String fileNameWInput
          DOCUMENT ME!
        • fileNameWRef
          String fileNameWRef
          DOCUMENT ME!
        • fillValue
          float fillValue
        • finePanelX
          JPanel finePanelX
          DOCUMENT ME!
        • finePanelY
          JPanel finePanelY
          DOCUMENT ME!
        • finePanelZ
          JPanel finePanelZ
          DOCUMENT ME!
        • fineRateTextX
          JTextField fineRateTextX
          DOCUMENT ME!
        • fineRateTextY
          JTextField fineRateTextY
          DOCUMENT ME!
        • fineRateTextZ
          JTextField fineRateTextZ
          DOCUMENT ME!
        • fineRateX
          float fineRateX
          DOCUMENT ME!
        • fineRateY
          float fineRateY
          DOCUMENT ME!
        • fineRateZ
          float fineRateZ
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • imageMax
          double imageMax
        • imageMin
          double imageMin
        • inputWeightImage
          ModelImage inputWeightImage
          DOCUMENT ME!
        • interp
          int interp
          DOCUMENT ME!
        • interp2
          int interp2
          DOCUMENT ME!
        • jtemCheckbox
          JCheckBox jtemCheckbox
          Turns on the JTEM full version of Powell's algorithm on or off
        • labelInterp2
          JLabel labelInterp2
          DOCUMENT ME!
        • LEVENBERG_MARQUARDT
          int LEVENBERG_MARQUARDT
        • lsCompleted
          boolean lsCompleted
          DOCUMENT ME!
        • lsImage
          ModelImage lsImage
          DOCUMENT ME!
        • lsMatrix
          TransMatrix lsMatrix
          DOCUMENT ME!
        • matchImage
          ModelImage matchImage
          DOCUMENT ME!
        • matrixComboBox
          JComboBox matrixComboBox
        • matrixDirectory
          String matrixDirectory
        • matrixLabel
          JLabel matrixLabel
        • maxIterations
          int maxIterations
          DOCUMENT ME!
        • maxIterations_def
          int maxIterations_def
          DOCUMENT ME!
        • maxIterationsText
          JTextField maxIterationsText
          DOCUMENT ME!
        • maxOfMinResol
          boolean maxOfMinResol
          DOCUMENT ME!
        • minMaxCheckbox
          JCheckBox minMaxCheckbox
          DOCUMENT ME!
        • multiThreadCheckBox
          JCheckBox multiThreadCheckBox
        • NL2SOL
          int NL2SOL
        • noneRadio
          JRadioButton noneRadio
          DOCUMENT ME!
        • numMinima
          int numMinima
          DOCUMENT ME!
        • numMinima_def
          int numMinima_def
          DOCUMENT ME!
        • numMinText
          JTextField numMinText
          DOCUMENT ME!
        • outOfBoundsComboBox
          JComboBox outOfBoundsComboBox
        • outOfBoundsIndex
          int outOfBoundsIndex
          Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum
        • outOfBoundsLabel
          JLabel outOfBoundsLabel
        • POWELL
          int POWELL
        • refImage
          ModelImage refImage
          DOCUMENT ME!
        • refWeightImage
          ModelImage refWeightImage
          DOCUMENT ME!
        • reg3
          AlgorithmRegOAR3D reg3
          DOCUMENT ME!
        • reg3E
          AlgorithmRegELSUNCOAR3D reg3E
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rotateBeginTextX
          JTextField rotateBeginTextX
          DOCUMENT ME!
        • rotateBeginTextY
          JTextField rotateBeginTextY
          DOCUMENT ME!
        • rotateBeginTextZ
          JTextField rotateBeginTextZ
          DOCUMENT ME!
        • rotateBeginX
          float rotateBeginX
          DOCUMENT ME!
        • rotateBeginY
          float rotateBeginY
          DOCUMENT ME!
        • rotateBeginZ
          float rotateBeginZ
          DOCUMENT ME!
        • rotateEndTextX
          JTextField rotateEndTextX
          DOCUMENT ME!
        • rotateEndTextY
          JTextField rotateEndTextY
          DOCUMENT ME!
        • rotateEndTextZ
          JTextField rotateEndTextZ
          DOCUMENT ME!
        • rotateEndX
          float rotateEndX
          DOCUMENT ME!
        • rotateEndY
          float rotateEndY
          DOCUMENT ME!
        • rotateEndZ
          float rotateEndZ
          DOCUMENT ME!
        • rotatePanel
          JPanel rotatePanel
          DOCUMENT ME!
        • rotateRangePanelX
          JPanel rotateRangePanelX
          DOCUMENT ME!
        • rotateRangePanelY
          JPanel rotateRangePanelY
          DOCUMENT ME!
        • rotateRangePanelZ
          JPanel rotateRangePanelZ
          DOCUMENT ME!
        • sampleCheckbox
          JCheckBox sampleCheckbox
          DOCUMENT ME!
        • searchAlgorithm
          int searchAlgorithm
        • textInput
          JTextField textInput
          DOCUMENT ME!
        • textRef
          JTextField textRef
          DOCUMENT ME!
        • transformCheckbox
          JCheckBox transformCheckbox
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • universalCheckbox
          JCheckBox universalCheckbox
          DOCUMENT ME!
        • userDirectoryLabel
          JLabel userDirectoryLabel
        • userDirectoryText
          JTextField userDirectoryText
        • valueLabel
          JLabel valueLabel
        • valueText
          JTextField valueText
        • voiRadio
          JRadioButton voiRadio
          DOCUMENT ME!
        • voisOnly
          boolean voisOnly
          DOCUMENT ME!
        • weighted
          boolean weighted
          DOCUMENT ME!
        • weightRadio
          JRadioButton weightRadio
          DOCUMENT ME!
        • xRadio
          JRadioButton xRadio
          DOCUMENT ME!
        • xSelected
          boolean xSelected
          DOCUMENT ME!
        • yRadio
          JRadioButton yRadio
          DOCUMENT ME!
        • ySelected
          boolean ySelected
          DOCUMENT ME!
        • zRadio
          JRadioButton zRadio
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationSIFT3D

      class JDialogRegistrationSIFT3D extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • baseImage
          ModelImage baseImage
          Base image - register match image to base image.
        • comboBoxImage
          JComboBox comboBoxImage
          Combo box with image names for choosing base image.
        • CUBOID_EXTREMA
          boolean CUBOID_EXTREMA
        • cuboidCheckBox
          JCheckBox cuboidCheckBox
        • ICOS_HIST
          boolean ICOS_HIST
        • icosahedralCheckBox
          JCheckBox icosahedralCheckBox
        • labelErrorThreshold
          JLabel labelErrorThreshold
        • labelGaussianWidth
          JLabel labelGaussianWidth
        • labelMatch
          JLabel labelMatch
        • labelMatchingThreshold
          JLabel labelMatchingThreshold
        • labelNumberIterations
          JLabel labelNumberIterations
        • matchCheckBox
          JCheckBox matchCheckBox
        • matchImage
          ModelImage matchImage
          Match image - register match image to base image.
        • refineCheckBox
          JCheckBox refineCheckBox
        • reg3D
          SIFT3D reg3D
          Algorithm to run from this dialog.
        • resultImage
          ModelImage resultImage
          Result image - image returned from registration algorithm.
        • SIFT3D_err_thresh_default
          double SIFT3D_err_thresh_default
        • SIFT3D_GAUSS_WIDTH_FCTR
          double SIFT3D_GAUSS_WIDTH_FCTR
        • SIFT3D_MATCH_MAX_DIST
          double SIFT3D_MATCH_MAX_DIST
        • SIFT3D_nn_thresh_default
          double SIFT3D_nn_thresh_default
        • SIFT3D_num_iter_default
          int SIFT3D_num_iter_default
        • SIFT3D_ORI_SOLID_ANGLE_WEIGHT
          boolean SIFT3D_ORI_SOLID_ANGLE_WEIGHT
        • SIFT3D_RANSAC_REFINE
          boolean SIFT3D_RANSAC_REFINE
        • solidCheckBox
          JCheckBox solidCheckBox
        • textErrorThreshold
          JTextField textErrorThreshold
        • textGaussianWidth
          JTextField textGaussianWidth
        • textMatch
          JTextField textMatch
        • textMatchingThreshold
          JTextField textMatchingThreshold
        • textNumberIterations
          JTextField textNumberIterations
        • useOCL
          boolean useOCL
        • userInterface
          ViewUserInterface userInterface
          Reference to userface.

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationTPSpline

      class JDialogRegistrationTPSpline extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      5973812592305647222L

      • Serialized Fields

        • baseImage
          ModelImage baseImage
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
          DOCUMENT ME!
        • coplanar
          boolean coplanar
          DOCUMENT ME!
        • DIM
          int DIM
          DOCUMENT ME!
        • matchImage
          ModelImage matchImage
          DOCUMENT ME!
        • matrixComboBox
          JComboBox matrixComboBox
        • matrixDirectory
          String matrixDirectory
        • matrixLabel
          JLabel matrixLabel
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • spline
          AlgorithmTPSpline spline
          DOCUMENT ME!
        • threeDButton
          JRadioButton threeDButton
        • titles
          String[] titles
          DOCUMENT ME!
        • twoDButton
          JRadioButton twoDButton
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • use3D
          boolean use3D
        • userDirectoryLabel
          JLabel userDirectoryLabel
        • userDirectoryText
          JTextField userDirectoryText
        • xSource
          double[] xSource
          DOCUMENT ME!
        • xTar
          double[] xTar
          DOCUMENT ME!
        • ySource
          double[] ySource
          DOCUMENT ME!
        • yTar
          double[] yTar
          DOCUMENT ME!
        • zSource
          double[] zSource
          DOCUMENT ME!
        • zTar
          double[] zTar
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRegistrationValidation

      class JDialogRegistrationValidation extends JDialogRegistrationLeastSquares implements Serializable

      • Serialized Fields

        • algoCost
          AlgorithmOptimizeFunctionBase algoCost
          Algorithm that implement cost functions, either a AlgorithmCostFunctions or AlgorithmCostFunctions2D
        • bin1
          int bin1
          Bin to use for pixel comparisons
        • currentCostFunct
          String currentCostFunct
          Description of the cost function being performed
        • doCorrelationRatioSmoothed
          JCheckBox doCorrelationRatioSmoothed
          Whether the available cost functions should be performed
        • doMutualInfoSmoothed
          JCheckBox doMutualInfoSmoothed
          Whether the available cost functions should be performed
        • doNormMutualInfoSmoothed
          JCheckBox doNormMutualInfoSmoothed
          Whether the available cost functions should be performed
        • doNormXCorr
          JCheckBox doNormXCorr
          Whether the available cost functions should be performed
        • simpleImg1
          ModelSimpleImage simpleImg1
          SimpleImages to describe ModelImage data, simpleImg2 is always registered image
        • simpleImg2
          ModelSimpleImage simpleImg2
          SimpleImages to describe ModelImage data, simpleImg2 is always registered image
        • tMatrix
          TransMatrix tMatrix
          Initial transmatrix for cost functions

    • Class gov.nih.mipav.view.dialogs.JDialogRegPatientPos

      class JDialogRegPatientPos extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7190471812525279048L

    • Class gov.nih.mipav.view.dialogs.JDialogRegularizedIsotropicDiffusion

      class JDialogRegularizedIsotropicDiffusion extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      781611739174870058L

      • Serialized Fields

        • checkBox25D
          JCheckBox checkBox25D
          DOCUMENT ME!
        • contrast
          float contrast
          DOCUMENT ME!
        • do25D
          boolean do25D
          DOCUMENT ME!
        • doOCL
          boolean doOCL
        • numIterations
          int numIterations
          DOCUMENT ME!
        • regIsoDiffusionAlgo
          AlgorithmRegularizedIsotropicDiffusion regIsoDiffusionAlgo
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • srcImage
          ModelImage srcImage
          DOCUMENT ME!
        • stdDev
          float stdDev
          DOCUMENT ME!
        • textContrast
          JTextField textContrast
          DOCUMENT ME!
        • textGaussian
          JTextField textGaussian
          DOCUMENT ME!
        • textNumberIterations
          JTextField textNumberIterations
          DOCUMENT ME!
        • useOCLCheckbox
          JCheckBox useOCLCheckbox

    • Class gov.nih.mipav.view.dialogs.JDialogRegVOILandmark

      class JDialogRegVOILandmark extends JDialogBase implements Serializable
      serialVersionUID:
      1515612809506343793L

      • Serialized Fields

        • algoRegVOILankmark
          AlgorithmRegVOILandmark algoRegVOILankmark
          DOCUMENT ME!
        • clonedImage
          ModelImage clonedImage
        • comboBoxOpt
          JComboBox comboBoxOpt
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelmaxRz
          JLabel labelmaxRz
          DOCUMENT ME!
        • labelmaxTx
          JLabel labelmaxTx
          DOCUMENT ME!
        • labelmaxTy
          JLabel labelmaxTy
          DOCUMENT ME!
        • labelminRz
          JLabel labelminRz
          DOCUMENT ME!
        • labelminTx
          JLabel labelminTx
          DOCUMENT ME!
        • labelminTy
          JLabel labelminTy
          DOCUMENT ME!
        • labelStep
          JLabel labelStep
          DOCUMENT ME!
        • position
          VOIContour position
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textmaxRz
          JTextField textmaxRz
          DOCUMENT ME!
        • textmaxTx
          JTextField textmaxTx
          DOCUMENT ME!
        • textmaxTy
          JTextField textmaxTy
          DOCUMENT ME!
        • textminRz
          JTextField textminRz
          DOCUMENT ME!
        • textminTx
          JTextField textminTx
          DOCUMENT ME!
        • textminTy
          JTextField textminTy
          DOCUMENT ME!
        • textStep
          JTextField textStep
          DOCUMENT ME!
        • tmpIntensity
          float[] tmpIntensity
          DOCUMENT ME!
        • tmpPosition
          WildMagic.LibFoundation.Mathematics.Vector3f[] tmpPosition
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRemovePlugin

      class JDialogRemovePlugin extends JDialogBase implements Serializable
      serialVersionUID:
      -6309199966911968353L

      • Serialized Fields

        • destroyFileCheckbox
          JCheckBox destroyFileCheckbox
          Toggles whether or not the plugin file should be deleted from MIPAV's class directory.
        • list
          JList list
          List of installed plugins.

    • Class gov.nih.mipav.view.dialogs.JDialogRemoveSlices

      class JDialogRemoveSlices extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7932215505116955663L

      • Serialized Fields

        • checkboxList
          JCheckBox[] checkboxList
          DOCUMENT ME!
        • checkboxPanel
          JPanel checkboxPanel
          DOCUMENT ME!
        • checkButton
          JButton checkButton
          DOCUMENT ME!
        • checkEvenButton
          JButton checkEvenButton
          DOCUMENT ME!
        • checkListRemove
          boolean[] checkListRemove
          DOCUMENT ME!
        • checkOddButton
          JButton checkOddButton
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • dontOpenFrame
          boolean dontOpenFrame
          DOCUMENT ME!
        • doReplace
          boolean doReplace
          DOCUMENT ME!
        • exampleLabel
          JLabel exampleLabel
          DOCUMENT ME!
        • exampleLabel2
          JLabel exampleLabel2
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • insertBlank
          boolean insertBlank
          If true, insert a blank rather than a weighted average
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • nSlices
          int nSlices
          DOCUMENT ME!
        • numChecked
          int numChecked
          DOCUMENT ME!
        • origExtents
          int[] origExtents
          DOCUMENT ME!
        • origNDims
          int origNDims
          DOCUMENT ME!
        • pressedCheckEven
          boolean pressedCheckEven
          DOCUMENT ME!
        • pressedCheckOdd
          boolean pressedCheckOdd
          DOCUMENT ME!
        • rangeField
          JTextField rangeField
          DOCUMENT ME!
        • removeSlicesAlgo
          AlgorithmRemoveSlices removeSlicesAlgo
          DOCUMENT ME!
        • replaceBox
          JCheckBox replaceBox
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • replaceSlicesAlgo
          AlgorithmReplaceRemovedSlices replaceSlicesAlgo
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • successful
          boolean successful
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • unCheckButton
          JButton unCheckButton
          DOCUMENT ME!
        • useRange
          JCheckBox useRange
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRemoveTSlices

      class JDialogRemoveTSlices extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -5187681503326982110L

      • Serialized Fields

        • checkboxList
          JCheckBox[] checkboxList
          DOCUMENT ME!
        • checkboxPanel
          JPanel checkboxPanel
          DOCUMENT ME!
        • checkButton
          JButton checkButton
          DOCUMENT ME!
        • checkListRemove
          boolean[] checkListRemove
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • nChecked
          int nChecked
          DOCUMENT ME!
        • nSlices
          int nSlices
          DOCUMENT ME!
        • removeTSlicesAlgo
          AlgorithmRemoveTSlices removeTSlicesAlgo
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • unCheckButton
          JButton unCheckButton
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogReorient

      class JDialogReorient extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogReplaceBlankSlicesWithAverages

      class JDialogReplaceBlankSlicesWithAverages extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogReplaceSlice

      class JDialogReplaceSlice extends JDialogBase implements Serializable
      serialVersionUID:
      -4522782534141992295L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogReplaceValue

      class JDialogReplaceValue extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -4321343995269931526L

    • Class gov.nih.mipav.view.dialogs.JDialogReslice

      class JDialogReslice extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      293226884205657186L

      • Serialized Fields

        • comboBoxInterp
          JComboBox comboBoxInterp
          Used for choosing interpolation.
        • image
          ModelImage image
          Image to reslice.
        • mode
          int mode
          Interpolation mode.
        • resliceAlgo
          AlgorithmReslice resliceAlgo
          Reslice algorithm.
        • resultImage
          ModelImage resultImage
          resliced image.

    • Class gov.nih.mipav.view.dialogs.JDialogRGBConcat

      class JDialogRGBConcat extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      4183252789435843400L

    • Class gov.nih.mipav.view.dialogs.JDialogRGBtoGray

      class JDialogRGBtoGray extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3780026821781916357L

      • Serialized Fields

        • blueValue
          float blueValue
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • equalButton
          JRadioButton equalButton
          DOCUMENT ME!
        • equalRange
          boolean equalRange
        • equalRangeButton
          JRadioButton equalRangeButton
        • fInfoBase
          FileInfoBase fInfoBase
          DOCUMENT ME!
        • graphicsButton
          JRadioButton graphicsButton
          DOCUMENT ME!
        • greenValue
          float greenValue
          DOCUMENT ME!
        • imageA
          ModelImage imageA
          DOCUMENT ME!
        • intensityAverage
          boolean intensityAverage
          DOCUMENT ME!
        • labelB
          JLabel labelB
          DOCUMENT ME!
        • labelG
          JLabel labelG
          DOCUMENT ME!
        • labelMaxB
          JLabel labelMaxB
        • labelMaxG
          JLabel labelMaxG
        • labelMaxR
          JLabel labelMaxR
        • labelMinB
          JLabel labelMinB
        • labelMinG
          JLabel labelMinG
        • labelMinR
          JLabel labelMinR
        • labelR
          JLabel labelR
          DOCUMENT ME!
        • maxB
          float maxB
        • maxG
          float maxG
        • maxR
          float maxR
        • minB
          float minB
        • minG
          float minG
        • minR
          float minR
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • redValue
          float redValue
          set the values to the defaults -- based on a default of equal values.
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • RGBAlgo
          AlgorithmRGBtoGray RGBAlgo
          DOCUMENT ME!
        • textB
          JTextField textB
          DOCUMENT ME!
        • textG
          JTextField textG
          DOCUMENT ME!
        • textMaxB
          JTextField textMaxB
        • textMaxG
          JTextField textMaxG
        • textMaxR
          JTextField textMaxR
        • textMinB
          JTextField textMinB
        • textMinG
          JTextField textMinG
        • textMinR
          JTextField textMinR
        • textR
          JTextField textR
          DOCUMENT ME!
        • textThreshold
          JTextField textThreshold
          DOCUMENT ME!
        • threshold
          float threshold
          DOCUMENT ME!
        • thresholdAverage
          boolean thresholdAverage
          DOCUMENT ME!
        • thresholdCheckBox
          JCheckBox thresholdCheckBox
          DOCUMENT ME!
        • unequalRangeButton
          JRadioButton unequalRangeButton
        • userButton
          JRadioButton userButton
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogRGBtoGrays

      class JDialogRGBtoGrays extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      540686811347959955L

    • Class gov.nih.mipav.view.dialogs.JDialogRGBtoHSB

      class JDialogRGBtoHSB extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -3386283808285677422L

    • Class gov.nih.mipav.view.dialogs.JDialogRotate

      class JDialogRotate extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8408959889101739488L

      • Serialized Fields

        • image
          ModelImage image
          Source image for algorithm.
        • resultImage
          ModelImage resultImage
          Result image after algorithm has completed.
        • rotateAlgo
          AlgorithmRotate rotateAlgo
          DOCUMENT ME!
        • rotateAxis
          int rotateAxis
          Rotation axis.

    • Class gov.nih.mipav.view.dialogs.JDialogRuleBasedContrastEnhancement

      class JDialogRuleBasedContrastEnhancement extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogSaveDicom

      class JDialogSaveDicom extends JDialogBase implements Serializable
      serialVersionUID:
      7303665224054251504L

      • Serialized Fields

        • additionalTagsList
          Hashtable<String,String> additionalTagsList
        • autofillButton
          JButton autofillButton
          DOCUMENT ME!
        • dataType
          int dataType
        • dicomFileInfo
          FileInfoDicom dicomFileInfo
          DOCUMENT ME!
        • fileInfo
          FileInfoBase fileInfo
          DOCUMENT ME!
        • fillButton
          JButton fillButton
          DOCUMENT ME!
        • gbc
          GridBagConstraints gbc
          DOCUMENT ME!
        • isMultiFrame
          boolean isMultiFrame
        • lateralities
          String[] lateralities
          DOCUMENT ME!
        • laterality
          JComboBox laterality
          DOCUMENT ME!
        • layout
          GridBagLayout layout
          DOCUMENT ME!
        • modalities
          String[] modalities
          DOCUMENT ME!
        • parts
          String[] parts
          DOCUMENT ME!
        • patientBirthDate
          JTextField patientBirthDate
          DOCUMENT ME!
        • patientBirthTime
          JTextField patientBirthTime
          DOCUMENT ME!
        • patientComments
          JTextField patientComments
          DOCUMENT ME!
        • patientEthnicGroup
          JTextField patientEthnicGroup
          DOCUMENT ME!
        • patientID
          JTextField patientID
          DOCUMENT ME!
        • patientName
          JTextField patientName
          DOCUMENT ME!
        • patientOrientation
          JTextField patientOrientation
          DOCUMENT ME!
        • patientOtherIDs
          JTextField patientOtherIDs
          DOCUMENT ME!
        • patientOtherNames
          JTextField patientOtherNames
          DOCUMENT ME!
        • patientPanel
          JPanel patientPanel
          DOCUMENT ME!
        • patientSex
          JComboBox patientSex
          DOCUMENT ME!
        • positions
          String[] positions
          DOCUMENT ME!
        • requiredPanel
          JPanel requiredPanel
          DOCUMENT ME!
        • seriesBody
          JComboBox seriesBody
          DOCUMENT ME!
        • seriesDate
          JTextField seriesDate
          DOCUMENT ME!
        • seriesDescrip
          JTextField seriesDescrip
          DOCUMENT ME!
        • seriesLarge
          JTextField seriesLarge
          DOCUMENT ME!
        • seriesMod
          JComboBox seriesMod
          DOCUMENT ME!
        • seriesNo
          JTextField seriesNo
          DOCUMENT ME!
        • seriesOp
          JTextField seriesOp
          DOCUMENT ME!
        • seriesPanel
          JPanel seriesPanel
          DOCUMENT ME!
        • seriesPerfPhy
          JTextField seriesPerfPhy
          DOCUMENT ME!
        • seriesPos
          JComboBox seriesPos
          DOCUMENT ME!
        • seriesProtocol
          JTextField seriesProtocol
          DOCUMENT ME!
        • seriesSmall
          JTextField seriesSmall
          DOCUMENT ME!
        • seriesStepDate
          JTextField seriesStepDate
          DOCUMENT ME!
        • seriesStepDescrip
          JTextField seriesStepDescrip
          DOCUMENT ME!
        • seriesStepID
          JTextField seriesStepID
          DOCUMENT ME!
        • seriesStepTime
          JTextField seriesStepTime
          DOCUMENT ME!
        • seriesTime
          JTextField seriesTime
          DOCUMENT ME!
        • seriesUID
          JTextField seriesUID
          DOCUMENT ME!
        • sexes
          String[] sexes
          DOCUMENT ME!
        • studyAccNumber
          JTextField studyAccNumber
          DOCUMENT ME!
        • studyAge
          JTextField studyAge
          DOCUMENT ME!
        • studyDate
          JTextField studyDate
          DOCUMENT ME!
        • studyDescrip
          JTextField studyDescrip
          DOCUMENT ME!
        • studyDiag
          JTextField studyDiag
          DOCUMENT ME!
        • studyHist
          JTextField studyHist
          DOCUMENT ME!
        • studyID
          JTextField studyID
          DOCUMENT ME!
        • studyOcc
          JTextField studyOcc
          DOCUMENT ME!
        • studyPanel
          JPanel studyPanel
          DOCUMENT ME!
        • studyPhyRead
          JTextField studyPhyRead
          DOCUMENT ME!
        • studyPhyRec
          JTextField studyPhyRec
          DOCUMENT ME!
        • studyRefPhy
          JTextField studyRefPhy
          DOCUMENT ME!
        • studySize
          JTextField studySize
          DOCUMENT ME!
        • studyTime
          JTextField studyTime
          DOCUMENT ME!
        • studyUID
          JTextField studyUID
          DOCUMENT ME!
        • studyWeight
          JTextField studyWeight
          DOCUMENT ME!
        • tabPane
          JTabbedPane tabPane
          DOCUMENT ME!
        • tagsImportedFromNonDicomImage
          Hashtable<String,String> tagsImportedFromNonDicomImage
          DICOM tags extracted from the image we want to save. Example: dicom_0xNNNN el_0xNNNN tags stored in MINC headers.
        • tagsList
          Hashtable<String,JComponent> tagsList
          The additional tags list is a list of tags the DTI group has requested.
        • UI
          ViewUserInterface UI
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSaveMergedVOIs

      class JDialogSaveMergedVOIs extends JDialogBase implements Serializable

      • Serialized Fields

        • AxialVOIs
          InstanceVOI AxialVOIs
          Axial VOI instance
        • buttonAxial
          JButton buttonAxial
          Choose button for each VOI and ply file.
        • buttonCoronal
          JButton buttonCoronal
          Choose button for each VOI and ply file.
        • buttonPanel
          JPanel buttonPanel
          Button panel to hold the OK button, Cancel button, and Help button.
        • buttonPly
          JButton buttonPly
          Choose button for each VOI and ply file.
        • buttonSagittal
          JButton buttonSagittal
          Choose button for each VOI and ply file.
        • CoronalVOIs
          InstanceVOI CoronalVOIs
          Coronal VOI instance
        • labelAxialVOI
          JLabel labelAxialVOI
        • labelCoronalVOI
          JLabel labelCoronalVOI
        • labelPlyFile
          JLabel labelPlyFile
        • labelSagittalVOI
          JLabel labelSagittalVOI
        • msgPanel
          JPanel msgPanel
          Msg box to show the Prostate surface analysis related info.
        • PlyInstance
          InstanceVOI PlyInstance
          Ply file instance. This instance only uses the file dir and file name.
        • SagittalVOIs
          InstanceVOI SagittalVOIs
          Sagittal VOI instance
        • textFieldAxialVOI
          JTextField textFieldAxialVOI
          Text field for each VOI and ply file.
        • textFieldCoronalVOI
          JTextField textFieldCoronalVOI
          Text field for each VOI and ply file.
        • textFieldPlyFile
          JTextField textFieldPlyFile
          Text field for each VOI and ply file.
        • textFieldSagittalVOI
          JTextField textFieldSagittalVOI
          Text field for each VOI and ply file.
        • VOIsPanel
          JPanel VOIsPanel

    • Class gov.nih.mipav.view.dialogs.JDialogSaveMinc

      class JDialogSaveMinc extends JDialogBase implements Serializable
      serialVersionUID:
      5951116204923790986L

      • Serialized Fields

        • comboX
          JComboBox comboX
          DOCUMENT ME!
        • comboY
          JComboBox comboY
          DOCUMENT ME!
        • comboZ
          JComboBox comboZ
          DOCUMENT ME!
        • defaultAxisOrient
          int[] defaultAxisOrient
          DOCUMENT ME!
        • defaultSet
          boolean defaultSet
          DOCUMENT ME!
        • defaultTSpace
          float defaultTSpace
          DOCUMENT ME!
        • defaultTStart
          float defaultTStart
          DOCUMENT ME!
        • defaultXSpace
          float defaultXSpace
          DOCUMENT ME!
        • defaultXStart
          float defaultXStart
          Variables for holding default values. Then if the default values are used (as in, the user hit "OK" without changing any values), that option would be set in "options". This affects the way the script records.
        • defaultYSpace
          float defaultYSpace
          DOCUMENT ME!
        • defaultYStart
          float defaultYStart
          DOCUMENT ME!
        • defaultZSpace
          float defaultZSpace
          DOCUMENT ME!
        • defaultZStart
          float defaultZStart
          DOCUMENT ME!
        • fileInfo
          FileInfoBase fileInfo
          Variables for holding and storing file information.
        • options
          FileWriteOptions options
          DOCUMENT ME!
        • ori
          int[] ori
          Axes orientations.
        • orient
          int orient
          DOCUMENT ME!
        • orientLabel
          JLabel orientLabel
          Variables for the actual GUI; not all need to be global, but just as easy. The text fields and radio buttons do need to be global.
        • tSpace
          JTextField tSpace
        • tStart
          JTextField tStart
        • xSpace
          JTextField xSpace
          DOCUMENT ME!
        • xStart
          JTextField xStart
          DOCUMENT ME!
        • ySpace
          JTextField ySpace
          DOCUMENT ME!
        • yStart
          JTextField yStart
          DOCUMENT ME!
        • zSpace
          JTextField zSpace
          DOCUMENT ME!
        • zStart
          JTextField zStart
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSaveMincVersionChoice

      class JDialogSaveMincVersionChoice extends JDialogBase implements Serializable

      • Serialized Fields

        • comboBoxSaveMethod
          JComboBox comboBoxSaveMethod
          Whether to save as selected by dialog or always as analyze, interfile, or nifti.
        • minc1File
          JRadioButton minc1File
          Radio button to indicate that an Minc1 CDF mnc file should be written out.
        • minc2File
          JRadioButton minc2File
          Radio button to indicate that a Minc2 HDF5 mnc file should be written out.
        • okayPressed
          boolean okayPressed
          Whether the window was closed through the user clicking the OK button (and not just killing the dialog).

    • Class gov.nih.mipav.view.dialogs.JDialogSaveSlices

      class JDialogSaveSlices extends JDialogBase implements Serializable
      serialVersionUID:
      6208822935229525687L

      • Serialized Fields

        • afniEnabled
          boolean afniEnabled
          DOCUMENT ME!
        • corEnabled
          boolean corEnabled
          DOCUMENT ME!
        • dataType
          int dataType
        • dicomEnabled
          boolean dicomEnabled
        • dicomGroup
          ButtonGroup dicomGroup
        • dicomInfoPanel
          JPanel dicomInfoPanel
          Dicom options panel
        • enablePackBitWrite
          boolean enablePackBitWrite
          DOCUMENT ME!
        • encapJP2Checkbox
          JCheckBox encapJP2Checkbox
          Check box for specifying whether DICOM files should be saved as an encapsulated JPEG2000
        • enforceDistinctVolumeWriting
          boolean enforceDistinctVolumeWriting
        • enhancedDicomButton
          JRadioButton enhancedDicomButton
          All frames in one file
        • floatToShort
          boolean floatToShort
        • floatToShortCheckbox
          JCheckBox floatToShortCheckbox
        • fourDimEnabled
          boolean fourDimEnabled
          DOCUMENT ME!
        • geGenesisEnabled
          boolean geGenesisEnabled
        • geSigna4XEnabled
          boolean geSigna4XEnabled
        • isDouble
          boolean isDouble
        • isFloat
          boolean isFloat
        • labelDigitNumber
          JLabel labelDigitNumber
          DOCUMENT ME!
        • labelFirstSlice
          JLabel labelFirstSlice
          DOCUMENT ME!
        • labelFirstTimePeriod
          JLabel labelFirstTimePeriod
          DOCUMENT ME!
        • labelLastSlice
          JLabel labelLastSlice
          DOCUMENT ME!
        • labelLastTimePeriod
          JLabel labelLastTimePeriod
          DOCUMENT ME!
        • labelStartNumber
          JLabel labelStartNumber
          DOCUMENT ME!
        • maxTimeValue
          int maxTimeValue
          DOCUMENT ME!
        • maxValue
          int maxValue
          DOCUMENT ME!
        • mincEnabled
          boolean mincEnabled
        • minTimeValue
          int minTimeValue
          DOCUMENT ME!
        • minValue
          int minValue
          DOCUMENT ME!
        • multiFileCheckbox
          JCheckBox multiFileCheckbox
          DOCUMENT ME!
        • multiFileDicomButton
          JRadioButton multiFileDicomButton
        • options
          FileWriteOptions options
          DOCUMENT ME!
        • packBitCheckbox
          JCheckBox packBitCheckbox
          DOCUMENT ME!
        • saveAsEncapJP2
          boolean saveAsEncapJP2
          Whether DICOM files should be saved as an encapsulated JPEG2000
        • saveEnhancedDicom
          boolean saveEnhancedDicom
          Whether 3D or higher dimensionality dicom images should be saved as a single file
        • slicePanel
          JPanel slicePanel
          DOCUMENT ME!
        • stampSecondary
          boolean stampSecondary
          Whether to stamp DICOM files with the MIPAV secondary stamp
        • stampSecondaryCheckbox
          JCheckBox stampSecondaryCheckbox
          Check box for specifying whether DICOM files should be stamped with MIPAV information
        • textDigitNumber
          JTextField textDigitNumber
          DOCUMENT ME!
        • textFirstSlice
          JTextField textFirstSlice
          DOCUMENT ME!
        • textFirstTimePeriod
          JTextField textFirstTimePeriod
          DOCUMENT ME!
        • textLastSlice
          JTextField textLastSlice
          DOCUMENT ME!
        • textLastTimePeriod
          JTextField textLastTimePeriod
          DOCUMENT ME!
        • textStartNumber
          JTextField textStartNumber
          DOCUMENT ME!
        • tiffEnabled
          boolean tiffEnabled
          DOCUMENT ME!
        • tiffPanel
          JPanel tiffPanel
          DOCUMENT ME!
        • timeEnabled
          boolean timeEnabled
          DOCUMENT ME!
        • timePanel
          JPanel timePanel
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSaveVistaParams

      class JDialogSaveVistaParams extends JDialogBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogScaleSaliency

      class JDialogScaleSaliency extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogSCDSegmentation

      class JDialogSCDSegmentation extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogScriptableBase

      class JDialogScriptableBase extends JDialogBase implements Serializable
      serialVersionUID:
      1714695069613762132L

      • Serialized Fields

        • displayInNewFrame
          boolean displayInNewFrame
        • isComplete
          boolean isComplete
          Indicates whether the scripted algorithm completed successfully. Used to retain the status after the dialog has finalized the algorithm handle(s) in algorithmPerformed.
        • scriptParameters
          AlgorithmParameters scriptParameters
          Contains parameters used to run or record the dialog action, along with some common helper methods.

    • Class gov.nih.mipav.view.dialogs.JDialogScriptableTransform

      class JDialogScriptableTransform extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7786904359172693422L

      • Serialized Fields

        • algoTal
          AlgorithmTalairachTransform algoTal
          DOCUMENT ME!
        • algoTrans
          AlgorithmTransform algoTrans
          or if the source image is to be replaced.
        • clipCheckbox
          JCheckBox clipCheckbox
          DOCUMENT ME!
        • comboBoxImage
          JComboBox comboBoxImage
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • comboBoxTalTransform
          JComboBox comboBoxTalTransform
          DOCUMENT ME!
        • computeTImage
          JRadioButton computeTImage
          DOCUMENT ME!
        • constantFOV
          int constantFOV
          We use the constant to preserve the FOV. Either 1 or 0;
        • constantFOVradio
          JRadioButton constantFOVradio
          Radio button for constant FOV interpolation.
        • cropOrPad
          ButtonGroup cropOrPad
          DOCUMENT ME!
        • cropRadio
          JRadioButton cropRadio
          DOCUMENT ME!
        • current
          JLabel current
          DOCUMENT ME!
        • cXdim
          int cXdim
          DOCUMENT ME!
        • cXres
          float cXres
          DOCUMENT ME!
        • cYdim
          int cYdim
          DOCUMENT ME!
        • cYres
          float cYres
          DOCUMENT ME!
        • cZdim
          int cZdim
          DOCUMENT ME!
        • cZres
          float cZres
          DOCUMENT ME!
        • dataType
          int dataType
        • dims
          float[] dims
        • do25D
          boolean do25D
          DOCUMENT ME!
        • doClip
          boolean doClip
          DOCUMENT ME!
        • doInvMat
          boolean doInvMat
          DOCUMENT ME!
        • doPad
          boolean doPad
          DOCUMENT ME!
        • doRotateCenter
          boolean doRotateCenter
          DOCUMENT ME!
        • doTalairach
          boolean doTalairach
          DOCUMENT ME!
        • doUpdateOrigin
          boolean doUpdateOrigin
          DOCUMENT ME!
        • doVOI
          boolean doVOI
          DOCUMENT ME!
        • enableSATransform
          boolean enableSATransform
        • endMatchFOVradio
          JRadioButton endMatchFOVradio
          Radio button for slice start invalid input: '&' end matching interpolation.
        • fileClip
          boolean[] fileClip
        • fileInterp
          int[] fileInterp
        • fileMatrix
          JRadioButton fileMatrix
          DOCUMENT ME!
        • filePad
          boolean[] filePad
        • fileTransMatrix
          TransMatrix fileTransMatrix
          Stores the matrix read in from a file it then can be converted to the corrected axis orientation (i.e. world coordinate and/or left-hand coordinate systems).
        • filetVOI
          boolean[] filetVOI
        • fillValue
          float fillValue
        • image
          ModelImage image
          source image
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • imageMax
          double imageMax
        • imageMin
          double imageMin
        • interp
          int interp
          Interpolation method
        • interpFOVgroup
          ButtonGroup interpFOVgroup
          Button group for interpolation type, contant FOV or start, end matching.
        • invertCheckbox
          JCheckBox invertCheckbox
          DOCUMENT ME!
        • isSATransform
          boolean isSATransform
          is this a scanner anatomical transform (->AXIAL)
        • labelDimX
          JLabel labelDimX
          DOCUMENT ME!
        • labelDimY
          JLabel labelDimY
          DOCUMENT ME!
        • labelDimZ
          JLabel labelDimZ
          DOCUMENT ME!
        • labelOrigin
          JLabel labelOrigin
        • labelResX
          JLabel labelResX
          DOCUMENT ME!
        • labelResY
          JLabel labelResY
          DOCUMENT ME!
        • labelResZ
          JLabel labelResZ
          DOCUMENT ME!
        • labelRx
          JLabel labelRx
          DOCUMENT ME!
        • labelRy
          JLabel labelRy
          DOCUMENT ME!
        • labelRz
          JLabel labelRz
          DOCUMENT ME!
        • labelSKx
          JLabel labelSKx
          DOCUMENT ME!
        • labelSKy
          JLabel labelSKy
          DOCUMENT ME!
        • labelSKz
          JLabel labelSKz
          DOCUMENT ME!
        • labelSx
          JLabel labelSx
          DOCUMENT ME!
        • labelSy
          JLabel labelSy
          DOCUMENT ME!
        • labelSz
          JLabel labelSz
          DOCUMENT ME!
        • labelTransformDimX
          JLabel labelTransformDimX
        • labelTransformDimY
          JLabel labelTransformDimY
        • labelTransformDimZ
          JLabel labelTransformDimZ
        • labelTransformResX
          JLabel labelTransformResX
        • labelTransformResY
          JLabel labelTransformResY
        • labelTransformResZ
          JLabel labelTransformResZ
        • labelTx
          JLabel labelTx
          DOCUMENT ME!
        • labelTy
          JLabel labelTy
          DOCUMENT ME!
        • labelTz
          JLabel labelTz
          DOCUMENT ME!
        • leftHandSystem
          boolean leftHandSystem
          If true change matrix to the left-hand coordinate system.
        • magSlider
          JSlider magSlider
          DOCUMENT ME!
        • matrixDeterminationGroup
          ButtonGroup matrixDeterminationGroup
          DOCUMENT ME!
        • matrixDirectory
          String matrixDirectory
        • matrixFile
          String matrixFile
          DOCUMENT ME!
        • matrixFName
          JTextField matrixFName
          DOCUMENT ME!
        • max
          int max
          DOCUMENT ME!
        • maximum
          JLabel maximum
          DOCUMENT ME!
        • min
          int min
          DOCUMENT ME!
        • minimum
          JLabel minimum
          DOCUMENT ME!
        • noTransform
          JRadioButton noTransform
          DOCUMENT ME!
        • outOfBoundsComboBox
          JComboBox outOfBoundsComboBox
        • outOfBoundsIndex
          int outOfBoundsIndex
          Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum
        • outOfBoundsLabel
          JLabel outOfBoundsLabel
        • outputDimsGroup
          ButtonGroup outputDimsGroup
        • oXdim
          int oXdim
          DOCUMENT ME!
        • oXres
          float oXres
          DOCUMENT ME!
        • oYdim
          int oYdim
          DOCUMENT ME!
        • oYres
          float oYres
          DOCUMENT ME!
        • oZdim
          int oZdim
          DOCUMENT ME!
        • oZres
          float oZres
          DOCUMENT ME!
        • padRadio
          JRadioButton padRadio
          DOCUMENT ME!
        • preserveFOV
          boolean preserveFOV
          DOCUMENT ME!
        • preserveFOV2Button
          JRadioButton preserveFOV2Button
        • preserveFOVButton
          JRadioButton preserveFOVButton
        • preserveOutputDimsButton
          JRadioButton preserveOutputDimsButton
        • prevSelectedTransformRadioButton
          JRadioButton prevSelectedTransformRadioButton
        • quiet
          boolean quiet
        • RESAMPLE_STATUS_DEFAULT_TEXT
          String RESAMPLE_STATUS_DEFAULT_TEXT
        • resampleGroup
          ButtonGroup resampleGroup
          DOCUMENT ME!
        • resampleImage
          ModelImage resampleImage
          DOCUMENT ME!
        • resampleMatrixSourceButton
          JRadioButton resampleMatrixSourceButton
        • resampleMatrixTargetButton
          JRadioButton resampleMatrixTargetButton
        • resamplePanel
          JPanel resamplePanel
        • resampleSlider
          JRadioButton resampleSlider
          DOCUMENT ME!
        • resampleStatusTextField
          JTextField resampleStatusTextField
        • resampletoImage
          JRadioButton resampletoImage
          DOCUMENT ME!
        • resampletoMatrixFile
          JRadioButton resampletoMatrixFile
          DOCUMENT ME!
        • resampletoUser
          JRadioButton resampletoUser
          DOCUMENT ME!
        • resDimGroup
          ButtonGroup resDimGroup
        • resols
          float[] resols
        • resTransformGroup
          ButtonGroup resTransformGroup
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • rotationAxisGroup
          ButtonGroup rotationAxisGroup
          DOCUMENT ME!
        • rotCenter
          JRadioButton rotCenter
          DOCUMENT ME!
        • rotOrigin
          JRadioButton rotOrigin
          DOCUMENT ME!
        • separateDimResButton
          JRadioButton separateDimResButton
        • sourceXdim
          int[] sourceXdim
        • sourceXres
          float[] sourceXres
        • sourceYdim
          int[] sourceYdim
        • sourceYres
          float[] sourceYres
        • sourceZdim
          int[] sourceZdim
        • sourceZres
          float[] sourceZres
        • spline
          AlgorithmTPSpline spline
        • storedMatrix
          JRadioButton storedMatrix
          DOCUMENT ME!
        • storedMatrixBox
          JComboBox storedMatrixBox
        • tabbedPane
          JTabbedPane tabbedPane
          Tabbed pane
        • targetXdim
          int[] targetXdim
        • targetXres
          float[] targetXres
        • targetYdim
          int[] targetYdim
        • targetYres
          float[] targetYres
        • targetZdim
          int[] targetZdim
        • targetZres
          float[] targetZres
        • textDimX
          JTextField textDimX
          DOCUMENT ME!
        • textDimY
          JTextField textDimY
          DOCUMENT ME!
        • textDimZ
          JTextField textDimZ
          DOCUMENT ME!
        • textResX
          JTextField textResX
          DOCUMENT ME!
        • textResY
          JTextField textResY
          DOCUMENT ME!
        • textResZ
          JTextField textResZ
          DOCUMENT ME!
        • textRx
          JTextField textRx
          DOCUMENT ME!
        • textRy
          JTextField textRy
          DOCUMENT ME!
        • textRz
          JTextField textRz
          DOCUMENT ME!
        • textSKx
          JTextField textSKx
          DOCUMENT ME!
        • textSKy
          JTextField textSKy
          DOCUMENT ME!
        • textSKz
          JTextField textSKz
          DOCUMENT ME!
        • textSx
          JTextField textSx
          DOCUMENT ME!
        • textSy
          JTextField textSy
          DOCUMENT ME!
        • textSz
          JTextField textSz
          DOCUMENT ME!
        • textTransformDimX
          JTextField textTransformDimX
        • textTransformDimY
          JTextField textTransformDimY
        • textTransformDimZ
          JTextField textTransformDimZ
        • textTransformResX
          JTextField textTransformResX
        • textTransformResY
          JTextField textTransformResY
        • textTransformResZ
          JTextField textTransformResZ
        • textTx
          JTextField textTx
          DOCUMENT ME!
        • textTy
          JTextField textTy
          DOCUMENT ME!
        • textTz
          JTextField textTz
          DOCUMENT ME!
        • tInfo
          TalairachTransformInfo tInfo
          DOCUMENT ME!
        • TRANSFORM_STATUS_DEFAULT_TEXT
          String TRANSFORM_STATUS_DEFAULT_TEXT
        • transformStatusTextField
          JTextField transformStatusTextField
        • transformType
          int transformType
          DOCUMENT ME!
        • tVal
          String[] tVal
          DOCUMENT ME!
        • units
          int[] units
        • updateOriginCheckbox
          JCheckBox updateOriginCheckbox
          DOCUMENT ME!
        • userDefinedMatrix
          JRadioButton userDefinedMatrix
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • useSACenter
          boolean useSACenter
        • useSACenterBox
          JCheckBox useSACenterBox
          checkbox telling the algorithm to use the scanner coordinate center rather than the image center
        • valueLabel
          JLabel valueLabel
        • valueText
          JTextField valueText
        • voiCheckbox
          JCheckBox voiCheckbox
          DOCUMENT ME!
        • wcSystem
          boolean wcSystem
          If true change matrix to the world coordinate system.
        • xfrm
          TransMatrix xfrm
          DOCUMENT ME!
        • xyAspectRatio
          JCheckBox xyAspectRatio
          DOCUMENT ME!
        • xyzAspectRatio
          JCheckBox xyzAspectRatio
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogScriptRecorder

      class JDialogScriptRecorder extends JDialogBase implements Serializable
      serialVersionUID:
      -8409175669783444792L

      • Serialized Fields

        • editButton
          JButton editButton
          DOCUMENT ME!
        • instructionLabel
          JLabel instructionLabel
          DOCUMENT ME!
        • message
          String message
          DOCUMENT ME!
        • pauseButton
          JButton pauseButton
          DOCUMENT ME!
        • pauseButton2
          JButton pauseButton2
          DOCUMENT ME!
        • scriptRecorder
          ScriptRecorder scriptRecorder
          A reference to the global MIPAV script recorder. This dialog listens to changes in its status and script.
        • scriptTextArea
          JTextArea scriptTextArea
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSelectChannelSequence

      class JDialogSelectChannelSequence extends JDialogBase implements Serializable
      serialVersionUID:
      7969429539433435403L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogSelectDICOMColumnHeaders

      class JDialogSelectDICOMColumnHeaders extends JDialogBase implements Serializable
      serialVersionUID:
      5883528252352616682L

    • Class gov.nih.mipav.view.dialogs.JDialogSequentialScanningWatershed

      class JDialogSequentialScanningWatershed extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogServer

      class JDialogServer extends JDialogBase implements Serializable
      serialVersionUID:
      1348641833737787663L

      • Serialized Fields

        • alias
          String alias
          DOCUMENT ME!
        • aliasField
          JTextField aliasField
          DOCUMENT ME!
        • aliasLabel
          JLabel aliasLabel
          DOCUMENT ME!
        • ip
          String ip
          DOCUMENT ME!
        • ipField
          JTextField ipField
          DOCUMENT ME!
        • ipLabel
          JLabel ipLabel
          DOCUMENT ME!
        • port
          String port
          DOCUMENT ME!
        • portField
          JTextField portField
          DOCUMENT ME!
        • portLabel
          JLabel portLabel
          DOCUMENT ME!
        • server
          boolean server
          DOCUMENT ME!
        • title
          String title
          DOCUMENT ME!
        • titleField
          JTextField titleField
          DOCUMENT ME!
        • titleLabel
          JLabel titleLabel
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogShortcutEditor

      class JDialogShortcutEditor extends JDialogBase implements Serializable
      serialVersionUID:
      -6964789155088488701L

      • Serialized Fields

        • addShortcut
          JButton addShortcut
          add shortcut button.
        • currentShortcut
          KeyStroke currentShortcut
          Keystroke built from shortcut editor dialog.
        • defaultShortcutModel
          ViewTableModel defaultShortcutModel
          DOCUMENT ME!
        • defaultShortcutTable
          JTable defaultShortcutTable
          DOCUMENT ME!
        • masterScrollPane
          JScrollPane masterScrollPane
          master scroll pane in which to display all information.
        • removeShortcut
          JButton removeShortcut
          button for removing shortcuts.
        • scrollingBox
          Box scrollingBox
          Box to hold table information.
        • userDefinedShortcutModel
          ViewTableModel userDefinedShortcutModel
          DOCUMENT ME!
        • userDefinedShortcutTable
          JTable userDefinedShortcutTable
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogShortestPathWatershed

      class JDialogShortestPathWatershed extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogShowCosts

      class JDialogShowCosts extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7737847738523057492L

      • Serialized Fields

        • algoCost
          AlgorithmOptimizeFunctionBase algoCost
          Is either a AlgorithmCostFunction or a AlgorithmCostFunctions2D depending on images
        • bin1
          int bin1
          Number of bins for each image
        • bin1Text
          JTextField bin1Text
          User input of bins
        • correlationRatioSmoothed
          boolean correlationRatioSmoothed
        • currentCostFunct
          String currentCostFunct
          The current cost function
        • doCorrelationRatioSmoothed
          JCheckBox doCorrelationRatioSmoothed
          Whether the available cost functions should be performed
        • doMutualInfoSmoothed
          JCheckBox doMutualInfoSmoothed
          Whether the available cost functions should be performed
        • doNormMutualInfoSmoothed
          JCheckBox doNormMutualInfoSmoothed
          Whether the available cost functions should be performed
        • doNormXCorr
          JCheckBox doNormXCorr
          Whether the available cost functions should be performed
        • firstImage
          ModelImage firstImage
          Active image when algorithm is called.
        • imageComboBox
          JComboBox imageComboBox
          Image list for user to pick registered image
        • labelImage
          JLabel labelImage
          The registered image
        • mutualInfoSmoothed
          boolean mutualInfoSmoothed
        • normMutualInfoSmoothed
          boolean normMutualInfoSmoothed
        • normXCorr
          boolean normXCorr
        • possibleIntValues1
          double possibleIntValues1
          Initial guesses for bin values
        • secondImage
          ModelImage secondImage
          The registered image as specified by user through gui
        • simpleImg1
          ModelSimpleImage simpleImg1
          Holds extents, other info about firstImage and SecondImage
        • simpleImg2
          ModelSimpleImage simpleImg2
          Holds extents, other info about firstImage and SecondImage
        • smoothSize
          float smoothSize
          Optional smooth parameter for both cost functions
        • tMatrix
          TransMatrix tMatrix
          Identity matrix for testing cost
        • UI
          ViewUserInterface UI
          The MIPAV user interface

    • Class gov.nih.mipav.view.dialogs.JDialogSIFT

      class JDialogSIFT extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -1L

      • Serialized Fields

        • changeRemoveIndex
          boolean changeRemoveIndex
        • chooserButton
          JButton chooserButton
        • descriptorarg
          String descriptorarg
        • edge_thresh
          double edge_thresh
        • fileDir
          String[] fileDir
        • fileName
          String[] fileName
        • force_orientations
          boolean force_orientations
        • framesarg
          String framesarg
        • gssarg
          String gssarg
        • imageList
          JList imageList
        • imagePanel
          JPanel imagePanel
        • labelEdgeThresh
          JLabel labelEdgeThresh
        • labelFirstOctave
          JLabel labelFirstOctave
        • labelMagnification
          JLabel labelMagnification
        • labelNLevels
          JLabel labelNLevels
        • labelNOctaves
          JLabel labelNOctaves
        • labelNormThresh
          JLabel labelNormThresh
        • labelPeakThresh
          JLabel labelPeakThresh
        • labelRegister
          JLabel labelRegister
        • labelWindowSize
          JLabel labelWindowSize
        • magnif
          double magnif
        • metaarg
          String metaarg
        • model
          DefaultListModel<String> model
        • mosaic
          boolean mosaic
        • mosaicCheckBox
          JCheckBox mosaicCheckBox
        • norm_thresh
          double norm_thresh
        • O
          int O
        • omin
          int omin
        • orientationsCheckBox
          JCheckBox orientationsCheckBox
        • outarg
          String outarg
        • paramPanel
          JPanel paramPanel
        • peak_thresh
          double peak_thresh
        • read_framesarg
          String read_framesarg
        • readFrames
          boolean readFrames
        • readFramesCheckBox
          JCheckBox readFramesCheckBox
        • removeButton
          JButton removeButton
        • removeIndex
          int removeIndex
        • S
          int S
        • selectedDirectory
          String selectedDirectory
        • selectedFileName
          String selectedFileName
        • SIFTAlgo
          SIFT SIFTAlgo
        • srcNumber
          int srcNumber
        • tempFileDir
          String[] tempFileDir
        • tempFileName
          String[] tempFileName
        • textEdgeThresh
          JTextField textEdgeThresh
        • textFirstOctave
          JTextField textFirstOctave
        • textMagnification
          JTextField textMagnification
        • textNLevels
          JTextField textNLevels
        • textNOctaves
          JTextField textNOctaves
        • textNormThresh
          JTextField textNormThresh
        • textPeakThresh
          JTextField textPeakThresh
        • textWindowSize
          JTextField textWindowSize
        • userInterface
          ViewUserInterface userInterface
        • verbose
          boolean verbose
        • verboseCheckBox
          JCheckBox verboseCheckBox
        • window_size
          double window_size
        • writeDescriptor
          boolean writeDescriptor
        • writeDescriptorCheckBox
          JCheckBox writeDescriptorCheckBox
        • writeFrames
          boolean writeFrames
        • writeFramesCheckBox
          JCheckBox writeFramesCheckBox
        • writeGss
          boolean writeGss
        • writeGssCheckBox
          JCheckBox writeGssCheckBox
        • writeMeta
          boolean writeMeta
        • writeMetaCheckBox
          JCheckBox writeMetaCheckBox

    • Class gov.nih.mipav.view.dialogs.JDialogSIFTImageSimilarity

      class JDialogSIFTImageSimilarity extends JDialogScriptableBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogSimulatedExposureFusion

      class JDialogSimulatedExposureFusion extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogSingleMRIImageSNR

      class JDialogSingleMRIImageSNR extends JDialogBase implements Serializable
      serialVersionUID:
      4621550176907564448L

      • Serialized Fields

        • automatic
          boolean automatic
        • automaticCheckBox
          JCheckBox automaticCheckBox
        • backgroundButton
          JRadioButton backgroundButton
          DOCUMENT ME!
        • backgroundIndex
          int backgroundIndex
          DOCUMENT ME!
        • componentImage
          ViewJComponentEditImage componentImage
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelReceiver
          JLabel labelReceiver
          DOCUMENT ME!
        • numReceivers
          int numReceivers
          DOCUMENT ME!
        • signal2Button
          JRadioButton signal2Button
          DOCUMENT ME!
        • signal2Index
          int signal2Index
          DOCUMENT ME!
        • signalButton
          JRadioButton signalButton
          DOCUMENT ME!
        • signalIndex
          int signalIndex
          DOCUMENT ME!
        • snrAlgo
          AlgorithmSingleMRIImageSNR snrAlgo
          DOCUMENT ME!
        • textReceiver
          JTextField textReceiver
          DOCUMENT ME!
        • VOIGroup
          ButtonGroup VOIGroup
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSingleScaleHornSchunk

      class JDialogSingleScaleHornSchunk extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogSkeletonize

      class JDialogSkeletonize extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogSlantTransform

      class JDialogSlantTransform extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • columnButton
          JRadioButton columnButton
        • comboBoxFilterType
          JComboBox<String> comboBoxFilterType
        • FILTER_GREATER
          int FILTER_GREATER
        • FILTER_HARD
          int FILTER_HARD
        • FILTER_LESS
          int FILTER_LESS
        • FILTER_NN_GARROTE
          int FILTER_NN_GARROTE
        • FILTER_NONE
          int FILTER_NONE
        • FILTER_SOFT
          int FILTER_SOFT
        • FILTER_THRESHOLD_FIRM
          int FILTER_THRESHOLD_FIRM
        • filterType
          int filterType
        • filterVal1
          double filterVal1
        • filterVal2
          double filterVal2
        • inverseImage
          ModelImage inverseImage
        • labelVal1
          JLabel labelVal1
        • labelVal2
          JLabel labelVal2
        • rcGroup
          ButtonGroup rcGroup
        • rowButton
          JRadioButton rowButton
        • sAlgo
          SlantTransform sAlgo
        • srcImage
          ModelImage srcImage
        • textVal1
          JTextField textVal1
        • textVal2
          JTextField textVal2
        • transform
          int transform
        • transformImage
          ModelImage transformImage

    • Class gov.nih.mipav.view.dialogs.JDialogSliceAveraging

      class JDialogSliceAveraging extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -6973307260738815367L

      • Serialized Fields

        • allButton
          JRadioButton allButton
          DOCUMENT ME!
        • averagingNumber
          int averagingNumber
          DOCUMENT ME!
        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • fiveButton
          JRadioButton fiveButton
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • numberGroup
          ButtonGroup numberGroup
          DOCUMENT ME!
        • optionsPanel
          JPanel optionsPanel
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sAverAlgo
          AlgorithmSliceAveraging sAverAlgo
          DOCUMENT ME!
        • sevenButton
          JRadioButton sevenButton
          DOCUMENT ME!
        • sliceNumber
          int sliceNumber
          DOCUMENT ME!
        • threeButton
          JRadioButton threeButton
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSM2

      class JDialogSM2 extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogSmoothMesh

      class JDialogSmoothMesh extends JDialogBase implements Serializable
      serialVersionUID:
      -4644401872827443236L

      • Serialized Fields

        • alpha
          float alpha
          Alpha smoothing factor.
        • alphaText
          JTextField alphaText
          Text field for getting alpha smoothing factor.
        • iterations
          int iterations
          Number of iterations for smoothing formula.
        • iterationsText
          JTextField iterationsText
          Text field for getting iterations.
        • lambda
          float lambda
          positive scale factor.
        • lambdaText
          JTextField lambdaText
          Text field for getting lambda for smoothing.
        • limitCheckBox
          JCheckBox limitCheckBox
          If limitCheckBox is selected iterations stop when volume change from initial volume is greater than or equal to volumePercent.
        • mainPanel
          JPanel mainPanel
          main panel containing interface:
        • mu
          float mu
          negative scale factor.
        • muText
          JTextField muText
          Volume text field.
        • stiffness
          float stiffness
          stiffness.
        • stiffnessText
          JTextField stiffnessText
          Text field for getting stiffness for smoothing.
        • volumeLimit
          boolean volumeLimit
          flag indicates volume is greater than or equal to volumePercent.
        • volumePercent
          float volumePercent
          Volume percentage.
        • volumeText
          JTextField volumeText
          Volume text field.

    • Class gov.nih.mipav.view.dialogs.JDialogSnake

      class JDialogSnake extends JDialogBase implements Serializable
      serialVersionUID:
      -6160718529233426119L

      • Serialized Fields

        • boundaryDir
          int boundaryDir
          DOCUMENT ME!
        • boundaryDirBox
          JComboBox boundaryDirBox
          DOCUMENT ME!
        • boundaryIterations
          int boundaryIterations
          DOCUMENT ME!
        • groupNum
          int groupNum
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelCorrected
          JLabel labelCorrected
          DOCUMENT ME!
        • normFactor
          float normFactor
          DOCUMENT ME!
        • propagate
          JRadioButton propagate
          DOCUMENT ME!
        • propagationType
          int propagationType
          DOCUMENT ME!
        • removeOriginal
          boolean removeOriginal
          DOCUMENT ME!
        • removeOriginalCheckBox
          JCheckBox removeOriginalCheckBox
          DOCUMENT ME!
        • resolutionCheckbox
          JCheckBox resolutionCheckbox
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • scaleZ
          float scaleZ
          DOCUMENT ME!
        • singleSlice
          JRadioButton singleSlice
          DOCUMENT ME!
        • smoothness
          float smoothness
          DOCUMENT ME!
        • snakeAlgo
          AlgorithmSnake snakeAlgo
          DOCUMENT ME!
        • srcVOI
          VOI srcVOI
          DOCUMENT ME!
        • textBoundaryIterations
          JTextField textBoundaryIterations
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textGaussZ
          JTextField textGaussZ
          DOCUMENT ME!
        • textSmoothness
          JTextField textSmoothness
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • voiColor
          Color voiColor
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSobel

      class JDialogSobel extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • comboBoxKernelSize
          JComboBox comboBoxKernelSize
        • image
          ModelImage image
          DOCUMENT ME!
        • image25D
          boolean image25D
          Flag indicating if slices should be blurred independently.
        • image25DCheckbox
          JCheckBox image25DCheckbox
          DOCUMENT ME!
        • kernelSize
          int kernelSize
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sobelAlgo
          AlgorithmSobel sobelAlgo
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSpatialBroxOpticalFlow

      class JDialogSpatialBroxOpticalFlow extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogSpectralClustering

      class JDialogSpectralClustering extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • alg
          AlgorithmSpectralClustering alg
          handle to algorithm
        • blueBuffer
          float[] blueBuffer
        • br
          BufferedReader br
        • buttonImage
          JButton buttonImage
        • buttonPointsFile
          JButton buttonPointsFile
        • centroidPos
          double[][] centroidPos
        • directoryPoints
          String directoryPoints
        • extents
          int[] extents
        • fileNamePoints
          String fileNamePoints
        • filePoints
          File filePoints
        • greenBuffer
          float[] greenBuffer
        • groupNum
          int[] groupNum
        • havePoints
          boolean havePoints
        • image
          ModelImage image
          source image.
        • imageList
          JComboBox imageList
        • isMultifile
          boolean isMultifile
          boolean isMultifile
        • nDims
          int nDims
        • nPoints
          int nPoints
        • numberClusters
          int numberClusters
        • pos
          double[][] pos
        • redBuffer
          float[] redBuffer
        • resultImage
          ModelImage resultImage
          result image
        • resultsFileName
          String resultsFileName
        • resultsFileNameLabel
          JLabel resultsFileNameLabel
        • resultsFileNameText
          JTextField resultsFileNameText
        • scale
          double[] scale
        • scaleMax
          double scaleMax
        • scaleVariablesToUnitVariance
          boolean scaleVariablesToUnitVariance
        • textClusters
          JTextField textClusters
        • textImage
          JTextField textImage
        • textPointsFile
          JTextField textPointsFile
        • unitVarianceCheckBox
          JCheckBox unitVarianceCheckBox
        • weight
          double[] weight

    • Class gov.nih.mipav.view.dialogs.JDialogSphereGeneration

      class JDialogSphereGeneration extends JDialogBase implements Serializable
      serialVersionUID:
      0L

      • Serialized Fields

        • aggregatedButton
          JRadioButton aggregatedButton
        • constantButton
          JRadioButton constantButton
        • constrainedButton
          JRadioButton constrainedButton
        • extents
          int[] extents
        • highestForbiddenLabel
          JLabel highestForbiddenLabel
        • highestForbiddenNNDistance
          double highestForbiddenNNDistance
        • highestForbiddenText
          JTextField highestForbiddenText
        • highestRegenerationLabel
          JLabel highestRegenerationLabel
        • highestRegenerationNNDistance
          double highestRegenerationNNDistance
        • highestRegenerationText
          JTextField highestRegenerationText
        • initialRandomSpheres
          int initialRandomSpheres
        • initialSpheresLabel
          JLabel initialSpheresLabel
        • initialSpheresText
          JTextField initialSpheresText
        • lowestForbiddenLabel
          JLabel lowestForbiddenLabel
        • lowestForbiddenNNDistance
          double lowestForbiddenNNDistance
        • lowestForbiddenText
          JTextField lowestForbiddenText
        • maximumDistanceLabel
          JLabel maximumDistanceLabel
        • maximumDistanceText
          JTextField maximumDistanceText
        • maximumNearestNeighborDistance
          double maximumNearestNeighborDistance
        • maxRadius
          int maxRadius
        • maxRadiusLabel
          JLabel maxRadiusLabel
        • maxRadiusText
          JTextField maxRadiusText
        • minimumDistanceLabel
          JLabel minimumDistanceLabel
        • minimumDistanceText
          JTextField minimumDistanceText
        • minimumNearestNeighborDistance
          double minimumNearestNeighborDistance
        • minRadius
          int minRadius
        • numSpheres
          int numSpheres
        • numSpheresText
          JTextField numSpheresText
        • pattern
          int pattern
        • patternGroup
          ButtonGroup patternGroup
        • radiusDistribution
          int radiusDistribution
        • radiusGroup
          ButtonGroup radiusGroup
        • radiusLabel
          JLabel radiusLabel
        • radiusText
          JTextField radiusText
          DOCUMENT ME!
        • randomButton
          JRadioButton randomButton
        • regularButton
          JRadioButton regularButton
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sAlgo
          AlgorithmSphereGeneration sAlgo
          DOCUMENT ME!
        • uniformButton
          JRadioButton uniformButton
        • xDim
          int xDim
          DOCUMENT ME!
        • xDimText
          JTextField xDimText
          DOCUMENT ME!
        • yDim
          int yDim
          DOCUMENT ME!
        • yDimText
          JTextField yDimText
        • zDim
          int zDim
        • zDimText
          JTextField zDimText

    • Class gov.nih.mipav.view.dialogs.JDialogSplitAndMergeWatershed

      class JDialogSplitAndMergeWatershed extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • binCheckBox
          JCheckBox binCheckBox
        • binNumber
          int binNumber
        • createWatershedCheckBox
          JCheckBox createWatershedCheckBox
        • createWatershedLines
          boolean createWatershedLines
        • eightButton
          JRadioButton eightButton
        • fourButton
          JRadioButton fourButton
        • image
          ModelImage image
          DOCUMENT ME!
        • labelBins
          JLabel labelBins
        • labelThreshold
          JLabel labelThreshold
        • limitBins
          boolean limitBins
        • merge
          boolean merge
        • mergeCheckBox
          JCheckBox mergeCheckBox
        • mergeThreshold
          double mergeThreshold
        • neighborGroup
          ButtonGroup neighborGroup
        • neighborPanel
          JPanel neighborPanel
          DOCUMENT ME!
        • numNeighbor
          int numNeighbor
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textBins
          JTextField textBins
        • textThreshold
          JTextField textThreshold
        • watershedAlgo
          AlgorithmSplitAndMergeWatershed watershedAlgo
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogStandardDeviationThreshold

      class JDialogStandardDeviationThreshold extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • alg
          AlgorithmStandardDeviationThreshold alg
          handle to algorithm
        • algoVOI
          AlgorithmVOIProps algoVOI
          handle to algorithm
        • avgIntensity
          float avgIntensity
          average intensities in VOI
        • avgIntensityB
          float avgIntensityB
          average intensities in VOI
        • avgIntensityG
          float avgIntensityG
          average intensities in VOI
        • avgIntensityR
          float avgIntensityR
          average intensities in VOI
        • destinationPanel
          JPanel destinationPanel
          panels
        • destinationRadioGroup
          ButtonGroup destinationRadioGroup
          radio groups
        • groupNum
          int groupNum
          number for id of VOI
        • inverseThreshold
          boolean inverseThreshold
          boolean for inverse threshold
        • inverseThresholdCheckBox
          JCheckBox inverseThresholdCheckBox
          checkbox for inverse threshold
        • isColorImage
          boolean isColorImage
          boolean for color image
        • mainPanel
          JPanel mainPanel
          panels
        • maxIntensity
          float maxIntensity
          max intensities calculatd using std dev
        • maxIntensityB
          float maxIntensityB
          max intensities calculatd using std dev
        • maxIntensityG
          float maxIntensityG
          max intensities calculatd using std dev
        • maxIntensityR
          float maxIntensityR
          max intensities calculatd using std dev
        • minIntensity
          float minIntensity
          min intensities calculatd using std dev
        • minIntensityB
          float minIntensityB
          min intensities calculatd using std dev
        • minIntensityG
          float minIntensityG
          min intensities calculatd using std dev
        • minIntensityR
          float minIntensityR
          min intensities calculatd using std dev
        • newImageDestination
          boolean newImageDestination
          flags for destination and threshold
        • newImageRadio
          JRadioButton newImageRadio
          radio buttons
        • numPixels
          int numPixels
        • numStdDev
          float numStdDev
          number of standard deviations used in thresholding
        • numStdDevB
          float numStdDevB
          number of standard deviations used in thresholding
        • numStdDevG
          float numStdDevG
          number of standard deviations used in thresholding
        • numStdDevR
          float numStdDevR
          number of standard deviations used in thresholding
        • outMax
          double outMax
          image type max
        • outMin
          double outMin
          image type min
        • paintRadio
          JRadioButton paintRadio
          radio buttons
        • resultImage
          ModelImage resultImage
          src image, result image
        • scriptFail
          boolean scriptFail
          boolean telling if script failed
        • setMaxThresholdCheckBox
          JCheckBox setMaxThresholdCheckBox
          checkbox for inverse threshold
        • setMaxThresholdCheckBoxB
          JCheckBox setMaxThresholdCheckBoxB
          checkbox for inverse threshold
        • setMaxThresholdCheckBoxG
          JCheckBox setMaxThresholdCheckBoxG
          checkbox for inverse threshold
        • setMaxThresholdCheckBoxR
          JCheckBox setMaxThresholdCheckBoxR
          checkbox for inverse threshold
        • setMinThresholdCheckBox
          JCheckBox setMinThresholdCheckBox
          checkbox for inverse threshold
        • setMinThresholdCheckBoxB
          JCheckBox setMinThresholdCheckBoxB
          checkbox for inverse threshold
        • setMinThresholdCheckBoxG
          JCheckBox setMinThresholdCheckBoxG
          checkbox for inverse threshold
        • setMinThresholdCheckBoxR
          JCheckBox setMinThresholdCheckBoxR
          checkbox for inverse threshold
        • srcImage
          ModelImage srcImage
          src image, result image
        • srcVOI
          VOI srcVOI
          src VOI used for thresholding ME!
        • stdDev
          float stdDev
          standard deviations in VOI
        • stdDevB
          float stdDevB
          standard deviations in VOI
        • stdDevG
          float stdDevG
          standard deviations in VOI
        • stdDevR
          float stdDevR
          standard deviations in VOI
        • stdDevTextField
          JTextField stdDevTextField
          text fields
        • stdDevTextFieldB
          JTextField stdDevTextFieldB
          text fields
        • stdDevTextFieldG
          JTextField stdDevTextFieldG
          text fields
        • stdDevTextFieldR
          JTextField stdDevTextFieldR
          text fields
        • sumPixelInten
          double sumPixelInten
        • sumPixelIntenB
          double sumPixelIntenB
        • sumPixelIntenG
          double sumPixelIntenG
        • sumPixelIntenR
          double sumPixelIntenR
        • thresholdPanel
          JPanel thresholdPanel
          panels
        • thresholdParametersLeftPanel
          JPanel thresholdParametersLeftPanel
          panels
        • thresholdParametersPanel
          JPanel thresholdParametersPanel
          panels
        • thresholdParametersRightPanel
          JPanel thresholdParametersRightPanel
          panels
        • thresholdRadioGroup
          ButtonGroup thresholdRadioGroup
          radio groups
        • UI
          ViewUserInterface UI
          handle to UI
        • valuesOutside
          float valuesOutside
          intensity values to be used in thresholding
        • valuesOutsideB
          float valuesOutsideB
          intensity values to be used in thresholding
        • valuesOutsideG
          float valuesOutsideG
          intensity values to be used in thresholding
        • valuesOutsideR
          float valuesOutsideR
          intensity values to be used in thresholding
        • valuesOutsideTextField
          JTextField valuesOutsideTextField
          text fields
        • valuesOutsideTextFieldB
          JTextField valuesOutsideTextFieldB
          text fields
        • valuesOutsideTextFieldG
          JTextField valuesOutsideTextFieldG
          text fields
        • valuesOutsideTextFieldR
          JTextField valuesOutsideTextFieldR
          text fields
        • voiRegionsRadio
          JRadioButton voiRegionsRadio
          radio buttons
        • VOIs
          ViewVOIVector VOIs
          vois in image
        • voiStatsLeftPanel
          JPanel voiStatsLeftPanel
          panels
        • voiStatsPanel
          JPanel voiStatsPanel
          panels
        • voiStatsRightPanel
          JPanel voiStatsRightPanel
          panels
        • wholeImageRadio
          JRadioButton wholeImageRadio
          radio buttons
        • wholeImageThreshold
          boolean wholeImageThreshold
          flags for destination and threshold

    • Class gov.nih.mipav.view.dialogs.JDialogSubsample

      class JDialogSubsample extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3213495943646123969L

      • Serialized Fields

        • algoSub
          AlgorithmSubsample algoSub
          DOCUMENT ME!
        • by2Button
          JRadioButton by2Button
          DOCUMENT ME!
        • by4Button
          JRadioButton by4Button
          DOCUMENT ME!
        • by8Button
          JRadioButton by8Button
          DOCUMENT ME!
        • denom
          int denom
          DOCUMENT ME!
        • dim
          int dim
          Number of dimensions in an image e.g 2D, 3D
        • doPad
          boolean doPad
          The boolean value to determine whether to pad the original image or not.
        • doVOI
          boolean doVOI
          DOCUMENT ME!
        • extents
          int[] extents
          The extents of original image
        • image
          ModelImage image
          DOCUMENT ME!
        • label2OriginalExtentX
          JLabel label2OriginalExtentX
          Label for displaying the original extent X
        • label2OriginalExtentY
          JLabel label2OriginalExtentY
          Label for displaying the original extent Y
        • label2OriginalExtentZ
          JLabel label2OriginalExtentZ
          Label for displaying the original extent Z
        • labelPaddedExtentX
          JLabel labelPaddedExtentX
          Label for displaying the padded extent X
        • labelPaddedExtentY
          JLabel labelPaddedExtentY
          Label for displaying the padded extent Y
        • labelPaddedExtentZ
          JLabel labelPaddedExtentZ
          label for displaying the padded extent Z
        • newExtents
          int[] newExtents
          DOCUMENT ME!
        • oXres
          float oXres
          DOCUMENT ME!
        • oYres
          float oYres
          DOCUMENT ME!
        • oZres
          float oZres
          DOCUMENT ME!
        • padExtents
          int[] padExtents
          The extents of padded image
        • processIndep
          boolean processIndep
          DOCUMENT ME!
        • processIndepBox
          JCheckBox processIndepBox
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sigmas
          float[] sigmas
          DOCUMENT ME!
        • Sx
          float Sx
          DOCUMENT ME!
        • Sy
          float Sy
          DOCUMENT ME!
        • Sz
          float Sz
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • voiCheckBox
          JCheckBox voiCheckBox
          DOCUMENT ME!
        • xfrm
          TransMatrix xfrm
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSubset

      class JDialogSubset extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      7757821847126335458L

      • Serialized Fields

        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelSlice
          JLabel labelSlice
          DOCUMENT ME!
        • removeDim
          int removeDim
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • resultString
          String resultString
          DOCUMENT ME!
        • sliceNum
          int sliceNum
          DOCUMENT ME!
        • subsetAlgo
          AlgorithmSubset subsetAlgo
          DOCUMENT ME!
        • tButton
          JRadioButton tButton
          DOCUMENT ME!
        • textSlice
          JTextField textSlice
          DOCUMENT ME!
        • textString
          String textString
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • tSlices
          int tSlices
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • xButton
          JRadioButton xButton
          DOCUMENT ME!
        • xSlices
          int xSlices
          DOCUMENT ME!
        • yButton
          JRadioButton yButton
          DOCUMENT ME!
        • ySlices
          int ySlices
          DOCUMENT ME!
        • zButton
          JRadioButton zButton
          DOCUMENT ME!
        • zSlices
          int zSlices
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSubtractVOI

      class JDialogSubtractVOI extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3133054636469390689L

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogSurfaceReconstruction

      class JDialogSurfaceReconstruction extends JDialogBase implements Serializable

      • Serialized Fields

        • BallPivotingPanel
          JPanel BallPivotingPanel
        • buttonInputFile
          JButton buttonInputFile
        • buttonOutputFile
          JButton buttonOutputFile
        • buttonPanel
          JPanel buttonPanel
          Button panel to hold the OK button, Cancel button, and Help button.
        • chooser
          JFileChooser chooser
        • directoryInput
          String directoryInput
        • directoryOutput
          String directoryOutput
        • file_suffix
          String file_suffix
        • fileNameInput
          String fileNameInput
        • fileNameOutput
          String fileNameOutput
        • msgPanel
          JPanel msgPanel
          Msg box to show the Prostate surface analysis related info.
        • plyInputFilePanel
          JPanel plyInputFilePanel
        • plyOutputFilePanel
          JPanel plyOutputFilePanel
        • PoissonPanel
          JPanel PoissonPanel
        • textFieldAngleThreshold
          JTextField textFieldAngleThreshold
        • textFieldBallRadius
          JTextField textFieldBallRadius
        • textFieldClusteringRadius
          JTextField textFieldClusteringRadius
        • textFieldInputFile
          JTextField textFieldInputFile
        • textFieldOutputFile
          JTextField textFieldOutputFile
        • textOctreeDepth
          JTextField textOctreeDepth
        • textSamplePerNode
          JTextField textSamplePerNode
        • textSolverDivide
          JTextField textSolverDivide
        • UI
          ViewUserInterface UI

    • Class gov.nih.mipav.view.dialogs.JDialogSwap34

      class JDialogSwap34 extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8107279710815271509L

      • Serialized Fields

        • doClose
          boolean doClose
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageName
          String imageName
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • swap34Algo
          AlgorithmSwap34 swap34Algo
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogSwapDims

      class JDialogSwapDims extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8107279710815271509L

      • Serialized Fields

        • doClose
          boolean doClose
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • imageName
          String imageName
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • swapDimsAlgo
          AlgorithmSwapDims swapDimsAlgo
          DOCUMENT ME!
        • swapType
          int swapType

    • Class gov.nih.mipav.view.dialogs.JDialogSwapSlicesVolumes

      class JDialogSwapSlicesVolumes extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • appendButton
          JButton appendButton
          Button for appending selected rows to end of JTable
        • displayTable
          JTable displayTable
          The visible JTable for slice/volume reordering
        • inPlace
          boolean inPlace
          Whether to perform alg in place
        • mode
          JDialogSwapSlicesVolumes.SwapMode mode
          Swap mode, either 3D or 4D
        • newImage
          JRadioButton newImage
          Radio buttons for alg output options.
        • nSlices
          int nSlices
          Number of slices in mode
        • replaceImage
          JRadioButton replaceImage
          Radio buttons for alg output options.
        • sliceRenum
          int[][] sliceRenum
          Reordering of slices/volumes
        • srcImage
          ModelImage srcImage
          srcImage for keeping track of slices
        • swapAlgo
          AlgorithmSwapSlicesVolume swapAlgo
          Running algorithm
        • swapVolume
          ModelImage swapVolume
          Result image
        • undoModel
          DefaultTableModel undoModel
          Model to restore last model of JTable

    • Class gov.nih.mipav.view.dialogs.JDialogSWI

      class JDialogSWI extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • doErnst
          boolean doErnst
          The variable representing whether the blur should be performed.
        • guiBuilder
          GuiBuilder guiBuilder
        • image
          ModelImage image
          This source image is typically set by the constructor
        • magImage
          ModelImage magImage
        • magnitudeCombo
          JComboBox magnitudeCombo
        • maskThreshold
          double maskThreshold
        • maskThresholdField
          JTextField maskThresholdField
        • multFactor
          int multFactor
        • multFactorField
          JTextField multFactorField
        • phaseCombo
          JComboBox phaseCombo
        • phaseImage
          ModelImage phaseImage
        • resultImage
          ModelImage resultImage
          Result image.
        • resultImageName
          String resultImageName
        • showInterImages
          boolean showInterImages
        • showInterImagesBox
          JCheckBox showInterImagesBox
        • swiAlgo
          AlgorithmSWI swiAlgo
          This is the SWIs algorithm
        • titles
          String[] titles
        • xFilterSize
          int xFilterSize
        • xFilterSizeField
          JTextField xFilterSizeField
        • yFilterSize
          int yFilterSize
        • yFilterSizeField
          JTextField yFilterSizeField

    • Class gov.nih.mipav.view.dialogs.JDialogSymmetricNearestNeighbor

      class JDialogSymmetricNearestNeighbor extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogTalairach

      class JDialogTalairach extends JDialogBase implements Serializable
      serialVersionUID:
      -2923298916025034767L

      • Serialized Fields

        • anteriorPt
          JRadioButton anteriorPt
          DOCUMENT ME!
        • anteriorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt3Df
          DOCUMENT ME!
        • applyTalairachButton
          JButton applyTalairachButton
          DOCUMENT ME!
        • cancelTalairachButton
          JButton cancelTalairachButton
          DOCUMENT ME!
        • clearTalairachButton
          JButton clearTalairachButton
          DOCUMENT ME!
        • frame
          ViewJFrameTriImage frame
          DOCUMENT ME!
        • haveAnteriorPt
          boolean haveAnteriorPt
          DOCUMENT ME!
        • haveInferiorPt
          boolean haveInferiorPt
          DOCUMENT ME!
        • haveLeftPt
          boolean haveLeftPt
          DOCUMENT ME!
        • havePosteriorPt
          boolean havePosteriorPt
          DOCUMENT ME!
        • haveRightPt
          boolean haveRightPt
          DOCUMENT ME!
        • haveSuperiorPt
          boolean haveSuperiorPt
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • inferiorPt
          JRadioButton inferiorPt
          DOCUMENT ME!
        • inferiorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt3Df
          DOCUMENT ME!
        • leftPt
          JRadioButton leftPt
          DOCUMENT ME!
        • leftPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f leftPt3Df
          DOCUMENT ME!
        • posteriorPt
          JRadioButton posteriorPt
          DOCUMENT ME!
        • posteriorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt3Df
          DOCUMENT ME!
        • rightPt
          JRadioButton rightPt
          DOCUMENT ME!
        • rightPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f rightPt3Df
          DOCUMENT ME!
        • setTalairachButton
          JButton setTalairachButton
          DOCUMENT ME!
        • superiorPt
          JRadioButton superiorPt
          DOCUMENT ME!
        • superiorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f superiorPt3Df
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTalairachTransform

      class JDialogTalairachTransform extends JDialogBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogTamuraTexture

      class JDialogTamuraTexture extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • blueButton
          JRadioButton blueButton
          DOCUMENT ME!
        • coarsenessCheckBox
          JCheckBox coarsenessCheckBox
        • coarsenessThreshold
          double coarsenessThreshold
          coarsenessThreshold must be invalid input: '<'= 1.0. If coarsenessThreshold invalid input: '<' 1.0, select the largest k for which Ek >= coarsenessThreshold * Emax. If coarsenessThreshold = 1.0, select the largest k which gives Emax.
        • colorGroup
          ButtonGroup colorGroup
          DOCUMENT ME!
        • colorPanel
          JPanel colorPanel
          DOCUMENT ME!
        • contrastCheckBox
          JCheckBox contrastCheckBox
        • cSize
          int cSize
        • directionalityCheckBox
          JCheckBox directionalityCheckBox
        • doCoarseness
          boolean doCoarseness
        • doContrast
          boolean doContrast
        • doDirectionality
          boolean doDirectionality
        • greenButton
          JRadioButton greenButton
          DOCUMENT ME!
        • histogramBins
          int histogramBins
        • histogramThreshold
          double histogramThreshold
        • image
          ModelImage image
          DOCUMENT ME!
        • labelCoarsenessThreshold
          JLabel labelCoarsenessThreshold
        • labelCSize
          JLabel labelCSize
        • labelHistogramBins
          JLabel labelHistogramBins
        • labelHistogramThreshold
          JLabel labelHistogramThreshold
        • numOperators
          int numOperators
          DOCUMENT ME!
        • redButton
          JRadioButton redButton
          DOCUMENT ME!
        • resultImage
          ModelImage[] resultImage
          DOCUMENT ME!
        • RGBOffset
          int RGBOffset
          DOCUMENT ME!
        • textCoarsenessThreshold
          JTextField textCoarsenessThreshold
        • textCSize
          JTextField textCSize
        • textHistogramBins
          JTextField textHistogramBins
        • textHistogramThreshold
          JTextField textHistogramThreshold
        • textureAlgo
          AlgorithmTamuraTexture textureAlgo
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTemporalBroxOpticalFlow

      class JDialogTemporalBroxOpticalFlow extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogText

      class JDialogText extends JDialogBase implements Serializable
      serialVersionUID:
      3861014709972568409L

      • Serialized Fields

        • buttonPanel
          JPanel buttonPanel
          DOCUMENT ME!
        • DEFAULT_SIZE
          Dimension DEFAULT_SIZE
          Describes the initial size of the textual display area when the dialog is created. The value is given in pixel size rather than the number of characters since the display area has no characters to display.
        • followingScroll
          boolean followingScroll
          DOCUMENT ME!
        • message
          StringBuffer message
          DOCUMENT ME!
        • scrollPane
          JScrollPane scrollPane
          DOCUMENT ME!
        • textArea
          JEditorPane textArea
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTextGE

      class JDialogTextGE extends JDialogText implements Serializable
      serialVersionUID:
      419753934724528702L

      • Serialized Fields

        • convertButton
          JButton convertButton
          DOCUMENT ME!
        • fileInfo
          FileInfoBase[] fileInfo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • slice
          int slice
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTextGE4X

      class JDialogTextGE4X extends JDialogText implements Serializable

      • Serialized Fields

        • convertButton
          JButton convertButton
          DOCUMENT ME!
        • fileInfo
          FileInfoBase[] fileInfo
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • slice
          int slice
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTextureAnalysis

      class JDialogTextureAnalysis extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogTextureSegmentation

      class JDialogTextureSegmentation extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • contourButton
          JRadioButton contourButton
        • contourMask
          BitSet contourMask
        • destImage
          ModelImage destImage
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelSegmentNumber
          JLabel labelSegmentNumber
        • labelWindowSize
          JLabel labelWindowSize
        • nonNegativity
          boolean nonNegativity
        • nonNegativityCheckBox
          JCheckBox nonNegativityCheckBox
        • noVOIsButton
          JRadioButton noVOIsButton
        • pointButton
          JRadioButton pointButton
        • pt
          WildMagic.LibFoundation.Mathematics.Vector3f[] pt
        • removeSmallRegions
          boolean removeSmallRegions
        • removeSmallRegionsCheckBox
          JCheckBox removeSmallRegionsCheckBox
        • segmentCheckBox
          JCheckBox segmentCheckBox
        • segmentNumber
          int segmentNumber
        • textSegmentNumber
          JTextField textSegmentNumber
        • textureSegAlgo
          AlgorithmTextureSegmentation textureSegAlgo
          DOCUMENT ME!
        • textWindowSize
          JTextField textWindowSize
        • useContours
          boolean useContours
        • usePoints
          boolean usePoints
        • VOIGroup
          ButtonGroup VOIGroup
        • windowSize
          int windowSize

    • Class gov.nih.mipav.view.dialogs.JDialogThinning2D

      class JDialogThinning2D extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogThreshold

      class JDialogThreshold extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8143576591075984708L

      • Serialized Fields

        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • fillValue
          float fillValue
          DOCUMENT ME!
        • histogram
          ModelHistogram histogram
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • inverseCheckbox
          JCheckBox inverseCheckbox
          DOCUMENT ME!
        • isInverse
          boolean isInverse
          DOCUMENT ME!
        • labelThres2
          JLabel labelThres2
          DOCUMENT ME!
        • max
          float max
          DOCUMENT ME!
        • maxEntCheckbox
          JCheckBox maxEntCheckbox
          DOCUMENT ME!
        • min
          float min
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • otsuCheckbox
          JCheckBox otsuCheckbox
          DOCUMENT ME!
        • outMax
          double outMax
          DOCUMENT ME!
        • outMin
          double outMin
          DOCUMENT ME!
        • outputBox
          JComboBox outputBox
          Holds the choices for the outputType.
        • outputType
          int outputType
          Same data-type, binary, or unsigned byte mask.
        • regionFlag
          boolean regionFlag
          or if the source image is to be replaced.
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textFill
          JTextField textFill
          DOCUMENT ME!
        • textThres1
          JTextField textThres1
          DOCUMENT ME!
        • textThres2
          JTextField textThres2
          DOCUMENT ME!
        • thres1
          float thres1
          DOCUMENT ME!
        • thres2
          float thres2
          DOCUMENT ME!
        • thresholdAlgo
          AlgorithmThresholdDual thresholdAlgo
          DOCUMENT ME!
        • thresholdType
          int thresholdType
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogThreshold.CheckValueAction

      class CheckValueAction extends AbstractAction implements Serializable
      serialVersionUID:
      -1531686009578681460L

    • Class gov.nih.mipav.view.dialogs.JDialogThresholdLUT

      class JDialogThresholdLUT extends JDialogBase implements Serializable
      serialVersionUID:
      -3705234971745674752L

      • Serialized Fields

        • fillValue
          float fillValue
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelMax
          JLabel labelMax
          DOCUMENT ME!
        • labelMin
          JLabel labelMin
          DOCUMENT ME!
        • lowerThreshold
          float lowerThreshold
          DOCUMENT ME!
        • outputType
          int outputType
          DOCUMENT ME!
        • radioBinary
          JRadioButton radioBinary
          DOCUMENT ME!
        • radioRange
          JRadioButton radioRange
          DOCUMENT ME!
        • radioThresh
          JRadioButton radioThresh
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textFill
          JTextField textFill
          DOCUMENT ME!
        • textMax
          JTextField textMax
          DOCUMENT ME!
        • textMin
          JTextField textMin
          DOCUMENT ME!
        • thresholdAlgo
          AlgorithmThresholdDual thresholdAlgo
          DOCUMENT ME!
        • upperThreshold
          float upperThreshold
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogThresholdRGB

      class JDialogThresholdRGB extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      1903960650432668714L

      • Serialized Fields

        • applyToAllBox
          JCheckBox applyToAllBox
          false = apply algorithm only to VOI regions apply same threshold to all.
        • applyToBlueBox
          JCheckBox applyToBlueBox
          enable blue threshold.
        • applyToGreenBox
          JCheckBox applyToGreenBox
          enable green threshold.
        • applyToRedBox
          JCheckBox applyToRedBox
          enable red threshold.
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • fillValues
          float[] fillValues
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • inverseOptionBox
          JCheckBox inverseOptionBox
          choose inverse or no inverse threshold.
        • isInverse
          boolean isInverse
          inverse?
        • maxs
          float[] maxs
          DOCUMENT ME!
        • mins
          float[] mins
          Minimum and maximum values for red/gree/blue.
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • regionFlag
          boolean regionFlag
          or if the source image is to be replaced.
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textFills
          JTextField[] textFills
          DOCUMENT ME!
        • textThreshold1
          JTextField[] textThreshold1
          Text fields for lower invalid input: '&' upper thresholds and fill values.
        • textThreshold2
          JTextField[] textThreshold2
          DOCUMENT ME!
        • thresholdAlgoRGB
          AlgorithmThresholdDualRGB thresholdAlgoRGB
          DOCUMENT ME!
        • thresholdB
          float[] thresholdB
          DOCUMENT ME!
        • thresholdG
          float[] thresholdG
          DOCUMENT ME!
        • thresholdLabels1
          JLabel[] thresholdLabels1
          DOCUMENT ME!
        • thresholdLabels2
          JLabel[] thresholdLabels2
          DOCUMENT ME!
        • thresholdR
          float[] thresholdR
          lower [0] and upper [1] thresholds for RGB.
        • titles
          String[] titles
          DOCUMENT ME!
        • useChannel
          boolean[] useChannel
          tells whether or not to use the channels (red=0, green=1, blue=2).
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • VOIRegions
          JRadioButton VOIRegions
          DOCUMENT ME!
        • wholeImage
          JRadioButton wholeImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTiltCorrection

      class JDialogTiltCorrection extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • destinationGroup
          ButtonGroup destinationGroup
          DOCUMENT ME!
        • destinationPanel
          JPanel destinationPanel
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • helicalButton
          JRadioButton helicalButton
        • image
          ModelImage image
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • nonHelical
          boolean nonHelical
          Use serialVersionUID for interoperability.
        • nonHelicalButton
          JRadioButton nonHelicalButton
        • optionsPanel
          JPanel optionsPanel
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • textAngle
          JTextField textAngle
          DOCUMENT ME!
        • tiltAlgo
          AlgorithmTiltCorrection tiltAlgo
          DOCUMENT ME!
        • tiltAngle
          double tiltAngle
        • titles
          String[] titles
          DOCUMENT ME!
        • typeGroup
          ButtonGroup typeGroup
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTimeFitting

      class JDialogTimeFitting extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogTLRC

      class JDialogTLRC extends JDialogBase implements Serializable

      • Serialized Fields

        • acpcImage
          ModelImage acpcImage
        • anteriorPt
          JRadioButton anteriorPt
        • anteriorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt3Df
        • applyTalairachButton
          JButton applyTalairachButton
        • cancelTalairachButton
          JButton cancelTalairachButton
        • clearTalairachButton
          JButton clearTalairachButton
        • frame
          ViewJFrameTriImage frame
        • haveAnteriorPt
          boolean haveAnteriorPt
        • haveInferiorPt
          boolean haveInferiorPt
        • haveLeftPt
          boolean haveLeftPt
        • havePosteriorPt
          boolean havePosteriorPt
        • haveRightPt
          boolean haveRightPt
        • haveSuperiorPt
          boolean haveSuperiorPt
        • inferiorPt
          JRadioButton inferiorPt
        • inferiorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt3Df
        • interpolation
          int interpolation
        • leftPt
          JRadioButton leftPt
        • leftPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f leftPt3Df
        • originalImage
          ModelImage originalImage
        • posteriorPt
          JRadioButton posteriorPt
        • posteriorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt3Df
        • rightPt
          JRadioButton rightPt
        • rightPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f rightPt3Df
        • setTalairachButton
          JButton setTalairachButton
        • superiorPt
          JRadioButton superiorPt
        • superiorPt3Df
          WildMagic.LibFoundation.Mathematics.Vector3f superiorPt3Df
        • talairachImage
          ModelImage talairachImage
        • transform
          TalairachTransformInfo transform

    • Class gov.nih.mipav.view.dialogs.JDialogTopHat

      class JDialogTopHat extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogTransformBSpline

      class JDialogTransformBSpline extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      3877682545436641450L

      • Serialized Fields

        • algoTrans
          AlgorithmTransformBSpline algoTrans
          DOCUMENT ME!
        • chooserButton
          JButton chooserButton
          DOCUMENT ME!
        • controlMat
          float[][] controlMat
          DOCUMENT ME!
        • controlMat25D
          float[][][] controlMat25D
          DOCUMENT ME!
        • destExtents
          int[] destExtents
          DOCUMENT ME!
        • destMinExtent
          int destMinExtent
          DOCUMENT ME!
        • directory
          String directory
        • have25D
          boolean have25D
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • model
          DefaultListModel model
          DOCUMENT ME!
        • nDims
          int nDims
          DOCUMENT ME!
        • nltFile
          File nltFile
        • nltName
          String nltName
          DOCUMENT ME!
        • numberSlices
          int numberSlices
          DOCUMENT ME!
        • numControlPoints
          int numControlPoints
          DOCUMENT ME!
        • removeButton
          JButton removeButton
          DOCUMENT ME!
        • resolutions
          float[] resolutions
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • splineDegree
          int splineDegree
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTransformVOI

      class JDialogTransformVOI extends JDialogBase implements Serializable
      serialVersionUID:
      -8451501816656567049L

    • Class gov.nih.mipav.view.dialogs.JDialogTreMethod

      class JDialogTreMethod extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • bottomLeftBox
          JCheckBox bottomLeftBox
        • bottomRightBox
          JCheckBox bottomRightBox
        • generalThresholdPanel
          JPanel generalThresholdPanel
        • guiBuilder
          GuiBuilder guiBuilder
        • hardCheckBox
          JRadioButton hardCheckBox
        • hardNoiseField
          JTextField hardNoiseField
        • hardNoiseThreshold
          float hardNoiseThreshold
        • lowerLeftCorner
          boolean lowerLeftCorner
        • lowerRightCorner
          boolean lowerRightCorner
        • noCheckBox
          JRadioButton noCheckBox
        • noiseScale
          float noiseScale
        • smartCheckBox
          JRadioButton smartCheckBox
        • smartNoiseField
          JTextField smartNoiseField
        • thresholdGroup
          ButtonGroup thresholdGroup
        • thresholdMethod
          AlgorithmTreParams.Threshold thresholdMethod
        • topLeftBox
          JCheckBox topLeftBox
        • topRightBox
          JCheckBox topRightBox
        • totalThreshold
          JPanel totalThreshold
        • upperLeftCorner
          boolean upperLeftCorner
          Whether, during "smart-thresholding", noise should be calculated from a given corner
        • upperRightCorner
          boolean upperRightCorner

    • Class gov.nih.mipav.view.dialogs.JDialogTreT1

      class JDialogTreT1 extends JDialogTreMethod implements Serializable

      • Serialized Fields

        • angleIncrement
          double angleIncrement
        • b1Field
          JComboBox b1Field
        • b1ImageIndex
          int b1ImageIndex
        • calculateM0
          boolean calculateM0
        • calculateT1
          boolean calculateT1
          The list of possible maps that can be calculated
        • cAlgo
          AlgorithmTreT1 cAlgo
        • convFAFieldAr
          JTextField[] convFAFieldAr
        • convimageComboAr
          JComboBox[] convimageComboAr
        • convRepTime
          JTextField convRepTime
        • convSpec
          JPanel convSpec
        • direction
          int[] direction
        • doConvTre
          JRadioButton doConvTre
        • doHifiTre
          JRadioButton doHifiTre
        • doubleInvRadio
          JRadioButton doubleInvRadio
        • estimates
          double[] estimates
        • fieldStrengthGroup
          ButtonGroup fieldStrengthGroup
        • flipAngleAr
          JTextField[] flipAngleAr
        • hifiPanel
          JPanel hifiPanel
        • hifiSpec
          JPanel hifiSpec
        • inversionGroup
          ButtonGroup inversionGroup
        • inversionType
          AlgorithmTreParams.InversionType inversionType
        • invertT1toR1
          boolean invertT1toR1
        • irspgrCombo
          JComboBox[] irspgrCombo
        • irspgrData
          double[] irspgrData
        • irspgrFA
          double irspgrFA
        • irspgrFAField
          JTextField irspgrFAField
        • irspgrField
          JTextField[] irspgrField
        • irspgrGeneralPanel
          JPanel irspgrGeneralPanel
        • irspgrImageIndex
          int[] irspgrImageIndex
        • irspgrKy
          double irspgrKy
        • irspgrNum
          JTextField irspgrNum
        • irspgrPanel
          JScrollPane irspgrPanel
        • irspgrTI
          double[] irspgrTI
        • irspgrTr
          double[] irspgrTr
        • irspgrTR
          double irspgrTR
        • irspgrTRField
          JTextField irspgrTRField
        • isGEButton
          JRadioButton isGEButton
        • isSiemensButton
          JRadioButton isSiemensButton
        • leastSquaresCheck
          JCheckBox leastSquaresCheck
        • maxAngle
          double maxAngle
        • maxM0
          double maxM0
        • maxM0Field
          JTextField maxM0Field
        • maxT1
          double maxT1
        • maxT1Field
          JTextField maxT1Field
        • mriStrength
          AlgorithmTreParams.FieldStrength mriStrength
          The following GUI choices change algorithm operation using enums
        • Nsa
          int Nsa
        • Nti
          int Nti
        • numSlicesField
          JTextField numSlicesField
        • performStraightTreT1
          boolean performStraightTreT1
        • performTreT1HIFI
          boolean performTreT1HIFI
        • performTreT1withPreCalculatedB1Map
          boolean performTreT1withPreCalculatedB1Map
        • pointScale
          double pointScale
        • residuals
          double[] residuals
        • scale
          double scale
        • scaleIncrement
          double scaleIncrement
        • scannerType
          AlgorithmTreParams.ScannerType scannerType
        • showB1Check
          JCheckBox showB1Check
        • showB1Map
          boolean showB1Map
        • showM0Map
          JCheckBox showM0Map
        • showR1Map
          JCheckBox showR1Map
        • showT1Map
          JCheckBox showT1Map
        • singleInvRadio
          JRadioButton singleInvRadio
        • smoothB1Box
          JCheckBox smoothB1Box
        • smoothB1Field
          boolean smoothB1Field
        • spgrData
          double[] spgrData
        • spgrImageComboBoxAr
          JComboBox[] spgrImageComboBoxAr
        • spgrImageIndex
          int[] spgrImageIndex
        • spgrNumFA
          JTextField spgrNumFA
        • spgrPanel
          JScrollPane spgrPanel
        • spgrRepTime
          JTextField spgrRepTime
        • straightPanel
          JPanel straightPanel
        • t15Radio
          JRadioButton t15Radio
        • t30Radio
          JRadioButton t30Radio
        • tab
          JTabbedPane tab
        • titles
          String[] titles
          The GUI list of images
        • treFA
          double[] treFA
        • treLong
          JScrollPane treLong
        • treTR
          double treTR
        • uniformAngleSpacing
          boolean uniformAngleSpacing
        • useB1Map
          JCheckBox useB1Map
        • useWeights
          boolean useWeights
        • wList
          String[] wList
          The ordered list of images that the algorithm is dependent on.

    • Class gov.nih.mipav.view.dialogs.JDialogTreT2

      class JDialogTreT2 extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      8406327135505127177L

      • Serialized Fields

        • b1ImageIndex
          int b1ImageIndex
        • bestToWorst
          int[] bestToWorst
        • calculateB0
          boolean calculateB0
        • calculateM0
          boolean calculateM0
        • calculateT2
          boolean calculateT2
        • cAlgo
          AlgorithmTreT2 cAlgo
        • contraction
          double[] contraction
        • expansion
          double[] expansion
        • geScanner
          boolean geScanner
        • hardNoiseThreshold
          float hardNoiseThreshold
        • includeB1Map
          boolean includeB1Map
        • invertT2toR2
          boolean invertT2toR2
        • lowerLeftCorner
          boolean lowerLeftCorner
        • lowerRightCorner
          boolean lowerRightCorner
        • maxM0
          double maxM0
        • maxT2
          double maxT2
        • modelingComboBox
          JComboBox modelingComboBox
        • Nfa_phase0
          int Nfa_phase0
        • Nfa_phase180
          int Nfa_phase180
        • noiseScale
          float noiseScale
        • performApproxModeling
          boolean performApproxModeling
        • performConventionalModeling
          boolean performConventionalModeling
        • performConventionalWith0Phase
          boolean performConventionalWith0Phase
        • performConventionalWith180Phase
          boolean performConventionalWith180Phase
        • performFullModeling
          boolean performFullModeling
        • phaseRadios
          ArrayList<JRadioButton> phaseRadios
        • reflection
          double[] reflection
        • shrink
          double[] shrink
        • siemensScanner
          boolean siemensScanner
        • simplex
          double[][] simplex
        • simplexCentre
          double[] simplexCentre
        • simplexLineValues
          double[] simplexLineValues
        • simplexResiduals
          double[] simplexResiduals
        • ssfpImageIndex_phase0
          int[] ssfpImageIndex_phase0
        • ssfpImageIndex_phase180
          int[] ssfpImageIndex_phase180
        • t1ImageIndex
          int t1ImageIndex
        • treFA_phase0
          double[] treFA_phase0
        • treFA_phase180
          double[] treFA_phase180
        • treTR
          double treTR
        • twoPContraction
          double[] twoPContraction
        • twoPExpansion
          double[] twoPExpansion
        • twoPReflection
          double[] twoPReflection
        • twoPShrink
          double[] twoPShrink
        • twoPSimplex
          double[][] twoPSimplex
        • twoPSimplexCentre
          double[] twoPSimplexCentre
        • twoPSimplexLineValues
          double[] twoPSimplexLineValues
        • twoPSimplexResiduals
          double[] twoPSimplexResiduals
        • upperLeftCorner
          boolean upperLeftCorner
        • upperRightCorner
          boolean upperRightCorner
        • useHardThresholding
          boolean useHardThresholding
        • useSmartThresholding
          boolean useSmartThresholding
        • wList
          String[] wList

    • Class gov.nih.mipav.view.dialogs.JDialogTriFrameLinker

      class JDialogTriFrameLinker extends JDialogBase implements Serializable
      serialVersionUID:
      -4546169496119216251L

    • Class gov.nih.mipav.view.dialogs.JDialogTriImageTransformation

      class JDialogTriImageTransformation extends JDialogBase implements Serializable
      serialVersionUID:
      -6567165297005633024L

      • Serialized Fields

        • boxIndex
          int boxIndex
          DOCUMENT ME!
        • centerGroup
          ButtonGroup centerGroup
        • centerX
          double centerX
          angles are passed to setRotate.
        • centerY
          double centerY
          angles are passed to setRotate.
        • centerZ
          double centerZ
          angles are passed to setRotate.
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • crosshairButton
          JRadioButton crosshairButton
        • frame
          ViewJFrameTriImage frame
          Pointer back to frame that called this.
        • imageA
          ModelImage imageA
          Image to transform.
        • imageB
          ModelImage imageB
          Image B to transform, can be null.
        • imageCenterButton
          JRadioButton imageCenterButton
        • originButton
          JRadioButton originButton
        • progressBar
          ViewJProgressBar progressBar
          Progress bar.
        • protractorCommonVertexButton
          JRadioButton protractorCommonVertexButton
        • thetaXY
          double thetaXY
          DOCUMENT ME!
        • thetaXZ
          double thetaXZ
          DOCUMENT ME!
        • thetaZY
          double thetaZY
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogTrilateralFilter

      class JDialogTrilateralFilter extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogTrim

      class JDialogTrim extends JDialogBase implements Serializable
      serialVersionUID:
      2967441574461453380L

      • Serialized Fields

        • activeImage
          ModelImage activeImage
          The currently selected image
        • maskCurrent
          JLabel maskCurrent
          Labels for values of the mask trim points property
        • maskMaximum
          JLabel maskMaximum
          Labels for values of the mask trim points property
        • maskMinimum
          JLabel maskMinimum
          Labels for values of the mask trim points property
        • maskTrimSlider
          JSlider maskTrimSlider
          Sliders for setting the mask and voi trim parameters
        • trimCheckbox
          JCheckBox trimCheckbox
          Checkbox for whether adjacent points are trimmed
        • voiCurrent
          JLabel voiCurrent
          Labels for values of the voi trim points property
        • voiMaximum
          JLabel voiMaximum
          Labels for values of the voi trim points property
        • voiMinimum
          JLabel voiMinimum
          Labels for values of the voi trim points property
        • voiTrimSlider
          JSlider voiTrimSlider
          Sliders for setting the mask and voi trim parameters

    • Class gov.nih.mipav.view.dialogs.JDialogTVL1FLOW

      class JDialogTVL1FLOW extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogTwoMRIImagesSNR

      class JDialogTwoMRIImagesSNR extends JDialogBase implements Serializable
      serialVersionUID:
      -2992719068907961685L

      • Serialized Fields

        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • componentImage
          ViewJComponentEditImage componentImage
          DOCUMENT ME!
        • componentImage2
          ViewJComponentEditImage componentImage2
          DOCUMENT ME!
        • cost
          int cost
          DOCUMENT ME!
        • createRegCheckBox
          JCheckBox createRegCheckBox
          DOCUMENT ME!
        • createRegImage
          boolean createRegImage
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • image2
          ModelImage image2
          DOCUMENT ME!
        • imageComboBox
          JComboBox imageComboBox
          DOCUMENT ME!
        • labelCost
          JLabel labelCost
          DOCUMENT ME!
        • nBoundingVOIs
          int nBoundingVOIs
          DOCUMENT ME!
        • regCheckBox
          JCheckBox regCheckBox
          DOCUMENT ME!
        • register
          boolean register
          DOCUMENT ME!
        • signal2Button
          JRadioButton signal2Button
          DOCUMENT ME!
        • signal2Image
          int signal2Image
          DOCUMENT ME!
        • signal2Index
          int signal2Index
          DOCUMENT ME!
        • signalButton
          JRadioButton signalButton
          DOCUMENT ME!
        • signalImage
          int signalImage
          DOCUMENT ME!
        • signalIndex
          int signalIndex
          DOCUMENT ME!
        • snrAlgo
          AlgorithmTwoMRIImagesSNR snrAlgo
          DOCUMENT ME!
        • UI
          ViewUserInterface UI
          DOCUMENT ME!
        • VOIGroup
          ButtonGroup VOIGroup
          DOCUMENT ME!
        • VOIs
          ViewVOIVector VOIs
          DOCUMENT ME!
        • VOIs2
          ViewVOIVector VOIs2
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogUltErode

      class JDialogUltErode extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -7439335499053110688L

    • Class gov.nih.mipav.view.dialogs.JDialogUninstallPlugin

      class JDialogUninstallPlugin extends JDialogBase implements Serializable
      serialVersionUID:
      -8736744495208652866L

      • Serialized Fields

        • pluginTree
          JTree pluginTree
          The JTree that describes the plugin structure
        • ui
          ViewUserInterface ui
          The main user interface

    • Class gov.nih.mipav.view.dialogs.JDialogUnionFindComponentLabelling

      class JDialogUnionFindComponentLabelling extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogUnionFindWatershed

      class JDialogUnionFindWatershed extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogUnknownIO

      class JDialogUnknownIO extends JDialogBase implements Serializable
      serialVersionUID:
      960085709232971480L

      • Serialized Fields

        • imageType
          int imageType
          DOCUMENT ME!
        • list
          JList list
          DOCUMENT ME!
        • suffix
          String suffix
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogUnsharpMask

      class JDialogUnsharpMask extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -3776616289889677111L

    • Class gov.nih.mipav.view.dialogs.JDialogVABRA

      class JDialogVABRA extends JDialogBase implements Serializable
      serialVersionUID:
      6730316616430519395L

      • Serialized Fields

        • comboBoxImage
          JComboBox comboBoxImage
          drop-down box for selecting available images
        • imageA
          ModelImage imageA
          source image.
        • imageB
          ModelImage imageB
          target image

    • Class gov.nih.mipav.view.dialogs.JDialogVesselEnhancement

      class JDialogVesselEnhancement extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • alpha
          double alpha
        • beta
          double beta
        • c
          double c
        • gamma
          double gamma
        • image
          ModelImage image
          DOCUMENT ME!
        • is2D
          boolean is2D
        • nScales
          int nScales
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • sigma
          double[][] sigma
        • sigmaMaxX
          double sigmaMaxX
        • sigmaMaxY
          double sigmaMaxY
        • sigmaMaxZ
          double sigmaMaxZ
        • sigmaMinX
          double sigmaMinX
        • sigmaMinY
          double sigmaMinY
        • sigmaMinZ
          double sigmaMinZ
        • textAlpha
          JTextField textAlpha
        • textBeta
          JTextField textBeta
        • textC
          JTextField textC
        • textGamma
          JTextField textGamma
        • textNScales
          JTextField textNScales
        • textSigmaMaxX
          JTextField textSigmaMaxX
        • textSigmaMaxY
          JTextField textSigmaMaxY
        • textSigmaMaxZ
          JTextField textSigmaMaxZ
        • textSigmaMinX
          JTextField textSigmaMinX
        • textSigmaMinY
          JTextField textSigmaMinY
        • textSigmaMinZ
          JTextField textSigmaMinZ
        • vesselAlgo
          AlgorithmVesselEnhancement vesselAlgo
          DOCUMENT ME!
        • wb
          boolean wb
        • wbCheckBox
          JCheckBox wbCheckBox

    • Class gov.nih.mipav.view.dialogs.JDialogVOIBoolean

      class JDialogVOIBoolean extends JDialogBase implements Serializable

      • Serialized Fields

    • Class gov.nih.mipav.view.dialogs.JDialogVOIExtraction

      class JDialogVOIExtraction extends JDialogBase implements Serializable
      serialVersionUID:
      6131165470681736959L

    • Class gov.nih.mipav.view.dialogs.JDialogVOIHausdorffDistance

      class JDialogVOIHausdorffDistance extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogVOIHausdorffDistance.JPanelAddRemoveVOI

      class JPanelAddRemoveVOI extends JPanelTreeController implements Serializable
      serialVersionUID:
      -2076771728355899710L

    • Class gov.nih.mipav.view.dialogs.JDialogVOILogicalOperations

      class JDialogVOILogicalOperations extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogVOILogicalOperations.JPanelAddRemoveVOI

      class JPanelAddRemoveVOI extends JPanelTreeController implements Serializable
      serialVersionUID:
      -2076771728355899710L

    • Class gov.nih.mipav.view.dialogs.JDialogVOILogicalOperations.JPanelImageOptions

      class JPanelImageOptions extends JPanel implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogVOILogicalOperations.JPanelLogicalOptions

      class JPanelLogicalOptions extends JPanel implements Serializable
      serialVersionUID:
      -4726615904924397356L

    • Class gov.nih.mipav.view.dialogs.JDialogVOIShapeInterpolation

      class JDialogVOIShapeInterpolation extends JDialogBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogVOISplitter

      class JDialogVOISplitter extends JDialogBase implements Serializable
      serialVersionUID:
      4074062695729029005L

      • Serialized Fields

        • allSlicesRadio
          JRadioButton allSlicesRadio
          DOCUMENT ME!
        • b
          float b
        • currentSlice
          int currentSlice
          DOCUMENT ME!
        • endPt
          WildMagic.LibFoundation.Mathematics.Vector3f endPt
        • image
          ModelImage image
          DOCUMENT ME!
        • onlyActiveRadio
          JRadioButton onlyActiveRadio
        • radioGroup
          ButtonGroup radioGroup
        • slope
          float slope
        • startPt
          WildMagic.LibFoundation.Mathematics.Vector3f startPt
        • tol
          float tol

    • Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics

      class JDialogVOIStatistics extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -1354965054401181781L

      • Serialized Fields

        • activeVolume
          int activeVolume
        • addremove
          JDialogVOIStatistics.JPanelAddRemoveVOI addremove
          Panel to push/pull VOIs from full list to selectable list.
        • calculator
          AlgorithmVOIProps calculator
          DOCUMENT ME!
        • checkBoxPanel
          JPanelStatisticsList checkBoxPanel
          Panel holding statistics options.
        • checkList
          boolean[] checkList
          boolean array mirroring checkbox panel's selection.
        • doAllVolumes
          boolean doAllVolumes
        • doForce
          boolean doForce
          force precision to display at maximum.
        • everything
          JTabbedPane everything
          Tabbed pane that holds all components.
        • fileSelectorPanel
          JPanelFileSelection fileSelectorPanel
          Panel to select files.
        • highlighter
          JDialogVOIStatistics.VOIHighlighter highlighter
          Operator to provide listener access... could be done by /this/
        • image
          ModelImage image
          Global image reference to the currently active image during script running and recording.
        • initialActiveVolume
          int initialActiveVolume
        • logFileText
          StringBuffer logFileText
          The text of the log process to be written to file.
        • logModel
          ViewTableModel logModel
          Model where data is stored for the table.
        • logTable
          JTable logTable
          Table holding log of statistics calculated.
        • noisyProcess
          boolean noisyProcess
          Flag where true means notifying the user of stupid errors.
        • outputOptionsPanel
          JDialogVOIStatistics.JPanelStatisticsOptions outputOptionsPanel
          Panel holding statistics output options.
        • overwriteBox
          JCheckBoxMenuItem overwriteBox
          Check box item indicating if we're to always overwriteBox the statistics file.
        • precision
          int precision
          Number of digits after decimal place to allow.
        • processList
          ViewVOIVector processList
        • processType
          int processType
          DOCUMENT ME!
        • r
          JPanelPixelExclusionSelector.RangeType r
        • rangeMaximum
          float rangeMaximum
          DOCUMENT ME!
        • rangeMaximumB
          float rangeMaximumB
        • rangeMaximumG
          float rangeMaximumG
        • rangeMaximumR
          float rangeMaximumR
        • rangeMinimum
          float rangeMinimum
          DOCUMENT ME!
        • rangeMinimumB
          float rangeMinimumB
        • rangeMinimumG
          float rangeMinimumG
        • rangeMinimumR
          float rangeMinimumR
        • scriptRange
          JPanelPixelExclusionSelector.RangeType scriptRange
          When running as a script, holds the pixel exclusion range.
        • selectedList
          JList selectedList
          List of selected VOIs.
        • showTotals
          boolean showTotals
          DOCUMENT ME!
        • subsetAlgo
          AlgorithmSubset subsetAlgo
        • subsetImage
          ModelImage subsetImage
        • tableDestination
          File tableDestination
          Log file destination.
        • tableDestinationUsage
          int tableDestinationUsage
          Indicates options for OVERWRITE, APPEND for the xlat file.
        • tDim
          int tDim
        • toolBar
          JToolBar toolBar
          Toolbar.
        • userInterface
          ViewUserInterface userInterface
          Icon and log access.
        • volumesList
          JList volumesList
          List of available VOIs.
        • xUnits
          int xUnits
          The units printed to the logModel, set in createNewLogile
        • yUnits
          int yUnits
          The units printed to the logModel, set in createNewLogile
        • zUnits
          int zUnits
          The units printed to the logModel, set in createNewLogile

    • Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics.JPanelAddRemoveVOI

      class JPanelAddRemoveVOI extends JPanelListController implements Serializable
      serialVersionUID:
      -2076771728355899710L

    • Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics.JPanelStatisticFileFormatOptions

      class JPanelStatisticFileFormatOptions extends JPanel implements Serializable
      serialVersionUID:
      -4726615904924397356L

      • Serialized Fields

        • tabDelimited
          JRadioButton tabDelimited
          Radio button to choose a tab-delimited file.
        • xml
          JRadioButton xml
          Radio button to choose a XML file.

    • Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics.JPanelStatisticsOptions

      class JPanelStatisticsOptions extends JPanel implements Serializable
      serialVersionUID:
      6577076069976323730L

      • Serialized Fields

        • activeVolumeButton
          JRadioButton activeVolumeButton
          A radio button to select calculation only for the active volume
        • allVolumesButton
          JRadioButton allVolumesButton
          A radio button to select calculation for all volumes
        • byContour
          JRadioButton byContour
          A radio button to select calculation by VOI contour.
        • byContourSlice
          JRadioButton byContourSlice
          A radio button to select calculation by VOI contour.
        • bySlice
          JRadioButton bySlice
          A radio button to select calculation by VOI slice.
        • byTotalVOI
          JRadioButton byTotalVOI
          A radio button to select calculation by total VOI.
        • excluder
          JPanelPixelExclusionSelector excluder
          The Exclusion selector.
        • forceDecimal
          JCheckBox forceDecimal
          DOCUMENT ME!
        • precisionBox
          JComboBox precisionBox
          User can choose the precision to display.
        • showTotals
          JCheckBox showTotals
          A check box to opt for VOI totals.

    • Class gov.nih.mipav.view.dialogs.JDialogVOIStats

      class JDialogVOIStats extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      1618733051752245417L

      • Serialized Fields

        • activeVolume
          int activeVolume
        • activeVolumeButton
          JRadioButton activeVolumeButton
        • algoVOI
          AlgorithmVOIProps algoVOI
          Algorithm for computing VOI statistics
        • allVolumesButton
          JRadioButton allVolumesButton
        • applyButton
          JButton applyButton
          Applies bounding box/shading/name display and other UI changes to ModelImage
        • calcButton
          JButton calcButton
          Performs statistics calculations
        • checkboxBoundingBox
          JCheckBox checkboxBoundingBox
          Whether to display bounding box around VOI
        • checkboxIncludeForProcessing
          JCheckBox checkboxIncludeForProcessing
          Whether to include the selected VOI for statistics processing
        • checkboxOpacity
          JCheckBox checkboxOpacity
          Whether to display VOI with shading
        • checkboxSaveStats
          JCheckBox checkboxSaveStats
          Whether to save statistics to a file
        • checkboxVOIName
          JCheckBox checkboxVOIName
          Whether to display VOI name
        • colorButton
          JButton colorButton
          Allows VOI color to be selected
        • colorChooser
          ViewJColorChooser colorChooser
          Internal dialog box for selecting VOI color
        • colorVOI
          Color colorVOI
          The current color of the selected VOI
        • contourTextArea
          JTextArea contourTextArea
          Displays points and name of selected VOI or contour
        • currentOpacity
          JLabel currentOpacity
          Displays current opacity level in slider
        • doAllVolumes
          boolean doAllVolumes
        • excluder
          JPanelPixelExclusionSelector excluder
        • followVOISelectionBox
          JCheckBox followVOISelectionBox
          DOCUMENT ME!
        • frameBorder
          Border frameBorder
          DOCUMENT ME!
        • frameFollowsSelection
          boolean frameFollowsSelection
          DOCUMENT ME!
        • helpButton
          JButton helpButton
          Displays Stats dialog help
        • image
          ModelImage image
          Internal reference to the currently selected ModelImage
        • listPanel
          JPanelStatisticsList listPanel
          The list of statistics to calculate
        • opacitySlider
          JSlider opacitySlider
          The opacity slider for the selected VOI
        • popup
          JDialogVOIStats.VOITreePopup popup
          DOCUMENT ME!
        • processList
          ViewVOIVector[] processList
          List of VOI sets that will have statistics calculated
        • processListIndex
          int processListIndex
          Current set of VOIs that are being processed
        • rangeMaximum
          float rangeMaximum
          DOCUMENT ME!
        • rangeMaximumB
          float rangeMaximumB
        • rangeMaximumG
          float rangeMaximumG
        • rangeMaximumR
          float rangeMaximumR
        • rangeMinimum
          float rangeMinimum
          DOCUMENT ME!
        • rangeMinimumB
          float rangeMinimumB
        • rangeMinimumG
          float rangeMinimumG
        • rangeMinimumR
          float rangeMinimumR
        • root
          DefaultMutableTreeNode root
          A reference in the voiTree to the currently selected image
        • scriptRange
          JPanelPixelExclusionSelector.RangeType scriptRange
          When running as a script, holds the pixel exclusion range.
        • seedValue
          short seedValue
          The seed value last entered by the user
        • seedValueTF
          JTextField seedValueTF
          Watershed seed value
        • subsetAlgo
          AlgorithmSubset subsetAlgo
        • subsetImage
          ModelImage subsetImage
        • tDim
          int tDim
        • treeSelectionChange
          boolean treeSelectionChange
          DOCUMENT ME!
        • UIDfield
          JTextField UIDfield
          uid of the selected voi
        • updateTree
          boolean updateTree
        • voi
          VOI voi
          The selected VOI when the VOIStats dialogue was created
        • voiContourPane
          JScrollPane voiContourPane
          DOCUMENT ME!
        • voiHandler
          VOIHandlerInterface voiHandler
        • voiModel
          DefaultTreeModel voiModel
          The tree of VOIs, composed of an image with children VOIs
        • VOIName
          JTextField VOIName
          Name of the currently selected voi
        • VOIThicknessField
          JTextField VOIThicknessField
          Thickness of the currently selected voi
        • voiTree
          JTree voiTree
          The graphical representation of voiModel
        • voiTreePane
          JScrollPane voiTreePane
          Displays the orthoganal list of VOIs in the selected ModelImage
        • wholeImage
          VOI wholeImage
          VOI used for whole image processing

    • Class gov.nih.mipav.view.dialogs.JDialogWalshHadamardTransform

      class JDialogWalshHadamardTransform extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogWatershed

      class JDialogWatershed extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      -3432667720289138422L

      • Serialized Fields

        • buttonEnergyInput
          JButton buttonEnergyInput
          DOCUMENT ME!
        • choiceCheckBox
          JCheckBox choiceCheckBox
          DOCUMENT ME!
        • gmDirectory
          String gmDirectory
          DOCUMENT ME!
        • gmFileName
          String gmFileName
          DOCUMENT ME!
        • gmImage
          ModelImage gmImage
          DOCUMENT ME!
        • gmTextFile
          JTextField gmTextFile
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • labelCorrected
          JLabel labelCorrected
          DOCUMENT ME!
        • labelGaussX
          JLabel labelGaussX
          DOCUMENT ME!
        • labelGaussY
          JLabel labelGaussY
          DOCUMENT ME!
        • labelGaussZ
          JLabel labelGaussZ
          DOCUMENT ME!
        • normFactor
          float normFactor
          DOCUMENT ME!
        • resolutionCheckbox
          JCheckBox resolutionCheckbox
          difference between x,y resolutions (in plane) and z resolution (between planes).
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • scaleX
          float scaleX
          DOCUMENT ME!
        • scaleY
          float scaleY
          DOCUMENT ME!
        • scaleZ
          float scaleZ
          DOCUMENT ME!
        • textGaussX
          JTextField textGaussX
          DOCUMENT ME!
        • textGaussY
          JTextField textGaussY
          DOCUMENT ME!
        • textGaussZ
          JTextField textGaussZ
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • watershedAlgo
          AlgorithmWatershed watershedAlgo
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogWaveletFuse

      class JDialogWaveletFuse extends JDialogScriptableBase implements Serializable

    • Class gov.nih.mipav.view.dialogs.JDialogWaveletMultiscaleProducts

      class JDialogWaveletMultiscaleProducts extends JDialogScriptableBase implements Serializable

      • Serialized Fields

        • actualThreshold
          double actualThreshold
        • actualThresholdLabel
          JLabel actualThresholdLabel
        • actualThresholdText
          JTextField actualThresholdText
        • BayesCheckBox
          JCheckBox BayesCheckBox
        • denoiseCheckBox
          JCheckBox denoiseCheckBox
        • destImage
          ModelImage destImage
        • doBayesShrinkThresholdComputation
          boolean doBayesShrinkThresholdComputation
        • doDenoise
          boolean doDenoise
        • doWaveletImages
          boolean doWaveletImages
          DOCUMENT ME!
        • filterLength
          int filterLength
        • filterType
          int filterType
        • hardButton
          JRadioButton hardButton
        • image
          ModelImage image
          DOCUMENT ME!
        • MADButton
          JRadioButton MADButton
        • maximumButton
          JRadioButton maximumButton
        • maximumLevel
          int maximumLevel
        • maximumLevelsButton
          JRadioButton maximumLevelsButton
        • midButton
          JRadioButton midButton
        • minimumButton
          JRadioButton minimumButton
        • minimumLevel
          int minimumLevel
        • nonredundantButton
          JRadioButton nonredundantButton
        • numberOfLevels
          int numberOfLevels
        • redundant
          boolean redundant
        • redundantButton
          JRadioButton redundantButton
        • softButton
          JRadioButton softButton
        • STDButton
          JRadioButton STDButton
        • textFilterLength
          JTextField textFilterLength
          DOCUMENT ME!
        • textLevels
          JTextField textLevels
        • textMaximum
          JTextField textMaximum
        • textMinimum
          JTextField textMinimum
        • thresholdingType
          int thresholdingType
        • thresholdingTypeGroup
          ButtonGroup thresholdingTypeGroup
        • thresholdingTypeLabel
          JLabel thresholdingTypeLabel
        • thresholdLowPass
          boolean thresholdLowPass
        • thresholdLowPassCheckBox
          JCheckBox thresholdLowPassCheckBox
        • thresholdMultiplier
          double thresholdMultiplier
        • thresholdMultiplierLabel
          JLabel thresholdMultiplierLabel
        • thresholdMultiplierText
          JTextField thresholdMultiplierText
        • userLevelsButton
          JRadioButton userLevelsButton
        • varianceEstimator
          int varianceEstimator
        • varianceEstimatorLabel
          JLabel varianceEstimatorLabel
        • varianceGroup
          ButtonGroup varianceGroup
        • waveletAlgo
          AlgorithmRiceWaveletTools waveletAlgo
          DOCUMENT ME!
        • waveletCheckBox
          JCheckBox waveletCheckBox
          DOCUMENT ME!
        • waveletImage
          ModelImage[] waveletImage
          DOCUMENT ME!
        • xDim
          int xDim
        • yDim
          int yDim

    • Class gov.nih.mipav.view.dialogs.JDialogWaveletThreshold

      class JDialogWaveletThreshold extends JDialogScriptableBase implements Serializable
      serialVersionUID:
      5536998601413644702L

      • Serialized Fields

        • cNum
          int cNum
          or if the source image is to be replaced.
        • coefficientCombo
          JComboBox coefficientCombo
          DOCUMENT ME!
        • displayLoc
          int displayLoc
          DOCUMENT ME!
        • doWaveletImage
          boolean doWaveletImage
          DOCUMENT ME!
        • garrote
          JRadioButton garrote
          DOCUMENT ME!
        • hard
          JRadioButton hard
          DOCUMENT ME!
        • image
          ModelImage image
          DOCUMENT ME!
        • newImage
          JRadioButton newImage
          DOCUMENT ME!
        • replaceImage
          JRadioButton replaceImage
          DOCUMENT ME!
        • resultImage
          ModelImage resultImage
          DOCUMENT ME!
        • scad
          JRadioButton scad
          DOCUMENT ME!
        • soft
          JRadioButton soft
          DOCUMENT ME!
        • textThreshold
          JTextField textThreshold
          DOCUMENT ME!
        • threshold
          float threshold
          DOCUMENT ME!
        • thresholdType
          int thresholdType
          DOCUMENT ME!
        • titles
          String[] titles
          DOCUMENT ME!
        • userInterface
          ViewUserInterface userInterface
          DOCUMENT ME!
        • waveletAlgo
          AlgorithmWaveletThreshold waveletAlgo
          DOCUMENT ME!
        • waveletCheckBox
          JCheckBox waveletCheckBox
          DOCUMENT ME!
        • waveletImage
          ModelImage waveletImage
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogWinLevel

      class JDialogWinLevel extends JDialogBase implements Serializable
      serialVersionUID:
      -3270517526341902110L

      • Serialized Fields

        • allowChangesMinMax
          int allowChangesMinMax
          allow changes to the min and max boundaries *
        • allowChangesWin
          int allowChangesWin
          allow changes to the window and level boundaries *
        • closeButton
          JButton closeButton
          DOCUMENT ME!
        • dataSlice
          float[] dataSlice
          Reference to the image data of the slice presently displayed. Needed to calculate the max/min of the slice used to adjust the transfer function.
        • image
          ModelImage image
          Reference to the image that will be affected by the adjust of the window and level.
        • keyTyped
          boolean keyTyped
        • level
          float level
          Average of the min and max extents of the transfer window that describes the window size.
        • levelMaxFloat
          float levelMaxFloat
          the maxes and mins for window and level *
        • levelMinFloat
          float levelMinFloat
          the maxes and mins for window and level *
        • levelSlider
          JSlider levelSlider
          DOCUMENT ME!
        • levelSliderMax
          int levelSliderMax
          Stores the maximum slider value.
        • levelValTextField
          JTextField levelValTextField
          textfield inputs for window and level *
        • loadButton
          JButton loadButton
          DOCUMENT ME!
        • LUT
          ModelLUT LUT
          Reference to the LUT used to display the image.
        • max
          float max
        • maxImage
          float maxImage
          Image's maximum intensity.
        • maxSlider
          JSlider maxSlider
          DOCUMENT ME!
        • maxValTextField
          JTextField maxValTextField
          textfield inputs for window and level *
        • min
          float min
        • minImage
          float minImage
          Image's minimum intensity.
        • minMaxBInt
          float minMaxBInt
          b intercept for mapping of min/max sliders *
        • minMaxPanel
          JPanel minMaxPanel
          DOCUMENT ME!
        • minMaxSlope
          float minMaxSlope
          slope for mapping of min/max sliders *
        • minSlider
          JSlider minSlider
          DOCUMENT ME!
        • minValTextField
          JTextField minValTextField
          textfield inputs for window and level *
        • saveButton
          JButton saveButton
          DOCUMENT ME!
        • sliderLevMax
          JLabel sliderLevMax
        • sliderLevMin
          JLabel sliderLevMin
        • sliderMaxMax
          JLabel sliderMaxMax
          labels at top and bottom of sliders indicating slider bounds *
        • sliderMaxMin
          JLabel sliderMaxMin
          labels at top and bottom of sliders indicating slider bounds *
        • sliderMinMax
          JLabel sliderMinMax
          labels at top and bottom of sliders indicating slider bounds *
        • sliderMinMin
          JLabel sliderMinMin
          labels at top and bottom of sliders indicating slider bounds *
        • sliderWinMax
          JLabel sliderWinMax
        • sliderWinMin
          JLabel sliderWinMin
        • tabbedPane
          JTabbedPane tabbedPane
          tabbed pane for w/L and min/max *
        • window
          float window
          The size of the window.
        • windowLevelPanel
          JPanel windowLevelPanel
          DOCUMENT ME!
        • windowSlider
          JSlider windowSlider
          DOCUMENT ME!
        • windowSliderMax
          int windowSliderMax
          Stores the minimum slider value.
        • winMaxFloat
          float winMaxFloat
          the maxes and mins for window and level *
        • winMinFloat
          float winMinFloat
          the maxes and mins for window and level *
        • winValTextField
          JTextField winValTextField
          textfield inputs for window and level *
        • x
          float[] x
          Three arrays to save the coordinates of the LUT's transfer fucntion. z[] not used.
        • y
          float[] y
          DOCUMENT ME!
        • z
          float[] z
          DOCUMENT ME!

    • Class gov.nih.mipav.view.dialogs.JDialogZoom

      class JDialogZoom extends JDialogBase implements Serializable
      serialVersionUID:
      5271517126304850595L

      • Serialized Fields

        • bilinear
          JRadioButton bilinear
          Radio buttons for interpolation methods.
        • componentImage
          ViewJComponentEditImage componentImage
          Component image which this dialog belongs to.
        • cubic
          JRadioButton cubic
          Radio buttons for interpolation methods.
        • currentLabel
          JLabel currentLabel
          Value of current slider number.
        • intensityCheckbox
          JCheckBox intensityCheckbox
          Checkbox for displaying intensity values.
        • interpType
          Preferences.InterpolateDisplay interpType
          Method of interpolation
        • magSlider
          JSlider magSlider
          Slider used for zooming.
        • maximumLabel
          JLabel maximumLabel
          Labels to display max/min slider values.
        • maximumValueButton
          JButton maximumValueButton
          Buttons to set max/min slider values.
        • maximumValueField
          JTextField maximumValueField
          Text fields for user to enter max/min slider values.
        • minimumLabel
          JLabel minimumLabel
          Labels to display max/min slider values.
        • minimumValueButton
          JButton minimumValueButton
          Buttons to set max/min slider values.
        • minimumValueField
          JTextField minimumValueField
          Text fields for user to enter max/min slider values.
        • mode
          JDialogZoom.ZoomMode mode
          Mode of operation for the dialog
        • nearest
          JRadioButton nearest
          Radio buttons for interpolation methods.

    • Class gov.nih.mipav.view.dialogs.JFrameRegistrationMosaic

      class JFrameRegistrationMosaic extends JFrame implements Serializable
      serialVersionUID:
      2954367270283496349L

      • Serialized Fields

        • m_aabReference
          boolean[][] m_aabReference
          For masking, set to true if the reference image is written into the same location:.
        • m_aabReferenceBackup
          boolean[][] m_aabReferenceBackup
          backup:.
        • m_akBackupBorders
          javax.media.j3d.Shape3D[] m_akBackupBorders
          Backup shape for Undo:.
        • m_akBackupImages
          ModelImage[] m_akBackupImages
          Backup Image for Undo:.
        • m_akBackupPolygons
          javax.media.j3d.Shape3D[] m_akBackupPolygons
          Backup shape for Undo:.
        • m_akBackupTG
          javax.media.j3d.TransformGroup[] m_akBackupTG
          Backup Transform for Undo:.
        • m_akBorderShapes
          javax.media.j3d.Shape3D[] m_akBorderShapes
          Reference to the border shape data structure for changing the color based on which image is selected:.
        • m_akImages
          ModelImage[] m_akImages
          Reference to the model images:.
        • m_akImageTransforms
          javax.media.j3d.TransformGroup[] m_akImageTransforms
          Reference and tile image transformations:.
        • m_akPolygonShapes
          javax.media.j3d.Shape3D[] m_akPolygonShapes
          Reference to the texture-mapped polygon on which the image is displayed:.
        • m_bBruteForce
          boolean m_bBruteForce
          Brute force default is off:.
        • m_bDisplayTransform
          boolean m_bDisplayTransform
          Display transfromed image in separate window: set to false (no display).
        • m_bDoMultiThread
          boolean m_bDoMultiThread
        • m_bDoSubsample
          boolean m_bDoSubsample
          Default subsample set to true:.
        • m_bFileLoaded
          boolean m_bFileLoaded
          Boolean to check that a file is loaded before mouse operations are allowed to occur.
        • m_bFirst
          boolean m_bFirst
          For blending the reference and tile images, reference image is not blended with background, reset when initData() is called.
        • m_bResetAlpha
          boolean m_bResetAlpha
          To reset m_kReferenceAlpha:.
        • m_bSetScale
          boolean m_bSetScale
          True when scale factor should be used:.
        • m_fCoarseRate
          float m_fCoarseRate
          Default rotation coarse rate, set to 2 degrees:.
        • m_fFineRate
          float m_fFineRate
          Default rotation fine rate, set to 1 degree:.
        • m_fRotateBegin
          float m_fRotateBegin
          Default rotation start, set to negative 5 degrees:.
        • m_fRotateEnd
          float m_fRotateEnd
          Default rotation end, set to postive 5 degrees:.
        • m_fRotationRange
          float m_fRotationRange
          default rotation range (0).
        • m_fScale
          float m_fScale
          Scale factor for large images:.
        • m_fXScaleRange
          float m_fXScaleRange
          default x scale range (0).
        • m_fYScaleRange
          float m_fYScaleRange
          default y scale range (0).
        • m_iCost
          int m_iCost
          Default cost function, set to correlation ratio (smoothed, weighted):.
        • m_iDOF
          int m_iDOF
          Default degrees of freedom:.
        • m_iInterp
          int m_iInterp
          Default image interpolation, set to be bilinear interpolation:.
        • m_iInterp2
          int m_iInterp2
          Default interpolation for the transform algorithm:.
        • m_iMaxIterations
          int m_iMaxIterations
          Default number of iteration set to 2:.
        • m_iNumMinima
          int m_iNumMinima
          Default number of minima to test from level 8 at level 4 (set to 3):.
        • m_iOpen
          int m_iOpen
          index of the non-selected image:.
        • m_iOpenSave
          int m_iOpenSave
          Backup of the open index:.
        • m_iReference
          int m_iReference
          Index of the reference image:.
        • m_iReferenceSave
          int m_iReferenceSave
          Backup of the reference index:.
        • m_iScaleSteps
          int m_iScaleSteps
          default number of divisions for scale optimazation:.
        • m_iSelected
          int m_iSelected
          index of the selected image:
        • m_iTile
          int m_iTile
          Index of the tile image:.
        • m_iTranslationRange
          int m_iTranslationRange
          default x,y translation range (0).
        • m_iXClick
          int m_iXClick
          x,y positions of the mouse when one of the mouse buttons is pressed:.
        • m_iYClick
          int m_iYClick
          x,y positions of the mouse when one of the mouse buttons is pressed:.
        • m_kAdvancedOptionsButton
          JButton m_kAdvancedOptionsButton
          Launches the JDialogRegistrationOAR2D dialog to set registration options:.
        • m_kCanvas
          javax.media.j3d.Canvas3D m_kCanvas
          Drawing canvas:.
        • m_kCloseAllButton
          JButton m_kCloseAllButton
          Close all images and remove them from the scene:.
        • m_kCurrentTransform
          javax.media.j3d.Transform3D m_kCurrentTransform
          current transformation based on mouseDragged event:.
        • m_kHelpButton
          JButton m_kHelpButton
          Open the mosaic image help.
        • m_kMouseEvent
          MouseEvent m_kMouseEvent
          Reference to the mousePressed event:.
        • m_kOldTransform
          javax.media.j3d.Transform3D m_kOldTransform
          Accumulated transformation prior to current mouseDrag:.
        • m_kOpenReferenceButton
          JButton m_kOpenReferenceButton
          Open reference image:.
        • m_kOpenTileButton
          JButton m_kOpenTileButton
          Open tile image:.
        • m_kReferenceAlpha
          ModelImage m_kReferenceAlpha
          For blending between refernce and transformed tile images:.
        • m_kReferenceAlphaBackup
          ModelImage m_kReferenceAlphaBackup
          For blending between refernce and transformed tile images:.
        • m_kRegisterButton
          JButton m_kRegisterButton
          Initialize and start the registration based on how the user positioned the two images:.
        • m_kSaveButton
          JButton m_kSaveButton
          Save the mosaic image:.
        • m_kScene
          javax.media.j3d.BranchGroup m_kScene
          Scene graph root node:.
        • m_kTileAlpha
          ModelImage m_kTileAlpha
          For blending between refernce and transformed tile images:.
        • m_kToggleSelectedButton
          JButton m_kToggleSelectedButton
          Toggle which image is currently selected:.
        • m_kUndoButton
          JButton m_kUndoButton
          Undo the last registration for the mosaic image:.
        • m_kUniverse
          com.sun.j3d.utils.universe.SimpleUniverse m_kUniverse
          SimpleUniverse:.

    • Class gov.nih.mipav.view.dialogs.JPanelPixelExclusionSelector

      class JPanelPixelExclusionSelector extends JPanel implements Serializable
      serialVersionUID:
      1471564039185960351L

      • Serialized Fields

        • boundA
          JTextField boundA
          The lower bound of the exclusion
        • boundB
          JTextField boundB
          The upper bound of the exclusion
        • boundLB
          JTextField boundLB
          The lower blue bound of the exclusion
        • boundLG
          JTextField boundLG
          The lower green bound of the exclusion
        • boundLR
          JTextField boundLR
          The lower red bound of the exclusion
        • boundUB
          JTextField boundUB
          The upper blue bound of the exclusion
        • boundUG
          JTextField boundUG
          The upper green bound of the exclusion
        • boundUR
          JTextField boundUR
          The upper red bound of the exclusion
        • checkBoxPanel
          JPanelStatisticsList checkBoxPanel
          A reference to the JDialogVOIStatistic or JDialogVOIStats check box panel.
        • doColor
          boolean doColor
        • excludeSelection
          JComboBox excludeSelection
          Lists available exclusion types
        • lowerLimit
          Float lowerLimit
          The lower limit of the exclusion
        • lowerLimitB
          Float lowerLimitB
        • lowerLimitG
          Float lowerLimitG
        • lowerLimitR
          Float lowerLimitR
        • permitExclusion
          JCheckBox permitExclusion
          Whether pixels will be excluded from a calculation based on intensity values
        • rangeFlag
          JPanelPixelExclusionSelector.RangeType rangeFlag
          The range type that this pixel exclusion selector covers.
        • upperLimit
          Float upperLimit
          held for switching between states of the exclusion.
        • upperLimitB
          Float upperLimitB
        • upperLimitG
          Float upperLimitG
        • upperLimitR
          Float upperLimitR

    • Class gov.nih.mipav.view.dialogs.ScriptTreeNode

      class ScriptTreeNode extends DefaultMutableTreeNode implements Serializable

      • Serialized Fields

        • filePath
          String filePath
        • nodeType
          int nodeType

  • Package gov.nih.mipav.view.dialogs.reportbug

    • Class gov.nih.mipav.view.dialogs.reportbug.ReportBugBuilder

      class ReportBugBuilder extends JDialogBase implements Serializable
      serialVersionUID:
      -7015450168814651213L

      • Serialized Fields

        • attachedImages
          JTextArea attachedImages
          Text are for displaying the attached images
        • attachmentName
          String attachmentName
          Name of the image being attached.
        • browser
          JFileChooser browser
          File chooser for the user to select an existing file for attachment
        • bugTypeComboBox
          JComboBox bugTypeComboBox
        • descriptionField
          JTextPane descriptionField
          Text pane for user inputed bug description
        • directory
          JTextField directory
          Text field for the directory of a file being attached from the user's computer
        • emailField
          JTextField emailField
          Text field for user inputed email
        • fileNames
          ArrayList<String> fileNames
          ArrayList of all file names of report attachments
        • filePaths
          ArrayList<String> filePaths
          ArrayList of all file paths of report attachments
        • frame
          JFrame frame
          Frame for the GUI in which the form is presented
        • image
          File image
          Image file used to store images created through the screen capture function
        • isScreenCapAttached
          boolean isScreenCapAttached
          Hack-ish boolean to avoid double adding screen captures to the attachment list.
        • nameField
          JTextField nameField
          Text field for user inputed name
        • screenCap
          JButton screenCap
          Button to launch the create new image dialog
        • screenCapture
          JDialogCaptureScreen screenCapture
          Dialog used for taking screen captures
        • standardOS
          JTextField standardOS
          Text field for the user inputed operating system.
        • standardUrgency
          JTextField standardUrgency
          Text field for the user inputed urgency of the bug
        • standardVersion
          JTextField standardVersion
          Text field for the user inputed mipav version.
        • summaryField
          JTextField summaryField
          Text area for user inputed bug title

  • Package gov.nih.mipav.view.graphVisualization

  • Package gov.nih.mipav.view.input.spacenav

  • Package gov.nih.mipav.view.renderer

    • Class gov.nih.mipav.view.renderer.JDialogRendererAVI

      class JDialogRendererAVI extends JDialogBase implements Serializable
      serialVersionUID:
      -1983774099020785830L

      • Serialized Fields

        • applyWindowLevel
          boolean applyWindowLevel
          Flag to indicate to apply window level or not.
        • rate
          double rate
          Frame rate.
        • rateBox
          JTextField rateBox
          Frame rate textbox.
        • windowLevelCheckBox
          JCheckBox windowLevelCheckBox
          Window level check box.

    • Class gov.nih.mipav.view.renderer.JDialogVolViewResample

      class JDialogVolViewResample extends JDialogBase implements Serializable
      serialVersionUID:
      -1966951185588087479L

      • Serialized Fields

        • extents
          int[] extents
          Original dimensions extents value array.
        • extXInput
          JTextField extXInput
          Original X, Y, Z dimension extents values.
        • extXOutput
          JTextField extXOutput
          Power of 2 X, Y, Z dimension extents values.
        • extYInput
          JTextField extYInput
          Original X, Y, Z dimension extents values.
        • extYOutput
          JTextField extYOutput
          Power of 2 X, Y, Z dimension extents values.
        • extZInput
          JTextField extZInput
          Original X, Y, Z dimension extents values.
        • extZOutput
          JTextField extZOutput
          Power of 2 X, Y, Z dimension extents values.
        • forcePadding
          boolean forcePadding
          Flag to force the padding of blank images to the end of images.
        • forceResample
          boolean forceResample
          Boolean flag to do resample images.
        • imageA
          ModelImage imageA
          Model images A and B.
        • imageAOriginal
          ModelImage imageAOriginal
          The non-cloned image which we want to load into the renderer.
        • imageB
          ModelImage imageB
          Model images A and B.
        • leftPanelRenderMode
          int leftPanelRenderMode
          The left panel renderer mode.
        • LUTa
          ModelLUT LUTa
          Lookup table of the imageA, B.
        • LUTb
          ModelLUT LUTb
          Lookup table of the imageA, B.
        • m_iFilter
          int m_iFilter
          Resample filter type, default: Trilinear Interpoloation.
        • m_kFilterType
          JComboBox m_kFilterType
          Resample filter selection box.
        • m_kVolViewType
          String m_kVolViewType
          Type of ViewJFrameVolumeView object (using WildMagic or not)
        • nDim
          int nDim
          Number of available dimension.
        • newRes
          float[] newRes
          Resample resolutioin corresponding to Power of 2.
        • padButton
          JButton padButton
          Pad button is used for inserting blank images to the end of the image. This approach creates the power of 2 image. Pad Button is only enabled when the power of 2 value is greater than the slices number.
        • radioBrainSurfaceFlattenerR
          JRadioButton radioBrainSurfaceFlattenerR
          Radio button of the brainsurface flattener render mode in the right panel.
        • radioFlythruL
          JRadioButton radioFlythruL
          Radio button of the fly througth mode in the left panel.
        • radioNoneR
          JRadioButton radioNoneR
          Radio button of the none mode in the right panel.
        • radioRaycastR
          JRadioButton radioRaycastR
          Radio button of the raycast render mode in the right panel.
        • radioShearwarpR
          JRadioButton radioShearwarpR
          Radio button of the shearwarp render mode in the right panel.
        • radioSurfaceL
          JRadioButton radioSurfaceL
          Radio button of the surface render mode int the left panel.
        • radioSurfaceR
          JRadioButton radioSurfaceR
          Radio button of the surface render mode in the right panel.
        • radioSurfaceView
          JRadioButton radioSurfaceView
          Radio button of the surface view mode in the left panel.
        • res
          float[] res
          Original resolutioin arrray.
        • resampledImage
          ModelImage resampledImage
          Temp Model image.
        • RGBTA
          ModelRGB RGBTA
          Lookup table of the color imageA, B.
        • RGBTB
          ModelRGB RGBTB
          Lookup table of the color imageA, B.
        • rightPanelRenderMode
          int rightPanelRenderMode
          The right panel renderer mode.
        • segmentationImage
          ModelImage segmentationImage
          An image with areas designated as special (vessels, etc).
        • sr
          ViewJFrameVolumeView sr
          Reference to ViewJFrameSurfaceRenderer.
        • startupCommand
          String startupCommand
          The action command to send to the volume renderer after we start it (can be used to open a tab). Used by RFAST to open up the RFA simulation immediately.
        • volExtents
          int[] volExtents
          Resampled dimension value in Power of 2.
        • volSize
          int volSize
          Volume size X*Y*Z.

    • Class gov.nih.mipav.view.renderer.JPanelAVIChoice

      class JPanelAVIChoice extends JDialogBase implements Serializable
      serialVersionUID:
      -4246819535725354623L

      • Serialized Fields

        • compressionBox
          JComboBox compressionBox
          Combo box to select compression.
        • okayPressed
          boolean okayPressed
          Indicator for OK button pressed.
        • operating_system
          int operating_system
          Operating system type windows or Mac.
        • qualityField
          JTextField qualityField
          Text Field for M-JPEG quality.

    • Class gov.nih.mipav.view.renderer.JPanelRendererBase

      class JPanelRendererBase extends JPanel implements Serializable
      serialVersionUID:
      7175361900854772739L

      • Serialized Fields

        • applyButton
          JButton applyButton
          Apply button is used to apply the setting of the dialog.
        • cancelButton
          JButton cancelButton
          Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • cancelFlag
          boolean cancelFlag
          Flag indicating if the dialog had been cancelled or not.
        • closeButton
          JButton closeButton
          Close button is used to close the dialog.
        • helpButton
          JButton helpButton
          Help button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • isActiveImage
          boolean isActiveImage
          DOCUMENT ME!
        • mainPanel
          JPanel mainPanel
          The main control.
        • OKButton
          JButton OKButton
          OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • runInSeparateThread
          boolean runInSeparateThread
          Flag indicating if the algorithm should run in a separate thread. Default is true.
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

    • Class gov.nih.mipav.view.renderer.JPanelVolOpacityRGB

      class JPanelVolOpacityRGB extends JPanelVolOpacityBase implements Serializable
      serialVersionUID:
      8837612116721229202L

      • Serialized Fields

        • histogramABlue
          ModelHistogram histogramABlue
          Deprecated.
          imageA histogram of the Blue channel.
        • histogramAGreen
          ModelHistogram histogramAGreen
          Deprecated.
          imageA histogram of the Green channel.
        • histogramARed
          ModelHistogram histogramARed
          Deprecated.
          imageA histogram of the Red channel.
        • histogramBBlue
          ModelHistogram histogramBBlue
          Deprecated.
          imageB histogram, the Blue channel.
        • histogramBGreen
          ModelHistogram histogramBGreen
          Deprecated.
          imageB histogram, the Green channel.
        • histogramBRed
          ModelHistogram histogramBRed
          Deprecated.
          imageB histogram of the Red channel.
        • histogramGM_ABlue
          ModelHistogram histogramGM_ABlue
          Deprecated.
          imageA histogram of the Blue channel.
        • histogramGM_AGreen
          ModelHistogram histogramGM_AGreen
          Deprecated.
          imageA histogram of the Green channel.
        • histogramGM_ARed
          ModelHistogram histogramGM_ARed
          Deprecated.
          imageA histogram of the Red channel.
        • histogramGM_BBlue
          ModelHistogram histogramGM_BBlue
          Deprecated.
          imageB histogram, the Blue channel.
        • histogramGM_BGreen
          ModelHistogram histogramGM_BGreen
          Deprecated.
          imageB histogram, the Green channel.
        • histogramGM_BRed
          ModelHistogram histogramGM_BRed
          Deprecated.
          imageB histogram of the Red channel.
        • rendererProgressBar
          JProgressBar rendererProgressBar
          Deprecated.
          A reference to the volume renderer frame's progress bar.
        • RGBTA
          ModelRGB RGBTA
          Deprecated.
          Tagged for deletion - Matt, Ruida, Lee, ModelRGB table for imageA, B.
        • RGBTA_GM
          ModelRGB RGBTA_GM
          Deprecated.
          Tagged for deletion - Matt, Ruida, Lee, RGB table reference of the image A, B.
        • RGBTB
          ModelRGB RGBTB
          Deprecated.
          DOCUMENT ME!
        • RGBTB_GM
          ModelRGB RGBTB_GM
          Deprecated.
          DOCUMENT ME!
        • toolBar
          JToolBar toolBar
          Deprecated.
          ToolBar that hold the linear, horizontal mode etc.

    • Class gov.nih.mipav.view.renderer.MouseEventVector

      class MouseEventVector extends Object implements Serializable
      serialVersionUID:
      5183229064629196522L

      • Serialization Methods

        • readObject
          private void readObject(ObjectInputStream stream) throws IOException, ClassNotFoundException
          Called by some native invokeMethod. Provides a way to read this class out as a object stream. First, the size of the vector is read, then each mouseEvent into the vector, then the name, then the view. The view is read in as a String because it is not serializable. The read method corresponds to the write method, below.
          Parameters:
          stream - Object stream to read from.
          Throws:
          IOException - DOCUMENT ME!
          ClassNotFoundException - DOCUMENT ME!
        • writeObject
          private void writeObject(ObjectOutputStream stream) throws IOException
          Called by some native invokeMethod. Provides a way to write this class out as a object stream. First, the size of the vector is written, then each mouseEvent in the vector, then the name, then the view. The view is written out as a String because it is not serializable. The write method corresponds to the read method, above.
          Parameters:
          stream - Object stream to write to.
          Throws:
          IOException - DOCUMENT ME!

      • Serialized Fields

        • first
          boolean first
          First time accessed.
        • mode
          int mode
          Current mode.
        • mouseEvents
          Vector mouseEvents
          Vector to record mouse events.
        • name
          String name
          Name of the events.
        • state
          Object state
          State being recorded.
        • stateVector
          Vector stateVector
          Vector to record state changes.
        • view
          double[] view
          Parent frame transform3D view.

    • Class gov.nih.mipav.view.renderer.SceneState

      class SceneState extends Object implements Serializable
      serialVersionUID:
      9166009718509099407L

      • Serialized Fields

        • aClipVisible
          boolean aClipVisible
          Boolean visibility values for x, y, z, arbitrary clipping slider frames.
        • axisAngle
          float axisAngle
          Save the current.
        • axisX
          float axisX
          Save the current.
        • axisY
          float axisY
          Save the current.
        • axisZ
          float axisZ
          Save the current.
        • clipSliceA
          int clipSliceA
          Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.
        • clipSliceX
          int clipSliceX
          Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.
        • clipSliceXNeg
          int clipSliceXNeg
          Clipping slider values for the triplanar clipping slider x, y, z negative.
        • clipSliceY
          int clipSliceY
          Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.
        • clipSliceYNeg
          int clipSliceYNeg
          Clipping slider values for the triplanar clipping slider x, y, z negative.
        • clipSliceZ
          int clipSliceZ
          Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.
        • clipSliceZNeg
          int clipSliceZNeg
          Clipping slider values for the triplanar clipping slider x, y, z negative.
        • is6PlaneClipping
          boolean is6PlaneClipping
          Boolean flag to indicate if the 6 plane clipping mode is active.
        • isClipArbiPicked
          boolean isClipArbiPicked
          Boolean flag to indicate if the arbitary clipping mode is active.
        • isVolOpacityChanged
          boolean isVolOpacityChanged
          Boolean indicator for volume opacity changed.
        • isVolumeDisplayMode3D
          boolean isVolumeDisplayMode3D
          Boolean indicator for the current diaplay mode, volume render mode or slice render mode.
        • surfaceOpacity
          int surfaceOpacity
          Surface opacity slider value of the surface dialog.
        • transform
          float[] transform
          Current sceneRoot transform.
        • transformFunc
          TransferFunction transformFunc
          Currrent tranform function of the volume render look up table.
        • whichComp
          int whichComp
          Current active volume opacity control of the volume render.
        • x
          int x
          x, y, z triplanar slider values.
        • xClipVisible
          boolean xClipVisible
          Boolean visibility values for x, y, z, arbitrary clipping slider frames.
        • xNegClipVisible
          boolean xNegClipVisible
          Boolean visibility values for x, y, z negative clipping slider frames.
        • xOpacity
          int xOpacity
          x, y, z triplanar opacity slider values.
        • xVisible
          boolean xVisible
          Boolean visibility values for x, y, z triplanar.
        • y
          int y
          x, y, z triplanar slider values.
        • yClipVisible
          boolean yClipVisible
          Boolean visibility values for x, y, z, arbitrary clipping slider frames.
        • yNegClipVisible
          boolean yNegClipVisible
          Boolean visibility values for x, y, z negative clipping slider frames.
        • yOpacity
          int yOpacity
          x, y, z triplanar opacity slider values.
        • yVisible
          boolean yVisible
          Boolean visibility values for x, y, z triplanar.
        • z
          int z
          x, y, z triplanar slider values.
        • zClipVisible
          boolean zClipVisible
          Boolean visibility values for x, y, z, arbitrary clipping slider frames.
        • zNegClipVisible
          boolean zNegClipVisible
          Boolean visibility values for x, y, z negative clipping slider frames.
        • zOpacity
          int zOpacity
          x, y, z triplanar opacity slider values.
        • zVisible
          boolean zVisible
          Boolean visibility values for x, y, z triplanar.

    • Class gov.nih.mipav.view.renderer.ViewJComponentVolOpacityBase

      class ViewJComponentVolOpacityBase extends JComponent implements Serializable
      serialVersionUID:
      826985329858268537L

      • Serialized Fields

        • addPointFlag
          boolean addPointFlag
          DOCUMENT ME!
        • componentDim
          Dimension componentDim
          The outer dimension of the histogram component we will be drawing.
        • dim
          Dimension dim
          The histogram image dimension.
        • histogram
          ModelHistogram histogram
          The image histogram.
        • histogramBuffer
          int[] histogramBuffer
          DOCUMENT ME!
        • histogramMax
          double histogramMax
          DOCUMENT ME!
        • histogramMaxLog
          double histogramMaxLog
          DOCUMENT ME!
        • image
          ModelImage image
          The image whose histo lut we are displaying.
        • img
          Image img
          DOCUMENT ME!
        • logFlag
          boolean logFlag
          Whether to transform the histogram data by log10.
        • lutIndexBuffer
          int[] lutIndexBuffer
          DOCUMENT ME!
        • max
          float max
          DOCUMENT ME!
        • min
          float min
          DOCUMENT ME!
        • mode
          int mode
          The current mode of the histogram component.
        • newPointIndex
          int newPointIndex
          DOCUMENT ME!
        • offsetX
          int offsetX
          DOCUMENT ME!
        • offsetY
          int offsetY
          DOCUMENT ME!
        • parentListener
          ViewJComponentVolOpacityListener parentListener
        • parentPanel
          JPanelVolOpacityBase parentPanel
          The container of this histogram component.
        • pixBuffer
          int[] pixBuffer
          DOCUMENT ME!
        • range
          float range
          DOCUMENT ME!
        • stRange
          int stRange
          DOCUMENT ME!
        • tfActiveIndex
          int tfActiveIndex
          DOCUMENT ME!
        • transferFunction
          TransferFunction transferFunction
          DOCUMENT ME!

    • Class gov.nih.mipav.view.renderer.ViewJComponentVolOpacityRGB

      class ViewJComponentVolOpacityRGB extends ViewJComponentVolOpacityBase implements Serializable
      serialVersionUID:
      1208349901510241151L

      • Serialized Fields

        • lutIndexBuffer
          int[] lutIndexBuffer
          DOCUMENT ME!

  • Package gov.nih.mipav.view.renderer.flythroughview

    • Class gov.nih.mipav.view.renderer.flythroughview.JPanelFlythruMove

      class JPanelFlythruMove extends JPanelRendererBase implements Serializable
      serialVersionUID:
      6224214629454958231L

      • Serialized Fields

        • annotationNextButton
          JButton annotationNextButton
          DOCUMENT ME!
        • annotationPrevButton
          JButton annotationPrevButton
          DOCUMENT ME!
        • autoRunButton
          JButton autoRunButton
          Auto Run Button.
        • aviPlayButton
          JToggleButton aviPlayButton
          AVI Recorder Play button.
        • aviRecordButton
          JToggleButton aviRecordButton
          AVI Recorder record button.
        • aviStopButton
          JToggleButton aviStopButton
          AVI Recorder Stop button.
        • branchButton
          JButton branchButton
          DOCUMENT ME!
        • changedMode
          boolean changedMode
          flag to indicate current mode being changed.
        • contButton
          JToggleButton contButton
          Continue play button.
        • current
          int current
          index to the item list.
        • currEventTime
          long currEventTime
          Current mouse press event time stamp.
        • endButton
          JButton endButton
          DOCUMENT ME!
        • eventVector
          MouseEventVector eventVector
          Seqence of mouse events ( press, shift,and release as individual mouse event).
        • first
          boolean first
          Flag to indicate first event.
        • gazeDecreaseButton
          JButton gazeDecreaseButton
          DOCUMENT ME!
        • gazeIncrButton
          JButton gazeIncrButton
          DOCUMENT ME!
        • homeButton
          JButton homeButton
          DOCUMENT ME!
        • isPlaying
          boolean isPlaying
          Flag to indicating play mouse is running or not.
        • leftRotateButton
          JButton leftRotateButton
          DOCUMENT ME!
        • mediaPlayerButton
          JButton mediaPlayerButton
          MS media player button to play AVI file.
        • middleDownButton
          JButton middleDownButton
          DOCUMENT ME!
        • middleLeftButton
          JButton middleLeftButton
          DOCUMENT ME!
        • middleLeftButtonEmpty
          JButton middleLeftButtonEmpty
          Empty button group.
        • middleRightButton
          JButton middleRightButton
          DOCUMENT ME!
        • middleUpButton
          JButton middleUpButton
          DOCUMENT ME!
        • mode
          int mode
          Current mode, init to stop.
        • mouseCount
          int mouseCount
          Mouse event counter.
        • mouseEvents
          Vector mouseEvents
          Sequence of mouse events( press, shift and release as a whole mouse event).
        • mousePanel
          JPanel mousePanel
          Panel holds the mouse move buttons.
        • moviePanel
          JPanel moviePanel
          Movie control panel that hold mouse recorder and AVI movie control.
        • parentScene
          FlyThroughRenderInterface parentScene
          The parent fly thru render reference.
        • pauseButton
          JToggleButton pauseButton
          Pause button.
        • playButton
          JToggleButton playButton
          Display button.
        • playMouse
          JPanelFlythruMove.PlayMouse playMouse
          Reference to PlayMouse class object.
        • pressed
          boolean pressed
          If any of the mouse move button pressed.
        • prevEventTime
          long prevEventTime
          Previous mouse press event time stamp.
        • quickTimeButton
          JButton quickTimeButton
          Apple quick time player button to play quick time movie.
        • recordButton
          JToggleButton recordButton
          Recorder button.
        • reverseButton
          JButton reverseButton
          DOCUMENT ME!
        • rightDownButton
          JButton rightDownButton
          DOCUMENT ME!
        • rightLeftButton
          JButton rightLeftButton
          DOCUMENT ME!
        • rightRightButton
          JButton rightRightButton
          DOCUMENT ME!
        • rightRotateButton
          JButton rightRotateButton
          DOCUMENT ME!
        • rightUpButton
          JButton rightUpButton
          JButton group.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanelFlythruMove.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • stepButton
          JToggleButton stepButton
          Next step button.
        • stepDecreaseButton
          JButton stepDecreaseButton
          DOCUMENT ME!
        • stepIncrButton
          JButton stepIncrButton
          DOCUMENT ME!
        • stopButton
          JToggleButton stopButton
          Stop button.
        • time
          long time
          Time to wait for the next mouse event.
        • toolBar
          JToolBar toolBar
          Tool bar of the mouse recorder.

  • Package gov.nih.mipav.view.renderer.J3D

    • Class gov.nih.mipav.view.renderer.J3D.JPanelCamera

      class JPanelCamera extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      7970872222123739616L

      • Serialized Fields

        • buttonPanel
          JPanel buttonPanel
          Button panel.
        • degreeLabel
          JLabel degreeLabel
          Label of the rotation degree.
        • degreeText
          JTextField degreeText
          Textfield of the roation degree.
        • flyButton
          JRadioButton flyButton
          Raido Button group.
        • labelX
          JLabel labelX
          X, Y, Z labels inside the rotation panel.
        • labelY
          JLabel labelY
          X, Y, Z labels inside the rotation panel.
        • labelZ
          JLabel labelZ
          X, Y, Z labels inside the rotation panel.
        • leftDownButton
          JButton leftDownButton
          Left panel mouse button down.
        • leftDownButtonEmpty
          JButton leftDownButtonEmpty
          Left panel empty button.
        • leftLeftButton
          JButton leftLeftButton
          Left panel mouse button left.
        • leftRightButton
          JButton leftRightButton
          Left panel mouse button right.
        • leftUpButton
          JButton leftUpButton
          Left panel mouse button up.
        • leftUpButtonEmpty
          JButton leftUpButtonEmpty
          Empty button group.
        • middleDownButton
          JButton middleDownButton
          Middle panel down button.
        • middleLeftButton
          JButton middleLeftButton
          Middel panel left button.
        • middleLeftButtonEmpty
          JButton middleLeftButtonEmpty
          Middle panel empty button.
        • middleRightButton
          JButton middleRightButton
          Middle panel right button.
        • middleRightButtonEmpty
          JButton middleRightButtonEmpty
          Middle panel right button empty.
        • middleUpButton
          JButton middleUpButton
          Middel panel up button.
        • mode
          int mode
          Current mode std or fly.
        • mousePanel
          JPanel mousePanel
          Panel holds the mouse move buttons.
        • parentScene
          RenderViewBase parentScene
          Parent frame.
        • pressed
          boolean pressed
          If any of the mouse move button pressed.
        • radioX
          JRadioButton radioX
          Radio button of the X_AXIS mode option.
        • radioY
          JRadioButton radioY
          Radio button of the Y_AXIS mode option.
        • radioZ
          JRadioButton radioZ
          Radio button of the Z_AXIS mode option.
        • resetButton
          JButton resetButton
          Reset button.
        • rightDownButton
          JButton rightDownButton
          Right panel down button.
        • rightLeftButton
          JButton rightLeftButton
          Right panel left button.
        • rightRightButton
          JButton rightRightButton
          Right panel right button.
        • rightUpButton
          JButton rightUpButton
          Right panel up button.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanelCamera.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • snapButton
          JButton snapButton
          Camera button.
        • startButton
          JButton startButton
          Start button to auto snapshooting.
        • stdButton
          JRadioButton stdButton
          Auto snapshot button.
        • time
          long time
          Time to wait for the next mouse event.

    • Class gov.nih.mipav.view.renderer.J3D.JPanelClip

      class JPanelClip extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -3342110506544352170L

      • Serialized Fields

        • AclipPlanePts
          javax.vecmath.Vector4f[] AclipPlanePts
          Arbitrary clipping plane four corners points.
        • arbiMouseRotateBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseRotate arbiMouseRotateBehavior
          Mouse Rotate behavior of the arbitrary clipping plane.
        • arbiTG
          javax.media.j3d.TransformGroup arbiTG
          Tranform group for arbitrary clipping plane.
        • arbiTrans3d
          javax.media.j3d.Transform3D arbiTrans3d
          Transform3D group for clipSliceA frame box and ModelClip arbitrary clipping plane.
        • arbitrary_SG
          javax.media.j3d.Switch arbitrary_SG
          Arbitrary clipping plane switch group.
        • aSlice
          int aSlice
          Which arbitray clipping slice is currently displayed.
        • axisAngle
          float axisAngle
          Value attribute for the roation axis.
        • axisX
          float axisX
          Value attribute for the roation axis.
        • axisY
          float axisY
          Value attribute for the roation axis.
        • axisZ
          float axisZ
          Value attribute for the roation axis.
        • behaviorBG
          javax.media.j3d.BranchGroup behaviorBG
          The BranchGroup to which the arbitrary behaviors are attached and rotate.
        • boundingCheckA
          JCheckBox boundingCheckA
          Arbitrary and static clipping plane check box.
        • boundingCheckStatic
          JCheckBox boundingCheckStatic
          Arbitrary and static clipping plane check box.
        • boundingCheckStaticInv
          JCheckBox boundingCheckStaticInv
          Arbitrary and static clipping plane check box.
        • boundingCheckX
          JCheckBox boundingCheckX
          Check box to turn the clipping plane frame on and off.
        • boundingCheckXInv
          JCheckBox boundingCheckXInv
          X,Y,Z inverse clipping plane check box.
        • boundingCheckY
          JCheckBox boundingCheckY
          Check box to turn the clipping plane frame on and off.
        • boundingCheckYInv
          JCheckBox boundingCheckYInv
          X,Y,Z inverse clipping plane check box.
        • boundingCheckZ
          JCheckBox boundingCheckZ
          Check box to turn the clipping plane frame on and off.
        • boundingCheckZInv
          JCheckBox boundingCheckZInv
          X,Y,Z inverse clipping plane check box.
        • boxA
          JCheckBox boxA
          Static and static inverse, arbitrary clipping plane check box.
        • boxStatic
          JCheckBox boxStatic
          Static and static inverse, arbitrary clipping plane check box.
        • boxStaticInv
          JCheckBox boxStaticInv
          Static and static inverse, arbitrary clipping plane check box.
        • boxX
          JCheckBox boxX
          Check boxes that turn the image plane and the sliders on and off.
        • boxXInv
          JCheckBox boxXInv
          Check boxes that turn the image plane and the sliders on and off.
        • boxY
          JCheckBox boxY
          Check boxes that turn the image plane and the sliders on and off.
        • boxYInv
          JCheckBox boxYInv
          Check boxes that turn the image plane and the sliders on and off.
        • boxZ
          JCheckBox boxZ
          Check boxes that turn the image plane and the sliders on and off.
        • boxZInv
          JCheckBox boxZInv
          Check boxes that turn the image plane and the sliders on and off.
        • clipCount
          int clipCount
          Counters show the event number in the mouse recorder.
        • clipEvents
          MouseEventVector clipEvents
          Mouse event vector that record the clipping plane sliders changes.
        • clipSliceA
          ViewJComponentBoxSlice clipSliceA
          Arbitrary clipping plane yellow boundary indicator box.
        • clipSliceA_BG
          javax.media.j3d.BranchGroup clipSliceA_BG
          Arbitrary clipping branch group.
        • clipSliceAIndicator
          ViewJComponentBoxSlice clipSliceAIndicator
          Arbitrary clipping plane yellow boundary indicator box.
        • clipSliceAIndicator_BG
          javax.media.j3d.BranchGroup clipSliceAIndicator_BG
          Arbitrary clipping branch group.
        • clipSliceStatic
          ViewJComponentBoxSlice clipSliceStatic
          Static clipping plane boundary box.
        • clipSliceStaticInv
          ViewJComponentBoxSlice clipSliceStaticInv
          Static clipping plane boundary box.
        • clipSliceX
          ViewJComponentBoxSlice clipSliceX
          The bounding box frame around the clipping planes.
        • clipSliceXInv
          ViewJComponentBoxSlice clipSliceXInv
          X, Y, Z inverse clipping slice boundary box.
        • clipSliceY
          ViewJComponentBoxSlice clipSliceY
          The bounding box frame around the clipping planes.
        • clipSliceYInv
          ViewJComponentBoxSlice clipSliceYInv
          X, Y, Z inverse clipping slice boundary box.
        • clipSliceZ
          ViewJComponentBoxSlice clipSliceZ
          The bounding box frame around the clipping planes.
        • clipSliceZInv
          ViewJComponentBoxSlice clipSliceZInv
          X, Y, Z inverse clipping slice boundary box.
        • clipSliderStatic
          JSlider clipSliderStatic
          Static, static inverse and arbitrary clipping plane boundary box.
        • clipSliderStaticInv
          JSlider clipSliderStaticInv
          Static, static inverse and arbitrary clipping plane boundary box.
        • clipSliderX
          JSlider clipSliderX
          Sliders for the image planes.
        • clipSliderY
          JSlider clipSliderY
          Sliders for the image planes.
        • clipSliderZ
          JSlider clipSliderZ
          Sliders for the image planes.
        • colorButtonA
          JButton colorButtonA
          Color button for the arbitrary clipping plane frame.
        • colorButtonStatic
          JButton colorButtonStatic
          Color button for the static clipping plane frame.
        • colorButtonStaticInv
          JButton colorButtonStaticInv
          Color button for the static clipping plane frame.
        • colorButtonX
          JButton colorButtonX
          Color button for X clipping plane frame.
        • colorButtonXInv
          JButton colorButtonXInv
          Color button for X clipping plane frame.
        • colorButtonY
          JButton colorButtonY
          Color button for Y clipping plane frame.
        • colorButtonYInv
          JButton colorButtonYInv
          Color button for Y clipping plane frame.
        • colorButtonZ
          JButton colorButtonZ
          Color button for Z clipping plane frame.
        • colorButtonZInv
          JButton colorButtonZInv
          Color button for Z clipping plane frame.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser dialog.
        • enables
          boolean[] enables
          Enable flags for the 6 ( X, Y, Z and inverse ) clipping planes.
        • enablesArbi
          boolean[] enablesArbi
          Enable flags for the arbitrary clipping planes.
        • enablesStatic
          boolean[] enablesStatic
          Enable flags for the static clipping planes.
        • eqnA
          javax.vecmath.Vector4d eqnA
          Vector4D clipping equation of each clipping plane.
        • eqnPlanes
          javax.vecmath.Vector4d[] eqnPlanes
          Vetor holding the clipping plane equations.
        • eqnPlanesArbi
          javax.vecmath.Vector4d[] eqnPlanesArbi
          Vetor holding the clipping plane equations.
        • eqnPlanesStatic
          javax.vecmath.Vector4d[] eqnPlanesStatic
          Vetor holding the clipping plane equations.
        • eqnX
          javax.vecmath.Vector4d eqnX
          Vector4D clipping equation of each clipping plane.
        • eqnXInv
          javax.vecmath.Vector4d eqnXInv
          Vector4D clipping equation of each clipping plane.
        • eqnY
          javax.vecmath.Vector4d eqnY
          Vector4D clipping equation of each clipping plane.
        • eqnYInv
          javax.vecmath.Vector4d eqnYInv
          Vector4D clipping equation of each clipping plane.
        • eqnZ
          javax.vecmath.Vector4d eqnZ
          Vector4D clipping equation of each clipping plane.
        • eqnZInv
          javax.vecmath.Vector4d eqnZInv
          Vector4D clipping equation of each clipping plane.
        • extractButtonA
          JButton extractButtonA
          Extract arbitrary cliping plane button.
        • extractButtonS
          JButton extractButtonS
          Extract static eye cliping plane button.
        • intersectionPts
          javax.vecmath.Point3f[] intersectionPts
          intersectioin points coordinate.
        • iNumLights
          int iNumLights
          12 possible intersection points.
        • is6PlaneClipping
          boolean is6PlaneClipping
          Flag to indicate 6 plane clipping is active.
        • isClipArbiPicked
          boolean isClipArbiPicked
          Arbitrary clipping plane frame being picked or not.
        • isFirstTimeBuildTree
          boolean isFirstTimeBuildTree
          First time to build the clipping plane tree.
        • isStateChangedEvent
          boolean isStateChangedEvent
          Flag to indicate StateChangeEvent invoked.
        • isTransformChanged
          boolean isTransformChanged
          Flag to indicate tranformChanged event invoked.
        • labelA
          JLabel labelA
          Static cliiping slider labels.
        • labelAEnd
          JLabel labelAEnd
          Arbitrary clipping slider labels.
        • labelAMid
          JLabel labelAMid
          Arbitrary clipping slider labels.
        • labelAStart
          JLabel labelAStart
          Arbitrary clipping slider labels.
        • labelStatic
          JLabel labelStatic
          Static cliiping slider labels.
        • labelStaticEnd
          JLabel labelStaticEnd
          Static clipping plane labels.
        • labelStaticInv
          JLabel labelStaticInv
          Static cliiping slider labels.
        • labelStaticInvEnd
          JLabel labelStaticInvEnd
          Static inverse clipping plane labels.
        • labelStaticInvMid
          JLabel labelStaticInvMid
          Static inverse clipping plane labels.
        • labelStaticInvStart
          JLabel labelStaticInvStart
          Static inverse clipping plane labels.
        • labelStaticMid
          JLabel labelStaticMid
          Static clipping plane labels.
        • labelStaticStart
          JLabel labelStaticStart
          Static clipping plane labels.
        • labelX
          JLabel labelX
          Sliders labels.
        • labelXEnd
          JLabel labelXEnd
          Slider tick labels.
        • labelXEndInv
          JLabel labelXEndInv
          X clipping slider labels.
        • labelXInv
          JLabel labelXInv
          Sliders labels.
        • labelXMid
          JLabel labelXMid
          Slider tick labels.
        • labelXMidInv
          JLabel labelXMidInv
          X clipping slider labels.
        • labelXStart
          JLabel labelXStart
          Slider tick labels.
        • labelXStartInv
          JLabel labelXStartInv
          X clipping slider labels.
        • labelY
          JLabel labelY
          Sliders labels.
        • labelYEnd
          JLabel labelYEnd
          Y clipping slider labels.
        • labelYEndInv
          JLabel labelYEndInv
          Y inverse clipping slider labels.
        • labelYInv
          JLabel labelYInv
          Sliders labels.
        • labelYMid
          JLabel labelYMid
          Y clipping slider labels.
        • labelYMidInv
          JLabel labelYMidInv
          Y inverse clipping slider labels.
        • labelYStart
          JLabel labelYStart
          Y clipping slider labels.
        • labelYStartInv
          JLabel labelYStartInv
          Y inverse clipping slider labels.
        • labelZ
          JLabel labelZ
          Sliders labels.
        • labelZEnd
          JLabel labelZEnd
          Z clipping slider labels.
        • labelZEndInv
          JLabel labelZEndInv
          Z clipping slider labels.
        • labelZInv
          JLabel labelZInv
          Sliders labels.
        • labelZMid
          JLabel labelZMid
          Z clipping slider labels.
        • labelZMidInv
          JLabel labelZMidInv
          Z clipping slider labels.
        • labelZStart
          JLabel labelZStart
          Z clipping slider labels.
        • labelZStartInv
          JLabel labelZStartInv
          Z clipping slider labels.
        • m_aiImageA_backup
          int[] m_aiImageA_backup
          Backup of the data for undo:.
        • m_aiImageB_backup
          int[] m_aiImageB_backup
          ImageB backup buffer.
        • m_akLightBG
          javax.media.j3d.BranchGroup[] m_akLightBG
          Parent of each light bulb.
        • m_akLightMaterials
          javax.media.j3d.Material[] m_akLightMaterials
          Material properties for each light bulb.
        • m_akLightSpheres
          com.sun.j3d.utils.geometry.Sphere[] m_akLightSpheres
          Shapes representing light bulbs.
        • m_akLightTransformGroup
          javax.media.j3d.TransformGroup[] m_akLightTransformGroup
          Parent transform group.
        • m_kLightRoot
          javax.media.j3d.BranchGroup m_kLightRoot
          Parent of all the light bulbs.
        • maxBox
          float maxBox
          The largest of xBox,yBox,and zBox.
        • maxDim
          int maxDim
          The largest dimension of xDim, yDim and zDim.
        • mc
          javax.media.j3d.ModelClip mc
          Global model clip object.
        • mcArbi
          javax.media.j3d.ModelClip mcArbi
          Global model clip object.
        • mcArbiBG
          javax.media.j3d.BranchGroup mcArbiBG
          Branch group of the arbitrary clipping plane.
        • mcArbiExtendBG
          javax.media.j3d.BranchGroup mcArbiExtendBG
          Branch group of the arbitrary clipping plane.
        • mcArbiTG
          javax.media.j3d.TransformGroup mcArbiTG
          ModelClip arbitrary TransformGroup.
        • mcArbiTrans3D
          javax.media.j3d.Transform3D mcArbiTrans3D
          Transform3D group for clipSliceA frame box and ModelClip arbitrary clipping plane.
        • mcBG
          javax.media.j3d.BranchGroup mcBG
          Branch group of the 6 clipping planes.
        • mcExtendBG
          javax.media.j3d.BranchGroup mcExtendBG
          Branch group of the arbitrary clipping plane.
        • mcStatic
          javax.media.j3d.ModelClip mcStatic
          Global model clip object.
        • mcStaticBG
          javax.media.j3d.BranchGroup mcStaticBG
          Branch group of the static clipping plane.
        • objClipSliceA_BG
          javax.media.j3d.BranchGroup objClipSliceA_BG
          Arbitrary clipping branch group.
        • objClipSlices_BG
          javax.media.j3d.BranchGroup objClipSlices_BG
          root of all the clipping slices branch group.
        • objClipSliceStatic_BG
          javax.media.j3d.BranchGroup objClipSliceStatic_BG
          Static clipping branch group.
        • objClipSliceStaticInv_BG
          javax.media.j3d.BranchGroup objClipSliceStaticInv_BG
          Static clipping branch group.
        • objClipSliceX_BG
          javax.media.j3d.BranchGroup objClipSliceX_BG
          Parent for each individual clip slices branch group, childen of objClipSlices_BG.
        • objClipSliceXInv_BG
          javax.media.j3d.BranchGroup objClipSliceXInv_BG
          Parent of the -x, -y, -z clip slices branchgroup.
        • objClipSliceY_BG
          javax.media.j3d.BranchGroup objClipSliceY_BG
          Parent for each individual clip slices branch group, childen of objClipSlices_BG.
        • objClipSliceYInv_BG
          javax.media.j3d.BranchGroup objClipSliceYInv_BG
          Parent of the -x, -y, -z clip slices branchgroup.
        • objClipSliceZ_BG
          javax.media.j3d.BranchGroup objClipSliceZ_BG
          Parent for each individual clip slices branch group, childen of objClipSlices_BG.
        • objClipSliceZInv_BG
          javax.media.j3d.BranchGroup objClipSliceZInv_BG
          Parent of the -x, -y, -z clip slices branchgroup.
        • panelA
          JPanel panelA
          Arbitrary and static control panels.
        • panelS
          JPanel panelS
          Arbitrary and static control panels.
        • panelSInv
          JPanel panelSInv
          Arbitrary and static control panels.
        • panelX
          JPanel panelX
          Declare each clipping plane control panel.
        • panelXInv
          JPanel panelXInv
          Declare each clipping plane control panel.
        • panelY
          JPanel panelY
          Declare each clipping plane control panel.
        • panelYInv
          JPanel panelYInv
          Declare each clipping plane control panel.
        • panelZ
          JPanel panelZ
          Declare each clipping plane control panel.
        • panelZInv
          JPanel panelZInv
          Declare each clipping plane control panel.
        • radicalRatio
          float radicalRatio
          Arbitrary clipping plane expanding ratio.
        • recordEventName
          boolean recordEventName
          Flag indicates whether to record the clip event name.
        • rotationAxis
          javax.vecmath.AxisAngle4f rotationAxis
          Rotation axis to sync up the action for both ModelClip arbitrary clipping plane and the clipSliceA frame box transformGroup.
        • rotationCount
          int rotationCount
          Counters show the event number in the mouse recorder.
        • rotationEvent
          MouseEventVector rotationEvent
          mouse rotation event vector for the arbitrary clipping plane.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Used when the screen is small.
        • scrollPanel
          JPanelClip.DrawingPanel scrollPanel
          Scroll panel that holding all the control components.
        • sliderA
          JSlider sliderA
          Static, static inverse and arbitrary clipping plane boundary box.
        • sliderXInv
          JSlider sliderXInv
          Sliders for the image planes.
        • sliderYInv
          JSlider sliderYInv
          Sliders for the image planes.
        • sliderZInv
          JSlider sliderZInv
          Sliders for the image planes.
        • sSlice
          int sSlice
          Record the current static clipping slice number.
        • sSliceInv
          int sSliceInv
          Record the current static clipping slice number.
        • tabbedPane
          JTabbedPane tabbedPane
          Tabbed Panel that hold the each clipping planes control box.
        • textA
          JTextField textA
          Static and arbitrary text field.
        • textStatic
          JTextField textStatic
          Static and arbitrary text field.
        • textStaticInv
          JTextField textStaticInv
          Static and arbitrary text field.
        • textX
          JTextField textX
          Text fields that display the slice number when slider moves.
        • textXInv
          JTextField textXInv
          X, Y, Z inverse text field.
        • textY
          JTextField textY
          Text fields that display the slice number when slider moves.
        • textYInv
          JTextField textYInv
          X, Y, Z inverse text field.
        • textZ
          JTextField textZ
          Text fields that display the slice number when slider moves.
        • textZInv
          JTextField textZInv
          X, Y, Z inverse text field.
        • xBox
          float xBox
          xBox, yBox, zBox from the parent scene.
        • xDim
          int xDim
          Image X, Y, Z dimension.
        • xSlice
          int xSlice
          Which slice is currently displayed in the ZY plane.
        • xSliceInv
          int xSliceInv
          Which slice is currently displayed in the ZY plane.
        • yBox
          float yBox
          xBox, yBox, zBox from the parent scene.
        • yDim
          int yDim
          Image X, Y, Z dimension.
        • ySlice
          int ySlice
          Which slice is currently displayed in the XZ plane.
        • ySliceInv
          int ySliceInv
          Which slice is currently displayed in the XZ plane.
        • zBox
          float zBox
          xBox, yBox, zBox from the parent scene.
        • zDim
          int zDim
          Image X, Y, Z dimension.
        • zSlice
          int zSlice
          Which slice is currently displayed in the XY plane.
        • zSliceInv
          int zSliceInv
          Which slice is currently displayed in the XY plane.

    • Class gov.nih.mipav.view.renderer.J3D.JPanelLights

      class JPanelLights extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      8549491288085975699L

      • Serialized Fields

        • ambientRadio
          JRadioButton ambientRadio
          Radio button for different light type.
        • bNeedsRedraw
          boolean bNeedsRedraw
          Flag is set if one of the controls changed a value and the renderering needs to be redrawn when the mouse is released.
        • checkBoxShowLight
          JCheckBox checkBoxShowLight
          Check box to show the light bulb or not.
        • colorButton
          JButton colorButton
          Color button, checkBox On/Off.
        • colorChooser
          ViewJColorChooser colorChooser
          Color choose dialog reference.
        • colorLabel
          JLabel colorLabel
          Color label.
        • controlPanel
          JPanel controlPanel
          Control panel.
        • controlPanelBox
          Box controlPanelBox
          Control panel box that hold the control panel.
        • directionalRadio
          JRadioButton directionalRadio
          Directional light radio botton.
        • drawPanel
          JPanel drawPanel
          Scroll panel reference.
        • intensitySlider
          JSlider intensitySlider
          Intensity slider.
        • iSelect
          int iSelect
          index of currently selected one.
        • labelIntensity
          JLabel labelIntensity
          Light intensity label.
        • labelIntensityBegin
          JLabel labelIntensityBegin
          Light intensity label begin.
        • labelIntensityEnd
          JLabel labelIntensityEnd
          Light intensity label end.
        • labelIntensityMid
          JLabel labelIntensityMid
          Light intensity label middle.
        • labelShininess
          JLabel labelShininess
          Light shinness label.
        • labelShininessBegin
          JLabel labelShininessBegin
          Shinness label begin.
        • labelShininessEnd
          JLabel labelShininessEnd
          Shinness label end.
        • labelShininessMid
          JLabel labelShininessMid
          Shinness lable middle.
        • list
          JList list
          List of lights.
        • m_aiLightScale
          int[] m_aiLightScale
          Light scale factor array.
        • m_akLights
          GeneralLight[] m_akLights
          The structure for the light bulbs.
        • m_akModelLights
          GeneralLight[] m_akModelLights
          General light array.
        • m_akSoftwareLightsModel
          SoftwareLight[] m_akSoftwareLightsModel
          Soft light array.
        • m_akSoftwareLightsWorld
          SoftwareLight[] m_akSoftwareLightsWorld
          Lighting objects needed for software rendering.
        • m_akWorldLights
          GeneralLight[] m_akWorldLights
          World general light array.
        • m_kGPUVolumeRender
          VolumeTriPlanarRender m_kGPUVolumeRender
        • m_kLabelPosX
          JLabel m_kLabelPosX
          Label for slider X position.
        • m_kLabelPosY
          JLabel m_kLabelPosY
          Label for slider Y position.
        • m_kLabelPosZ
          JLabel m_kLabelPosZ
          Label for slider Z position.
        • m_kLabelTrgX
          JLabel m_kLabelTrgX
          Label for X light target position.
        • m_kLabelTrgY
          JLabel m_kLabelTrgY
          Label for Y light target position.
        • m_kLabelTrgZ
          JLabel m_kLabelTrgZ
          Label for Z light target position.
        • m_kPanelSurface
          JPanelSurface m_kPanelSurface
          surface panel reference.
        • m_kRenderSurface
          SurfaceRender m_kRenderSurface
          Parent render frame reference.
        • m_kSliderPosX
          JSlider m_kSliderPosX
          Light x position slider.
        • m_kSliderPosY
          JSlider m_kSliderPosY
          Light y position slider.
        • m_kSliderPosZ
          JSlider m_kSliderPosZ
          Light z position slider.
        • m_kSliderTrgX
          JSlider m_kSliderTrgX
          Light x target position slider.
        • m_kSliderTrgY
          JSlider m_kSliderTrgY
          Light y target position slider.
        • m_kSliderTrgZ
          JSlider m_kSliderTrgZ
          Light z target position slider.
        • m_kTextPosX
          JTextField m_kTextPosX
          X position text field.
        • m_kTextPosY
          JTextField m_kTextPosY
          Y position text field.
        • m_kTextPosZ
          JTextField m_kTextPosZ
          Z position text field.
        • m_kTextTrgX
          JTextField m_kTextTrgX
          X target position text field.
        • m_kTextTrgY
          JTextField m_kTextTrgY
          Y target position text field.
        • m_kTextTrgZ
          JTextField m_kTextTrgZ
          Z target position text field.
        • maxBox
          float maxBox
          x, y, z box size.
        • onOffCheckBox
          JCheckBox onOffCheckBox
          Light turn on/off check box.
        • onOffLabel
          JLabel onOffLabel
          Light turn on/off label.
        • pointRadio
          JRadioButton pointRadio
          Point light radio button.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanel scrollPanel
          Scroll the control panel when the frame changes size.
        • shininessPanel
          JPanel shininessPanel
          Shininess panel.
        • shininessSlider
          JSlider shininessSlider
          Shininess slider.
        • spotRadio
          JRadioButton spotRadio
          Spot light radio button.
        • textIntensity
          JTextField textIntensity
          Light intensity textfield.
        • textShininess
          JTextField textShininess
          Light shinness textfield.
        • xBox
          float xBox
          x, y, z box size.
        • yBox
          float yBox
          x, y, z box size.
        • zBox
          float zBox
          x, y, z box size.

    • Class gov.nih.mipav.view.renderer.J3D.JPanelRendererJ3D

      class JPanelRendererJ3D extends JPanelRendererBase implements Serializable

      • Serialized Fields

        • rayBasedRender
          VolumeRenderer rayBasedRender
          Raycast based renderer reference, raycast renderer or shear warp renderer.
        • renderBase
          RenderViewBase renderBase
          Render base.

    • Class gov.nih.mipav.view.renderer.J3D.JPanelSculptor

      class JPanelSculptor extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      4235930260988710821L

      • Serialized Fields

        • lineButton
          JToggleButton lineButton
          Line shape button.
        • m_iSculptHeight
          int m_iSculptHeight
          DOCUMENT ME!
        • m_iSculptWidth
          int m_iSculptWidth
          Window information for Sculpting:.
        • m_kApplySculptButton
          JButton m_kApplySculptButton
          Button to apply sculpt region to the volume.
        • m_kClearDrawOutlineButton
          JButton m_kClearDrawOutlineButton
          Button for clearing the sculpt region.
        • m_kDrawOutlineButton
          JToggleButton m_kDrawOutlineButton
          Toggle button is down while the mouse is used to draw the sculpt outline.
        • m_kInvertOutlineButton
          JButton m_kInvertOutlineButton
          Button for inverting the sculpt region.
        • m_kSaveSculptButton
          JButton m_kSaveSculptButton
          Button to save the sculpt image.
        • m_kTextureSculptor
          TextureSculptor m_kTextureSculptor
          DOCUMENT ME!
        • m_kUndoSculptButton
          JButton m_kUndoSculptButton
          Button to undo the sculpt and restor the original volume.
        • m_kVolumeSculptor
          VolumeSculptor m_kVolumeSculptor
          Sculptor object enables, draws and sculpts the volume based on the outline region drawn on screen. Handles drawing the sculpt region.
        • mainPanel
          JPanel mainPanel
          Control panel for volume sculpting.
        • rectButton
          JToggleButton rectButton
          Rectangle shape button.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JPanelSculptor.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • surRender
          SurfaceRender surRender
          SurfaceRender reference.
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          Toolbar builder reference.

    • Class gov.nih.mipav.view.renderer.J3D.JPanelVolOpacity

      class JPanelVolOpacity extends JPanelVolOpacityBase implements Serializable
      serialVersionUID:
      -2618795264166878795L

      • Serialized Fields

        • histogramA
          ModelHistogram histogramA
          Deprecated.
          Histogram reference for image A.
        • histogramB
          ModelHistogram histogramB
          Deprecated.
          Histogram reference for image B.
        • histogramGM_A
          ModelHistogram histogramGM_A
          Deprecated.
          Histogram reference for imageA GM.
        • histogramGM_B
          ModelHistogram histogramGM_B
          Deprecated.
          Histogram reference for imageB GM.
        • rendererProgressBar
          JProgressBar rendererProgressBar
          Deprecated.
          A reference to the volume renderer frame's progress bar.

    • Class gov.nih.mipav.view.renderer.J3D.JPanelVolOpacityBase

      class JPanelVolOpacityBase extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -5320201609864903620L

      • Serialized Fields

        • blendSlider
          JSlider blendSlider
          Deprecated.
          Opacity slider of texture 3D volume opacity changes.
        • componentOpacityA
          ViewJComponentVolOpacityBase componentOpacityA
          Deprecated.
          Reference to compoment opacity control A.
        • componentOpacityB
          ViewJComponentVolOpacityBase componentOpacityB
          Deprecated.
          Reference to compoment opacity control B.
        • componentOpacityGM_A
          ViewJComponentVolOpacityBase componentOpacityGM_A
          Deprecated.
          Reference to compoment opacity control A GM Rescale.
        • componentOpacityGM_B
          ViewJComponentVolOpacityBase componentOpacityGM_B
          Deprecated.
          Reference to compoment opacity control B GM Rescale.
        • GMCheckBox
          JCheckBox GMCheckBox
          Deprecated.
          Gradient Magnitude Check box of the grey scale image.
        • gradMagRescale_A
          ModelImage gradMagRescale_A
          Deprecated.
          Model image of the gradient magnitude of image A rescaled to have value in the range [0:255].
        • gradMagRescale_B
          ModelImage gradMagRescale_B
          Deprecated.
          Model image of the gradient magnitude of image B rescaled to have value in the range [0:255].
        • imageA
          ModelImage imageA
          Deprecated.
          Model image A.
        • imageB
          ModelImage imageB
          Deprecated.
          Model image B.
        • labelsTable
          Hashtable labelsTable
          Deprecated.
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • labelsTableB
          Hashtable labelsTableB
          Deprecated.
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • labelsTableGM_A
          Hashtable labelsTableGM_A
          Deprecated.
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • labelsTableGM_B
          Hashtable labelsTableGM_B
          Deprecated.
          Historgram dialog slider labels of the imageA, B and GM imageA, B.
        • m_kVolumeViewer
          VolumeTriPlanarInterface m_kVolumeViewer
          Deprecated.
          Render base.
        • middleLabelValueA
          float middleLabelValueA
          Deprecated.
          DOCUMENT ME!
        • middleLabelValueB
          float middleLabelValueB
          Deprecated.
          DOCUMENT ME!
        • middleLabelValueGM_A
          float middleLabelValueGM_A
          Deprecated.
          DOCUMENT ME!
        • middleLabelValueGM_B
          float middleLabelValueGM_B
          Deprecated.
          DOCUMENT ME!
        • mouseSlider
          JSlider mouseSlider
          Deprecated.
          DOCUMENT ME!
        • mouseSliderB
          JSlider mouseSliderB
          Deprecated.
          DOCUMENT ME!
        • mouseSliderGM_A
          JSlider mouseSliderGM_A
          Deprecated.
          DOCUMENT ME!
        • mouseSliderGM_B
          JSlider mouseSliderGM_B
          Deprecated.
          DOCUMENT ME!
        • opacitySliderLabelsA
          JLabel[] opacitySliderLabelsA
          Deprecated.
          The labels below the opacity slider.
        • opacitySliderLabelsB
          JLabel[] opacitySliderLabelsB
          Deprecated.
          The labels below the opacity slider.
        • opacitySliderLabelsGM_A
          JLabel[] opacitySliderLabelsGM_A
          Deprecated.
          DOCUMENT ME!
        • opacitySliderLabelsGM_B
          JLabel[] opacitySliderLabelsGM_B
          Deprecated.
          DOCUMENT ME!
        • panelOpacityA
          JPanel panelOpacityA
          Deprecated.
          Panels that hold the the control components (opacity maps).
        • panelOpacityB
          JPanel panelOpacityB
          Deprecated.
          DOCUMENT ME!
        • panelOpacityGM_A
          JPanel panelOpacityGM_A
          Deprecated.
          DOCUMENT ME!
        • panelOpacityGM_B
          JPanel panelOpacityGM_B
          Deprecated.
          DOCUMENT ME!
        • rangeText
          JTextField rangeText
          Deprecated.
          X range text field in the imageA, B histogram dialog.
        • rangeTextB
          JTextField rangeTextB
          Deprecated.
          X range text field in the imageA, B histogram dialog.
        • rangeTextGM_A
          JTextField rangeTextGM_A
          Deprecated.
          X range text field in the Gradient Magnitude imageA, B histogram dialog.
        • rangeTextGM_B
          JTextField rangeTextGM_B
          Deprecated.
          X range text field in the Gradient Magnitude imageA, B histogram dialog.
        • scaleRangeA
          float scaleRangeA
          Deprecated.
          Scale range value according to the image min and max.
        • scaleRangeB
          float scaleRangeB
          Deprecated.
          Scale range value according to the image min and max.
        • scaleRangeGM_A
          float scaleRangeGM_A
          Deprecated.
          Scale range value according to the image min and max.
        • scaleRangeGM_B
          float scaleRangeGM_B
          Deprecated.
          Scale range value according to the image min and max.
        • tabbedPane
          JTabbedPane tabbedPane
          Deprecated.
          Tabbed pane that contains the list of opacity functions.
        • xRangeTextA
          JTextField xRangeTextA
          Deprecated.
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • xRangeTextB
          JTextField xRangeTextB
          Deprecated.
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • xRangeTextGM_A
          JTextField xRangeTextGM_A
          Deprecated.
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • xRangeTextGM_B
          JTextField xRangeTextGM_B
          Deprecated.
          X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextA
          JTextField yRangeTextA
          Deprecated.
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextB
          JTextField yRangeTextB
          Deprecated.
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextGM_A
          JTextField yRangeTextGM_A
          Deprecated.
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.
        • yRangeTextGM_B
          JTextField yRangeTextGM_B
          Deprecated.
          Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

    • Class gov.nih.mipav.view.renderer.J3D.PlaneRender

      class PlaneRender extends VolumeCanvas3D implements Serializable
      serialVersionUID:
      2025132936439496099L

      • Serialized Fields

        • m_aiLocalImageExtents
          int[] m_aiLocalImageExtents
          The image dimensions in x,y,z:.
        • m_akColors
          javax.vecmath.Color3f[] m_akColors
          Set of colors used to draw the X and Y Bars and the Z box:.
        • m_akImageComponent
          javax.media.j3d.ImageComponent2D[] m_akImageComponent
          Image component 2D. Used to store the ModelImage data as textures.
        • m_bDrawAxes
          boolean m_bDrawAxes
          when true, the axis labels (P-> L-> S->) will be drawn
        • m_bDrawXHairs
          boolean m_bDrawXHairs
          Turns on drawing of the X,Y bars and the Axis labels:.
        • m_bEntryPointSelect
          boolean m_bEntryPointSelect
          Boolean to turn on/off the RFA probe entry point selection with mouse:.
        • m_bFirstDrag
          boolean m_bFirstDrag
          Change the mouse cursor with the first mouseDrag event
        • m_bLeftMousePressed
          boolean m_bLeftMousePressed
          True when the left mouse has been pressed, set to false when the left mouse button is released.
        • m_bMemoryUsage
          boolean m_bMemoryUsage
          Whether to store all the data in ImageComponent2D array or not:.
        • m_bPatientOrientation
          boolean m_bPatientOrientation
          Actual image orietation.
        • m_bRightMousePressed
          boolean m_bRightMousePressed
          Flag indicating if the right mouse button is currently pressed down:
        • m_fCenterX
          float m_fCenterX
          The center of the X,Y bar cross hairs, in plane coordinates:.
        • m_fCenterY
          float m_fCenterY
          The center of the X,Y bar cross hairs, in plane coordinates:.
        • m_fMaxBox
          float m_fMaxBox
          Numbers dicatating the size of the plane based on the extents and resolutions of the image.
        • m_fX0
          float m_fX0
          lower x-bound of the texture-mapped polygon:
        • m_fX1
          float m_fX1
          upper x-bound of the texture-mapped polygon:
        • m_fXBox
          float m_fXBox
          Numbers dicatating the size of the plane based on the extents and resolutions of the image.
        • m_fXRange
          float m_fXRange
          Width of the texture-mapped polygon:
        • m_fXTranslate
          float m_fXTranslate
          X direction mouse translation.
        • m_fY0
          float m_fY0
          lower y-bound of the texture-mapped polygon:
        • m_fY1
          float m_fY1
          upper y-bound of the texture-mapped polygon:
        • m_fYBox
          float m_fYBox
          Numbers dicatating the size of the plane based on the extents and resolutions of the image.
        • m_fYRange
          float m_fYRange
          Height of the texture-mapped polygon:
        • m_fYTranslate
          float m_fYTranslate
          Y direction mouse translatioin.
        • m_fZoomScale
          float m_fZoomScale
          Image scaling from Zoom:.
        • m_iPlaneOrientation
          int m_iPlaneOrientation
          Which dimension of the ModelImage to render.
        • m_iSlice
          int m_iSlice
          Which slice is currently displayed in the XY plane.
        • m_kActiveImage
          ModelImage m_kActiveImage
          Current active image for manipulating the LUT by dragging with the right-mouse down.
        • m_kActiveLookupTable
          ModelStorageBase m_kActiveLookupTable
          The current active lookup table:
        • m_kCanvas
          VolumeCanvas3D m_kCanvas
          The Canvas3D object on which the plane is drawn.
        • m_kCurrentTransform
          javax.media.j3d.Transform3D m_kCurrentTransform
          current zoom transformation
        • m_kDisplayedImage
          javax.media.j3d.ImageComponent2D m_kDisplayedImage
          The current displayed texture, based on the value of m_iSlice.
        • m_kImageA
          ModelImage m_kImageA
          Current image A.
        • m_kImageB
          ModelImage m_kImageB
          Current image B.
        • m_kLabelX
          String m_kLabelX
          x-axis label:
        • m_kLabelY
          String m_kLabelY
          y-axis label:
        • m_kMouseTranslate
          MouseTranslation m_kMouseTranslate
          Mouse translate behavior.
        • m_kMouseZoom
          MouseZoomBehavior m_kMouseZoom
          Mouse zoom behavior.
        • m_kObjRootBG
          javax.media.j3d.BranchGroup m_kObjRootBG
          The BranchGroup root of the scene managed by the simple universe. The root has a single child, a TransformGroup, that manages all of the actual objects.
        • m_kOrderedGroup
          javax.media.j3d.OrderedGroup m_kOrderedGroup
          Root order group of the image scene graph.
        • m_kParent
          ViewJFrameVolumeView m_kParent
          Reference to the parent frame:.
        • m_kPatientSlice
          PatientSlice m_kPatientSlice
          PatientSlice contains all the Patient Coordinate System view-specific data for rendering this component:
        • m_kRFA_BranchGroup
          javax.media.j3d.BranchGroup m_kRFA_BranchGroup
          Branch group for the RFA indicator point.
        • m_kTextBranchGroup
          javax.media.j3d.BranchGroup m_kTextBranchGroup
          Branch group to hold the texture image.
        • m_kTextTransformGroup
          javax.media.j3d.TransformGroup m_kTextTransformGroup
          Transform group to hold the texture images.
        • m_kTexture
          javax.media.j3d.Texture2D m_kTexture
          The 2D texture for the texture-mapped polygon.
        • m_kTranslationTG
          javax.media.j3d.TransformGroup m_kTranslationTG
          Group dictating how the plane is translated.
        • m_kUniverse
          com.sun.j3d.utils.universe.SimpleUniverse m_kUniverse
          The SimpleUniverse object which is the parent of everything else in the scene.
        • m_kWinLevel
          WindowLevel m_kWinLevel

    • Class gov.nih.mipav.view.renderer.J3D.RenderViewBase

      class RenderViewBase extends VolumeCanvas3D implements Serializable
      serialVersionUID:
      2913636735677876386L

      • Serialized Fields

        • background
          javax.media.j3d.Background background
          The background node for the canvas.
        • bounds
          javax.media.j3d.BoundingSphere bounds
          A BoundingSphere that contains the entire scene. This bound is used for all scheduling, including lighting and mouse behaviors.
        • boxFrame
          ViewJComponentBoxFrame boxFrame
          The outside box frame.
        • canvas
          VolumeCanvas3D canvas
          The Canvas3D object on which the surfaces are drawn and where the picking happens.
        • captureFrame
          ViewJFrameRenderCamera captureFrame
          Camera snapshot frame.
        • captureImage
          ModelImage captureImage
          The resulting ModelImage of the camera snapshot.
        • config
          GraphicsConfiguration config
          The config used to extends the Canvas3D class.
        • displayMode
          int displayMode
          Indicates which image is to be acted upon when two images are displayed.
        • imageA
          ModelImage imageA
          Reference to the image A of this frame.
        • imageB
          ModelImage imageB
          Reference to the image Bof this frame.
        • LUTa
          ModelLUT LUTa
          Reference to LUT for image A.
        • LUTb
          ModelLUT LUTb
          Reference to LUT for image B.
        • objBehaviorBG
          javax.media.j3d.BranchGroup objBehaviorBG
          The BranchGroup to which the standard behaviors are attached, zoom and rotate.
        • objBoxFrameBG
          javax.media.j3d.BranchGroup objBoxFrameBG
          Parent of the whole box frame.
        • objRootBG
          javax.media.j3d.BranchGroup objRootBG
          The BranchGroup root of the scene managed by the simple universe. The root has a single child, a TransformGroup, that manages all of the actual scene objects.
        • rotationAngle
          int rotationAngle
          Rotation angle when the camera takes snapshot.
        • rotationAxis
          int rotationAxis
          Rotation axis when the camera takes snapshot.
        • rotationControlPanel
          JPanelCamera rotationControlPanel
          Camera control dialog box.
        • rotationTimes
          int rotationTimes
          Number of rotation during the camera auto snapshotting.
        • rotationTotal
          int rotationTotal
          The total rotation degree, fixing one bug.
        • sceneRootTG
          javax.media.j3d.TransformGroup sceneRootTG
          A TransformGroup object to which all the scene objects are attached, including 3D images, surface, behavior, and lights.
        • sliderEvents
          MouseEventVector sliderEvents
          Slider events used by the mouse recorder.
        • transRotation
          javax.media.j3d.Transform3D transRotation
          transform rotation of the volume image during camera snapshot.
        • transRotationMatrix
          javax.media.j3d.Transform3D transRotationMatrix
          Rotation matrix.
        • triPlanarViewBG
          javax.media.j3d.BranchGroup triPlanarViewBG
          Triplanar view branch group, which hold the three plane view and the slice box frame view.
        • universe
          com.sun.j3d.utils.universe.SimpleUniverse universe
          The SimpleUniverse object which is the parent of everything else in the scene.
        • viewPanel
          JPanelView viewPanel
          View dialog associated with surface plotter or renderer.

    • Class gov.nih.mipav.view.renderer.J3D.ViewJComponentVolOpacity

      class ViewJComponentVolOpacity extends ViewJComponentVolOpacityBase implements Serializable
      serialVersionUID:
      -5441344478555285964L

      • Serialized Fields

        • myParent
          RenderViewBase myParent
          DOCUMENT ME!
        • opacityCount
          int opacityCount
          Opacity slider event count.
        • opacityEvents
          MouseEventVector opacityEvents
          Opacity slider changed events, which is used by the mouse recorder.

    • Class gov.nih.mipav.view.renderer.J3D.ViewJFrameRenderCamera

      class ViewJFrameRenderCamera extends ViewJFrameBase implements Serializable
      serialVersionUID:
      -6223794265610151148L

      • Serialized Fields

        • borderColor
          Color borderColor
          color for the line border surrounding each image in the light-box.
        • borderSize
          int borderSize
          spacing for the line border surrounding each image in the light-box.
        • componentImageVector
          Vector componentImageVector
          DOCUMENT ME!
        • currentSelectedSlice
          int currentSelectedSlice
          DOCUMENT ME!
        • currentSlice
          int currentSlice
          current info -- this slice info refers to the *real* slice number, not the page index for a slice on a page.
        • deleteButton
          JButton deleteButton
          Delete the captured image button.
        • deleteSelection
          JMenuItem deleteSelection
          Delete menu icon item.
        • extractButton
          JButton extractButton
          Extract the selected image button.
        • extractSelection
          JMenuItem extractSelection
          Extrace menu icon item.
        • firstTime
          boolean firstTime
          DOCUMENT ME!
        • frameHeight
          int frameHeight
          DOCUMENT ME!
        • frameStartLocation
          Point frameStartLocation
          DOCUMENT ME!
        • frameWidth
          int frameWidth
          frame information.
        • gridColor
          Color gridColor
          color for the region in-between the images in the light-box.
        • gridColumn
          int gridColumn
          DOCUMENT ME!
        • gridRow
          int gridRow
          value for the number of rows (number of images along the y-axis) and columns (number of images along the x-axis) in the light-box.

          Note that both row and column set to 1 cannot make sense, but that one or the other will be the 'dependent variable' as defined by the row_dependent boolean var.

          A value of 0 means that the dependent variable will automatically be sized to its maximum size that can fit nicely on the screen.

        • gridSpacing
          int gridSpacing
          spacing between images in the light-box.
        • group
          ButtonGroup group
          DOCUMENT ME!
        • imageBorderVector
          Vector imageBorderVector
          DOCUMENT ME!
        • imageBufferA
          float[] imageBufferA
          DOCUMENT ME!
        • imageHeight
          int imageHeight
          DOCUMENT ME!
        • imagePanelSizeX
          int imagePanelSizeX
          per num visible images information.
        • imagePanelSizeY
          int imagePanelSizeY
          per num visible images information.
        • imagePanelVector
          Vector imagePanelVector
          DOCUMENT ME!
        • imageWidth
          int imageWidth
          DOCUMENT ME!
        • lastSelectedSlice
          int lastSelectedSlice
          DOCUMENT ME!
        • magMax
          float magMax
          DOCUMENT ME!
        • magMin
          float magMin
          DOCUMENT ME!
        • magnification
          float magnification
          magnification of images in the light-box (mag is a percentage).
        • maxPagePanelSizeX
          int maxPagePanelSizeX
          DOCUMENT ME!
        • maxPagePanelSizeY
          int maxPagePanelSizeY
          DOCUMENT ME!
        • menuBar
          JMenuBar menuBar
          variables for the menubar.
        • modelImageVector
          Vector modelImageVector
          DOCUMENT ME!
        • numTotalSlices
          int numTotalSlices
          DOCUMENT ME!
        • pagePanel
          JPanel pagePanel
          Number of pages in this frame will always be one.
        • pagePanelSizeX
          int pagePanelSizeX
          DOCUMENT ME!
        • pagePanelSizeY
          int pagePanelSizeY
          DOCUMENT ME!
        • pageScrollPanel
          JScrollPane pageScrollPanel
          Scroll panel to handle the frame scolling.
        • parentFrame
          RenderViewBase parentFrame
          DOCUMENT ME!
        • pBarVisible
          boolean pBarVisible
          Flag indicating if a whether of not the progress bar is visible.
        • pixBuffer
          int[] pixBuffer
          DOCUMENT ME!
        • progressBar
          ViewJProgressBar progressBar
          Progress bar object.
        • progressBarLocation
          Point progressBarLocation
          Progress bar default location.
        • progressMode
          int progressMode
          Progress mode - either standard, no cancel, or no progress bar.
        • row_dependent
          boolean row_dependent
          indicates which--row or column--should be dependent on the other.

          the default is the number of rows is the dependent variable, and is dependent apon the total number of images and the number of columns. Don't confuse the reading to be "This display is (t/f) dependent on the row." It -could- be read as "The display is a column-independent (t/f) matrix".

        • selectedBorderColor
          Color selectedBorderColor
          color for the line border surrounding each selected image in the light-box.
        • selectedBorderSize
          int selectedBorderSize
          spacing for the selected line border surrounding each image in the light-box.
        • selectedImages
          Vector selectedImages
          the selectedImages contains the *real* slice numbers -- not the index of a slice on a page. So the maximum number in the vector will be numTotalSlices - 1.
        • srcImage
          ModelImage srcImage
          Reference to imageA.
        • tBar
          JToolBar tBar
          Frame ToolBar.
        • toolbarPanel
          JPanel toolbarPanel
          variables for the toolbar.
        • unselectedBorderColor
          Color unselectedBorderColor
          DOCUMENT ME!
        • xScreen
          int xScreen
          DOCUMENT ME!
        • yScreen
          int yScreen
          DOCUMENT ME!

    • Class gov.nih.mipav.view.renderer.J3D.ViewJFrameVolumeView

      class ViewJFrameVolumeView extends ViewJFrameBase implements Serializable
      serialVersionUID:
      1898957906984534260L

      • Serialized Fields

        • axialOrientation
          boolean axialOrientation
          Indicates that image orientation is unknown type or not.
        • brainsurfaceFlattenerRender
          MjCorticalAnalysis brainsurfaceFlattenerRender
          Rendering the brainsurfaceFlattener objects.
        • cameraPanel
          JPanel cameraPanel
          DOCUMENT ME!
        • clipBox
          JPanel clipBox
          DOCUMENT ME!
        • clipButton
          JButton clipButton
          Button to invoke all the six clipping planes.
        • clipDisableButton
          JButton clipDisableButton
          Button to disable all the six clipping planes.
        • clipMaskButton
          JButton clipMaskButton
          Button to crop the clip volume.
        • clipMaskUndoButton
          JButton clipMaskUndoButton
          Button to undo crop the clip volume.
        • clipPanel
          JPanel clipPanel
          DOCUMENT ME!
        • clipPlaneButton
          JButton clipPlaneButton
          Button to invoke clipping planes.
        • clipSaveButton
          JButton clipSaveButton
          Button to save clipped region.
        • compound
          Border compound
          Panel Border view.
        • config
          GraphicsConfiguration config
          Configuration param, which will pass down to each render's constructor.
        • displayPanel
          JPanel displayPanel
          DOCUMENT ME!
        • dualImagePane
          JSplitPane dualImagePane
          dual image pane that holds the left and right panel.
        • dualImagePanel
          JPanel dualImagePanel
          The image panel to hold two Canvas3D.
        • dualLeftPanel
          JPanel dualLeftPanel
          Left panel of the dual panel view.
        • dualRightPanel
          JPanel dualRightPanel
          Right panel of the dual panel view.
        • etchedBorder
          Border etchedBorder
          Panel Border view.
        • firstTimeVolView
          boolean firstTimeVolView
          Keep track of whether we're switching to the volume renderer for the first time.
        • flythruControl
          JPanelVirtualEndoscopySetup flythruControl
          Fly through setup control panel.
        • flythruMoveControl
          JPanelFlythruMove flythruMoveControl
          Fly through movement control panel.
        • flythruMovePanel
          JPanel flythruMovePanel
          View panel contains the fly thru control panel.
        • flythruOptions
          FlythruRender.SetupOptions flythruOptions
          Fly through options.
        • flythruPanel
          JPanel flythruPanel
          Fly through panel.
        • flythruRender
          FlythruRender flythruRender
          Reference to fly through renderer.
        • flythruSurfaceButton
          JButton flythruSurfaceButton
          Surface load button.
        • flythruTabVector
          Vector flythruTabVector
          DOCUMENT ME!
        • flyThruToolbar
          JToolBar flyThruToolbar
          Flythru toolbar.
        • histoLUTPanel
          JPanel histoLUTPanel
          Control panel for the surface renderer.
        • imageAOriginal
          ModelImage imageAOriginal
          Reference to the imageA original copy.
        • imageOrientation
          int imageOrientation
          Image orientation: coronal, sagittal, axial, unknown.
        • imagePanel
          JPanel imagePanel
          The image panel to hold one Canvas3D.
        • intensityDialog
          JDialogIntensityPaint intensityDialog
          DOCUMENT ME!
        • isBrainsurfaceFlattenerEnable
          boolean isBrainsurfaceFlattenerEnable
          Indicate if the brainsurface flattener render is enabled from the resample dialog or not.
        • isEndoscopyEnable
          boolean isEndoscopyEnable
          Indicate if the fly through render is enabled from the resample dialog or not.
        • isoImageA
          ModelImage isoImageA
          Isotropic version image A, B, used by the shear warp renderer.
        • isoImageB
          ModelImage isoImageB
          Isotropic version image A, B, used by the shear warp renderer.
        • isRayCastEnable
          boolean isRayCastEnable
          Indicate if the raycast render is enabled from the resample dialog or not.
        • isShearWarpEnable
          boolean isShearWarpEnable
          Indicate if the shear warp render is enabled from the resample dialog or not.
        • isSurfaceRenderEnable
          boolean isSurfaceRenderEnable
          Indicate if the surface render is enabled from the resample dialog or not.
        • isSurfaceViewEnable
          boolean isSurfaceViewEnable
          Indicate if the surface view is enabled from the resample dialog or not.
        • leftPanelRenderMode
          int leftPanelRenderMode
          The left panel renderer mode.
        • lightPanel
          JPanel lightPanel
          DOCUMENT ME!
        • loweredbevel
          Border loweredbevel
          Panel Border view.
        • m_akPlaneRender
          PlaneRender[] m_akPlaneRender
          The three slice views displayed as texture-mapped polygons:.
        • m_kBrainsurfaceFlattenerPanel
          JPanel m_kBrainsurfaceFlattenerPanel
          Control panels for the Brainsurface Flattener:.
        • m_kGeodesicPanel
          JPanel m_kGeodesicPanel
          Control panel for drawing geodesic curves.
        • m_kSculptPanel
          JPanel m_kSculptPanel
          Control panel for volume sculpting.
        • maxPanelWidth
          int maxPanelWidth
          The max width of the control panels.
        • menuBar
          JMenuBar menuBar
          Menu bar.
        • menuObj
          ViewMenuBuilder menuObj
          Menu items storage.
        • modelViewLabel
          JLabel modelViewLabel
          Labels for the current position in 3D ModelView coordinates:.
        • modelViewLabelVals
          JLabel[] modelViewLabelVals
          DOCUMENT ME!
        • mousePanel
          JPanel mousePanel
          DOCUMENT ME!
        • opacityDialog
          JDialogOpacityControls opacityDialog
          DOCUMENT ME!
        • opacityPanel
          JPanel opacityPanel
          DOCUMENT ME!
        • orient
          int[] orient
          Orientations of the three axes.
        • paddingImageA
          ModelImage paddingImageA
          Padding imageA with blank images feeding.
        • paddingImageB
          ModelImage paddingImageB
          Padding imageB with blank images feeding.
        • paintGrowDialog
          JDialogPaintGrow paintGrowDialog
          Control panels of the triplanar view.
        • panelHistogram
          JFrameHistogram panelHistogram
          LUT control panel of the gray scale image.
        • panelLabels
          JPanel panelLabels
          Panel containing the position labels:.
        • panelToolbar
          JPanel panelToolbar
          Panel that holds the toolbars.
        • parallelButton
          JToggleButton parallelButton
          Rendering parallel rotation button.
        • patientSliceLabel
          JLabel patientSliceLabel
          Labels for the current position in PatientSlice coordinates:.
        • patientSliceLabelVals
          JLabel[] patientSliceLabelVals
          DOCUMENT ME!
        • pressedBorder
          Border pressedBorder
          Panel Border view.
        • probePanel
          JPanel probePanel
          DOCUMENT ME!
        • radioCOMPOSITE
          JRadioButton radioCOMPOSITE
          Radio button of the COMPOSITE mode option.
        • radioCOMPOSITEShear
          JRadioButton radioCOMPOSITEShear
          Radio button of the COMPOSITE mode option.
        • radioMIP
          JRadioButton radioMIP
          Radio button of the MIP mode option.
        • radioMIPShear
          JRadioButton radioMIPShear
          Radio button of the MIP mode option.
        • radioSURFACE
          JRadioButton radioSURFACE
          Radio button of the SURFACE mode option.
        • radioSURFACEFAST
          JRadioButton radioSURFACEFAST
          Radio button of the SURFACE mode option.
        • radioSURFACEShear
          JRadioButton radioSURFACEShear
          Radio button of the SURFACE mode option.
        • radioSurrenderCOMPOSITE
          JRadioButton radioSurrenderCOMPOSITE
          Radio button of the surface render composite mode.
        • radioSurrenderLIGHT
          JRadioButton radioSurrenderLIGHT
          Radio button of the surface render lighting mode.
        • radioXRAY
          JRadioButton radioXRAY
          Radio button of the XRAY mode option.
        • radioXRAYShear
          JRadioButton radioXRAYShear
          Radio button of the XRAY mode option.
        • raisedbevel
          Border raisedbevel
          Panel Border view.
        • raycastCameraPanel
          JPanel raycastCameraPanel
          DOCUMENT ME!
        • raycastOptionsPanel
          JPanel raycastOptionsPanel
          Control panels for the raycast render.
        • raycastRender
          VolumeRendererRayCast raycastRender
          DOCUMENT ME!
        • raycastTabVector
          Vector raycastTabVector
          DOCUMENT ME!
        • rayCastToolBar
          JToolBar rayCastToolBar
          Raycast toolbar.
        • redBorder
          Border redBorder
          Panel Border view.
        • resampleDialog
          JDialogVolViewResample resampleDialog
          Reference to resample dialog, use to null out the resample dialog in this frame.
        • rfaButton
          JButton rfaButton
          Button for RFA.
        • rfaSeparator
          JButton rfaSeparator
          RFA separator.
        • RGBTA
          ModelRGB RGBTA
          Lookup table of the color imageA, B.
        • RGBTB
          ModelRGB RGBTB
          Lookup table of the color imageA, B.
        • rightPane
          JSplitPane rightPane
          The view pane that contains the image view and tri-planar view panels.
        • rightPanelRenderMode
          int rightPanelRenderMode
          The right panel renderer mode.
        • screenHeight
          int screenHeight
          Screen width, screen height.
        • screenWidth
          int screenWidth
          Screen width, screen height.
        • sculptHeight
          int sculptHeight
          Sculpt region height.
        • sculptWidth
          int sculptWidth
          Sculpt region width.
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • shearwarpCameraPanel
          JPanel shearwarpCameraPanel
          DOCUMENT ME!
        • shearwarpOptionsPanel
          JPanel shearwarpOptionsPanel
          Control panels for the shearwarp render.
        • shearwarpRender
          VolumeRendererShearWarp shearwarpRender
          DOCUMENT ME!
        • shearwarpTabVector
          Vector shearwarpTabVector
          DOCUMENT ME!
        • shearWarpToolBar
          JToolBar shearWarpToolBar
          Shearwarp toolbar.
        • slicePanel
          JPanel slicePanel
          DOCUMENT ME!
        • storeTabbedPaneIndex
          int storeTabbedPaneIndex
          Previoius tab index recorder.
        • surfacePanel
          JPanel surfacePanel
          DOCUMENT ME!
        • surRender
          SurfaceRender surRender
          Three types of renderer.
        • surTabVector
          Vector surTabVector
          For each render, use the vector to store the currently active tabs.
        • surView
          SurfaceView surView
          Surface View reference
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          Toolbar builder reference.
        • triImagePanel
          JPanel triImagePanel
          Tri image planar render panels.
        • unparallelButton
          JToggleButton unparallelButton
          Rendering unparallel rotaion button.
        • viewPanel
          JPanel viewPanel
          DOCUMENT ME!
        • viewToolBar
          JToolBar viewToolBar
          The top one render view switch toolbar.
        • volToolBar
          JToolBar volToolBar
          Surface Render toolbar.

    • Class gov.nih.mipav.view.renderer.J3D.VolumeCanvas3D

      class VolumeCanvas3D extends javax.media.j3d.Canvas3D implements Serializable
      serialVersionUID:
      5377755312667171175L

      • Serialized Fields

        • m_bTestFrameRate
          boolean m_bTestFrameRate
        • m_dAccumulatedTime
          double m_dAccumulatedTime
          Framerate Performance parameters:
        • m_dFrameRate
          double m_dFrameRate
          Framerate Performance parameters:
        • m_dLastTime
          double m_dLastTime
          Framerate Performance parameters:
        • m_iAccumulatedFrameCount
          int m_iAccumulatedFrameCount
          Framerate Performance parameters:
        • m_iFrameCount
          int m_iFrameCount
          Framerate Performance parameters:
        • m_iMaxTimer
          int m_iMaxTimer
          Framerate Performance parameters:
        • m_iTimer
          int m_iTimer
          Framerate Performance parameters:

  • Package gov.nih.mipav.view.renderer.J3D.model.file

  • Package gov.nih.mipav.view.renderer.J3D.model.structures

  • Package gov.nih.mipav.view.renderer.J3D.surfaceview

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JDialogSimpleText

      class JDialogSimpleText extends JDialogBase implements Serializable
      serialVersionUID:
      1577016550517413391L

      • Serialized Fields

        • field
          JTextField field
          Text field to enter name in.
        • name
          String name
          Name for the view.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JDialogSurfaceAVI

      class JDialogSurfaceAVI extends JDialogBase implements Serializable
      serialVersionUID:
      -475364340269669481L

      • Serialized Fields

        • rate
          double rate
          Frame rate per second.
        • rateBox
          JTextField rateBox
          Text field for the frame rate per second.
        • subSample
          int subSample
          Subsample flag.
        • subSampleCBox
          JComboBox subSampleCBox
          Sub sampel combo box.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JFrameSurfaceMaterialProperties

      class JFrameSurfaceMaterialProperties extends JFrame implements Serializable
      serialVersionUID:
      3077827124095959620L

      • Serialized Fields

        • AFTER
          int AFTER
          Before/After index values for the two displayed spheres, canvases, and display panels:.
        • BEFORE
          int BEFORE
          Before/After index values for the two displayed spheres, canvases, and display panels:.
        • m_akMaterialPreset
          javax.media.j3d.Material[] m_akMaterialPreset
          Pre-defined materials
        • m_bColorApplied
          boolean m_bColorApplied
          keeps track of whether or not color has been applied to surface (for backup on cancel)
        • m_fShininess
          float m_fShininess
          specular coefficient
        • m_iNumPreset
          int m_iNumPreset
          Preset Material's examples:.
        • m_iSurfaceIndex
          int m_iSurfaceIndex
          the index of the surface that is being changed in the JPanelSurface
        • m_iWhichButton
          int m_iWhichButton
          Which button is pressed to activate the JColorChooser:.
        • m_kAmbient
          javax.vecmath.Color3f m_kAmbient
          Current color values:.
        • m_kAmbientColorButton
          JButton m_kAmbientColorButton
          Material Properties color buttons:.
        • m_kColorChooser
          JColorChooser m_kColorChooser
          Color Chooser dialog:.
        • m_kDiffuse
          javax.vecmath.Color3f m_kDiffuse
          diffuse color
        • m_kDiffuseColorButton
          JButton m_kDiffuseColorButton
          diffuse color button
        • m_kEmissive
          javax.vecmath.Color3f m_kEmissive
          emissive color
        • m_kEmissiveColorButton
          JButton m_kEmissiveColorButton
          emissive color button
        • m_kImagePane
          JSplitPane m_kImagePane
          Split pane for displaying the canvases side-by-side:.
        • m_kImagePanel
          JPanel[] m_kImagePanel
          Canvas display panels:.
        • m_kMainPane
          JSplitPane m_kMainPane
          Split pane for displaying the rendered spheres above the interface:.
        • m_kMaterialNew
          javax.media.j3d.Material m_kMaterialNew
          Materials for new vales and backup:.
        • m_kMaterialPanel
          JPanel m_kMaterialPanel
          Window display panels: Material properties buttons/slider panel:.
        • m_kMaterialSave
          javax.media.j3d.Material m_kMaterialSave
          Saved Material for backup
        • m_kParent
          JPanelSurface m_kParent
          Parent class:.
        • m_kShininessSlider
          JSlider m_kShininessSlider
          Shininess slider.
        • m_kSpecular
          javax.vecmath.Color3f m_kSpecular
          Specular color component
        • m_kSpecularColorButton
          JButton m_kSpecularColorButton
          Specular color button

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelDisplay

      class JPanelDisplay extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      926266253314679850L

      • Serialized Fields

        • boundingCheck
          JCheckBox boundingCheck
          Check box for turning box on and off.
        • coarse
          JTextField coarse
          Coarse and fine value text field.
        • coarseLabel
          JLabel coarseLabel
          Coarse and fine value label.
        • coarseValue
          float coarseValue
          Coarse and fine value.
        • colorButton
          JButton colorButton
          Color button for changing color.
        • colorButtonBackground
          JButton colorButtonBackground
          Color button for changing z color.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser dialog.
        • cubePanel
          JPanel cubePanel
          Panel for the rotation cube.
        • cubicCheck
          JCheckBox cubicCheck
          Check box for cubic control.
        • fine
          JTextField fine
          Coarse and fine value text field.
        • fineLabel
          JLabel fineLabel
          Coarse and fine value label.
        • fineValue
          float fineValue
          Coarse and fine value.
        • flag
          boolean flag
          Flag indicating if the red bounding box is on or off.
        • radioButtonGroupProjections
          ButtonGroup radioButtonGroupProjections
          Button group for projections.
        • radioButtonOrthographic
          JRadioButton radioButtonOrthographic
          Radio Button for Orthographic rendering.
        • radioButtonPerspective
          JRadioButton radioButtonPerspective
          Radio Button for Perspective rendering.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JPanelDisplay.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • viewAlignedButton
          JRadioButton viewAlignedButton
          Radio Button for Perspective rendering.
        • viewButton
          JRadioButton viewButton
          Radio Button for Orthographic rendering.
        • viewTextureButtonGroup
          ButtonGroup viewTextureButtonGroup
          Button group for projections.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelGeodesic

      class JPanelGeodesic extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      4382184418236793404L

      • Serialized Fields

        • drawLabel
          JLabel drawLabel
          Geodesic line draw control label.
        • flythruGeodesic
          Geodesic flythruGeodesic
          DOCUMENT ME!
        • flythruRender
          FlythruRender flythruRender
          FlythruRender reference.
        • m_bPickSetFlyThru
          boolean m_bPickSetFlyThru
          Initialzied to true when the the Geodesic.setPickCanvas funtion is called.
        • m_bPickSetSurface
          boolean m_bPickSetSurface
          DOCUMENT ME!
        • m_fDijkstraCurrent
          float m_fDijkstraCurrent
          DOCUMENT ME!
        • m_fDijkstraPrevious
          float m_fDijkstraPrevious
          DOCUMENT ME!
        • m_fDijkstraTotal
          float m_fDijkstraTotal
          DOCUMENT ME!
        • m_fEuclidianCurrent
          float m_fEuclidianCurrent
          Values for the current path length between the last two selected points:
        • m_fEuclidianPrevious
          float m_fEuclidianPrevious
          Values for the previous current path length between the last two selected points:
        • m_fEuclidianTotal
          float m_fEuclidianTotal
          Values for the total path lengths:.
        • m_fGeodesicSmoothCurrent
          float m_fGeodesicSmoothCurrent
          DOCUMENT ME!
        • m_fGeodesicSmoothPrevious
          float m_fGeodesicSmoothPrevious
          DOCUMENT ME!
        • m_fGeodesicSmoothTotal
          float m_fGeodesicSmoothTotal
          DOCUMENT ME!
        • m_kCheckLivewire
          JCheckBox m_kCheckLivewire
          Toggle between LiveWire Interaction and point invalid input: '&' click interaction:.
        • m_kClearAllCutsButton
          JButton m_kClearAllCutsButton
          DOCUMENT ME!
        • m_kClearAllGeodesicButton
          JButton m_kClearAllGeodesicButton
          DOCUMENT ME!
        • m_kClearLastCutButton
          JButton m_kClearLastCutButton
          DOCUMENT ME!
        • m_kClearLastGeodesicButton
          JButton m_kClearLastGeodesicButton
          Button for deleting the geodesic.
        • m_kCutGeodesicButton
          JButton m_kCutGeodesicButton
          Button for cutting the mesh along the geodesic:.
        • m_kDijkstraDistance
          JLabel m_kDijkstraDistance
          DOCUMENT ME!
        • m_kDijkstraDistanceValueLast
          JLabel m_kDijkstraDistanceValueLast
          DOCUMENT ME!
        • m_kDijkstraDistanceValueTotal
          JLabel m_kDijkstraDistanceValueTotal
          DOCUMENT ME!
        • m_kDisplayButtonGroup
          ButtonGroup m_kDisplayButtonGroup
          DOCUMENT ME!
        • m_kDisplayDijkstra
          JRadioButton m_kDisplayDijkstra
          DOCUMENT ME!
        • m_kDisplayEuclidian
          JRadioButton m_kDisplayEuclidian
          DOCUMENT ME!
        • m_kDisplayGeodesic
          JRadioButton m_kDisplayGeodesic
          Radio buttons for displaying the smoothed geodesic, dijkstra's path, or the euclidian path:.
        • m_kDrawGeodesicButton
          JToggleButton m_kDrawGeodesicButton
          Geodesic drawing interface Toggle button is down while points are added to the curve:.
        • m_kEuclidianDistance
          JLabel m_kEuclidianDistance
          Labels to indicate the path length between the picked points, in Euclidian distance, geodesic smoothed distance, and Dijkstra's path mesh distance. Two labels each, one for the distances between the last two points picked, and one for the total length of the curve, from starting point to end point:
        • m_kEuclidianDistanceValueLast
          JLabel m_kEuclidianDistanceValueLast
          DOCUMENT ME!
        • m_kEuclidianDistanceValueTotal
          JLabel m_kEuclidianDistanceValueTotal
          DOCUMENT ME!
        • m_kFinishClosedGeodesicButton
          JButton m_kFinishClosedGeodesicButton
          DOCUMENT ME!
        • m_kFinishOpenGeodesicButton
          JButton m_kFinishOpenGeodesicButton
          DOCUMENT ME!
        • m_kGeodesicSmoothDistance
          JLabel m_kGeodesicSmoothDistance
          DOCUMENT ME!
        • m_kGeodesicSmoothDistanceValueLast
          JLabel m_kGeodesicSmoothDistanceValueLast
          DOCUMENT ME!
        • m_kGeodesicSmoothDistanceValueTotal
          JLabel m_kGeodesicSmoothDistanceValueTotal
          DOCUMENT ME!
        • m_kGeodesicToggleWireframe
          JToggleButton m_kGeodesicToggleWireframe
          DOCUMENT ME!
        • mainPanel
          JPanel mainPanel
          the main control panel.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JPanelGeodesic.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • surfaceGeodesic
          Geodesic surfaceGeodesic
          Geodesic reference.
        • surPickLabel
          JLabel surPickLabel
          Label to indicate that enable Surface pickable before drawing geodesic line.
        • surRender
          SurfaceRender surRender
          SurfaceRender reference.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelMouse

      class JPanelMouse extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -3554229077099968128L

      • Serialized Fields

        • changedMode
          boolean changedMode
          flag to indicate current mode being changed.
        • contButton
          JToggleButton contButton
          Continue play button.
        • currentEventVector
          MouseEventVector currentEventVector
          Current event vector used by the save AVI.
        • currentObject
          Object currentObject
          current SceneState object being recorded by SaveAVI.
        • currentTransform
          javax.media.j3d.Transform3D currentTransform
          Current transform3D object used in Save AVI.
        • events
          Vector events
          Vector that holds mouse or change events.
        • eventVector
          MouseEventVector eventVector
          Global mouse event vector.
        • first
          boolean first
          Flag to indicate first event.
        • goButton
          JButton goButton
          Go to button.
        • isArbitraryRotation
          boolean isArbitraryRotation
          Flag indicates that arbitrary clipping plane is triggered or not.
        • isPlaying
          boolean isPlaying
          Flag to indicating play mouse is running or not.
        • listModel
          DefaultListModel listModel
          List to record info for each mouse, change events.
        • mainPanel
          JPanel mainPanel
          The main control panel.
        • mjpegQuality
          float mjpegQuality
          Param to save AVI.
        • mode
          int mode
          Current mode, init to stop.
        • mouseCount
          int mouseCount
          Mouse event counter.
        • movieButton
          JButton movieButton
          Save AVI button .
        • myParent
          SurfaceRender myParent
          Reference to ViewJFrameSurfaceRenderer.
        • nameChangeVector
          MouseEventVector nameChangeVector
          Used by name change dialog to change name of the selected item.
        • newButton
          JButton newButton
          This button add at head of the list.
        • parentScene
          RenderViewBase parentScene
          Parent scene.
        • pauseButton
          JToggleButton pauseButton
          Pause button.
        • playButton
          JToggleButton playButton
          Display button.
        • playMouse
          JPanelMouse.PlayMouse playMouse
          Reference to PlayMouse class object.
        • process
          int process
          Process id used by the save AVI.
        • recordButton
          JToggleButton recordButton
          Recorder button.
        • recorderToAVI
          JPanelMouse.RecordMouse recorderToAVI
          Reference to RecordMouse object class.
        • removeAllButton
          JButton removeAllButton
          Remove all items in the item list.
        • removeButton
          JButton removeButton
          Remove the selected item in the item list.
        • resetTransform
          javax.media.j3d.Transform3D resetTransform
          Current transform3D object.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JPanelMouse.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • setMouseVectorFlag
          boolean setMouseVectorFlag
          flag to indicate the first time mouse tranform event happpened.
        • sliceDialog
          JPanelSlices sliceDialog
          Dialog to turn the slices control box on and off.
        • sliderCount
          int sliderCount
          Slider moves event counter.
        • stepButton
          JToggleButton stepButton
          Next step button.
        • stopButton
          JToggleButton stopButton
          Stop button.
        • toolBar
          JToolBar toolBar
          Tool bar of the mouse recorder.
        • transformChange
          boolean transformChange
          Flag indicates that a transform changed event is invoked.
        • viewList
          JList viewList
          View list of the mouse recorder display list.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelSlices

      class JPanelSlices extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -8359831093707979536L

      • Serialized Fields

        • boundingBoxPanel
          JPanel boundingBoxPanel
          Bounding box control panel.
        • boundingCheck
          JCheckBox[] boundingCheck
          Check box for turning bounding boxes on and off.
        • boxX
          JCheckBox boxX
          Check boxes that turn the image plane on and off.
        • boxY
          JCheckBox boxY
          Check boxes that turn the image plane on and off.
        • boxZ
          JCheckBox boxZ
          Check boxes that turn the image plane on and off.
        • colorButton
          JButton[] colorButton
          Color button for changing bounding box color.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser dialog.
        • controlPanel
          JPanel controlPanel
          Main panel for sliders.
        • current
          int current
          Current event vector index.
        • labelT
          JLabel labelT
          Labels next to sliders.
        • labelX
          JLabel labelX
          Labels next to sliders.
        • labelX1
          JLabel labelX1
          Labels beneath sliders.
        • labelXEnd
          JLabel labelXEnd
          Labels beneath sliders.
        • labelXMid
          JLabel labelXMid
          Labels beneath sliders.
        • labelY
          JLabel labelY
          Labels next to sliders.
        • labelY1
          JLabel labelY1
          Labels beneath sliders.
        • labelYEnd
          JLabel labelYEnd
          Labels beneath sliders.
        • labelYMid
          JLabel labelYMid
          Labels beneath sliders.
        • labelZ
          JLabel labelZ
          Labels next to sliders.
        • labelZ1
          JLabel labelZ1
          Labels beneath sliders.
        • labelZEnd
          JLabel labelZEnd
          Labels beneath sliders.
        • labelZMid
          JLabel labelZMid
          Labels beneath sliders.
        • opacityControlPanel
          JPanel opacityControlPanel
          Opacity control panel.
        • opacityLabelX
          JLabel opacityLabelX
          The opacity slider label.
        • opacityLabelY
          JLabel opacityLabelY
          The opacity slider label.
        • opacityLabelZ
          JLabel opacityLabelZ
          The opacity slider label.
        • opacitySliderLabelsX
          JLabel[] opacitySliderLabelsX
          The labels below the opacity slider.
        • opacitySliderLabelsY
          JLabel[] opacitySliderLabelsY
          The labels below the opacity slider.
        • opacitySliderLabelsZ
          JLabel[] opacitySliderLabelsZ
          The labels below the opacity slider.
        • opacitySliderX
          JSlider opacitySliderX
          Opacity slider, not enabled yet.
        • opacitySliderY
          JSlider opacitySliderY
          Opacity slider, not enabled yet.
        • opacitySliderZ
          JSlider opacitySliderZ
          Opacity slider, not enabled yet.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JPanelSlices.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • setSliderFlag
          boolean setSliderFlag
          Flag to indicate the first time slider name changes.
        • slicePosition
          WildMagic.LibFoundation.Mathematics.Vector3f slicePosition
        • sliceVisible
          boolean[] sliceVisible
          Flags indicating if the image slices are on or off.
        • sliderT
          JSlider sliderT
          Sliders for the image planes.
        • sliderX
          JSlider sliderX
          Sliders for the image planes.
        • sliderY
          JSlider sliderY
          Sliders for the image planes.
        • sliderZ
          JSlider sliderZ
          Sliders for the image planes.
        • tDim
          int tDim
          x, y, z and time dimension values.
        • textT
          JTextField textT
          Text fields that display the slice number next to the sliders.
        • textX
          JTextField textX
          Text fields that display the slice number next to the sliders.
        • textY
          JTextField textY
          Text fields that display the slice number next to the sliders.
        • textZ
          JTextField textZ
          Text fields that display the slice number next to the sliders.
        • tSlice
          int tSlice
          Which time slice is currently displayed.
        • xDim
          int xDim
          x, y, z and time dimension values.
        • xOpacitySlice
          int xOpacitySlice
          x, y, z opacity slider values.
        • xProbe
          int xProbe
          Probe x, y, z position.
        • xSlice
          int xSlice
          Which slice is currently displayed in the ZY plane.
        • yDim
          int yDim
          x, y, z and time dimension values.
        • yOpacitySlice
          int yOpacitySlice
          x, y, z opacity slider values.
        • yProbe
          int yProbe
          Probe x, y, z position.
        • ySlice
          int ySlice
          Which slice is currently displayed in the XZ plane.
        • zDim
          int zDim
          x, y, z and time dimension values.
        • zOpacitySlice
          int zOpacitySlice
          x, y, z opacity slider values.
        • zProbe
          int zProbe
          Probe x, y, z position.
        • zSlice
          int zSlice
          Which slice is currently displayed in the XY plane.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelSurface

      class JPanelSurface extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -4600563188022683359L

      • Serialized Fields

        • activeLightBulbIndex
          int activeLightBulbIndex
          Record the current active index of light bulb, which is being picked.
        • areaLabel
          JLabel areaLabel
          The area label.
        • areaText
          JTextField areaText
          Displays the area of triangle.
        • colorButton
          JButton colorButton
          The color button, which calls a color chooser.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser for when the user wants to change the color of the surface.
        • colorLabel
          JLabel colorLabel
          The color button label.
        • comboLabel
          JLabel comboLabel
          The polygon mode combo box label.
        • currentIndex
          int currentIndex
          Current surface index being highlighted.
        • decimateButton
          JButton decimateButton
          Decimate button.
        • detailLabel
          JLabel detailLabel
          The level of detail slider label.
        • detailSlider
          JSlider detailSlider
          Level of detail slider.
        • detailSliderLabels
          JLabel[] detailSliderLabels
          The labels below the detail slider.
        • extents
          int[] extents
        • findArbitraryClipping
          boolean findArbitraryClipping
          flag indicates arbitrary clpping bounding frame being picked.
        • findProbe
          boolean findProbe
          flag indicates the probe being picked.
        • levelSButton
          JButton levelSButton
          Save surface button.
        • levelVButton
          JButton levelVButton
          Save surface button.
        • levelWButton
          JButton levelWButton
          Save surface button.
        • levelXMLButton
          JButton levelXMLButton
          Save surface button.
        • lightArray
          javax.media.j3d.Light[] lightArray
          An array of eight lights that can be used for illuminating the surfaces in the scene. The lights at indices 0 and 7 are initially enabled; the other lights are initially disabled. The default positions for the lights are at the 8 corners of the cube [0,1]^3. Light 0 is at (0,0,0) and light 7 is at (1,1,1), thereby providing suitable lighting for the visible surfaces in the scene. Other lights can be enabled as desired through the light attribute dialog.
        • lightArrayBG
          javax.media.j3d.BranchGroup[] lightArrayBG
          The branch groups to which the lights are attached.
        • lightBulbs
          ViewJComponentLightBulbs lightBulbs
          The structure for the light bulbs.
        • m_aiMapIndexToJPanelLightsIndex
          int[] m_aiMapIndexToJPanelLightsIndex
          The index of the lights in JPanelLights is different from the order maintained here. This array maps from our index to JPanelLights' index.
        • m_aiMapJPanelLightsIndexToIndex
          int[] m_aiMapJPanelLightsIndexToIndex
          The index of the lights in JPanelLights is different from the order maintained here. This array maps from JPanelLights' index to our index.
        • m_akLights
          GeneralLight[] m_akLights
          The description of the lights so they can be duplicated in the "Advanced Material Properties" dialog:.
        • m_kAdvancedMaterialOptionsButton
          JButton m_kAdvancedMaterialOptionsButton
          The material options button, which launches the material editor window.
        • m_kFiberTractGroup
          javax.media.j3d.BranchGroup m_kFiberTractGroup
          For displaying the fiber bundle tracts in the orthogonal slice view:
        • m_kGeodesicGroup
          javax.media.j3d.BranchGroup m_kGeodesicGroup
          For drawing the geodesic lines on the triangle mesh:.
        • m_kLightsControl
          JPanelLights m_kLightsControl
          Light dialog for when the user clicks the light button.
        • m_kPathPositionTG
          javax.media.j3d.TransformGroup m_kPathPositionTG
          For drawing the flythru path in the triangle mesh:.
        • m_kStereoButton
          JButton m_kStereoButton
          Stereo render button, launches the JStereoWindow for viewing the ModelTriangleMesh in stereo:.
        • m_kSurfaceTextureButton
          JButton m_kSurfaceTextureButton
          Opens SurfaceTexture dialog:.
        • maxBox
          float maxBox
          ModelImage max dimension: (Extents * resolutions).
        • mSurfaceMask
          SurfaceMask mSurfaceMask
          Surface mask.
        • mSurfacePaint
          SurfacePaint mSurfacePaint
          Paint interface/algorithm for allowing the user to interactively paint the vertices of the ModelTriangleMesh.
        • opacityLabel
          JLabel opacityLabel
          The opacity slider label.
        • opacitySlider
          JSlider opacitySlider
          Opacity slider, not enabled yet.
        • opacitySliderLabels
          JLabel[] opacitySliderLabels
          The labels below the opacity slider.
        • parentScene
          SurfaceRender parentScene
          The parent object that holds necessary the structures to which the surfaces will be added and modified.
        • pickCanvas
          com.sun.j3d.utils.picking.PickCanvas pickCanvas
          The PickCanvas object that ties together the canvas and the surfaces branch group to allow pick operations on the scene.
        • polygonModeCB
          JComboBox polygonModeCB
          The combo box for the polygon mode to display.
        • resolutions
          float[] resolutions
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • setSurfaceOpacityFlag
          boolean setSurfaceOpacityFlag
          Indicator for the opacity slider moves.
        • smooth1Button
          JButton smooth1Button
          Smooth button.
        • smooth2Button
          JButton smooth2Button
          Smooth button.
        • smooth3Button
          JButton smooth3Button
          Smooth button.
        • sphere
          com.sun.j3d.utils.geometry.Sphere sphere
          Sphere showing where the user clicked in the surface.
        • sphereBranch
          javax.media.j3d.BranchGroup sphereBranch
          Branch group parent of the sphere.
        • sphereShowing
          boolean sphereShowing
          Flag indicating if the sphere is currently showing.
        • sphereTransform
          javax.media.j3d.TransformGroup sphereTransform
          Transform group parent of the sphere.
        • staticLightBehaviorBG
          javax.media.j3d.BranchGroup staticLightBehaviorBG
          Static light hehavior branch group.
        • staticLightBG
          javax.media.j3d.BranchGroup staticLightBG
          The branch group that holds the static light bulb.
        • staticLightBulb
          ViewJComponentLightBulbs staticLightBulb
          The structure for the static light bulb.
        • staticLightTG
          javax.media.j3d.TransformGroup staticLightTG
          The transform group that holds the static light branch group.
        • staticLightTranslate
          com.sun.j3d.utils.behaviors.mouse.MouseTranslate staticLightTranslate
          Static light translate behavior.
        • staticLightZoom
          com.sun.j3d.utils.behaviors.mouse.MouseZoom staticLightZoom
          Static light zoom behavior.
        • surfaceBackFaceCB
          JCheckBox surfaceBackFaceCB
          Check Box for surface back face culling.
        • surfaceClipCB
          JCheckBox surfaceClipCB
          Check Box for surface clpping of the volume render.
        • surfaceDirectoryName
          String surfaceDirectoryName
          The directory where a surface file was last loaded/saved. Defaults to MIPAV default directory.
        • surfaceList
          JList surfaceList
          The list box in the dialog for surfaces.
        • surfaceOpacityEvents
          MouseEventVector surfaceOpacityEvents
          Surface opacity changes event queue.
        • surfaceOpacitySlice
          int surfaceOpacitySlice
          Surface volume opacity.
        • surfacePickableCB
          JCheckBox surfacePickableCB
          Check Box for surface pickable.
        • surfaceRootBG
          javax.media.j3d.BranchGroup surfaceRootBG
          The branch group that holds all the surfaces together.
        • surfaceRootTG
          javax.media.j3d.TransformGroup surfaceRootTG
          The transform group to which the model lights are attached.
        • surfaceSliderCount
          int surfaceSliderCount
          Counter for surface opacity slider moves.
        • surfaceTransparencyCB
          JCheckBox surfaceTransparencyCB
          Check Box for surface transparency.
        • surfaceVector
          Vector<SurfaceAttributes> surfaceVector
          A list of the surfaces. The elements are of type SurfaceAttributes.
        • triangleLabel
          JLabel triangleLabel
          The number of triangles label.
        • triangleText
          JTextField triangleText
          Displays the number of triangles.
        • volumeLabel
          JLabel volumeLabel
          The volume label.
        • volumeText
          JTextField volumeText
          Displays the volume of triangle.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelSurfaceTexture

      class JPanelSurfaceTexture extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      7562070328632922435L

      • Serialized Fields

        • mHistogram
          JFrameHistogram mHistogram
          Display the independent LUT for Black/White images.
        • mImageA
          ModelImage mImageA
          ModelImage used to generate the 3D texture:.
        • mImageALink
          ModelImage mImageALink
          Reference to ModelImage A for linking the texture to the imageA LUT.
        • mImageAsTextureRadioButton
          JRadioButton mImageAsTextureRadioButton
          RadioButton for turing on the surface image texture:.
        • mImageAsVertexColorRadioButton
          JRadioButton mImageAsVertexColorRadioButton
          RadioButton for turing on the surface image per-vertex color:.
        • mImageDirName
          String mImageDirName
          Stores the currently-loaded ModelImage directory name:.
        • mImageFileName
          String mImageFileName
          Stores the currently-loaded ModelImage file name:.
        • mImageFileNameLabel
          JLabel mImageFileNameLabel
          Display the currently-loaded ModelImage file name:.
        • mImageNoneRadioButton
          JRadioButton mImageNoneRadioButton
          RadioButton for turing off the surface image:.
        • mLoadImageButton
          JButton mLoadImageButton
          Load a new ModelImage:.
        • mLUTButtonGroup
          ButtonGroup mLUTButtonGroup
          Grouping the radio buttons:.
        • mLUTImageA
          ModelImage mLUTImageA
          Independent ModelImage for independent LUT.
        • mLUTModel
          ModelLUT mLUTModel
          The LUT associated with the ModelImage imageA:.
        • mLUTSeparate
          ModelLUT mLUTSeparate
          The LUT associated with the independent texture LUT:.
        • mModelLUTRadioButton
          JRadioButton mModelLUTRadioButton
          Use the ModelImage LUT.
        • mNewLUTRadioButton
          JRadioButton mNewLUTRadioButton
          Use a separate LUT.
        • mPatientSlice
          PatientSlice mPatientSlice
          Renders the ModelImage data with LUT changes.
        • mRGBModel
          ModelRGB mRGBModel
          The RGB LUT associated with the ModelImage imageA:.
        • mRGBSeparate
          ModelRGB mRGBSeparate
          The RGB LUT associated with the independent texture LUT:.
        • mSurfaceTextureImage
          javax.media.j3d.ImageComponent3D mSurfaceTextureImage
          The ModelImage texture with LUT changes, used with the Texture3D.
        • mTexture
          javax.media.j3d.Texture3D mTexture
          3D Texture used to display the ModelImage data as a texture mapped onto the ModelTriangleMesh.
        • mTextureButtonGroup
          ButtonGroup mTextureButtonGroup
          Grouping the radio buttons:.
        • mTextureStatus
          int mTextureStatus
          Currently selected ModelImage display type:.
        • mTextureUnitState
          javax.media.j3d.TextureUnitState[] mTextureUnitState
          TextureUnitState contains texture information for the rendered surfaces:.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelView

      class JPanelView extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -8408530937731996131L

      • Serialized Fields

        • flyBehavior
          FlyBehaviorRenderer flyBehavior
          Fly behavior reference.
        • flyButton
          JRadioButton flyButton
          Fly behaviro radio button.
        • flyText
          String flyText
          User message explain how the mouse moves in fly mode.
        • labels
          JLabel[] labels
          speed control slider labels.
        • leftDownButton
          JButton leftDownButton
          DOCUMENT ME!
        • leftLeftButton
          JButton leftLeftButton
          DOCUMENT ME!
        • leftRightButton
          JButton leftRightButton
          DOCUMENT ME!
        • leftUpButton
          JButton leftUpButton
          Arrow button references.
        • middleDownButton
          JButton middleDownButton
          DOCUMENT ME!
        • middleLeftButton
          JButton middleLeftButton
          DOCUMENT ME!
        • middleRightButton
          JButton middleRightButton
          DOCUMENT ME!
        • middleUpButton
          JButton middleUpButton
          DOCUMENT ME!
        • mode
          int mode
          Current behavior mode.
        • modeGroup
          ButtonGroup modeGroup
          Radio button group reference.
        • mouseText
          JTextArea mouseText
          Text field reference that hold the user message.
        • pointerBehavior
          PointerBehaviorRenderer pointerBehavior
          Pointer behavior reference, not used now.
        • pressed
          boolean pressed
          Flag to indicate mouse pressed or not.
        • ptrButton
          JRadioButton ptrButton
          Point behavior button.
        • rightDownButton
          JButton rightDownButton
          DOCUMENT ME!
        • rightLeftButton
          JButton rightLeftButton
          DOCUMENT ME!
        • rightRightButton
          JButton rightRightButton
          DOCUMENT ME!
        • rightUpButton
          JButton rightUpButton
          DOCUMENT ME!
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JPanelView.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • stdBehavior
          com.sun.j3d.utils.behaviors.vp.ViewPlatformBehavior stdBehavior
          Standard behavior reference.
        • stdButton
          JRadioButton stdButton
          Standard behavior button.
        • stdText
          String stdText
          User message explain how the mouse moves in stardard mode.
        • time
          long time
          Standard mouse tread waiting time.
        • velocitySlider
          JSlider velocitySlider
          fly Speed control slider.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.JStereoWindow

      class JStereoWindow extends JFrame implements Serializable
      serialVersionUID:
      -2284771559648676504L

      • Serialized Fields

        • m_akUniverse
          com.sun.j3d.utils.universe.SimpleUniverse[] m_akUniverse
          Three SimpleUniverses, one for each canavas:.
        • m_dEyeSeparation
          double m_dEyeSeparation
          Original eye separation, read from the canvas.view.physicalbody.
        • m_iCurrentUniverse
          int m_iCurrentUniverse
          The current universe to be initialized:.
        • m_iStereoUpdateCount
          int m_iStereoUpdateCount
          First time the stereo canvas is rendered, set to true:.
        • m_kD
          Dimension m_kD
          BufferedImage Dimensions (power of two).
        • m_kDisplayPane
          JSplitPane m_kDisplayPane
          The JSplitPane displaying the left and right eye views:.
        • m_kEyeSep_Slider
          JSlider m_kEyeSep_Slider
          Focal-length, (eye separation) slider.
        • m_kLeftCanvas
          VolumeCanvas3D m_kLeftCanvas
          Left-eye view canvas:.
        • m_kLeftImagePanel
          JPanel m_kLeftImagePanel
          Left Image Panel, holds the canvas for the left-eye view:.
        • m_kMainPane
          JSplitPane m_kMainPane
          The JSplitPane displaying different views and the user-interface:.
        • m_kRGStereo
          BufferedImage m_kRGStereo
          BufferedImage containing the Anagyphy stereo image:.
        • m_kRightCanvas
          VolumeCanvas3D m_kRightCanvas
          Right-eye view canvas:.
        • m_kRightImagePanel
          JPanel m_kRightImagePanel
          Right Image Panel, holds the canvas for the right-eye view:.
        • m_kStereoCanvas
          VolumeCanvas3D m_kStereoCanvas
          Stereo canvas:.
        • m_kStereoPane
          JSplitPane m_kStereoPane
          The JSplitPane displaying the left and right eye views and the stereo view:.
        • m_kStereoPanel
          JPanel m_kStereoPanel
          Stereo Image Panel, holds the canvas for the Anaglyph stereo view:.
        • m_kStereoShape
          javax.media.j3d.Shape3D m_kStereoShape
          Texture-mapped polygon for displaying the Anaglyph stereo image as a texture:.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceRender

      class SurfaceRender extends RenderViewBase implements Serializable
      serialVersionUID:
      608959413602233595L

      • Serialized Fields

        • boxPanel
          JPanelDisplay boxPanel
          Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.
        • boxSlices
          ViewJComponentBoxSlice[] boxSlices
          The frame around the AXIAL, CORONAL, SAGITTAL slices:
        • boxSliceVertices
          javax.vecmath.Vector3f[][] boxSliceVertices
          The transformed boxSlices frames used to sample the volume data along diagonal slices:
        • clipPanel
          JPanelClip clipPanel
          Dialog to turn the clipping palne box on and off.
        • componentVolImage
          ViewJComponentSurfaceVolume componentVolImage
          Volume image object.
        • cubicBehaviorBG
          javax.media.j3d.BranchGroup cubicBehaviorBG
          The cubic roational behavior branch group.
        • cubicBG
          javax.media.j3d.BranchGroup cubicBG
          Cubic branch group.
        • cubicRotate
          com.sun.j3d.utils.behaviors.mouse.MouseRotate cubicRotate
          Cubic mouse rotation behavior.
        • cubicTG
          javax.media.j3d.TransformGroup cubicTG
          Cubic transform group.
        • currentTransform
          javax.media.j3d.Transform3D currentTransform
          Current transform matrix.
        • currentTransformType
          int currentTransformType
          Current transform changes type.
        • first6ClipPlane
          boolean first6ClipPlane
          flag indicate the first time 6 clipping plane branch switch.
        • firstClipArbi
          boolean firstClipArbi
          flag indicate the first time arbitrary clipping plane branch switch.
        • geodesicPanel
          JPanelGeodesic geodesicPanel
          Geodesic panel.
        • imageA
          ModelImage imageA
          Current image A.
        • imageB
          ModelImage imageB
          Current image B.
        • imageVolBufferA
          float[] imageVolBufferA
          Buffer that holds image A volume data.
        • imageVolBufferB
          float[] imageVolBufferB
          Buffer that holds image B volume data.
        • isEntryPoint
          boolean isEntryPoint
          Flag indicates that probe rotate around the entry point or not.
        • isTriPlanarVolView
          boolean isTriPlanarVolView
          Mode is tri-planar volume view or not.
        • isViewTextureAligned
          boolean isViewTextureAligned
          Flag to indicate whether the view volume texture is aligned or not.
        • m_bRenderModeLighting
          boolean m_bRenderModeLighting
          Flag set when texture volume is being rendered using lights.
        • m_dOriginalScreenScale
          double m_dOriginalScreenScale
          Zoomfactor, zooming in screen scale space, and is relative to original position, this stores that original position:.
        • m_kObjBoxSliceProbe_TG
          javax.media.j3d.TransformGroup[] m_kObjBoxSliceProbe_TG
          TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice BOXES:
        • m_kObjPlaneProbe_TG
          javax.media.j3d.TransformGroup[] m_kObjPlaneProbe_TG
          TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice PLANES:
        • m_kProbeTransform
          javax.media.j3d.Transform3D m_kProbeTransform
          The Transform3D used to position the planes based on the Probe position and angle. The planes are rotates about the intersection between the probe and the plane, which may or may not be in the center of the plane. This transform allows non-origin rotations by conactenating the translation to the origin, rotation, and translation matricies into one transform, which is used to set the Transforms for the TransformGroups above and also to sample the ModelImage data on the diagonal slice:
        • m_kRFACoordMaps
          javax.vecmath.Vector4f[][] m_kRFACoordMaps
          Texture mapping for the RFA probe rotation:
        • m_kSoftwareLightSet
          SoftwareLightSet m_kSoftwareLightSet
          Used to compute software lighting of composite texture volume.
        • m_kSoftwareMaterial
          SoftwareMaterial m_kSoftwareMaterial
          DOCUMENT ME!
        • maxBox
          float maxBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • mousePanel
          JPanelMouse mousePanel
          Dialog for recording and playing back mouse events.
        • mouseRotateBehavior
          MouseRotateExt mouseRotateBehavior
          Mouse Rotate behavior.
        • mouseTranslateBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseTranslateBehavior
          Mouse Translate behavior.
        • mouseZoomBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseZoomBehavior
          Mouse Zoom behavior.
        • myEyePoint
          javax.vecmath.Point3d myEyePoint
          Initial center viewing point of the image.
        • objBoxSlices_BG
          javax.media.j3d.BranchGroup[] objBoxSlices_BG
          BranchGroup[] containing the slice BOXES:
        • objPlane_BG
          javax.media.j3d.BranchGroup[] objPlane_BG
          BranchGroup[] containing the image planes.
        • objTransSlices_TG
          javax.media.j3d.TransformGroup[] objTransSlices_TG
          Group dictating how the XY plane is translated.
        • parallelRotation
          boolean parallelRotation
          Parallel rotation flag.
        • parallelScaleT3D
          javax.media.j3d.Transform3D parallelScaleT3D
          Transformation matrix.
        • parent
          ViewJFrameBase parent
          Controls for the image. ViewJFrameVolumeView
        • probePanel
          JPanelProbe probePanel
          Dialog for loading and displaying probes.
        • rayBasedRender
          VolumeRenderer rayBasedRender
          Raycast based renderer reference, raycast renderer or shear warp renderer.
        • resols
          float[] resols
          Resolutions of image A.
        • rotationAlpha
          javax.media.j3d.Alpha rotationAlpha
        • rotationCount
          int rotationCount
          fix one bug from threading.
        • sculptorPanel
          JPanelSculptor sculptorPanel
          Sculptor panel.
        • segmentationImage
          ModelImage segmentationImage
          Image with areas marked with values indicating that they are special tissue types (vessels, etc).
        • sliceImageComponent2D
          javax.media.j3d.ImageComponent2D[] sliceImageComponent2D
          Each Texture2D adds a ImageComponent2D:
        • slicePanel
          JPanelSlices slicePanel
          Dialog to turn the slices control box on and off.
        • sliceTextures
          javax.media.j3d.Texture2D[] sliceTextures
          ViewJComponentTriSliceImages -> Texture2D to display the image slices:
        • sliceTransparency
          javax.media.j3d.TransparencyAttributes[] sliceTransparency
          ViewJComponentTriSliceImages -> Texture2D transparency values:
        • surfacePanel
          JPanelSurface surfacePanel
          Dialog for loading and displaying surfaces.
        • surfaceTexturePanel
          JPanelSurfaceTexture surfaceTexturePanel
          Panel for displaying the SurfaceTexture interface:
        • switchGroup
          javax.media.j3d.Switch switchGroup
          Tri planar view and the 3D texture volume view switch group.
        • tDim
          int tDim
          Dimensions of image A.
        • texture
          VolumeTexture texture
          Reference to 3D texture node for the volume.
        • transformCubic
          javax.media.j3d.Transform3D transformCubic
          Cubic tansform3D.
        • transformNode3d
          javax.media.j3d.Transform3D transformNode3d
          Setup the initial position of the image, added to ScenerootTG transform group.
        • triSliceGeometry
          javax.media.j3d.Shape3D[] triSliceGeometry
        • triSliceImages
          ViewJComponentTriSliceImage[] triSliceImages
          ImageRenderers for the AXIAL, CORONAL, SAGITTAL slices:
        • view
          javax.media.j3d.View view
          View object in rendering a three dimensional scene from one viewpoint.
        • volBG
          javax.media.j3d.BranchGroup volBG
          Volume branch group.
        • volOpacityPanel
          JPanelVolumeOpacity volOpacityPanel
          Volume opacity control dialog.
        • volRenderBG
          javax.media.j3d.BranchGroup volRenderBG
          Volume render branch group.
        • volRenderNode
          NodeVolumeTextureRender volRenderNode
          Add here.
        • volRenderOG
          javax.media.j3d.OrderedGroup volRenderOG
          Volume render order group, specify the rendering order.
        • volumeDisplayMode3D
          boolean volumeDisplayMode3D
          If true display 3D volume as a 3D texture map or 2D array of texture maps. If false display 3 orthogonal image planes.
        • xBox
          float xBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • xDim
          int xDim
          Dimensions of image A.
        • yBox
          float yBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • yDim
          int yDim
          Dimensions of image A.
        • zBox
          float zBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • zDim
          int zDim
          Dimensions of image A.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceView

      class SurfaceView extends SurfaceRender implements Serializable
      serialVersionUID:
      608959413602233595L

      • Serialized Fields

        • boxPanel
          JPanelDisplay boxPanel
          Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.
        • boxSlices
          ViewJComponentBoxSlice[] boxSlices
          The frame around the AXIAL, CORONAL, SAGITTAL slices:
        • boxSliceVertices
          javax.vecmath.Vector3f[][] boxSliceVertices
          The transformed boxSlices frames used to sample the volume data along diagonal slices:
        • bufferFactor
          int bufferFactor
          Buffer factor, 1 usually, 4 for color images.
        • clipPanel
          JPanelClip clipPanel
          Dialog to turn the clipping palne box on and off.
        • cubicBehaviorBG
          javax.media.j3d.BranchGroup cubicBehaviorBG
          The cubic roational behavior branch group.
        • cubicBG
          javax.media.j3d.BranchGroup cubicBG
          Cubic branch group.
        • cubicRotate
          com.sun.j3d.utils.behaviors.mouse.MouseRotate cubicRotate
          Cubic mouse rotation behavior.
        • cubicTG
          javax.media.j3d.TransformGroup cubicTG
          Cubic transform group.
        • currentTransform
          javax.media.j3d.Transform3D currentTransform
          Current transform matrix.
        • currentTransformType
          int currentTransformType
          Current transform changes type.
        • first6ClipPlane
          boolean first6ClipPlane
          flag indicate the first time 6 clipping plane branch switch.
        • firstClipArbi
          boolean firstClipArbi
          flag indicate the first time arbitrary clipping plane branch switch.
        • geodesicPanel
          JPanelGeodesic geodesicPanel
          Geodesic panel.
        • imageA
          ModelImage imageA
          Current image A.
        • imageB
          ModelImage imageB
          Current image B.
        • isEntryPoint
          boolean isEntryPoint
          Flag indicates that probe rotate around the entry point or not.
        • m_bRenderModeLighting
          boolean m_bRenderModeLighting
          Flag set when texture volume is being rendered using lights.
        • m_dOriginalScreenScale
          double m_dOriginalScreenScale
          Zoomfactor, zooming in screen scale space, and is relative to original position, this stores that original position:.
        • m_kObjBoxSliceProbe_TG
          javax.media.j3d.TransformGroup[] m_kObjBoxSliceProbe_TG
          TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice BOXES:
        • m_kObjPlaneProbe_TG
          javax.media.j3d.TransformGroup[] m_kObjPlaneProbe_TG
          TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice PLANES:
        • m_kProbeTransform
          javax.media.j3d.Transform3D m_kProbeTransform
          The Transform3D used to position the planes based on the Probe position and angle. The planes are rotates about the intersection between the probe and the plane, which may or may not be in the center of the plane. This transform allows non-origin rotations by conactenating the translation to the origin, rotation, and translation matricies into one transform, which is used to set the Transforms for the TransformGroups above and also to sample the ModelImage data on the diagonal slice:
        • m_kRFACoordMaps
          javax.vecmath.Vector4f[][] m_kRFACoordMaps
          Texture mapping for the RFA probe rotation:
        • m_kSoftwareLightSet
          SoftwareLightSet m_kSoftwareLightSet
          Used to compute software lighting of composite texture volume.
        • m_kSoftwareMaterial
          SoftwareMaterial m_kSoftwareMaterial
          DOCUMENT ME!
        • maxBox
          float maxBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • mousePanel
          JPanelMouse mousePanel
          Dialog for recording and playing back mouse events.
        • mouseRotateBehavior
          MouseRotateExt mouseRotateBehavior
          Mouse Rotate behavior.
        • mouseTranslateBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseTranslateBehavior
          Mouse Translate behavior.
        • mouseZoomBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseZoomBehavior
          Mouse Zoom behavior.
        • myEyePoint
          javax.vecmath.Point3d myEyePoint
          Initial center viewing point of the image.
        • objPlane_BG
          javax.media.j3d.BranchGroup[] objPlane_BG
          BranchGroup[] containing the image planes.
        • objTransSlices_TG
          javax.media.j3d.TransformGroup[] objTransSlices_TG
          Group dictating how the XY plane is translated.
        • parallelRotation
          boolean parallelRotation
          Parallel rotation flag.
        • parallelScaleT3D
          javax.media.j3d.Transform3D parallelScaleT3D
          Transformation matrix.
        • parent
          ViewJFrameBase parent
          Controls for the image. ViewJFrameVolumeView
        • probePanel
          JPanelProbe probePanel
          Dialog for loading and displaying probes.
        • resols
          float[] resols
          Resolutions of image A.
        • rotationCount
          int rotationCount
          fix one bug from threading.
        • segmentationImage
          ModelImage segmentationImage
          Image with areas marked with values indicating that they are special tissue types (vessels, etc).
        • slicePanel
          JPanelSlices slicePanel
          Dialog to turn the slices control box on and off.
        • surfacePanel
          JPanelSurface surfacePanel
          Dialog for loading and displaying surfaces.
        • surfaceTexturePanel
          JPanelSurfaceTexture surfaceTexturePanel
          Panel for displaying the SurfaceTexture interface:
        • switchGroup
          javax.media.j3d.Switch switchGroup
          Tri planar view and the 3D texture volume view switch group.
        • tDim
          int tDim
          Dimensions of image A.
        • transformCubic
          javax.media.j3d.Transform3D transformCubic
          Cubic tansform3D.
        • transformNode3d
          javax.media.j3d.Transform3D transformNode3d
          Setup the initial position of the image, added to ScenerootTG transform group.
        • view
          javax.media.j3d.View view
          View object in rendering a three dimensional scene from one viewpoint.
        • volBG
          javax.media.j3d.BranchGroup volBG
          Volume branch group.
        • volRenderBG
          javax.media.j3d.BranchGroup volRenderBG
          Volume render branch group.
        • volRenderOG
          javax.media.j3d.OrderedGroup volRenderOG
          Volume render order group, specify the rendering order.
        • volumeDisplayMode3D
          boolean volumeDisplayMode3D
          If true display 3D volume as a 3D texture map or 2D array of texture maps. If false display 3 orthogonal image planes.
        • xBox
          float xBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • xDim
          int xDim
          Dimensions of image A.
        • yBox
          float yBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • yDim
          int yDim
          Dimensions of image A.
        • zBox
          float zBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • zDim
          int zDim
          Dimensions of image A.

  • Package gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.JPanelBrainSurfaceFlattener

      class JPanelBrainSurfaceFlattener extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -2749305357977770854L

      • Serialized Fields

        • m_bFileLoaded
          boolean m_bFileLoaded
          DOCUMENT ME!
        • m_bFirstSurface
          boolean m_bFirstSurface
          DOCUMENT ME!
        • m_iGridY
          int m_iGridY
          DOCUMENT ME!
        • m_kButtonLoadImage
          JButton m_kButtonLoadImage
          DOCUMENT ME!
        • m_kButtonLoadSurface
          JButton m_kButtonLoadSurface
          DOCUMENT ME!
        • m_kCenter
          javax.vecmath.Point3f m_kCenter
          DOCUMENT ME!
        • m_kDisablePick
          JRadioButton m_kDisablePick
          DOCUMENT ME!
        • m_kDisplayButtonGroup
          ButtonGroup m_kDisplayButtonGroup
          DOCUMENT ME!
        • m_kDisplayPlane
          JRadioButton m_kDisplayPlane
          DOCUMENT ME!
        • m_kDisplaySphere
          JRadioButton m_kDisplaySphere
          DOCUMENT ME!
        • m_kFile
          File m_kFile
          DOCUMENT ME!
        • m_kImage
          ModelImage m_kImage
          DOCUMENT ME!
        • m_kImageDir
          String m_kImageDir
          DOCUMENT ME!
        • m_kImageFile
          String m_kImageFile
          DOCUMENT ME!
        • m_kLabelFileName
          JLabel m_kLabelFileName
          DOCUMENT ME!
        • m_kLabelFileNameImage
          JLabel m_kLabelFileNameImage
          DOCUMENT ME!
        • m_kLatLonLines
          JCheckBox m_kLatLonLines
          DOCUMENT ME!
        • m_kLUTa
          ModelLUT m_kLUTa
          DOCUMENT ME!
        • m_kLUTImageA
          ModelImage m_kLUTImageA
          DOCUMENT ME!
        • m_kNumLatText
          JTextField m_kNumLatText
          DOCUMENT ME!
        • m_kNumLonText
          JTextField m_kNumLonText
          DOCUMENT ME!
        • m_kPanelBrainsurfaceFlattenerLUT
          JFrameHistogram m_kPanelBrainsurfaceFlattenerLUT
          DOCUMENT ME!
        • m_kParentFrame
          ViewJFrameVolumeView m_kParentFrame
          DOCUMENT ME!
        • m_kPickButtonGroup
          ButtonGroup m_kPickButtonGroup
          DOCUMENT ME!
        • m_kPickCorrespondence
          JRadioButton m_kPickCorrespondence
          DOCUMENT ME!
        • m_kPickPuncture
          JRadioButton m_kPickPuncture
          DOCUMENT ME!
        • m_kSurfaceDir
          String m_kSurfaceDir
          DOCUMENT ME!
        • m_kTriangleMesh
          ModelTriangleMesh m_kTriangleMesh
          DOCUMENT ME!
        • m_kView
          MjCorticalAnalysis m_kView
          DOCUMENT ME!

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjCorticalAnalysis

      class MjCorticalAnalysis extends RenderViewBase implements Serializable
      serialVersionUID:
      -6130870790192175575L

      • Serialized Fields

        • m_aiTriIndex
          int[] m_aiTriIndex
          DOCUMENT ME!
        • m_akPickColors
          javax.vecmath.Color3f[] m_akPickColors
          Colors for the picked points:.
        • m_akTriColors
          javax.vecmath.Color4f[] m_akTriColors
          DOCUMENT ME!
        • m_bCurvatureColors
          boolean m_bCurvatureColors
          Flag set to indicate whether curvature colors are rendered on the mesh surface. If not, then average convexity colors are rendered.
        • m_bInflationInitialized
          boolean m_bInflationInitialized
          Flag set once inflation processing has been initialized.
        • m_bMousePressed
          boolean m_bMousePressed
          Mouse events. Setting mousePressed and mouseReleased explicitly when the mouse events are received has deals with getting multiply mouse event notifications for the same mouse press.
        • m_bMouseReleased
          boolean m_bMouseReleased
          DOCUMENT ME!
        • m_bPickCorrespondenceEnabled
          boolean m_bPickCorrespondenceEnabled
          Turned on when picking with the mouse is enabled:.
        • m_bPickPunctureEnabled
          boolean m_bPickPunctureEnabled
          DOCUMENT ME!
        • m_iNumPicked
          int m_iNumPicked
          number of picked points displayed.
        • m_iRunningNumPicked
          int m_iRunningNumPicked
          DOCUMENT ME!
        • m_kCortical
          MjCorticalMesh m_kCortical
          Cortical mesh to be used in rendering scene.
        • m_kGeometryArrayPlane
          javax.media.j3d.GeometryArray m_kGeometryArrayPlane
          DOCUMENT ME!
        • m_kGeometryArraySphere
          javax.media.j3d.GeometryArray m_kGeometryArraySphere
          DOCUMENT ME!
        • m_kLUTConvexity
          ModelLUT m_kLUTConvexity
          DOCUMENT ME!
        • m_kLUTCurvature
          ModelLUT m_kLUTCurvature
          local reference to ModelLUT.
        • m_kMeshBranchRoot
          javax.media.j3d.BranchGroup m_kMeshBranchRoot
          BranchGroups for the Meshlines, for deleting and recreating the meshlines when the user changes the number of latitude and longitude lines:.
        • m_kMeshLinesBranchRoot
          javax.media.j3d.BranchGroup m_kMeshLinesBranchRoot
          DOCUMENT ME!
        • m_kMouseEvent
          MouseEvent m_kMouseEvent
          DOCUMENT ME!
        • m_kPanel
          JPanelBrainSurfaceFlattener m_kPanel
          DOCUMENT ME!
        • m_kPickCanvas
          com.sun.j3d.utils.picking.PickCanvas m_kPickCanvas
          DOCUMENT ME!
        • m_kShapeMesh
          javax.media.j3d.Shape3D m_kShapeMesh
          DOCUMENT ME!
        • m_kShapePlane
          javax.media.j3d.Shape3D m_kShapePlane
          DOCUMENT ME!
        • m_kShapeSphere
          javax.media.j3d.Shape3D m_kShapeSphere
          DOCUMENT ME!
        • m_kSwitchDisplay
          javax.media.j3d.Switch m_kSwitchDisplay
          Switch between displaying the Sphere and the Plane:.
        • m_kSwitchLinesMesh
          javax.media.j3d.Switch m_kSwitchLinesMesh
          This node contains the latitude/longitude renderings for the mesh which can be enabled/disabled.
        • m_kSwitchLinesPlane
          javax.media.j3d.Switch m_kSwitchLinesPlane
          This node contains the latitude/longitude renderings for the plane which can be enabled/disabled.
        • m_kSwitchLinesPlaneBranch
          javax.media.j3d.BranchGroup m_kSwitchLinesPlaneBranch
          DOCUMENT ME!
        • m_kSwitchLinesSphere
          javax.media.j3d.Switch m_kSwitchLinesSphere
          This node contains the latitude/longitude renderings for the sphere which can be enabled/disabled.
        • m_kSwitchLinesSphereBranch
          javax.media.j3d.BranchGroup m_kSwitchLinesSphereBranch
          DOCUMENT ME!
        • m_kTransformGroupActive
          javax.media.j3d.TransformGroup m_kTransformGroupActive
          Currently selected transform that gets modified by the handler for the keyboard behavior.
        • m_kTransformGroupMesh
          javax.media.j3d.TransformGroup m_kTransformGroupMesh
          DOCUMENT ME!
        • m_kTransformGroupPlane
          javax.media.j3d.TransformGroup m_kTransformGroupPlane
          DOCUMENT ME!
        • m_kTransformGroupPoseMesh
          javax.media.j3d.TransformGroup m_kTransformGroupPoseMesh
          This node contains all of the cortical mesh related nodes in the scene which can be manipulated as a group.
        • m_kTransformGroupPosePlane
          javax.media.j3d.TransformGroup m_kTransformGroupPosePlane
          This node contains all of the plane related nodes in the scene which can be manipulated as a group.
        • m_kTransformGroupPoseSphere
          javax.media.j3d.TransformGroup m_kTransformGroupPoseSphere
          This node contains all of the sphere related nodes in the scene which can be manipulated as a group.
        • m_kTransformGroupSphere
          javax.media.j3d.TransformGroup m_kTransformGroupSphere
          DOCUMENT ME!
        • m_kTriangleMesh
          ModelTriangleMesh m_kTriangleMesh
          Geometry for the rendering of the cortical mesh is maintained here so that the scene can be updated when the mesh is inflated.
        • MAX_POINTS
          int MAX_POINTS
          DOCUMENT ME!
        • MESH
          int MESH
          DOCUMENT ME!
        • PLANE
          int PLANE
          DOCUMENT ME!
        • SPHERE
          int SPHERE
          DOCUMENT ME!

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjVector2f

      class MjVector2f extends javax.vecmath.Vector2f implements Serializable
      serialVersionUID:
      -1076716465909115350L

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjVector3f

      class MjVector3f extends javax.vecmath.Vector3f implements Serializable
      serialVersionUID:
      -3573463090318350522L

  • Package gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview.FlythruRender

      class FlythruRender extends SurfaceRender implements Serializable
      serialVersionUID:
      -3255657270255875848L

      • Serialized Fields

        • buffer
          short[] buffer
          DOCUMENT ME!
        • capScreenHeight
          int capScreenHeight
          DOCUMENT ME!
        • capScreenWidth
          int capScreenWidth
          DOCUMENT ME!
        • currEventTime
          long currEventTime
          Current mouse press event time stamp.
        • directory
          String directory
          DOCUMENT ME!
        • extents
          int[] extents
          DOCUMENT ME!
        • fileType
          String fileType
          DOCUMENT ME!
        • imageCounter
          int imageCounter
          DOCUMENT ME!
        • imageToMovie
          JpegImagesToMovie imageToMovie
          DOCUMENT ME!
        • kCanvas
          VolumeCanvas3D kCanvas
          DOCUMENT ME!
        • kImage
          ModelImage kImage
          DOCUMENT ME!
        • m_aiBranchIndexUnvisitedMax
          int[] m_aiBranchIndexUnvisitedMax
          DOCUMENT ME!
        • m_aiBranchIndexUnvisitedMin
          int[] m_aiBranchIndexUnvisitedMin
          This is the range of path samples for each branch that are unvisited.
        • m_aiMeshConnectivity
          int[] m_aiMeshConnectivity
          DOCUMENT ME!
        • m_iLastSelectedBranchIndex
          int m_iLastSelectedBranchIndex
          Keep track of the last branch that was selected (at a branch point).
        • m_kAnnotateList
          FlyPathAnnotateList m_kAnnotateList
          This is for the collection of annotation points.
        • m_kAnnotatePointGroup
          javax.media.j3d.Group m_kAnnotatePointGroup
          DOCUMENT ME!
        • m_kBranchConnectShape
          javax.media.j3d.Shape3D m_kBranchConnectShape
          DOCUMENT ME!
        • m_kBranchPathShape
          javax.media.j3d.Shape3D m_kBranchPathShape
          This is the Java3D geometry for the path.
        • m_kControlFrame
          JPanelVirtualEndoscopySetup m_kControlFrame
          This is the control frame which may need to be updated as the view changes.
        • m_kFlyPathBehavior
          FlyPathBehavior m_kFlyPathBehavior
          Keep track of the FlyPathBehavior because it knows about the view from the path.
        • m_kFlyPathGraphCurve
          FlyPathGraphCurve m_kFlyPathGraphCurve
          DOCUMENT ME!
        • m_kFlyPathGraphSamples
          FlyPathGraphSamples m_kFlyPathGraphSamples
          This is the path extracted from the skeletonization.
        • m_kGeodesicGroup
          javax.media.j3d.Group m_kGeodesicGroup
          DOCUMENT ME!
        • m_kMeanCurvaturesLUT
          ModelLUT m_kMeanCurvaturesLUT
          DOCUMENT ME!
        • m_kMeshCurvatures
          ModelTriangleMeshCurvatures m_kMeshCurvatures
          DOCUMENT ME!
        • m_kMouseRotateBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseRotate m_kMouseRotateBehavior
          DOCUMENT ME!
        • m_kNormalColorPathUnvisited
          javax.vecmath.Color3f m_kNormalColorPathUnvisited
          DOCUMENT ME!
        • m_kNormalColorPathVisited
          javax.vecmath.Color3f m_kNormalColorPathVisited
          These are the colors to use when rendering the normal/selected branch that is unvisited/visited.
        • m_kOptions
          FlythruRender.SetupOptions m_kOptions
          These are the setup options passed to the constructor which we need to keep track of in case we need to use them outside the constructor.
        • m_kPickCanvas
          com.sun.j3d.utils.picking.PickCanvas m_kPickCanvas
          Used for picking.
        • m_kPointLight
          javax.media.j3d.PointLight m_kPointLight
          DOCUMENT ME!
        • m_kSceneRoot
          javax.media.j3d.BranchGroup m_kSceneRoot
          These are part of the scene and view.
        • m_kSelectColorPathUnvisited
          javax.vecmath.Color3f m_kSelectColorPathUnvisited
          DOCUMENT ME!
        • m_kSelectColorPathVisited
          javax.vecmath.Color3f m_kSelectColorPathVisited
          DOCUMENT ME!
        • m_kSkeleton
          Skeleton3D m_kSkeleton
          This it skeletonization of the binary volume.
        • m_kSurface
          ModelTriangleMesh m_kSurface
          This is the surface geometry and its properties.
        • m_kSurfaceCurveSegments
          ModelTriangleMeshCurveSegments m_kSurfaceCurveSegments
          DOCUMENT ME!
        • m_kSurfaceGeometry
          javax.media.j3d.IndexedGeometryArray m_kSurfaceGeometry
          DOCUMENT ME!
        • m_kSurfaceGeometryInfo
          com.sun.j3d.utils.geometry.GeometryInfo m_kSurfaceGeometryInfo
          This is the Java3D geometry for the surface.
        • m_kSurfaceMesh
          ModelTriangleMesh m_kSurfaceMesh
          DOCUMENT ME!
        • m_kSurfaceShape
          javax.media.j3d.Shape3D m_kSurfaceShape
          DOCUMENT ME!
        • m_kUniverse
          com.sun.j3d.utils.universe.SimpleUniverse m_kUniverse
          The simple universe contains a single canvas, a viewing platform, and a scene graph. The scene graph will contain all objects involved in the rendering.
        • m_kVolumeLayout
          ModelImage3DLayout m_kVolumeLayout
          Describes the organization of the volume data in a linear array.
        • movieMake
          MovieMaker movieMake
          DOCUMENT ME!
        • parentFrame
          ViewJFrameVolumeView parentFrame
          DOCUMENT ME!
        • pixels
          int[] pixels
          DOCUMENT ME!
        • pressed
          boolean pressed
          If any of the mouse move button pressed.
        • prevEventTime
          long prevEventTime
          Previous mouse press event time stamp.
        • rendererProgressBar
          JProgressBar rendererProgressBar
          A local reference to the volume renderer frame's progress bar.
        • robot
          Robot robot
          DOCUMENT ME!
        • saveCounter
          int saveCounter
          DOCUMENT ME!
        • time
          long time
          Time to wait for the next mouse event.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview.JPanelVirtualEndoscopySetup

      class JPanelVirtualEndoscopySetup extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      5676430934584329807L

      • Serialized Fields

        • contentBox
          Box contentBox
          Box layout for control panel.
        • continueUpdate
          boolean continueUpdate
          Flag indicates to continue update the surface render and plane render or not.
        • directory
          String directory
          File name and directory.
        • endoscopyImage
          ModelImage endoscopyImage
          Loaded endoscopy image file.
        • fileName
          String fileName
          File name and directory.
        • flythruButtonLoadImage
          JButton flythruButtonLoadImage
          DOCUMENT ME!
        • flythruLabelFileName
          JLabel flythruLabelFileName
          DOCUMENT ME!
        • kDialogSmooth
          JDialogSmoothMesh kDialogSmooth
          Surface smooth control panel reference.
        • kFile
          File kFile
          File to open the mask suface.
        • kPanelButton
          JPanel kPanelButton
          Button panel.
        • m_bShowMeanCurvatures
          boolean m_bShowMeanCurvatures
          Flag indicates to show pseudo color or not.
        • m_kButtonLoadSurface
          JButton m_kButtonLoadSurface
          DOCUMENT ME!
        • m_kCheckBoxShowCurvatures
          JCheckBox m_kCheckBoxShowCurvatures
          DOCUMENT ME!
        • m_kComboSegmentSurfaceBranchSamplesReductionFactor
          JComboBox m_kComboSegmentSurfaceBranchSamplesReductionFactor
          Surface sample reduction factor.
        • m_kContinueUpdate
          JCheckBox m_kContinueUpdate
          DOCUMENT ME!
        • m_kDecimalFormat
          DecimalFormat m_kDecimalFormat
          Used to create text representations of numbers.
        • m_kLabelBranch
          JLabel m_kLabelBranch
          DOCUMENT ME!
        • m_kLabelDirection
          JLabel m_kLabelDirection
          DOCUMENT ME!
        • m_kLabelDistance
          JLabel m_kLabelDistance
          DOCUMENT ME!
        • m_kLabelFileName
          JLabel m_kLabelFileName
          Automatically inserted by JBuilder Designer.
        • m_kLabelOrientation
          JLabel m_kLabelOrientation
          DOCUMENT ME!
        • m_kLabelPosition
          JLabel m_kLabelPosition
          DOCUMENT ME!
        • m_kLabelStepGaze
          JLabel m_kLabelStepGaze
          DOCUMENT ME!
        • m_kMeanCurvaturesLUT
          ModelLUT m_kMeanCurvaturesLUT
          kMean curvature LUT. Pseudo color look up table.
        • m_kOptions
          FlythruRender.SetupOptions m_kOptions
          Image option panel.
        • m_kTextBranch
          JTextField m_kTextBranch
          DOCUMENT ME!
        • m_kTextDirection
          JTextField m_kTextDirection
          DOCUMENT ME!
        • m_kTextDistance
          JTextField m_kTextDistance
          DOCUMENT ME!
        • m_kTextMaxNumBranches
          JTextField m_kTextMaxNumBranches
          maximum number of branches created for the endoscopy view.
        • m_kTextMinBranchLength
          JTextField m_kTextMinBranchLength
          minimum branch length.
        • m_kTextOrientation
          JTextField m_kTextOrientation
          DOCUMENT ME!
        • m_kTextPercentBSplineNumControlPoints
          JTextField m_kTextPercentBSplineNumControlPoints
          BSpline control points fraction of branch samples.
        • m_kTextPosition
          JTextField m_kTextPosition
          DOCUMENT ME!
        • m_kTextStepGaze
          JTextField m_kTextStepGaze
          DOCUMENT ME!
        • m_kTriangleMesh
          ModelTriangleMesh m_kTriangleMesh
          Keep a copy of the loaded triangle mesh and any other properties associated with the surface.
        • m_kView
          FlythruRender m_kView
          Applet that is associated with the controls in this frame.
        • parentFrame
          ViewJFrameVolumeView parentFrame
          Keep a reference to the ViewJFrameVolumeView.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanelVirtualEndoscopySetup.DrawingPanel scrollPanel
          Scroll panel that holding all the control components.
        • surfaceDir
          String surfaceDir
          Loaded mask surface image directory.
        • updateButton
          JButton updateButton
          continue update button.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview.ViewJSimpleProgressBar

      class ViewJSimpleProgressBar extends ViewJProgressBar implements Serializable
      serialVersionUID:
      -8035459499734828360L

      • Serialized Fields

        • m_fRangeMax
          float m_fRangeMax
          DOCUMENT ME!
        • m_fRangeMin
          float m_fRangeMin
          Remember the range of input values for the progress bar. It is not required that the minimum be less than the maximum.
        • m_iLastValue
          int m_iLastValue
          Remember the value passed to the setValue method of the JProgressBar. When valid, should be in range [0,RESOLUTION).

  • Package gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.JPanelMousePlotter

      class JPanelMousePlotter extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -8105261993244718879L

      • Serialized Fields

        • changedMode
          boolean changedMode
          flag to indicate current mode being changed.
        • contButton
          JToggleButton contButton
          Continue play button.
        • current
          int current
          index to the item list.
        • currentEventVector
          MouseEventVectorPlotter currentEventVector
          Current event vector used by the save AVI.
        • currentObject
          Object currentObject
          current SceneState object being recorded by SaveAVI.
        • currentTransform
          javax.media.j3d.Transform3D currentTransform
          Current transform3D object used in Save AVI.
        • events
          Vector<MouseEventVectorPlotter> events
          Vector that holds mouse or change events.
        • eventVector
          MouseEventVectorPlotter eventVector
          Global mouse event vector.
        • first
          boolean first
          Flag to indicate first event.
        • goButton
          JButton goButton
          Go to button.
        • isPlaying
          boolean isPlaying
          Flag to indicating play mouse is running or not.
        • listModel
          DefaultListModel listModel
          List to record info for each mouse, change events.
        • mjpegQuality
          float mjpegQuality
          DOCUMENT ME!
        • mode
          int mode
          Current mode, init to stop.
        • mouseCount
          int mouseCount
          Mouse event counter.
        • movieButton
          JButton movieButton
          Save AVI button .
        • myParentPlotter
          SurfacePlotter myParentPlotter
          Reference to ViewJFrameSurfacePlotter.
        • nameChangeVector
          MouseEventVectorPlotter nameChangeVector
          Used by name change dialog to change name of the selected item.
        • newButton
          JButton newButton
          This button add at head of the list.
        • parentScene
          RenderViewBase parentScene
          Parent scene.
        • pauseButton
          JToggleButton pauseButton
          Pause button.
        • playButton
          JToggleButton playButton
          Display button.
        • playMouse
          JPanelMousePlotter.PlayMouse playMouse
          Reference to PlayMouse class object.
        • process
          int process
          Process id used by the save AVI.
        • recordButton
          JToggleButton recordButton
          Recorder button.
        • recorderToAVI
          JPanelMousePlotter.RecordMouse recorderToAVI
          Reference to RecordMouse object class.
        • removeAllButton
          JButton removeAllButton
          Remove all items in the item list.
        • removeButton
          JButton removeButton
          Remove the selected item in the item list.
        • resetTransform
          javax.media.j3d.Transform3D resetTransform
          Current transform3D object.
        • setMouseVectorFlag
          boolean setMouseVectorFlag
          flag to indicate the first time mouse tranform event happpened.
        • sliderCount
          int sliderCount
          Slider moves event counter.
        • stepButton
          JToggleButton stepButton
          Next step button.
        • stopButton
          JToggleButton stopButton
          Stop button.
        • toolBar
          JToolBar toolBar
          Tool bar of the mouse recorder.
        • transformChange
          boolean transformChange
          DOCUMENT ME!
        • viewList
          JList viewList
          View list of the mouse recorder display list.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.JPanelSurfaceBox

      class JPanelSurfaceBox extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -1435246141584042105L

      • Serialized Fields

        • boundingCheck
          JCheckBox boundingCheck
          Check box for turning box on and off.
        • buttonPanel
          JPanel buttonPanel
          DOCUMENT ME!
        • coarse
          JTextField coarse
          DOCUMENT ME!
        • coarseLabel
          JLabel coarseLabel
          DOCUMENT ME!
        • coarseValue
          float coarseValue
          DOCUMENT ME!
        • colorButton
          JButton colorButton
          Color button for changing color.
        • colorButtonBackground
          JButton colorButtonBackground
          Color button for changing z color.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser dialog.
        • cubePanel
          JPanel cubePanel
          Panel for the rotation cube.
        • cubicCheck
          JCheckBox cubicCheck
          Check box for cubic control.
        • fine
          JTextField fine
          DOCUMENT ME!
        • fineLabel
          JLabel fineLabel
          DOCUMENT ME!
        • fineValue
          float fineValue
          DOCUMENT ME!
        • flag
          boolean flag
          Flag indicating if box is on or off.
        • radioButtonGroupProjections
          ButtonGroup radioButtonGroupProjections
          Button group for projections.
        • radioButtonOrthographic
          JRadioButton radioButtonOrthographic
          Radio Button for Orthographic rendering.
        • radioButtonPerspective
          JRadioButton radioButtonPerspective
          Radio Button for Perspective rendering.
        • viewAlignedButton
          JRadioButton viewAlignedButton
          Radio Button for Perspective rendering.
        • viewButton
          JRadioButton viewButton
          Radio Button for Orthographic rendering.
        • viewTextureButtonGroup
          ButtonGroup viewTextureButtonGroup
          Button group for projections.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.MouseEventVectorPlotter

      class MouseEventVectorPlotter extends Object implements Serializable
      serialVersionUID:
      -6069342266407301187L

      • Serialization Methods

        • readObject
          private void readObject(ObjectInputStream stream) throws IOException, ClassNotFoundException
          Called by some native invokeMethod. Provides a way to read this class out as a object stream. First, the size of the vector is read, then each mouseEvent into the vector, then the name, then the view. The view is read in as a String because it is not serializable. The read method corresponds to the write method, below.
          Parameters:
          stream - Object stream to read from.
          Throws:
          IOException - If the matrix being read in by the JDialogMouseRecorder has the incorrect size.
          ClassNotFoundException - DOCUMENT ME!
        • writeObject
          private void writeObject(ObjectOutputStream stream) throws IOException
          Called by some native invokeMethod. Provides a way to write this class out as a object stream. First, the size of the vector is written, then each mouseEvent in the vector, then the name, then the view. The view is written out as a String because it is not serializable. The write method corresponds to the read method, above.
          Parameters:
          stream - Object stream to write to.
          Throws:
          IOException - DOCUMENT ME!

      • Serialized Fields

        • first
          boolean first
          First time accessed.
        • mode
          int mode
          Current mode.
        • mouseEvents
          Vector mouseEvents
          Vector to record mouse events.
        • name
          String name
          Name of the events.
        • state
          Object state
          State being recorded.
        • stateVector
          Vector stateVector
          Vector to record state changes.
        • view
          javax.media.j3d.Transform3D view
          Parent frame transform3D view.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.SceneStatePlotter

      class SceneStatePlotter extends Object implements Serializable
      serialVersionUID:
      5063961369724570657L

      • Serialized Fields

        • transform
          javax.media.j3d.Transform3D transform
          Current sceneRoot transform.
        • z
          int z
          DOCUMENT ME!
        • zVisible
          boolean zVisible
          DOCUMENT ME!

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.SurfacePlotter

      class SurfacePlotter extends RenderViewBase implements Serializable
      serialVersionUID:
      -1650691820947415108L

      • Serialized Fields

        • boxDialog
          JPanelSurfaceBox boxDialog
          Dialog for recording and playing back mouse events.
        • componentImageXY
          ViewJComponentSurface componentImageXY
          Main component found in this frame.
        • controlPanel
          JPanel controlPanel
          the control panel that hold the z slider.
        • current
          int current
          Current event vector index.
        • extents
          int[] extents
          Extents of image.
        • imageBranch
          javax.media.j3d.BranchGroup imageBranch
          Branch parent of the image in the scene, needed so image can be made invisible when another surface is loaded.
        • isVisible
          boolean isVisible
          Flag indicating if the image is currently visible.
        • itemLine
          JCheckBoxMenuItem itemLine
          Check box menu item indicating if surface should be in line mode or full mode.
        • label1
          JLabel label1
          Label for slider, "1".
        • label100
          JLabel label100
          Label for slider, "100".
        • label50
          JLabel label50
          Label for slider, "50".
        • labelZ
          JLabel labelZ
          Label that says "Z (1-100)".
        • LUTa
          ModelLUT LUTa
          LUT that dictates how the vertices of the quad mesh are colored.
        • mainPanel
          JPanel mainPanel
          The main control panel.
        • mouseDialog
          JPanelMousePlotter mouseDialog
          Mouse recorder dialog associated with surface plotter.
        • mouseRotateBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseRotate mouseRotateBehavior
          Mouse Rotate behavior.
        • mouseTranslateBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseTranslateBehavior
          Mouse Translate behavior.
        • mouseZoomBehavior
          com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseZoomBehavior
          Mouse Zoom behavior.
        • myEyePoint
          javax.vecmath.Point3d myEyePoint
          Initial center viewing point of the image.
        • objTransXY
          javax.media.j3d.TransformGroup objTransXY
          Transform group guiding how image is displayed.
        • openingMenuBar
          JMenuBar openingMenuBar
          Menu bar.
        • panelToolbar
          JPanel panelToolbar
          Panel that holds the toolbars.
        • parallelScaleT3D
          javax.media.j3d.Transform3D parallelScaleT3D
          Transformation matrix.
        • setSliderFlag
          boolean setSliderFlag
          Flag to indicate the first time slider name changes.
        • slice
          int slice
          Current slice of 3D image, used to figure out XY plane to plot.
        • sliderEvents
          MouseEventVectorPlotter sliderEvents
          Slider events used by the mouse recorder.
        • sliderFrame
          JSlider sliderFrame
          Slider for frame/slice of image.
        • sliderZ
          JSlider sliderZ
          3, 1-100%, dictating where the image in the surface should be displayed.
        • t3d_XY_t
          javax.media.j3d.Transform3D t3d_XY_t
          Actual transform of the image.
        • textZ
          JTextField textZ
          Text field displaying the percentage of the slider.
        • texUnitStateBXY
          javax.media.j3d.TextureUnitState[] texUnitStateBXY
          Texture creating appearance for the "back" of the image. Needs to be array even though there will be only 1 item.
        • texUnitStateFXY
          javax.media.j3d.TextureUnitState[] texUnitStateFXY
          Texture creating appearance for the "front" of the image. Needs to be array even though there will be only 1 item.
        • visibleBox
          JCheckBox visibleBox
          Check box for whether or not the image should be visible.
        • xRes
          float xRes
          X and Y resolution.
        • yRes
          float yRes
          X and Y resolution.
        • zSlice
          int zSlice
          Z slice, which image of 1-100 are we showing.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.ViewJComponentSurface

      class ViewJComponentSurface extends ViewJComponentBase implements Serializable
      serialVersionUID:
      -870321457925828704L

      • Serialized Fields

        • cConnect
          int[] cConnect
          Vertex connection array.
        • cVertex
          javax.vecmath.Point3f[] cVertex
          Vertex array.
        • frame
          RenderViewBase frame
          Frame where the plotted surface is displayed.
        • imageA
          ModelImage imageA
          Structure holding image.
        • imageBufferA
          float[] imageBufferA
          Buffer which holds the pixel data.
        • imageExtents
          int[] imageExtents
          Extents of the image.
        • lineMode
          boolean lineMode
          Flag indicating if the surface is currently in line mode (true) or fill mode (false).
        • LUTa
          ModelLUT LUTa
          Lookup table for image.
        • lutBufferRemapped
          int[] lutBufferRemapped
          Used to remap the LUT appropriately.
        • maxBox
          float maxBox
          MaxBox value from the parent frame.
        • pixBuffer
          int[] pixBuffer
          Buffer used to store ARGB images of the image presently being displayed.
        • plottedRoot
          javax.media.j3d.BranchGroup plottedRoot
          Branch group that is the parent of the plotted surface.
        • qMesh
          ModelQuadMesh qMesh
          Quad mesh. This is the core of the component.
        • sampleSize
          int sampleSize
          Sample size. This determines how many triangles are used in the quad mesh.
        • xBox
          float xBox
          xBox, yBox and zBox values from the parent frame.
        • yBox
          float yBox
          xBox, yBox and zBox values from the parent frame.
        • zBox
          float zBox
          xBox, yBox and zBox values from the parent frame.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.ViewJFramePlotterView

      class ViewJFramePlotterView extends ViewJFrameBase implements Serializable
      serialVersionUID:
      8972056170229565046L

      • Serialized Fields

        • cameraPanel
          JPanel cameraPanel
          DOCUMENT ME!
        • compound
          Border compound
          Panel Border view.
        • config
          GraphicsConfiguration config
          Configuration param, which will pass down to each render's constructor.
        • imagePanel
          JPanel imagePanel
          The image panel to hold one Canvas3D.
        • itemLine
          JCheckBoxMenuItem itemLine
          Image line mode check box.
        • loweredbevel
          Border loweredbevel
          Panel Border view.
        • mousePanel
          JPanel mousePanel
          DOCUMENT ME!
        • openingMenuBar
          JMenuBar openingMenuBar
          Menu bar.
        • panelToolbar
          JPanel panelToolbar
          Toolbar panel.
        • plotterRender
          SurfacePlotter plotterRender
          Surface plotter view.
        • raisedbevel
          Border raisedbevel
          Panel Border view.
        • screenHeight
          int screenHeight
          Screen width, screen height.
        • screenWidth
          int screenWidth
          Screen width, screen height.
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • sliderControlPanel
          JPanel sliderControlPanel
          DOCUMENT ME!
        • surfaceBoxPanel
          JPanel surfaceBoxPanel
          DOCUMENT ME!
        • surTabVector
          Vector surTabVector
          DOCUMENT ME!
        • tabbedPane
          JTabbedPane tabbedPane
          The main tabbed pane in the volume view frame.
        • tabVector
          Vector tabVector
          For each render, use the vector to store the currently active tabs.
        • viewPanel
          JPanel viewPanel
          Control panel for the surface renderer.

  • Package gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.JDialogBurnParameter

      class JDialogBurnParameter extends JDialogBase implements Serializable
      serialVersionUID:
      -1568251410627012713L

      • Serialized Fields

        • diameter
          float diameter
          DOCUMENT ME!
        • diameterField
          JTextField diameterField
          DOCUMENT ME!
        • ok
          boolean ok
          DOCUMENT ME!
        • opacity
          float opacity
          DOCUMENT ME!
        • probePanel
          JPanelProbe probePanel
          DOCUMENT ME!
        • radius
          float radius
          DOCUMENT ME!
        • time
          float time
          DOCUMENT ME!
        • timeField
          JTextField timeField
          DOCUMENT ME!
        • voltage
          float voltage
          DOCUMENT ME!
        • voltageField
          JTextField voltageField
          DOCUMENT ME!
        • volume
          float volume
          DOCUMENT ME!

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.JPanelProbe

      class JPanelProbe extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -2467552118438070016L

      • Serialized Fields

        • bonePresetButton
          JButton bonePresetButton
          DOCUMENT ME!
        • burnBackFaceCB
          JCheckBox burnBackFaceCB
          burning point back face culling check box.
        • burnBase
          BurnBase burnBase
          Burn base reference.
        • burnClipCB
          JCheckBox burnClipCB
          burning point clipping check box.
        • burnIndex
          int burnIndex
          Current burning point index being hightlighted.
        • burningPtTransVector
          javax.vecmath.Vector3f burningPtTransVector
          Burning point coordinate vector in world coordinate system.
        • burnList
          JList burnList
          Burn list that hold the burning point names.
        • calcButton
          JButton calcButton
          Calculat button.
        • center
          javax.vecmath.Point3f center
          Burning point coordinate.
        • centerLabel
          JLabel centerLabel
          burning point center label.
        • clipping
          boolean clipping
          Burning surface being clipped or not.
        • colorButton
          JButton colorButton
          Burning point color button.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser when the user changes the color of the surface.
        • colorLabel
          JLabel colorLabel
          Burning point color label.
        • culling
          boolean culling
          Burning surface being culled ( back face bulling ) or not.
        • cursorMode
          int cursorMode
          curreent cursor nevigation mode.
        • diffVolumeLabel
          JLabel diffVolumeLabel
          Volume difference label for the current treatment.
        • diffVolumeText
          JTextField diffVolumeText
          Volume difference text.
        • drawingPane
          JPanelProbe.DrawingPane drawingPane
          Associate structure of the scroll pane to resize the panel properly.
        • endPtTransVector
          javax.vecmath.Vector3f endPtTransVector
          End point coordinate vector in the world coordinate system.
        • entryPointLabel
          JLabel entryPointLabel
          entry point label.
        • entryPointPanel
          JPanel entryPointPanel
          Panel that hold the entry point roation check box.
        • entryPointRotationCB
          JCheckBox entryPointRotationCB
          entry point rotation check box.
        • liverPresetButton
          JButton liverPresetButton
          Liver segmentation preset opacity transform function control button.
        • loadVisualizationButton
          JButton loadVisualizationButton
          Load button for the opacity transform function.
        • m_kProbeTwistLabel
          JLabel m_kProbeTwistLabel
          DOCUMENT ME!
        • m_kProbeTwistSlider
          JSlider m_kProbeTwistSlider
          Rotation/Twist around the direction of the probe:.
        • maxBox
          float maxBox
          The maximum of the fram box values.
        • noTargetTreatment
          TreatmentInformation noTargetTreatment
          Treatment information to be used if the user wants to burn without any target surface.
        • opacity
          float opacity
          Burning point opacity.
        • opacityLabel
          JLabel opacityLabel
          The opacity slider label.
        • opacitySlider
          JSlider opacitySlider
          burning point surface opacity slider.
        • opacitySliderLabels
          JLabel[] opacitySliderLabels
          burning point surface opacity slider label.
        • parentFrame
          ViewJFrameVolumeView parentFrame
          Volume view frame work reference.
        • probe
          Probe probe
          Probe reference.
        • probeList
          JList probeList
          Probes list.
        • probeResetButton
          JToggleButton probeResetButton
          Reset probe nevigation mode.
        • probeTargetButton
          JToggleButton probeTargetButton
          Control the tri-planar probe nevigation mode.
        • radiusLabel
          JLabel radiusLabel
          burning point diameter label.
        • resultLabel
          JLabel resultLabel
          result label to show the bone, vasculature detection information message.
        • saveVisualizationButton
          JButton saveVisualizationButton
          Save button for the opacity tranform function.
        • scroller
          JScrollPane scroller
          Scroll pane that control the resizing of the panel.
        • semiXLabel
          JLabel semiXLabel
          burning point semi axis X label.
        • semiXText
          JTextField semiXText
          burning point semi axis X text field.
        • semiYLabel
          JLabel semiYLabel
          burning point semi axis Y label.
        • semiYText
          JTextField semiYText
          burning point semi axis Y text field.
        • semiZLabel
          JLabel semiZLabel
          burning point semi axis Z label.
        • semiZText
          JTextField semiZText
          burning point semi axis Z text field.
        • showBurnLabels
          boolean showBurnLabels
          Flag indicates the show burning text label or not.
        • showBurnLabelsCB
          JCheckBox showBurnLabelsCB
          Show the burning text label checkbox.
        • skinPresetButton
          JButton skinPresetButton
          Skin segmentation preset opacity transform function control button.
        • sliderX
          JSlider sliderX
          The probe X slider that control the probe push and pull movements.
        • snapToTarget
          boolean snapToTarget
          Whether to snap to center of a target surface when it is selected; defaults to true.
        • snapToTargetCB
          JCheckBox snapToTargetCB
          Checkbox indicating whether to snap to center of a target surface when it is selected.
        • startPtTransVector
          javax.vecmath.Vector3f startPtTransVector
          Start point ( invisible ) coordinate vector in world coordinate system.
        • tabbedPane
          JTabbedPane tabbedPane
          The main tabbed pane in the volume view frame.
        • tabPanel
          JPanel tabPanel
          The main tab contrl panel.
        • targetList
          JList targetList
          Surface target list (tumors).
        • targetVolumeText
          JTextField targetVolumeText
          Label containing the volume of the current target surface.
        • targetXText
          JTextField targetXText
          X label for the center coordinate of the current target surface.
        • targetYText
          JTextField targetYText
          Y label for the center coordinate of the current target surface.
        • targetZText
          JTextField targetZText
          Z label for the center coordinate of the current target surface.
        • tipLengthCB
          JComboBox tipLengthCB
          Combo box for indicating the length of the probe tip. Currently used just by CoolTip probe.
        • toolBar
          JToolBar toolBar
          Tool bar.
        • totalVolumeLabel
          JLabel totalVolumeLabel
          Burning points total volume label.
        • totalVolumeText
          JTextField totalVolumeText
          Burning point total volume text.
        • traverseButton
          JToggleButton traverseButton
          Control the tri-planar default view nevigation mode.
        • treatmentVector
          Vector<TreatmentInformation> treatmentVector
          List of treatment sets.
        • volumeLabel
          JLabel volumeLabel
          buring point volume label.
        • volumeText
          JTextField volumeText
          burning pont volume text box.
        • xBox
          float xBox
          Parent frame box value.
        • xLabel
          JLabel xLabel
          burning point X, Y, Z coordinate label.
        • xLabelEntry
          JLabel xLabelEntry
          entry point X, Y, Z coordinate label.
        • xRes
          float xRes
          The resolutions of the (possibly respampled) image (the one shown in the renderer).
        • xSliderS
          JSlider xSliderS
          slider that controls the probe moves along the x direction.
        • xText
          JTextField xText
          burning point X, Y, Z coordinate text box.
        • xTextEntry
          JTextField xTextEntry
          entry point X, Y, Z coordinate text box.
        • yBox
          float yBox
          Parent frame box value.
        • yLabel
          JLabel yLabel
          burning point X, Y, Z coordinate label.
        • yLabelEntry
          JLabel yLabelEntry
          entry point X, Y, Z coordinate label.
        • yRes
          float yRes
          The resolutions of the (possibly respampled) image (the one shown in the renderer).
        • ySliderS
          JSlider ySliderS
          slider that controls the probe moves along the y direction.
        • yText
          JTextField yText
          burning point X, Y, Z coordinate text box.
        • yTextEntry
          JTextField yTextEntry
          entry point X, Y, Z coordinate text box.
        • zBox
          float zBox
          Parent frame box value.
        • zLabel
          JLabel zLabel
          burning point X, Y, Z coordinate label.
        • zLabelEntry
          JLabel zLabelEntry
          entry point X, Y, Z coordinate label.
        • zRes
          float zRes
          The resolutions of the (possibly respampled) image (the one shown in the renderer).
        • zSliderS
          JSlider zSliderS
          slider that controls the probe moves along the z direction.
        • zText
          JTextField zText
          burning point X, Y, Z coordinate text box.
        • zTextEntry
          JTextField zTextEntry
          entry point X, Y, Z coordinate text box.

    • Class gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.JPanelProbe.DrawingPane

      class DrawingPane extends JPanel implements Serializable
      serialVersionUID:
      199157917084746068L

  • Package gov.nih.mipav.view.renderer.J3D.volumeview

    • Class gov.nih.mipav.view.renderer.J3D.volumeview.JPanelRenderOptionsRayCast

      class JPanelRenderOptionsRayCast extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      -6813615755994835860L

      • Serialized Fields

        • blurBox
          JCheckBox blurBox
          Blur image check box.
        • buttonPanel
          JPanel buttonPanel
          Button Panel.
        • colorButton
          JButton colorButton
          Color button for changing color.
        • colorButtonBackground
          JButton colorButtonBackground
          Color button for changing z color.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser dialog.
        • diffuseButton
          JButton diffuseButton
          Diffuse color button for vertex material.
        • m_kRadioGroupMaxRenExtent
          ButtonGroup m_kRadioGroupMaxRenExtent
          DOCUMENT ME!
        • m_kRadioMaxRenExtent_1024
          JRadioButton m_kRadioMaxRenExtent_1024
          DOCUMENT ME!
        • m_kRadioMaxRenExtent_128
          JRadioButton m_kRadioMaxRenExtent_128
          DOCUMENT ME!
        • m_kRadioMaxRenExtent_256
          JRadioButton m_kRadioMaxRenExtent_256
          DOCUMENT ME!
        • m_kRadioMaxRenExtent_512
          JRadioButton m_kRadioMaxRenExtent_512
          DOCUMENT ME!
        • m_kRadioMaxRenExtent_64
          JRadioButton m_kRadioMaxRenExtent_64
          Radio Button Group for the Render Image Target size of the raycast rendered image. Target sizes options are preset to be typical texture sizes:
        • myParent
          VolumeRendererRayCast myParent
          Volume rendering parent frame.
        • radioButtonGroupProjections
          ButtonGroup radioButtonGroupProjections
          Button group for projections.
        • radioButtonOrthographic
          JRadioButton radioButtonOrthographic
          Radio Button for Orthographic rendering.
        • radioButtonPerspective
          JRadioButton radioButtonPerspective
          Radio Button for Perspective rendering.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanelRenderOptionsRayCast.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • spaceText
          JTextField spaceText
          Text field of the ray trace space size.
        • specularButton
          JButton specularButton
          Specular color button for vertex material.
        • stepText
          JTextField stepText
          Text field of the ray trace step size.

    • Class gov.nih.mipav.view.renderer.J3D.volumeview.JPanelRenderOptionsShearWarp

      class JPanelRenderOptionsShearWarp extends JPanelRendererJ3D implements Serializable
      serialVersionUID:
      4059526095627109190L

      • Serialized Fields

        • buttonPanel
          JPanel buttonPanel
          Button Panel.
        • colorButton
          JButton colorButton
          Color button for changing color.
        • colorButtonBackground
          JButton colorButtonBackground
          Color button for changing z color.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser dialog.
        • myParent
          VolumeRendererShearWarp myParent
          Volume rendering parent frame.
        • radioButtonGroupProjections
          ButtonGroup radioButtonGroupProjections
          Button group for projections.
        • radioButtonOrthographic
          JRadioButton radioButtonOrthographic
          Radio Button for Orthographic rendering.
        • radioButtonPerspective
          JRadioButton radioButtonPerspective
          Radio Button for Perspective rendering.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanelRenderOptionsShearWarp.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • stepText
          JTextField stepText
          Text field of the ray trace step size.

    • Class gov.nih.mipav.view.renderer.J3D.volumeview.VolumeRenderer

      class VolumeRenderer extends RenderViewBase implements Serializable
      serialVersionUID:
      -6617098263675852750L

      • Serialized Fields

        • boxSliceX
          ViewJComponentBoxSlice boxSliceX
          The frame around the x slice.
        • componentImageXY
          ViewJComponentRenderImage componentImageXY
          Component holding the texture of the XY plane image.
        • currentTransform
          javax.media.j3d.Transform3D currentTransform
          Current transform matrix.
        • currentTransType
          int currentTransType
          Current transform type.
        • extents
          int[] extents
          Extents of image A, same as xDim, yDim, etc.
        • imageA
          ModelImage imageA
          Current image A.
        • imageB
          ModelImage imageB
          Current image B.
        • isRotate
          boolean isRotate
          Flag indicating mouse rotation, avoid image disappearing problem.
        • kDefaultAppearance
          javax.media.j3d.Appearance kDefaultAppearance
          Original Appearance obj of the ImageComponent2D texture.
        • kShape
          javax.media.j3d.Shape3D kShape
          Shape object of the volume renderer.
        • lightControl
          JPanelLights lightControl
          light control panel.
        • m_bMouseListen
          boolean m_bMouseListen
          Flag to turn mouseListener on or off.
        • m_bTestFrameRate
          boolean m_bTestFrameRate
        • m_dAccumulatedTime
          double m_dAccumulatedTime
          Framerate Performance parameters:
        • m_dFrameRate
          double m_dFrameRate
          Framerate Performance parameters:
        • m_dLastTime
          double m_dLastTime
          Framerate Performance parameters:
        • m_iAccumulatedFrameCount
          int m_iAccumulatedFrameCount
          Framerate Performance parameters:
        • m_iFrameCount
          int m_iFrameCount
          Framerate Performance parameters:
        • m_iMaxTimer
          int m_iMaxTimer
          Framerate Performance parameters:
        • m_iTimer
          int m_iTimer
          Framerate Performance parameters:
        • m_kImage
          BufferedImage m_kImage
          Buffer image for the volume renderer.
        • m_kImageComponent
          javax.media.j3d.ImageComponent2D m_kImageComponent
          Image component 2D to hold the volume renderer properties.
        • m_kSoftwareLightSet
          SoftwareLightSet m_kSoftwareLightSet
          Set of lights to use for software-based lighting.
        • m_kSoftwareMaterial
          SoftwareMaterial m_kSoftwareMaterial
          Material properties to use for software-based lighting.
        • m_kTextureXY
          javax.media.j3d.Texture2D m_kTextureXY
          2D texture of the volume renderer.
        • maxBox
          float maxBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • maxRenExtent
          int maxRenExtent
          max Extent of X, Y dimensions.
        • mouseBehaviorRotate
          com.sun.j3d.utils.behaviors.mouse.MouseRotate mouseBehaviorRotate
          Mouse rotate behavior.
        • mouseBehaviorTranslate
          com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseBehaviorTranslate
          Mouse translate behavior.
        • mouseBehaviorZoom
          com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseBehaviorZoom
          Mouse zoom behavior.
        • mouseReleased
          boolean mouseReleased
          Flag to indicate whether the mouseReleased event triggered or not.
        • objBoxSliceX
          javax.media.j3d.BranchGroup objBoxSliceX
          Parent of the x slice.
        • objTransSliceX
          javax.media.j3d.TransformGroup objTransSliceX
          Member variables used to display the rendered image on the texture-mapped polygon, stored so that they can be updated as the render target image size is changed by the user-interface:.
        • objTransXY
          javax.media.j3d.TransformGroup objTransXY
          Group dictating how the XY plane is translated.
        • objXYPlane
          javax.media.j3d.BranchGroup objXYPlane
          Parent of the XY plane image.
        • optionsPanel
          JPanelRendererBase optionsPanel
          Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.
        • parallelRotation
          boolean parallelRotation
          Parallel rotation flag.
        • pBar
          ViewJProgressBar pBar
          Actual bar which fills with color as the percentage of completion increases.
        • pixBufferA_XY
          int[] pixBufferA_XY
          Buffer that holds image A pixel data for the XY plane, used to build displayable image.
        • pixBufferB_XY
          int[] pixBufferB_XY
          Buffer that holds image B pixel data for the XY plane, used to build displayable image.
        • resols
          float[] resols
          Resolutions of image A.
        • shapeBG
          javax.media.j3d.BranchGroup shapeBG
          DOCUMENT ME!
        • shapeSliceBG
          javax.media.j3d.BranchGroup shapeSliceBG
          DOCUMENT ME!
        • sliderT
          JSlider sliderT
          Sliders for the image planes.
        • surfaceRender
          SurfaceRender surfaceRender
          Surface renderer reference.
        • tDim
          int tDim
          Dimensions of image A.
        • textT
          JTextField textT
          Text fields that display the slice number next to the sliders.
        • tSlice
          int tSlice
          Which time slice is currently displayed.
        • units
          int[] units
          Units of measure of imageA.
        • updateWinlevel
          boolean updateWinlevel
          Update the window level flag, call by the plane renderer.
        • xBox
          float xBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • xDim
          int xDim
          Dimensions of image A.
        • yBox
          float yBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • yDim
          int yDim
          Dimensions of image A.
        • zBox
          float zBox
          Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.
        • zDim
          int zDim
          Dimensions of image A.
        • zSlice
          int zSlice
          Which slice is currently displayed in the XY plane.

    • Class gov.nih.mipav.view.renderer.J3D.volumeview.VolumeRendererRayCast

      class VolumeRendererRayCast extends VolumeRenderer implements Serializable
      serialVersionUID:
      7864871507214707172L

    • Class gov.nih.mipav.view.renderer.J3D.volumeview.VolumeRendererShearWarp

      class VolumeRendererShearWarp extends VolumeRenderer implements Serializable
      serialVersionUID:
      -3304622158293691309L

  • Package gov.nih.mipav.view.renderer.WildMagic

    • Class gov.nih.mipav.view.renderer.WildMagic.GPURenderBase

      class GPURenderBase extends WildMagic.LibApplications.OpenGLApplication.JavaApplication3D implements Serializable
      serialVersionUID:
      9069227710441839806L

      • Serialized Fields

        • currentLocation
          WildMagic.LibFoundation.Mathematics.Vector3f currentLocation
        • defaultVelocityRotational
          double defaultVelocityRotational
        • defaultVelocityTranslational
          double defaultVelocityTranslational
          3D MOUSE MOTION CONSTANTS
        • dpiScale
          double dpiScale
        • hyperstack
          VolumeImage[] hyperstack
        • hyperstackColormap
          WildMagic.LibGraphics.Rendering.Texture hyperstackColormap
        • isSpaceNavCodeRunning
          boolean isSpaceNavCodeRunning
        • m_akLights
          WildMagic.LibGraphics.Rendering.Light[] m_akLights
          Lights from JPanelLight
        • m_bDispose
          boolean m_bDispose
        • m_bDoClip
          boolean m_bDoClip
        • m_bExtract
          boolean m_bExtract
        • m_bFirstDrag
          boolean m_bFirstDrag
          Change the mouse cursor with the first mouseDrag event
        • m_bInit
          boolean m_bInit
          Set to true when init() is called:
        • m_bModified
          boolean m_bModified
          Minimizes rendering, only render when modified is true.
        • m_bMouseDrag
          boolean m_bMouseDrag
          keeps track if the user is currently dragging with the mouse
        • m_bPickPending
          boolean m_bPickPending
          Set to true when there is a pending pick operation
        • m_bShared
          boolean m_bShared
        • m_bSnapshot
          boolean m_bSnapshot
          Set to true when recording.
        • m_bSurfaceMaskUpdate
          boolean m_bSurfaceMaskUpdate
          Set to true when the surface mask should be recalculated.
        • m_bSurfaceUpdate
          boolean m_bSurfaceUpdate
          Set to true when the surface has been added or modified.
        • m_bTestFrameRate
          boolean m_bTestFrameRate
          For testing the frame rate:
        • m_bVisible
          boolean m_bVisible
          Flag for indicating the that Java Container is visible or not:
        • m_fMax
          float m_fMax
          Normalized volume extents:
        • m_fX
          float m_fX
          Normalized volume extents:
        • m_fY
          float m_fY
          Normalized volume extents:
        • m_fZ
          float m_fZ
          Normalized volume extents:
        • m_iCaptureFPS
          int m_iCaptureFPS
        • m_iMovieCounter
          int m_iMovieCounter
        • m_iScreenCaptureCounter
          int m_iScreenCaptureCounter
          Screen capture counter.
        • m_iXPick
          int m_iXPick
          Picking support:
        • m_iYPick
          int m_iYPick
          Picking support:
        • m_kAnimator
          com.jogamp.opengl.util.Animator m_kAnimator
          Animator object, displays scene in rendering loop (similar to GLUTMainLoop()
        • m_kCuller
          WildMagic.LibGraphics.SceneGraph.Culler m_kCuller
          Culling out-of-view objects:
        • m_kDeleteList
          Vector<VolumeObject> m_kDeleteList
        • m_kDisplayList
          Vector<VolumeObject> m_kDisplayList
          List of objects displayed in the scene.
        • m_kPicker
          WildMagic.LibGraphics.Collision.Picker m_kPicker
          For processing picking:
        • m_kSceneToWorld
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kSceneToWorld
        • m_kTranslate
          WildMagic.LibFoundation.Mathematics.Vector3f m_kTranslate
          Scene translation, centers the scene:
        • m_kVolumeImageA
          VolumeImage m_kVolumeImageA
          VolumeImage for ModelImageA, contains data and textures.
        • m_kVolumeImageA_New
          VolumeImage m_kVolumeImageA_New
        • m_kVolumeImageA_Old
          VolumeImage m_kVolumeImageA_Old
        • m_kVolumeImageB
          VolumeImage m_kVolumeImageB
          VolumeImage for ModelImageB, contains data and textures.
        • m_kVolumeImageB_New
          VolumeImage m_kVolumeImageB_New
        • m_kVolumeImageB_Old
          VolumeImage m_kVolumeImageB_Old
        • m_kWinLevel
          WindowLevel m_kWinLevel
          Window-level interface.
        • m_kXRotate
          WildMagic.LibFoundation.Mathematics.Matrix3f m_kXRotate
          Basic rotations for fixed input use:
        • m_kYRotate
          WildMagic.LibFoundation.Mathematics.Matrix3f m_kYRotate
          Basic rotations for fixed input use:
        • m_kZRotate
          WildMagic.LibFoundation.Mathematics.Matrix3f m_kZRotate
          Basic rotations for fixed input use:
        • m_spkCull
          WildMagic.LibGraphics.Rendering.CullState m_spkCull
          Culling: turns backface/frontface culling on/off:
        • m_spkScene
          WildMagic.LibGraphics.SceneGraph.Node m_spkScene
          Scene-graph root node:
        • mouseRot
          double mouseRot
        • nearPlane
          float nearPlane
        • rotPower
          double rotPower
        • rotScalar
          double rotScalar
        • transPower
          double transPower
        • transScalar
          double transScalar
        • updateBoundingCube
          boolean updateBoundingCube
        • useMouseRotationCutoffs
          boolean useMouseRotationCutoffs
        • useMouseTranslationCutoffs
          boolean useMouseTranslationCutoffs
        • zVector
          WildMagic.LibFoundation.Mathematics.Vector3f zVector
        • ZXDistanceStep
          float ZXDistanceStep
        • ZYDistanceStep
          float ZYDistanceStep
        • ZZDistanceStep
          float ZZDistanceStep

    • Class gov.nih.mipav.view.renderer.WildMagic.PlaneRender_WM

      class PlaneRender_WM extends GPURenderBase implements Serializable
      serialVersionUID:
      2025132936439496099L

      • Serialized Fields

        • isAnnotationEnabled
          boolean isAnnotationEnabled
        • isMouseFlythru
          boolean isMouseFlythru
        • isPathFlythru
          boolean isPathFlythru
        • latestVolumePt
          WildMagic.LibFoundation.Mathematics.Vector3f latestVolumePt
        • m_aaiColorSwap
          int[][] m_aaiColorSwap
          Axis labels color assignments.
        • m_aakColors
          WildMagic.LibFoundation.Mathematics.ColorRGB[][] m_aakColors
          Set of colors used to draw the axis labels.
        • m_abAxisFlip
          boolean[] m_abAxisFlip
          ModelImage axis flip.
        • m_adCos
          double[] m_adCos
        • m_adSin
          double[] m_adSin
        • m_afResolutions
          float[] m_afResolutions
        • m_aiAxisOrder
          int[] m_aiAxisOrder
          ModelImage axis orientation.
        • m_aiLocalImageExtents
          int[] m_aiLocalImageExtents
          The image dimensions in x,y,z:.
        • m_aiUnits
          int[] m_aiUnits
        • m_akCLoc
          WildMagic.LibFoundation.Mathematics.Vector3f[] m_akCLoc
          Camera Locations, for rendering the different Axial, Sagittal and Coronal views.
        • m_akCoords
          WildMagic.LibFoundation.Mathematics.Vector3f[] m_akCoords
          Camera Direction, UP, and Right vectors, for rendering the different Axial, Sagittal and Coronal views.
        • m_bCleanup
          boolean m_bCleanup
        • m_bDrawAxes
          boolean m_bDrawAxes
          when true, the axis labels (P-> L-> S->) will be drawn
        • m_bDrawXHairs
          boolean m_bDrawXHairs
          Turns on drawing of the X,Y bars and the Axis labels:.
        • m_bIsMouseActive
          boolean m_bIsMouseActive
        • m_bLeftMousePressed
          boolean m_bLeftMousePressed
          True when the left mouse has been pressed, set to false when the left mouse button is released.
        • m_bPatientOrientation
          boolean m_bPatientOrientation
          Actual image orientation.
        • m_bRightMousePressed
          boolean m_bRightMousePressed
          Flag indicating if the right mouse button is currently pressed down:
        • m_bShowSurface
          boolean m_bShowSurface
        • m_bShowVOIs
          boolean m_bShowVOIs
        • m_bUpdateSpacing
          boolean m_bUpdateSpacing
        • m_fMaxBox
          float m_fMaxBox
          Numbers dictating the size of the plane based on the extents and resolutions of the image.
        • m_fMouseY
          float m_fMouseY
          For zooming with the mouse.
        • m_fX0
          float m_fX0
          lower x-bound of the texture-mapped polygon:
        • m_fX1
          float m_fX1
          upper x-bound of the texture-mapped polygon:
        • m_fXBox
          float m_fXBox
          Numbers dictating the size of the plane based on the extents and resolutions of the image.
        • m_fXRange
          float m_fXRange
          Width of the texture-mapped polygon:
        • m_fY0
          float m_fY0
          lower y-bound of the texture-mapped polygon:
        • m_fY1
          float m_fY1
          upper y-bound of the texture-mapped polygon:
        • m_fYBox
          float m_fYBox
          Numbers dictating the size of the plane based on the extents and resolutions of the image.
        • m_fYRange
          float m_fYRange
          Height of the texture-mapped polygon:
        • m_fZoomScale
          float m_fZoomScale
          Image scaling from Zoom:.
        • m_iCirclePts
          int m_iCirclePts
        • m_iLabelX_SpacingX
          int m_iLabelX_SpacingX
        • m_iLabelX_SpacingY
          int m_iLabelX_SpacingY
        • m_iLabelY_SpacingX
          int m_iLabelY_SpacingX
        • m_iLabelY_SpacingY
          int m_iLabelY_SpacingY
        • m_iPlaneOrientation
          int m_iPlaneOrientation
          Which dimension of the ModelImage to render.
        • m_iSlice
          int m_iSlice
          Which slice is currently displayed in the XY plane.
        • m_kActiveImage
          ModelImage m_kActiveImage
          Current active image for manipulating the LUT by dragging with the right-mouse down.
        • m_kActiveLookupTable
          ModelStorageBase m_kActiveLookupTable
          The current active lookup table:
        • m_kBallPoint
          WildMagic.LibGraphics.SceneGraph.Polyline m_kBallPoint
        • m_kCenter
          WildMagic.LibFoundation.Mathematics.Vector3f m_kCenter
        • m_kLabelX
          String m_kLabelX
          x-axis label:
        • m_kLabelXDisplay
          String m_kLabelXDisplay
        • m_kLabelY
          String m_kLabelY
          y-axis label:
        • m_kParent
          VolumeTriPlanarInterface m_kParent
          Parent user-interface and display frame.
        • m_kPatientPt
          WildMagic.LibFoundation.Mathematics.Vector3f m_kPatientPt
        • m_kPVWMatrix
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kPVWMatrix
        • m_kVOIAttr
          WildMagic.LibGraphics.SceneGraph.Attributes m_kVOIAttr
        • m_kVolumeScale
          WildMagic.LibFoundation.Mathematics.Vector3f m_kVolumeScale
        • m_kVolumeScaleInv
          WildMagic.LibFoundation.Mathematics.Vector3f m_kVolumeScaleInv
        • m_kXArrow
          WildMagic.LibGraphics.SceneGraph.TriMesh[] m_kXArrow
          x-axis arrow
        • m_kYArrow
          WildMagic.LibGraphics.SceneGraph.TriMesh[] m_kYArrow
          y-axis arrow
        • m_kZState
          WildMagic.LibGraphics.Rendering.ZBufferState m_kZState
        • m_spkScreenCamera
          WildMagic.LibGraphics.Rendering.Camera m_spkScreenCamera
          Drawing the axis arrows in screen-space.

    • Class gov.nih.mipav.view.renderer.WildMagic.VolumeRenderState

      class VolumeRenderState extends Object implements Serializable
      serialVersionUID:
      4937933351322531830L

      • Serialized Fields

        • ArbitratyEquation
          WildMagic.LibFoundation.Mathematics.Matrix3f ArbitratyEquation
        • BackgroundColor
          Color BackgroundColor
        • Blend
          int Blend
        • BlendColor
          Color BlendColor
        • BlueA
          TransferFunction BlueA
        • BlueB
          TransferFunction BlueB
        • BlueOnA
          boolean BlueOnA
        • BlueOnB
          boolean BlueOnB
        • BoundingBoxColor
          Color BoundingBoxColor
        • Camera
          float[] Camera
        • CameraLocation
          WildMagic.LibFoundation.Mathematics.Vector3f CameraLocation
        • Center
          WildMagic.LibFoundation.Mathematics.Vector3f Center
        • ClipColors
          Color[] ClipColors
        • ClipDisplayed
          boolean[] ClipDisplayed
        • ClipEnabled
          boolean[] ClipEnabled
        • ClipValues
          int[] ClipValues
        • CustomAlpha
          int CustomAlpha
        • DestinationBlend
          int DestinationBlend
        • DisplayRayCast
          boolean DisplayRayCast
        • DisplaySlices
          boolean DisplaySlices
        • DisplaySurface
          boolean DisplaySurface
        • DualDividerLocation
          int DualDividerLocation
        • Equation
          int Equation
        • ExtendedState
          int ExtendedState
        • ExtractionIntensityLevel
          int ExtractionIntensityLevel
        • GreenA
          TransferFunction GreenA
        • GreenB
          TransferFunction GreenB
        • GreenOnA
          boolean GreenOnA
        • GreenOnB
          boolean GreenOnB
        • ImageA
          VolumeImage ImageA
        • ImageB
          VolumeImage ImageB
        • IPD
          float IPD
        • Lights
          WildMagic.LibGraphics.Rendering.Light[] Lights
        • LightSelected
          int LightSelected
        • LUTa
          ModelLUT LUTa
        • LUTb
          ModelLUT LUTb
        • MainDividerLocation
          int MainDividerLocation
        • MultiHistogram
          boolean MultiHistogram
        • MultiHistoWidgets
          Vector<ClassificationWidget> MultiHistoWidgets
        • ObjectLocation
          float[] ObjectLocation
        • ObjectRotation
          WildMagic.LibFoundation.Mathematics.Matrix3f ObjectRotation
        • Opacity
          int[] Opacity
        • OpacityA
          TransferFunction OpacityA
        • OpacityB
          TransferFunction OpacityB
        • OpacityGMA
          TransferFunction OpacityGMA
        • OpacityGMB
          TransferFunction OpacityGMB
        • OpacityGMOnA
          boolean OpacityGMOnA
        • OpacityGMOnB
          boolean OpacityGMOnB
        • OtherBlue
          TransferFunction OtherBlue
        • OtherGreen
          TransferFunction OtherGreen
        • OtherImageDirectory
          String OtherImageDirectory
        • OtherImageName
          String OtherImageName
        • OtherLUT
          ModelStorageBase OtherLUT
        • OtherRed
          TransferFunction OtherRed
        • OtherTransfer
          TransferFunction OtherTransfer
        • Perspective
          boolean Perspective
        • PlanesDividerLocation
          int PlanesDividerLocation
        • PlaneZoom
          float[] PlaneZoom
        • Radiological
          boolean Radiological
        • RedA
          TransferFunction RedA
        • RedB
          TransferFunction RedB
        • RedOnA
          boolean RedOnA
        • RedOnB
          boolean RedOnB
        • ReleasedSamples
          int ReleasedSamples
        • RenderMode
          int RenderMode
        • RGBa
          ModelRGB RGBa
        • RGBb
          ModelRGB RGBb
        • RotationSamples
          int RotationSamples
        • SculptDrawn
          boolean SculptDrawn
        • SculptImage
          byte[] SculptImage
        • SculptShape
          int SculptShape
        • SelectedSurface
          int SelectedSurface
        • SelectedTab
          int SelectedTab
        • Show4D
          boolean Show4D
        • ShowAxes
          boolean ShowAxes
        • ShowBoundingBox
          boolean ShowBoundingBox
        • ShowCrossHairs
          boolean ShowCrossHairs
        • ShowOrientationCube
          boolean ShowOrientationCube
        • ShowSlice
          boolean[] ShowSlice
        • ShowSliceBox
          boolean[] ShowSliceBox
        • ShowVOI
          boolean ShowVOI
        • SliceColor
          Color[] SliceColor
        • SourceBlend
          int SourceBlend
        • StereoType
          int StereoType
        • SurfaceList
          Vector<SurfaceState> SurfaceList
        • TabbedList
          Vector<String> TabbedList
        • TextureEnabled
          boolean TextureEnabled
        • TextureOn
          boolean TextureOn
        • TransferA
          TransferFunction TransferA
        • TransferB
          TransferFunction TransferB
        • UseOtherImage
          boolean UseOtherImage
        • UseOtherLUT
          boolean UseOtherLUT
        • VolumeBlend
          int VolumeBlend
        • WidgetSelected
          int WidgetSelected
        • WindowSize
          Dimension WindowSize
        • WindowX
          int WindowX
        • WindowY
          int WindowY

    • Class gov.nih.mipav.view.renderer.WildMagic.VolumeTriPlanarInterface

      class VolumeTriPlanarInterface extends JFrame implements Serializable
      serialVersionUID:
      1898957906984534260L

      • Serialized Fields

        • bf_flyPanel
          JPanel bf_flyPanel
          Panel to hold the BrainSurfaceFlattener or Flythrough views.
        • brainsurfaceFlattenerRender
          CorticalAnalysisRender brainsurfaceFlattenerRender
          Rendering the brainsurfaceFlattener objects.
        • clipButton
          JButton clipButton
          Button to invoke all the six clipping planes.
        • clipDisableButton
          JButton clipDisableButton
          Button to disable all the six clipping planes.
        • clipGUI
          JPanelClip_WM clipGUI
          Clipping user-interface panel:
        • clipMaskButton
          JButton clipMaskButton
          Button to crop the clip volume.
        • clipMaskUndoButton
          JButton clipMaskUndoButton
          Button to undo crop the clip volume.
        • clipPlaneButton
          JButton clipPlaneButton
          Button to invoke clipping planes.
        • clipSaveButton
          JButton clipSaveButton
          Button to save clipped region.
        • customBlendGUI
          JPanelCustomBlend customBlendGUI
          Multihistogram panel:
        • displayGUI
          JPanelDisplay_WM displayGUI
          Display options panel:
        • dualPane
          JSplitPane dualPane
          For displaying the BrainSurfaceFlattener or Flythrough renderers.
        • flythruControl
          JPanelVirtualEndoscopySetup_WM flythruControl
          Flythough setup panel:
        • flythruMoveControl
          JPanelFlythruMove flythruMoveControl
          Flythough Move panel:
        • frameHistogram
          JFrameHistogram frameHistogram
        • geodesicGUI
          JPanelGeodesic_WM geodesicGUI
          Geodesic user-interface panel:
        • gpuPanel
          JPanel gpuPanel
          The image panel to hold one Canvas3D.
        • m_akPlaneRender
          PlaneRender_WM[] m_akPlaneRender
          The three slice views displayed as texture-mapped polygons:.
        • m_b4D
          boolean m_b4D
        • m_bDependentInterfaceInit
          boolean m_bDependentInterfaceInit
        • m_iVOICount
          int m_iVOICount
        • m_kAnnotationAnimationPanel
          JPanelAnnotationAnimation m_kAnnotationAnimationPanel
        • m_kFlyThroughRender
          FlyThroughRender m_kFlyThroughRender
          Flythrough renderer:
        • m_kLightsPanel
          JPanelLights_WM m_kLightsPanel
          Light panel
        • m_kLoadButton
          JButton m_kLoadButton
        • m_kRecordToggle
          JToggleButton m_kRecordToggle
        • m_kSaveButton
          JButton m_kSaveButton
        • m_kVOIInterface
          VOILatticeManagerInterface m_kVOIInterface
        • m_kVolOpacityPanel
          JPanelVolumeOpacity m_kVolOpacityPanel
          Opacity panel.
        • m_kVolume4DGUI
          JPanelVolume4D m_kVolume4DGUI
        • m_kVolumeImageA
          VolumeImage m_kVolumeImageA
          VolumeImage contains data and textures for ModelImage A.
        • m_kVolumeImageB
          VolumeImage m_kVolumeImageB
          VolumeImage contains data and textures for ModelImage B.
        • mainPane
          JSplitPane mainPane
        • maxPanelWidth
          int maxPanelWidth
          The max width of the control panels.
        • menuBar
          JMenuBar menuBar
          Menu bar.
        • menuObj
          ViewMenuBuilder menuObj
          Menu items storage.
        • mouseGUI
          JPanel3DMouse_WM mouseGUI
          3D mouse user-interface panel:
        • multiHistogramGUI
          JPanelMultiDimensionalTransfer multiHistogramGUI
          Multihistogram panel:
        • navigationGUI
          JPanelNavigation navigationGUI
          Navigation mode user-interface panel
        • panelAxial
          JPanel panelAxial
          Axial view panel.
        • panelCoronal
          JPanel panelCoronal
          Coronal view panel.
        • panelSagittal
          JPanel panelSagittal
          Sagittal view panel.
        • panelToolbar
          JPanel panelToolbar
          Panel that holds the toolbars.
        • panelToolBarGBC
          GridBagConstraints panelToolBarGBC
          Constraints on panelToolbar layout:
        • positionsPanel
          JPanelPositions positionsPanel
        • prevHeight
          int prevHeight
        • raycastRenderWM
          VolumeTriPlanarRender raycastRenderWM
          Volume/Slice/Surface renderer.
        • rendererGUI
          JPanelRenderMode_WM rendererGUI
          Renderer mode user-interface panel
        • rightPane
          JSplitPane rightPane
          The view pane that contains the image view and tri-planar view panels.
        • screenHeight
          int screenHeight
          Current frame width and height.
        • screenWidth
          int screenWidth
          Current frame width and height.
        • sculptGUI
          JPanelSculptor_WM sculptGUI
          Sculpting user-interface panel:
        • sliceGUI
          JPanelSlices_WM sliceGUI
          3D Slice-view user-interface panel:
        • surfaceGUI
          JPanelSurface_WM surfaceGUI
          3D Surface user-interface panel:
        • surfaceTextureGUI
          JPanelSurfaceTexture_WM surfaceTextureGUI
          Surface Texture user-interface panel:
        • tabbedPane
          JTabbedPane tabbedPane
          The main tabbed pane in the volume view frame.
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          Toolbar builder reference.
        • triImagePanel
          JPanel triImagePanel
          Tri image planar render panels.
        • userInterface
          ViewUserInterface userInterface
          Reference to the user interface.
        • viewToolBar
          JToolBar viewToolBar
          The top one render view switch toolbar.
        • voiMenu
          JMenu voiMenu

    • Class gov.nih.mipav.view.renderer.WildMagic.VolumeTriPlanarInterface.IntVector

      class IntVector extends Vector<Integer> implements Serializable
      serialVersionUID:
      -7551972247476811252L

    • Class gov.nih.mipav.view.renderer.WildMagic.VolumeTriPlanarRender

      class VolumeTriPlanarRender extends VolumeTriPlanarRenderBase implements Serializable
      serialVersionUID:
      4387274360968910837L

    • Class gov.nih.mipav.view.renderer.WildMagic.VolumeTriPlanarRenderBase

      class VolumeTriPlanarRenderBase extends GPURenderBase implements Serializable
      serialVersionUID:
      -8415814666722429687L

      • Serialized Fields

        • animateCurve
          boolean animateCurve
        • animateLatticeModel
          LatticeModel animateLatticeModel
        • animateLattices
          boolean animateLattices
        • animateSlice
          boolean animateSlice
        • animateStop
          boolean animateStop
        • annotatePtsCounter
          int annotatePtsCounter
          number of annotate points along the specified path.
        • annotatePtsList
          Vector<WildMagic.LibFoundation.Mathematics.Vector3f> annotatePtsList
          annotate path planning points list
        • cameraPosition
          WildMagic.LibFoundation.Mathematics.Vector3f cameraPosition
        • container
          VolumeTriPlanarRenderBase.JPanelGPU container
          main container for this object, contains the scroll pane and the depth slider:
        • fSample_mouseDragged
          float fSample_mouseDragged
          sample rate when mouse is dragged.
        • fSample_mouseReleased
          float fSample_mouseReleased
          sample rate when mouse is released.
        • isAnnotateEnabled
          boolean isAnnotateEnabled
          is annotation mode is enabled or not.
        • isMouseControlEnabled
          boolean isMouseControlEnabled
          is mouse control enabled or not.
        • isNavigationEnabled
          boolean isNavigationEnabled
          is nagivation mode enabled or not.
        • isPathPlanningEnabled
          boolean isPathPlanningEnabled
          is path planning mode enabled or not.
        • kGeometryBranchPath
          WildMagic.LibGraphics.SceneGraph.Polyline kGeometryBranchPath
        • kPoly
          WildMagic.LibGraphics.SceneGraph.Polyline kPoly
        • kPolyNode
          WildMagic.LibGraphics.SceneGraph.Node kPolyNode
        • lattice
          VOIVector lattice
        • latticeClip
          boolean latticeClip
        • latticeClipAxes
          WildMagic.LibFoundation.Mathematics.Vector3f[] latticeClipAxes
        • latticeClipBox
          WildMagic.LibFoundation.Mathematics.Box3f latticeClipBox
        • latticeClipExtents
          float[] latticeClipExtents
        • latticeClipPos
          WildMagic.LibFoundation.Mathematics.Vector3f latticeClipPos
        • m_afArbEquation
          float[] m_afArbEquation
          Arbitrary clip plane equation:
        • m_afArbEquationInv
          float[] m_afArbEquationInv
        • m_akSceneTarget
          WildMagic.LibGraphics.Rendering.Texture[] m_akSceneTarget
        • m_akSlicesColor
          WildMagic.LibFoundation.Mathematics.ColorRGB[] m_akSlicesColor
        • m_bArbClipOn
          boolean m_bArbClipOn
          Enable Arbitrary clip plane:
        • m_bCrop
          boolean m_bCrop
          Set to true when cropping the volume in the shader.
        • m_bDisplay
          boolean m_bDisplay
        • m_bDisplaySecond
          boolean m_bDisplaySecond
          Enables/Disables rendering the second pass. When disabled, the back-facing polygons of the proxy-geometry are shown instead of the volume:
        • m_bDropper
          boolean m_bDropper
        • m_bErase
          boolean m_bErase
        • m_bFirstDisplay
          boolean m_bFirstDisplay
        • m_bFirstRender
          boolean m_bFirstRender
          The first time the frame is rendererd use the shader to calculate the normals for the volume data.
        • m_bGeodesicEnabled
          boolean m_bGeodesicEnabled
          Geodesic enabled on/off.
        • m_bPaint
          boolean m_bPaint
        • m_bPaintCan
          boolean m_bPaintCan
        • m_bPaintEnabled
          boolean m_bPaintEnabled
          Painting parameters:
        • m_bPickCorrespondence
          boolean m_bPickCorrespondence
          BrainSurfaceFlattener pick correspondence enabled on/off.
        • m_bPlay4D
          boolean m_bPlay4D
        • m_bPlay4DVOIs
          boolean m_bPlay4DVOIs
        • m_bResetImages
          boolean m_bResetImages
        • m_bUpdateCenterOnDisplay
          boolean m_bUpdateCenterOnDisplay
        • m_bWriteImage
          boolean m_bWriteImage
        • m_fAnimateRate
          float m_fAnimateRate
        • m_iAnimateCount
          int m_iAnimateCount
        • m_iBrushSize
          int m_iBrushSize
        • m_iExtractLevel
          int m_iExtractLevel
          Intensity level for GPU-surface extraction.
        • m_iStereo
          int m_iStereo
          Stereo on/off.
        • m_kArbitraryClip
          WildMagic.LibFoundation.Mathematics.Vector4f m_kArbitraryClip
        • m_kArbitraryClipInv
          WildMagic.LibFoundation.Mathematics.Vector4f m_kArbitraryClipInv
        • m_kDTIDisplay
          VolumeDTI m_kDTIDisplay
          DTI renderer.
        • m_kFBO
          WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kFBO
        • m_kFlyPathGraphCurve
          FlyPathGraphCurve m_kFlyPathGraphCurve
          Fly path curve.
        • m_kNewCenter
          WildMagic.LibFoundation.Mathematics.Vector3f m_kNewCenter
        • m_kNormalColorPathUnvisited
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kNormalColorPathUnvisited
          Color for the parts of the path that have not yet been visited (Dark Green)
        • m_kPaintColor
          WildMagic.LibFoundation.Mathematics.ColorRGBA m_kPaintColor
        • m_kSculptor
          Sculptor_WM m_kSculptor
          New sculpting object for WM-based sculpting.
        • m_kSlices
          VolumeSlices m_kSlices
          3D Slice renderer.
        • m_kVolumeBox
          VolumeBoundingBox m_kVolumeBox
          Volume bounding box renderer.
        • m_kVolumeClip
          VolumeClip m_kVolumeClip
          Clipping planes renderer
        • m_kVolumeCube
          VolumeOrientationCube m_kVolumeCube
          Orientation cube renderer
        • m_kVolumeRayCast
          VolumeRayCast m_kVolumeRayCast
          GPU-based ray cast renderer.
        • m_pkPlane
          WildMagic.LibGraphics.SceneGraph.TriMesh m_pkPlane
        • m_pkScreenCamera
          WildMagic.LibGraphics.Rendering.Camera m_pkScreenCamera
        • m_spkPlaneEffect
          WildMagic.LibGraphics.Effects.ShaderEffect m_spkPlaneEffect
        • navigationBehavior
          NavigationBehavior navigationBehavior
          navigation behavior.
        • opacityLabel
          JLabel opacityLabel
        • opacitySlider
          JSlider opacitySlider
          Opacity sliders for when this renderer is displayed as a stand-alone app.
        • plane
          WildMagic.LibGraphics.SceneGraph.TriMesh plane
        • planeName
          String planeName
        • planeVOI
          VOI planeVOI
        • profile
          boolean profile
        • screenShotRotateCount
          int screenShotRotateCount
        • screenShots
          Vector<BufferedImage> screenShots
        • segmentIndex
          int segmentIndex
        • sharedDrawable
          com.jogamp.opengl.GLOffscreenAutoDrawable sharedDrawable
        • sharedRenderer
          VolumeTriPlanarRender sharedRenderer
        • sliceDir
          int sliceDir
        • sphereClip
          WildMagic.LibFoundation.Mathematics.Vector3f sphereClip
        • sphereRadius
          float sphereRadius
        • takeScreenShot
          boolean takeScreenShot

  • Package gov.nih.mipav.view.renderer.WildMagic.AAM

    • Class gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMShapeCollection

      class CAAMShapeCollection extends Vector<CAAMShape> implements Serializable

      • Serialized Fields

        • m_dAvgSize
          double m_dAvgSize
          The average shape size (calculated during alignment).
        • m_MeanShapeBeforeTS
          CAAMShape m_MeanShapeBeforeTS
          The meanshape prior to tangent space projection (calculated during alignment).
        • m_szPath
          String m_szPath
          Path to the .asf files (if any).

    • Class gov.nih.mipav.view.renderer.WildMagic.AAM.EigenvalueDecomposition

      class EigenvalueDecomposition extends Object implements Serializable

      • Serialized Fields

        • d
          double[] d
          Arrays for internal storage of eigenvalues.
          internal storage of eigenvalues.
        • e
          double[] e
          Arrays for internal storage of eigenvalues.
          internal storage of eigenvalues.
        • H
          double[][] H
          Array for internal storage of nonsymmetric Hessenberg form.
          internal storage of nonsymmetric Hessenberg form.
        • issymmetric
          boolean issymmetric
          Symmetry flag.
          internal symmetry flag.
        • n
          int n
          Row and column dimension (square matrix).
          matrix dimension.
        • ort
          double[] ort
          Working storage for nonsymmetric algorithm.
          working storage for nonsymmetric algorithm.
        • V
          double[][] V
          Array for internal storage of eigenvectors.
          internal storage of eigenvectors.

    • Class gov.nih.mipav.view.renderer.WildMagic.AAM.SingularValueDecomposition

      class SingularValueDecomposition extends Object implements Serializable

      • Serialized Fields

        • m
          int m
          Row and column dimensions.
          row dimension.
        • n
          int n
          Row and column dimensions.
          row dimension.
        • s
          double[] s
          Array for internal storage of singular values.
          internal storage of singular values.
        • U
          double[][] U
          Arrays for internal storage of U and V.
          internal storage of U.
        • V
          double[][] V
          Arrays for internal storage of U and V.
          internal storage of U.

  • Package gov.nih.mipav.view.renderer.WildMagic.BallPivoting

  • Package gov.nih.mipav.view.renderer.WildMagic.brainflattenerview_WM

    • Class gov.nih.mipav.view.renderer.WildMagic.brainflattenerview_WM.CorticalAnalysisRender

      class CorticalAnalysisRender extends GPURenderBase implements Serializable
      serialVersionUID:
      -6130870790192175575L

      • Serialized Fields

        • m_aiTriIndex
          int[] m_aiTriIndex
          Point indices of the puncture triangle.
        • m_akPickColors
          WildMagic.LibFoundation.Mathematics.ColorRGB[] m_akPickColors
          Colors for the picked points:.
        • m_akTriColors
          WildMagic.LibFoundation.Mathematics.ColorRGBA[] m_akTriColors
          puncture triangle color
        • m_bCurvatureColors
          boolean m_bCurvatureColors
          Flag set to indicate whether curvature colors are rendered on the mesh surface. If not, then average convexity colors are rendered.
        • m_bDisplayLines
          boolean m_bDisplayLines
          Toggle latitude/longitude display on/off.
        • m_bFirst
          boolean m_bFirst
          First time the scene is rendered.
        • m_bInflationInitialized
          boolean m_bInflationInitialized
          Flag set once inflation processing has been initialized.
        • m_bPickCorrespondenceEnabled
          boolean m_bPickCorrespondenceEnabled
          Turned on when picking with the mouse is enabled:.
        • m_bPickPunctureEnabled
          boolean m_bPickPunctureEnabled
          Enable/disable picking puncture triangle
        • m_iNumLat
          int m_iNumLat
        • m_iNumLon
          int m_iNumLon
        • m_iNumPicked
          int m_iNumPicked
          number of picked points displayed.
        • m_iRunningNumPicked
          int m_iRunningNumPicked
          Cycle through the number of correspondence points.
        • m_kCortical
          MjCorticalMesh_WM m_kCortical
          Cortical mesh to be used in rendering scene.
        • m_kCylinder
          VolumeSurface m_kCylinder
          Cylinder renderer
        • m_kCylinderLines
          VolumeNode m_kCylinderLines
          Cylinder longitude/latitude lines.
        • m_kCylinderPoints
          VolumeNode m_kCylinderPoints
          Scene-graph node for displaying correspondence points on the cylinder.
        • m_kLUTConvexity
          ModelLUT m_kLUTConvexity
          LUT for the triangle mesh convexity colors.
        • m_kLUTCurvature
          ModelLUT m_kLUTCurvature
          local reference to ModelLUT.
        • m_kMeshLines
          WildMagic.LibGraphics.SceneGraph.Node m_kMeshLines
          TriMesh longitude/latitude lines.
        • m_kMeshPoints
          WildMagic.LibGraphics.SceneGraph.Node m_kMeshPoints
          Scene-graph node for displaying correspondence points on the TriMesh surface.
        • m_kPanel
          JPanelBrainSurfaceFlattener_WM m_kPanel
          BrainSurfaceFlattener User-Interface panel
        • m_kParent
          VolumeTriPlanarInterface m_kParent
          Parent user-interface and display frame.
        • m_kSphere
          VolumeSurface m_kSphere
          Sphere renderer.
        • m_kSphereLines
          VolumeNode m_kSphereLines
          Sphere longitude/latitude lines.
        • m_kSpherePoints
          VolumeNode m_kSpherePoints
          Scene-graph node for displaying correspondence points on the sphere.
        • MAX_POINTS
          int MAX_POINTS
          Maximum number of correspondence points.

    • Class gov.nih.mipav.view.renderer.WildMagic.brainflattenerview_WM.JPanelBrainSurfaceFlattener_WM

      class JPanelBrainSurfaceFlattener_WM extends JPanel implements Serializable
      serialVersionUID:
      -2749305357977770854L

      • Serialized Fields

        • cancelButton
          JButton cancelButton
          Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • m_bFileLoaded
          boolean m_bFileLoaded
          Set to true when a surface has been loaded
        • m_bFirstSurface
          boolean m_bFirstSurface
          Causes the surface LUT to be calculated for the first time.
        • m_iGridY
          int m_iGridY
          Keeps track of the user-interface position in the main panel.
        • m_kDisablePick
          JRadioButton m_kDisablePick
          Enable/disable correspondence picking
        • m_kDisplayButtonGroup
          ButtonGroup m_kDisplayButtonGroup
          ButtonGroup for the plane/surface display selection.
        • m_kDisplayPlane
          JRadioButton m_kDisplayPlane
          Toggle displaying the plane on/off
        • m_kDisplaySphere
          JRadioButton m_kDisplaySphere
          Toggle displaying the sphere on/off
        • m_kInsidePanel
          JPanel m_kInsidePanel
          Panel container.
        • m_kLatLonLines
          JCheckBox m_kLatLonLines
          Toggle display of latitude/longitude lines on/off.
        • m_kLUTa
          ModelLUT m_kLUTa
          Color LUT based on Volume Data
        • m_kLUTImageA
          ModelImage m_kLUTImageA
          Volume data for LUT
        • m_kNumLatText
          JTextField m_kNumLatText
          Text box for entering the number of latitude lines.
        • m_kNumLonText
          JTextField m_kNumLonText
          Text box for entering the number of longitude lines.
        • m_kPanelBrainsurfaceFlattenerLUT
          JFrameHistogram m_kPanelBrainsurfaceFlattenerLUT
          LUT Panel based on surface curvature.
        • m_kPickButtonGroup
          ButtonGroup m_kPickButtonGroup
          Picking button group -- switch between picking correspondence points and the puncture triangle.
        • m_kPickCorrespondence
          JRadioButton m_kPickCorrespondence
          Correspondence point picking.
        • m_kPickPuncture
          JRadioButton m_kPickPuncture
          Puncture triangle picking.
        • m_kTriangleMesh
          WildMagic.LibGraphics.SceneGraph.TriMesh m_kTriangleMesh
          Brain Surface TriMesh
        • m_kView
          CorticalAnalysisRender m_kView
          Brain Surface Renderer.
        • m_kVolumeViewer
          VolumeTriPlanarInterface m_kVolumeViewer
          Parent user-interface frame.
        • mainPanel
          JPanel mainPanel
          The main control.
        • OKButton
          JButton OKButton
          OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

  • Package gov.nih.mipav.view.renderer.WildMagic.Decimate

  • Package gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.DTIColorDisplay

      class DTIColorDisplay extends ViewJFrameBase implements Serializable

      • Serialized Fields

        • adjustExp
          float adjustExp
          adjust exp *
        • adjustExpPanel
          JPanel adjustExpPanel
          panels *
        • adjustExpSlider
          JSlider adjustExpSlider
          various sliders in dialog *
        • adjustExpTextField
          JTextField adjustExpTextField
          textfields *
        • alg
          AlgorithmDTIColorDisplay alg
          handle to the algorithm *
        • anisotropyBrowseButton
          JButton anisotropyBrowseButton
          buttons *
        • anisotropyFilename
          String anisotropyFilename
          names of eigenvector and anisotropy files*
        • anisotropyImage
          ModelImage anisotropyImage
          anisotropy src image *
        • anisotropyLabel
          JLabel anisotropyLabel
          labels *
        • anisotropyMax
          float anisotropyMax
          anisotropy max *
        • anisotropyMaxPanel
          JPanel anisotropyMaxPanel
          panels *
        • anisotropyMaxSlider
          JSlider anisotropyMaxSlider
          various sliders in dialog *
        • anisotropyMaxTextField
          JTextField anisotropyMaxTextField
          textfields *
        • anisotropyMin
          float anisotropyMin
          anisotropy min *
        • anisotropyMinPanel
          JPanel anisotropyMinPanel
          panels *
        • anisotropyMinSlider
          JSlider anisotropyMinSlider
          various sliders in dialog *
        • anisotropyMinTextField
          JTextField anisotropyMinTextField
          textfields *
        • anisotropyPath
          JTextField anisotropyPath
          textfields *
        • bottomPanel
          JPanel bottomPanel
          panels *
        • captureImageButton
          JButton captureImageButton
          buttons *
        • colorPanel
          JPanel colorPanel
          panels *
        • colorRangePanel
          JPanel colorRangePanel
          panels *
        • colorRangeSlider
          JSlider colorRangeSlider
          various sliders in dialog *
        • colorRangeTextField
          JTextField colorRangeTextField
          textfields *
        • colorWheel
          ColorWheel colorWheel
          Color Wheels *
        • colorWheelChoicesPanel
          JPanel colorWheelChoicesPanel
          panels *
        • colorWheelComboBox
          JComboBox colorWheelComboBox
          color wheel choices combo box *
        • colorWheelPanel
          JPanel colorWheelPanel
          panels *
        • componentImage
          ViewJComponentDTIImage componentImage
          ViewJComponentDTIImage *
        • currentColorWheelType
          String currentColorWheelType
          String indicating current color wheel type *
        • currentRectangle
          Rectangle currentRectangle
          rectangle for screen capture*
        • currentResultImageSlicesLabel
          JLabel currentResultImageSlicesLabel
          labels *
        • dimGreenPanel
          JPanel dimGreenPanel
          panels *
        • dimGreenSlider
          JSlider dimGreenSlider
          various sliders in dialog *
        • dimGreenTextField
          JTextField dimGreenTextField
          textfields *
        • eigenvectorBrowseButton
          JButton eigenvectorBrowseButton
          buttons *
        • eigenvectorLabel
          JLabel eigenvectorLabel
          labels *
        • eigenvectorPath
          JTextField eigenvectorPath
          textfields *
        • eigvecFilename
          String eigvecFilename
          names of eigenvector and anisotropy files*
        • eigvecSrcImage
          ModelImage eigvecSrcImage
          eigenvector src image *
        • filesPanel
          JPanel filesPanel
          panels *
        • flag
          boolean flag
          flag needed when performing restore defaults *
        • gamma
          float gamma
          gamma correction *
        • gammaPanel
          JPanel gammaPanel
          panels *
        • gammaSlider
          JSlider gammaSlider
          various sliders in dialog *
        • gammaTextField
          JTextField gammaTextField
          textfields *
        • gbc
          GridBagConstraints gbc
          GridbagConstraints *
        • gbl
          GridBagLayout gbl
          GridBagLayout *
        • heightResFactor
          float heightResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • heuristicParametersPanel
          JPanel heuristicParametersPanel
          panels *
        • imageBufferA
          float[] imageBufferA
          Buffer used to store image intensities the presently viewed slice of image A.
        • in
          BufferedReader in
          Buffered Reader for loading params *
        • isMultiply
          boolean isMultiply
          boolean for truncate/multiply *
        • loadButton
          JButton loadButton
          buttons *
        • LUTa
          ModelLUT LUTa
          LUT of input image *
        • magButton
          JButton magButton
          buttons *
        • magLabel
          JLabel magLabel
          labels *
        • mainPanel
          JPanel mainPanel
          panels *
        • maxAdjustExp
          float maxAdjustExp
          mins and maxes for heuristic parameters*
        • maxAdjustExpLabel
          JLabel maxAdjustExpLabel
          labels *
        • maxAnisotropyMax
          float maxAnisotropyMax
          mins and maxes for heuristic parameters*
        • maxAnisotropyMaxLabel
          JLabel maxAnisotropyMaxLabel
          labels *
        • maxAnisotropyMin
          float maxAnisotropyMin
          mins and maxes for heuristic parameters*
        • maxAnisotropyMinLabel
          JLabel maxAnisotropyMinLabel
          labels *
        • maxColorRange
          float maxColorRange
          mins and maxes for heuristic parameters*
        • maxColorRangeLabel
          JLabel maxColorRangeLabel
          labels *
        • maxDimGreen
          float maxDimGreen
          mins and maxes for heuristic parameters*
        • maxDimGreenLabel
          JLabel maxDimGreenLabel
          labels *
        • maxGamma
          float maxGamma
          mins and maxes for heuristic parameters*
        • maxGammaLabel
          JLabel maxGammaLabel
          labels *
        • maxResultImageSlicesLabel
          JLabel maxResultImageSlicesLabel
          labels *
        • maxSatBlue
          float maxSatBlue
          mins and maxes for heuristic parameters*
        • maxSatBlueLabel
          JLabel maxSatBlueLabel
          labels *
        • maxSatVsTheta
          float maxSatVsTheta
          mins and maxes for heuristic parameters*
        • maxSatVsThetaLabel
          JLabel maxSatVsThetaLabel
          labels *
        • maxStevensBeta
          float maxStevensBeta
          mins and maxes for heuristic parameters*
        • maxStevensBetaLabel
          JLabel maxStevensBetaLabel
          labels *
        • minAdjustExp
          float minAdjustExp
          mins and maxes for heuristic parameters*
        • minAdjustExpLabel
          JLabel minAdjustExpLabel
          labels *
        • minAnisotropyMax
          float minAnisotropyMax
          mins and maxes for heuristic parameters*
        • minAnisotropyMaxLabel
          JLabel minAnisotropyMaxLabel
          labels *
        • minAnisotropyMin
          float minAnisotropyMin
          mins and maxes for heuristic parameters*
        • minAnisotropyMinLabel
          JLabel minAnisotropyMinLabel
          labels *
        • minColorRange
          float minColorRange
          mins and maxes for heuristic parameters*
        • minColorRangeLabel
          JLabel minColorRangeLabel
          labels *
        • minDimGreen
          float minDimGreen
          mins and maxes for heuristic parameters*
        • minDimGreenLabel
          JLabel minDimGreenLabel
          labels *
        • minGamma
          float minGamma
          mins and maxes for heuristic parameters*
        • minGammaLabel
          JLabel minGammaLabel
          labels *
        • minResultImageSlicesLabel
          JLabel minResultImageSlicesLabel
          labels *
        • minSatBlue
          float minSatBlue
          mins and maxes for heuristic parameters*
        • minSatBlueLabel
          JLabel minSatBlueLabel
          labels *
        • minSatVsTheta
          float minSatVsTheta
          mins and maxes for heuristic parameters*
        • minSatVsThetaLabel
          JLabel minSatVsThetaLabel
          labels *
        • minStevensBeta
          float minStevensBeta
          mins and maxes for heuristic parameters*
        • minStevensBetaLabel
          JLabel minStevensBetaLabel
          labels *
        • multRadio
          JRadioButton multRadio
          radio buttons for truncate/multiply *
        • nImage
          int nImage
          Number of slices in a 3D dataset.
        • nTImage
          int nTImage
          Number of time sequences in a 4D dataset.
        • numSlices
          int numSlices
          num slices for result image *
        • okButton
          JButton okButton
          buttons *
        • okPanel
          JPanel okPanel
          panels *
        • optionsPanel
          JPanel optionsPanel
          panels *
        • out
          BufferedWriter out
          Buffered Writer for saving params *
        • pB
          float pB
          blue saturation *
        • pC
          float pC
          color range *
        • pG
          float pG
          green saturation *
        • pixBuffer
          int[] pixBuffer
          Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageA intensities as a index into a LUT.
        • pS
          float pS
          saturation vs theta *
        • refLabel1
          JLabel refLabel1
          labels *
        • refLabel2
          JLabel refLabel2
          labels *
        • refLabel3
          JLabel refLabel3
          labels *
        • refPanel
          JPanel refPanel
          panels *
        • resols
          float[] resols
          Storage of the image voxel resolutions. One resolution value per dimension.
        • restoreDefaultsButton
          JButton restoreDefaultsButton
          buttons *
        • restoreDefaultsPanel
          JPanel restoreDefaultsPanel
          panels *
        • resultImage
          ModelImage resultImage
          result image *
        • resultImagePanel
          JPanel resultImagePanel
          panels *
        • resultImageSlider
          JSlider resultImageSlider
          various sliders in dialog *
        • resultImageSliderPanel
          JPanel resultImageSliderPanel
          panels *
        • resultPanel
          JPanel resultPanel
          panels *
        • resultScrollPanel
          JScrollPane resultScrollPanel
          scroll pane for result image *
        • satBluePanel
          JPanel satBluePanel
          panels *
        • satBlueSlider
          JSlider satBlueSlider
          various sliders in dialog *
        • satBlueTextField
          JTextField satBlueTextField
          textfields *
        • satVsThetaPanel
          JPanel satVsThetaPanel
          panels *
        • satVsThetaSlider
          JSlider satVsThetaSlider
          various sliders in dialog *
        • satVsThetaTextField
          JTextField satVsThetaTextField
          textfields *
        • saveButton
          JButton saveButton
          buttons *
        • saveLoadPanel
          JPanel saveLoadPanel
          panels *
        • stevensBeta
          float stevensBeta
          steven's beta *
        • stevensBetaPanel
          JPanel stevensBetaPanel
          panels *
        • stevensBetaSlider
          JSlider stevensBetaSlider
          various sliders in dialog *
        • stevensBetaTextField
          JTextField stevensBetaTextField
          textfields *
        • tempPanel
          JPanel tempPanel
          panels *
        • title
          String title
          dialog title and version *
        • titledBorder
          TitledBorder titledBorder
          titled border for certain components *
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          ViewToolBarBuilder *
        • toolbarPanel
          JPanel toolbarPanel
          panels *
        • topPanel
          JPanel topPanel
          panels *
        • truncMultPanel
          JPanel truncMultPanel
          panels *
        • truncMultRadioGroup
          ButtonGroup truncMultRadioGroup
          radio group for truncate/multiply *
        • truncRadio
          JRadioButton truncRadio
          radio buttons for truncate/multiply *
        • tSlice
          int tSlice
          Image time sequence number of image that is displayed. Zero indexed based.
        • type
          String type
          type of color wheel ABSVAL, NOSYMM, ROTATIONALSYMM, MIRRORSYMM *
        • units
          int[] units
          Storage of the resolution units of measure. For example, mm, cm, inches ...
        • unMagButton
          JButton unMagButton
          buttons *
        • widthResFactor
          float widthResFactor
          Storage for correction parameters where datasets have non isotropic values.
        • zoom
          float zoom
          current zoom for result image *
        • zoomOneButton
          JButton zoomOneButton
          buttons *
        • zSlice
          int zSlice
          current z slice *

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.DTIPipeline

      class DTIPipeline extends JDialogBase implements Serializable

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIEstimateTensor

      class JPanelDTIEstimateTensor extends JPanel implements Serializable
      serialVersionUID:
      -6738722246165232246L

      • Serialized Fields

        • calcTensor
          JButton calcTensor
        • comboBoxDTI_Algorithm
          JComboBox comboBoxDTI_Algorithm
          menu for selecting dti algorithm:
        • displayExit
          JCheckBox displayExit
          Check boxes enable the user to save and display output images:
        • displayIntensity
          JCheckBox displayIntensity
        • displayTensor
          JCheckBox displayTensor
        • EPIpanel
          JPanelEPIDistortionCorrection EPIpanel
        • m_aakDWIList
          String[][] m_aakDWIList
        • m_aiMatrixEntries
          int[] m_aiMatrixEntries
        • m_bUseXRes
          boolean m_bUseXRes
        • m_bUseYRes
          boolean m_bUseYRes
        • m_bUseZRes
          boolean m_bUseZRes
        • m_fMeanNoise
          float m_fMeanNoise
        • m_fResX
          float m_fResX
        • m_fResY
          float m_fResY
        • m_fResZ
          float m_fResZ
        • m_iBOrig
          int m_iBOrig
        • m_iDimX
          int m_iDimX
        • m_iDimY
          int m_iDimY
        • m_iSlices
          int m_iSlices
        • m_iWeights
          int m_iWeights
        • m_kBMatrix
          WildMagic.LibFoundation.Mathematics.GMatrixd m_kBMatrix
        • m_kDWIImage
          ModelImage m_kDWIImage
        • m_kRawFormat
          String m_kRawFormat
        • mainPanel
          JPanel mainPanel
          main panel
        • maskImage
          ModelImage maskImage
          Mask image for the tensor calculation
        • outputDirTextField
          JTextField outputDirTextField
          output directory
        • pipeline
          DTIPipeline pipeline
          parent dialog
        • saveExit
          JCheckBox saveExit
        • saveIntensity
          JCheckBox saveIntensity
        • saveTensor
          JCheckBox saveTensor
        • serif12
          Font serif12
        • tensorImage
          ModelImage tensorImage
          Diffusion tensor image:
        • textListFile
          JTextField textListFile
          DWI .list location:
        • textMaskimage
          JTextField textMaskimage
          mask image location:

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIFiberTracking

      class JPanelDTIFiberTracking extends JPanel implements Serializable
      serialVersionUID:
      3303854496014433147L

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIImportData

      class JPanelDTIImportData extends JPanel implements Serializable

      • Serialized Fields

        • activeDWIButton
          JRadioButton activeDWIButton
        • angCorrGT
          double[][] angCorrGT
          DOCUMENT ME!
        • BMatrixButton
          JRadioButton BMatrixButton
        • browseDWIButton
          JRadioButton browseDWIButton
        • bvalGradAppButton
          JButton bvalGradAppButton
          DOCUMENT ME!
        • bvalGradFileLabel
          JLabel bvalGradFileLabel
          DOCUMENT ME!
        • checkSiemens
          boolean checkSiemens
        • clearDWITableButton
          JButton clearDWITableButton
        • currDir
          String currDir
          current directory *
        • dtiparams
          DTIParameters dtiparams
        • dtiStudioButton
          JRadioButton dtiStudioButton
          Radio button to save gradBval text file in DTIStudio format
        • DWIButtonPanel
          JPanel DWIButtonPanel
        • DWIOpenPanel
          JPanel DWIOpenPanel
        • fatshiftBox
          JComboBox fatshiftBox
          DOCUMENT ME!
        • fatShiftLabel
          JLabel fatShiftLabel
          DOCUMENT ME!
        • filebvalGradTxtName
          String filebvalGradTxtName
          bValGrad test file name from user
        • fileInfoPARREC
          FileInfoPARREC fileInfoPARREC
        • foldOverBox
          JComboBox foldOverBox
          DOCUMENT ME!
        • foldOverLabel
          JLabel foldOverLabel
          DOCUMENT ME!
        • frame
          ViewJFrameImage frame
        • fslButton
          JRadioButton fslButton
          Radio button to save gradBval text file in FSL format
        • gradBvalText
          int gradBvalText
          int to determine which format user selects for gradBval test file
        • gradCreatetable
          double[][] gradCreatetable
          DOCUMENT ME!
        • gradientButton
          JRadioButton gradientButton
        • gradOPBox
          JComboBox gradOPBox
          DOCUMENT ME!
        • gradOPLabel
          JLabel gradOPLabel
          DOCUMENT ME!
        • gradResBox
          JComboBox gradResBox
          DOCUMENT ME!
        • gradResLabel
          JLabel gradResLabel
          DOCUMENT ME!
        • gradResWOP
          String gradResWOP
        • invertedBox
          JComboBox invertedBox
          DOCUMENT ME!
        • invertedLabel
          JLabel invertedLabel
          DOCUMENT ME!
        • isBmatFile
          boolean isBmatFile
        • isDWICellEditBox
          JCheckBox isDWICellEditBox
          DOCUMENT ME!
        • isJonesBox
          JCheckBox isJonesBox
          DOCUMENT ME!
        • isKirbyBox
          JCheckBox isKirbyBox
          DOCUMENT ME!
        • lastStackFlag
          boolean lastStackFlag
        • loadBValGradFileButton
          JButton loadBValGradFileButton
        • loadTable
          JPanel loadTable
        • m_kDWIImage
          ModelImage m_kDWIImage
          Diffusion Tensor image.
        • m_kT2Image
          ModelImage m_kT2Image
          T2 image.
        • mipavStandardButton
          JRadioButton mipavStandardButton
          Radio button to save gradBval text file in mipavStandard format
        • mosaicToSliceAlgo
          AlgorithmMosaicToSlices mosaicToSliceAlgo
        • negXCheckBox
          JCheckBox negXCheckBox
          DOCUMENT ME!
        • negYCheckBox
          JCheckBox negYCheckBox
          DOCUMENT ME!
        • negZCheckBox
          JCheckBox negZCheckBox
          DOCUMENT ME!
        • newDTIparams
          DTIParameters newDTIparams
        • numVolumes
          int numVolumes
          number of Volumes in DWI Image
        • openDWIButton
          JButton openDWIButton
          DOCUMENT ME!
        • openedImageCheckBox
          JCheckBox openedImageCheckBox
          DOCUMENT ME!
        • openFile
          ViewOpenFileUI openFile
        • openImageNames
          Vector<String> openImageNames
        • openT2Button
          JButton openT2Button
          DOCUMENT ME!
        • osBox
          JComboBox osBox
          DOCUMENT ME!
        • osLabel
          JLabel osLabel
          DOCUMENT ME!
        • outputTextArea
          JTextArea outputTextArea
          TextArea of main dialogfor text output.*
        • parDTIParams
          DTIParameters parDTIParams
        • parNExamName
          String parNExamName
        • parNfoldover
          String parNfoldover
        • parNoffCentre
          double[] parNoffCentre
        • parNorient
          int parNorient
        • parNPatientPosition
          String parNPatientPosition
        • parNProtocolName
          String parNProtocolName
        • parNsliceAng
          double[] parNsliceAng
        • parNversion
          String parNversion
        • patientOrientBox
          JComboBox patientOrientBox
          DOCUMENT ME!
        • patientOrientLabel
          JLabel patientOrientLabel
          DOCUMENT ME!
        • patientPosBox
          JComboBox patientPosBox
          DOCUMENT ME!
        • patientPosLabel
          JLabel patientPosLabel
          DOCUMENT ME!
        • philRelBox
          JComboBox philRelBox
          DOCUMENT ME!
        • philRelLabel
          JLabel philRelLabel
          DOCUMENT ME!
        • pipeline
          DTIPipeline pipeline
        • rev_angCorrGT
          double[][] rev_angCorrGT
          DOCUMENT ME!
        • saveBvalGradButton
          JButton saveBvalGradButton
        • saveGradchooser
          JFileChooser saveGradchooser
          chooser for save gradBval text dialog
        • scrollPane
          JScrollPane scrollPane
        • serif12
          Font serif12
        • sliceAng0
          double sliceAng0
        • sliceAng1
          double sliceAng1
        • sliceAng2
          double sliceAng2
        • space
          String space
          DOCUMENT ME!
        • srcBvalGradTable
          JTable srcBvalGradTable
        • srcPanel
          JPanel srcPanel
        • srcTableModel
          DefaultTableModel srcTableModel
          table model for the srcimages.
        • t2FileLabel
          JLabel t2FileLabel
          DOCUMENT ME!
        • t2frame
          ViewJFrameImage t2frame
        • t2OpenPanel
          JPanel t2OpenPanel
        • textBvalGradFile
          JTextField textBvalGradFile
          DOCUMENT ME!
        • textDWIDataimage
          JTextField textDWIDataimage
        • textT2image
          JTextField textT2image
          DOCUMENT ME!
        • ui
          ViewUserInterface ui
        • useT2CheckBox
          JCheckBox useT2CheckBox
          DOCUMENT ME!

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIParametersPanel

      class JPanelDTIParametersPanel extends JInterfaceBase implements Serializable
      serialVersionUID:
      2778749302064237729L

      • Serialized Fields

        • displayMode
          int displayMode
        • glyphsList
          JComboBox glyphsList
          list to hold the glyphs type name
        • m_fFAMax
          float m_fFAMax
        • m_fFAMin
          float m_fFAMin
        • m_fFraction
          float m_fFraction
        • m_fMaxAngle
          float m_fMaxAngle
        • m_iCurrentGroup
          int m_iCurrentGroup
          Number of currently loaded fiber bundle groups.
        • m_iCurrentTrackCount
          int m_iCurrentTrackCount
        • m_iDimX
          int m_iDimX
        • m_iDimY
          int m_iDimY
        • m_iDimZ
          int m_iDimZ
        • m_iMaxTractLength
          int m_iMaxTractLength
        • m_iMinTractLength
          int m_iMinTractLength
        • m_kCExclude
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kCExclude
        • m_kCIgnore
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kCIgnore
        • m_kCInclude
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kCInclude
        • m_kColorButton
          JButton m_kColorButton
          Color button for changing the color of the fiber bundles.
        • m_kColorChooser
          ViewJColorChooser m_kColorChooser
          Color chooser for when the user wants to change the color of the fiber bundle tracts.
        • m_kCurrentStartList
          Vector<WildMagic.LibFoundation.Mathematics.Vector3f> m_kCurrentStartList
        • m_kDisplaySlider
          JSlider m_kDisplaySlider
          User-control over the number of glyphs displayed in GPUVolumeRender
        • m_kDTIImage
          ModelImage m_kDTIImage
        • m_kExclude
          JRadioButton m_kExclude
        • m_kFAMaxThreshold
          JTextField m_kFAMaxThreshold
        • m_kFAMinThreshold
          JTextField m_kFAMinThreshold
        • m_kGroupList
          Vector<Integer> m_kGroupList
          Keeps track of the groups of polylines loaded.
        • m_kIgnore
          JRadioButton m_kIgnore
        • m_kImage
          ModelImage m_kImage
        • m_kInclude
          JRadioButton m_kInclude
        • m_kMaxAngle
          JTextField m_kMaxAngle
        • m_kMaxLength
          JTextField m_kMaxLength
        • m_kMinLength
          JTextField m_kMinLength
        • m_kSliderLabel
          JLabel m_kSliderLabel
        • m_kTractList
          JList m_kTractList
          The list box in the dialog for fiber bundle tracts.
        • m_kUseEllipsoids
          JCheckBox m_kUseEllipsoids
          Checkbox for switching between polylines and ellipsoids.
        • m_kUseVOICheck
          JCheckBox m_kUseVOICheck
          When selected, only tracts that intersect the VOI are displayed.
        • m_kUseVolumeColor
          JCheckBox m_kUseVolumeColor
          Checkbox for turning on/off volume color for the polylines.
        • m_kVOIList
          JList m_kVOIList
          The list box in the dialog for 3D VOIs.
        • m_kVOIParamsList
          Vector<JPanelDTIParametersPanel.VOIParams> m_kVOIParamsList
        • m_kVolumeDisplay
          VolumeTriPlanarRender m_kVolumeDisplay
        • m_kVoxelStepsize
          JTextField m_kVoxelStepsize
        • parentFrame
          VolumeTriPlanarInterfaceDTI parentFrame

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIPreprocessing

      class JPanelDTIPreprocessing extends JPanel implements Serializable
      serialVersionUID:
      -4309868934393418962L

      • Serialized Fields

        • b0MatrixFileName
          String b0MatrixFileName
          File name for the B0 to T2 transformation matrix (needed to populate the next panel in the DTIPipeline)
        • b0toStructMatrix
          TransMatrix b0toStructMatrix
          The transformation matrix describing the transformation from registering B0 to T2 image. If that step in the process is skipped, this defaults to the identity matrix:
        • blanklabel
          JLabel blanklabel
        • buttonPanel
          JPanel buttonPanel
        • coarseRateX
          float coarseRateX
        • coarseRateY
          float coarseRateY
        • coarseRateZ
          float coarseRateZ
        • comboBoxCostFunct
          JComboBox comboBoxCostFunct
          DOCUMENT ME!
        • comboBoxDOF
          JComboBox comboBoxDOF
          DOCUMENT ME!
        • comboBoxInterp
          JComboBox comboBoxInterp
          DOCUMENT ME!
        • correctGradTransCheckbox
          JCheckBox correctGradTransCheckbox
        • cost
          int cost
          DOCUMENT ME!
        • costT2
          int costT2
          DOCUMENT ME!
        • DOF
          int DOF
          DOCUMENT ME!
        • DOFT2
          int DOFT2
          DOCUMENT ME!
        • doGraph
          boolean doGraph
        • doMultiThread
          boolean doMultiThread
        • doSubsample
          boolean doSubsample
        • fastMode
          boolean fastMode
        • fineRateX
          float fineRateX
        • fineRateY
          float fineRateY
        • fineRateZ
          float fineRateZ
        • imageB0
          ModelImage imageB0
          The B0 image from the original 4D DWI image series, extracted from the DWI volume:
        • imageT2
          ModelImage imageT2
          The T2 image that the B0 image is registered to. This may be the original T2 if it matched the extents/resultions of the other image Or it is the resampled T2 image
        • imageUpdatedDWI
          ModelImage imageUpdatedDWI
          After the B0 image is registered to the T2 image the B0 sub-volume is replaced in the original DWI image, creating a new 4D DWI image:
        • interp
          int interp
          DOCUMENT ME!
        • interpT2
          int interpT2
          DOCUMENT ME!
        • labelCost
          JLabel labelCost
        • labelDOF
          JLabel labelDOF
        • labelInternal
          JLabel labelInternal
        • labelInterp
          JLabel labelInterp
        • mainPanel
          JPanel mainPanel
        • matrixComboBox
          JComboBox matrixComboBox
          DOCUMENT ME!
        • matrixDirText
          JTextField matrixDirText
          DOCUMENT ME!
        • maxIterations
          int maxIterations
        • maxOfMinResol
          boolean maxOfMinResol
        • numMinima
          int numMinima
        • OKButton
          JButton OKButton
        • openDirButton
          JButton openDirButton
        • outputCommand
          String outputCommand
          action command when the user presses the browse button to select the output directory:
        • outputDir
          JTextField outputDir
          output directory enables user to choose where to save files to.
        • performEPICheckbox
          JCheckBox performEPICheckbox
        • pipeline
          DTIPipeline pipeline
        • preProsLabel
          JLabel preProsLabel
        • preProsText
          JTextField preProsText
        • progressBar
          ViewJProgressBar progressBar
          Progress bar that will listen to a dialog's algorithm (and reflect current progress)
        • refImageNumText
          JTextField refImageNumText
          user-input for the B0 sub-volume number in the 4D DWI image
        • reg3
          AlgorithmRegOAR3D reg3
          DOCUMENT ME!
        • reg35
          AlgorithmRegOAR35D reg35
          DOCUMENT ME!
        • registerTo
          int registerTo
        • result35RegImage
          ModelImage result35RegImage
        • rotateBeginX
          float rotateBeginX
        • rotateBeginY
          float rotateBeginY
        • rotateBeginZ
          float rotateBeginZ
        • rotateEndX
          float rotateEndX
        • rotateEndY
          float rotateEndY
        • rotateEndZ
          float rotateEndZ
        • serif12
          Font serif12
        • serif12B
          Font serif12B
        • skipPreCheckbox
          JCheckBox skipPreCheckbox
        • structOptPanel
          JPanel structOptPanel
        • transformB0Checkbox
          JCheckBox transformB0Checkbox
        • transformB0label
          JLabel transformB0label
        • transformB0MatCheckbox
          JCheckBox transformB0MatCheckbox
        • transformDWICheckbox
          JCheckBox transformDWICheckbox
          DOCUMENT ME!
        • transformMatDWICheckbox
          JCheckBox transformMatDWICheckbox

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIVisualization

      class JPanelDTIVisualization extends JPanel implements Serializable
      serialVersionUID:
      8011148684175711251L

      • Serialized Fields

        • loadButton
          JButton loadButton
          Button enabled when all required images are loaded. Pressing 'Load' launches the Volume DTI Renderer.
        • m_kAnisotropyImage
          ModelImage m_kAnisotropyImage
          Anisotropy image *
        • m_kDTIColorImage
          ModelImage m_kDTIColorImage
          result image *
        • m_kDTIImage
          ModelImage m_kDTIImage
          Diffusion Tensor image.
        • m_kEigenValueImage
          ModelImage m_kEigenValueImage
          EigenValue image *
        • m_kEigenVectorImage
          ModelImage m_kEigenVectorImage
          Eigenvector image *
        • m_kT2Image
          ModelImage m_kT2Image
          Anisotropy image *
        • m_kTractFile
          File m_kTractFile
          Tract input file.
        • m_kTractPath
          JTextField m_kTractPath
          Fiber bundle tract file input path name text box.
        • mainPanel
          JPanel mainPanel
          main panel *
        • parentFrame
          JDialog parentFrame
          Parent dialog, when this panel is created as a stand-alone dialog: *
        • textDTIColorImage
          JTextField textDTIColorImage
          Text boxes for the tensor, color image, eigen vector, eigen value, and functional anisotropy files:
        • textDTIimage
          JTextField textDTIimage
          Text boxes for the tensor, color image, eigen vector, eigen value, and functional anisotropy files:
        • textEValueImage
          JTextField textEValueImage
          Text boxes for the tensor, color image, eigen vector, eigen value, and functional anisotropy files:
        • textEVimage
          JTextField textEVimage
          Text boxes for the tensor, color image, eigen vector, eigen value, and functional anisotropy files:
        • textFAimage
          JTextField textFAimage
          Text boxes for the tensor, color image, eigen vector, eigen value, and functional anisotropy files:
        • textT2image
          JTextField textT2image
          Text boxes for the tensor, color image, eigen vector, eigen value, and functional anisotropy files:

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelEPIDistortionCorrection

      class JPanelEPIDistortionCorrection extends JPanel implements Serializable
      serialVersionUID:
      5817025147038892937L

      • Serialized Fields

        • B0MatrixFile
          JTextField B0MatrixFile
        • B0toStructTransPanel
          JPanel B0toStructTransPanel
        • computeDefFieldCommand
          String computeDefFieldCommand
        • computeDeformationFieldButton
          JButton computeDeformationFieldButton
          button for computing the deformation field:
        • computeEpiCommand
          String computeEpiCommand
        • computeEpiCorrectionButton
          JButton computeEpiCorrectionButton
          button for applying the deformation field to the input 4D image
        • DefLoadPanel
          JPanel DefLoadPanel
        • deformationB0T2
          ModelImage deformationB0T2
          deformation field from registering the B0 volume to the resampled T2 volume with VABRA
        • deformationB0T2Text
          JTextField deformationB0T2Text
        • deformedDWI
          ModelImage deformedDWI
          DWI image series after applying the list of deformation fields
        • displayDeformationField
          JCheckBox displayDeformationField
          output image display options:
        • displayEPIResult
          JCheckBox displayEPIResult
        • displayRegisteredB0
          JCheckBox displayRegisteredB0
        • DWITransPanel
          JPanel DWITransPanel
        • loadAllMatrixComand
          String loadAllMatrixComand
        • loadB0MatrixComand
          String loadB0MatrixComand
        • loadDeformationFieldCommand
          String loadDeformationFieldCommand
        • loadDWICommand
          String loadDWICommand
        • loadT2Command
          String loadT2Command
          button commands
        • mainPanel
          JPanel mainPanel
          main panel
        • matB0T2
          TransMatrix matB0T2
          Transformation matrix from registering B0 to T2.
        • matRegistered
          TransMatrix[] matRegistered
          Array of transformation matrices after registering the DWI image series to the B0 reference volume.
        • matricesFile
          JTextField matricesFile
        • outputCommand
          String outputCommand
        • outputDir
          JTextField outputDir
        • OutputPanel
          JPanel OutputPanel
        • pipeline
          DTIPipeline pipeline
          reference to the DTI Pipeline
        • refImageNumText
          JTextField refImageNumText
          Text fields for entering the input images:
        • registeredB0
          ModelImage registeredB0
          B0 volume extracted from the DWI series.
        • registeredDWI
          ModelImage registeredDWI
          DWI image series that has been registered within series to the B0 volume.
        • RegisteredDWIPanel
          JPanel RegisteredDWIPanel
        • registeredDWIText
          JTextField registeredDWIText
        • resampledT2
          ModelImage resampledT2
          Structural T2 image, resampled to match the DWI image series.
        • resampledT2Text
          JTextField resampledT2Text
        • T2loadPanel
          JPanel T2loadPanel

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.VolumeTriPlanarInterfaceDTI

      class VolumeTriPlanarInterfaceDTI extends VolumeTriPlanarInterface implements Serializable
      serialVersionUID:
      1898957906984534260L

      • Serialized Fields

        • DTIParametersPanel
          JPanel DTIParametersPanel
        • DTIparamsPanel
          JPanelDTIParametersPanel DTIparamsPanel
        • m_kAnisotropyImage
          ModelImage m_kAnisotropyImage
          Anisotropy image
        • m_kDTIColorImage
          ModelImage m_kDTIColorImage
          Diffusion Tensor image.
        • m_kDTIImage
          ModelImage m_kDTIImage
          Diffusion Tensor image.
        • m_kEigenValueImage
          ModelImage m_kEigenValueImage
          EigenValue image
        • m_kEigenVectorImage
          ModelImage m_kEigenVectorImage
          Eigenvector image
        • m_kParentDir
          String m_kParentDir

    • Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.VolumeTriPlanerRenderDTI

      class VolumeTriPlanerRenderDTI extends VolumeTriPlanarRender implements Serializable
      serialVersionUID:
      237088312722258458L

      • Serialized Fields

        • m_bSlicePickEnabled
          boolean m_bSlicePickEnabled
        • m_bSlicePickPending
          boolean m_bSlicePickPending
        • updatingFiberTrack
          boolean updatingFiberTrack

  • Package gov.nih.mipav.view.renderer.WildMagic.flythroughview

    • Class gov.nih.mipav.view.renderer.WildMagic.flythroughview.FlyThroughRender

      class FlyThroughRender extends GPURenderBase implements Serializable
      serialVersionUID:
      -6130870790192175575L

      • Serialized Fields

        • m_aiBranchIndexUnvisitedMax
          int[] m_aiBranchIndexUnvisitedMax
          This is the range of path samples for each branch that are unvisited.
        • m_aiBranchIndexUnvisitedMin
          int[] m_aiBranchIndexUnvisitedMin
          This is the range of path samples for each branch that are unvisited.
        • m_akColorBackup
          WildMagic.LibFoundation.Mathematics.ColorRGB[] m_akColorBackup
          Original surface color for undoing the pseudo-color curvature map.
        • m_iLastSelectedBranchIndex
          int m_iLastSelectedBranchIndex
          Keep track of the last branch that was selected (at a branch point).
        • m_kAnnotateList
          FlyPathAnnotateList_WM m_kAnnotateList
          Annotations along the fly path.
        • m_kCenter
          WildMagic.LibFoundation.Mathematics.Vector3f m_kCenter
          Center of Mesh
        • m_kControlFrame
          JPanelVirtualEndoscopySetup_WM m_kControlFrame
          This is the control frame which may need to be updated as the view changes.
        • m_kCortical
          MjCorticalMesh_WM m_kCortical
          Calculating the mesh curvatures.
        • m_kFlyPathBehavior
          FlyPathBehavior_WM m_kFlyPathBehavior
          Fly path behavior.
        • m_kFlyPathGraphCurve
          FlyPathGraphCurve m_kFlyPathGraphCurve
          Fly path curve.
        • m_kLight
          WildMagic.LibGraphics.Rendering.Light m_kLight
          Lighting in the scene.
        • m_kLightShader
          SurfaceLightingEffect m_kLightShader
          Lighting effect.
        • m_kMaskImage
          ModelImage m_kMaskImage
          ModelImage used to generate the fly path.
        • m_kMeanCurvaturesLUT
          ModelLUT m_kMeanCurvaturesLUT
          kMean curvature LUT. Pseudo color look up table.
        • m_kNormalColorPathUnvisited
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kNormalColorPathUnvisited
          Color for the parts of the path that have not yet been visited (Dark Green)
        • m_kNormalColorPathVisited
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kNormalColorPathVisited
          Color for the parts of the path that have been visited (Light Green)
        • m_kOptions
          FlyThroughRender.SetupOptions m_kOptions
          Setup options.
        • m_kParent
          VolumeTriPlanarInterface m_kParent
          Parent user-interface and display frame.
        • m_kRotation
          WildMagic.LibGraphics.SceneGraph.Node m_kRotation
          Mouse rotation.
        • m_kSelectColorPathUnvisited
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kSelectColorPathUnvisited
          Color for selecting previously-unvisited parts of the path at a branch (Dark Red)
        • m_kSelectColorPathVisited
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kSelectColorPathVisited
          Color for selecting previously-visited parts of the path at a branch (Red)
        • m_kSkeleton
          Skeleton3D m_kSkeleton
          3D Skeleton of the ModelImage.
        • m_kSurface
          WildMagic.LibGraphics.SceneGraph.TriMesh m_kSurface
          The surface to fly through.
        • m_kVolumeLayout
          ModelImage3DLayout m_kVolumeLayout
          3D Layout of the ModelImage.
        • pressed
          boolean pressed
          If any of the mouse move button pressed.

    • Class gov.nih.mipav.view.renderer.WildMagic.flythroughview.JPanelVirtualEndoscopySetup_WM

      class JPanelVirtualEndoscopySetup_WM extends JPanelRendererBase implements Serializable
      serialVersionUID:
      5676430934584329807L

      • Serialized Fields

        • contentBox
          Box contentBox
          Box layout for control panel.
        • continueUpdate
          boolean continueUpdate
          Flag indicates to continue update the surface render and plane render or not.
        • directory
          String directory
          File name and directory.
        • endoscopyImage
          ModelImage endoscopyImage
          Loaded endoscopy image file.
        • fileName
          String fileName
          File name and directory.
        • flythruButtonLoadImage
          JButton flythruButtonLoadImage
          Load image button.
        • flythruLabelFileName
          JLabel flythruLabelFileName
          Image file name label.
        • kPanelButton
          JPanel kPanelButton
          Button panel.
        • m_bShowMeanCurvatures
          boolean m_bShowMeanCurvatures
          Flag indicates to show pseudo color or not.
        • m_kCheckBoxShowCurvatures
          JCheckBox m_kCheckBoxShowCurvatures
          Show curvature colors check box.
        • m_kComboSegmentSurfaceBranchSamplesReductionFactor
          JComboBox m_kComboSegmentSurfaceBranchSamplesReductionFactor
          Surface sample reduction factor.
        • m_kContinueUpdate
          JCheckBox m_kContinueUpdate
          Continuous update check box.
        • m_kDecimalFormat
          DecimalFormat m_kDecimalFormat
          Used to create text representations of numbers.
        • m_kLabelBranch
          JLabel m_kLabelBranch
          Branch label.
        • m_kLabelDirection
          JLabel m_kLabelDirection
          View direction label.
        • m_kLabelDistance
          JLabel m_kLabelDistance
          Path distance label.
        • m_kLabelFileName
          JLabel m_kLabelFileName
          Automatically inserted by JBuilder Designer.
        • m_kLabelOrientation
          JLabel m_kLabelOrientation
          Orientation label.
        • m_kLabelPosition
          JLabel m_kLabelPosition
          Current path position label.
        • m_kLabelStepGaze
          JLabel m_kLabelStepGaze
          Step gaze label.
        • m_kOptions
          FlyThroughRender.SetupOptions m_kOptions
          Image option panel.
        • m_kTextBranch
          JTextField m_kTextBranch
          Current branch text box.
        • m_kTextDirection
          JTextField m_kTextDirection
          View direction text box.
        • m_kTextDistance
          JTextField m_kTextDistance
          Distance along path text box.
        • m_kTextMaxNumBranches
          JTextField m_kTextMaxNumBranches
          maximum number of branches created for the endoscopy view.
        • m_kTextMinBranchLength
          JTextField m_kTextMinBranchLength
          minimum branch length.
        • m_kTextOrientation
          JTextField m_kTextOrientation
          Orientation text box.
        • m_kTextPercentBSplineNumControlPoints
          JTextField m_kTextPercentBSplineNumControlPoints
          BSpline control points fraction of branch samples.
        • m_kTextPosition
          JTextField m_kTextPosition
          Position text box.
        • m_kTextStepGaze
          JTextField m_kTextStepGaze
          Step gaze text box.
        • m_kView
          FlyThroughRender m_kView
          Renderer for displaying the scene-graph.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanelVirtualEndoscopySetup_WM.DrawingPanel scrollPanel
          Scroll panel that holding all the control components.
        • updateButton
          JButton updateButton
          continue update button.

  • Package gov.nih.mipav.view.renderer.WildMagic.Interface

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.FileInfoSurfaceGiftiXML_WM

      class FileInfoSurfaceGiftiXML_WM extends FileInfoSurfaceRefXML implements Serializable
      serialVersionUID:
      819907577181061024L

      • Serialized Fields

        • connectivity
          Vector<Integer> connectivity
          Vector to hold the connection index.
        • coordinates
          Vector<WildMagic.LibFoundation.Mathematics.Vector3f> coordinates
          Vector to hold the 3D coordinate positions
        • m_kMaterial
          WildMagic.LibGraphics.Rendering.MaterialState m_kMaterial
          Material properties of the surface:.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.FileInfoSurfaceRefXML_WM

      class FileInfoSurfaceRefXML_WM extends FileInfoSurfaceRefXML implements Serializable
      serialVersionUID:
      819907577181061024L

      • Serialized Fields

        • m_kMaterial
          WildMagic.LibGraphics.Rendering.MaterialState m_kMaterial
          Material properties of the surface:.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JDialogDTIInput

      class JDialogDTIInput extends JInterfaceBase implements Serializable
      serialVersionUID:
      9207590841799033846L

      • Serialized Fields

        • m_aakDWIList
          String[][] m_aakDWIList
          List of file names for the Diffusion Weighted Images, from the .path file.
        • m_aiMatrixEntries
          int[] m_aiMatrixEntries
          keeps track of unique entries in the BMatrix
        • m_bUseXRes
          boolean m_bUseXRes
          Set to true if the slice resolution is read from the .list file: (xRes)
        • m_bUseYRes
          boolean m_bUseYRes
          Set to true if the slice resolution is read from the .list file: (yRes)
        • m_bUseZRes
          boolean m_bUseZRes
          Set to true if the slice resolution is read from the .list file: (zRes)
        • m_fMeanNoise
          float m_fMeanNoise
          Mean noise vale read from the .list file
        • m_fResX
          float m_fResX
          Slice thickness read from .list file
        • m_fResY
          float m_fResY
          Slice thickness read from .list file
        • m_fResZ
          float m_fResZ
          Slice thickness read from .list file
        • m_iBOrig
          int m_iBOrig
          Number of different BMatrix rows:
        • m_iDimX
          int m_iDimX
          X-dimensions for Diffusion Weighted Images.
        • m_iDimY
          int m_iDimY
          Y-dimensions for Diffusion Weighted Images.
        • m_iSlices
          int m_iSlices
          Number of slices in the Diffusion Weighted Images series.
        • m_iType
          int m_iType
          Dialog type.
        • m_iWeights
          int m_iWeights
          Number of weights in the Diffusion Weighted Images series.
        • m_kAnisotropyImage
          ModelImage m_kAnisotropyImage
          Anisotropy image *
        • m_kAnisotropyPath
          JTextField m_kAnisotropyPath
          Anisotropy file input path name text box.
        • m_kBMatrix
          WildMagic.LibFoundation.Mathematics.GMatrixd m_kBMatrix
          General matrix storing BMatrix values.
        • m_kDTIImage
          ModelImage m_kDTIImage
          Diffusion Tensor image.
        • m_kDTIPath
          JTextField m_kDTIPath
          Diffusion Tensor file input path name text box.
        • m_kDWIMaskImage
          ModelImage m_kDWIMaskImage
          Mask image for calculating the DTI image.
        • m_kDWIMaskPath
          JTextField m_kDWIMaskPath
          Diffusion Weighted Images Mask file input path name text box.
        • m_kDWIPath
          JTextField m_kDWIPath
          Diffusion Weighted Images .list file input path name text box.
        • m_kEigenValueImage
          ModelImage m_kEigenValueImage
          EigenValue image *
        • m_kEigenVectorImage
          ModelImage m_kEigenVectorImage
          Eigenvector image *
        • m_kEigenVectorPath
          JTextField m_kEigenVectorPath
          EigenVector file input path name text box.
        • m_kLUTa
          ModelLUT m_kLUTa
          LUT of input image *
        • m_kOpenB0
          JCheckBox m_kOpenB0
        • m_kParentDir
          String m_kParentDir
          parent directory for the DTI output images.
        • m_kRawFormat
          String m_kRawFormat
          raw image format read from the .list file:
        • m_kReconstructTracts
          JCheckBox m_kReconstructTracts
          Checkbox for tract reconstruction.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JDialogVolumeAnnotation

      class JDialogVolumeAnnotation extends JDialogAnnotation implements Serializable
      serialVersionUID:
      6726637420209273103L

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JFrameSurfaceMaterialProperties_WM

      class JFrameSurfaceMaterialProperties_WM extends JFrame implements Serializable
      serialVersionUID:
      3077827124095959620L

      • Serialized Fields

        • AFTER
          int AFTER
          Before/After index values for the two displayed spheres, canvases, and display panels:.
        • BEFORE
          int BEFORE
          Before/After index values for the two displayed spheres, canvases, and display panels:.
        • m_akMaterialPreset
          WildMagic.LibGraphics.Rendering.MaterialState[] m_akMaterialPreset
          Pre-defined materials
        • m_akSurfaceMaterial
          SurfaceMaterialDisplay[] m_akSurfaceMaterial
        • m_bColorApplied
          boolean m_bColorApplied
          keeps track of whether or not color has been applied to surface (for backup on cancel)
        • m_fShininess
          float m_fShininess
          specular coefficient
        • m_iNumPreset
          int m_iNumPreset
          Preset Material's examples:.
        • m_iSurfaceIndex
          int m_iSurfaceIndex
          the index of the surface that is being changed in the JPanelSurface
        • m_iWhichButton
          int m_iWhichButton
          Which button is pressed to activate the JColorChooser:.
        • m_kAmbient
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kAmbient
          Current color values:.
        • m_kAmbientColorButton
          JButton m_kAmbientColorButton
          Material Properties color buttons:.
        • m_kAnimator
          com.jogamp.opengl.util.Animator m_kAnimator
        • m_kColorChooser
          JColorChooser m_kColorChooser
          Color Chooser dialog:.
        • m_kDiffuse
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kDiffuse
          diffuse color
        • m_kDiffuseColorButton
          JButton m_kDiffuseColorButton
          diffuse color button
        • m_kEmissive
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kEmissive
          emissive color
        • m_kEmissiveColorButton
          JButton m_kEmissiveColorButton
          emissive color button
        • m_kImagePane
          JSplitPane m_kImagePane
          Split pane for displaying the canvases side-by-side:.
        • m_kImagePanel
          JPanel[] m_kImagePanel
          Canvas display panels:.
        • m_kMainPane
          JSplitPane m_kMainPane
          Split pane for displaying the rendered spheres above the interface:.
        • m_kMaterialNew
          WildMagic.LibGraphics.Rendering.MaterialState m_kMaterialNew
          Materials for new vales and backup:.
        • m_kMaterialPanel
          JPanel m_kMaterialPanel
          Window display panels: Material properties buttons/slider panel:.
        • m_kMaterialSave
          WildMagic.LibGraphics.Rendering.MaterialState m_kMaterialSave
          Saved Material for backup
        • m_kParent
          JPanelSurface_WM m_kParent
          Parent class:.
        • m_kShininessSlider
          JSlider m_kShininessSlider
          Shininess slider.
        • m_kSpecular
          WildMagic.LibFoundation.Mathematics.ColorRGB m_kSpecular
          Specular color component
        • m_kSpecularColorButton
          JButton m_kSpecularColorButton
          Specular color button

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JInterfaceBase

      class JInterfaceBase extends JDialog implements Serializable
      serialVersionUID:
      1185755612726454935L

      • Serialized Fields

        • cancelButton
          JButton cancelButton
          Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.
        • colorChooser
          ViewJColorChooser colorChooser
          Color chooser dialog.
        • mainPanel
          JPanel mainPanel
          The main control.
        • OKButton
          JButton OKButton
          OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JInterfaceBase.DrawingPanel

      class DrawingPanel extends JPanel implements Serializable
      serialVersionUID:
      -6456589720445279985L

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanel3DMouse_WM

      class JPanel3DMouse_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      2858702077770704429L

      • Serialized Fields

        • buttonfine
          JButton buttonfine
        • buttonnormal
          JButton buttonnormal
        • chckbxfine
          JCheckBox chckbxfine
        • chckbxForwardsbackwards
          JCheckBox chckbxForwardsbackwards
        • chckbxLeftright
          JCheckBox chckbxLeftright
        • chckbxRotationRX
          JCheckBox chckbxRotationRX
        • chckbxRotationRy
          JCheckBox chckbxRotationRy
        • chckbxRotationRz
          JCheckBox chckbxRotationRz
        • chckbxUpdown
          JCheckBox chckbxUpdown
        • gbc_1
          GridBagConstraints gbc_1
        • gbc_2
          GridBagConstraints gbc_2
        • gbc_3
          GridBagConstraints gbc_3
        • gbc_4
          GridBagConstraints gbc_4
        • gbc_5
          GridBagConstraints gbc_5
        • inMenu
          boolean inMenu
        • labelX1
          JLabel labelX1
          Labels beneath sliders.
        • labelXEnd
          JLabel labelXEnd
          Labels beneath sliders.
        • labelXMid
          JLabel labelXMid
          Labels beneath sliders.
        • lblRotation
          JLabel lblRotation
        • lblRotations
          JLabel lblRotations
        • lblTranslation
          JLabel lblTranslation
        • lblTranslations
          JLabel lblTranslations
        • leftRighticon
          JLabel leftRighticon
        • leftRighticon_1
          JLabel leftRighticon_1
        • mouseRotationCutoffSlider
          JSlider mouseRotationCutoffSlider
          Mouse rotation sensitivity cutoff slider
        • mouseRotationSpeedSlider
          JSlider mouseRotationSpeedSlider
          Mouse rotation speed slider.
        • mouseTranslationCutoffSlider
          JSlider mouseTranslationCutoffSlider
        • mouseTranslationSpeedSlider
          JSlider mouseTranslationSpeedSlider
          Mouse translation speed slider.
        • rollIcon
          JLabel rollIcon
        • rotationCutoffTextField
          JTextField rotationCutoffTextField
          Text fields that display the sensitivity number next to the sliders.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • spinIcon
          JLabel spinIcon
        • tilticon
          JLabel tilticon
        • translationCutoffTextField
          JTextField translationCutoffTextField
        • zInvertCheckBox
          JCheckBox zInvertCheckBox
          Invert movement checkbox

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelAnnotationAnimation

      class JPanelAnnotationAnimation extends JInterfaceBase implements Serializable

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelClip_WM

      class JPanelClip_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      -3342110506544352170L

      • Serialized Fields

        • clipColor
          JButton[] clipColor
        • clipLabel
          JLabel[] clipLabel
        • clipPanel
          JPanel[] clipPanel
        • clipSlider
          JSlider[] clipSlider
        • clipText
          JTextField[] clipText
        • clipValue
          int[] clipValue
        • displayClip
          JCheckBox[] displayClip
        • enableClip
          JCheckBox[] enableClip
        • extract
          JButton[] extract
        • labelEnd
          JLabel[] labelEnd
        • labelMid
          JLabel[] labelMid
        • labelStart
          JLabel[] labelStart
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Used when the screen is small.
        • scrollPanel
          JPanel scrollPanel
          Scroll panel that holding all the control components.
        • tabbedPane
          JTabbedPane tabbedPane
          Tabbed Panel that hold the each clipping planes control box.
        • thicknessSlider
          JSlider thicknessSlider

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelCustomBlend

      class JPanelCustomBlend extends JInterfaceBase implements Serializable
      serialVersionUID:
      -6719268114423090548L

      • Serialized Fields

        • alphaSlider
          JSlider alphaSlider
        • colorButton
          JButton colorButton
        • m_bUpdate
          boolean m_bUpdate
        • m_kBlendEquationColor
          JComboBox m_kBlendEquationColor
          The combo box for the Blend Equation mode to display.
        • m_kDstBlend
          JComboBox m_kDstBlend
        • m_kLogicOp
          JComboBox m_kLogicOp
          The combo box for the Logic Operation mode to display.
        • m_kSrcBlend
          JComboBox m_kSrcBlend
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelDisplay_WM

      class JPanelDisplay_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      926266253314679850L

      • Serialized Fields

        • boundingCheck
          JCheckBox boundingCheck
          Check box for turning box on and off.
        • cameraNearPlane
          JSlider cameraNearPlane
          Slider for moving the camera near-plane in/out from the eye position.
        • cameraXLabel
          JLabel cameraXLabel
          Camera move parameter labels
        • cameraXTurnLabel
          JLabel cameraXTurnLabel
          Camera turn parameter labels
        • cameraYLabel
          JLabel cameraYLabel
          Camera move parameter labels
        • cameraYTurnLabel
          JLabel cameraYTurnLabel
          Camera turn parameter labels
        • cameraZLabel
          JLabel cameraZLabel
          Camera move parameter labels
        • colorButton
          JButton colorButton
          Color button for changing color.
        • colorButtonBackground
          JButton colorButtonBackground
          Color button for changing z color.
        • cubePanel
          JPanel cubePanel
          Panel for the rotation cube.
        • cubicCheck
          JCheckBox cubicCheck
          Check box for cubic control.
        • flag
          boolean flag
          Flag indicating if the red bounding box is on or off.
        • objectXRotLabel
          JLabel objectXRotLabel
          Object rotation parameter labels.
        • objectYRotLabel
          JLabel objectYRotLabel
          Object rotation parameter labels.
        • objectZRotLabel
          JLabel objectZRotLabel
          Object rotation parameter labels.
        • planeConstantSlider
          JSlider planeConstantSlider
          Slider to adjust the front clipping plane constant.
        • radioButtonGroupProjections
          ButtonGroup radioButtonGroupProjections
          Button group for projections.
        • radioButtonOrthographic
          JRadioButton radioButtonOrthographic
          Radio Button for Orthographic rendering.
        • radioButtonPerspective
          JRadioButton radioButtonPerspective
          Radio Button for Perspective rendering.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JInterfaceBase.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • viewAlignedButton
          JRadioButton viewAlignedButton
          Radio Button for Perspective rendering.
        • viewButton
          JRadioButton viewButton
          Radio Button for Orthographic rendering.
        • viewTextureButtonGroup
          ButtonGroup viewTextureButtonGroup
          Button group for projections.
        • xCameraMove
          float xCameraMove
          Camera move parameter values.
        • xCameraMoveText
          JTextField xCameraMoveText
          Camera move parameter text-field.
        • xCameraTurn
          float xCameraTurn
          Camera move parameter values
        • xCameraTurnText
          JTextField xCameraTurnText
          Camera move parameter text-field
        • xObjectRotate
          float xObjectRotate
          Object rotation angle parameter values.
        • xObjectRotateText
          JTextField xObjectRotateText
          Object rotation parameter text-field.
        • yCameraMove
          float yCameraMove
          Camera move parameter values.
        • yCameraMoveText
          JTextField yCameraMoveText
          Camera move parameter text-field.
        • yCameraTurn
          float yCameraTurn
          Camera move parameter values
        • yCameraTurnText
          JTextField yCameraTurnText
          Camera move parameter text-field
        • yObjectRotate
          float yObjectRotate
          Object rotation angle parameter values.
        • yObjectRotateText
          JTextField yObjectRotateText
          Object rotation parameter text-field.
        • zCameraMove
          float zCameraMove
          Camera move parameter values.
        • zCameraMoveText
          JTextField zCameraMoveText
          Camera move parameter text-field.
        • zObjectRotate
          float zObjectRotate
          Object rotation angle parameter values.
        • zObjectRotateText
          JTextField zObjectRotateText
          Object rotation parameter text-field.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelGeodesic_WM

      class JPanelGeodesic_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      4382184418236793404L

      • Serialized Fields

        • drawLabel
          JLabel drawLabel
          Geodesic line draw control label.
        • m_fDijkstraCurrent
          float m_fDijkstraCurrent
          Current Dijkstra path length.
        • m_fDijkstraPrevious
          float m_fDijkstraPrevious
          Previous Dijkstra path length.
        • m_fDijkstraTotal
          float m_fDijkstraTotal
          Total Dijkstra path length.
        • m_fEuclidianCurrent
          float m_fEuclidianCurrent
          Values for the current path length between the last two selected points:
        • m_fEuclidianPrevious
          float m_fEuclidianPrevious
          Values for the previous current path length between the last two selected points:
        • m_fEuclidianTotal
          float m_fEuclidianTotal
          Values for the total path lengths:.
        • m_fGeodesicSmoothCurrent
          float m_fGeodesicSmoothCurrent
          Current Geodesic path length
        • m_fGeodesicSmoothPrevious
          float m_fGeodesicSmoothPrevious
          Previous Geodesic path length
        • m_fGeodesicSmoothTotal
          float m_fGeodesicSmoothTotal
          Total Geodesic path length
        • m_kCheckLivewire
          JCheckBox m_kCheckLivewire
          Toggle between LiveWire Interaction and point invalid input: '&' click interaction:.
        • m_kClearAllCutsButton
          JButton m_kClearAllCutsButton
          Clearsall cuts.
        • m_kClearAllGeodesicButton
          JButton m_kClearAllGeodesicButton
          Clearsall Geodesic components.
        • m_kClearLastCutButton
          JButton m_kClearLastCutButton
          Clear the last cut.
        • m_kClearLastGeodesicButton
          JButton m_kClearLastGeodesicButton
          Button for deleting the geodesic.
        • m_kCutGeodesicButton
          JButton m_kCutGeodesicButton
          Button for cutting the mesh along the geodesic:.
        • m_kDijkstraDistance
          JLabel m_kDijkstraDistance
          Label displaying the current Dijkstra path length.
        • m_kDijkstraDistanceValueLast
          JLabel m_kDijkstraDistanceValueLast
          Label displaying the previous Dijkstra path length.
        • m_kDijkstraDistanceValueTotal
          JLabel m_kDijkstraDistanceValueTotal
          Label displaying the total Dijkstra path length.
        • m_kDisplayButtonGroup
          ButtonGroup m_kDisplayButtonGroup
          ButtonGroup for the different path display options.
        • m_kDisplayDijkstra
          JRadioButton m_kDisplayDijkstra
          Display Dijkstra's path.
        • m_kDisplayEuclidian
          JRadioButton m_kDisplayEuclidian
          Display the Euclidian path.
        • m_kDisplayGeodesic
          JRadioButton m_kDisplayGeodesic
          Radio buttons for displaying the smoothed geodesic, dijkstra's path, or the euclidian path:.
        • m_kDrawGeodesicButton
          JToggleButton m_kDrawGeodesicButton
          Geodesic drawing interface Toggle button is down while points are added to the curve:.
        • m_kEuclidianDistance
          JLabel m_kEuclidianDistance
          Label displaying the current Euclidian path length.
        • m_kEuclidianDistanceValueLast
          JLabel m_kEuclidianDistanceValueLast
          Label displaying the previous Euclidian path length.
        • m_kEuclidianDistanceValueTotal
          JLabel m_kEuclidianDistanceValueTotal
          Label displaying the total Euclidian path length.
        • m_kFinishClosedGeodesicButton
          JButton m_kFinishClosedGeodesicButton
          Close and finish the Geodesic path.
        • m_kFinishOpenGeodesicButton
          JButton m_kFinishOpenGeodesicButton
          Finish the Geodesic path without closing.
        • m_kGeodesicSmoothDistance
          JLabel m_kGeodesicSmoothDistance
          Label displaying the current Geodesic path length.
        • m_kGeodesicSmoothDistanceValueLast
          JLabel m_kGeodesicSmoothDistanceValueLast
          Label displaying the previous Geodesic path length.
        • m_kGeodesicSmoothDistanceValueTotal
          JLabel m_kGeodesicSmoothDistanceValueTotal
          Label displaying the total Geodesic path length.
        • m_kGeodesicToggleWireframe
          JToggleButton m_kGeodesicToggleWireframe
          Toggle wireframe
        • m_kSurfacePanel
          JPanelSurface_WM m_kSurfacePanel
          Surface panel.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JInterfaceBase.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • surfaceGeodesic
          Geodesic_WM surfaceGeodesic
          Geodesic reference.
        • surPickLabel
          JLabel surPickLabel
          Label to indicate that enable Surface pickable before drawing geodesic line.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelLights_WM

      class JPanelLights_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      8549491288085975699L

      • Serialized Fields

        • ambientRadio
          JRadioButton ambientRadio
          Radio button for different light type.
        • colorButton
          JButton colorButton
          Color button, checkBox On/Off.
        • colorLabel
          JLabel colorLabel
          Color label.
        • controlPanel
          JPanel controlPanel
          Control panel.
        • controlPanelBox
          Box controlPanelBox
          Control panel box that hold the control panel.
        • directionalRadio
          JRadioButton directionalRadio
          Directional light radio botton.
        • drawPanel
          JPanel drawPanel
          Scroll panel reference.
        • intensitySlider
          JSlider intensitySlider
          Intensity slider.
        • iSelect
          int iSelect
          index of currently selected one.
        • labelIntensity
          JLabel labelIntensity
          Light intensity label.
        • labelIntensityBegin
          JLabel labelIntensityBegin
          Light intensity label begin.
        • labelIntensityEnd
          JLabel labelIntensityEnd
          Light intensity label end.
        • labelIntensityMid
          JLabel labelIntensityMid
          Light intensity label middle.
        • list
          JList list
          List of lights.
        • m_aiLightScale
          int[] m_aiLightScale
          Light scale factor array.
        • m_akLights
          WildMagic.LibGraphics.Rendering.Light[] m_akLights
          The structure for the light bulbs.
        • m_kLabelPosX
          JLabel m_kLabelPosX
          Label for slider X position.
        • m_kLabelPosY
          JLabel m_kLabelPosY
          Label for slider Y position.
        • m_kLabelPosZ
          JLabel m_kLabelPosZ
          Label for slider Z position.
        • m_kLabelTrgX
          JLabel m_kLabelTrgX
          Label for X light target position.
        • m_kLabelTrgY
          JLabel m_kLabelTrgY
          Label for Y light target position.
        • m_kLabelTrgZ
          JLabel m_kLabelTrgZ
          Label for Z light target position.
        • m_kSliderPosX
          JSlider m_kSliderPosX
          Light x position slider.
        • m_kSliderPosY
          JSlider m_kSliderPosY
          Light y position slider.
        • m_kSliderPosZ
          JSlider m_kSliderPosZ
          Light z position slider.
        • m_kSliderTrgX
          JSlider m_kSliderTrgX
          Light x target position slider.
        • m_kSliderTrgY
          JSlider m_kSliderTrgY
          Light y target position slider.
        • m_kSliderTrgZ
          JSlider m_kSliderTrgZ
          Light z target position slider.
        • m_kTextPosX
          JTextField m_kTextPosX
          X position text field.
        • m_kTextPosY
          JTextField m_kTextPosY
          Y position text field.
        • m_kTextPosZ
          JTextField m_kTextPosZ
          Z position text field.
        • m_kTextTrgX
          JTextField m_kTextTrgX
          X target position text field.
        • m_kTextTrgY
          JTextField m_kTextTrgY
          Y target position text field.
        • m_kTextTrgZ
          JTextField m_kTextTrgZ
          Z target position text field.
        • maxBox
          float maxBox
          x, y, z box size.
        • onOffCheckBox
          JCheckBox onOffCheckBox
          Light turn on/off check box.
        • onOffLabel
          JLabel onOffLabel
          Light turn on/off label.
        • pointRadio
          JRadioButton pointRadio
          Point light radio button.
        • scroller
          JScrollPane scroller
          Scroll pane.
        • scrollPanel
          JPanel scrollPanel
          Scroll the control panel when the frame changes size.
        • spotRadio
          JRadioButton spotRadio
          Spot light radio button.
        • textIntensity
          JTextField textIntensity
          Light intensity textfield.
        • xBox
          float xBox
          x, y, z box size.
        • yBox
          float yBox
          x, y, z box size.
        • zBox
          float zBox
          x, y, z box size.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelMultiDimensionalTransfer

      class JPanelMultiDimensionalTransfer extends JInterfaceBase implements Serializable
      serialVersionUID:
      926266253314679850L

      • Serialized Fields

        • alphaSlider
          JSlider alphaSlider
          Alpha blend slider.
        • boundaryEmphasisSlider
          JSlider boundaryEmphasisSlider
          Boundary emphasis slider slider.
        • colorButton
          JButton colorButton
          Color button for changing color.
        • gmAxis
          ViewJComponentGraphAxes gmAxis
        • helpPanel
          JPanel helpPanel
        • histogramPanel
          JPanel histogramPanel
          Panel containing the 2D Histogram display canvas:
        • imageAxis
          ViewJComponentGraphAxes imageAxis
          Graph axes helper classes for displaying the axes of the 2D Histogram:
        • loadButton
          JButton loadButton
          Read new multi-histogram widgets from file.
        • m_kGroup
          ButtonGroup m_kGroup
          Button group for the widget type:
        • m_kMultiHistogram
          VolumeImageMultiDimensionalTransfer m_kMultiHistogram
          Displays the 2D Histogram and widgets:
        • saveButton
          JButton saveButton
          Save the current multi-histogram widgets to file.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JPanel scrollPanel
          Scroll panel that holding the all the control components.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelNavigation

      class JPanelNavigation extends JInterfaceBase implements Serializable
      serialVersionUID:
      3015333092796701354L

      • Serialized Fields

        • addAnnotateButton
          JToggleButton addAnnotateButton
          button for adding annotation points for the path planning
        • cameraRotationDegreeLabel
          JLabel cameraRotationDegreeLabel
          camera rotation degree label
        • cameraRotationDegreeSlider
          JSlider cameraRotationDegreeSlider
          camera rotation degree slider
        • clearPathButton
          JButton clearPathButton
          cleaning the planned path button.
        • createPathButton
          JButton createPathButton
          create path planning path button.
        • mouseControlRadio
          JRadioButton mouseControlRadio
          Radio check button for mouse control.
        • navigationCheckBox
          JCheckBox navigationCheckBox
          Navigation (fly-thru) checkbox
        • pathPlanningRadio
          JRadioButton pathPlanningRadio
          Radio check button the path planning.
        • radioButtonGroupFlyMode
          ButtonGroup radioButtonGroupFlyMode
          radio check button for fly-thru mode.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelPositions

      class JPanelPositions extends JInterfaceBase implements Serializable
      serialVersionUID:
      4578542603991193148L

      • Serialized Fields

        • absoluteLabel
          JLabel absoluteLabel
          Labels for the current absolute position:.
        • absoluteLabelVals
          JLabel[] absoluteLabelVals
          Labels for the current absolute position values:.
        • absolutePanel
          JPanel absolutePanel
          JPanel containing the absoulte position labels:.
        • modelViewLabel
          JLabel modelViewLabel
          Labels for the current position in 3D ModelView coordinates.
        • modelViewLabelVals
          JLabel[] modelViewLabelVals
          Displayed values for the current position in 3D ModelView coordinates.
        • neurologicalView
          JRadioButton neurologicalView
        • panelLabels
          JPanel panelLabels
          Panel containing the position labels:.
        • patientSliceLabel
          JLabel patientSliceLabel
          Labels for the current position in PatientSlice coordinates.
        • patientSliceLabelVals
          JLabel[] patientSliceLabelVals
          Displayed values for the current position in PatientSlice coordinates.
        • radiologicalView
          JRadioButton radiologicalView
        • scannerLabel
          JLabel scannerLabel
          Labels for the current scanner position:.
        • scannerLabelVals
          JLabel[] scannerLabelVals
          Labels for the current scanner position values:.
        • scannerPanel
          JPanel scannerPanel
          JPanel containing the scanner position labels:.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelRenderMode_WM

      class JPanelRenderMode_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      3015333092796701354L

      • Serialized Fields

        • cameraRotationDegreeLabel
          JLabel cameraRotationDegreeLabel
          camera rotation degree label
        • cameraRotationDegreeSlider
          JSlider cameraRotationDegreeSlider
          camera rotation degree slider
        • m_fIPD
          float m_fIPD
          IPD number.
        • m_kDisplaySlicesCheck
          JCheckBox m_kDisplaySlicesCheck
          Turn display 3D Slices on/off
        • m_kDisplaySurfaceCheck
          JCheckBox m_kDisplaySurfaceCheck
          Turn display 3D TriMesh Surface on/off
        • m_kDisplayVOICheck
          JCheckBox m_kDisplayVOICheck
          Turn display VOIs on/off
        • m_kDisplayVolumeCheck
          JCheckBox m_kDisplayVolumeCheck
          Turn display volume on/off
        • m_kExtractTriMesh
          JButton m_kExtractTriMesh
          Button for extracting a TriMesh surface based on the ray-cast volume rendered in Surface mode
        • m_kIntensityTF
          JTextField m_kIntensityTF
          Text box for setting the intensity level for extraction.
        • m_kIPDSlider
          JSlider m_kIPDSlider
          Opacity slider.
        • m_kStereoModeCB
          JComboBox m_kStereoModeCB
          The combo box for the polygon mode to display.
        • m_kVolumeBlendSlider
          JSlider m_kVolumeBlendSlider
          Volume alpha-blending slider.
        • m_kVolumeSamplesSliderMouseDragged
          JSlider m_kVolumeSamplesSliderMouseDragged
          Volume number of samples slider when mouse Dragged.
        • m_kVolumeSamplesSliderMouseReleased
          JSlider m_kVolumeSamplesSliderMouseReleased
          Volume number of samples slider when mouse released.
        • mkCurrent
          JLabel mkCurrent
          Label that gives current value of slider.
        • mouseRotationSpeedSlider
          JSlider mouseRotationSpeedSlider
          Mouse rotation speed slider.
        • mouseTranslationSpeedSlider
          JSlider mouseTranslationSpeedSlider
          Mouse translation speed slider.
        • mouseZoomSpeedSlider
          JSlider mouseZoomSpeedSlider
          Mouse zoom speed slider.
        • radioCOMPOSITE
          JRadioButton radioCOMPOSITE
          Radio button of the COMPOSITE mode option.
        • radioCustom
          JRadioButton radioCustom
          Radio button of the Custom blend mode option.
        • radioMIP
          JRadioButton radioMIP
          Radio button of the MIP mode option.
        • radioMULTIHISTO
          JCheckBox radioMULTIHISTO
          Checkbox for the Multi-histo mode option.
        • radioSURFACE
          JRadioButton radioSURFACE
          Radio button of the SURFACE mode option.
        • radioSURFACEFAST
          JRadioButton radioSURFACEFAST
          Radio button of the SURFACE mode option.
        • radioSurrenderCOMPOSITE
          JRadioButton radioSurrenderCOMPOSITE
          Radio button of the surface render composite mode.
        • radioXRAY
          JRadioButton radioXRAY
          Radio button of the XRAY mode option.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • serif12
          Font serif12
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.
        • serif12B
          Font serif12B
          Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSculptor_WM

      class JPanelSculptor_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      4235930260988710821L

      • Serialized Fields

        • lineButton
          JToggleButton lineButton
          Line shape button.
        • m_iSculptHeight
          int m_iSculptHeight
          Window width information for Sculpting.
        • m_iSculptWidth
          int m_iSculptWidth
          Window width information for Sculpting.
        • m_kApplyAllButton
          JButton m_kApplyAllButton
          Button to apply sculpt region to the volume.
        • m_kApplySculptButton
          JButton m_kApplySculptButton
          Button to apply sculpt region to the volume.
        • m_kClearDrawOutlineButton
          JButton m_kClearDrawOutlineButton
          Button for clearing the sculpt region.
        • m_kDrawOutlineButton
          JToggleButton m_kDrawOutlineButton
          Toggle button is down while the mouse is used to draw the sculpt outline.
        • m_kInvertOutlineButton
          JButton m_kInvertOutlineButton
          Button for inverting the sculpt region.
        • m_kSaveSculptButton
          JButton m_kSaveSculptButton
          Button to save the sculpt image.
        • m_kUndoAllButton
          JButton m_kUndoAllButton
        • m_kUndoSculptButton
          JButton m_kUndoSculptButton
          Button to undo the sculpt and restor the original volume.
        • rectButton
          JToggleButton rectButton
          Rectangle shape button.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JInterfaceBase.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • toolbarBuilder
          ViewToolBarBuilder toolbarBuilder
          Toolbar builder reference.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSlices_WM

      class JPanelSlices_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      -8359831093707979536L

      • Serialized Fields

        • boundingBoxPanel
          JPanel boundingBoxPanel
          Bounding box control panel.
        • boundingCheck
          JCheckBox[] boundingCheck
          Check box for turning bounding boxes on and off.
        • boxX
          JCheckBox boxX
          Check boxes that turn the image plane on and off.
        • boxY
          JCheckBox boxY
          Check boxes that turn the image plane on and off.
        • boxZ
          JCheckBox boxZ
          Check boxes that turn the image plane on and off.
        • colorButton
          JButton[] colorButton
          Color button for changing bounding box color.
        • controlPanel
          JPanel controlPanel
          Main panel for sliders.
        • labelT
          JLabel labelT
          Labels next to sliders.
        • labelX
          JLabel labelX
          Labels next to sliders.
        • labelX1
          JLabel labelX1
          Labels beneath sliders.
        • labelXEnd
          JLabel labelXEnd
          Labels beneath sliders.
        • labelXMid
          JLabel labelXMid
          Labels beneath sliders.
        • labelY
          JLabel labelY
          Labels next to sliders.
        • labelY1
          JLabel labelY1
          Labels beneath sliders.
        • labelYEnd
          JLabel labelYEnd
          Labels beneath sliders.
        • labelYMid
          JLabel labelYMid
          Labels beneath sliders.
        • labelZ
          JLabel labelZ
          Labels next to sliders.
        • labelZ1
          JLabel labelZ1
          Labels beneath sliders.
        • labelZEnd
          JLabel labelZEnd
          Labels beneath sliders.
        • labelZMid
          JLabel labelZMid
          Labels beneath sliders.
        • opacityControlPanel
          JPanel opacityControlPanel
          Opacity control panel.
        • opacityLabelX
          JLabel opacityLabelX
          The opacity slider label.
        • opacityLabelY
          JLabel opacityLabelY
          The opacity slider label.
        • opacityLabelZ
          JLabel opacityLabelZ
          The opacity slider label.
        • opacitySliderLabelsX
          JLabel[] opacitySliderLabelsX
          The labels below the opacity slider.
        • opacitySliderLabelsY
          JLabel[] opacitySliderLabelsY
          The labels below the opacity slider.
        • opacitySliderLabelsZ
          JLabel[] opacitySliderLabelsZ
          The labels below the opacity slider.
        • opacitySliderX
          JSlider opacitySliderX
          Opacity slider, not enabled yet.
        • opacitySliderY
          JSlider opacitySliderY
          Opacity slider, not enabled yet.
        • opacitySliderZ
          JSlider opacitySliderZ
          Opacity slider, not enabled yet.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • scrollPanel
          JInterfaceBase.DrawingPanel scrollPanel
          Scroll panel that holding the all the control components.
        • sliceVisible
          boolean[] sliceVisible
          Flags indicating if the image slices are on or off.
        • sliderT
          JSlider sliderT
          Sliders for the image planes.
        • sliderX
          JSlider sliderX
          Sliders for the image planes.
        • sliderY
          JSlider sliderY
          Sliders for the image planes.
        • sliderZ
          JSlider sliderZ
          Sliders for the image planes.
        • tDim
          int tDim
          x, y, z and time dimension values.
        • textT
          JTextField textT
          Text fields that display the slice number next to the sliders.
        • textX
          JTextField textX
          Text fields that display the slice number next to the sliders.
        • textY
          JTextField textY
          Text fields that display the slice number next to the sliders.
        • textZ
          JTextField textZ
          Text fields that display the slice number next to the sliders.
        • tSlice
          int tSlice
          Which time slice is currently displayed.
        • xDim
          int xDim
          x, y, z and time dimension values.
        • xOpacitySlice
          int xOpacitySlice
          x, y, z opacity slider values.
        • xProbe
          int xProbe
          Probe x, y, z position.
        • xSlice
          int xSlice
          Which slice is currently displayed in the ZY plane.
        • yDim
          int yDim
          x, y, z and time dimension values.
        • yOpacitySlice
          int yOpacitySlice
          x, y, z opacity slider values.
        • yProbe
          int yProbe
          Probe x, y, z position.
        • ySlice
          int ySlice
          Which slice is currently displayed in the XZ plane.
        • zDim
          int zDim
          x, y, z and time dimension values.
        • zOpacitySlice
          int zOpacitySlice
          x, y, z opacity slider values.
        • zProbe
          int zProbe
          Probe x, y, z position.
        • zSlice
          int zSlice
          Which slice is currently displayed in the XY plane.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSurface_WM

      class JPanelSurface_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      -4600563188022683359L

      • Serialized Fields

        • areaLabel
          JLabel areaLabel
          The area label.
        • areaText
          JTextField areaText
          Displays the area of triangle.
        • colorButton
          JButton colorButton
          The color button, which calls a color chooser.
        • colorLabel
          JLabel colorLabel
          The color button label.
        • comboLabel
          JLabel comboLabel
          The polygon mode combo box label.
        • convexHull
          JButton convexHull
          Smooth button.
        • decimateButton
          JButton decimateButton
          Decimate button.
        • decimationPercentage
          double decimationPercentage
          Decimation Percentage
        • detailLabel
          JLabel detailLabel
          The level of detail slider label.
        • detailSlider
          JSlider detailSlider
          Level of detail slider.
        • detailSliderLabels
          JLabel[] detailSliderLabels
          The labels below the detail slider.
        • extractConnected
          JButton extractConnected
          Smooth button.
        • invertNormals
          JButton invertNormals
          Smooth button.
        • listModel
          DefaultListModel<String> listModel
        • m_akSurfaceStates
          Vector<SurfaceState> m_akSurfaceStates
        • m_kAdvancedMaterialOptionsButton
          JButton m_kAdvancedMaterialOptionsButton
          The material options button, which launches the material editor window.
        • m_kSurfacePaint
          SurfacePaint_WM m_kSurfacePaint
          Paint tool-bar (contained in the SurfacePaint class)
        • m_kSurfaceTextureButton
          JButton m_kSurfaceTextureButton
          Opens SurfaceTexture dialog:.
        • opacityLabel
          JLabel opacityLabel
          The opacity slider label.
        • opacitySlider
          JSlider opacitySlider
          Opacity slider, not enabled yet.
        • opacitySliderLabels
          JLabel[] opacitySliderLabels
          The labels below the opacity slider.
        • polygonModeCB
          JComboBox polygonModeCB
          The combo box for the polygon mode to display.
        • polylineCounter
          int polylineCounter
          constant polyline counter
        • polylineCounterList
          DefaultListModel polylineCounterList
          Polyline counter list invalid input: '<'index, groupID>
        • polylineList
          JList polylineList
          Polyline list box in the dialog for surfaces.
        • savePLYSurfaceButton
          JButton savePLYSurfaceButton
          Save .PLY surface button.
        • saveSTLSurfaceButton
          JButton saveSTLSurfaceButton
          Save .STL surface button.
        • saveSurfaceButton
          JButton saveSurfaceButton
          Save surface button.
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.
        • smooth1Button
          JButton smooth1Button
          Smooth button.
        • smooth2Button
          JButton smooth2Button
          Smooth button.
        • smooth3Button
          JButton smooth3Button
          Smooth button.
        • subdivideTriangles
          JButton subdivideTriangles
          Smooth button.
        • surfaceBackFaceCB
          JCheckBox surfaceBackFaceCB
          Check Box for surface back face culling.
        • surfaceClipCB
          JCheckBox surfaceClipCB
          Check Box for surface clpping of the volume render.
        • surfaceList
          JList<String> surfaceList
          The list box in the dialog for surfaces.
        • surfacePickableCB
          JCheckBox surfacePickableCB
          Check Box for surface picking.
        • surfaceTransparencyCB
          JCheckBox surfaceTransparencyCB
          Check Box for surface transparency.
        • tmesh
          TriangleMesh[] tmesh
          triangle mesh for decimation.
        • triangleLabel
          JLabel triangleLabel
          The number of triangles label.
        • triangleText
          JTextField triangleText
          Displays the number of triangles.
        • volumeCoordsCheck
          JCheckBox volumeCoordsCheck
          loads mesh files in basic volume coordinates
        • volumeLabel
          JLabel volumeLabel
          The volume label.
        • volumeText
          JTextField volumeText
          Displays the volume of triangle.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSurfaceTexture_WM

      class JPanelSurfaceTexture_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      7562070328632922435L

      • Serialized Fields

        • m_kSurfacePanel
          JPanelSurface_WM m_kSurfacePanel
          Surface panel
        • mHistogram
          JFrameHistogram mHistogram
          Display the independent LUT for Black/White images.
        • mImageA
          ModelImage mImageA
          ModelImage used to generate the 3D texture:.
        • mImageALink
          ModelImage mImageALink
          Reference to ModelImage A for linking the texture to the imageA LUT.
        • mImageAsTextureCheck
          JCheckBox mImageAsTextureCheck
          RadioButton for turing on the surface image texture:.
        • mImageButtonGroup
          ButtonGroup mImageButtonGroup
          Grouping the radio buttons:.
        • mImageDirName
          String mImageDirName
          Stores the currently-loaded ModelImage directory name:.
        • mImageFileName
          String mImageFileName
          Stores the currently-loaded ModelImage file name:.
        • mImageFileNameLabel
          JLabel mImageFileNameLabel
          Display the currently-loaded ModelImage file name:.
        • mLoadImageButton
          JButton mLoadImageButton
          Load a new ModelImage:.
        • mLUTButtonGroup
          ButtonGroup mLUTButtonGroup
          Grouping the radio buttons:.
        • mLUTImageA
          ModelImage mLUTImageA
          Independent ModelImage for independent LUT.
        • mLUTModel
          ModelStorageBase mLUTModel
          The LUT associated with the ModelImage imageA:.
        • mLUTSeparate
          ModelStorageBase mLUTSeparate
          The LUT associated with the independent texture LUT:.
        • mModelImageRadioButton
          JRadioButton mModelImageRadioButton
          Use the ModelImage LUT.
        • mModelLUTRadioButton
          JRadioButton mModelLUTRadioButton
          Use the ModelImage LUT.
        • mNewImageRadioButton
          JRadioButton mNewImageRadioButton
          Use a separate LUT.
        • mNewLUTRadioButton
          JRadioButton mNewLUTRadioButton
          Use a separate LUT.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelVolume4D

      class JPanelVolume4D extends JInterfaceBase implements Serializable
      serialVersionUID:
      -5083630753484806459L

      • Serialized Fields

        • m_k4DSlider
          JSlider m_k4DSlider
        • m_kFrameRateSlider
          JSlider m_kFrameRateSlider
        • scroller
          JScrollPane scroller
          The scroll pane holding the panel content. Useful when the screen is small.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.SurfaceExtractor

      class SurfaceExtractor extends WildMagic.LibImagics.Extraction.ExtractSurfaceTetra implements Serializable

      • Serialized Fields

        • dicomMatrix
          TransMatrix dicomMatrix
          Dicom Matrix
        • direction
          int[] direction
          Surface direction
        • m_fXDelta
          float m_fXDelta
          Relative voxel size.
        • m_fYDelta
          float m_fYDelta
          Relative voxel size.
        • m_fZDelta
          float m_fZDelta
          Relative voxel size.
        • startLocation
          float[] startLocation
          Surface 3D location

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.SurfaceExtractorCubes

      class SurfaceExtractorCubes extends WildMagic.LibImagics.Extraction.ExtractSurfaceCubes implements Serializable

      • Serialized Fields

        • dicomMatrix
          TransMatrix dicomMatrix
          Dicom Matrix
        • m_afStartLocation
          float[] m_afStartLocation
          Surface 3D location
        • m_aiDirection
          int[] m_aiDirection
          Surface direction
        • m_fXDelta
          float m_fXDelta
          Relative voxel size.
        • m_fYDelta
          float m_fYDelta
          Relative voxel size.
        • m_fZDelta
          float m_fZDelta
          Relative voxel size.

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.SurfacePaint_WM

      class SurfacePaint_WM extends JInterfaceBase implements Serializable
      serialVersionUID:
      -3767599197318881261L

      • Serialized Fields

        • m_bEnabled
          boolean m_bEnabled
          Enables painting
        • m_kPanel
          JPanelSurface_WM m_kPanel
          Surface panel.
        • mBrushSize
          int mBrushSize
          current paint brush size
        • mBrushSizeText
          JTextField mBrushSizeText
          Paint brush size text field
        • mButtonGroup
          ButtonGroup mButtonGroup
          Button group for paint functions:
        • mColorChooser
          JColorChooser mColorChooser
          Color Chooser dialog.
        • mColorPaintButton
          JButton mColorPaintButton
          Color selection button
        • mDropperButton
          JToggleButton mDropperButton
          Paint dropper button
        • mEraseAllButton
          JButton mEraseAllButton
          Erase all button
        • mEraserButton
          JToggleButton mEraserButton
          Eraser paint button
        • mOpacity
          float mOpacity
          Current paint opacity
        • mOpacityPaintButton
          JButton mOpacityPaintButton
          Opacity paint button
        • mPaintBrushButton
          JToggleButton mPaintBrushButton
          Paint brush button
        • mPaintCanButton
          JToggleButton mPaintCanButton
          Paint can button
        • mPaintColor
          WildMagic.LibFoundation.Mathematics.ColorRGBA mPaintColor
          Current paint color
        • mPaintGrowDialog
          JDialogPaintGrow mPaintGrowDialog
          Paint Grow Dialog.
        • mPaintToolBar
          JToolBar mPaintToolBar
          Paint user-interface ToolBar

    • Class gov.nih.mipav.view.renderer.WildMagic.Interface.SurfaceState

      class SurfaceState extends Object implements Serializable
      serialVersionUID:
      -489331431277320685L

  • Package gov.nih.mipav.view.renderer.WildMagic.Knees

  • Package gov.nih.mipav.view.renderer.WildMagic.Navigation

    • Class gov.nih.mipav.view.renderer.WildMagic.Navigation.NavigationPicker

      class NavigationPicker extends WildMagic.LibGraphics.Collision.Picker implements Serializable
      serialVersionUID:
      -9171618026409224678L

      • Serialized Fields

        • m_fTMax
          float m_fTMax
        • m_fTMin
          float m_fTMin
        • m_kDirection
          WildMagic.LibFoundation.Mathematics.Vector3f m_kDirection
        • m_kOrigin
          WildMagic.LibFoundation.Mathematics.Vector3f m_kOrigin
        • Records
          Vector<WildMagic.LibGraphics.Collision.PickRecord> Records
          Picking records along the mouse click point.

  • Package gov.nih.mipav.view.renderer.WildMagic.ProstateFramework

  • Package gov.nih.mipav.view.renderer.WildMagic.ProstateFramework.liblinearsvm

  • Package gov.nih.mipav.view.renderer.WildMagic.ProstateFramework.libsvm

  • Package gov.nih.mipav.view.renderer.WildMagic.Render

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.BoundingBoxEffect

      class BoundingBoxEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      7377691694355531644L

      • Serialized Fields

        • background
          WildMagic.LibFoundation.Mathematics.ColorRGB background
        • color
          WildMagic.LibFoundation.Mathematics.ColorRGB color
        • origin
          WildMagic.LibFoundation.Mathematics.Vector3f origin
        • plane
          WildMagic.LibFoundation.Mathematics.Vector3f plane
        • range
          WildMagic.LibFoundation.Mathematics.Vector3f range
        • scale
          WildMagic.LibFoundation.Mathematics.Vector3f scale

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.ImageReduceEffect

      class ImageReduceEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      8646199208619749718L

      • Serialized Fields

        • m_dNumSamples
          double m_dNumSamples

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.ImageRegistrationGPU

      class ImageRegistrationGPU extends WildMagic.LibApplications.OpenGLApplication.JavaApplication3D implements Serializable
      serialVersionUID:
      3444862706603129509L

      • Serialized Fields

        • m_afBracket
          float[] m_afBracket
        • m_afBracketB
          float[] m_afBracketB
        • m_afPt
          float[] m_afPt
        • m_afStartPoint
          float[] m_afStartPoint
        • m_afUnitDirections
          float[] m_afUnitDirections
        • m_akCollapse2D
          VolumeHistogramEffect m_akCollapse2D
        • m_akCollapseColumns
          VolumeHistogramEffect m_akCollapseColumns
        • m_akCollapseRows
          VolumeHistogramEffect m_akCollapseRows
        • m_akImageReduceEntropy
          ImageReduceEffect m_akImageReduceEntropy
        • m_bCalcLineMin
          boolean m_bCalcLineMin
        • m_bCleanUp
          boolean m_bCleanUp
        • m_bDisplay
          boolean m_bDisplay
        • m_bDispose
          boolean m_bDispose
        • m_bDisposeComplete
          boolean m_bDisposeComplete
        • m_bInit
          boolean m_bInit
        • m_bStatus
          boolean m_bStatus
        • m_dHx
          double m_dHx
        • m_dHxy
          double m_dHxy
        • m_dHy
          double m_dHy
        • m_dOverlap
          double m_dOverlap
        • m_fDim
          float m_fDim
        • m_fMinDist
          float m_fMinDist
        • m_fPtLength
          float m_fPtLength
        • m_fRigid
          float m_fRigid
        • m_fUnitTolerance
          float m_fUnitTolerance
        • m_iRenderLoops
          int m_iRenderLoops
        • m_kAlpha
          WildMagic.LibGraphics.Rendering.AlphaState m_kAlpha
        • m_kBracketNewOut
          WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kBracketNewOut
        • m_kBracketOut
          WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kBracketOut
        • m_kBracketPoints
          WildMagic.LibGraphics.SceneGraph.Polypoint m_kBracketPoints
        • m_kCalcTransform
          LineMinimizationEffect m_kCalcTransform
        • m_kEntropyOut
          WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kEntropyOut
        • m_kEntropyPoints2D
          WildMagic.LibGraphics.SceneGraph.Polypoint m_kEntropyPoints2D
        • m_kFrame
          JFrame m_kFrame
        • m_kFromOrigin
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kFromOrigin
        • m_kFromOriginInv
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kFromOriginInv
        • m_kHistogramOutput
          WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kHistogramOutput
        • m_kHistogramOutputB
          WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kHistogramOutputB
        • m_kHistogramPoints2D
          WildMagic.LibGraphics.SceneGraph.Polypoint m_kHistogramPoints2D
        • m_kImageA
          ModelSimpleImage m_kImageA
        • m_kImageB
          ModelSimpleImage m_kImageB
        • m_kImageEffectDual
          VolumeHistogramEffect m_kImageEffectDual
        • m_kImageLineMinDual
          LineMinimizationEffect m_kImageLineMinDual
        • m_kImageLineMinPass2a
          LineMinimizationEffect m_kImageLineMinPass2a
        • m_kImagePointsDual
          WildMagic.LibGraphics.SceneGraph.Polypoint m_kImagePointsDual
        • m_kImageTransform
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kImageTransform
        • m_kImageTransformd
          WildMagic.LibFoundation.Mathematics.Matrix4d m_kImageTransformd
        • m_kMoving
          ModelSimpleImage m_kMoving
        • m_kNameA
          String m_kNameA
        • m_kNameB
          String m_kNameB
        • m_kTarget
          ModelSimpleImage m_kTarget
        • m_kTextureA
          WildMagic.LibGraphics.Rendering.Texture m_kTextureA
        • m_kTextureB
          WildMagic.LibGraphics.Rendering.Texture m_kTextureB
        • m_kToOrigin
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kToOrigin
        • m_kToOriginInv
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kToOriginInv
        • m_kTransformOut
          WildMagic.LibRenderers.OpenGLRenderer.OpenGLFrameBuffer m_kTransformOut
        • m_kTransformPoints
          WildMagic.LibGraphics.SceneGraph.Polypoint m_kTransformPoints

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.LineMinimizationEffect

      class LineMinimizationEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      7303288656271198298L

      • Serialized Fields

        • m_afPt
          float[] m_afPt
        • m_afStartPoint
          float[] m_afStartPoint
        • m_afUnitDirections
          float[] m_afUnitDirections
        • m_aiExtents
          int[] m_aiExtents
        • m_dNumSamples
          float m_dNumSamples
        • m_fDim
          float m_fDim
        • m_fMin1
          float m_fMin1
        • m_fMin2
          float m_fMin2
        • m_fMinDist
          float m_fMinDist
        • m_fPtLength
          float m_fPtLength
        • m_fRigid
          float m_fRigid
        • m_fScale1
          float m_fScale1
        • m_fScale2
          float m_fScale2
        • m_fUnitTolerance
          float m_fUnitTolerance
        • m_iHeight
          int m_iHeight
        • m_iWidth
          int m_iWidth
        • m_kFromOrigin
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kFromOrigin
        • m_kToOrigin
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kToOrigin

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MipavLightingEffect

      class MipavLightingEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      4315576697840371407L

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.OrderIndpTransparencyEffect

      class OrderIndpTransparencyEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      -1254697242675646161L

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.PolylineVector

      class PolylineVector extends Vector<WildMagic.LibGraphics.SceneGraph.Polyline> implements Serializable
      serialVersionUID:
      -7579112007899203250L

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.ScaledTextureEffect

      class ScaledTextureEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      -2514458768937685922L

      • Serialized Fields

        • m_fScale
          float m_fScale

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.SurfaceClipEffect

      class SurfaceClipEffect extends VolumeClipEffect implements Serializable
      serialVersionUID:
      8502686732859951115L

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.SurfaceExtractImage

      class SurfaceExtractImage extends WildMagic.LibGraphics.Rendering.GraphicsImage implements Serializable
      serialVersionUID:
      -8778385831984000534L

      • Serialized Fields

        • Data
          int[] Data
        • Max
          int Max
        • Min
          int Min
        • TriTable
          Vector<int[]> TriTable

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.SurfaceLightingEffect

      class SurfaceLightingEffect extends VolumeClipEffect implements Serializable
      serialVersionUID:
      5100923838093263591L

      • Serialized Fields

        • m_bPerPixelLighting
          boolean m_bPerPixelLighting
        • m_bUseNewImage
          boolean m_bUseNewImage
        • m_bUseNewLUT
          boolean m_bUseNewLUT
        • m_fBlend
          float m_fBlend
        • m_iReverseFace
          int m_iReverseFace
        • m_kColorMapNew
          WildMagic.LibGraphics.Rendering.GraphicsImage m_kColorMapNew
        • m_kImageNew
          ModelImage m_kImageNew
        • m_kLUTNew
          ModelStorageBase m_kLUTNew
        • m_kPPixelLighting
          WildMagic.LibGraphics.Shaders.PixelShader m_kPPixelLighting
        • m_kPVertexLighting
          WildMagic.LibGraphics.Shaders.PixelShader m_kPVertexLighting
        • m_kVolumeImage
          VolumeImage m_kVolumeImage
        • m_kVolumeImageNew
          WildMagic.LibGraphics.Rendering.GraphicsImage m_kVolumeImageNew
        • m_kVolumeLUTNew
          WildMagic.LibGraphics.Rendering.Texture m_kVolumeLUTNew
        • m_kVolumeTextureNew
          WildMagic.LibGraphics.Rendering.Texture m_kVolumeTextureNew
        • m_kVPixelLighting
          WildMagic.LibGraphics.Shaders.VertexShader m_kVPixelLighting
        • m_kVVertexLighting
          WildMagic.LibGraphics.Shaders.VertexShader m_kVVertexLighting

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.SurfaceMaterialDisplay

      class SurfaceMaterialDisplay extends WildMagic.LibApplications.OpenGLApplication.JavaApplication3D implements Serializable
      serialVersionUID:
      1567185245264397021L

      • Serialized Fields

        • m_akLights
          WildMagic.LibGraphics.Rendering.Light[] m_akLights
        • m_bInit
          boolean m_bInit
        • m_bMain
          boolean m_bMain
        • m_kCuller
          WildMagic.LibGraphics.SceneGraph.Culler m_kCuller
        • m_kLightShader
          MipavLightingEffect m_kLightShader
        • m_pkMaterial
          WildMagic.LibGraphics.Rendering.MaterialState m_pkMaterial
        • m_spkScene
          WildMagic.LibGraphics.SceneGraph.Node m_spkScene
        • m_spkSphere
          WildMagic.LibGraphics.SceneGraph.TriMesh m_spkSphere

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeCalcEffect

      class VolumeCalcEffect extends VolumeClipEffect implements Serializable
      serialVersionUID:
      -4844378132828150930L

      • Serialized Fields

        • m_afMinMax
          float[] m_afMinMax
          stores the gradient magnitude filter on/off value:
        • m_bIsColor
          boolean m_bIsColor
          When true the volume data is color.

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeClipEffect

      class VolumeClipEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      -833857381096103948L

      • Serialized Fields

        • m_aafClipData
          float[][] m_aafClipData
          stores t=clip plane information:
        • m_afClipAll
          boolean[] m_afClipAll
          Turn clipping on/off per-axis aligned clip plane, eye-clip planes and arbitrary plane.
        • m_afClipOBBAxis0
          float[] m_afClipOBBAxis0
        • m_afClipOBBAxis1
          float[] m_afClipOBBAxis1
        • m_afClipOBBAxis2
          float[] m_afClipOBBAxis2
        • m_afClipOBBExtent
          float[] m_afClipOBBExtent
        • m_afClipSphereCenter
          float[] m_afClipSphereCenter
        • m_afClipSphereScale
          float[] m_afClipSphereScale
        • m_afDoClip
          float[] m_afDoClip
          Turn clipping on/off.
        • m_afVolumeMatrix
          float[] m_afVolumeMatrix
        • m_bClipOBB
          boolean m_bClipOBB
        • m_bClipSphere
          boolean m_bClipSphere

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeHistogramEffect

      class VolumeHistogramEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      547439954218104278L

      • Serialized Fields

        • m_aiExtents
          int[] m_aiExtents
        • m_fMin1
          float m_fMin1
        • m_fMin2
          float m_fMin2
        • m_fScale1
          float m_fScale1
        • m_fScale2
          float m_fScale2
        • m_fUseZSlice
          float m_fUseZSlice
        • m_fZSlice
          float m_fZSlice
        • m_iHeight
          int m_iHeight
        • m_iWidth
          int m_iWidth
        • m_kImageTransform
          WildMagic.LibFoundation.Mathematics.Matrix4f m_kImageTransform
        • m_kImageTransformd
          WildMagic.LibFoundation.Mathematics.Matrix4d m_kImageTransformd

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeImage

      class VolumeImage extends Object implements Serializable
      serialVersionUID:
      -7254697711265907746L

      • Serialization Methods

      • Serialized Fields

        • m_akGradientMagMinMax
          WildMagic.LibFoundation.Mathematics.Vector2f[] m_akGradientMagMinMax
          3D sub-images (4D data)
        • m_akHistoTCoord
          WildMagic.LibFoundation.Mathematics.Vector2f[] m_akHistoTCoord
          Texture coordinates for displaying histogram in 2D
        • m_bGMInit
          boolean m_bGMInit
          Set to true if the Gradient Magnitude texture map has been initialized.
        • m_bHistoInit
          boolean m_bHistoInit
          Set to true when the multi-histogram histogram texture has been initialized.
        • m_bNormalsInit
          boolean m_bNormalsInit
          Set to true if the Normal Map has been initialized.
        • m_fDRRNormalize
          float m_fDRRNormalize
        • m_fMax
          float m_fMax
          Image scale factors for display in 3D
        • m_fX
          float m_fX
          Image scale factors for display in 3D
        • m_fY
          float m_fY
          Image scale factors for display in 3D
        • m_fZ
          float m_fZ
          Image scale factors for display in 3D
        • m_iMaxExtent
          int m_iMaxExtent
        • m_iTimeSlice
          int m_iTimeSlice
          Current position in time (4D data)
        • m_iTimeSteps
          int m_iTimeSteps
          Total number of time-slices (4D data)
        • m_kColorMap
          WildMagic.LibGraphics.Rendering.GraphicsImage m_kColorMap
          Data storage for color map:
        • m_kColorMapTarget
          WildMagic.LibGraphics.Rendering.Texture m_kColorMapTarget
          Texture object for color map:
        • m_kDir
          String m_kDir
          Directory for calculated images
        • m_kHisto
          WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kHisto
          Histogram data for multi-histogram interface
        • m_kHistoTarget
          WildMagic.LibGraphics.Rendering.Texture m_kHistoTarget
          Texture object for data:
        • m_kImage
          ModelImage m_kImage
          Reference to ModelImage image
        • m_kImageGM
          ModelImage m_kImageGM
        • m_kLUT
          ModelLUT m_kLUT
          ModelLUT
        • m_kNormal
          WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kNormal
          Data storage for normals:
        • m_kNormalMapTarget
          WildMagic.LibGraphics.Rendering.Texture m_kNormalMapTarget
          Texture object for normal map:
        • m_kOpacityMap_GM
          WildMagic.LibGraphics.Rendering.GraphicsImage m_kOpacityMap_GM
          GraphicsImage contains GM opacity transfer function data:
        • m_kOpacityMapTarget_GM
          WildMagic.LibGraphics.Rendering.Texture m_kOpacityMapTarget_GM
          Texture contains texture filter modes and GraphicsImage for opacity transfer function:
        • m_kPostfix
          String m_kPostfix
          Image name post-fix typically either 'A' or 'B'
        • m_kRGBT
          ModelRGB m_kRGBT
          ModelRGB
        • m_kScratchTarget
          WildMagic.LibGraphics.Rendering.Texture m_kScratchTarget
          Texture object for GPU computations:
        • m_kSurfaceImage
          WildMagic.LibGraphics.Rendering.GraphicsImage m_kSurfaceImage
          Data storage for surfaces:
        • m_kSurfaceTarget
          WildMagic.LibGraphics.Rendering.Texture m_kSurfaceTarget
          Texture object for surfaces:
        • m_kVolume
          WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kVolume
          Data storage for volume:
        • m_kVolumeGM
          WildMagic.LibGraphics.Rendering.GraphicsImage[] m_kVolumeGM
          Data storage for volume gradient magnitude:
        • m_kVolumeGMTarget
          WildMagic.LibGraphics.Rendering.Texture m_kVolumeGMTarget
          Texture object for volume gradient magnitude data:
        • m_kVolumeTarget
          WildMagic.LibGraphics.Rendering.Texture m_kVolumeTarget
          Texture object for data:
        • opacityTransferFn
          TransferFunction opacityTransferFn
        • surfaceColor
          Vector<WildMagic.LibFoundation.Mathematics.ColorRGB> surfaceColor
          A vector of BitSet masks, one for each surface loaded into the viewer.
        • surfaceMask
          Vector<BitSet> surfaceMask
          A vector of BitSet masks, one for each surface loaded into the viewer.
        • surfaceNames
          Vector<String> surfaceNames
          A vector of the mask names, so they can be accessed by name:

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeImageCrop

      class VolumeImageCrop extends VolumeImageViewer implements Serializable
      serialVersionUID:
      -3884075404385493867L

      • Serialized Fields

        • m_kClipEffect
          VolumeClipEffect m_kClipEffect
        • m_kVolumeViewMatrix
          float[] m_kVolumeViewMatrix

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeImageExtract

      class VolumeImageExtract extends VolumeImageViewer implements Serializable
      serialVersionUID:
      5118167091752659025L

      • Serialized Fields

        • m_afNewResolutions
          float[] m_afNewResolutions
        • m_aiNewExtents
          int[] m_aiNewExtents
        • m_bDisplayFirst
          boolean m_bDisplayFirst
        • m_bDisplaySecond
          boolean m_bDisplaySecond
        • m_iExtractLevel
          int m_iExtractLevel
          Intensity level for GPU-surface extraction.
        • m_kCalcImage
          WildMagic.LibGraphics.Rendering.GraphicsImage m_kCalcImage
        • m_kCalcImage2
          SurfaceExtractImage m_kCalcImage2
        • m_kClipEffect
          VolumeClipEffect m_kClipEffect
        • m_pkVolumeCalcTarget
          WildMagic.LibGraphics.Rendering.Texture m_pkVolumeCalcTarget
        • m_pkVolumeCalcTarget2
          WildMagic.LibGraphics.Rendering.Texture m_pkVolumeCalcTarget2
        • m_spkEffect2
          VolumeCalcEffect m_spkEffect2

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeImageSurfaceMask

      class VolumeImageSurfaceMask extends VolumeImageViewer implements Serializable
      serialVersionUID:
      -6880453836501887284L

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeImageViewer

      class VolumeImageViewer extends WildMagic.LibApplications.OpenGLApplication.JavaApplication3D implements Serializable
      serialVersionUID:
      -2042201391319899982L

      • Serialized Fields

        • dpiScale
          double dpiScale
        • elapsedTime
          double elapsedTime
          Elapsed time (in milliseconds) -- time it took for algorithm to run.
        • m_bDisplay
          boolean m_bDisplay
        • m_bDispose
          boolean m_bDispose
        • m_bInit
          boolean m_bInit
        • m_iSlice
          int m_iSlice
        • m_kAnimator
          com.jogamp.opengl.util.Animator m_kAnimator
        • m_kCull
          WildMagic.LibGraphics.Rendering.CullState m_kCull
        • m_kCuller
          WildMagic.LibGraphics.SceneGraph.Culler m_kCuller
        • m_kFrame
          Frame m_kFrame
        • m_kParent
          VolumeTriPlanarInterface m_kParent
        • m_kVolumeImage
          VolumeImage m_kVolumeImage
        • m_pkPlane
          WildMagic.LibGraphics.SceneGraph.TriMesh m_pkPlane
        • m_spkEffect
          WildMagic.LibGraphics.Effects.ShaderEffect m_spkEffect
        • m_spkScene
          WildMagic.LibGraphics.SceneGraph.Node m_spkScene
        • startTime
          long startTime

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumePlaneEffect

      class VolumePlaneEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      -5399442879177045664L

      • Serialized Fields

        • m_bShowSurface
          boolean m_bShowSurface
        • m_bTransparent
          boolean m_bTransparent
        • m_fBlend
          float m_fBlend
        • m_kPShader
          WildMagic.LibGraphics.Shaders.PixelShader m_kPShader
        • m_kVolumeImageA
          VolumeImage m_kVolumeImageA
          Shared volume data and textures.
        • m_kVolumeImageB
          VolumeImage m_kVolumeImageB
          Shared volume data and textures.
        • rgbA
          ModelRGB rgbA
        • rgbB
          ModelRGB rgbB

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumePreRenderEffect

      class VolumePreRenderEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      -9019623746108147953L

      • Serialized Fields

        • m_kPos
          WildMagic.LibFoundation.Mathematics.Vector3f m_kPos

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeShaderEffectMultiPass

      class VolumeShaderEffectMultiPass extends VolumeClipEffect implements Serializable
      serialVersionUID:
      5580825290512790813L

      • Serialized Fields

        • m_aafLight
          float[][] m_aafLight
        • m_afABBlendParam
          float[] m_afABBlendParam
        • m_afBlendParam
          float[] m_afBlendParam
        • m_akLevWidget
          ClassificationWidgetState[] m_akLevWidget
        • m_bGradientMag
          boolean m_bGradientMag
        • m_bMultiHisto
          boolean m_bMultiHisto
        • m_fMaxLength
          float m_fMaxLength
        • m_fSamples
          float m_fSamples
        • m_iBlend
          int m_iBlend
        • m_iDstBlend
          int m_iDstBlend
        • m_iPasses
          int m_iPasses
        • m_iSrcBlend
          int m_iSrcBlend
        • m_iUsedWidgets
          int m_iUsedWidgets
        • m_iWhichShader
          int m_iWhichShader
          Indicates which shader to use (MIP, DDR, CMP, SUR, CMP_SUR, MULTIHISTO):
        • m_kBlendColor
          WildMagic.LibFoundation.Mathematics.ColorRGBA m_kBlendColor
        • m_kPShaderCMP
          WildMagic.LibGraphics.Shaders.PixelShader m_kPShaderCMP
          PixelShader program and data for Composite mode:
        • m_kRGBT
          ModelRGB m_kRGBT
        • m_kSceneTarget
          WildMagic.LibGraphics.Rendering.Texture m_kSceneTarget
          Reference to the SceneImage texture:
        • m_kVolumeImageA
          VolumeImage m_kVolumeImageA
          Shared volume data and textures.
        • m_kVolumeImageB
          VolumeImage m_kVolumeImageB
          Shared volume data and textures.
        • m_pkVShader
          WildMagic.LibGraphics.Shaders.VertexShader m_pkVShader

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeShaderEffectMultiPassDynamic

      class VolumeShaderEffectMultiPassDynamic extends VolumeShaderEffectMultiPass implements Serializable
      serialVersionUID:
      -4552046274082477860L

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VolumeVOIEffect

      class VolumeVOIEffect extends WildMagic.LibGraphics.Effects.ShaderEffect implements Serializable
      serialVersionUID:
      8243388938991470076L

      • Serialized Fields

        • minRange
          float minRange

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.VSEMD_MultipleImages

      class VSEMD_MultipleImages extends VolumeShaderEffectMultiPass implements Serializable
      serialVersionUID:
      -4552046274082477860L

      • Serialized Fields

        • hyperstack
          VolumeImage[] hyperstack
        • hyperstackColormap
          WildMagic.LibGraphics.Rendering.Texture hyperstackColormap
        • imageOn
          boolean[] imageOn
        • lut
          String[] lut

  • Package gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer.CircleClassificationWidget

      class CircleClassificationWidget extends ClassificationWidget implements Serializable
      serialVersionUID:
      -4180814068815939724L

      • Serialization Methods

      • Serialized Fields

        • m_fCenterScale
          float m_fCenterScale
          Distance scale used to position the center sphere control-point out from the center of the circle/ellipse.
        • m_fRadiusX
          float m_fRadiusX
          The radius of the circle in the x-direction.
        • m_fRadiusY
          float m_fRadiusY
          The radius of the circle in the y-direction.
        • m_kCenterDir
          WildMagic.LibFoundation.Mathematics.Vector2f m_kCenterDir
          Direction used to position the center sphere control-point out from the center of the circle/ellipse.

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer.ClassificationWidget

      class ClassificationWidget extends Object implements Serializable
      serialVersionUID:
      8150358952544808439L

      • Serialization Methods

      • Serialized Fields

        • m_iHeight
          int m_iHeight
          Canvas width and height
        • m_iWidth
          int m_iWidth
          Canvas width and height
        • m_kLowerSphere
          WildMagic.LibGraphics.SceneGraph.TriMesh m_kLowerSphere
          The lower-sphere control point of the widget, controls the shape/size of the widget
        • m_kMiddleSphere
          WildMagic.LibGraphics.SceneGraph.TriMesh m_kMiddleSphere
          The middle-sphere control point of the widget, controls the color transfer function inside the widget.
        • m_kMouseOffset
          WildMagic.LibFoundation.Mathematics.Vector2f m_kMouseOffset
          Mouse offset used for dragging the widget. Stored in screen (MouseEvent) coordinates
        • m_kOutline
          WildMagic.LibGraphics.SceneGraph.Polyline m_kOutline
          Polyline outlines the widget in red when selected, or blue when non selected.
        • m_kPicked
          WildMagic.LibGraphics.SceneGraph.Spatial m_kPicked
          Currently picked, or active part of this widget, may be the mesh or one of the control-point spheres. When null no part of this widget is currently active.
        • m_kTMax
          WildMagic.LibFoundation.Mathematics.Vector2f m_kTMax
          Maximum texture coordinates for the 2D histogram. The 2D Histogram is truncated based on a minimum threshold value, so the entire histogram may not be used depending on the data.
        • m_kTMin
          WildMagic.LibFoundation.Mathematics.Vector2f m_kTMin
          Minimum texture coordinates for the 2D histogram. The 2D Histogram is truncated based on a minimum threshold value, so the entire histogram may not be used depending on the data.
        • m_kUpperSphere
          WildMagic.LibGraphics.SceneGraph.TriMesh m_kUpperSphere
          The upper-sphere control point of the widget, controls the shape/size of the widget
        • m_kWidget
          WildMagic.LibGraphics.SceneGraph.Node m_kWidget
          The top-level node containing the widget graphic data structures (triangle meshes and transformations)
        • m_kWidgetEfect
          ClassificationWidgetEffect m_kWidgetEfect
          The shader effect used to render the inside color transfer function of the widget, based on the position of the widget and the position of the middle (green) sphere control-point.
        • m_kWidgetMesh
          WildMagic.LibGraphics.SceneGraph.TriMesh m_kWidgetMesh
          The TriMesh representing the shape of the widget.
        • m_kWidgetState
          ClassificationWidgetState m_kWidgetState
          Shader effect state, for reading from disk:

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer.ClassificationWidgetEffect

      class ClassificationWidgetEffect extends WildMagic.LibGraphics.Effects.TextureEffect implements Serializable
      serialVersionUID:
      3379141203039832123L

      • Serialization Methods

      • Serialized Fields

        • m_kCurrentText
          String m_kCurrentText
          Current GLSL code for the widget program.
        • m_kLUTMap
          WildMagic.LibGraphics.Rendering.Texture m_kLUTMap
          color look-up table Texture:
        • m_kLUTName
          String m_kLUTName
          color look-up table name.
        • m_kTexture
          WildMagic.LibGraphics.Rendering.Texture m_kTexture
          Texture used in the histogram.
        • m_kWidgetState
          ClassificationWidgetState m_kWidgetState
          Current state of the widget encapsulated in the GLSL parameters needed for the Volume renderer GLSL program:
        • mainPixelShader1
          String mainPixelShader1
          First part of the GLSL code for the pixel shader program for all widgets:
        • mainPixelShader2
          String mainPixelShader2
          GLSL main code part 2 for all widget types.
        • mainPixelShaderCircle
          String mainPixelShaderCircle
          GLSL function call for the circle widget:
        • mainPixelShaderSquare
          String mainPixelShaderSquare
          GLSL function call for the square widget:
        • mainPixelShaderTriangle
          String mainPixelShaderTriangle
          GLSL function call for the triangle widget:

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer.ClassificationWidgetState

      class ClassificationWidgetState extends Object implements Serializable
      serialVersionUID:
      711728604033191355L

      • Serialized Fields

        • BoundaryEmphasis
          float[] BoundaryEmphasis
          contribution of the boundary emphasis slider and therefor the contribution of the 2nd derivative of the data.
        • Center
          float[] Center
          Widget Center:
        • Color
          float[] Color
          Default color for the color transfer function is white:
        • InvertLUT
          boolean InvertLUT
        • LeftLine
          float[] LeftLine
          Transfer function left line:
        • MidLine
          float[] MidLine
          Transfer function mid-line:
        • Radius
          float[] Radius
          Transfer function radius:
        • RightLine
          float[] RightLine
          Transfer function right line:
        • Shift
          float[] Shift
          Transfer function shift:
        • Type
          int Type
        • UseColorMap
          float[] UseColorMap
          turns the widget color map on/off in the GLSL shader code.
        • UseWidget
          float[] UseWidget
          turns the widget on/off in the GLSL shader code.
        • XRatio
          float[] XRatio
          Transfer function y-ratios:
        • YRatio
          float[] YRatio
          Transfer function y-ratios:

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer.SquareClassificationWidget

      class SquareClassificationWidget extends ClassificationWidget implements Serializable
      serialVersionUID:
      -4180814068815939724L

      • Serialization Methods

      • Serialized Fields

        • m_fCenterX
          float m_fCenterX
          Current parameterized coordinates for the center control point in X (used to maintain relative position when resizing the widget).
        • m_fCenterY
          float m_fCenterY
          Current parameterized coordinates for the center control point in Y (used to maintain relative position when resizing the widget).

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer.TriangleClassificationWidget

      class TriangleClassificationWidget extends ClassificationWidget implements Serializable
      serialVersionUID:
      -3903003012355432310L

      • Serialization Methods

      • Serialized Fields

        • m_fCenterX
          float m_fCenterX
          Current parameterized coordinates for the center control point in X (used to maintain relative position when resizing the widget).
        • m_fCenterY
          float m_fCenterY
          Current parameterized coordinates for the center control point in Y (used to maintain relative position when resizing the widget).
        • m_kLeftSphere
          WildMagic.LibGraphics.SceneGraph.TriMesh m_kLeftSphere

    • Class gov.nih.mipav.view.renderer.WildMagic.Render.MultiDimensionalTransfer.VolumeImageMultiDimensionalTransfer

      class VolumeImageMultiDimensionalTransfer extends VolumeImageViewer implements Serializable
      serialVersionUID:
      401740242306942355L

      • Serialized Fields

        • container
          JPanel container
          main container for this object:
        • m_akWidgets
          Vector<ClassificationWidget> m_akWidgets
          The list of widgets displayed on the 2D Histogram.
        • m_bAdded
          boolean m_bAdded
          When true a new Widget was added with the mouse.
        • m_bFirstAdded
          boolean m_bFirstAdded
        • m_bPickPending
          boolean m_bPickPending
          When true there is a pending mouse pick to process.
        • m_bUpdateLev
          boolean m_bUpdateLev
        • m_iCurrent
          int m_iCurrent
          The ID of the active and previously active widget.
        • m_iLUTIndex
          int m_iLUTIndex
        • m_iMouseButton
          int m_iMouseButton
          Stores which button was pressed during mouse drag.
        • m_iMouseX
          int m_iMouseX
          Stores the mouse position for picking.
        • m_iMouseY
          int m_iMouseY
          Stores the mouse position for picking.
        • m_iPicked
          int m_iPicked
          The ID of the
        • m_iPrevious
          int m_iPrevious
          The ID of the active and previously active widget.
        • m_kCurrentColor
          WildMagic.LibFoundation.Mathematics.ColorRGBA m_kCurrentColor
          The current color to use to create a new Widget.
        • m_kInterface
          JInterfaceBase m_kInterface
          Reference to the containing JPanel.
        • m_kTMax
          WildMagic.LibFoundation.Mathematics.Vector2f m_kTMax
        • m_kTMin
          WildMagic.LibFoundation.Mathematics.Vector2f m_kTMin
          The bounds on the 2D Histogram texture coordinates used to display the 2D Histogram. The texture coordinates are clamped to show only the portions of the texture that are above a threshold value.
        • m_kWidgetType
          String m_kWidgetType
          Defines the current selected widget type.
        • MAX_WIDGETS
          int MAX_WIDGETS
          The maximum number of widgets that can be added to the display. More can be added, but then the Volume Renderer GLSL program should be changed to add the new widgets.

  • Package gov.nih.mipav.view.renderer.WildMagic.TBI

  • Package gov.nih.mipav.view.renderer.WildMagic.WormUntwisting