Package gov.nih.mipav.model.algorithms

Class AlgorithmSplitAndMergeWatershed

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmSplitAndMergeWatershed

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmSplitAndMergeWatershed
extends AlgorithmBase

Author:

ilb Separate dark VOIs on a constant light background only works if you do lower completion first. Reference: 1.) Fast watershed algorithms: analysis and extensions by Bogdan P. Dobrin, Timo Viero, and Moncef Gabbouj. 2.) The Watershed Transform: Definitions, Algorithms, and Parallelization Strategies by Jos B.T.M. Roerdink and Arnold Meijster, Fundamentals Informaticae 41 (2001), pp. 187-228. 3.) Automated Sulcal Segmentation Using Watersheds on the Cortical Surface by Maryam E. Rettmann, Xiao Han, Chenyang Xu, and Jerry L. Prince, NeuroImage 15, 2002, Section Merging of Catchment Basins, p.338. Reference 2 makes the following criticism about this algorithm: 'Isolated' regions. When computing the watershed transform, regions in the image may arise which are completely surrounded by watershed pixels. In some implementations of watershed transforms by topographical distance, such regions may in fact become temporarily or permanently 'isolated'. This is a defect of the particular implementation, since, according to Corollary 3.1, watershed pixels should be propagated. Such 'problems' are often solved by ad hoc modifications of the implementation, which still do not correctly implement the definition.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	AlgorithmSplitAndMergeWatershed.indexValueComparator
private class	AlgorithmSplitAndMergeWatershed.indexValueItem

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private int	binNumber
private boolean	createWatershedLines
private static final int	INIT
private static final int	INOQ
private boolean	limitBins
private boolean	merge
private double	mergeThreshold
private static final int	NARM
private int	numNeighbor
private static final int	PIAP
private static final int	WSHED

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

destFlag, destImage, image25D, mask, 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
AlgorithmSplitAndMergeWatershed(ModelImage destImage, ModelImage srcImage, int numNeighbor, boolean limitBins, int binNumber, boolean createWatershedLines, boolean merge, double mergeThreshold)

Method Summary

Modifier and Type	Method	Description
void	runAlgorithm()	Actually runs the algorithm.
void	runBW()
private void	runColor()

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

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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

WSHED

private static final int WSHED

See Also:

• Constant Field Values

NARM

private static final int NARM

See Also:

• Constant Field Values

INOQ

private static final int INOQ

See Also:

• Constant Field Values

INIT

private static final int INIT

See Also:

• Constant Field Values

PIAP

private static final int PIAP

See Also:

• Constant Field Values

numNeighbor

private int numNeighbor

limitBins

private boolean limitBins

binNumber

private int binNumber

createWatershedLines

private boolean createWatershedLines

merge

private boolean merge

mergeThreshold

private double mergeThreshold

Constructor Details

AlgorithmSplitAndMergeWatershed

public AlgorithmSplitAndMergeWatershed(ModelImage destImage,
 ModelImage srcImage,
 int numNeighbor,
 boolean limitBins,
 int binNumber,
 boolean createWatershedLines,
 boolean merge,
 double mergeThreshold)

Method Details

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

runBW

public void runBW()

runColor

private void runColor()