Field Detail

• serialVersionUID

  private static final long serialVersionUID

  Use serialVersionUID for interoperability.

  See Also:

  Constant Field Values

• XPLANE

  public static final int XPLANE

  Used in determining if all points on the contour have the same x-value

  See Also:

  Constant Field Values

• YPLANE

  public static final int YPLANE

  Used in determining if all points on the contour have the same y-value

  See Also:

  Constant Field Values

• ZPLANE

  public static final int ZPLANE

  Used in determining if all points on the contour have the same z-value

  See Also:

  Constant Field Values

• NOT_A_PLANE

  public static final int NOT_A_PLANE

  If the points on the contour are not on the x,y, or z-plane.

  See Also:

  Constant Field Values

• UPPER_LEFT

  public static final int UPPER_LEFT

  See Also:

  Constant Field Values

• UPPER_RIGHT

  public static final int UPPER_RIGHT

  See Also:

  Constant Field Values

• LOWER_LEFT

  public static final int LOWER_LEFT

  See Also:

  Constant Field Values

• LOWER_RIGHT

  public static final int LOWER_RIGHT

  See Also:

  Constant Field Values

• UPPER_MIDDLE

  public static final int UPPER_MIDDLE

  See Also:

  Constant Field Values

• LEFT_MIDDLE

  public static final int LEFT_MIDDLE

  See Also:

  Constant Field Values

• RIGHT_MIDDLE

  public static final int RIGHT_MIDDLE

  See Also:

  Constant Field Values

• LOWER_MIDDLE

  public static final int LOWER_MIDDLE

  See Also:

  Constant Field Values

• NOT_A_POINT

  public static final int NOT_A_POINT

  Used in places which usually remember an index into a point vector. Indicates that the index should not be used.

  See Also:

  Constant Field Values

• UP

  protected static final int UP

  The up arrow key.

  See Also:

  Constant Field Values

• LEFT

  protected static final int LEFT

  The left arrow key.

  See Also:

  Constant Field Values

• DOWN

  protected static final int DOWN

  The down arrow key.

  See Also:

  Constant Field Values

• RIGHT

  protected static final int RIGHT

  The right arrow key.

  See Also:

  Constant Field Values

• active

  protected 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

• gcPt

  protected WildMagic.LibFoundation.Mathematics.Vector3f gcPt

  Stores the geometric center of the contour of a VOI.

• averagePt

  protected WildMagic.LibFoundation.Mathematics.Vector3f averagePt

  Stores the average of the contour of a VOI.

• cenMassPt

  protected WildMagic.LibFoundation.Mathematics.Vector3f cenMassPt

  Stores the black and white center of mass of the contour of a VOI.

• cenMassPtR

  protected WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtR

  Stores the red center of mass of the contour of a VOI.

• cenMassPtG

  protected WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtG

  Stores the green center of mass of the contour of a VOI.

• cenMassPtB

  protected WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtB

  Stores the blue center of mass of the contour of a VOI.

• fixed

  protected boolean fixed

  Flag that indicates if the VOI is movable.

• label

  protected java.lang.String label

  Label (Name) for this member of the VOI.

• autoLabel

  protected boolean autoLabel

  Automatically generate the label, unless it is set explicitly:

• lastPoint

  protected int lastPoint

  Keeps track of the last near point value (for keyboard moving of individual pts.

• nearPoint

  protected int nearPoint

  Flag used to indicate if the cursor is near a point of the VOI member.

• nearBoundPoint

  protected int nearBoundPoint

  Flag used to indicate if the cursor is near a point on the VOI bounding box.

• voiGroup

  protected VOI voiGroup

  Reference to the containing VOI object.

• process

  protected 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.

• doGeometricCenterLabel

  private boolean doGeometricCenterLabel

  If doGeometricCenterLabel = true and if active == false and if closed = true, execute drawGeometricCenterLabel when in drawSelf

• m_bUpdateMask

  protected boolean m_bUpdateMask

  Set to true if the contour changes, so the mask will update when needed.

• m_bUpdateBounds

  protected boolean m_bUpdateBounds

  Set to true if the contour bounding-box needs updating.

• m_bUpdateGeometricCenter

  protected boolean m_bUpdateGeometricCenter

  Set to true if the geometric center needs updating.

• m_bUpdateAverage

  protected boolean m_bUpdateAverage

  Set to true if the geometric center needs updating.

• m_bReloadPoints

  protected boolean m_bReloadPoints

• m_bUpdatePlane

  protected boolean m_bUpdatePlane

  Set to true if the contour plane needs updating.

• m_iVOIType

  protected int m_iVOIType

  VOI type of this contour.

• m_iAnchorIndex

  protected int m_iAnchorIndex

  Anchor point.

• closed

  protected boolean closed

  True when this is a closed contour.

• m_bSplit

  protected boolean m_bSplit

  True is this is a split-line contour.

• m_bQuickLUT

  protected boolean m_bQuickLUT

  True is this is a QuickLUT contour.

• m_iPlane

  protected int m_iPlane

  Current plane of this contour.

• m_akImageMinMax

  protected WildMagic.LibFoundation.Mathematics.Vector3f[] m_akImageMinMax

  Current contour bounding-box.

• m_kColor

  protected WildMagic.LibFoundation.Mathematics.ColorRGBA m_kColor

  Contour color.

• m_kVolumeVOI

  protected transient VolumeVOI m_kVolumeVOI

  Data structure for drawing this contour in the GPU VolumeRenderer

• volumeDisplayRange

  protected float volumeDisplayRange

  Used to display 3D VOIs in the three orthogonal views of the data in the volume renderer

• numPixels

  protected int numPixels

  Number of pixels in the array used in graphing intensity along the boundary.

• m_kPositionSum

  protected WildMagic.LibFoundation.Mathematics.Vector3f m_kPositionSum

• UNKNOWN_SUBTYPE

  public static final int UNKNOWN_SUBTYPE

  available subtypes for VOI

  See Also:

  Constant Field Values

• CIRCLE

  public static final int CIRCLE

  See Also:

  Constant Field Values

• SQUARE

  public static final int SQUARE

  See Also:

  Constant Field Values

• subtype

  private int subtype

  initialize subtype to unknown

• display

  protected boolean display

  displays the voi in the volume renderer:

• xPts

  private float[] xPts

• yPts

  private float[] yPts

• zPts

  private float[] zPts

Constructor Detail

• VOIBase

  public VOIBase()

  Default Constructor. Initializes the Vector : start and the amount to increment the vector by.,

• VOIBase

  public VOIBase​(boolean bFixed,
                 boolean bClosed)

  Constructor sets the fixed and closed flags.

  Parameters:

  bFixed - true if this contour cannot be changed.

  bClosed - true if this contour is closed.

• VOIBase

  public VOIBase​(boolean bFixed,
                 boolean bClosed,
                 java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kIn)

  Constructor, sets the fixed and closed flags and positions.

  Parameters:

  bFixed - true if this contour cannot be changed.

  bClosed - true if this contour is closed.

  kIn - positions.

• VOIBase

  public VOIBase​(boolean bFixed,
                 boolean bClosed,
                 WildMagic.LibFoundation.Mathematics.Vector3f kIn)

• VOIBase

  public VOIBase​(VOIBase kBase)

  Copies the input VOIBase into a new VOIBase object.

  Parameters:

  kBase -

• VOIBase

  public VOIBase​(VOIBase kBase,
                 int iPropDir)

  Copies the input contour and changes it's slice +/-

  Parameters:

  kBase -

  iPropDir -

• VOIBase

  public VOIBase​(VOIBase kBase,
                 TransMatrix tMatrix)

  Copies the input VOIBase, transformed by the input TransMatrix.

  Parameters:

  kBase - VOI to copy.

  tMatrix - transformation

Method Detail

• sortCrossingPoints

  private static void sortCrossingPoints​(float[] aiList,
                                         int iNumElements)

  Sorts the edge crossing points in place.

  Parameters:

  aiList - list of positions

  iNumElements - number of positions.

• addElement

  public void addElement​(float x,
                         float y,
                         float z)

  Adds a point to the curve.

  Parameters:

  x - x coordinate of point

  y - y coordinate of point

  z - z coordinate of point

• addElement

  public void addElement​(int x,
                         int y,
                         int z)

  Adds a point to the curve.

  Parameters:

  x - x coordinate of point

  y - y coordinate of point

  z - z coordinate of point

• area

  public double area()

• calcIntensity

  public float calcIntensity​(ModelImage kImage,
                             int t)

  Calculated the total intensity contained within this contour.

  Parameters:

  kImage -

  Returns:

  total intensity.

• calcIntensity

  public java.util.Vector<java.lang.Float> calcIntensity​(ModelImage kImage,
                                                         WildMagic.LibFoundation.Mathematics.Vector3f kValues,
                                                         float ignoreMin,
                                                         float ignoreMax,
                                                         JPanelPixelExclusionSelector.RangeType rangeFlag)

  Finds values contained within this contour, based on the rangeFlag, ignorMin and ignoreMax.

  Parameters:

  kImage - input image.

  ignoreMin - intensity minimum.

  ignoreMax - intensity maximum.

  rangeFlag - flag indicating (between, outside, none).

  Returns:

  list of values inside this contour that fit the parameters.

• calcIntensityThreshold

  public float calcIntensityThreshold​(ModelImage kImage,
                                      float threshold,
                                      int t)

  Calculates the total intensity contained within this contour, equal to of greater than the threshold.

  Parameters:

  kImage - input image

  threshold -

  Returns:

  total intensity of image contained within this contour, greater than threshold.

• calcRGBIntensity

  public java.util.Vector<WildMagic.LibFoundation.Mathematics.ColorRGB> calcRGBIntensity​(ModelImage kImage,
                                                                                         WildMagic.LibFoundation.Mathematics.ColorRGB kMin,
                                                                                         WildMagic.LibFoundation.Mathematics.ColorRGB kMax,
                                                                                         WildMagic.LibFoundation.Mathematics.ColorRGB kSum,
                                                                                         float ignoreMinR,
                                                                                         float ignoreMaxR,
                                                                                         float ignoreMinG,
                                                                                         float ignoreMaxG,
                                                                                         float ignoreMinB,
                                                                                         float ignoreMaxB,
                                                                                         JPanelPixelExclusionSelector.RangeType rangeFlag)

  Finds values contained within this contour, based on the rangeFlag, ignoreMinR, ignoreMaxR, ignoreMinG, ignoreMaxG, ignoreMinB, and ignoreMaxB.

  Parameters:

  kImage - input image.

  kMin - .

  kMax - .

  kSum - .

  ignoreMinR - intensity minimum red.

  ignoreMaxR - intensity maximum red.

  ignoreMinG - intensity minimum green.

  ignoreMaxG - intensity maximum green.

  ignoreMinB - intensity minimum blue.

  ignoreMaxB - intensity maximum blue.

  rangeFlag - flag indicating (between, outside, none).

  Returns:

  list of values inside this contour that fit the parameters.

• calcRGBIntensity

  public float calcRGBIntensity​(ModelImage kImage,
                                int RGorB)

  Calculates the total intensity contained within this contour for the input color channel.

  Parameters:

  kImage -

  RGorB - (Red = 0; Green = 1; Blue = 2)

  Returns:

  total intensity contained within this contour, for the input image and color channel.

• calcRGBIntensityThreshold

  public float calcRGBIntensityThreshold​(ModelImage kImage,
                                         int RGorB,
                                         float threshold)

  Calculates the total intensity contained within this contour for the input color channel, that is greater than or equal to the input threshold value.

  Parameters:

  kImage -

  RGorB - (Red = 0; Green = 1; Blue = 2)

  threshold -

  Returns:

  total intensity greater than the threshold contained within this contour, for the input image and color channel.

• clone

  public abstract VOIBase clone()

  Overrides:

  clone in class java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>

• contains

  public boolean contains​(float iX,
                          float iY)

  Returns true if the input iX, iY is contained within this contour. The z-value of the contour is ignored.

  Parameters:

  iX -

  iY -

  Returns:

• contain

  public boolean contain​(float iX,
                         float iY)

  This is used by SVM boundary training to identify the prostate boundary VOI landmark points.

  Parameters:

  iX -

  iY -

  Returns:

• contains

  public boolean contains​(float iX,
                          float iY,
                          float iZ)

  Returns true if the input iX,iY,iZ is contained within this contour.

  Parameters:

  iX -

  iY -

  iZ -

  Returns:

• contains

  public boolean contains​(int _x,
                          int _y,
                          boolean forceReload)

• createVolumeVOI

  public VolumeVOI createVolumeVOI​(VolumeImage kVolumeImage,
                                   WildMagic.LibFoundation.Mathematics.Vector3f kTranslate)

  Creates the VolumeVOI data structure for rendering this contour in the GPU VolumeRenderer

  Parameters:

  kVolumeImage -

  kTranslate -

  Returns:

  VolumeVOI

• display

  public void display​(boolean show)

  Turns the display setting on/off for the VolumeVOI displayed in the volume renderer.

  Parameters:

  show -

• cycleActivePt

  public void cycleActivePt​(int keyCode)

  Cycles through the active points on the curve.

  Parameters:

  keyCode - int arrow key (up/down/left/right)

• delete

  public void delete​(int iPos)

  Deletes the specified position on the curve.

  Parameters:

  iPos - position on the curve to delete.

• dispose

  public void dispose()

  Deletes local data members.

• distanceToVOI

  public float distanceToVOI​(int iX,
                             int iY,
                             int iZ)

  Returns the smallest distance from the input point to this contour.

  Parameters:

  iX - input x-position

  iY - input y-position

  iZ - input z-position

  Returns:

  smallest distance from the input to the contour.

• equals

  public boolean equals​(java.lang.Object o)

  Specified by:

  equals in interface java.util.Collection<WildMagic.LibFoundation.Mathematics.Vector3f>

  Specified by:

  equals in interface java.util.List<WildMagic.LibFoundation.Mathematics.Vector3f>

  Overrides:

  equals in class java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>

• exportArrays

  public void exportArrays​(float[] x,
                           float[] y,
                           float[] z)

  Exports the float arrays of the points of the curve.

  Parameters:

  x - array of x coordinates

  y - array of y coordinates

  z - array of z coordinates

• exportArrays

  public void exportArrays​(int[] x,
                           int[] y,
                           int[] z)

  Exports the arrays of the points of the curve in int array format.

  Parameters:

  x - array of x coordinates

  y - array of y coordinates

  z - array of z coordinates

• fillVolume

  public void fillVolume​(ModelImage kVolume,
                         java.util.BitSet kMask,
                         boolean bIntersection,
                         int iValue)

  Renders this contour into the input ModelImage or the input BitSet mask.

  Parameters:

  kVolume - if non-null this contour is rendered into the ModelImage.

  kMask - if non-null this contour is rendered into the mask.

  bIntersection - when true the contour rendered as an intersection with other contours.

  iValue - value to write into the input image.

• findVOIIndentations2D

  public int findVOIIndentations2D​(ModelImage kImage,
                                   int sliceNum,
                                   java.util.Vector<VOIBase> curves,
                                   boolean displayIndentations)

• findPositionAndCurvature

  public int findPositionAndCurvature​(java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> positions,
                                      java.util.Vector<java.lang.Float> curvatures,
                                      boolean smoothCurvature,
                                      double[] meanCurvature,
                                      double[] stdDevCurvature,
                                      double[] meanNegativeCurvature,
                                      double negativeHysteresisFraction,
                                      double positiveHysteresisFraction,
                                      int[] numberOfIndentations,
                                      int consecutiveNegativeNeeded,
                                      double negativeCurvatureNeeded,
                                      double[] totalLength)

  Finds the position/curvature along a VOI. To fill in missing samples requires smoothing spline interpolation.

  Parameters:

  positions - Vector that is filled with the distance along the VOI in millimeters for example

  curvatures - the corresponding curvature along the contour

  smooth - if true smooth before finding curvature

  meanCurvature -

  stdDevCurvature -

  meanNegativeCurvature -

  negativeHysteresisFraction -

  positiveHysteresisFraction -

  numberOfIndentations -

  consecutiveNegativeNeeded -

  negativeCurvatureNeeded -

  Returns:

  the number of points in the position and curvature array that have valid data.

• findPositionAndIntensity

  public int findPositionAndIntensity​(ModelImage kImage,
                                      java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> positions,
                                      java.util.Vector<WildMagic.LibFoundation.Mathematics.ColorRGB> colors)

  Finds the position/intensity along a VOI.

  Parameters:

  positions - Vector that is filled with the distance along the VOI in millimeters for example

  colors - the corresponding intensities along the line

  Returns:

  the number of points in the position and intensity array that have valid data.

• findPositionAndIntensity

  public void findPositionAndIntensity​(WildMagic.LibFoundation.Mathematics.Vector3f kStart,
                                       WildMagic.LibFoundation.Mathematics.Vector3f kEnd,
                                       ModelImage kImage,
                                       java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> positions,
                                       java.util.Vector<WildMagic.LibFoundation.Mathematics.ColorRGB> colors)

  Finds the positions and intensities along a line-segment of the VOI.

  Parameters:

  kStart - start position on the VOI.

  kEnd - end position on the VOI

  kImage - input image to read intensity values from

  positions - output list of positions

  colors - output list of colors.

• getActivePt

  public WildMagic.LibFoundation.Mathematics.Vector3f getActivePt()

  Gets the Vector3f of the active point.

  Returns:

  Vector3f the active point's Vector3f

• getAnchor

  public int getAnchor()

  Returns the anchor point.

  Returns:

• getAverage

  public WildMagic.LibFoundation.Mathematics.Vector3f getAverage()

• getBounds

  public void getBounds​(float[] x,
                        float[] y,
                        float[] z)

  Calculates the bounds of the contour.

  Parameters:

  x - two element array where x[0] = min extent of the Contour and x[1] = max extent of the Contour in the x dimension

  y - two element array where y[0] = min extent of the Contour and y[1] = max extent of the Contour in the y dimension

  z - two element array where z[0] = min extent of the Contour and z[1] = max extent of the Contour in the z dimension

• getBounds

  public void getBounds​(int[] x,
                        int[] y,
                        int[] z)

  Calculates the bounds of the contour.

  Parameters:

  x - two element array where x[0] = min extent of the Contour and x[1] = max extent of the Contour in the x dimension

  y - two element array where y[0] = min extent of the Contour and y[1] = max extent of the Contour in the y dimension

  z - two element array where z[0] = min extent of the Contour and z[1] = max extent of the Contour in the z dimension

• getCenterOfMass

  public WildMagic.LibFoundation.Mathematics.Vector3f getCenterOfMass​(ModelImage kImage)

  Gets the center of mass of the contour for a given image

  Parameters:

  kImage - input image.

  Returns:

  center of mass for this contour and the input image.

• getCenterOfMass

  public void getCenterOfMass​(ModelImage kImage,
                              WildMagic.LibFoundation.Mathematics.Vector3f centerPt,
                              int c)

  Gets the center of mass of the contour for the image and color-channel c.

  Parameters:

  kImage - input image.

  centerPt - output point.

  c - color channel.

• getCenterOfMassB

  public WildMagic.LibFoundation.Mathematics.Vector3f getCenterOfMassB​(ModelImage kImage)

  Gets the blue center of mass of the contour.

  Parameters:

  kImage - input image.

  Returns:

  returns the center of mass

• getCenterOfMassG

  public WildMagic.LibFoundation.Mathematics.Vector3f getCenterOfMassG​(ModelImage kImage)

  Gets the green center of mass of the contour.

  Parameters:

  kImage - input image.

  Returns:

  returns the center of mass

• getCenterOfMassR

  public WildMagic.LibFoundation.Mathematics.Vector3f getCenterOfMassR​(ModelImage kImage)

  Gets the red center of mass of the contour.

  Parameters:

  kImage - input image.

  Returns:

  returns the center of mass

• getContourID

  public int getContourID()

  Returns the contour ID: the index of this contour into the VOI.

  Returns:

  contour ID, or -1 if this contour is not contained in a VOI.

• getDoGeometricCenterLabel

  public boolean getDoGeometricCenterLabel()

  If doGeometricCenterLabel = true and active == false and closed = true, execute drawGeometricCenterLabel when in drawSelf

  Returns:

  doGeometricCenterLabel

• getGeometricCenter

  public WildMagic.LibFoundation.Mathematics.Vector3f getGeometricCenter()

  Gets the geometric center of the contour.

  Returns:

  returns the geometric center

• getGeometricCenterA

  public WildMagic.LibFoundation.Mathematics.Vector3f getGeometricCenterA()

• getGroup

  public VOI getGroup()

  Returns the VOI object that contains this contour.

  Returns:

  the VOI object that contains this contour.

• getImageBoundingBox

  public WildMagic.LibFoundation.Mathematics.Vector3f[] getImageBoundingBox()

  Returns the contour bounding-box.

  Returns:

  Vector3f[] with the bounding-box minimum in [0] and the maximum in [1].

• getLabel

  public java.lang.String getLabel()

  Gets the label of the VOI.

  Returns:

  label as a String

• getLastNumPixels

  public int getLastNumPixels()

  Accessor that returns the number of points used in the most recent intensity calculation of this contour.

  Returns:

  the number of points used in the most recent intensity calculation

• getLengthPtToPt

  public double getLengthPtToPt​(float[] resolutions)

  Returns the total length of this contour, based on the input resolutions.

  Parameters:

  resolutions - .

  Returns:

  total length of this contour, scaled by the resolutions.

• getLengthPtToPt

  public double getLengthPtToPt​(float[][] resolutions)

  Returns the total length of this contour, based on the input resolutions.

  Parameters:

  resolutions - .

  Returns:

  total length of this contour, scaled by the resolutions.

• getLengthString

  public java.lang.String getLengthString​(int iPos0,
                                          int iPos1,
                                          float[] afResolutions,
                                          int[] aiUnits)

  Returns the length of this contour between the two positions along the contour. Based on the input resolutions and units.

  Parameters:

  iPos0 - first position on this contour.

  iPos1 - second position on this contour.

  afResolutions - resolutions.

  aiUnits - units.

  Returns:

  String with the length and units labeled.

• getAllContourPoints

  public java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> getAllContourPoints()

• getMaskPositions

  public java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> getMaskPositions()

• getName

  public java.lang.String getName()

  Gets the name of the VOI that contains this contour, null if this contour is not contained in a VOI.

  Returns:

  String

• getNearBoundPoint

  public int getNearBoundPoint()

• getNearPoint

  public int getNearPoint()

  Returns the point on the curve nearest the cursor, calculated by nearLine, etc.

  Returns:

  point on the curve nearest the cursor.

• getNumVoxels

  public int getNumVoxels()

• getPlane

  public int getPlane()

  Determines if the points on the contour lie on either the x,y,or z-planes. Or not on any plane.

  Returns:

  XPLANE, YPLANE, ZPLANE or NOT_A_PLANE.

• getProcess

  public boolean getProcess()

  Accessor that returns the process.

  Returns:

  the process

• getSelectedPoint

  public int getSelectedPoint()

  Returns the last selected point.

  Returns:

• getSubtype

  public int getSubtype()

• getTotalLengthString

  public java.lang.String getTotalLengthString​(float[] afResolutions,
                                               int[] aiUnits)

  Returns the total length of this contour as a string. Based on the input resolutions and units.

  Parameters:

  afResolutions -

  aiUnits -

  Returns:

  String with the length and units labeled.

• getType

  public int getType()

  Returns the type of this contour.

  Returns:

  type of this contour.

• deleteVolumeVOI

  public void deleteVolumeVOI()

• getVolumeVOI

  public VolumeVOI getVolumeVOI()

  Returns the VolumeVOI data member used to draw this contour in the GPU VOlumeRenderer.

  Returns:

  VolumeVOI for rendering this contour in the GPU VolumeRenderer.

• importArrays

  public void importArrays​(float[] x,
                           float[] y,
                           float[] z,
                           int n)

  Imports new position values into this contour.

  Parameters:

  x - array of x-positions.

  y - array of y-positions.

  z - array of z-positions.

  n - number of values.

• importArrays

  public void importArrays​(int[] x,
                           int[] y,
                           int[] z,
                           int n)

  Imports new position values into this contour.

  Parameters:

  x - array of x-positions.

  y - array of y-positions.

  z - array of z-positions.

  n - number of values.

• importPoints

  public void importPoints​(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)

  Imports new position values into this contour.

  Parameters:

  pt - array of points to import into this contour.

• isActive

  public boolean isActive()

  Accessor to flag that indicates if an VOI is active.

  Returns:

  flag indicating if an VOI is active

• isClosed

  public boolean isClosed()

  Flag used to indicate type of contour: true = closed contour (i.e. contour end points are connected) false = open contour

  Returns:

  flag whether the voi contour is closed.

• isFixed

  public boolean isFixed()

  Accessor to flag that indicates if an VOI is fixed (movable).

  Returns:

  flag indicating if an VOI is fixed

• isM_bUpdateBounds

  public boolean isM_bUpdateBounds()

• isM_bUpdateGeometricCenter

  public boolean isM_bUpdateGeometricCenter()

• isQuickLUT

  public boolean isQuickLUT()

  Returns true if this is a QuickLUT contour.

  Returns:

• isSplit

  public boolean isSplit()

  Returns true if this is a split-line contour.

  Returns:

• nearLine

  public boolean nearLine​(int iX,
                          int iY,
                          int iZ)

  Returns true if the input position is near the outline of this contour.

  Parameters:

  iX - input x-position.

  iY - input y-position.

  iZ - input z-position

  Returns:

  true if the input position is 'near' the outline of this contour.

• nearLine

  public boolean nearLine​(int iX,
                          int iY,
                          int iZ,
                          int tol)

  Returns true if the input position is near the outline of this contour. Based on the input tolerance.

  Parameters:

  iX - input x-position.

  iY - input y-position.

  iZ - input z-position

  tol - tolerance value for determining if the position is near this contour.

  Returns:

  true if the input position is 'near' the outline of this contour.

• planeFit

  public WildMagic.LibFoundation.Mathematics.Plane3f planeFit()

  Fits a plane to the points in this contour and returns the plane.

  Returns:

• reloadPoints

  public void reloadPoints()

  Reloads points in this array for speed purposes.

• setActive

  public void setActive​(boolean active)

  Sets flag to indicate whether or not VOI is active.

  Parameters:

  active - flag sets the activity status of a flag

• setAnchor

  public void setAnchor()

  Sets the anchor point.

• setClosed

  public void setClosed​(boolean bClosed)

  Sets this contour as open or closed.

  Parameters:

  bClosed -

• setDoGeometricCenterLabel

  public void setDoGeometricCenterLabel​(boolean doGeometricCenterLabel)

  If doGeometricCenterLabel = true and active == false and closed = true, execute drawGeometricCenterLabel when in drawSelf

  Parameters:

  doGeometricCenterLabel -

• setFixed

  public void setFixed​(boolean fixed)

  Sets flag to indicate whether or not VOI is fixed.

  Parameters:

  fixed - flag sets the fixed status of a flag

• setGroup

  public void setGroup​(VOI kGroup)

  Sets the VOI object that contains this contour.

  Parameters:

  kGroup - VOI container for this contour.

• setLabel

  public void setLabel​(java.lang.String str)

  Sets the label of the VOI.

  Parameters:

  str - the label

• setMask

  public void setMask​(java.util.BitSet kMask,
                      int xDim,
                      int yDim,
                      boolean XOR,
                      int polarity)

• setMaskSlice

  public void setMaskSlice​(java.util.BitSet kMask,
                           int xDim,
                           boolean XOR,
                           int polarity)

• setNearBoundPoint

  public void setNearBoundPoint​(int i)

  Sets the near boundary point.

  Parameters:

  i -

• setNearPoint

  public void setNearPoint​(int i)

  Sets the near point.

  Parameters:

  i -

• setPlane

  public void setPlane​(int iPlane)

• setProcess

  public void setProcess​(boolean process)

  Sets whether the shape is included in processing.

  Parameters:

  flag - the process flag

• setQuickLUT

  public void setQuickLUT​(boolean bQuickLUT)

  Sets the QuickLUT flag.

  Parameters:

  bQuickLUT -

• setSelectedPoint

  public void setSelectedPoint​(int i)

  Sets the selected point.

  Parameters:

  i -

• setSplit

  public void setSplit​(boolean bSplit)

  Sets the split flag.

  Parameters:

  bSplit -

• setSubtype

  public void setSubtype​(int subtype)

• getVolumeDisplayRange

  public float getVolumeDisplayRange()

• setVolumeDisplayRange

  public void setVolumeDisplayRange​(float range)

• slice

  public int slice()

  Returns the slice value of the contour on every plane. If the contour does not exist on the x-plane, returns its value on the y-plane. If the contour does not exist on the y-plane, returns its value on the z-plane. Use slice(int iPlane) for a more reliable value.

  Returns:

• slice

  public int slice​(int iPlane)

  Returns the point value the contour has in common if it lies in the given plane. If the contour does not exist on the given plane, -1 is returned.

  Returns:

• transform

  public void transform​(TransMatrix tMatrix)

  Copies the input VOIBase, transformed by the input TransMatrix.

  Parameters:

  kBase - VOI to copy.

  tMatrix - transformation

• trimPoints

  public void trimPoints​(double constraint,
                         boolean tFlag)

  Trims a contour and then removes collinear points in the resulting contour. If the perpendicular distance from the middle point to the line defined by the 1st and 3rd point is small than the middle point is removed.

  Parameters:

  constraint - factor that controls the number of points removed. A larger constraint removes more points 0.50 typical - removes most "almost/and collinear" points 0.00 - removes only "collinear" points

  tFlag - if true, trim collinear points

• update

  public void update()

  The contour has changed, set the update flags so statistics are recalculated when needed.

• update

  public void update​(WildMagic.LibFoundation.Mathematics.ColorRGBA kColor)

  Set the color of this contour.

  Parameters:

  kColor - new color for this contour.

• update

  public void update​(WildMagic.LibFoundation.Mathematics.Vector3f kTranslate)

  The contour has been translated, this function translates the geometric center and bounding-box so they don't need to be recalculated.

  Parameters:

  kTranslate - amount by which the contour was translated.

• containsX

  private boolean containsX​(int y,
                            int z)

• containsY

  private boolean containsY​(int x,
                            int z)

• containsZ

  private boolean containsZ​(int x,
                            int y)

• fill

  private void fill​(float[][] aaiCrossingPoints,
                    int[] aiNumCrossings,
                    int iXMin,
                    int iXMax,
                    int iZ,
                    ModelImage kVolume,
                    java.util.BitSet kMask,
                    boolean bIntersection,
                    int iValue)

  Helper function for rendering this contour onto the z-plane. Pixels are determined to be inside or outside the contour based on the parameters, aaiCrossingPoints and aiNumCrossings, using a scan-conversion algorithm that traverses each row and column of the bounding box of the sculpt region coloring inside points as it goes.

  Parameters:

  aaiCrossingPoints - column crossing points.

  aiNumCrossings - number of crossing points per row.

  iXMin - contour bounding box x-minimum.

  iYMin - contour bounding box y-minimum.

  iXMax - contour bounding box x-maximum.

  iYMax - contour bounding box y-maximum.

  iZ - z-plane slice to render into.

  kVolume - output: when non-null this contour is rendered into the input image.

  kMask - output: when non-null this contour is rendered into the input BitSet mask.

  bIntersection - when true the contour rendered as an intersection with other contours.

  iValue - value to write into the input image.

• fill_X

  private void fill_X​(float[][] aaiCrossingPoints,
                      int[] aiNumCrossings,
                      int iYMin,
                      int iYMax,
                      int iX,
                      ModelImage kVolume,
                      java.util.BitSet kMask,
                      boolean bIntersection,
                      int iValue)

  Helper function for rendering this contour onto the x-plane. Pixels are determined to be inside or outside the contour based on the parameters, aaiCrossingPoints and aiNumCrossings, using a scan-conversion algorithm that traverses each row and column of the bounding box of the sculpt region coloring inside points as it goes.

  Parameters:

  aaiCrossingPoints - column crossing points.

  aiNumCrossings - number of crossing points per row.

  iYMin - contour bounding box y-minimum.

  iZMin - contour bounding box z-minimum.

  iYMax - contour bounding box y-maximum.

  iZMax - contour bounding box z-maximum.

  iX - x-plane slice to render into.

  kVolume - output: when non-null this contour is rendered into the input image.

  kMask - output: when non-null this contour is rendered into the input BitSet mask.

  bIntersection - when true the contour rendered as an intersection with other contours.

  iValue - value to write into the input image.

• fill_Y

  private void fill_Y​(float[][] aaiCrossingPoints,
                      int[] aiNumCrossings,
                      int iXMin,
                      int iXMax,
                      int iY,
                      ModelImage kVolume,
                      java.util.BitSet kMask,
                      boolean bIntersection,
                      int iValue)

  Helper function for rendering this contour onto the y-plane. Pixels are determined to be inside or outside the contour based on the parameters, aaiCrossingPoints and aiNumCrossings, using a scan-conversion algorithm that traverses each row and column of the bounding box of the sculpt region coloring inside points as it goes.

  Parameters:

  aaiCrossingPoints - column crossing points.

  aiNumCrossings - number of crossing points per row.

  iXMin - contour bounding box x-minimum.

  iZMin - contour bounding box z-minimum.

  iXMax - contour bounding box x-maximum.

  iZMax - contour bounding box z-maximum.

  iY - y-plane slice to render into.

  kVolume - output: when non-null this contour is rendered into the input image.

  kMask - output: when non-null this contour is rendered into the input BitSet mask.

  bIntersection - when true the contour rendered as an intersection with other contours.

  iValue - value to write into the input image.

• fillVolume

  private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> fillVolume​(java.util.BitSet kMask,
                                                                                    int xDim,
                                                                                    int yDim)

  Renders this contour into the input mask.

  Parameters:

  kMask - input mask.

  xDim - x-dimensions of the input mask.

  yDim - y-dimension of the input mask.

• fillX

  private void fillX​(int iX,
                     java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kMaskPositions,
                     java.util.BitSet kMask,
                     int xDim,
                     int yDim)

• fillY

  private void fillY​(int iY,
                     java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kMaskPositions,
                     java.util.BitSet kMask,
                     int xDim,
                     int yDim)

• fillZ

  private void fillZ​(int iZ,
                     java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kMaskPositions,
                     java.util.BitSet kMask,
                     int xDim,
                     int yDim)

• outlineRegion

  private void outlineRegion​(float[][] aaiCrossingPoints,
                             int[] aiNumCrossings,
                             int iXMin,
                             int iXMax)

  Helper function computes the set of spans indicated by column crossings for rendering this contour into the z-plane.

  Parameters:

  aaiCrossingPoints - output: x-values that the contour crosses

  aiNumCrossings - output: number of crossing points per row.

  iXMin - the minimum x-value of this contour.

  iXMax - the maximum x-value of this contour.

• outlineRegion_X

  private void outlineRegion_X​(float[][] aaiCrossingPoints,
                               int[] aiNumCrossings,
                               int iYMin,
                               int iYMax)

  Helper function computes the set of spans indicated by column crossings for rendering this contour into the x-plane.

  Parameters:

  aaiCrossingPoints - output: z-values that the contour crosses

  aiNumCrossings - output: number of crossing points per row.

  iXMin - the minimum y-value of this contour.

  iXMax - the maximum y-value of this contour.

• outlineRegion_Y

  private void outlineRegion_Y​(float[][] aaiCrossingPoints,
                               int[] aiNumCrossings,
                               int iXMin,
                               int iXMax)

  Helper function computes the set of spans indicated by column crossings for rendering this contour into the y-plane.

  Parameters:

  aaiCrossingPoints - output: z-values that the contour crosses

  aiNumCrossings - output: number of crossing points per row.

  iXMin - the minimum x-value of this contour.

  iXMax - the maximum x-value of this contour.

• areaTwice

  protected float areaTwice​(float ptAx,
                            float ptAy,
                            float ptBx,
                            float ptBy,
                            float ptCx,
                            float ptCy)

  Calculates twice the area (cross product of two vectors) of a triangle given three points. This is a private function only called by the function "contains".

  Parameters:

  ptAx - x-coordinate of the first point of the triangle

  ptAy - y-coordinate of the first point of the triangle

  ptBx - x-coordinate of the second point of the triangle

  ptBy - y-coordinate of the second point of the triangle

  ptCx - x-coordinate of the third point of the triangle

  ptCy - y-coordinate of the third point of the triangle

  Returns:

  twice the area of the triangle if CCw or -2*area if CW