Package gov.nih.mipav.model.algorithms

Class AlgorithmGaussianMixtureModelEM

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmGaussianMixtureModelEM

All Implemented Interfaces:

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

public class AlgorithmGaussianMixtureModelEM
extends AlgorithmBase

Copyright (c) 1995 The Board of Trustees of Purdue University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose, without fee, and without written agreement is hereby granted, provided that the above copyright notice and the following two paragraphs appear in all copies of this software. In no event shall Purdue University be liable to any party for direct, indirect, special, incidental, or consequential damages arising out of the use of this software and its documentation, even if Purdue University has been advised of the possibility of such damage. Purdue University specifically disclaims any warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The software provided hereunder is on an "as is" basis, and Purdue Univeristy has no obligation to provide maintenance, support, updates, enhancements, or modifications. This is a port of cluster-3.6.7 developed by: Charles A. Bouman; School of ECE, Purdue University Michael Shapiro; NCSA Gregory W. Cook; School of ECE, Purdue University C. Brian Atkins; School of ECE, Purdue University Hui Cheng; School of ECE, Purdue University Jennifer G. Dy; School of ECE, Purdue University Sean Borman; Department of Electrical Engineering, University of Notre Dame This is software for doing unsupervised clustering. This is done by estimating the parameters of a Gaussian mixture model using the EM algorithm.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	AlgorithmGaussianMixtureModelEM.ClassData
(package private) class	AlgorithmGaussianMixtureModelEM.ClassSig
(package private) class	AlgorithmGaussianMixtureModelEM.SigSet
(package private) class	AlgorithmGaussianMixtureModelEM.SubSig

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	CLUSTER_DIAG
private int	CLUSTER_FULL
private int	clusterMessageVerboseLevel
(package private) double[]	compute_constants_col
private boolean	compute_constants_first
private int[]	compute_constants_indx
(package private) double[][]	compute_constants_y
private double	COVAR_DYNAMIC_RANGE
private java.lang.String	data_file_directory
private java.lang.String	data_file_name
private boolean	distance_first
private AlgorithmGaussianMixtureModelEM.SigSet	distance_S
private AlgorithmGaussianMixtureModelEM.ClassSig	distance_Sig3
private AlgorithmGaussianMixtureModelEM.SubSig	distance_SubSig3
private boolean	full
private int	init_num_of_subclasses
private java.lang.String	input_file_directory
private java.lang.String	input_file_name
private int	number_of_clusters
private java.lang.String	parameter_input_file_directory
private java.lang.String	parameter_input_file_name
private java.lang.String	parameter_output_file_directory
private java.lang.String	parameter_output_file_name
private boolean	reduce_order_first
private AlgorithmGaussianMixtureModelEM.SigSet	reduce_order_S
private AlgorithmGaussianMixtureModelEM.ClassSig	reduce_order_Sig3
(package private) AlgorithmGaussianMixtureModelEM.SubSig	reduce_order_SubSig3
private int	SIGNATURE_TYPE_MIXED
private AlgorithmGaussianMixtureModelEM.SigSet	Smin

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
AlgorithmGaussianMixtureModelEM()
AlgorithmGaussianMixtureModelEM(int clusterMessageVerboseLevel, int init_num_of_subclasses, java.lang.String input_file_directory, java.lang.String input_file_name, java.lang.String parameter_output_file_directory, java.lang.String parameter_output_file_name, boolean full, int number_of_clusters)
AlgorithmGaussianMixtureModelEM(java.lang.String parameter_input_file_directory, java.lang.String parameter_input_file_name, java.lang.String file_directory, java.lang.String file_name, boolean classify)

Method Summary

Modifier and Type	Method	Description
private void	add_SubSigs(AlgorithmGaussianMixtureModelEM.SubSig SubSig1, AlgorithmGaussianMixtureModelEM.SubSig SubSig2, AlgorithmGaussianMixtureModelEM.SubSig SubSig3, int nbands)
private double	AverageVariance(AlgorithmGaussianMixtureModelEM.ClassSig Sig, int nbands)
private void	classify()
private void	ClassLogLikelihood(double[] vector, double[] ll, AlgorithmGaussianMixtureModelEM.SigSet S)
private void	ClassLogLikelihood_init(AlgorithmGaussianMixtureModelEM.SigSet S)
void	clust()
private int	clust_invert(double[][] a, int n, double[] det_man, int[] det_exp, int[] indx, double[][] y, double[] col)
private void	compute_constants(AlgorithmGaussianMixtureModelEM.ClassSig Sig, int nbands)
private void	copy_ClassSig(AlgorithmGaussianMixtureModelEM.ClassSig Sig1, AlgorithmGaussianMixtureModelEM.ClassSig Sig2, int nbands)
private void	copy_SubSig(AlgorithmGaussianMixtureModelEM.SubSig SubSig1, AlgorithmGaussianMixtureModelEM.SubSig SubSig2, int nbands)
void	demoClassify()
void	demoClustDiag()
void	demoClustDiag5()
void	demoClustFull()
void	demoClustFull5()
void	demoSplitClasses()
private void	DiagonalizeMatrix(double[][] R, int nbands)
private double	distance(AlgorithmGaussianMixtureModelEM.SubSig SubSig1, AlgorithmGaussianMixtureModelEM.SubSig SubSig2, int nbands)
private void	get_class(java.io.RandomAccessFile raFile, AlgorithmGaussianMixtureModelEM.SigSet S)
private void	get_subclass(java.io.RandomAccessFile raFile, AlgorithmGaussianMixtureModelEM.SigSet S, AlgorithmGaussianMixtureModelEM.ClassSig C)
private AlgorithmGaussianMixtureModelEM.ClassData	I_AllocClassData(AlgorithmGaussianMixtureModelEM.SigSet S, AlgorithmGaussianMixtureModelEM.ClassSig C, int npixels)
private void	I_DeallocClassData(AlgorithmGaussianMixtureModelEM.SigSet S, AlgorithmGaussianMixtureModelEM.ClassSig C)
private void	I_DeallocClassSig(AlgorithmGaussianMixtureModelEM.SigSet S)
private void	I_DeallocSigSet(AlgorithmGaussianMixtureModelEM.SigSet S)
private void	I_DeallocSubSig(AlgorithmGaussianMixtureModelEM.ClassSig C)
private java.lang.String	I_GetClassTitle(AlgorithmGaussianMixtureModelEM.ClassSig C)
private java.lang.String	I_GetSigTitle(AlgorithmGaussianMixtureModelEM.SigSet S)
private void	I_InitSigSet(AlgorithmGaussianMixtureModelEM.SigSet S)
private AlgorithmGaussianMixtureModelEM.ClassSig	I_NewClassSig(AlgorithmGaussianMixtureModelEM.SigSet S)
private AlgorithmGaussianMixtureModelEM.SubSig	I_NewSubSig(AlgorithmGaussianMixtureModelEM.SigSet S, AlgorithmGaussianMixtureModelEM.ClassSig C)
private void	I_ReadSigSet(java.io.RandomAccessFile raFile, AlgorithmGaussianMixtureModelEM.SigSet S)
private void	I_SetClassTitle(AlgorithmGaussianMixtureModelEM.ClassSig C, java.lang.String title)
private void	I_SetSigTitle(AlgorithmGaussianMixtureModelEM.SigSet S, java.lang.String title)
private void	I_SigSetNBands(AlgorithmGaussianMixtureModelEM.SigSet S, int nbands)
private void	I_WriteSigSet(java.io.RandomAccessFile raFile, AlgorithmGaussianMixtureModelEM.SigSet S)
private int	invert(double[][] a, int n)
private double	loglike(double[] x, AlgorithmGaussianMixtureModelEM.SubSig sSig, int nbands)
private void	lubksb(double[][] a, int[] indx, double[] b)
private int	ludcmp(double[][] a, int n, int[] indx, double[] d)
private void	normalize_pi(AlgorithmGaussianMixtureModelEM.ClassSig Sig)
private void	reduce_order(AlgorithmGaussianMixtureModelEM.ClassSig Sig, int nbands, int[] min_ii, int[] min_jj)
private void	reestimate(AlgorithmGaussianMixtureModelEM.ClassSig Sig, int nbands, double Rmin, int option)
private double	refine_clusters(AlgorithmGaussianMixtureModelEM.ClassSig Sig, int nbands, double Rmin, int option)
private double	regroup(AlgorithmGaussianMixtureModelEM.ClassSig Sig, int nbands)
void	runAlgorithm()	Actually runs the algorithm.
private void	save_ClassSig(AlgorithmGaussianMixtureModelEM.ClassSig Sig1, AlgorithmGaussianMixtureModelEM.SigSet S, int nbands)
private void	seed(AlgorithmGaussianMixtureModelEM.ClassSig Sig, int nbands, double Rmin, int option)
private void	splitClasses()
private int	subcluster(AlgorithmGaussianMixtureModelEM.SigSet S, int Class_Index, int desired_num, int option, double Rmin, int[] Max_num)

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, 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

clusterMessageVerboseLevel

private int clusterMessageVerboseLevel

init_num_of_subclasses

private int init_num_of_subclasses

input_file_directory

private java.lang.String input_file_directory

input_file_name

private java.lang.String input_file_name

data_file_directory

private java.lang.String data_file_directory

data_file_name

private java.lang.String data_file_name

parameter_input_file_directory

private java.lang.String parameter_input_file_directory

parameter_input_file_name

private java.lang.String parameter_input_file_name

parameter_output_file_directory

private java.lang.String parameter_output_file_directory

parameter_output_file_name

private java.lang.String parameter_output_file_name

full

private boolean full

number_of_clusters

private int number_of_clusters

SIGNATURE_TYPE_MIXED

private final int SIGNATURE_TYPE_MIXED

See Also:

Constant Field Values

COVAR_DYNAMIC_RANGE

private double COVAR_DYNAMIC_RANGE

CLUSTER_FULL

private final int CLUSTER_FULL

See Also:

Constant Field Values

CLUSTER_DIAG

private final int CLUSTER_DIAG

See Also:

Constant Field Values

Smin

private AlgorithmGaussianMixtureModelEM.SigSet Smin

compute_constants_indx

private int[] compute_constants_indx

compute_constants_y

double[][] compute_constants_y

compute_constants_col

double[] compute_constants_col

compute_constants_first

private boolean compute_constants_first

reduce_order_S

private AlgorithmGaussianMixtureModelEM.SigSet reduce_order_S

reduce_order_Sig3

private AlgorithmGaussianMixtureModelEM.ClassSig reduce_order_Sig3

reduce_order_SubSig3

AlgorithmGaussianMixtureModelEM.SubSig reduce_order_SubSig3

reduce_order_first

private boolean reduce_order_first

distance_S

private AlgorithmGaussianMixtureModelEM.SigSet distance_S

distance_Sig3

private AlgorithmGaussianMixtureModelEM.ClassSig distance_Sig3

distance_SubSig3

private AlgorithmGaussianMixtureModelEM.SubSig distance_SubSig3

distance_first

private boolean distance_first

Constructor Detail

AlgorithmGaussianMixtureModelEM

public AlgorithmGaussianMixtureModelEM()

AlgorithmGaussianMixtureModelEM

public AlgorithmGaussianMixtureModelEM(int clusterMessageVerboseLevel,
                                       int init_num_of_subclasses,
                                       java.lang.String input_file_directory,
                                       java.lang.String input_file_name,
                                       java.lang.String parameter_output_file_directory,
                                       java.lang.String parameter_output_file_name,
                                       boolean full,
                                       int number_of_clusters)

AlgorithmGaussianMixtureModelEM

public AlgorithmGaussianMixtureModelEM(java.lang.String parameter_input_file_directory,
                                       java.lang.String parameter_input_file_name,
                                       java.lang.String file_directory,
                                       java.lang.String file_name,
                                       boolean classify)

Method Detail

demoClustFull

public void demoClustFull()

demoClustDiag

public void demoClustDiag()

demoClustFull5

public void demoClustFull5()

demoClustDiag5

public void demoClustDiag5()

demoClassify

public void demoClassify()

demoSplitClasses

public void demoSplitClasses()

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

clust

public void clust()

I_InitSigSet

private void I_InitSigSet(AlgorithmGaussianMixtureModelEM.SigSet S)

I_SigSetNBands

private void I_SigSetNBands(AlgorithmGaussianMixtureModelEM.SigSet S,
                            int nbands)

I_SetSigTitle

private void I_SetSigTitle(AlgorithmGaussianMixtureModelEM.SigSet S,
                           java.lang.String title)

I_SetClassTitle

private void I_SetClassTitle(AlgorithmGaussianMixtureModelEM.ClassSig C,
                             java.lang.String title)

I_NewClassSig

private AlgorithmGaussianMixtureModelEM.ClassSig I_NewClassSig(AlgorithmGaussianMixtureModelEM.SigSet S)

I_NewSubSig

private AlgorithmGaussianMixtureModelEM.SubSig I_NewSubSig(AlgorithmGaussianMixtureModelEM.SigSet S,
                                                           AlgorithmGaussianMixtureModelEM.ClassSig C)

I_AllocClassData

private AlgorithmGaussianMixtureModelEM.ClassData I_AllocClassData(AlgorithmGaussianMixtureModelEM.SigSet S,
                                                                   AlgorithmGaussianMixtureModelEM.ClassSig C,
                                                                   int npixels)

AverageVariance

private double AverageVariance(AlgorithmGaussianMixtureModelEM.ClassSig Sig,
                               int nbands)

subcluster

private int subcluster(AlgorithmGaussianMixtureModelEM.SigSet S,
                       int Class_Index,
                       int desired_num,
                       int option,
                       double Rmin,
                       int[] Max_num)

seed

private void seed(AlgorithmGaussianMixtureModelEM.ClassSig Sig,
                  int nbands,
                  double Rmin,
                  int option)

DiagonalizeMatrix

private void DiagonalizeMatrix(double[][] R,
                               int nbands)

compute_constants

private void compute_constants(AlgorithmGaussianMixtureModelEM.ClassSig Sig,
                               int nbands)

clust_invert

private int clust_invert(double[][] a,
                         int n,
                         double[] det_man,
                         int[] det_exp,
                         int[] indx,
                         double[][] y,
                         double[] col)

ludcmp

private int ludcmp(double[][] a,
                   int n,
                   int[] indx,
                   double[] d)

lubksb

private void lubksb(double[][] a,
                    int[] indx,
                    double[] b)

normalize_pi

private void normalize_pi(AlgorithmGaussianMixtureModelEM.ClassSig Sig)

refine_clusters

private double refine_clusters(AlgorithmGaussianMixtureModelEM.ClassSig Sig,
                               int nbands,
                               double Rmin,
                               int option)

regroup

private double regroup(AlgorithmGaussianMixtureModelEM.ClassSig Sig,
                       int nbands)

loglike

private double loglike(double[] x,
                       AlgorithmGaussianMixtureModelEM.SubSig sSig,
                       int nbands)

reestimate

private void reestimate(AlgorithmGaussianMixtureModelEM.ClassSig Sig,
                        int nbands,
                        double Rmin,
                        int option)

save_ClassSig

private void save_ClassSig(AlgorithmGaussianMixtureModelEM.ClassSig Sig1,
                           AlgorithmGaussianMixtureModelEM.SigSet S,
                           int nbands)

copy_ClassSig

private void copy_ClassSig(AlgorithmGaussianMixtureModelEM.ClassSig Sig1,
                           AlgorithmGaussianMixtureModelEM.ClassSig Sig2,
                           int nbands)

copy_SubSig

private void copy_SubSig(AlgorithmGaussianMixtureModelEM.SubSig SubSig1,
                         AlgorithmGaussianMixtureModelEM.SubSig SubSig2,
                         int nbands)

reduce_order

private void reduce_order(AlgorithmGaussianMixtureModelEM.ClassSig Sig,
                          int nbands,
                          int[] min_ii,
                          int[] min_jj)

distance

private double distance(AlgorithmGaussianMixtureModelEM.SubSig SubSig1,
                        AlgorithmGaussianMixtureModelEM.SubSig SubSig2,
                        int nbands)

add_SubSigs

private void add_SubSigs(AlgorithmGaussianMixtureModelEM.SubSig SubSig1,
                         AlgorithmGaussianMixtureModelEM.SubSig SubSig2,
                         AlgorithmGaussianMixtureModelEM.SubSig SubSig3,
                         int nbands)

I_DeallocSubSig

private void I_DeallocSubSig(AlgorithmGaussianMixtureModelEM.ClassSig C)

I_DeallocSigSet

private void I_DeallocSigSet(AlgorithmGaussianMixtureModelEM.SigSet S)

I_DeallocClassSig

private void I_DeallocClassSig(AlgorithmGaussianMixtureModelEM.SigSet S)

I_DeallocClassData

private void I_DeallocClassData(AlgorithmGaussianMixtureModelEM.SigSet S,
                                AlgorithmGaussianMixtureModelEM.ClassSig C)

I_WriteSigSet

private void I_WriteSigSet(java.io.RandomAccessFile raFile,
                           AlgorithmGaussianMixtureModelEM.SigSet S)

I_GetSigTitle

private java.lang.String I_GetSigTitle(AlgorithmGaussianMixtureModelEM.SigSet S)

I_GetClassTitle

private java.lang.String I_GetClassTitle(AlgorithmGaussianMixtureModelEM.ClassSig C)

classify

private void classify()

I_ReadSigSet

private void I_ReadSigSet(java.io.RandomAccessFile raFile,
                          AlgorithmGaussianMixtureModelEM.SigSet S)

get_class

private void get_class(java.io.RandomAccessFile raFile,
                       AlgorithmGaussianMixtureModelEM.SigSet S)

get_subclass

private void get_subclass(java.io.RandomAccessFile raFile,
                          AlgorithmGaussianMixtureModelEM.SigSet S,
                          AlgorithmGaussianMixtureModelEM.ClassSig C)

ClassLogLikelihood_init

private void ClassLogLikelihood_init(AlgorithmGaussianMixtureModelEM.SigSet S)

invert

private int invert(double[][] a,
                   int n)

ClassLogLikelihood

private void ClassLogLikelihood(double[] vector,
                                double[] ll,
                                AlgorithmGaussianMixtureModelEM.SigSet S)

splitClasses

private void splitClasses()