Package gov.nih.mipav.model.algorithms

Class AlgorithmVOIExtractionPaint

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmVOIExtractionPaint

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmVOIExtractionPaint
extends AlgorithmBase

DOCUMENT ME!

Nested Class Summary

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

Thread.Builder, Thread.State, 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 BitSet	mask	DOCUMENT ME!
private BitSet	mask2	DOCUMENT ME!
private BitSet	maskAll	DOCUMENT ME!
private BitSet	maskE	DOCUMENT ME!
private BitSet	maskExpanded
private int[][]	maskList	DOCUMENT ME!
private BitSet	maskN	DOCUMENT ME!
private BitSet	maskS	DOCUMENT ME!
private BitSet	maskW	DOCUMENT ME!
private int	neighbors	DOCUMENT ME!
private int[][]	nextMaskList	DOCUMENT ME!
private 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 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, BitSet srcPaint, int xDimen, int yDimen, int zDimen, short voiID)	Construct the extractor for paint extraction to a VOI.

Method Summary

Modifier and Type	Method	Description
private void	calcInPlace()	Calculates the VOI extraction.
void	finalize()	Prepares this class for destruction.
Vector<Polygon>	findPaintBorder(int slice)	Finds a set of lines which surround the paint in the image.
void	runAlgorithm()	Starts the program.
void	setPaintMask(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, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

addedVOI

private VOI addedVOI

DOCUMENT ME!

length

private int length

xDim2*yDim2.

expandedLength

private int expandedLength

(xDim2+2)*(yDim2+2)

mask

private BitSet mask

DOCUMENT ME!

mask2

private BitSet mask2

DOCUMENT ME!

maskAll

private BitSet maskAll

DOCUMENT ME!

maskE

private BitSet maskE

DOCUMENT ME!

maskList

private int[][] maskList

DOCUMENT ME!

maskN

private BitSet maskN

DOCUMENT ME!

maskS

private BitSet maskS

DOCUMENT ME!

maskW

private BitSet maskW

DOCUMENT ME!

neighbors

private int neighbors

DOCUMENT ME!

nextMaskList

private int[][] nextMaskList

DOCUMENT ME!

outMask

private 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 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 BitSet maskExpanded

Constructor Details

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,
 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 Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

findPaintBorder

public Vector<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(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