Package gov.nih.mipav.model.algorithms

Class AlgorithmHistogramSliceMatch

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmHistogramSliceMatch

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmHistogramSliceMatch
extends AlgorithmBase

Algorithm that matches or transforms a match or source slice so as to make its histogram equal to the histogram of a base slice. In order to easily note the great similarity of the histograms, the histogram displays must both be in linear mode rather than log mode so that small differences are not exaggerated. The algorithm is as follows: 1.) Make the histogram for the match image. 2.) Make the histogram cumulative. 3.) Create the scaled cumulative histogram mapping scaled so that the last bin of mapping has the range of the base image. 4.) For the base image create a histogram with the same number of bins as the match image. 5.) Make the histogram cumulative. 6.) Create the scaled cumulative histogram cumHist scaled so that the last bin of cumHist has the range of the base image. 7.) For each value of mapping[i] find the cumHist[j] that is closest in value. 8.) In remap[i] put the value of srcImage corresponding to the jth bin. 9.) For each srcBuffer[i] find the bin number brightnessLevel and replace the srcBuffer[i] with the remap[brightnessLevel]. References: 1.) Digital Image Processing by Rafael C. Gonzalez and Richard E. Woods, Addison-Wesley Publishing Company, 1992, pp. 173-182. 2.) Two-Dimensional Signal and Image Processing by Jae S. Lim, Prentice-Hall, Inc., 1990, pp. 453-459.

According to Freedman and Diaconis as summarized in "Recent Developments in NonParametric Density Estimation" by Alan Julian Izenman, Journal of the American Statistical Association, March, 1991, Vol. 86, No. 413, pp. 205 - 224: The ideal histogram bin width W is given by W = 2(IQR)pow(N,-1/3) where IQR is the inrterquartile range(the 75 percentile minus the 25th percentile) and N is the number of available samples.

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 float	bufMax	DOCUMENT ME!
private float	bufMin	DOCUMENT ME!
private boolean	isColorImage	DOCUMENT ME!
private int	referenceSlice

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
AlgorithmHistogramSliceMatch(ModelImage srcImg, int referenceSlice)	Constructor for 3D images in which changes are returned to the source image.
AlgorithmHistogramSliceMatch(ModelImage destImg, ModelImage srcImg, int referenceSlice)	Constructor for 3D images in which changes are placed in a predetermined destination image.

Method Summary

Modifier and Type	Method	Description
private void	calcInPlace()	Histogram equalizing of slices to reference slice.
private void	calcStoreInDest()	This function produces a new image that has had all slices histogram equalized to reference slice. places filtered image in the destination image.
private void	filter(float[] srcBuffer, float[] baseBuffer)	just break up each RGB image into these separate monochrome images sliceFilter and then reassemble int aRGB.
void	finalize()	Prepares this class for destruction.
private void	findBufferMinMax(float[] buf, int bufStart, int bufEnd)	Finds the local maximum and minimum values in the given range in order, as given by the starting and stoping values.
private float	getIdealWidth(float[] srcBuffer)	find the ideal bin width
void	runAlgorithm()	starts the algorithm.

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

bufMax

private float bufMax

DOCUMENT ME!

bufMin

private float bufMin

DOCUMENT ME!

isColorImage

private boolean isColorImage

DOCUMENT ME!

referenceSlice

private int referenceSlice

Constructor Details

AlgorithmHistogramSliceMatch

public AlgorithmHistogramSliceMatch(ModelImage srcImg,
 int referenceSlice)

Constructor for 3D images in which changes are returned to the source image.

Parameters:

srcImg - source image model

referenceSlice -

AlgorithmHistogramSliceMatch

public AlgorithmHistogramSliceMatch(ModelImage destImg,
 ModelImage srcImg,
 int referenceSlice)

Constructor for 3D images in which changes are placed in a predetermined destination image.

Parameters:

destImg - image model where result image is to stored

srcImg - source image model

referenceSlice -

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

calcInPlace

private void calcInPlace()

Histogram equalizing of slices to reference slice. Replaces the original image with the filtered image.

calcStoreInDest

private void calcStoreInDest()

This function produces a new image that has had all slices histogram equalized to reference slice. places filtered image in the destination image.

filter

private void filter(float[] srcBuffer,
 float[] baseBuffer)

just break up each RGB image into these separate monochrome images sliceFilter and then reassemble int aRGB.

Parameters:

srcBuffer - source buffer

baseBuffer - base Buffer

getIdealWidth

private float getIdealWidth(float[] srcBuffer)

find the ideal bin width

findBufferMinMax

private void findBufferMinMax(float[] buf,
 int bufStart,
 int bufEnd)

Finds the local maximum and minimum values in the given range in order, as given by the starting and stoping values.

Parameters:

buf - float array of values

bufStart - where to begin looking

bufEnd - where to stop