Package gov.nih.mipav.model.algorithms.filters

Class AlgorithmSWI

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.filters.AlgorithmSWI

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmSWI
extends AlgorithmBase

This class recalculates mo and dceFullTre to provide better estimates using the inverse Ernst equation

Author:

Justin Senseney (SenseneyJ@mail.nih.gov)

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	brainMask	Denotes which pixels undergo SWI processing.
private ModelImage	iCenter
private ModelImage	iFinal
private ModelImage	iImage
private boolean	inScript	Denotes whether the algorithm is run in a script/JIST, if so showInterImages just stores images for later access.
private ModelImage	kCenterImage
private ModelImage	kImage
private ModelImage	magImage
private double	maskThreshold
private int	multFactor
private ModelImage	phaseImage
private ModelImage	phaseMask
private boolean	showInterImages	Whether intermediate images should be displayed during pipeline processing
private int	xDim	X dimension length
private int	xFilterSize
private double	xFilterTopLeft
private int	yDim	Y dimension length
private int	yFilterSize
private double	yFilterTopLeft
private int	zDim	Z dimension length

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
AlgorithmSWI(boolean inScript, ModelImage resultImage, ModelImage magImage, ModelImage phaseImage, double maskThreshold, int roFilterSize, int peFilterSize, int multFactor, boolean showInterImages)	Constructor.

Method Summary

Modifier and Type	Method	Description
private void	calc2D()
private void	calc3D()
private ModelImage	createBrainMask()
private ModelImage	createiImage(double[] realData, double[] imagData)
private ModelImage	createKCenterImage(ModelImage kImage)
private ModelImage	createkImage(ModelImage iImage)
void	finalize()	Prepares this class for destruction.
private ModelImage	generateIFinal(ModelImage iImage, ModelImage iCenterImage, BitSet brainMaskSet, double[] ixRealFinal, double[] ixImagFinal)
private ModelImage	generateMagEnhanced(double[] phaseMaskData, ModelImage magnitude)
private ModelImage	generatePhaseMask(BitSet brainMaskSet, double[] ixRealFinal, double[] ixImagFinal, double[] phaseMaskData)
ModelImage	getBrainMask()
ModelImage	getiCenter()
ModelImage	getiFinal()
ModelImage	getiImage()
ModelImage	getkCenterImage()
ModelImage	getkImage()
ModelImage	getPhaseMask()
private void	rescaleToComplex(ModelImage magImage, ModelImage phaseImage, double[] realData, double[] imagData)
void	runAlgorithm()	Starts the algorithm.
private ModelImage	runiFFTonKCenter(ModelImage kCenterImage)

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

magImage

private ModelImage magImage

phaseImage

private ModelImage phaseImage

maskThreshold

private double maskThreshold

xFilterSize

private int xFilterSize

yFilterSize

private int yFilterSize

multFactor

private int multFactor

xDim

private int xDim

X dimension length

yDim

private int yDim

Y dimension length

zDim

private int zDim

Z dimension length

xFilterTopLeft

private double xFilterTopLeft

yFilterTopLeft

private double yFilterTopLeft

showInterImages

private boolean showInterImages

Whether intermediate images should be displayed during pipeline processing

kImage

private ModelImage kImage

iImage

private ModelImage iImage

brainMask

private ModelImage brainMask

Denotes which pixels undergo SWI processing.

kCenterImage

private ModelImage kCenterImage

iFinal

private ModelImage iFinal

phaseMask

private ModelImage phaseMask

inScript

private boolean inScript

Denotes whether the algorithm is run in a script/JIST, if so showInterImages just stores images for later access.

iCenter

private ModelImage iCenter

Constructor Details

AlgorithmSWI

public AlgorithmSWI(boolean inScript,
 ModelImage resultImage,
 ModelImage magImage,
 ModelImage phaseImage,
 double maskThreshold,
 int roFilterSize,
 int peFilterSize,
 int multFactor,
 boolean showInterImages)

Constructor.

Parameters:

resultImage - Result image model

srcImg - Source image model.

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the algorithm. At the conclusion of this method, AlgorithmBase reports to any algorithm listeners that this algorithm has completed. This method is not usually called explicitly by a controlling dialog. Instead, see AlgorithmBase.run() or start().

Specified by:

runAlgorithm in class AlgorithmBase

calc2D

private void calc2D()

calc3D

private void calc3D()

generateMagEnhanced

private ModelImage generateMagEnhanced(double[] phaseMaskData,
 ModelImage magnitude)

generatePhaseMask

private ModelImage generatePhaseMask(BitSet brainMaskSet,
 double[] ixRealFinal,
 double[] ixImagFinal,
 double[] phaseMaskData)

generateIFinal

private ModelImage generateIFinal(ModelImage iImage,
 ModelImage iCenterImage,
 BitSet brainMaskSet,
 double[] ixRealFinal,
 double[] ixImagFinal)

runiFFTonKCenter

private ModelImage runiFFTonKCenter(ModelImage kCenterImage)

createKCenterImage

private ModelImage createKCenterImage(ModelImage kImage)

createkImage

private ModelImage createkImage(ModelImage iImage)

createiImage

private ModelImage createiImage(double[] realData,
 double[] imagData)

createBrainMask

private ModelImage createBrainMask()

rescaleToComplex

private void rescaleToComplex(ModelImage magImage,
 ModelImage phaseImage,
 double[] realData,
 double[] imagData)

getkImage

public ModelImage getkImage()

getiImage

public ModelImage getiImage()

getBrainMask

public ModelImage getBrainMask()

getkCenterImage

public ModelImage getkCenterImage()

getiFinal

public ModelImage getiFinal()

getPhaseMask

public ModelImage getPhaseMask()

getiCenter

public ModelImage getiCenter()