Package gov.nih.mipav.model.algorithms

Class AlgorithmTreT1

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTProcess

gov.nih.mipav.model.algorithms.AlgorithmTreT1

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmTreT1
extends AlgorithmTProcess

This class is adapted from the ImageJ version originally written by Sean Deoni while working at the National Institutes of Health. This class performs T1 calculations given any number of SPGR and IRSPGR images.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	AlgorithmTreT1.CalculateT1
private class	AlgorithmTreT1.CalculateT1UsingConventionalTreT1Inner
private class	AlgorithmTreT1.CalculteT1UsingTreT1HIFIInner

Nested classes/interfaces inherited from class gov.nih.mipav.model.algorithms.AlgorithmTProcess

AlgorithmTProcess.CalculateT

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private double	angleIncrement
private int	b1ImageIndex
private double[][][]	b1ResultData
private ModelImage	b1ResultStack
private ViewJFrameImage	b1ResultWindow
private boolean	calculateM0
private boolean	calculateT1
private boolean	completed
private int[]	direction
private boolean	doubleInversion
private double[]	estimates
private boolean	geScanner
private boolean	invertT1toR1
private double[]	irspgrData
private double	irspgrFA
private int[]	irspgrImageIndex
private double	irspgrKy
private double[]	irspgrTI
private double[]	irspgrTr
private double	irspgrTR
private ModelImage	largestImage
private double[][][]	m0ResultData
private ModelImage	m0ResultStack
private ViewJFrameImage	m0ResultWindow
private double	maxAngle
private double	maxM0
private double	maxT1
private int	Nsa
private int	Nti
private boolean	onefiveTField
private boolean	performStraightTreT1
private boolean	performTreT1HIFI
private boolean	performTreT1withPreCalculatedB1Map
private double	pointScale
private double[][][]	r1ResultData
private ModelImage	r1ResultStack
private ViewJFrameImage	r1ResultWindow
private double[]	residuals
private double	scale
private double	scaleIncrement
private boolean	showB1Map
private boolean	siemensScanner
private boolean	singleInversion
private boolean	smoothB1Field
private double[]	spgrData
private int[]	spgrImageIndex
private double[][][]	t1ResultData
private ModelImage	t1ResultStack
private ViewJFrameImage	t1ResultWindow	The frames for result images (if null at end of algorithm src ModelImage is destroyed)
private boolean	threeTField
private String[]	titles
private double[]	treFA
private double	treTR
private boolean	uniformAngleSpacing
private boolean	useWeights
private String[]	wList

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmTProcess

computeDataThreads, do4D, Gaussian, hardNoiseThreshold, loadDataThreads, lowerLeftCorner, lowerRightCorner, MAX_PROCESS, noiseScale, nSlices, processDataThreads, upperLeftCorner, upperRightCorner, useHardThresholding, useSmartThresholding

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
AlgorithmTreT1(double treTR, double irspgrTR, double irspgrKy, double irspgrFA, double maxT1, double maxM0, double[] treFA, double[] irspgrTr2, double[] irspgrTI, double[] spgrData, double[] irspgrData, double scale, double pointScale, double scaleIncrement, double[] estimates, double[] residuals, int[] direction, int[] spgrImageIndex, int[] irspgrImageIndex, int b1ImageIndex, double angleIncrement, int nsa, int nti, double maxAngle, boolean smoothB1Field, boolean performStraightTreT1, boolean performTreT1withPreCalculatedB1Map, boolean performTreT1HIFI, boolean doubleInversion, boolean singleInversion, boolean geScanner, boolean siemensScanner, boolean threeTField, boolean onefiveTField, boolean calculateT1, boolean showB1Map, boolean calculateM0, boolean invertT1toR1, boolean useWeights, boolean uniformAngleSpacing, boolean upperLeftCorner, boolean upperRightCorner, boolean lowerLeftCorner, boolean lowerRightCorner, boolean useSmartThresholding, boolean useHardThresholding, float noiseScale, float hardNoiseThreshold, String[] wList, String[] titles)
AlgorithmTreT1(ModelImage destImage, ModelImage srcImage, double treTR, double irspgrTR, double irspgrKy, double irspgrFA, double maxT1, double maxM0, double[] treFA, double[] irspgrTr2, double[] irspgrTI, double[] spgrData, double[] irspgrData, double scale, double pointScale, double scaleIncrement, double[] estimates, double[] residuals, int[] direction, int[] spgrImageIndex, int[] irspgrImageIndex, int b1ImageIndex, double angleIncrement, int nsa, int nti, double maxAngle, boolean smoothB1Field, boolean performStraightTreT1, boolean performTreT1withPreCalculatedB1Map, boolean performTreT1HIFI, boolean doubleInversion, boolean singleInversion, boolean geScanner, boolean siemensScanner, boolean threeTField, boolean onefiveTField, boolean calculateT1, boolean showB1Map, boolean calculateM0, boolean invertT1toR1, boolean useWeights, boolean uniformAngleSpacing, boolean upperLeftCorner, boolean upperRightCorner, boolean lowerLeftCorner, boolean lowerRightCorner, boolean useSmartThresholding, boolean useHardThresholding, float noiseScale, float hardNoiseThreshold, String[] wList, String[] titles)

Method Summary

Modifier and Type	Method	Description
boolean	calculateT1UsingConventionalTreT1()
boolean	calculateT1UsingTreT1HIFI()
protected void	computeProcessors()
protected void	displayImages()	This method is used in both the conventional and HIFI case to display result images
void	finalize()	Prepares this class for destruction.
ModelImage	getB1ResultStack()
ModelImage	getM0ResultStack()
ModelImage	getR1ResultStack()
ModelImage	getT1ResultStack()
private void	init()	Initializes local variables that are internal to tre.
private void	initializeDisplayImages(ModelImage image)	This method initializes the final images as near-clones of the largest image in the set
private void	loadFinalData(ModelImage image, double[][][] data)
void	runAlgorithm()	Actually runs the algorithm.
double	signalResiduals(double x, double[] spgrData, double[] irspgrData, double Inversion, int Nfa, int Nti, double[] treFA, double treTR, double[] irspgrTr, double[] irspgrTI, double irspgrFA)

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmTProcess

cloneFileInfo

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

t1ResultStack

private ModelImage t1ResultStack

m0ResultStack

private ModelImage m0ResultStack

r1ResultStack

private ModelImage r1ResultStack

b1ResultStack

private ModelImage b1ResultStack

t1ResultData

private double[][][] t1ResultData

m0ResultData

private double[][][] m0ResultData

r1ResultData

private double[][][] r1ResultData

b1ResultData

private double[][][] b1ResultData

largestImage

private ModelImage largestImage

treTR

private double treTR

irspgrTR

private double irspgrTR

irspgrKy

private double irspgrKy

irspgrFA

private double irspgrFA

maxT1

private double maxT1

maxM0

private double maxM0

treFA

private double[] treFA

irspgrTr

private double[] irspgrTr

irspgrTI

private double[] irspgrTI

spgrData

private double[] spgrData

irspgrData

private double[] irspgrData

scale

private double scale

pointScale

private double pointScale

scaleIncrement

private double scaleIncrement

estimates

private double[] estimates

residuals

private double[] residuals

direction

private int[] direction

spgrImageIndex

private int[] spgrImageIndex

irspgrImageIndex

private int[] irspgrImageIndex

b1ImageIndex

private int b1ImageIndex

angleIncrement

private double angleIncrement

Nsa

private int Nsa

Nti

private int Nti

maxAngle

private double maxAngle

smoothB1Field

private boolean smoothB1Field

performStraightTreT1

private boolean performStraightTreT1

performTreT1withPreCalculatedB1Map

private boolean performTreT1withPreCalculatedB1Map

performTreT1HIFI

private boolean performTreT1HIFI

doubleInversion

private boolean doubleInversion

singleInversion

private boolean singleInversion

geScanner

private boolean geScanner

siemensScanner

private boolean siemensScanner

threeTField

private boolean threeTField

onefiveTField

private boolean onefiveTField

calculateT1

private boolean calculateT1

showB1Map

private boolean showB1Map

calculateM0

private boolean calculateM0

invertT1toR1

private boolean invertT1toR1

useWeights

private boolean useWeights

uniformAngleSpacing

private boolean uniformAngleSpacing

wList

private String[] wList

titles

private String[] titles

completed

private boolean completed

t1ResultWindow

private ViewJFrameImage t1ResultWindow

The frames for result images (if null at end of algorithm src ModelImage is destroyed)

m0ResultWindow

private ViewJFrameImage m0ResultWindow

r1ResultWindow

private ViewJFrameImage r1ResultWindow

b1ResultWindow

private ViewJFrameImage b1ResultWindow

Constructor Details

AlgorithmTreT1

public AlgorithmTreT1(double treTR,
 double irspgrTR,
 double irspgrKy,
 double irspgrFA,
 double maxT1,
 double maxM0,
 double[] treFA,
 double[] irspgrTr2,
 double[] irspgrTI,
 double[] spgrData,
 double[] irspgrData,
 double scale,
 double pointScale,
 double scaleIncrement,
 double[] estimates,
 double[] residuals,
 int[] direction,
 int[] spgrImageIndex,
 int[] irspgrImageIndex,
 int b1ImageIndex,
 double angleIncrement,
 int nsa,
 int nti,
 double maxAngle,
 boolean smoothB1Field,
 boolean performStraightTreT1,
 boolean performTreT1withPreCalculatedB1Map,
 boolean performTreT1HIFI,
 boolean doubleInversion,
 boolean singleInversion,
 boolean geScanner,
 boolean siemensScanner,
 boolean threeTField,
 boolean onefiveTField,
 boolean calculateT1,
 boolean showB1Map,
 boolean calculateM0,
 boolean invertT1toR1,
 boolean useWeights,
 boolean uniformAngleSpacing,
 boolean upperLeftCorner,
 boolean upperRightCorner,
 boolean lowerLeftCorner,
 boolean lowerRightCorner,
 boolean useSmartThresholding,
 boolean useHardThresholding,
 float noiseScale,
 float hardNoiseThreshold,
 String[] wList,
 String[] titles)

AlgorithmTreT1

public AlgorithmTreT1(ModelImage destImage,
 ModelImage srcImage,
 double treTR,
 double irspgrTR,
 double irspgrKy,
 double irspgrFA,
 double maxT1,
 double maxM0,
 double[] treFA,
 double[] irspgrTr2,
 double[] irspgrTI,
 double[] spgrData,
 double[] irspgrData,
 double scale,
 double pointScale,
 double scaleIncrement,
 double[] estimates,
 double[] residuals,
 int[] direction,
 int[] spgrImageIndex,
 int[] irspgrImageIndex,
 int b1ImageIndex,
 double angleIncrement,
 int nsa,
 int nti,
 double maxAngle,
 boolean smoothB1Field,
 boolean performStraightTreT1,
 boolean performTreT1withPreCalculatedB1Map,
 boolean performTreT1HIFI,
 boolean doubleInversion,
 boolean singleInversion,
 boolean geScanner,
 boolean siemensScanner,
 boolean threeTField,
 boolean onefiveTField,
 boolean calculateT1,
 boolean showB1Map,
 boolean calculateM0,
 boolean invertT1toR1,
 boolean useWeights,
 boolean uniformAngleSpacing,
 boolean upperLeftCorner,
 boolean upperRightCorner,
 boolean lowerLeftCorner,
 boolean lowerRightCorner,
 boolean useSmartThresholding,
 boolean useHardThresholding,
 float noiseScale,
 float hardNoiseThreshold,
 String[] wList,
 String[] titles)

Method Details

init

private void init()

Initializes local variables that are internal to tre.

computeProcessors

protected void computeProcessors()

Specified by:

computeProcessors in class AlgorithmTProcess

displayImages

protected void displayImages()

This method is used in both the conventional and HIFI case to display result images

Specified by:

displayImages in class AlgorithmTProcess

calculateT1UsingTreT1HIFI

public boolean calculateT1UsingTreT1HIFI()

calculateT1UsingConventionalTreT1

public boolean calculateT1UsingConventionalTreT1()

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

signalResiduals

public double signalResiduals(double x,
 double[] spgrData,
 double[] irspgrData,
 double Inversion,
 int Nfa,
 int Nti,
 double[] treFA,
 double treTR,
 double[] irspgrTr,
 double[] irspgrTI,
 double irspgrFA)

getT1ResultStack

public ModelImage getT1ResultStack()

getM0ResultStack

public ModelImage getM0ResultStack()

getR1ResultStack

public ModelImage getR1ResultStack()

getB1ResultStack

public ModelImage getB1ResultStack()

initializeDisplayImages

private void initializeDisplayImages(ModelImage image)

This method initializes the final images as near-clones of the largest image in the set

Parameters:

image -

loadFinalData

private void loadFinalData(ModelImage image,
 double[][][] data)