Package gov.nih.mipav.model.file

Class FileInfoAfni

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable
    public class FileInfoAfni
extends FileInfoBase
    This structures contains the information that describes how an Afni image is stored on disk.
    See Also:
    FileAfni, Serialized Form

    • Field Detail

      • serialVersionUID

        private static final long serialVersionUID
        Use serialVersionUID for interoperability.
        See Also:
        Constant Field Values

      • HEAD_ANAT_TYPE

        public static final int HEAD_ANAT_TYPE
        AFNI typeString head anatomical.
        See Also:
        Constant Field Values

      • HEAD_FUNC_TYPE

        public static final int HEAD_FUNC_TYPE
        AFNI typeString head functional.
        See Also:
        Constant Field Values

      • GEN_ANAT_TYPE

        public static final int GEN_ANAT_TYPE
        AFNI typeString general anatomical.
        See Also:
        Constant Field Values

      • GEN_FUNC_TYPE

        public static final int GEN_FUNC_TYPE
        AFNI typeString general functional.
        See Also:
        Constant Field Values

      • ANAT_SPGR_TYPE

        public static final int ANAT_SPGR_TYPE
        funcType for anatType == true.

        At this time, Anat codes 0..10 are treated identically by all AFNI programs. Code 11 marks the dataset as a "bucket" type, which is treated differently in the display; a chooser allows you to specify which sub-brick from the bucket should be used to make the underlay image.

        See Also:
        Constant Field Values

      • acquisitionDuration

        private float acquisitionDuration
        DOCUMENT ME!

      • AFNIOrigExtents

        private int[] AFNIOrigExtents
        DOCUMENT ME!

      • AFNIOrigResolutions

        private float[] AFNIOrigResolutions
        DOCUMENT ME!

      • AFNITypeString

        private int AFNITypeString
        DOCUMENT ME!

      • AFNIViewType

        private int AFNIViewType
        DOCUMENT ME!

      • alpha

        private WildMagic.LibFoundation.Mathematics.Vector3f alpha
        DOCUMENT ME!

      • alphaArray

        private WildMagic.LibFoundation.Mathematics.Vector3f[] alphaArray
        arrays of 12 values used for Talairach conversions.

      • anotherPt

        private WildMagic.LibFoundation.Mathematics.Vector3f anotherPt
        DOCUMENT ME!

      • anteriorPt

        private WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt
        markers used for +ACPC to +tlrc transformation.

      • beta

        private WildMagic.LibFoundation.Mathematics.Vector3f beta
        DOCUMENT ME!

      • betaArray

        private WildMagic.LibFoundation.Mathematics.Vector3f[] betaArray
        DOCUMENT ME!

      • botX

        private int[] botX
        DOCUMENT ME!

      • botY

        private int[] botY
        DOCUMENT ME!

      • botZ

        private int[] botZ
        DOCUMENT ME!

      • brickLabsString

        private java.lang.String[] brickLabsString
        Name for each sub-brick

      • brickStatAux

        private float[] brickStatAux
        DOCUMENT ME!

      • datasetName

        private java.lang.String datasetName
        DOCUMENT ME!

      • firstPt

        private WildMagic.LibFoundation.Mathematics.Vector3f firstPt
        DOCUMENT ME!

      • funcType

        private int funcType
        DOCUMENT ME!

      • gamma

        private WildMagic.LibFoundation.Mathematics.Vector3f gamma
        DOCUMENT ME!

      • gammaArray

        private WildMagic.LibFoundation.Mathematics.Vector3f[] gammaArray
        DOCUMENT ME!

      • gapArray

        private int[] gapArray
        If planeGap is not -1, then gapArray contains the values at which zero filling gaps are present.

      • highXmm

        private float highXmm
        DOCUMENT ME!

      • highYmm

        private float highYmm
        DOCUMENT ME!

      • highZmm

        private float highZmm
        DOCUMENT ME!

      • idcodeDate

        private java.lang.String idcodeDate
        DOCUMENT ME!

      • idcodeString

        private java.lang.String idcodeString
        DOCUMENT ME!

      • inferiorEdge

        private WildMagic.LibFoundation.Mathematics.Vector3f inferiorEdge
        DOCUMENT ME!

      • inferiorPt

        private WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt
        DOCUMENT ME!

      • isDicom

        private boolean isDicom
        DOCUMENT ME!

      • label1

        private java.lang.String label1
        DOCUMENT ME!

      • label2

        private java.lang.String label2
        DOCUMENT ME!

      • leftPt

        private WildMagic.LibFoundation.Mathematics.Vector3f leftPt
        DOCUMENT ME!

      • lowXmm

        private float lowXmm
        DOCUMENT ME!

      • lowYmm

        private float lowYmm
        DOCUMENT ME!

      • lowZmm

        private float lowZmm
        DOCUMENT ME!

      • marksFlag

        private int marksFlag
        DOCUMENT ME!

      • marksFlags

        private int marksFlags
        DOCUMENT ME!

      • noteDate001

        private java.lang.String noteDate001
        DOCUMENT ME!

      • noteDate002

        private java.lang.String noteDate002
        DOCUMENT ME!

      • noteDate003

        private java.lang.String noteDate003
        DOCUMENT ME!

      • noteDate004

        private java.lang.String noteDate004
        DOCUMENT ME!

      • noteDate005

        private java.lang.String noteDate005
        DOCUMENT ME!

      • noteNumber001

        private java.lang.String noteNumber001
        DOCUMENT ME!

      • noteNumber002

        private java.lang.String noteNumber002
        DOCUMENT ME!

      • noteNumber003

        private java.lang.String noteNumber003
        DOCUMENT ME!

      • noteNumber004

        private java.lang.String noteNumber004
        DOCUMENT ME!

      • noteNumber005

        private java.lang.String noteNumber005
        DOCUMENT ME!

      • origDicom

        private boolean origDicom
        DOCUMENT ME!

      • OriginalPosteriorMargin

        private WildMagic.LibFoundation.Mathematics.Vector3f OriginalPosteriorMargin
        DOCUMENT ME!

      • OriginalSuperiorEdge

        private WildMagic.LibFoundation.Mathematics.Vector3f OriginalSuperiorEdge
        DOCUMENT ME!

      • pcie

        private WildMagic.LibFoundation.Mathematics.Vector3f pcie
        The posterior commisure inferior edge. pcie is the coordinated transformed inferiorEdge

      • planeGap

        private 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

        private WildMagic.LibFoundation.Mathematics.Vector3f posteriorMargin
        DOCUMENT ME!

      • posteriorPt

        private WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt
        DOCUMENT ME!

      • rightPt

        private WildMagic.LibFoundation.Mathematics.Vector3f rightPt
        DOCUMENT ME!

      • rr

        private WildMagic.LibFoundation.Mathematics.Vector3f rr
        rr is the dicom ordered original image Talairach center location.

      • rrArray

        private WildMagic.LibFoundation.Mathematics.Vector3f[] rrArray
        DOCUMENT ME!

      • slicesWithTimeOffsets

        private int slicesWithTimeOffsets
        DOCUMENT ME!

      • statAux

        private float[] statAux
        DOCUMENT ME!

      • subBrickNumber

        private int subBrickNumber
        Specifies sub-brick that this file-info belongs to

      • superiorEdge

        private WildMagic.LibFoundation.Mathematics.Vector3f superiorEdge
        markers used for +orig to +ACPC transformation.

      • superiorPt

        private WildMagic.LibFoundation.Mathematics.Vector3f superiorPt
        DOCUMENT ME!

      • TalairachCenter

        private WildMagic.LibFoundation.Mathematics.Vector3f TalairachCenter
        DOCUMENT ME!

      • tAxisOffsets

        private float[] tAxisOffsets
        If TAXIS_NUMS[1] > 0, then this array gives the time offsets of the

      • timeOrigin

        private float timeOrigin
        DOCUMENT ME!

      • timeStep

        private float timeStep
        DOCUMENT ME!

      • topX

        private int[] topX
        DOCUMENT ME!

      • topY

        private int[] topY
        DOCUMENT ME!

      • topZ

        private int[] topZ
        DOCUMENT ME!

      • translation

        private WildMagic.LibFoundation.Mathematics.Vector3f translation
        DOCUMENT ME!

      • zAxisOffset

        private float zAxisOffset
        DOCUMENT ME!

      • zAxisStep

        private float zAxisStep
        DOCUMENT ME!

    • Constructor Detail

      • FileInfoAfni

        public FileInfoAfni​(java.lang.String name,
                    java.lang.String directory,
                    int format)
        File info storage constructor.
        Parameters:
        name - file name
        directory - directory
        format - file format

    • Method Detail

      • displayAboutInfo

        public void displayAboutInfo​(JDialogBase dlog,
                             TransMatrix matrix)
        Displays the file information.
        Specified by:
        displayAboutInfo in class FileInfoBase
        Parameters:
        dlog - dialog box that is written to
        matrix - transformation matrix

      • getAFNIOrigExtents

        public int[] getAFNIOrigExtents()
        Returns the dimensions of the dicom ordered +orig AFNI image.
        Returns:
        the array contain dicom ordered +orig image dimensions

      • getAFNIOrigResolutions

        public float[] getAFNIOrigResolutions()
        Return the resolutions of the dicom ordered +orig AFNI image return the array containing the dicom ordered +orig image resolutions.
        Returns:
        DOCUMENT ME!

      • getAFNITypeString

        public int getAFNITypeString()
        Returns integer telling if file is AFNI HEAD_ANAT_TYPE, HEAD_FUNC_TYPE, GEN_ANAT_TYPE, or GEN_FUNC_TYPE.
        Returns:
        returns AFNITypeString

      • getAFNIViewType

        public int getAFNIViewType()
        Returns integer telling if file is AFNI +orig, +acpc, or +tlrc.
        Returns:
        returns AFNIViewType

      • getAlpha

        public WildMagic.LibFoundation.Mathematics.Vector3f getAlpha()
        Returns T00, T01, and T02 in the transformation matrix.
        Returns:
        returns alpha

      • getAlphaArray

        public WildMagic.LibFoundation.Mathematics.Vector3f[] getAlphaArray()
        Returns array of T00, T01, and T02 in the transformation matrix.
        Returns:
        returns alphaArray

      • getAnotherPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getAnotherPt()
        Returns another mid-sag marker point for +orig to +acpc transformation in dataset ordering.
        Returns:
        returns marker point

      • getAnteriorPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getAnteriorPt()
        Returns most anterior point marker for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns marker point

      • getBeta

        public WildMagic.LibFoundation.Mathematics.Vector3f getBeta()
        Returns T10, T11, and T12 in the transformation matrix.
        Returns:
        returns beta

      • getBetaArray

        public WildMagic.LibFoundation.Mathematics.Vector3f[] getBetaArray()
        Returns array of T10, T11, and T12 in the transformation matrix.
        Returns:
        returns betaArray

      • getBotX

        public int[] getBotX()
        Returns array of bottom X boundaries for conversion to Talairach space.
        Returns:
        returns botX

      • getBotY

        public int[] getBotY()
        Returns array of bottom Y boundaries for conversion to Talairach space.
        Returns:
        returns botY

      • getBotZ

        public int[] getBotZ()
        Returns array of bottom Z boundaries for conversion to Talairach space.
        Returns:
        returns botZ

      • getBrickLabsString

        public java.lang.String[] getBrickLabsString()
        Returns the brick labs string for identifying sub-bricks.

      • getFirstPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getFirstPt()
        Returns first mid-sag point marker point for +orig to +acpc transformation in dataset ordering.
        Returns:
        returns marker point

      • getFuncType

        public int getFuncType()
        Gets the function type.
        Returns:
        funcType

      • getGamma

        public WildMagic.LibFoundation.Mathematics.Vector3f getGamma()
        Returns T20, T21, and T22 in the transformation matrix.
        Returns:
        returns gamma

      • getGammaArray

        public WildMagic.LibFoundation.Mathematics.Vector3f[] getGammaArray()
        Returns array of T20, T21, and T22 in the transformation matrix.
        Returns:
        returns gammaArray

      • getGapArray

        public int[] getGapArray()
        Returns array of coordinate values at which gap is present.
        Returns:
        returns gapArray

      • getHighXmm

        public float getHighXmm()
        Returns the highest x location in millimeters.
        Returns:
        highest x location in millimeters

      • getHighYmm

        public float getHighYmm()
        Returns the highest y location in millimeters.
        Returns:
        highest y location in millimeters

      • getHighZmm

        public float getHighZmm()
        Returns the highest z location in millimeters.
        Returns:
        highest z location in millimeters

      • getInferiorEdge

        public WildMagic.LibFoundation.Mathematics.Vector3f getInferiorEdge()
        Returns PC inferior edge marker point for +orig to +acpc transformation in dataset ordering.
        Returns:
        returns marker point

      • getInferiorPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getInferiorPt()
        Returns most inferior point marker for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns marker point

      • getLeftPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getLeftPt()
        Returns most left point marker for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns marker point

      • getLowXmm

        public float getLowXmm()
        Returns the lowest x location in millimeters.
        Returns:
        lowest x location in millimeters

      • getLowYmm

        public float getLowYmm()
        Returns the lowest Y location in millimeters.
        Returns:
        lowest Y location in millimeters

      • getLowZmm

        public float getLowZmm()
        Returns the lowest Z location in millimeters.
        Returns:
        lowest Z location in millimeters

      • getMarksFlag

        public int getMarksFlag()
        DOCUMENT ME!
        Returns:
        marksFlag

      • getMarksFlags

        public int getMarksFlags()
        DOCUMENT ME!
        Returns:
        marksFlags

      • getOriginalPosteriorMargin

        public WildMagic.LibFoundation.Mathematics.Vector3f getOriginalPosteriorMargin()
        Returns AC posterior margin marker point for +orig to +acpc transformation in dicom ordering using numbers not adjusted for resolution and origin.
        Returns:
        returns marker point

      • getOriginalSuperiorEdge

        public WildMagic.LibFoundation.Mathematics.Vector3f getOriginalSuperiorEdge()
        Returns AC superior edge marker point for +orig to +acpc transformation in dicom ordering using numbers not adjusted for resolution and origin.
        Returns:
        returns marker point

      • getpcie

        public WildMagic.LibFoundation.Mathematics.Vector3f getpcie()
        Returns posterior commissure inferior edge for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns marker point

      • getPlaneGap

        public int getPlaneGap()
        Returns -1 if no plane gap is present, 0 = x gap, 1 = y gap, 2 = z gap.
        Returns:
        returns planeGap

      • getPosteriorMargin

        public WildMagic.LibFoundation.Mathematics.Vector3f getPosteriorMargin()
        Returns AC posterior margin marker point for +orig to +acpc transformation in dataset ordering.
        Returns:
        returns marker point

      • getPosteriorPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getPosteriorPt()
        Returns most posterior point marker for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns marker point

      • getRightPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getRightPt()
        Returns most right point marker for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns marker point

      • getrr

        public WildMagic.LibFoundation.Mathematics.Vector3f getrr()
        Returns the location of the Talairach center in the dicom order +orig anatomical image in voxel indices.
        Returns:
        returns rr

      • getrrArray

        public WildMagic.LibFoundation.Mathematics.Vector3f[] getrrArray()
        Returns array of the location of the Talairach center in the dicom order +orig anatomical image in voxel indices.
        Returns:
        returns rrArray

      • getSlicesWithTimeOffsets

        public int getSlicesWithTimeOffsets()
        Gets slicesWithTimeOffsets.
        Returns:
        slicesWithTimeOffsets

      • getSuperiorEdge

        public WildMagic.LibFoundation.Mathematics.Vector3f getSuperiorEdge()
        Returns AC superior edge marker point for +orig to +acpc transformation in dataset ordering.
        Returns:
        returns marker point

      • getSuperiorPt

        public WildMagic.LibFoundation.Mathematics.Vector3f getSuperiorPt()
        Returns most superior point marker for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns marker point

      • getTalairachCenter

        public WildMagic.LibFoundation.Mathematics.Vector3f getTalairachCenter()
        Returns Talairach center for +acpc to +tlrc transformation in dicom ordering.
        Returns:
        returns TalairachCenter

      • getTAxisOffsets

        public float[] getTAxisOffsets()
        Gets time axis offsets.
        Returns:
        tAxisOffsets

      • getTimeStep

        public float getTimeStep()
        Gets timeStep.
        Returns:
        timeStep

      • getTopX

        public int[] getTopX()
        Returns array of top X boundaries for conversion to Talairach space.
        Returns:
        returns topX

      • getTopY

        public int[] getTopY()
        Returns array of top Y boundaries for conversion to Talairach space.
        Returns:
        returns topY

      • getTopZ

        public int[] getTopZ()
        Returns array of top Z boundaries for conversion to Talairach space.
        Returns:
        returns topZ

      • getTranslation

        public WildMagic.LibFoundation.Mathematics.Vector3f getTranslation()
        Returns T03, T13, and T23 in the transformationmatrix.
        Returns:
        returns translation

      • setAcquisitionDuration

        public void setAcquisitionDuration​(float acquisitionDuration)
        Sets acquisition duration.
        Parameters:
        acquisitionDuration - Value to set.

      • setAFNIOrigExtents

        public void setAFNIOrigExtents​(int[] extents)
        Sets the dimensions of the dicom ordered +orig image.
        Parameters:
        extents - the array with dimensions of the dicom ordered +orig image

      • setAFNIOrigResolutions

        public void setAFNIOrigResolutions​(float[] resolutions)
        Sets the resolutions of the dicom ordered +orig image.
        Parameters:
        resolutions - the array with resolutions of the dicom ordered +orig image

      • setAFNITypeString

        public void setAFNITypeString​(int AFNITypeString)
        Sets the AFNITypeString to HEAD_ANAT_TYPE, HEAD_FUNC_TYPE, GEN_ANAT_TYPE, or GEN_FUNC_TYPE.
        Parameters:
        AFNITypeString - The type.

      • setAFNIViewType

        public void setAFNIViewType​(int AFNIViewType)
        Sets the AFNIViewType to AFNI_ORIG, AFNI_APCPC, or AFNI_TLRC.
        Parameters:
        AFNIViewType - The view type.

      • setAlpha

        public void setAlpha​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets T00, T01, and T02 in the transformation matrix.
        Parameters:
        pt - - the alpha point coordinates

      • setAlphaArray

        public void setAlphaArray​(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)
        Sets array of T00, T01, and T02 in the transformation matrix.
        Parameters:
        pt - - the array of alpha point coordinates

      • setAnotherPt

        public void setAnotherPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets another mid-sag point marker for orig to ACPC transformation in dataset ordering.
        Parameters:
        pt - - the marker point coordinates

      • setAnteriorPt

        public void setAnteriorPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the most anterior point marker for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - - the marker point coordinates

      • setBeta

        public void setBeta​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets T10, T11, and T12 in the transformation matrix.
        Parameters:
        pt - -the beta point coordinates

      • setBetaArray

        public void setBetaArray​(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)
        Sets array of T10, T11, and T12 in the transformation matrix.
        Parameters:
        pt - -the array of beta point coordinates

      • setBotX

        public void setBotX​(int[] botX)
        Sets array of the bottom x bounding box boundaries in Talairach conversion.
        Parameters:
        botX - - the array of bottom x boundaries

      • setBotY

        public void setBotY​(int[] botY)
        Sets array of the bottom y bounding box boundaries in Talairach conversion.
        Parameters:
        botY - - the array of bottom y boundaries

      • setBotZ

        public void setBotZ​(int[] botZ)
        Sets array of the bottom z bounding box boundaries in Talairach conversion.
        Parameters:
        botZ - - the array of bottom z boundaries

      • setBrickLabsString

        public void setBrickLabsString​(java.lang.String[] brickLabsString)

      • setBrickStatAux

        public void setBrickStatAux​(float[] brickStatAux)
        Sets brickStatAux The BRICK_STATAUX attribute allows you to attach statistical distribution information to arbitrary sub-bricks of a bucket dataset.
        Parameters:
        brickStatAux - auxiliary statistical information about sub-bricks

      • setDatasetName

        public void setDatasetName​(java.lang.String datasetName)
        Sets datasetName.
        Parameters:
        datasetName - Dataset name to set.

      • setFirstPt

        public void setFirstPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the first mid-sag marker for orig to ACPC transformation in dataset ordering.
        Parameters:
        pt - - the marker point coordinates

      • setFuncType

        public void setFuncType​(int funcType)
        Sets the function type.
        Parameters:
        funcType - Function type to set.

      • setGamma

        public void setGamma​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets T20, T21, and T22 in the transformation matrix.
        Parameters:
        pt - -the gamma point coordinates

      • setGammaArray

        public void setGammaArray​(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)
        Sets array of T20, T21, and T22 in the transformation matrix.
        Parameters:
        pt - - the array of gamma point coordinates

      • setGapArray

        public void setGapArray​(int[] gapArray)
        Sets array of gap values for plane gap not equal to -1.
        Parameters:
        gapArray - DOCUMENT ME!

      • setHighXmm

        public void setHighXmm​(float highXmm)
        Sets the value of the highest x location in millimeters.
        Parameters:
        highXmm - DOCUMENT ME!

      • setHighYmm

        public void setHighYmm​(float highYmm)
        Sets the value of the highest y location in millimeters.
        Parameters:
        highYmm - DOCUMENT ME!

      • setHighZmm

        public void setHighZmm​(float highZmm)
        Sets the value of the highest z location in millimeters.
        Parameters:
        highZmm - DOCUMENT ME!

      • setIDCodeDate

        public void setIDCodeDate​(java.lang.String idcodeDate)
        Sets IDCodeDate.
        Parameters:
        idcodeDate - Code date to set.

      • setIDCodeString

        public void setIDCodeString​(java.lang.String idcodeString)
        Sets IDCodeString.
        Parameters:
        idcodeString - Code string to set.

      • setInferiorEdge

        public void setInferiorEdge​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the PC superior edge marker for orig to ACPC transformation in dataset ordering.
        Parameters:
        pt - the marker point coordinates

      • setInferiorPt

        public void setInferiorPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the most inferior point marker for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - the marker point coordinates

      • setLabel1

        public void setLabel1​(java.lang.String label1)
        Sets label1.
        Parameters:
        label1 - Label 1 to set.

      • setLabel2

        public void setLabel2​(java.lang.String label2)
        Sets label2.
        Parameters:
        label2 - Label 2 to set.

      • setLeftPt

        public void setLeftPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the most left point marker for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - the marker point coordinates

      • setLowXmm

        public void setLowXmm​(float lowXmm)
        Sets the value of the lowest x location in millimeters.
        Parameters:
        lowXmm - DOCUMENT ME!

      • setLowYmm

        public void setLowYmm​(float lowYmm)
        Sets the value of the lowest y location in millimeters.
        Parameters:
        lowYmm - DOCUMENT ME!

      • setLowZmm

        public void setLowZmm​(float lowZmm)
        Sets the value of the lowest z location in millimeters.
        Parameters:
        lowZmm - DOCUMENT ME!

      • setMarksFlag

        public void setMarksFlag​(int marksFlag)
        DOCUMENT ME!
        Parameters:
        marksFlag - int

      • setMarksFlags

        public void setMarksFlags​(int marksFlags)
        DOCUMENT ME!
        Parameters:
        marksFlags - int

      • setNoteDate001

        public void setNoteDate001​(java.lang.String noteDate001)
        Sets noteDate001.
        Parameters:
        noteDate001 - Value to set.

      • setNoteDate002

        public void setNoteDate002​(java.lang.String noteDate002)
        Sets noteDate002.
        Parameters:
        noteDate002 - Value to set.

      • setNoteDate003

        public void setNoteDate003​(java.lang.String noteDate003)
        Sets noteDate003.
        Parameters:
        noteDate003 - Value to set.

      • setNoteDate004

        public void setNoteDate004​(java.lang.String noteDate004)
        Sets noteDate004.
        Parameters:
        noteDate004 - Value to set.

      • setNoteDate005

        public void setNoteDate005​(java.lang.String noteDate005)
        Sets noteDate005.
        Parameters:
        noteDate005 - Value to set.

      • setNoteNumber001

        public void setNoteNumber001​(java.lang.String noteNumber001)
        Sets noteNumber001.
        Parameters:
        noteNumber001 - Value to set.

      • setNoteNumber002

        public void setNoteNumber002​(java.lang.String noteNumber002)
        Sets noteNumber002.
        Parameters:
        noteNumber002 - Value to set.

      • setNoteNumber003

        public void setNoteNumber003​(java.lang.String noteNumber003)
        Sets noteNumber003.
        Parameters:
        noteNumber003 - Value to set.

      • setNoteNumber004

        public void setNoteNumber004​(java.lang.String noteNumber004)
        Sets noteNumber004.
        Parameters:
        noteNumber004 - Value to set.

      • setNoteNumber005

        public void setNoteNumber005​(java.lang.String noteNumber005)
        Sets noteNumber005.
        Parameters:
        noteNumber005 - Value to set.

      • setOrigDicom

        public void setOrigDicom​(boolean origDicom)
        Sets origDicom.
        Parameters:
        origDicom - Value to set.

      • setOriginalPosteriorMargin

        public void setOriginalPosteriorMargin​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the AC posterior margin marker for orig to ACPC transformation in dicom ordering using numbers not adjusted for origin and resolution.
        Parameters:
        pt - the marker point coordinates

      • setOriginalSuperiorEdge

        public void setOriginalSuperiorEdge​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the AC superior edge marker for orig to ACPC transformation in dicom ordering using numbers not adjusted for origin and resolution.
        Parameters:
        pt - - the marker point coordinates

      • setpcie

        public void setpcie​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the posterior commissure inferior edge for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - the marker point coordinates

      • setPlaneGap

        public void setPlaneGap​(int planeGap)
        Sets planeGap to -1 for no gap, 0 = x gap, 1 = y gap, 2 = z gap.
        Parameters:
        planeGap - The plane gap.

      • setPosteriorMargin

        public void setPosteriorMargin​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the AC posterior margin marker for orig to ACPC transformation in dataset ordering.
        Parameters:
        pt - the marker point coordinates

      • setPosteriorPt

        public void setPosteriorPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the most posterior point marker for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - - the marker point coordinates

      • setRightPt

        public void setRightPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the most right point marker for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - - the marker point coordinates

      • setrr

        public void setrr​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the Talairach center voxel inidces in the dicom ordered original image.
        Parameters:
        pt - - the rr point coordinates

      • setrrArray

        public void setrrArray​(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)
        Sets array of the Talairach center voxel inidces in the dicom ordered original image.
        Parameters:
        pt - - the array of rr point coordinates

      • setSlicesWithTimeOffsets

        public void setSlicesWithTimeOffsets​(int slicesWithTimeOffsets)
        Sets slicesWithTimeOffsets.
        Parameters:
        slicesWithTimeOffsets - Value to set.

      • setStatAux

        public void setStatAux​(float[] statAux)
        Sets statAux. Stat aux applies statistical information to the second sub-brick of a func dataset of type FUNC_COR_TYPE, FUNC_TT_TYPE, FUNC_FT_TYPE, FUNC_CT_TYPE, FUNC_BT_TYPE, FUNC_BN_TYPE, FUNC_GT_TYPE, or FUNC_PT_TYPE
        Parameters:
        statAux - Value to set.

      • setSubBrickNumber

        public void setSubBrickNumber​(int i)

      • setSuperiorEdge

        public void setSuperiorEdge​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the AC superior edge marker for orig to ACPC transformation in dataset ordering.
        Parameters:
        pt - - the marker point coordinates

      • setSuperiorPt

        public void setSuperiorPt​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the most superior point marker for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - - the marker point coordinates

      • setTalairachCenter

        public void setTalairachCenter​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets the Talairach center point for +acpc to +tlrc transformation in dicom ordering.
        Parameters:
        pt - - the Talairach center coordinates

      • setTAxisOffsets

        public void setTAxisOffsets​(float[] tAxisOffsets)
        Sets time axis offsets.
        Parameters:
        tAxisOffsets - Time axis offsets to set.

      • setTimeOrigin

        public void setTimeOrigin​(float timeOrigin)
        Sets timeOrigin.
        Parameters:
        timeOrigin - Value to set.

      • setTimeStep

        public void setTimeStep​(float timeStep)
        Sets timeStep.
        Parameters:
        timeStep - Value to set.

      • setTopX

        public void setTopX​(int[] topX)
        Sets array of the top x bounding box boundaries in Talairach conversion.
        Parameters:
        topX - - the array of top x boundaries

      • setTopY

        public void setTopY​(int[] topY)
        Sets array of the top y bounding box boundaries in Talairach conversion.
        Parameters:
        topY - - the array of top y boundaries

      • setTopZ

        public void setTopZ​(int[] topZ)
        Sets array of the top z bounding box boundaries in Talairach conversion.
        Parameters:
        topZ - - the array of top z boundaries

      • setTranslation

        public void setTranslation​(WildMagic.LibFoundation.Mathematics.Vector3f pt)
        Sets T03, T13 and T23 in the transformation matrix.
        Parameters:
        pt - - the translation point coordinates

      • setZAxisOffset

        public void setZAxisOffset​(float zAxisOffset)
        Sets z axis offset.
        Parameters:
        zAxisOffset - Value to set.

      • setZAxisStep

        public void setZAxisStep​(float zAxisStep)
        Sets z axis step.
        Parameters:
        zAxisStep - Value to set.