java.lang.Object
- java.util.AbstractCollection<E>
- - java.util.AbstractList<E>
  - - java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>
    - - gov.nih.mipav.model.structures.VOIBase

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<WildMagic.LibFoundation.Mathematics.Vector3f>, java.util.Collection<WildMagic.LibFoundation.Mathematics.Vector3f>, java.util.List<WildMagic.LibFoundation.Mathematics.Vector3f>, java.util.RandomAccess

Direct Known Subclasses:

VOIContour, VOILine, VOIPoint, VOIPolyLineSlice, VOIProtractor, VOIText
```
public abstract class VOIBase
extends java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>
```
Base which holds the functions common to both Contour, Line and Point type VOI. Abstract class.

Version:

0.1 Jul 22, 1998

Author:

Matthew McAuliffe

See Also:

VOILine, $Logfile: /mipav/src/gov/nih/mipav/model/structures/VOIBase.java $ $Revision: 56 $ $Date: 2/24/06 3:34p $, Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`protected boolean`	`active`	Flag indicating whether or not a VOI is active (selected).
`protected boolean`	`autoLabel`	Automatically generate the label, unless it is set explicitly:
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`averagePt`	Stores the average of the contour of a VOI.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`cenMassPt`	Stores the black and white center of mass of the contour of a VOI.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`cenMassPtB`	Stores the blue center of mass of the contour of a VOI.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`cenMassPtG`	Stores the green center of mass of the contour of a VOI.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`cenMassPtR`	Stores the red center of mass of the contour of a VOI.
`static int`	`CIRCLE`
`protected boolean`	`closed`	True when this is a closed contour.
`protected boolean`	`display`	displays the voi in the volume renderer:
`private boolean`	`doGeometricCenterLabel`	If doGeometricCenterLabel = true and if active == false and if closed = true, execute drawGeometricCenterLabel when in drawSelf
`protected static int`	`DOWN`	The down arrow key.
`protected boolean`	`fixed`	Flag that indicates if the VOI is movable.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`gcPt`	Stores the geometric center of the contour of a VOI.
`protected java.lang.String`	`label`	Label (Name) for this member of the VOI.
`protected int`	`lastPoint`	Keeps track of the last near point value (for keyboard moving of individual pts.
`protected static int`	`LEFT`	The left arrow key.
`static int`	`LEFT_MIDDLE`
`static int`	`LOWER_LEFT`
`static int`	`LOWER_MIDDLE`
`static int`	`LOWER_RIGHT`
`protected WildMagic.LibFoundation.Mathematics.Vector3f[]`	`m_akImageMinMax`	Current contour bounding-box.
`protected boolean`	`m_bQuickLUT`	True is this is a QuickLUT contour.
`protected boolean`	`m_bReloadPoints`
`protected boolean`	`m_bSplit`	True is this is a split-line contour.
`protected boolean`	`m_bUpdateAverage`	Set to true if the geometric center needs updating.
`protected boolean`	`m_bUpdateBounds`	Set to true if the contour bounding-box needs updating.
`protected boolean`	`m_bUpdateGeometricCenter`	Set to true if the geometric center needs updating.
`protected boolean`	`m_bUpdateMask`	Set to true if the contour changes, so the mask will update when needed.
`protected boolean`	`m_bUpdatePlane`	Set to true if the contour plane needs updating.
`protected int`	`m_iAnchorIndex`	Anchor point.
`protected int`	`m_iPlane`	Current plane of this contour.
`protected int`	`m_iVOIType`	VOI type of this contour.
`protected WildMagic.LibFoundation.Mathematics.ColorRGBA`	`m_kColor`	Contour color.
`protected WildMagic.LibFoundation.Mathematics.Vector3f`	`m_kPositionSum`
`protected VolumeVOI`	`m_kVolumeVOI`	Data structure for drawing this contour in the GPU VolumeRenderer
`protected int`	`nearBoundPoint`	Flag used to indicate if the cursor is near a point on the VOI bounding box.
`protected int`	`nearPoint`	Flag used to indicate if the cursor is near a point of the VOI member.
`static int`	`NOT_A_PLANE`	If the points on the contour are not on the x,y, or z-plane.
`static int`	`NOT_A_POINT`	Used in places which usually remember an index into a point vector.
`protected int`	`numPixels`	Number of pixels in the array used in graphing intensity along the boundary.
`protected boolean`	`process`	If true this flag indicates that the shape should be included (applied) when processing the image.
`protected static int`	`RIGHT`	The right arrow key.
`static int`	`RIGHT_MIDDLE`
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`static int`	`SQUARE`
`private int`	`subtype`	initialize subtype to unknown
`static int`	`UNKNOWN_SUBTYPE`	available subtypes for VOI
`protected static int`	`UP`	The up arrow key.
`static int`	`UPPER_LEFT`
`static int`	`UPPER_MIDDLE`
`static int`	`UPPER_RIGHT`
`protected VOI`	`voiGroup`	Reference to the containing VOI object.
`protected float`	`volumeDisplayRange`	Used to display 3D VOIs in the three orthogonal views of the data in the volume renderer
`static int`	`XPLANE`	Used in determining if all points on the contour have the same x-value
`private float[]`	`xPts`
`static int`	`YPLANE`	Used in determining if all points on the contour have the same y-value
`private float[]`	`yPts`
`static int`	`ZPLANE`	Used in determining if all points on the contour have the same z-value
`private float[]`	`zPts`

Fields inherited from class java.util.Vector
capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList
modCount

Constructor Summary

Constructors
Constructor	Description
`VOIBase()`	Default Constructor.
`VOIBase(boolean bFixed, boolean bClosed)`	Constructor sets the fixed and closed flags.
`VOIBase(boolean bFixed, boolean bClosed, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kIn)`	Constructor, sets the fixed and closed flags and positions.
`VOIBase(boolean bFixed, boolean bClosed, WildMagic.LibFoundation.Mathematics.Vector3f kIn)`
`VOIBase(VOIBase kBase)`	Copies the input VOIBase into a new VOIBase object.
`VOIBase(VOIBase kBase, int iPropDir)`	Copies the input contour and changes it's slice +/-
`VOIBase(VOIBase kBase, TransMatrix tMatrix)`	Copies the input VOIBase, transformed by the input TransMatrix.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addElement(float x, float y, float z)`	Adds a point to the curve.
`void`	`addElement(int x, int y, int z)`	Adds a point to the curve.
`double`	`area()`
`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.
`float`	`calcIntensity(ModelImage kImage, int t)`	Calculated the total intensity contained within this contour.
`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.
`float`	`calcIntensityThreshold(ModelImage kImage, float threshold, int t)`	Calculates the total intensity contained within this contour, equal to of greater than the threshold.
`float`	`calcRGBIntensity(ModelImage kImage, int RGorB)`	Calculates the total intensity contained within this contour for the input color channel.
`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.
`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.
`abstract VOIBase`	`clone()`
`boolean`	`contain(float iX, float iY)`	This is used by SVM boundary training to identify the prostate boundary VOI landmark points.
`boolean`	`contains(float iX, float iY)`	Returns true if the input iX, iY is contained within this contour.
`boolean`	`contains(float iX, float iY, float iZ)`	Returns true if the input iX,iY,iZ is contained within this contour.
`boolean`	`contains(int _x, int _y, boolean forceReload)`
`private boolean`	`containsX(int y, int z)`
`private boolean`	`containsY(int x, int z)`
`private boolean`	`containsZ(int x, int y)`
`VolumeVOI`	`createVolumeVOI(VolumeImage kVolumeImage, WildMagic.LibFoundation.Mathematics.Vector3f kTranslate)`	Creates the VolumeVOI data structure for rendering this contour in the GPU VolumeRenderer
`void`	`cycleActivePt(int keyCode)`	Cycles through the active points on the curve.
`void`	`delete(int iPos)`	Deletes the specified position on the curve.
`void`	`deleteVolumeVOI()`
`void`	`display(boolean show)`	Turns the display setting on/off for the VolumeVOI displayed in the volume renderer.
`void`	`dispose()`	Deletes local data members.
`float`	`distanceToVOI(int iX, int iY, int iZ)`	Returns the smallest distance from the input point to this contour.
`boolean`	`equals(java.lang.Object o)`
`void`	`exportArrays(float[] x, float[] y, float[] z)`	Exports the float arrays of the points of the curve.
`void`	`exportArrays(int[] x, int[] y, int[] z)`	Exports the arrays of the points of the curve in int array format.
`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.
`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.
`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.
`void`	`fillVolume(ModelImage kVolume, java.util.BitSet kMask, boolean bIntersection, int iValue)`	Renders this contour into the input ModelImage or the input BitSet mask.
`private java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>`	`fillVolume(java.util.BitSet kMask, int xDim, int yDim)`	Renders this contour into the input mask.
`private void`	`fillX(int iX, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kMaskPositions, java.util.BitSet kMask, int xDim, int yDim)`
`private void`	`fillY(int iY, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kMaskPositions, java.util.BitSet kMask, int xDim, int yDim)`
`private void`	`fillZ(int iZ, java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> kMaskPositions, java.util.BitSet kMask, int xDim, int yDim)`
`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.
`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.
`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.
`int`	`findVOIIndentations2D(ModelImage kImage, int sliceNum, java.util.Vector<VOIBase> curves, boolean displayIndentations)`
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getActivePt()`	Gets the Vector3f of the active point.
`java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>`	`getAllContourPoints()`
`int`	`getAnchor()`	Returns the anchor point.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getAverage()`
`void`	`getBounds(float[] x, float[] y, float[] z)`	Calculates the bounds of the contour.
`void`	`getBounds(int[] x, int[] y, int[] z)`	Calculates the bounds of the contour.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getCenterOfMass(ModelImage kImage)`	Gets the center of mass of the contour for a given image
`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.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getCenterOfMassB(ModelImage kImage)`	Gets the blue center of mass of the contour.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getCenterOfMassG(ModelImage kImage)`	Gets the green center of mass of the contour.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getCenterOfMassR(ModelImage kImage)`	Gets the red center of mass of the contour.
`int`	`getContourID()`	Returns the contour ID: the index of this contour into the VOI.
`boolean`	`getDoGeometricCenterLabel()`	If doGeometricCenterLabel = true and active == false and closed = true, execute drawGeometricCenterLabel when in drawSelf
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getGeometricCenter()`	Gets the geometric center of the contour.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getGeometricCenterA()`
`VOI`	`getGroup()`	Returns the VOI object that contains this contour.
`WildMagic.LibFoundation.Mathematics.Vector3f[]`	`getImageBoundingBox()`	Returns the contour bounding-box.
`java.lang.String`	`getLabel()`	Gets the label of the VOI.
`int`	`getLastNumPixels()`	Accessor that returns the number of points used in the most recent intensity calculation of this contour.
`double`	`getLengthPtToPt(float[] resolutions)`	Returns the total length of this contour, based on the input resolutions.
`double`	`getLengthPtToPt(float[][] resolutions)`	Returns the total length of this contour, based on the input resolutions.
`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.
`java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>`	`getMaskPositions()`
`java.lang.String`	`getName()`	Gets the name of the VOI that contains this contour, null if this contour is not contained in a VOI.
`int`	`getNearBoundPoint()`
`int`	`getNearPoint()`	Returns the point on the curve nearest the cursor, calculated by nearLine, etc.
`int`	`getNumVoxels()`
`int`	`getPlane()`	Determines if the points on the contour lie on either the x,y,or z-planes.
`boolean`	`getProcess()`	Accessor that returns the process.
`int`	`getSelectedPoint()`	Returns the last selected point.
`int`	`getSubtype()`
`java.lang.String`	`getTotalLengthString(float[] afResolutions, int[] aiUnits)`	Returns the total length of this contour as a string.
`int`	`getType()`	Returns the type of this contour.
`float`	`getVolumeDisplayRange()`
`VolumeVOI`	`getVolumeVOI()`	Returns the VolumeVOI data member used to draw this contour in the GPU VOlumeRenderer.
`void`	`importArrays(float[] x, float[] y, float[] z, int n)`	Imports new position values into this contour.
`void`	`importArrays(int[] x, int[] y, int[] z, int n)`	Imports new position values into this contour.
`void`	`importPoints(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)`	Imports new position values into this contour.
`boolean`	`isActive()`	Accessor to flag that indicates if an VOI is active.
`boolean`	`isClosed()`	Flag used to indicate type of contour: true = closed contour (i.e.
`boolean`	`isFixed()`	Accessor to flag that indicates if an VOI is fixed (movable).
`boolean`	`isM_bUpdateBounds()`
`boolean`	`isM_bUpdateGeometricCenter()`
`boolean`	`isQuickLUT()`	Returns true if this is a QuickLUT contour.
`boolean`	`isSplit()`	Returns true if this is a split-line contour.
`boolean`	`nearLine(int iX, int iY, int iZ)`	Returns true if the input position is near the outline of this contour.
`boolean`	`nearLine(int iX, int iY, int iZ, int tol)`	Returns true if the input position is near the outline of this contour.
`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.
`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.
`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.
`WildMagic.LibFoundation.Mathematics.Plane3f`	`planeFit()`	Fits a plane to the points in this contour and returns the plane.
`void`	`reloadPoints()`	Reloads points in this array for speed purposes.
`void`	`setActive(boolean active)`	Sets flag to indicate whether or not VOI is active.
`void`	`setAnchor()`	Sets the anchor point.
`void`	`setClosed(boolean bClosed)`	Sets this contour as open or closed.
`void`	`setDoGeometricCenterLabel(boolean doGeometricCenterLabel)`	If doGeometricCenterLabel = true and active == false and closed = true, execute drawGeometricCenterLabel when in drawSelf
`void`	`setFixed(boolean fixed)`	Sets flag to indicate whether or not VOI is fixed.
`void`	`setGroup(VOI kGroup)`	Sets the VOI object that contains this contour.
`void`	`setLabel(java.lang.String str)`	Sets the label of the VOI.
`void`	`setMask(java.util.BitSet kMask, int xDim, int yDim, boolean XOR, int polarity)`
`void`	`setMaskSlice(java.util.BitSet kMask, int xDim, boolean XOR, int polarity)`
`void`	`setNearBoundPoint(int i)`	Sets the near boundary point.
`void`	`setNearPoint(int i)`	Sets the near point.
`void`	`setPlane(int iPlane)`
`void`	`setProcess(boolean process)`	Sets whether the shape is included in processing.
`void`	`setQuickLUT(boolean bQuickLUT)`	Sets the QuickLUT flag.
`void`	`setSelectedPoint(int i)`	Sets the selected point.
`void`	`setSplit(boolean bSplit)`	Sets the split flag.
`void`	`setSubtype(int subtype)`
`void`	`setVolumeDisplayRange(float range)`
`int`	`slice()`	Returns the slice value of the contour on every plane.
`int`	`slice(int iPlane)`	Returns the point value the contour has in common if it lies in the given plane.
`private static void`	`sortCrossingPoints(float[] aiList, int iNumElements)`	Sorts the edge crossing points in place.
`void`	`transform(TransMatrix tMatrix)`	Copies the input VOIBase, transformed by the input TransMatrix.
`void`	`trimPoints(double constraint, boolean tFlag)`	Trims a contour and then removes collinear points in the resulting contour.
`void`	`update()`	The contour has changed, set the update flags so statistics are recalculated when needed.
`void`	`update(WildMagic.LibFoundation.Mathematics.ColorRGBA kColor)`	Set the color of this contour.
`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.

Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clear, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, firstElement, forEach, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, iterator, lastElement, lastIndexOf, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeIf, removeRange, replaceAll, retainAll, set, setElementAt, setSize, size, sort, spliterator, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection
parallelStream, stream, toArray

- 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

Class VOIBase

Field Summary

Fields inherited from class java.util.Vector

Fields inherited from class java.util.AbstractList

Constructor Summary

Method Summary

Methods inherited from class java.util.Vector

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Collection

Field Detail

serialVersionUID

XPLANE

YPLANE

ZPLANE

NOT_A_PLANE

UPPER_LEFT

UPPER_RIGHT

LOWER_LEFT

LOWER_RIGHT

UPPER_MIDDLE

LEFT_MIDDLE

RIGHT_MIDDLE

LOWER_MIDDLE

NOT_A_POINT

UP

LEFT

DOWN

RIGHT

active

gcPt

averagePt

cenMassPt

cenMassPtR

cenMassPtG

cenMassPtB

fixed

label

autoLabel

lastPoint

nearPoint

nearBoundPoint

voiGroup

process

doGeometricCenterLabel

m_bUpdateMask

m_bUpdateBounds

m_bUpdateGeometricCenter

m_bUpdateAverage

m_bReloadPoints

m_bUpdatePlane

m_iVOIType

m_iAnchorIndex

closed

m_bSplit

m_bQuickLUT

m_iPlane

m_akImageMinMax

m_kColor

m_kVolumeVOI

volumeDisplayRange

numPixels

m_kPositionSum

UNKNOWN_SUBTYPE

CIRCLE

SQUARE

subtype

display

xPts

yPts

zPts

Constructor Detail

VOIBase

VOIBase

VOIBase

VOIBase

VOIBase

VOIBase

VOIBase

Method Detail

sortCrossingPoints