Package gov.nih.mipav.model.algorithms

Class AlgorithmVOIExtraction

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmVOIExtraction

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmVOIExtraction
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 Color[]	colorTable	DOCUMENT ME!
private int	connected
private short[]	expImgBuffer	DOCUMENT ME!
private short[]	grayScaleArray	DOCUMENT ME!
private short[]	imgBuffer	DOCUMENT ME!
private BitSet	mask	DOCUMENT ME!
private BitSet	mask2	DOCUMENT ME!
private BitSet	maskAll	DOCUMENT ME!
private BitSet	maskExpanded
private short[][]	maskList	DOCUMENT ME!
private String[]	nameTable	DOCUMENT ME!
private short[][]	nextMaskList	DOCUMENT ME!
private int	numVOIAdded
private short[]	objBuffer	DOCUMENT ME!
private BitSet	outMask	DOCUMENT ME!
private int[]	VOIIndexArray	DOCUMENT ME!
private int	xDim	DOCUMENT ME!
private int	xDimE	DOCUMENT ME!
private int	yDim	DOCUMENT ME!
private int	yDimE	DOCUMENT ME!

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

destFlag, destImage, image25D, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmVOIExtraction(ModelImage srcImg)	Creates a new AlgorithmVOIExtraction object.

Method Summary

Modifier and Type	Method	Description
private void	calcInPlace()	Calculates the VOI extraction.
private void	calcInPlace2()	From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.6 Inner Boundary Tracing, pp. 191-192.
void	disposeLocal()	DOCUMENT ME!
private void	extendedBoundaryTracing()	From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.8 Extended Boundary Tracing, pp. 195-196.
void	finalize()	Prepares this class for destruction.
VOI	getAddedVOI()	Retrieve the VOI generated by the mask to voi extraction.
int	getNumVOIAdded()
private void	outerBoundaryTracing()	From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.7 Outer Boundary Tracing, p. 193.
void	runAlgorithm()	Starts the program.
void	setColorTable(Color[] colorTable)	DOCUMENT ME!
void	setNameTable(String[] nameTable)	DOCUMENT ME!
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, short objectValue)	Sets the mask of all points in the 4 connected region with a gray scale value of objectValue Uses iteration.
private void	setRegionOutMaskI(int xStart, int yStart, short objectValue)	Sets the mask of all points in the 4 connected region with a gray scale value of objectValue 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!

colorTable

private Color[] colorTable

DOCUMENT ME!

expImgBuffer

private short[] expImgBuffer

DOCUMENT ME!

grayScaleArray

private short[] grayScaleArray

DOCUMENT ME!

imgBuffer

private short[] imgBuffer

DOCUMENT ME!

mask

private BitSet mask

DOCUMENT ME!

mask2

private BitSet mask2

DOCUMENT ME!

maskAll

private BitSet maskAll

DOCUMENT ME!

maskList

private short[][] maskList

DOCUMENT ME!

nameTable

private String[] nameTable

DOCUMENT ME!

nextMaskList

private short[][] nextMaskList

DOCUMENT ME!

objBuffer

private short[] objBuffer

DOCUMENT ME!

outMask

private BitSet outMask

DOCUMENT ME!

VOIIndexArray

private int[] VOIIndexArray

DOCUMENT ME!

xDim

private int xDim

DOCUMENT ME!

xDimE

private int xDimE

DOCUMENT ME!

yDim

private int yDim

DOCUMENT ME!

yDimE

private int yDimE

DOCUMENT ME!

maskExpanded

private BitSet maskExpanded

connected

private int connected

numVOIAdded

private int numVOIAdded

Constructor Details

AlgorithmVOIExtraction

public AlgorithmVOIExtraction(ModelImage srcImg)

Creates a new AlgorithmVOIExtraction object.

Parameters:

srcImg - source image model

Method Details

disposeLocal

public void disposeLocal()

DOCUMENT ME!

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

setColorTable

public void setColorTable(Color[] colorTable)

DOCUMENT ME!

Parameters:

colorTable - DOCUMENT ME!

setNameTable

public void setNameTable(String[] nameTable)

DOCUMENT ME!

Parameters:

nameTable - DOCUMENT ME!

extendedBoundaryTracing

private void extendedBoundaryTracing()

From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.8 Extended Boundary Tracing, pp. 195-196.

outerBoundaryTracing

private void outerBoundaryTracing()

From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.7 Outer Boundary Tracing, p. 193.

calcInPlace2

private void calcInPlace2()

From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.6 Inner Boundary Tracing, pp. 191-192. "Algorithm 6.6 works for all regions larger than one pixel. It is able to find region borders but does not find borders of region holes, which may be located by identifying border elements unallocated thus far to borders. The search for border elements always starts after a traced border is closed, and the search for "unused" border elements can continue in the same way as the search for the first border element. Note that if objects are of unit width, more conditions must be added." Can be used with either connected = 4 or connected = 8. Much less memory than calcInPlace.

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,
 short objectValue)

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

objectValue - the gray scale value of the object

setRegionOutMaskI

private void setRegionOutMaskI(int xStart,
 int yStart,
 short objectValue)

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

objectValue - the gray scale value of the object

getAddedVOI

public VOI getAddedVOI()

Retrieve the VOI generated by the mask to voi extraction.

Returns:

The generated VOI object.

getNumVOIAdded

public int getNumVOIAdded()