java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmSpectralClustering

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.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 java.lang.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, java.lang.String resultsFileName, float[] redBuffer, float[] greenBuffer, float[] blueBuffer, double scaleMax, boolean scaleVariablesToUnitVariance)`

Method Summary

All Methods Instance Methods Concrete Methods
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, 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

image
```
private ModelImage image
```

scale
```
private double[] scale
```

pos
```
private double[][] pos
```

groupNum
```
private int[] groupNum
```

centroidPos
```
private double[][] centroidPos
```

resultsFileName

private java.lang.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 Detail

AlgorithmSpectralClustering

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

Method Detail
- 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()
```

Class AlgorithmSpectralClustering

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

image

scale

pos

groupNum

centroidPos

resultsFileName

redBuffer

greenBuffer

blueBuffer

scaleMax

useColorHistogram

scaleVariablesToUnitVariance

nDims

nPoints

numberClusters

A

scale2

D

L

jobz

range

uplo

il

iu

abstol

numEigenvaluesFound

eigenvalues

X

work

lwork

iwork

ifail

info

found

Y

totalWeight

centroidDistances

Constructor Detail

AlgorithmSpectralClustering

Method Detail

finalize

runAlgorithm

eval

selfTest