Package gov.nih.mipav.model.file

Class FileInfoAfni

java.lang.Object
gov.nih.mipav.model.structures.ModelSerialCloneable
gov.nih.mipav.model.file.FileInfoBase
gov.nih.mipav.model.file.FileInfoAfni
All Implemented Interfaces:
Serializable, Cloneable
public class FileInfoAfni extends FileInfoBase
This structures contains the information that describes how an Afni image is stored on disk.
See Also:

  • Field Details

    • serialVersionUID

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

    • AFNI_ORIG

      public static final int AFNI_ORIG
      AFNI view type Original.
      See Also:

    • AFNI_ACPC

      public static final int AFNI_ACPC
      AFNI view type ACPC.
      See Also:

    • AFNI_TLRC

      public static final int AFNI_TLRC
      AFNI view type Talairach.
      See Also:

    • HEAD_ANAT_TYPE

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

    • HEAD_FUNC_TYPE

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

    • GEN_ANAT_TYPE

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

    • GEN_FUNC_TYPE

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

    • 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:

    • ANAT_FSE_TYPE

      public static final int ANAT_FSE_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_EPI_TYPE

      public static final int ANAT_EPI_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_MRAN_TYPE

      public static final int ANAT_MRAN_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_CT_TYPE

      public static final int ANAT_CT_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_SPECT_TYPE

      public static final int ANAT_SPECT_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_PET_TYPE

      public static final int ANAT_PET_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_MRA_TYPE

      public static final int ANAT_MRA_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_BMAP_TYPE

      public static final int ANAT_BMAP_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_DIFF_TYPE

      public static final int ANAT_DIFF_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_OMRI_TYPE

      public static final int ANAT_OMRI_TYPE
      DOCUMENT ME!
      See Also:

    • ANAT_BUCK_TYPE

      public static final int ANAT_BUCK_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_FIM_TYPE

      public static final int FUNC_FIM_TYPE
      1 value.
      See Also:

    • FUNC_THR_TYPE

      public static final int FUNC_THR_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_COR_TYPE

      public static final int FUNC_COR_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_TT_TYPE

      public static final int FUNC_TT_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_FT_TYPE

      public static final int FUNC_FT_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_ZT_TYPE

      public static final int FUNC_ZT_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_CT_TYPE

      public static final int FUNC_CT_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_BT_TYPE

      public static final int FUNC_BT_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_BN_TYPE

      public static final int FUNC_BN_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_GT_TYPE

      public static final int FUNC_GT_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_PT_TYPE

      public static final int FUNC_PT_TYPE
      DOCUMENT ME!
      See Also:

    • FUNC_BUCK_TYPE

      public static final int FUNC_BUCK_TYPE
      DOCUMENT ME!
      See Also:

    • 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 String[] brickLabsString
      Name for each sub-brick

    • brickStatAux

      private float[] brickStatAux
      DOCUMENT ME!

    • datasetName

      private 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 String idcodeDate
      DOCUMENT ME!

    • idcodeString

      private 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 String label1
      DOCUMENT ME!

    • label2

      private 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 String noteDate001
      DOCUMENT ME!

    • noteDate002

      private String noteDate002
      DOCUMENT ME!

    • noteDate003

      private String noteDate003
      DOCUMENT ME!

    • noteDate004

      private String noteDate004
      DOCUMENT ME!

    • noteDate005

      private String noteDate005
      DOCUMENT ME!

    • noteNumber001

      private String noteNumber001
      DOCUMENT ME!

    • noteNumber002

      private String noteNumber002
      DOCUMENT ME!

    • noteNumber003

      private String noteNumber003
      DOCUMENT ME!

    • noteNumber004

      private String noteNumber004
      DOCUMENT ME!

    • noteNumber005

      private 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 Details

    • FileInfoAfni

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

  • Method Details

    • 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 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(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(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(String idcodeDate)
      Sets IDCodeDate.
      Parameters:
      idcodeDate - Code date to set.

    • setIDCodeString

      public void setIDCodeString(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(String label1)
      Sets label1.
      Parameters:
      label1 - Label 1 to set.

    • setLabel2

      public void setLabel2(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(String noteDate001)
      Sets noteDate001.
      Parameters:
      noteDate001 - Value to set.

    • setNoteDate002

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

    • setNoteDate003

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

    • setNoteDate004

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

    • setNoteDate005

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

    • setNoteNumber001

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

    • setNoteNumber002

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

    • setNoteNumber003

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

    • setNoteNumber004

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

    • setNoteNumber005

      public void setNoteNumber005(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.