Package gov.nih.mipav.model.algorithms

Class AlgorithmSpectralClustering

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmSpectralClustering

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmSpectralClustering
extends AlgorithmBase

Author:

William Gandler This program is an implementation of the algorithm described in "On Spectral Clustering: Analysis and an algorithm" by Andrew Y. Ng, Michael I. Jordan, and Yair Weiss. This forms clusters of nonconvex objects in black and white images or in text data files.

Nested Class Summary

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private double[][]	A
private double	abstol
private float[]	blueBuffer
private double[][]	centroidDistances
private double[][]	centroidPos
private double[][]	D
private double[]	eigenvalues
private boolean[]	found
private float[]	greenBuffer
private int[]	groupNum
private int[]	ifail
private int	il
private ModelImage	image
private int[]	info
private int	iu
private int[]	iwork
private char	jobz
private double[][]	L
private int	lwork
private int	nDims
private int	nPoints
private int	numberClusters
private int[]	numEigenvaluesFound
private double[][]	pos
private char	range
private float[]	redBuffer
private String	resultsFileName
private double[]	scale
private double[]	scale2
private double	scaleMax
private boolean	scaleVariablesToUnitVariance
private int[]	totalWeight
private char	uplo
private boolean	useColorHistogram
private double[]	work
private double[][]	X
private double[][]	Y

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
AlgorithmSpectralClustering(ModelImage image, double[][] pos, double[] scale, int[] groupNum, double[][] centroidPos, String resultsFileName, float[] redBuffer, float[] greenBuffer, float[] blueBuffer, double scaleMax, boolean scaleVariablesToUnitVariance)

Method Summary

Modifier and Type	Method	Description
private double	eval(double sigma)
void	finalize()	Prepares this class for destruction.
void	runAlgorithm()	Starts the algorithm.
private void	selfTest()

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, 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

image

private ModelImage image

scale

private double[] scale

pos

private double[][] pos

groupNum

private int[] groupNum

centroidPos

private double[][] centroidPos

resultsFileName

private String resultsFileName

redBuffer

private float[] redBuffer

greenBuffer

private float[] greenBuffer

blueBuffer

private float[] blueBuffer

scaleMax

private double scaleMax

useColorHistogram

private boolean useColorHistogram

scaleVariablesToUnitVariance

private boolean scaleVariablesToUnitVariance

nDims

private int nDims

nPoints

private int nPoints

numberClusters

private int numberClusters

A

private double[][] A

scale2

private double[] scale2

D

private double[][] D

L

private double[][] L

jobz

private char jobz

range

private char range

uplo

private char uplo

il

private int il

iu

private int iu

abstol

private double abstol

numEigenvaluesFound

private int[] numEigenvaluesFound

eigenvalues

private double[] eigenvalues

X

private double[][] X

work

private double[] work

lwork

private int lwork

iwork

private int[] iwork

ifail

private int[] ifail

info

private int[] info

found

private boolean[] found

Y

private double[][] Y

totalWeight

private int[] totalWeight

centroidDistances

private double[][] centroidDistances

Constructor Details

AlgorithmSpectralClustering

public AlgorithmSpectralClustering(ModelImage image,
 double[][] pos,
 double[] scale,
 int[] groupNum,
 double[][] centroidPos,
 String resultsFileName,
 float[] redBuffer,
 float[] greenBuffer,
 float[] blueBuffer,
 double scaleMax,
 boolean scaleVariablesToUnitVariance)

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the algorithm.

Specified by:

runAlgorithm in class AlgorithmBase

eval

private double eval(double sigma)

selfTest

private void selfTest()