Package gov.nih.mipav.model.algorithms

Class AlgorithmHMRF_EM

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmHMRF_EM

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmHMRF_EM
extends AlgorithmBase

This is a port of the MATLAB files HMRF_EM.m and MRF_MAP.m written by Quan Wang to Java. % Copyright by Quan Wang, 2012/04/25 % Please cite: Quan Wang. HMRF-EM-image: Implementation of the % Hidden Markov Random Field Model and its Expectation-Maximization % Algorithm. arXiv:1207.3510 [cs.CV], 2012. Copyright (c) 2012, Quan Wang All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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 int	colorWeighting
private static int	EQUAL_WEIGHTS
private float	gaussianSigma
private static int	GRAPHIC_WEIGHTS
private int	maxEMIterations
private int	maxMAPIterations
private int	numberClusters
private java.lang.String	resultsFileName
private boolean	showMAPplot

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
AlgorithmHMRF_EM()	AlgorithmHMRF_EM - default constructor.
AlgorithmHMRF_EM(ModelImage destImg, ModelImage srcImg, int colorWeighting, int numberClusters, float gaussianSigma, int maxEMIterations, int maxMAPIterations, boolean showMAPplot, java.lang.String resultsFileName)	AlgorithmHMRF_EM.

Method Summary

Modifier and Type	Method	Description
void	finalize()	finalize -
void	runAlgorithm()	Starts the program.

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

EQUAL_WEIGHTS

private static final int EQUAL_WEIGHTS

See Also:

Constant Field Values

GRAPHIC_WEIGHTS

private static final int GRAPHIC_WEIGHTS

See Also:

Constant Field Values

colorWeighting

private int colorWeighting

numberClusters

private int numberClusters

gaussianSigma

private float gaussianSigma

maxEMIterations

private int maxEMIterations

maxMAPIterations

private int maxMAPIterations

showMAPplot

private boolean showMAPplot

resultsFileName

private java.lang.String resultsFileName

Constructor Detail

AlgorithmHMRF_EM

public AlgorithmHMRF_EM()

AlgorithmHMRF_EM - default constructor.

AlgorithmHMRF_EM

public AlgorithmHMRF_EM(ModelImage destImg,
                        ModelImage srcImg,
                        int colorWeighting,
                        int numberClusters,
                        float gaussianSigma,
                        int maxEMIterations,
                        int maxMAPIterations,
                        boolean showMAPplot,
                        java.lang.String resultsFileName)

AlgorithmHMRF_EM.

Parameters:

destImg - DOCUMENT ME!

srcImg - DOCUMENT ME!

colorWeighting -

numberClusters -

gaussianSigma -

maxEMIterations -

maxMAPIterations -

showMAPplot -

resultsFileName -

Method Detail

finalize

public void finalize()

finalize -

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase