Package gov.nih.mipav.model.algorithms

Class AlgorithmEfficientWatershed

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmEfficientWatershed

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmEfficientWatershed
extends AlgorithmBase

Author:

ilb Reference: * 1.) The Watershed Transform: Definitions, Algorithms, and Parallelization Strategies by Jos B.T.M. Roerdink and Arnold Meijster, Fundamentals Informaticae 41 (2001), pp. 187-228. Algorithm 4.1 Vincent-Soille watershed algorithm 2.) Image Processing, Analysis, and Machine Vision 4th edition International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Section 6.3.4 Watershed segmentation, pp. 229-232. 3.) Watersheds in Digital Spaces: An Efficient Algorithm Based on Immersion Simulations by Luc Vincent and Pierre Soille, IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 13, No. 6, June, 1991, pp. 583-598. 4.) Fast watershed algorithms: analysis and extensions by Bogdan P. Dobrin, Timo Viero, and Moncef Gabbouj. 5.) Watershed-Based Segmentation of 3D MR Data for Volume Quantization by J. Sijbers, P. Scheunders, M. Verhoye, A. Van Der Linden, D. van Dyck, and E. Raman, Magnetic Resonance Imaging, Vol. 15, No. 6, 1997, pp. 679-688. 6.) 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. The ImageJ version has 3 differences with the original article pseudocode as noted in comments. Reference 2 states "Further improvements of the watershed segmentation based on immersion simulations are given in [Dobrin et al., 1994]." Reference 4 states: "Vincent invalid input: '&' Soille algorithm produces a tesselation of the image into its disjoint catchment basins. Pixels lying exactly half-way between the two catchment basins, should be assigned to watersheds. Studying the operation of Vincent and Soille algorithms, we will show that this is not always the case. The algorithm has a tendency to generate large watershed regions, because it does not propagate only catchment basin labels but also watershed labels.... Therefore, the algorithm produces an ambiguous result when propagating watershed lines to a region. Another drawback of this algorithm is given by the oscillation in the pixel assignment rule. It is relatively easy to see ... that the value of the current pixel, i.e. the pixel whose value is to be determined, can change multiple times depending on its local neighborhood. For example, the current pixel can firstly be assigned to watersheds and then immediately to a catchment basin label or vice versa. As a result, the operation of the algorithm is inconsistent in several critical pixel configurations." Reference 5 uses a 3D version of this algorithm with 26 connectivity.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	AlgorithmEfficientWatershed.indexValueComparator
private class	AlgorithmEfficientWatershed.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 static final int	INIT
private boolean	limitBins
private static final int	MASK
private boolean	merge
private double	mergeThreshold
private int	numNeighbor
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
AlgorithmEfficientWatershed(ModelImage destImage, ModelImage srcImage, int numNeighbor, boolean limitBins, int binNumber, boolean merge, double mergeThreshold)

Method Summary

Modifier and Type	Method	Description
void	run2D()
void	run3D()
void	runAlgorithm()	Actually runs the algorithm.

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

MASK

private static final int MASK

See Also:

• Constant Field Values

WSHED

private static final int WSHED

See Also:

• Constant Field Values

INIT

private static final int INIT

See Also:

• Constant Field Values

numNeighbor

private int numNeighbor

limitBins

private boolean limitBins

binNumber

private int binNumber

merge

private boolean merge

mergeThreshold

private double mergeThreshold

Constructor Details

AlgorithmEfficientWatershed

public AlgorithmEfficientWatershed(ModelImage destImage,
 ModelImage srcImage,
 int numNeighbor,
 boolean limitBins,
 int binNumber,
 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

run2D

public void run2D()

run3D

public void run3D()