java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmVOIExtractionPaint

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmVOIExtractionPaint
extends AlgorithmBase
```
DOCUMENT ME!

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private VOI`	`addedVOI`	DOCUMENT ME!
`private int`	`expandedLength`	(xDim2+2)*(yDim2+2)
`private int`	`length`	xDim2*yDim2.
`private java.util.BitSet`	`mask`	DOCUMENT ME!
`private java.util.BitSet`	`mask2`	DOCUMENT ME!
`private java.util.BitSet`	`maskAll`	DOCUMENT ME!
`private java.util.BitSet`	`maskE`	DOCUMENT ME!
`private java.util.BitSet`	`maskExpanded`
`private int[][]`	`maskList`	DOCUMENT ME!
`private java.util.BitSet`	`maskN`	DOCUMENT ME!
`private java.util.BitSet`	`maskS`	DOCUMENT ME!
`private java.util.BitSet`	`maskW`	DOCUMENT ME!
`private int`	`neighbors`	DOCUMENT ME!
`private int[][]`	`nextMaskList`	DOCUMENT ME!
`private java.util.BitSet`	`outMask`	DOCUMENT ME!
`private int`	`smallLength`	xDim * yDim.
`private int`	`smallPos`	DOCUMENT ME!
`private int`	`smallPos3D`	DOCUMENT ME!
`private int`	`smallX`	DOCUMENT ME!
`private int`	`smallY`	DOCUMENT ME!
`private ModelImage`	`srcImage`	DOCUMENT ME!
`private java.util.BitSet`	`srcPaintMask`	DOCUMENT ME!
`private int`	`testPos`	x + y*xDim.
`private short`	`voiIDnum`	DOCUMENT ME!
`private int`	`x`	current x position.
`private int`	`xDim`	DOCUMENT ME!
`private int`	`xDim2`	DOCUMENT ME!
`private int`	`xDim4`	DOCUMENT ME!
`private int`	`xt`	DOCUMENT ME!
`private int`	`y`	current y position.
`private int`	`yDim`	DOCUMENT ME!
`private int`	`yDim2`	DOCUMENT ME!
`private int`	`yt`	DOCUMENT ME!
`private int`	`z`	current z slice.
`private int`	`zDim`	extent of z dimension in the in the source image.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmVOIExtractionPaint(ModelImage sourceImage)`	Constructor for finding the borders of the paint on various slices of an image.
`AlgorithmVOIExtractionPaint(ModelImage sourceImage, java.util.BitSet srcPaint, int xDimen, int yDimen, int zDimen, short voiID)`	Construct the extractor for paint extraction to a VOI.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcInPlace()`	Calculates the VOI extraction.
`void`	`finalize()`	Prepares this class for destruction.
`java.util.Vector<java.awt.Polygon>`	`findPaintBorder(int slice)`	Finds a set of lines which surround the paint in the image.
`void`	`runAlgorithm()`	Starts the program.
`void`	`setPaintMask(java.util.BitSet mask)`	Changes the paint mask that we look for borders in.
`private void`	`setRegionMaskAll()`	Sets the mask of all points in the 4 connected region with a gray scale value.
`private void`	`setRegionMaskI(int xStart, int yStart, int offset)`	Sets the mask of all points in the 4 connected region with a gray scale value of objectValue Uses iteration.
`private void`	`setRegionMaskIFalse(int xStart, int yStart, int offset)`	Sets the mask of all points in the 4 connected region with a gray scale value of objectValue.
`private void`	`setRegionOutMaskI(int xStart, int yStart, int offset)`	Sets the mask of all points in the 4 connected region with a srcPaintMask equal to false Uses iteration.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

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

- Field Detail
  - addedVOI
```
private VOI addedVOI
```
    DOCUMENT ME!
  - length
```
private int length
```
    xDim2*yDim2.
  - expandedLength
```
private int expandedLength
```
    (xDim2+2)*(yDim2+2)
  - mask
```
private java.util.BitSet mask
```
    DOCUMENT ME!
  - mask2
```
private java.util.BitSet mask2
```
    DOCUMENT ME!
  - maskAll
```
private java.util.BitSet maskAll
```
    DOCUMENT ME!
  - maskE
```
private java.util.BitSet maskE
```
    DOCUMENT ME!
  - maskList
```
private int[][] maskList
```
    DOCUMENT ME!
  - maskN
```
private java.util.BitSet maskN
```
    DOCUMENT ME!
  - maskS
```
private java.util.BitSet maskS
```
    DOCUMENT ME!
  - maskW
```
private java.util.BitSet maskW
```
    DOCUMENT ME!
  - neighbors
```
private int neighbors
```
    DOCUMENT ME!
  - nextMaskList
```
private int[][] nextMaskList
```
    DOCUMENT ME!
  - outMask
```
private java.util.BitSet outMask
```
    DOCUMENT ME!
  - smallLength
```
private int smallLength
```
    xDim * yDim.
  - smallPos
```
private int smallPos
```
    DOCUMENT ME!
  - smallPos3D
```
private int smallPos3D
```
    DOCUMENT ME!
  - smallX
```
private int smallX
```
    DOCUMENT ME!
  - smallY
```
private int smallY
```
    DOCUMENT ME!
  - srcImage
```
private ModelImage srcImage
```
    DOCUMENT ME!
  - srcPaintMask
```
private java.util.BitSet srcPaintMask
```
    DOCUMENT ME!
  - testPos
```
private int testPos
```
    x + y*xDim.
  - voiIDnum
```
private short voiIDnum
```
    DOCUMENT ME!
  - x
```
private int x
```
    current x position.
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - xDim2
```
private int xDim2
```
    DOCUMENT ME!
  - xDim4
```
private int xDim4
```
    DOCUMENT ME!
  - xt
```
private int xt
```
    DOCUMENT ME!
  - yt
```
private int yt
```
    DOCUMENT ME!
  - y
```
private int y
```
    current y position.
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - yDim2
```
private int yDim2
```
    DOCUMENT ME!
  - z
```
private int z
```
    current z slice.
  - zDim
```
private int zDim
```
    extent of z dimension in the in the source image.
  - maskExpanded
```
private java.util.BitSet maskExpanded
```
- Constructor Detail
  - AlgorithmVOIExtractionPaint
```
public AlgorithmVOIExtractionPaint(ModelImage sourceImage)
```
    Constructor for finding the borders of the paint on various slices of an image.
    
    Parameters:
    
    sourceImage - the image that has been painted
  - AlgorithmVOIExtractionPaint
```
public AlgorithmVOIExtractionPaint(ModelImage sourceImage,
                                   java.util.BitSet srcPaint,
                                   int xDimen,
                                   int yDimen,
                                   int zDimen,
                                   short voiID)
```
    Construct the extractor for paint extraction to a VOI.
    
    Parameters:
    
    sourceImage - the image that has been painted
    
    srcPaint - the paint bitmap
    
    xDimen - the x dimension of the image
    
    yDimen - the y dimension of the image
    
    zDimen - the z dimension of the image
    
    voiID - the VOI number to give to the generated VOI
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - findPaintBorder
```
public java.util.Vector<java.awt.Polygon> findPaintBorder(int slice)
```
    Finds a set of lines which surround the paint in the image.
    
    Parameters:
    
    slice - the slice to find the paint borders on
    
    Returns:
    
    DOCUMENT ME!
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setPaintMask
```
public void setPaintMask(java.util.BitSet mask)
```
    Changes the paint mask that we look for borders in.
    
    Parameters:
    
    mask - the new mask to search through
  - calcInPlace
```
private void calcInPlace()
```
    Calculates the VOI extraction.
  - setRegionMaskAll
```
private void setRegionMaskAll()
```
    Sets the mask of all points in the 4 connected region with a gray scale value.
  - setRegionMaskI
```
private void setRegionMaskI(int xStart,
                            int yStart,
                            int offset)
```
    Sets the mask of all points in the 4 connected region with a gray scale value of objectValue Uses iteration.
    
    Parameters:
    
    xStart - the x coordinate of the starting point
    
    yStart - the y coordinate of the starting point
    
    offset - offset into z plane of srcPaintMask
  - setRegionMaskIFalse
```
private void setRegionMaskIFalse(int xStart,
                                 int yStart,
                                 int offset)
```
    Sets the mask of all points in the 4 connected region with a gray scale value of objectValue. Uses iteration.
    
    Parameters:
    
    xStart - the x coordinate of the starting point
    
    yStart - the y coordinate of the starting point
    
    offset - offset into z plane of srcPaintMask
  - setRegionOutMaskI
```
private void setRegionOutMaskI(int xStart,
                               int yStart,
                               int offset)
```
    Sets the mask of all points in the 4 connected region with a srcPaintMask equal to false Uses iteration.
    
    Parameters:
    
    xStart - the x coordinate of the starting point
    
    yStart - the y coordinate of the starting point
    
    offset - offset into z plane of srcPaintMask

Class AlgorithmVOIExtractionPaint

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

addedVOI

length

expandedLength

mask

mask2

maskAll

maskE

maskList

maskN

maskS

maskW

neighbors

nextMaskList

outMask

smallLength

smallPos

smallPos3D

smallX

smallY

srcImage

srcPaintMask

testPos

voiIDnum

x

xDim

xDim2

xDim4

xt

yt

y

yDim

yDim2

z

zDim

maskExpanded

Constructor Detail

AlgorithmVOIExtractionPaint

AlgorithmVOIExtractionPaint

Method Detail

finalize

findPaintBorder

runAlgorithm

setPaintMask

calcInPlace

setRegionMaskAll

setRegionMaskI

setRegionMaskIFalse

setRegionOutMaskI