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

All Methods Instance Methods Concrete Methods
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()
```

Class AlgorithmGaussianMixtureModelEM

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

clusterMessageVerboseLevel

init_num_of_subclasses

input_file_directory

input_file_name

data_file_directory

data_file_name

parameter_input_file_directory

parameter_input_file_name

parameter_output_file_directory

parameter_output_file_name

full

number_of_clusters

SIGNATURE_TYPE_MIXED

COVAR_DYNAMIC_RANGE

CLUSTER_FULL

CLUSTER_DIAG

Smin

compute_constants_indx

compute_constants_y

compute_constants_col

compute_constants_first

reduce_order_S

reduce_order_Sig3

reduce_order_SubSig3

reduce_order_first

distance_S

distance_Sig3

distance_SubSig3

distance_first

Constructor Detail

AlgorithmGaussianMixtureModelEM

AlgorithmGaussianMixtureModelEM

AlgorithmGaussianMixtureModelEM

Method Detail

demoClustFull

demoClustDiag

demoClustFull5

demoClustDiag5

demoClassify

demoSplitClasses

runAlgorithm

clust

I_InitSigSet

I_SigSetNBands

I_SetSigTitle

I_SetClassTitle

I_NewClassSig

I_NewSubSig

I_AllocClassData

AverageVariance

subcluster

seed

DiagonalizeMatrix

compute_constants

clust_invert

ludcmp

lubksb

normalize_pi

refine_clusters

regroup

loglike

reestimate

save_ClassSig

copy_ClassSig

copy_SubSig

reduce_order

distance

add_SubSigs