Package gov.nih.mipav.model.algorithms

Class AlgorithmMixGaussEM

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmMixGaussEM

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmMixGaussEM
extends AlgorithmBase

Author:

aailb Copyright (c) 2016, Mo Chen 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 Neither the name of nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 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

Modifier and Type	Class	Description
(package private) class	AlgorithmMixGaussEM.model

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	iter
private int[]	label
private double[]	llh
private AlgorithmMixGaussEM.model	mixGaussOut
(package private) RandomNumberGen	randomGen
private double[][]	X

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
AlgorithmMixGaussEM()

Method Summary

Modifier and Type	Method	Description
double[]	dirichletRnd(double ain, double[] m)
int[]	discreteRnd(double[] pin, int n)
private double[][]	expectation(double[][] X, AlgorithmMixGaussEM.model mod)
double	gamrnd(double a, double b)
private double[]	gaussRnd(double[] mu, double[][] Sigma)
private double[][]	gaussRnd(double[] mu, double[][] Sigma, int n)
private double[][]	initialization(double[][] X, int init)
private double[][]	initialization(double[][] X, int[] init)
private double[][]	initialization(double[][] X, AlgorithmMixGaussEM.model init)
private double[]	loggausspdf(double[][] Xin, double[] mu, double[][] Sigma)
double[]	logsumexp(double[][] ain, int dim)
private AlgorithmMixGaussEM.model	maximization(double[][] X, double[][] R)
private void	mixGaussEm(double[][] X, int init)
void	mixGaussEm_demo()
private void	mixGaussPred(double[][] R, double[][] X, AlgorithmMixGaussEM.model mod)
void	mixGaussRnd(int d, int k, int n)
private void	plot(double[] llh)
private void	plotClass(double[][] X, int[] label, String title)
void	runAlgorithm()	Actually runs the algorithm.
void	test_dirichletRnd()
void	test_discreteRnd()
void	test_gamrnd()
void	test_gaussRnd()
void	test_gaussRnd2()

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

X

private double[][] X

label

private int[] label

mixGaussOut

private AlgorithmMixGaussEM.model mixGaussOut

llh

private double[] llh

iter

private int iter

randomGen

RandomNumberGen randomGen

Constructor Details

AlgorithmMixGaussEM

public AlgorithmMixGaussEM()

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

mixGaussEm_demo

public void mixGaussEm_demo()

mixGaussRnd

public void mixGaussRnd(int d,
 int k,
 int n)

test_discreteRnd

public void test_discreteRnd()

discreteRnd

public int[] discreteRnd(double[] pin,
 int n)

test_dirichletRnd

public void test_dirichletRnd()

dirichletRnd

public double[] dirichletRnd(double ain,
 double[] m)

test_gamrnd

public void test_gamrnd()

gamrnd

public double gamrnd(double a,
 double b)

test_gaussRnd2

public void test_gaussRnd2()

gaussRnd

private double[] gaussRnd(double[] mu,
 double[][] Sigma)

test_gaussRnd

public void test_gaussRnd()

gaussRnd

private double[][] gaussRnd(double[] mu,
 double[][] Sigma,
 int n)

plotClass

private void plotClass(double[][] X,
 int[] label,
 String title)

mixGaussPred

private void mixGaussPred(double[][] R,
 double[][] X,
 AlgorithmMixGaussEM.model mod)

mixGaussEm

private void mixGaussEm(double[][] X,
 int init)

initialization

private double[][] initialization(double[][] X,
 int init)

initialization

private double[][] initialization(double[][] X,
 int[] init)

initialization

private double[][] initialization(double[][] X,
 AlgorithmMixGaussEM.model init)

expectation

private double[][] expectation(double[][] X,
 AlgorithmMixGaussEM.model mod)

loggausspdf

private double[] loggausspdf(double[][] Xin,
 double[] mu,
 double[][] Sigma)

maximization

private AlgorithmMixGaussEM.model maximization(double[][] X,
 double[][] R)

plot

private void plot(double[] llh)

logsumexp

public double[] logsumexp(double[][] ain,
 int dim)