java.lang.Object
- gov.nih.mipav.model.structures.ModelSerialCloneable
- - gov.nih.mipav.model.structures.VOI

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable
```
public class VOI
extends ModelSerialCloneable
```
This the Volume Of Interest (VOI) structure. An image can have 32565 different VOIs. A VOI can have multiple contours in a single slice or in other slices. VOIs can be additive or subtractive so that doughnut like objects can be made. A VOI can be different types: annotation, point, line, protractor, polyline and contour. Event-handling routines: to add this object to send out events for listening objects, at least the following 3 methods must be present: addListener, removeListener, fireEvent as present below.

Version:

0.1 Oct 27, 1997

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`private boolean`	`active`
`static int`	`ADDITIVE`	Mask as ones - i.e. put ones to indicate VOI location
`static int`	`ANNOTATION`	Indicates that the VOI is of type ANNOTATION for adding text annotations to an image.
`static int`	`BACK`	Static Variables for VOI and VOI Contour selection.
`static int`	`BACKWARD`	Static Variables for VOI and VOI Contour selection.
`static int`	`BOUNDARY`	Indicates only the boundary of the VOI should be displayed.
`private boolean`	`boundingBox`	If true the bounding box of the VOI should be displayed.
`static int`	`CARDIOLOGY`	Indicates that the VOI is of type CARDIOLOGY, special VOI for specific tasks needed in cardiology.
`private java.awt.Color`	`color`	Indicates the color or the VOI.
`private java.util.ArrayList<java.lang.String>`	`comments`
`static int`	`CONTOUR`	Indicates that the VOI is of type CONTOUR.
`private ViewJFrameGraph`	`contourGraph`	ViewJFrameGraph for graphing contours in this VOI
`private VOIBaseVector`	`curves`	A vector array of curves per slice.
`private int`	`curveType`	Indicates the type of VOI (i.e.
`private int`	`displayMode`	Indicates if the VOI should be shown as a boundary or a solid.
`private java.lang.String`	`extension`	extension of voi file name of voi was read in through file
`private boolean`	`fixed`	If true the VOI cannot be moved, if false this VOI can be moved.
`static int`	`FORWARD`	Static Variables for VOI and VOI Contour selection.
`static int`	`FRONT`	Static Variables for VOI and VOI Contour selection.
`private short`	`ID`	ID of the VOI, also used when choosing the display color.
`private float`	`ignoreMax`	Sets the maximum intensity value for operations on B & W images segmented by this VOI
`private float`	`ignoreMaxB`	Sets the maximum blue intensity value for operations on RGB images segmented by this VOI
`private float`	`ignoreMaxG`	Sets the maximum green intensity value for operations on RGB images segmented by this VOI
`private float`	`ignoreMaxR`	Sets the maximum red intensity value for operations on RGB images segmented by this VOI
`private float`	`ignoreMin`	Sets the minimum intensity value for operations on B & W images segmented by this VOI
`private float`	`ignoreMinB`	Sets the minimum blue intensity value for operations on RGB images segmented by this VOI
`private float`	`ignoreMinG`	Sets the minimum green intensity value for operations on RGB images segmented by this VOI
`private float`	`ignoreMinR`	Sets the minimum red intensity value for operations on RGB images segmented by this VOI
`static int`	`LINE`	Indicates that the VOI is of type Line made up of two points.
`javax.swing.event.EventListenerList`	`listenerList`	VOIListeners that are updated when this VOI changes
`private java.lang.String`	`name`	Name of the VOI stored as a string.
`int`	`NOT_A_POINT`	int indicating that no point was found.
`private float`	`opacity`	When in the solid display mode indicates how opaque the VOI should be.
`static int`	`POINT`	Indicates that the POINT is of type Line made up of a single point.
`private int`	`polarity`	Indicates if the VOI should mask ones or mask as zeros.
`static int`	`POLYLINE`	Indicates that the VOI is of type POLYLINE type of contour - end points NOT connected.
`static int`	`POLYLINE_SLICE`	Indicates that the VOI is of type POLYLINE that will go through more than one slice.
`private boolean`	`process`	If true this flag indicates that the VOI should be included (applied) when processing the image.
`static int`	`PROTRACTOR`	Indicates that the VOI is of type PROTRACTOR used to measure angles.
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`static int`	`SOLID`	Indicates that the VOI should be displayed as a solid and not just a boundary.
`static int`	`SUBTRACTIVE`	Mask as zeros - i.e. put zeros to indicate where the VOI is located
`private int`	`thickness`	The thickness of the VOI lines
`private int`	`UID`	Unique ID for saving & retrieving.
`private boolean`	`visible`	If true the VOI is visible.
`private short`	`watershedID`	Used to objects a label or ID inconjuction with the watershed algorithm.
`private float[]`	`xBounds`	The x - dimension bounds: xBounds [0] = min and xBounds[1] = max.
`private float[]`	`yBounds`	The y - dimension bounds: yBounds [0] = min and yBounds[1] = max.
`private float[]`	`zBounds`	The z - dimension bounds: zBounds [0] = min and zBounds[1] = max.

Constructor Summary

Constructors
Constructor	Description
`VOI(short id, java.lang.String name)`	Create a VOI with the given id and name.
`VOI(short id, java.lang.String name, int curveType, float presetHue)`	Constructs a Volume of Interest (VOI).
`VOI(short id, java.lang.String name, int curveType, float presetHue, int initialCapacity)`	Constructs a Volume of Interest (VOI).
`VOI(VOI kVOI)`	Copies the VOI into a new VOI object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`void`	`addVOIListener(VOIListener listener)`	adds the update listener.
`double`	`area()`	Finds the area of the entire VOI of the VOIContour type only.
`double`	`calcLargestDistance(java.util.BitSet mask, int[] extents, float[] res)`	Calculate the distance of the largest line segment contained entirely within the VOI
`static double`	`calcLargestDistance(java.util.BitSet mask, int[] extents, float xRes, float yRes, float zRes, float[] xPts, float[] yPts, float[] zPts, WildMagic.LibFoundation.Mathematics.Vector3f kPos1, WildMagic.LibFoundation.Mathematics.Vector3f kPos2)`
`java.lang.Object`	`clone()`	Clone function that calls the super (modelserializable) clone and then manually copies references to the transient VOIListeners (eventlistenerlist)
`void`	`createActiveContourBinaryMask(java.util.BitSet mask, int xDim, int yDim)`	Creates a binary mask at every slice.
`void`	`createBinaryImage(ModelImage image, boolean XOR, boolean onlyActive)`	Forms a binary representation of the VOI into the image.
`java.util.BitSet`	`createBinaryMask(int xDim, int yDim, int slice)`	Creates a binary mask at a slice for that slice only.
`java.util.BitSet`	`createBinaryMask(int xDim, int yDim, int slice, VOIBase contour)`	Creates a binary mask at a slice for that slice and element only.
`void`	`createBinaryMask(int xDim, int yDim, int slice, java.util.BitSet mask, boolean XOR, boolean onlyActive)`	Creates a binary mask at a slice.
`void`	`createBinaryMask3D(java.util.BitSet mask, int xDim, int yDim, boolean XOR, boolean onlyActive)`	Creates a 3D binary mask.
`void`	`createOneElementBinaryMask3D(java.util.BitSet mask, int xDim, int yDim, boolean XOR, boolean onlyActive, int elementNum)`	Creates a 3D binary mask.
`void`	`createShortImage(ModelImage image, int offset, boolean XOR, boolean onlyActive)`	Creates a short image of the VOI.
`short[]`	`createShortMask(short[] mask, int xDim, int yDim, int zDim, boolean XOR)`	Creates a short mask at a slice.
`void`	`createUByteImage(ModelImage image, int offset, boolean XOR, boolean onlyActive)`	Creates a short image of the VOI.
`private static double[]`	`determineMaxAvg(float xRes, float yRes, float zRes, float[] xPts, float[] yPts, float[] zPts)`	Gathers max and average statistics to build guessing intervals
`void`	`dispose()`
`boolean`	`equals(java.lang.String str)`	two VOIs are the same if they have the same name.
`WildMagic.LibFoundation.Mathematics.Vector3f[]`	`exportAllPoints()`	Get Vector3fs from the VOI; can only use with Point.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`exportPoint()`	Returns the first point.
`java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>`	`exportPoints(int slice)`	Get Vector3fs from the VOI; can only use with Point.
`java.util.Vector<java.awt.Polygon>`	`exportPolygon(int iSlice)`
`void`	`finalize()`
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`findMaxWidth(WildMagic.LibFoundation.Mathematics.Vector3f pt, double[] maxDistance, boolean bOnlyActive)`	This is used by the method maxWidth.
`protected void`	`fireVOIBaseAdded(VOIBase curve)`	Fires a VOI event based on the VOI. calls the listener's `addedVOI()` method.
`protected void`	`fireVOIBaseRemoved(VOIBase curve)`	Fires a VOI event based on the VOI. calls the listener's `removedVOI()` method.
`protected void`	`fireVOIColorChange(java.awt.Color color)`	Deprecated.
`protected void`	`fireVOIselection()`	Fires a VOI event based on the VOI. calls the listener's `removedVOI()` method.
`private static void`	`gatherBoundedPoints(java.util.ArrayList<java.lang.Integer> orig, java.util.ArrayList<java.lang.Integer> term, double lowerBound, double upperBound, float xRes, float yRes, float zRes, float[] xPts, float[] yPts, float[] zPts)`	Gathers the points that fall within the required bounds
`boolean`	`getBoundingBoxFlag()`	Accessor that returns the bounding box flag.
`void`	`getBounds(float[] x, float[] y, float[] z)`	Calculates the extents or boundary of the voi in x, y, and z.
`void`	`getBounds(int[] x, int[] y, int[] z)`	Calculates the extents or boundary of the voi in x, y, and z.
`java.awt.Color`	`getColor()`	Accessor that returns the VOI's color.
`java.util.ArrayList<java.lang.String>`	`getComments()`
`ViewJFrameGraph`	`getContourGraph()`	Returns the contour graph associated with this voi.
`VOIBaseVector`	`getCurves()`	Accessor that returns the curves making up the VOI.
`int`	`getCurveType()`	Accessor that returns the curve type.
`int`	`getDisplayMode()`	Accessor that returns the display mode.
`java.lang.String`	`getExtension()`	Accessor that returns the VOI extension.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getGeometricCenter()`	Returns the geometric center of the VOI (only contour).
`short`	`getID()`	Accessor that returns the ID.
`private static double`	`getLargest(java.util.BitSet mask, int[] extents, java.util.ArrayList<java.lang.Integer> orig, java.util.ArrayList<java.lang.Integer> term, float xRes, float yRes, float zRes, float[] xPoints, float[] yPoints, float[] zPoints, WildMagic.LibFoundation.Mathematics.Vector3f kPos1, WildMagic.LibFoundation.Mathematics.Vector3f kPos2)`	Finds the largest line that lies within entirely within the VOI.
`float`	`getMaximumIgnore()`	Accessor that returns the maximum of the range of intensities to ignore.
`float`	`getMaximumIgnoreB()`	Accessor that returns the maximum of the range of blue intensities to ignore.
`float`	`getMaximumIgnoreG()`	Accessor that returns the maximum of the range of green intensities to ignore.
`float`	`getMaximumIgnoreR()`	Accessor that returns the maximum of the range of red intensities to ignore.
`float`	`getMinimumIgnore()`	Accessor that returns the minimum of the range of intensities to ignore.
`float`	`getMinimumIgnoreB()`	Accessor that returns the minimum of the range of blue intensities to ignore.
`float`	`getMinimumIgnoreG()`	Accessor that returns the minimum of the range of green intensities to ignore.
`float`	`getMinimumIgnoreR()`	Accessor that returns the minimum of the range of red intensities to ignore.
`java.lang.String`	`getName()`	Accessor that returns the name of the VOI.
`int`	`getNumPoints()`	Get the number of points in the VOI file.
`float`	`getOpacity()`	Accessor that returns the opacity of the VOI.
`void`	`getPointCoordinates(float[] coord)`	This method is used to get the coordinates of a single VOIPoint.
`int`	`getPolarity()`	Accessor that returns.
`int`	`getPositionAndIntensity(int slice, int contourNo, WildMagic.LibFoundation.Mathematics.Vector3f[] position, float[] intensity, float[] imageBuffer, int xDim)`	Gets the position and intensity for this VOI if it's a line.
`boolean`	`getProcess()`	Accessor that returns whether voi is included in processing.
`int`	`getSize()`	Returns the number of contours in this VOI.
`java.util.Vector<VOIBase>`	`getSliceCurves(int iSlice)`	Returns a list of contours on a given slice.
`java.util.Vector<VOIBase>`	`getSliceCurves(int iPlane, int iSlice)`	Returns a list of contours for the given image orientation and slice.
`int`	`getSliceSize(int iSlice)`	Returns the number of contours for a given slice.
`int`	`getSliceSize(int iPlane, int iSlice)`	Returns the number of contours for a given image orientation and slice in a 3D image.
`java.util.Vector<VOIBase>[]`	`getSortedCurves(int iDim)`	Sorts the contours based on the image default orientation.
`java.util.Vector<VOIBase>[]`	`getSortedCurves(int iPlane, int iDim)`	Sorts the contours based on a given image orientation and the desired image depth for that orientation.
`int`	`getThickness()`	Returns the thickness of the VOI
`int`	`getUID()`	Accessor that returns the Unique ID (original hash code for object).
`int`	`getVOISlices()`	Returns the number of z slices actually containing part of the voi
`short`	`getWatershedID()`	getWatershedID - accessor that returns the watershedID.
`boolean`	`hasListener(VOIListener listener)`
`VOIBase`	`importCurve(float[] x, float[] y, float[] z)`	Imports a new curve into this voi.
`void`	`importCurve(int[] x, int[] y, int[] z)`
`void`	`importCurve(VOIBase curve)`	Imports the curve into the VOI.
`void`	`importCurve(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)`	Imports the curve into the VOI, testing for which type.
`void`	`importNewVOI(int slice, int voiSlice, VOI voi, boolean resize)`	Imports just the VOIs in a slice into this VOI.
`void`	`importPoint(WildMagic.LibFoundation.Mathematics.Vector3f point)`	Import a new point into this VOI.
`void`	`importPoint(WildMagic.LibFoundation.Mathematics.Vector3f point, boolean notifyListener)`	Import a new point into this VOI.
`void`	`importPolygon(java.awt.Polygon gon, int slice)`	Imports the polygon into the VOI (must be a contour).
`boolean`	`isActive()`	Accessor that tells if the VOI is active.
`boolean`	`isAllActive()`	Returns true iff all contours in this VOI are active.
`boolean`	`isEmpty()`	Test whether or not the VOI is empty.
`boolean`	`isFixed()`	Accessor that tells if VOI is fixed.
`boolean`	`isVisible()`	Accessor that tells if the VOI is visible.
`WildMagic.LibFoundation.Mathematics.Vector3f[]`	`maxWidth(boolean bOnlyActive)`	Finds 2 points that form the maximum width of the VOI.
`void`	`moveVOI(int slice, int xDim, int yDim, int zDim, int xM, int yM, int zM)`	Move VOI to a new position.
`boolean`	`nearLine(int x, int y, int slice)`	Tests if a point is near a line.
`boolean`	`nearPoint(int x, int y, int slice)`	Tests if a point is near a point.
`(package private) void`	`notifyParentVOIProcess(boolean flag)`	Allows VOIBase's to set their parent's process flag without affecting other contours.
`float`	`pointToContour(int x, int y, int z)`	Finds the minimum distance from a point to a contour.
`void`	`removeAllVOIListeners()`
`void`	`removeCurve(VOIBase kCurve)`	Clears VOI of all curves at a slice.
`void`	`removeCurves()`	Clears VOI of all curves.
`void`	`removeCurves(int slice)`	Deprecated.
`void`	`removeVOIListener(VOIListener listener)`	removes the update listener.
`void`	`setActive(boolean act)`	Sets whether or not the VOI is active.
`void`	`setAllActive(boolean flag)`	Sets all contours in the VOI as active or inactive.
`void`	`setBoundingBoxFlag(boolean flag)`	Accessor that sets the flag to the parameter.
`void`	`setColor(float hue)`	Accessor that sets the color to the parameter.
`void`	`setColor(java.awt.Color color)`	Accessor that sets the color to the parameter.
`void`	`setComments(java.lang.String comment)`
`void`	`setContourGraph(ViewJFrameGraph newGraph)`	Accessor that sets the contourGraph to the parameter.
`void`	`setCurves(VOIBaseVector newCurves)`	Sets the list of contours in this VOI to a new list.
`void`	`setCurveType(int curveType)`	Accessor that sets the curveType to the parameter.
`void`	`setDisplayMode(int mode)`	Accessor that sets the display mode to the parameter.
`void`	`setExtension(java.lang.String extension)`	Sets the VOI extenstion of voi file name of voi was read in through file
`void`	`setFixed(boolean fixed)`	Sets whether or not the VOI is fixed.
`void`	`setID(short ID)`	Accessor that sets the ID to the parameter.
`void`	`setMaximumIgnore(float max)`	Accessor that sets the maximum of the range of intensities to ignore.
`void`	`setMaximumIgnoreB(float max)`	Accessor that sets the maximum of the range of blue intensities to ignore.
`void`	`setMaximumIgnoreG(float max)`	Accessor that sets the maximum of the range of green intensities to ignore.
`void`	`setMaximumIgnoreR(float max)`	Accessor that sets the maximum of the range of red intensities to ignore.
`void`	`setMinimumIgnore(float min)`	Accessor that sets the minimum of the range of intensities to ignore.
`void`	`setMinimumIgnoreB(float min)`	Accessor that sets the minimum of the range of blue intensities to ignore.
`void`	`setMinimumIgnoreG(float min)`	Accessor that sets the minimum of the range of green intensities to ignore.
`void`	`setMinimumIgnoreR(float min)`	Accessor that sets the minimum of the range of red intensities to ignore.
`void`	`setName(java.lang.String name)`	Accessor that sets the VOI's name to the parameter.
`void`	`setOnlyID(short ID)`	Accessor that sets the ID to the parameter.
`void`	`setOpacity(float opacity)`	Accessor that sets the opacity to the parameter.
`void`	`setPolarity(int polarity)`	Accessor that sets the polarity to the parameter.
`void`	`setProcess(boolean flag)`	Accessor that sets the flag to the parameter.
`void`	`setThickness(int newThickness)`	Sets the thickness of the VOI
`void`	`setUID(int uid)`	Sets the unique ID (for saving/retreiving treatment details).
`void`	`setWatershedID(short wID)`	Accessor that sets the ID to the parameter.
`void`	`setXYDim(int xDim, int yDim)`	Deprecated.
`java.lang.String`	`toString()`
`void`	`trim()`	Trims all active contours in the VOI based on the Preferences getTrim and getTrimAdjacent values.
`void`	`update()`
`void`	`updateActive()`

Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable
nativeClone

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

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Use serialVersionUID for interoperability.
    
    See Also:
    
    Constant Field Values
  - FORWARD
```
public static final int FORWARD
```
    Static Variables for VOI and VOI Contour selection.
    
    See Also:
    
    Constant Field Values
  - BACKWARD
```
public static final int BACKWARD
```
    Static Variables for VOI and VOI Contour selection.
    
    See Also:
    
    Constant Field Values
  - FRONT
```
public static final int FRONT
```
    Static Variables for VOI and VOI Contour selection.
    
    See Also:
    
    Constant Field Values
  - BACK
```
public static final int BACK
```
    Static Variables for VOI and VOI Contour selection.
    
    See Also:
    
    Constant Field Values
  - BOUNDARY
```
public static final int BOUNDARY
```
    Indicates only the boundary of the VOI should be displayed.
    
    See Also:
    
    Constant Field Values
  - SOLID
```
public static final int SOLID
```
    Indicates that the VOI should be displayed as a solid and not just a boundary.
    
    See Also:
    
    Constant Field Values
  - ADDITIVE
```
public static final int ADDITIVE
```
    Mask as ones - i.e. put ones to indicate VOI location
    
    See Also:
    
    Constant Field Values
  - SUBTRACTIVE
```
public static final int SUBTRACTIVE
```
    Mask as zeros - i.e. put zeros to indicate where the VOI is located
    
    See Also:
    
    Constant Field Values
  - CONTOUR
```
public static final int CONTOUR
```
    Indicates that the VOI is of type CONTOUR.
    
    See Also:
    
    Constant Field Values
  - POLYLINE
```
public static final int POLYLINE
```
    Indicates that the VOI is of type POLYLINE type of contour - end points NOT connected.
    
    See Also:
    
    Constant Field Values
  - LINE
```
public static final int LINE
```
    Indicates that the VOI is of type Line made up of two points.
    
    See Also:
    
    Constant Field Values
  - POINT
```
public static final int POINT
```
    Indicates that the POINT is of type Line made up of a single point.
    
    See Also:
    
    Constant Field Values
  - PROTRACTOR
```
public static final int PROTRACTOR
```
    Indicates that the VOI is of type PROTRACTOR used to measure angles.
    
    See Also:
    
    Constant Field Values
  - ANNOTATION
```
public static final int ANNOTATION
```
    Indicates that the VOI is of type ANNOTATION for adding text annotations to an image.
    
    See Also:
    
    Constant Field Values
  - CARDIOLOGY
```
public static final int CARDIOLOGY
```
    Indicates that the VOI is of type CARDIOLOGY, special VOI for specific tasks needed in cardiology.
    
    See Also:
    
    Constant Field Values
  - POLYLINE_SLICE
```
public static final int POLYLINE_SLICE
```
    Indicates that the VOI is of type POLYLINE that will go through more than one slice.
    
    See Also:
    
    Constant Field Values
  - NOT_A_POINT
```
public final int NOT_A_POINT
```
    int indicating that no point was found.
    
    See Also:
    
    Constant Field Values
  - boundingBox
```
private boolean boundingBox
```
    If true the bounding box of the VOI should be displayed.
  - color
```
private java.awt.Color color
```
    Indicates the color or the VOI.
  - thickness
```
private int thickness
```
    The thickness of the VOI lines
  - contourGraph
```
private transient ViewJFrameGraph contourGraph
```
    ViewJFrameGraph for graphing contours in this VOI
  - curves
```
private VOIBaseVector curves
```
    A vector array of curves per slice.
  - curveType
```
private int curveType
```
    Indicates the type of VOI (i.e. CONTOUR, POLYLINE, LINE, POINT, PROTRACTOR, etc. ... )
  - displayMode
```
private int displayMode
```
    Indicates if the VOI should be shown as a boundary or a solid.
  - fixed
```
private boolean fixed
```
    If true the VOI cannot be moved, if false this VOI can be moved.
  - ID
```
private short ID
```
    ID of the VOI, also used when choosing the display color.
  - ignoreMax
```
private float ignoreMax
```
    Sets the maximum intensity value for operations on B & W images segmented by this VOI
  - ignoreMin
```
private float ignoreMin
```
    Sets the minimum intensity value for operations on B & W images segmented by this VOI
  - ignoreMaxR
```
private float ignoreMaxR
```
    Sets the maximum red intensity value for operations on RGB images segmented by this VOI
  - ignoreMinR
```
private float ignoreMinR
```
    Sets the minimum red intensity value for operations on RGB images segmented by this VOI
  - ignoreMaxG
```
private float ignoreMaxG
```
    Sets the maximum green intensity value for operations on RGB images segmented by this VOI
  - ignoreMinG
```
private float ignoreMinG
```
    Sets the minimum green intensity value for operations on RGB images segmented by this VOI
  - ignoreMaxB
```
private float ignoreMaxB
```
    Sets the maximum blue intensity value for operations on RGB images segmented by this VOI
  - ignoreMinB
```
private float ignoreMinB
```
    Sets the minimum blue intensity value for operations on RGB images segmented by this VOI
  - name
```
private java.lang.String name
```
    Name of the VOI stored as a string.
  - opacity
```
private float opacity
```
    When in the solid display mode indicates how opaque the VOI should be. Zero is transparent and one is opaque.
  - polarity
```
private int polarity
```
    Indicates if the VOI should mask ones or mask as zeros.
  - process
```
private boolean process
```
    If true this flag indicates that the VOI should be included (applied) when processing the image.
  - UID
```
private int UID
```
    Unique ID for saving & retrieving.
  - visible
```
private boolean visible
```
    If true the VOI is visible.
  - watershedID
```
private short watershedID
```
    Used to objects a label or ID inconjuction with the watershed algorithm.
  - xBounds
```
private float[] xBounds
```
    The x - dimension bounds: xBounds [0] = min and xBounds[1] = max.
  - yBounds
```
private float[] yBounds
```
    The y - dimension bounds: yBounds [0] = min and yBounds[1] = max.
  - zBounds
```
private float[] zBounds
```
    The z - dimension bounds: zBounds [0] = min and zBounds[1] = max.
  - extension
```
private java.lang.String extension
```
    extension of voi file name of voi was read in through file
  - active
```
private boolean active
```
  - listenerList
```
public transient javax.swing.event.EventListenerList listenerList
```
    VOIListeners that are updated when this VOI changes
  - comments
```
private java.util.ArrayList<java.lang.String> comments
```
- Constructor Detail
  - VOI
```
public VOI(short id,
           java.lang.String name)
```
    Create a VOI with the given id and name.
    
    Parameters:
    
    id - identifier of VOI
    
    name - name of the VOI
  - VOI
```
public VOI(short id,
           java.lang.String name,
           int curveType,
           float presetHue)
```
    Constructs a Volume of Interest (VOI).
    
    Parameters:
    
    id - identifier of VOI
    
    name - name of the VOI
    
    curveType - type of curve, either a line or a contour
    
    presetHue - If presetHue >= 0.0, use this value as the hue
  - VOI
```
public VOI(short id,
           java.lang.String name,
           int curveType,
           float presetHue,
           int initialCapacity)
```
    Constructs a Volume of Interest (VOI).
    
    Parameters:
    
    id - identifier of VOI
    
    name - name of the VOI
    
    curveType - type of curve, either a line or a contour
    
    presetHue - If presetHue >= 0.0, use this value as the hue
  - VOI
```
public VOI(VOI kVOI)
```
    Copies the VOI into a new VOI object.
    
    Parameters:
    
    kVOI - VOI to copy.
- Method Detail
  - calcLargestDistance
```
public static double calcLargestDistance(java.util.BitSet mask,
                                         int[] extents,
                                         float xRes,
                                         float yRes,
                                         float zRes,
                                         float[] xPts,
                                         float[] yPts,
                                         float[] zPts,
                                         WildMagic.LibFoundation.Mathematics.Vector3f kPos1,
                                         WildMagic.LibFoundation.Mathematics.Vector3f kPos2)
```
  - determineMaxAvg
```
private static double[] determineMaxAvg(float xRes,
                                        float yRes,
                                        float zRes,
                                        float[] xPts,
                                        float[] yPts,
                                        float[] zPts)
```
    Gathers max and average statistics to build guessing intervals
  - gatherBoundedPoints
```
private static void gatherBoundedPoints(java.util.ArrayList<java.lang.Integer> orig,
                                        java.util.ArrayList<java.lang.Integer> term,
                                        double lowerBound,
                                        double upperBound,
                                        float xRes,
                                        float yRes,
                                        float zRes,
                                        float[] xPts,
                                        float[] yPts,
                                        float[] zPts)
```
    Gathers the points that fall within the required bounds
  - getLargest
```
private static double getLargest(java.util.BitSet mask,
                                 int[] extents,
                                 java.util.ArrayList<java.lang.Integer> orig,
                                 java.util.ArrayList<java.lang.Integer> term,
                                 float xRes,
                                 float yRes,
                                 float zRes,
                                 float[] xPoints,
                                 float[] yPoints,
                                 float[] zPoints,
                                 WildMagic.LibFoundation.Mathematics.Vector3f kPos1,
                                 WildMagic.LibFoundation.Mathematics.Vector3f kPos2)
```
    Finds the largest line that lies within entirely within the VOI.
  - addVOIListener
```
public void addVOIListener(VOIListener listener)
```
    adds the update listener.
    
    Parameters:
    
    listener - VOIListener.
  - area
```
public double area()
```
    Finds the area of the entire VOI of the VOIContour type only.
    
    Returns:
    
    returns the area
  - calcLargestDistance
```
public double calcLargestDistance(java.util.BitSet mask,
                                  int[] extents,
                                  float[] res)
```
    Calculate the distance of the largest line segment contained entirely within the VOI
    
    Parameters:
    
    xRes -
    
    yRes -
    
    zRes -
    
    Returns:
    
    largestDistance
  - clone
```
public java.lang.Object clone()
```
    Clone function that calls the super (modelserializable) clone and then manually copies references to the transient VOIListeners (eventlistenerlist)
    
    Overrides:
    
    clone in class ModelSerialCloneable
    
    Returns:
    
    The cloned object. Null if there was an error.
  - createActiveContourBinaryMask
```
public void createActiveContourBinaryMask(java.util.BitSet mask,
                                          int xDim,
                                          int yDim)
```
    Creates a binary mask at every slice.
    
    Parameters:
    
    mask - the binary mask
    
    xDim - x dimension, used to index into the image
    
    yDim - y dimension, used to index into the image
  - createBinaryImage
```
public void createBinaryImage(ModelImage image,
                              boolean XOR,
                              boolean onlyActive)
```
    Forms a binary representation of the VOI into the image.
    
    Parameters:
    
    image - boolean image where VOI bits are to be set.
    
    XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
    
    onlyActive - Only mask regions that are active (i.e. selected )
  - createBinaryMask
```
public java.util.BitSet createBinaryMask(int xDim,
                                         int yDim,
                                         int slice)
```
    Creates a binary mask at a slice for that slice only.
    
    Parameters:
    
    xDim - x dimension, used to index into the image
    
    yDim - y dimension, used to index into the image
    
    slice - slice to create mask at
    
    Returns:
    
    mask the binary mask
  - createBinaryMask
```
public void createBinaryMask(int xDim,
                             int yDim,
                             int slice,
                             java.util.BitSet mask,
                             boolean XOR,
                             boolean onlyActive)
```
    Creates a binary mask at a slice.
    
    Parameters:
    
    xDim - x dimension, used to index into the image
    
    yDim - y dimension, used to index into the image
    
    slice - slice to create mask at
    
    mask - the binary mask
    
    XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
    
    onlyActive - Only mask regions that are active (i.e. selected )
  - createBinaryMask
```
public java.util.BitSet createBinaryMask(int xDim,
                                         int yDim,
                                         int slice,
                                         VOIBase contour)
```
    Creates a binary mask at a slice for that slice and element only.
    
    Parameters:
    
    xDim - x dimension, used to index into the image
    
    yDim - y dimension, used to index into the image
    
    slice - slice to create mask at
    
    contour - element of VOI
    
    Returns:
    
    mask the binary mask
  - createBinaryMask3D
```
public void createBinaryMask3D(java.util.BitSet mask,
                               int xDim,
                               int yDim,
                               boolean XOR,
                               boolean onlyActive)
```
    Creates a 3D binary mask.
    
    Parameters:
    
    mask - mask written into
    
    xDim - x-dimensions of the image.
    
    yDim - y-dimensions of the images.
    
    XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
    
    onlyActive - Only mask regions that are active (i.e. selected )
  - createOneElementBinaryMask3D
```
public void createOneElementBinaryMask3D(java.util.BitSet mask,
                                         int xDim,
                                         int yDim,
                                         boolean XOR,
                                         boolean onlyActive,
                                         int elementNum)
```
    Creates a 3D binary mask.
    
    Parameters:
    
    mask - mask written into
    
    xDim - x-dimensions of the image.
    
    yDim - y-dimensions of the images.
    
    XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
    
    onlyActive - Only mask regions that are active (i.e. selected )
  - createShortImage
```
public void createShortImage(ModelImage image,
                             int offset,
                             boolean XOR,
                             boolean onlyActive)
```
    Creates a short image of the VOI. Positions within the VOI are set to the VOI's watershed ID.
    
    Parameters:
    
    image - short image where VOI labels are to be set.
    
    offset - value added to watershedID - normally 1
    
    XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
    
    onlyActive - Only mask regions that are active (i.e. selected )
  - createShortMask
```
public short[] createShortMask(short[] mask,
                               int xDim,
                               int yDim,
                               int zDim,
                               boolean XOR)
```
    Creates a short mask at a slice.
    
    Parameters:
    
    mask - the short mask
    
    xDim - x dimension, used to index into the image
    
    yDim - y dimension, used to index into the image
    
    zDim - z dimension, used to index into the image
    
    XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
    
    Returns:
    
    returns the mask
  - createUByteImage
```
public void createUByteImage(ModelImage image,
                             int offset,
                             boolean XOR,
                             boolean onlyActive)
```
    Creates a short image of the VOI. Positions within the VOI are set to the VOI's watershed ID.
    
    Parameters:
    
    image - short image where VOI labels are to be set.
    
    offset - value added to watershedID - normally 1
    
    XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
    
    onlyActive - Only mask regions that are active (i.e. selected )
  - dispose
```
public void dispose()
```
  - equals
```
public boolean equals(java.lang.String str)
```
    two VOIs are the same if they have the same name.
    
    Parameters:
    
    str - name of the VOI to compare this to.
    
    Returns:
    
    true if the names of the VOIs are equal.
  - exportAllPoints
```
public WildMagic.LibFoundation.Mathematics.Vector3f[] exportAllPoints()
```
    Get Vector3fs from the VOI; can only use with Point.
    
    Returns:
    
    array of points at the slice
  - exportPoint
```
public WildMagic.LibFoundation.Mathematics.Vector3f exportPoint()
```
    Returns the first point.
    
    Returns:
    
    return the first point from the VOIPoint object
  - exportPoints
```
public java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f> exportPoints(int slice)
```
    Get Vector3fs from the VOI; can only use with Point.
    
    Parameters:
    
    slice - index of slice
    
    Returns:
    
    array of points at the slice
  - finalize
```
public void finalize()
              throws java.lang.Throwable
```
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.Throwable
  - getBoundingBoxFlag
```
public boolean getBoundingBoxFlag()
```
    Accessor that returns the bounding box flag.
    
    Returns:
    
    the process
  - getBounds
```
public void getBounds(float[] x,
                      float[] y,
                      float[] z)
```
    Calculates the extents or boundary of the voi in x, y, and z.
    
    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 extents or boundary of the voi in x, y, and z.
    
    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
  - getColor
```
public java.awt.Color getColor()
```
    Accessor that returns the VOI's color.
    
    Returns:
    
    the color
  - getComments
```
public java.util.ArrayList<java.lang.String> getComments()
```
  - getContourGraph
```
public ViewJFrameGraph getContourGraph()
```
    Returns the contour graph associated with this voi.
    
    Returns:
    
    contour graph associated with this voi.
  - getCurves
```
public VOIBaseVector getCurves()
```
    Accessor that returns the curves making up the VOI.
    
    Returns:
    
    the curves
  - getCurveType
```
public int getCurveType()
```
    Accessor that returns the curve type.
    
    Returns:
    
    the curve type
  - getDisplayMode
```
public int getDisplayMode()
```
    Accessor that returns the display mode.
    
    Returns:
    
    the display mode
  - getExtension
```
public java.lang.String getExtension()
```
    Accessor that returns the VOI extension.
    
    Returns:
    
    extension of voi file name of voi was read in through file
  - getGeometricCenter
```
public WildMagic.LibFoundation.Mathematics.Vector3f getGeometricCenter()
```
    Returns the geometric center of the VOI (only contour).
    
    Returns:
    
    returns the geometric center
  - getID
```
public short getID()
```
    Accessor that returns the ID.
    
    Returns:
    
    the ID
  - getMaximumIgnore
```
public float getMaximumIgnore()
```
    Accessor that returns the maximum of the range of intensities to ignore.
    
    Returns:
    
    The maximum.
  - getMinimumIgnore
```
public float getMinimumIgnore()
```
    Accessor that returns the minimum of the range of intensities to ignore.
    
    Returns:
    
    The minimum.
  - getMaximumIgnoreR
```
public float getMaximumIgnoreR()
```
    Accessor that returns the maximum of the range of red intensities to ignore.
    
    Returns:
    
    The maximum.
  - getMinimumIgnoreR
```
public float getMinimumIgnoreR()
```
    Accessor that returns the minimum of the range of red intensities to ignore.
    
    Returns:
    
    The minimum.
  - getMaximumIgnoreG
```
public float getMaximumIgnoreG()
```
    Accessor that returns the maximum of the range of green intensities to ignore.
    
    Returns:
    
    The maximum.
  - getMinimumIgnoreG
```
public float getMinimumIgnoreG()
```
    Accessor that returns the minimum of the range of green intensities to ignore.
    
    Returns:
    
    The minimum.
  - getMaximumIgnoreB
```
public float getMaximumIgnoreB()
```
    Accessor that returns the maximum of the range of blue intensities to ignore.
    
    Returns:
    
    The maximum.
  - getMinimumIgnoreB
```
public float getMinimumIgnoreB()
```
    Accessor that returns the minimum of the range of blue intensities to ignore.
    
    Returns:
    
    The minimum.
  - getName
```
public java.lang.String getName()
```
    Accessor that returns the name of the VOI.
    
    Returns:
    
    the name
  - getNumPoints
```
public int getNumPoints()
```
    Get the number of points in the VOI file.
    
    Returns:
    
    numPoints number of points
  - getOpacity
```
public float getOpacity()
```
    Accessor that returns the opacity of the VOI.
    
    Returns:
    
    the opacity
  - getPointCoordinates
```
public void getPointCoordinates(float[] coord)
```
    This method is used to get the coordinates of a single VOIPoint.
    
    Parameters:
    
    coord - this float array contains the x-coordinate in the first element and the y coordinate in the second element
  - getPolarity
```
public int getPolarity()
```
    Accessor that returns.
    
    Returns:
    
    the polarity
  - getPositionAndIntensity
```
public int getPositionAndIntensity(int slice,
                                   int contourNo,
                                   WildMagic.LibFoundation.Mathematics.Vector3f[] position,
                                   float[] intensity,
                                   float[] imageBuffer,
                                   int xDim)
```
    Gets the position and intensity for this VOI if it's a line.
    
    Parameters:
    
    slice - slice where the line is located
    
    contourNo - the contour within the image slice
    
    position - position of the line (x-coordinates)
    
    intensity - intensity of the line (y-coordinates)
    
    imageBuffer - image buffer
    
    xDim - x dimension
    
    Returns:
    
    the number of points in the position and intensity array that have a valid data.
  - getProcess
```
public boolean getProcess()
```
    Accessor that returns whether voi is included in processing.
    
    Returns:
    
    the process
  - getSize
```
public int getSize()
```
    Returns the number of contours in this VOI.
    
    Returns:
    
    number of contours in this VOI.
  - getSliceCurves
```
public java.util.Vector<VOIBase> getSliceCurves(int iSlice)
```
    Returns a list of contours on a given slice.
    
    Parameters:
    
    iSlice - the slice in the image.
    
    Returns:
    
    list of contours for the slice.
  - getSliceCurves
```
public java.util.Vector<VOIBase> getSliceCurves(int iPlane,
                                                int iSlice)
```
    Returns a list of contours for the given image orientation and slice.
    
    Parameters:
    
    iPlane - , the plane direction to slice the 3D image (x, y, or z).
    
    iSlice - the slice number.
    
    Returns:
    
    list of contours.
  - getSliceSize
```
public int getSliceSize(int iSlice)
```
    Returns the number of contours for a given slice.
    
    Parameters:
    
    iSlice - the slice number in the 3D image.
    
    Returns:
    
    number of contours for the slice.
  - getSliceSize
```
public int getSliceSize(int iPlane,
                        int iSlice)
```
    Returns the number of contours for a given image orientation and slice in a 3D image.
    
    Parameters:
    
    iPlane - the plane direction to slice the 3D image (x,y, or z).
    
    iSlice - the slice number.
    
    Returns:
    
    the number of contours.
  - getSortedCurves
```
public java.util.Vector<VOIBase>[] getSortedCurves(int iDim)
```
    Sorts the contours based on the image default orientation.
    
    Parameters:
    
    iDim - the number of slices in the image for the default z-direction of the image.
    
    Returns:
    
    an array of contour lists, one list per slice in the image.
  - getSortedCurves
```
public java.util.Vector<VOIBase>[] getSortedCurves(int iPlane,
                                                   int iDim)
```
    Sorts the contours based on a given image orientation and the desired image depth for that orientation.
    
    Parameters:
    
    iPlane - the direction to slice the 3D image (x, y, or z).
    
    iDim - the number of slice in the given orientation.
    
    Returns:
    
    an array of contour lists, one per slice in the image.
  - getThickness
```
public int getThickness()
```
    Returns the thickness of the VOI
    
    Returns:
  - getUID
```
public int getUID()
```
    Accessor that returns the Unique ID (original hash code for object).
    
    Returns:
    
    the unique ID
  - getVOISlices
```
public int getVOISlices()
```
    Returns the number of z slices actually containing part of the voi
    
    Returns:
  - getWatershedID
```
public short getWatershedID()
```
    getWatershedID - accessor that returns the watershedID.
    
    Returns:
    
    the ID
  - hasListener
```
public boolean hasListener(VOIListener listener)
```
  - importCurve
```
public VOIBase importCurve(float[] x,
                           float[] y,
                           float[] z)
```
    Imports a new curve into this voi.
    
    Parameters:
    
    x - x-positions of the curve.
    
    y - y-positions of the curve.
    
    z - z-positions of the curve.
    
    Returns:
    
    the new VOIBase object created by the importCurve.
  - importCurve
```
public void importCurve(int[] x,
                        int[] y,
                        int[] z)
```
  - importCurve
```
public void importCurve(WildMagic.LibFoundation.Mathematics.Vector3f[] pt)
```
    Imports the curve into the VOI, testing for which type.
    
    Parameters:
    
    pt - array of 3D points to import
  - importCurve
```
public void importCurve(VOIBase curve)
```
    Imports the curve into the VOI.
    
    Parameters:
    
    curve - curve to import
  - importNewVOI
```
public void importNewVOI(int slice,
                         int voiSlice,
                         VOI voi,
                         boolean resize)
```
    Imports just the VOIs in a slice into this VOI.
    
    Parameters:
    
    slice - slice indicates the slice where the contour(s) is to be located
    
    voiSlice - voiSlice indicates the slice where the contour(s) is to be copied from
    
    voi - added to VOI
    
    resize - when true clear the existing curves.
  - importPoint
```
public void importPoint(WildMagic.LibFoundation.Mathematics.Vector3f point)
```
    Import a new point into this VOI. This VOI must be of type POINT.
    
    Parameters:
    
    point -
  - importPoint
```
public void importPoint(WildMagic.LibFoundation.Mathematics.Vector3f point,
                        boolean notifyListener)
```
    Import a new point into this VOI. This VOI must be of type POINT.
    
    Parameters:
    
    point -
  - importPolygon
```
public void importPolygon(java.awt.Polygon gon,
                          int slice)
```
    Imports the polygon into the VOI (must be a contour).
    
    Parameters:
    
    gon - polygon to import
    
    slice - index of slice of new polygon
  - exportPolygon
```
public java.util.Vector<java.awt.Polygon> exportPolygon(int iSlice)
```
  - isActive
```
public boolean isActive()
```
    Accessor that tells if the VOI is active.
    
    Returns:
    
    boolean active
  - isAllActive
```
public boolean isAllActive()
```
    Returns true iff all contours in this VOI are active.
    
    Returns:
    
    true iff all contours in this VOI are active.
  - isEmpty
```
public boolean isEmpty()
```
    Test whether or not the VOI is empty.
    
    Returns:
    
    boolean result of test
  - isFixed
```
public boolean isFixed()
```
    Accessor that tells if VOI is fixed. A fixed VOI cannot be modified.
    
    Returns:
    
    boolean fixed
  - isVisible
```
public boolean isVisible()
```
    Accessor that tells if the VOI is visible.
    
    Returns:
    
    boolean visible
  - maxWidth
```
public WildMagic.LibFoundation.Mathematics.Vector3f[] maxWidth(boolean bOnlyActive)
```
    Finds 2 points that form the maximum width of the VOI.
    
    Returns:
    
    returns the two points.
  - moveVOI
```
public void moveVOI(int slice,
                    int xDim,
                    int yDim,
                    int zDim,
                    int xM,
                    int yM,
                    int zM)
```
    Move VOI to a new position.
    
    Parameters:
    
    slice - slice where the VOI is located
    
    xDim - x dimension maximum
    
    yDim - y dimension maximum
    
    zDim - z dimension maximum
    
    xM - amount in pixels to move the line in the x direction
    
    yM - amount in pixels to move the line in the y direction
    
    zM - amount in pixels to move the line in the z direction
  - nearLine
```
public boolean nearLine(int x,
                        int y,
                        int slice)
```
    Tests if a point is near a line.
    
    Parameters:
    
    x - x coordinate of line
    
    y - y coordinate of line
    
    slice - index of slice in curve array
    
    Returns:
    
    result of test
  - nearPoint
```
public boolean nearPoint(int x,
                         int y,
                         int slice)
```
    Tests if a point is near a point.
    
    Parameters:
    
    x - x coordinate of point
    
    y - y coordinate of point
    
    slice - index of slice in curve array
    
    Returns:
    
    result of test
  - pointToContour
```
public float pointToContour(int x,
                            int y,
                            int z)
```
    Finds the minimum distance from a point to a contour. If the point is in a contour, the distance is given a negative sign. If the point is outside contours, the distance is given a positive sign. The contour points are connected by straight line segments between the points so simply find the distances from the point to each line segment comprising the contours.
    
    Parameters:
    
    x - input x-position
    
    y - input y-position
    
    z - input z-position
    
    Returns:
    
    minDistance
  - removeAllVOIListeners
```
public void removeAllVOIListeners()
```
  - removeCurve
```
public void removeCurve(VOIBase kCurve)
```
    Clears VOI of all curves at a slice.
    
    Parameters:
    
    slice - index of slice of curves to remove
  - removeCurves
```
public void removeCurves()
```
    Clears VOI of all curves.
    
    Parameters:
    
    slice - index of slice of curves to remove
  - removeCurves
```
@Deprecated
public void removeCurves(int slice)
```
    Deprecated.
    
    Clears VOI of all curves at a slice.
    
    Parameters:
    
    slice - index of slice of curves to remove
  - removeVOIListener
```
public void removeVOIListener(VOIListener listener)
```
    removes the update listener.
    
    Parameters:
    
    listener - VOIListener to remove.
  - setActive
```
public void setActive(boolean act)
```
    Sets whether or not the VOI is active.
    
    Parameters:
    
    act - boolean to set active to
  - setAllActive
```
public void setAllActive(boolean flag)
```
    Sets all contours in the VOI as active or inactive.
    
    Parameters:
    
    flag - boolean to set VOI active or inactive
  - setBoundingBoxFlag
```
public void setBoundingBoxFlag(boolean flag)
```
    Accessor that sets the flag to the parameter.
    
    Parameters:
    
    flag - the visible flag
  - setColor
```
public void setColor(java.awt.Color color)
```
    Accessor that sets the color to the parameter.
    
    Parameters:
    
    color - the color
  - setColor
```
public void setColor(float hue)
```
    Accessor that sets the color to the parameter.
    
    Parameters:
    
    hue - the color of the VOI
  - setComments
```
public void setComments(java.lang.String comment)
```
  - setContourGraph
```
public void setContourGraph(ViewJFrameGraph newGraph)
```
    Accessor that sets the contourGraph to the parameter.
    
    Parameters:
    
    newGraph - the graph
  - setCurves
```
public void setCurves(VOIBaseVector newCurves)
```
    Sets the list of contours in this VOI to a new list.
    
    Parameters:
    
    newCurves - new list of VOIBase contours.
  - setCurveType
```
public void setCurveType(int curveType)
```
    Accessor that sets the curveType to the parameter.
    
    Parameters:
    
    curveType - the curve type
  - setDisplayMode
```
public void setDisplayMode(int mode)
```
    Accessor that sets the display mode to the parameter.
    
    Parameters:
    
    mode - the display mode
  - setExtension
```
public void setExtension(java.lang.String extension)
```
    Sets the VOI extenstion of voi file name of voi was read in through file
    
    Parameters:
    
    extension -
  - setFixed
```
public void setFixed(boolean fixed)
```
    Sets whether or not the VOI is fixed.
    
    Parameters:
    
    fixed - boolean to set fixed to
  - setID
```
public void setID(short ID)
```
    Accessor that sets the ID to the parameter.
    
    Parameters:
    
    ID - the ID
  - setMaximumIgnore
```
public void setMaximumIgnore(float max)
```
    Accessor that sets the maximum of the range of intensities to ignore.
    
    Parameters:
    
    max - The maximum.
  - setMinimumIgnore
```
public void setMinimumIgnore(float min)
```
    Accessor that sets the minimum of the range of intensities to ignore.
    
    Parameters:
    
    min - The minimum.
  - setMaximumIgnoreR
```
public void setMaximumIgnoreR(float max)
```
    Accessor that sets the maximum of the range of red intensities to ignore.
    
    Parameters:
    
    max - The maximum.
  - setMinimumIgnoreR
```
public void setMinimumIgnoreR(float min)
```
    Accessor that sets the minimum of the range of red intensities to ignore.
    
    Parameters:
    
    min - The minimum.
  - setMaximumIgnoreG
```
public void setMaximumIgnoreG(float max)
```
    Accessor that sets the maximum of the range of green intensities to ignore.
    
    Parameters:
    
    max - The maximum.
  - setMinimumIgnoreG
```
public void setMinimumIgnoreG(float min)
```
    Accessor that sets the minimum of the range of green intensities to ignore.
    
    Parameters:
    
    min - The minimum.
  - setMaximumIgnoreB
```
public void setMaximumIgnoreB(float max)
```
    Accessor that sets the maximum of the range of blue intensities to ignore.
    
    Parameters:
    
    max - The maximum.
  - setMinimumIgnoreB
```
public void setMinimumIgnoreB(float min)
```
    Accessor that sets the minimum of the range of blue intensities to ignore.
    
    Parameters:
    
    min - The minimum.
  - setName
```
public void setName(java.lang.String name)
```
    Accessor that sets the VOI's name to the parameter.
    
    Parameters:
    
    name - the name
  - setOnlyID
```
public void setOnlyID(short ID)
```
    Accessor that sets the ID to the parameter.
    
    Parameters:
    
    ID - the ID
  - setOpacity
```
public void setOpacity(float opacity)
```
    Accessor that sets the opacity to the parameter.
    
    Parameters:
    
    opacity - the opacity
  - setPolarity
```
public void setPolarity(int polarity)
```
    Accessor that sets the polarity to the parameter.
    
    Parameters:
    
    polarity - the polarity
  - setProcess
```
public void setProcess(boolean flag)
```
    Accessor that sets the flag to the parameter.
    
    Parameters:
    
    flag - the process flag
  - notifyParentVOIProcess
```
void notifyParentVOIProcess(boolean flag)
```
    Allows VOIBase's to set their parent's process flag without affecting other contours. If not all contours are in the same state, this will not be set.
    
    Parameters:
    
    flag - the process flag
  - setThickness
```
public void setThickness(int newThickness)
```
    Sets the thickness of the VOI
    
    Parameters:
    
    newThickness - the new thickness
  - setUID
```
public void setUID(int uid)
```
    Sets the unique ID (for saving/retreiving treatment details).
    
    Parameters:
    
    uid - - unique ID
  - setWatershedID
```
public void setWatershedID(short wID)
```
    Accessor that sets the ID to the parameter.
    
    Parameters:
    
    wID - the ID
  - setXYDim
```
public void setXYDim(int xDim,
                     int yDim)
```
    Deprecated.
    
    Accessor that sets xDim and yDim.
    
    Parameters:
    
    xDim - x dimension
    
    yDim - y dimension
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - trim
```
public void trim()
```
    Trims all active contours in the VOI based on the Preferences getTrim and getTrimAdjacent values.
  - update
```
public void update()
```
  - updateActive
```
public void updateActive()
```
  - findMaxWidth
```
private WildMagic.LibFoundation.Mathematics.Vector3f findMaxWidth(WildMagic.LibFoundation.Mathematics.Vector3f pt,
                                                                  double[] maxDistance,
                                                                  boolean bOnlyActive)
```
    This is used by the method maxWidth.
    
    Parameters:
    
    pt - calculate the distance from this point to any point on any of the contours which form the VOI.
    
    maxDistance - single array value to keep track of the largest
    
    Returns:
    
    the maximum width of the VOI
  - fireVOIBaseAdded
```
protected void fireVOIBaseAdded(VOIBase curve)
```
    Fires a VOI event based on the VOI. calls the listener's addedVOI() method.
    
    Parameters:
    
    curve - new curve added to this VOI.
  - fireVOIBaseRemoved
```
protected void fireVOIBaseRemoved(VOIBase curve)
```
    Fires a VOI event based on the VOI. calls the listener's removedVOI() method.
    
    Parameters:
    
    curve - curve removed from this VOI.
  - fireVOIColorChange
```
protected void fireVOIColorChange(java.awt.Color color)
```
    Deprecated.
    
    Parameters:
    
    color -
  - fireVOIselection
```
protected void fireVOIselection()
```
    Fires a VOI event based on the VOI. calls the listener's removedVOI() method.

Class VOI

Field Summary

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

FORWARD

BACKWARD

FRONT

BACK

BOUNDARY

SOLID

ADDITIVE

SUBTRACTIVE

CONTOUR

POLYLINE

LINE

POINT

PROTRACTOR

ANNOTATION

CARDIOLOGY

POLYLINE_SLICE

NOT_A_POINT

boundingBox

color

thickness

contourGraph

curves

curveType

displayMode

fixed

ID

ignoreMax

ignoreMin

ignoreMaxR

ignoreMinR

ignoreMaxG

ignoreMinG

ignoreMaxB

ignoreMinB

name

opacity

polarity

process

UID

visible

watershedID

xBounds

yBounds

zBounds

extension

active

listenerList

comments

Constructor Detail

VOI

VOI

VOI

VOI

Method Detail

calcLargestDistance

determineMaxAvg

gatherBoundedPoints

getLargest

addVOIListener

area

calcLargestDistance

clone

createActiveContourBinaryMask

createBinaryImage

createBinaryMask

createBinaryMask

createBinaryMask

createBinaryMask3D

createOneElementBinaryMask3D

createShortImage

createShortMask

createUByteImage