Package gov.nih.mipav.model.algorithms

Class AlgorithmHistogram2Dim

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmHistogram2Dim

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmHistogram2Dim
extends AlgorithmBase

This algorithm creates a two dimensional histogram of the data in 2 black and white images or 1 color image. if doLinearRescale is true, the range of data in the second image is rescaled to be the same as the range of data in the first image. That is the second image minimum is rescaled to the first image minimum and the second image maximum is rescaled to the first image maximum. Also, if linear rescaling is used the number of bins in the second image is set equal to the number of bins in the first image. The default number of bins equals the min(256,maximum value - minimum value + 1) if the data is not float or double. If the data is float or double, the default number of bins is 256. ch1 = 0 to ch1 = bin1 - 2 all have a width of (bin1 - 1)/range1, but ch1 = bin1 - 1 has no width, it is a single value at max1. bin ch1 = 0 covers min1 invalid input: '<'= ch1 invalid input: '<' min1 + (max1 - min1)/(bin1 - 1) bin ch1 = 1 covers min1 + (max1 - min1)/(bin1 - 1) invalid input: '<'= ch1 invalid input: '<' min1 + 2*(max1 - min1)/(bin1 - 1) bin ch1 = bin1 - 2 covers min1 + (bin1 - 2)*(max - min1)/(bin1 - 1) invalid input: '<'= ch1 invalid input: '<' max1 bin ch1 = bin1 - 1 covers only max1 The processing for maximum values is specially handled to prevent loss of top bin counts from rounding errors.

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 ModelImage	baseImage	Image for Y-axis of Histogram
private int	bin1	Number of bins for Image1
private int	bin2	Number of bins for Image2
private boolean	doLinearRescale	Boolean value.
private boolean	doLogResult	Boolean value.
private boolean	useBlue	For color images only.
private boolean	useGreen	For color images only.
private boolean	useRed	For color images only.

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
AlgorithmHistogram2Dim(ModelImage destImg, ModelImage srcImg, boolean doLinearRescale, boolean doLogResult, int bin1, int bin2, boolean useRed, boolean useGreen, boolean useBlue)	Constructor for images in which 2D histogram is placed in a predetermined destination image.
AlgorithmHistogram2Dim(ModelImage destImg, ModelImage srcImg, ModelImage baseImage, boolean doLinearRescale, boolean doLogResult, int bin1, int bin2)	Constructor for images in which 2D histogram is placed in a predetermined destination image.

Method Summary

Modifier and Type	Method	Description
private void	calcStoreInDest()	This function produces a 2D histogram image with srcImage values represented across the x axis and baseImage values represented across the y axis.
private void	calcStoreInDestColor()	This function produces a 2D histogram image with first color values represented across the x axis and second color values represented across the y axis.
void	finalize()	Prepares this class for destruction.
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

baseImage

private ModelImage baseImage

Image for Y-axis of Histogram

bin1

private int bin1

Number of bins for Image1

bin2

private int bin2

Number of bins for Image2

doLinearRescale

private boolean doLinearRescale

Boolean value. If true baseImage (Image2) is rescaled to the range of source image (Image1)

doLogResult

private boolean doLogResult

Boolean value. If true, the log of the result image is displayed for better visualization

useBlue

private boolean useBlue

For color images only. If true blue image is used as one of the images to create a 2D Histogram

useGreen

private boolean useGreen

For color images only. If true green image is used as one of the images to create a 2D Histogram

useRed

private boolean useRed

For color images only. If true red image is used as one of the images to create a 2D Histogram

Constructor Details

AlgorithmHistogram2Dim

public AlgorithmHistogram2Dim(ModelImage destImg,
 ModelImage srcImg,
 ModelImage baseImage,
 boolean doLinearRescale,
 boolean doLogResult,
 int bin1,
 int bin2)

Constructor for images in which 2D histogram is placed in a predetermined destination image. Used for 2 black and white images

Parameters:

destImg - image model where result image is to stored

srcImg - image for x axis of histogram

baseImage - image for y axis of histogram

doLinearRescale - If true rescales the Image2 data to the range of Image1 data

doLogResult - If true, displays the log of the result image for better visualization

bin1 - Number of bins on x-axis (Image1)

bin2 - Number of bins in y-axis (Image2)

AlgorithmHistogram2Dim

public AlgorithmHistogram2Dim(ModelImage destImg,
 ModelImage srcImg,
 boolean doLinearRescale,
 boolean doLogResult,
 int bin1,
 int bin2,
 boolean useRed,
 boolean useGreen,
 boolean useBlue)

Constructor for images in which 2D histogram is placed in a predetermined destination image. Used for 1 color image.

Parameters:

destImg - image model where result image is to stored

srcImg - source image model

doLinearRescale - If true rescales the Image2 data to the range of Image1 data

doLogResult - If true, displays the log of the result image for better visualization

bin1 - Number of bins on x-axis (Image1)

bin2 - Number of bins in y-axis (Image2)

useRed - For color images only. If true red image is used as one of the images to create a 2D Histogram

useGreen - For color images only. If true green image is used as one of the images to create a 2D Histogram

useBlue - For color images only. If true blue image is used as one of the images to create a 2D Histogram

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

calcStoreInDest

private void calcStoreInDest()

This function produces a 2D histogram image with srcImage values represented across the x axis and baseImage values represented across the y axis.

calcStoreInDestColor

private void calcStoreInDestColor()

This function produces a 2D histogram image with first color values represented across the x axis and second color values represented across the y axis.