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

All Implemented Interfaces:

AlgorithmInterface, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmProstateFeaturesSaveAutoTrain
extends AlgorithmBase
implements AlgorithmInterface
```
This class save the Coherence Enhanced Diffusion (CED) 2D slice based features, which are Hurst index and Haralick features. The input is the CED 2D slice, the output is SVM feature array.

Author:

Ruida Cheng

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 ModelImage`	`classificationImage`	classification image to hold the SVM readable features.
`private AlgorithmCoherenceEnhancingDiffusion`	`coherenceEnhancingDiffusionAlgo`
`private boolean`	`coherenceEnhancingDiffusionFilter`
`private ModelImage`	`coherenceEnhancingDiffusionImage`
`private ModelImage`	`destImage`
`private AlgorithmFrequencyFilter`	`gaborAlgo`
`private boolean`	`gaborFilter`
`private ModelImage`	`gaborImage`
`private AlgorithmGaussianBlur`	`gaussianAlgo`
`private boolean`	`gaussianFilter`
`private ModelImage`	`gaussianImage`
`private AlgorithmGradientMagnitude`	`gmAlgo`
`private boolean`	`gmFilter`
`private ModelImage`	`gmImage`
`private float[][][]`	`haralickBuffer`
`private boolean`	`haralickFilter`
`private AlgorithmHurstIndex`	`hurstAlgo`
`private boolean`	`hurstFilter`
`private ModelImage`	`hurstImage`
`private AlgorithmIHN3Correction`	`IHN3CorrectionAlgo`
`private boolean`	`IHN3CorrectionFilter`
`private ModelImage`	`IHN3CorrectionImage`
`private ModelImage`	`image`	source image.
`private boolean`	`imageIntensityFilter`	flag to indicate the image intensity filter enabled or not.
`private AlgorithmChangeType`	`invertAlgo`
`private boolean`	`invertFilter`
`private ModelImage`	`invertImage`
`private AlgorithmMean`	`meanAlgo`
`private boolean`	`meanFilter`
`private ModelImage`	`meanImage`
`private AlgorithmMedian`	`medianAlgo`
`private boolean`	`medianFilter`
`private ModelImage`	`medianImage`
`private AlgorithmMode`	`modeAlgo`
`private boolean`	`modeFilter`
`private ModelImage`	`modeImage`
`private int`	`numberFeatures`	number features.
`private AlgorithmRegularizedIsotropicDiffusion`	`regisotropicDiffusionAlgo`
`private boolean`	`regisotropicDiffusionFilter`
`private ModelImage`	`regisotropicDiffusionImage`
`private int`	`totalHaralickFilters`
`private VOIVector`	`VOIs`	source imag VOIs.
`private AlgorithmRiceWaveletTools`	`waveletAlgo`
`private boolean`	`waveletFilter`
`private ModelImage[]`	`waveletImage`

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, 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
`AlgorithmProstateFeaturesSaveAutoTrain(ModelImage destImg, ModelImage classImage, ModelImage srcImg, boolean imageIntensityFilter, boolean coherenceEnhancingDiffusionFilter, boolean regisotropicDiffusionFilter, boolean IHN3CorrectionFilter, boolean modeFilter, boolean meanFilter, boolean medianFilter, boolean invertFilter, boolean haralickFilter, boolean gaborFilter, boolean hurstFilter, boolean waveletFilter, boolean gaussianFilter, boolean gmFilter, int numberFeatures)`	Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
`private void`	`calculate()`	DOCUMENT ME!
`private void`	`calculateCoherenceEnhancingDiffusion()`
`private void`	`calculateGabor()`	Generate Gabor filter.
`private void`	`calculateGaussian()`	generate the gaussian filter.
`private void`	`calculateGM()`	generate the gradient magnitude image.
`private void`	`calculateHaralick()`	Genernate Haralick images.
`private void`	`calculateHurstIndex()`	Generate hurst index image.
`void`	`calculateIHN3Correction()`
`private void`	`calculateInvert()`	Generate the invert image.
`private void`	`calculateMean()`	Generate mean image.
`private void`	`calculateMedian()`	Generate the median image.
`private void`	`calculateMode()`
`private void`	`calculateRegIsotropicDiffusion()`
`private void`	`calculateWavelet()`	Generate the wavelet image
`void`	`finalize()`	Prepares this class for destruction.
`void`	`runAlgorithm()`	Starts the program.
`int`	`whichClass(int pos, int centerX, int centerY, int xDim, int yDim)`

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

destImage
```
private ModelImage destImage
```

classificationImage
```
private ModelImage classificationImage
```
classification image to hold the SVM readable features.

image
```
private ModelImage image
```
source image.

VOIs
```
private VOIVector VOIs
```
source imag VOIs.

imageIntensityFilter
```
private boolean imageIntensityFilter
```
flag to indicate the image intensity filter enabled or not.

coherenceEnhancingDiffusionFilter

private boolean coherenceEnhancingDiffusionFilter

coherenceEnhancingDiffusionImage

private ModelImage coherenceEnhancingDiffusionImage

coherenceEnhancingDiffusionAlgo

private AlgorithmCoherenceEnhancingDiffusion coherenceEnhancingDiffusionAlgo

regisotropicDiffusionFilter

private boolean regisotropicDiffusionFilter

regisotropicDiffusionImage

private ModelImage regisotropicDiffusionImage

regisotropicDiffusionAlgo

private AlgorithmRegularizedIsotropicDiffusion regisotropicDiffusionAlgo

IHN3CorrectionFilter
```
private boolean IHN3CorrectionFilter
```

IHN3CorrectionImage
```
private ModelImage IHN3CorrectionImage
```

IHN3CorrectionAlgo

private AlgorithmIHN3Correction IHN3CorrectionAlgo

modeFilter
```
private boolean modeFilter
```

modeImage
```
private ModelImage modeImage
```

modeAlgo
```
private AlgorithmMode modeAlgo
```

meanFilter
```
private boolean meanFilter
```

meanImage
```
private ModelImage meanImage
```

meanAlgo
```
private AlgorithmMean meanAlgo
```

medianFilter
```
private boolean medianFilter
```

medianImage
```
private ModelImage medianImage
```

medianAlgo
```
private AlgorithmMedian medianAlgo
```

invertFilter
```
private boolean invertFilter
```

invertImage
```
private ModelImage invertImage
```

invertAlgo
```
private AlgorithmChangeType invertAlgo
```

haralickFilter
```
private boolean haralickFilter
```

haralickBuffer
```
private float[][][] haralickBuffer
```

totalHaralickFilters
```
private int totalHaralickFilters
```

gaborFilter
```
private boolean gaborFilter
```

gaborImage
```
private ModelImage gaborImage
```

gaborAlgo

private AlgorithmFrequencyFilter gaborAlgo

gaussianFilter
```
private boolean gaussianFilter
```

gaussianImage
```
private ModelImage gaussianImage
```

gaussianAlgo

private AlgorithmGaussianBlur gaussianAlgo

gmFilter
```
private boolean gmFilter
```

gmImage
```
private ModelImage gmImage
```

gmAlgo

private AlgorithmGradientMagnitude gmAlgo

hurstFilter
```
private boolean hurstFilter
```

hurstImage
```
private ModelImage hurstImage
```

hurstAlgo
```
private AlgorithmHurstIndex hurstAlgo
```

waveletFilter
```
private boolean waveletFilter
```

waveletImage
```
private ModelImage[] waveletImage
```

waveletAlgo

private AlgorithmRiceWaveletTools waveletAlgo

numberFeatures
```
private int numberFeatures
```
number features.

Constructor Detail

AlgorithmProstateFeaturesSaveAutoTrain

public AlgorithmProstateFeaturesSaveAutoTrain(ModelImage destImg,
                                              ModelImage classImage,
                                              ModelImage srcImg,
                                              boolean imageIntensityFilter,
                                              boolean coherenceEnhancingDiffusionFilter,
                                              boolean regisotropicDiffusionFilter,
                                              boolean IHN3CorrectionFilter,
                                              boolean modeFilter,
                                              boolean meanFilter,
                                              boolean medianFilter,
                                              boolean invertFilter,
                                              boolean haralickFilter,
                                              boolean gaborFilter,
                                              boolean hurstFilter,
                                              boolean waveletFilter,
                                              boolean gaussianFilter,
                                              boolean gmFilter,
                                              int numberFeatures)

Constructor.

Parameters:: destImg -; classImage -; srcImg -; imageIntensityFilter - flag for image intensity filter.; coherenceEnhancingDiffusionFilter - flag for CED filter.; regisotropicDiffusionFilter - flag for iso-tropic diffusion filter.; IHN3CorrectionFilter - flag for N3 correction filter.; modeFilter - flag for mode filter.; meanFilter - flag for mean filter.; medianFilter - flag for median filter.; invertFilter - flag for invert filter.; haralickFilter - flag for filter.; gaborFilter - flag for filter.; hurstFilter - flag for index filter.; waveletFilter - flag for filter.; gaussianFilter - flag for filter.; gmFilter - flag for gradient magnitude filter.; numberFeatures - number features.

Method Detail
- finalize
```
public void finalize()
```
  Prepares this class for destruction.
  
  Overrides:
  
  finalize in class AlgorithmBase
- runAlgorithm
```
public void runAlgorithm()
```
  Starts the program.
  
  Specified by:
  
  runAlgorithm in class AlgorithmBase
- calculateWavelet
```
private void calculateWavelet()
```
  Generate the wavelet image
- calculateHurstIndex
```
private void calculateHurstIndex()
```
  Generate hurst index image.
- calculateGM
```
private void calculateGM()
```
  generate the gradient magnitude image.
- calculateGaussian
```
private void calculateGaussian()
```
  generate the gaussian filter.
- calculateGabor
```
private void calculateGabor()
```
  Generate Gabor filter.
- calculateInvert
```
private void calculateInvert()
```
  Generate the invert image.
- calculateMedian
```
private void calculateMedian()
```
  Generate the median image.
- calculateMean
```
private void calculateMean()
```
  Generate mean image.
- calculateMode
```
private void calculateMode()
```
- calculateRegIsotropicDiffusion
```
private void calculateRegIsotropicDiffusion()
```
- calculateCoherenceEnhancingDiffusion
```
private void calculateCoherenceEnhancingDiffusion()
```
- calculateIHN3Correction
```
public void calculateIHN3Correction()
```
- calculate
```
private void calculate()
```
  DOCUMENT ME!
- calculateHaralick
```
private void calculateHaralick()
```
  Genernate Haralick images.
- whichClass
```
public int whichClass(int pos,
                      int centerX,
                      int centerY,
                      int xDim,
                      int yDim)
```
- algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
  Description copied from interface: AlgorithmInterface
  
  Called after an algorithm this listener is registered to exits (maybe successfully, maybe not). If the algorithm is run in a separate thread, this call will be made within that thread. If not, this call will be made from that same, shared thread.
  
  Specified by:
  
  algorithmPerformed in interface AlgorithmInterface
  
  Parameters:
  
  algorithm - the algorithm which has just completed

Class AlgorithmProstateFeaturesSaveAutoTrain

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

destImage

classificationImage

image

VOIs

imageIntensityFilter

coherenceEnhancingDiffusionFilter

coherenceEnhancingDiffusionImage

coherenceEnhancingDiffusionAlgo

regisotropicDiffusionFilter

regisotropicDiffusionImage

regisotropicDiffusionAlgo

IHN3CorrectionFilter

IHN3CorrectionImage

IHN3CorrectionAlgo

modeFilter

modeImage

modeAlgo

meanFilter

meanImage

meanAlgo

medianFilter

medianImage

medianAlgo

invertFilter

invertImage

invertAlgo

haralickFilter

haralickBuffer

totalHaralickFilters

gaborFilter

gaborImage

gaborAlgo

gaussianFilter

gaussianImage

gaussianAlgo

gmFilter

gmImage

gmAlgo

hurstFilter

hurstImage

hurstAlgo

waveletFilter

waveletImage

waveletAlgo

numberFeatures

Constructor Detail

AlgorithmProstateFeaturesSaveAutoTrain

Method Detail

finalize

runAlgorithm

calculateWavelet

calculateHurstIndex

calculateGM

calculateGaussian

calculateGabor

calculateInvert

calculateMedian

calculateMean

calculateMode

calculateRegIsotropicDiffusion

calculateCoherenceEnhancingDiffusion

calculateIHN3Correction

calculate

calculateHaralick

whichClass

algorithmPerformed