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

All Methods Instance Methods Concrete Methods
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

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

Class AlgorithmHMRF_EM

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

EQUAL_WEIGHTS

GRAPHIC_WEIGHTS

colorWeighting

numberClusters

gaussianSigma

maxEMIterations

maxMAPIterations

showMAPplot

resultsFileName

Constructor Detail

AlgorithmHMRF_EM

AlgorithmHMRF_EM

Method Detail

finalize

runAlgorithm