Package gov.nih.mipav.model.algorithms

Class AlgorithmTreT2

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTProcess

gov.nih.mipav.model.algorithms.AlgorithmTreT2

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmTreT2
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 T2 calculations given any number of SPGR images.

Nested Class Summary

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

AlgorithmTProcess.CalculateT

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	b0ResultStack
private ViewJFrameImage	b0ResultWindow
private java.lang.String	b1ImageName
private int[]	bestToWorst
private double[]	contraction
private JDialogTreT2	dialog	The dialog for accessing GUI specific information, also set during scripting.
private double[]	expansion
private boolean	hardInterrupt
private ModelImage	m0ResultStack
private ViewJFrameImage	m0ResultWindow
private ModelImage	r2ResultStack
private ViewJFrameImage	r2ResultWindow
private double[]	reflection
private double[]	shrink
private double[][]	simplex
private double[]	simplexCentre
private double[]	simplexLineValues
private double[]	simplexResiduals
private java.lang.String[]	ssfpImageNames_phase0
private java.lang.String[]	ssfpImageNames_phase180
private java.lang.String	t1ImageName
private ModelImage	t2ResultStack
private ViewJFrameImage	t2ResultWindow	The frames for result images (if null at end of algorithm src ModelImage is destroyed)
private double[]	treFA_phase0
private double[]	treFA_phase180
private double[]	twoPContraction
private double[]	twoPExpansion
private double[]	twoPReflection
private double[]	twoPShrink
private double[][]	twoPSimplex
private double[]	twoPSimplexCentre
private double[]	twoPSimplexLineValues
private double[]	twoPSimplexResiduals

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
AlgorithmTreT2(ModelImage destImage, ModelImage srcImage, JDialogTreT2 dialog, double[] treFAPhase0, double[] treFAPhase180, java.lang.String[] ssfpImageNamesPhase0, java.lang.String[] ssfpImageNamesPhase180, java.lang.String t1ImageName, java.lang.String b1ImageName, double[] simplexLineValues, double[] simplexResiduals, double[] simplexCentre, double[] reflection, double[] expansion, double[] contraction, double[] shrink, double[][] simplex, double[] twoPSimplexLineValues, double[] twoPSimplexResiduals, double[] twoPSimplexCentre, double[] twoPReflection, double[] twoPExpansion, double[] twoPContraction, double[] twoPShrink, double[][] twoPSimplex, int[] bestToWorst, java.lang.String[] wList)
AlgorithmTreT2(JDialogTreT2 dialog, double[] treFAPhase0, double[] treFAPhase180, java.lang.String[] ssfpImageNamesPhase0, java.lang.String[] ssfpImageNamesPhase180, java.lang.String t1ImageName, java.lang.String b1ImageName, double[] simplexLineValues, double[] simplexResiduals, double[] simplexCentre, double[] reflection, double[] expansion, double[] contraction, double[] shrink, double[][] simplex, double[] twoPSimplexLineValues, double[] twoPSimplexResiduals, double[] twoPSimplexCentre, double[] twoPReflection, double[] twoPExpansion, double[] twoPContraction, double[] twoPShrink, double[][] twoPSimplex, int[] bestToWorst, java.lang.String[] wList)

Method Summary

Modifier and Type	Method	Description
double	calculate2PResiduals(double[] simplexLineValues, double b0, double t1, double tr, double[] Signal, double[] sina, double[] cosa, double[] phaseIncrements, int N)
void	calculateBestToWorst(double[] simplexResiduals, int[] bestToWorst, int numVertices)
double	calculateResiduals(double[] simplexLineValues, double t1, double tr, double[] Signal, double[] sina, double[] cosa, double[] phaseIncrements, int N)
void	calculateT2with0Phase()
void	calculateT2with180Phase()
void	calculateT2withApproximateModeling()
void	calculateT2withFullModeling()
double	calculateTwoPResiduals(double[] simplexLineValues, double b0, double t1, double tr, double[] Signal, double[] sina, double[] cosa, double[] phaseIncrements, int N)
protected void	computeProcessors()
protected void	displayImages()
void	finalize()	Prepares this class for destruction.
ModelImage	getB0ResultStack()
ModelImage	getM0ResultStack()
ModelImage	getR2ResultStack()
ModelImage	getT2ResultStack()
void	reduceB0Field(double[][] b0Field, double resonancePeriod, int width, int height)
void	resetSliceToZero(double[][] field, int width, int height)
void	runAlgorithm()	Actually runs the algorithm.
void	smoothField(double[][] field, float[][] fieldValues, int width, int height, int k)
void	smoothFieldB(double[][] field, int width, int height)
void	swapMatrixForVector(double[][] fieldField, float[][] fieldValues, int k, int width, int height)
void	swapMatrixForVectorB(double[][] fieldField, float[][] fieldValues, int k, int width, int height)
void	threePDownHillSimplex(double[] optimization, double[] initialGuess, double t1, double tr, double[] ssfpSampleData, double[] sina, double[] cosa, double[] phaseIncrements, int N)
void	twoPDownHillSimplex(double[] optimization, double[] initialGuess, double b0, double t1, double tr, double[] ssfpSampleData, double[] sina, double[] cosa, double[] phaseIncrements, int N)

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, 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

treFA_phase0

private final double[] treFA_phase0

treFA_phase180

private final double[] treFA_phase180

simplexLineValues

private double[] simplexLineValues

simplexResiduals

private double[] simplexResiduals

simplexCentre

private double[] simplexCentre

reflection

private double[] reflection

expansion

private double[] expansion

contraction

private double[] contraction

shrink

private double[] shrink

simplex

private double[][] simplex

twoPSimplexLineValues

private double[] twoPSimplexLineValues

twoPSimplexResiduals

private double[] twoPSimplexResiduals

twoPSimplexCentre

private double[] twoPSimplexCentre

twoPReflection

private double[] twoPReflection

twoPExpansion

private double[] twoPExpansion

twoPContraction

private double[] twoPContraction

twoPShrink

private double[] twoPShrink

twoPSimplex

private double[][] twoPSimplex

bestToWorst

private int[] bestToWorst

hardInterrupt

private boolean hardInterrupt

t2ResultStack

private ModelImage t2ResultStack

m0ResultStack

private ModelImage m0ResultStack

r2ResultStack

private ModelImage r2ResultStack

b0ResultStack

private ModelImage b0ResultStack

t2ResultWindow

private ViewJFrameImage t2ResultWindow

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

m0ResultWindow

private ViewJFrameImage m0ResultWindow

r2ResultWindow

private ViewJFrameImage r2ResultWindow

b0ResultWindow

private ViewJFrameImage b0ResultWindow

ssfpImageNames_phase0

private java.lang.String[] ssfpImageNames_phase0

ssfpImageNames_phase180

private java.lang.String[] ssfpImageNames_phase180

t1ImageName

private java.lang.String t1ImageName

b1ImageName

private java.lang.String b1ImageName

dialog

private final JDialogTreT2 dialog

The dialog for accessing GUI specific information, also set during scripting.

Constructor Detail

AlgorithmTreT2

public AlgorithmTreT2(JDialogTreT2 dialog,
                      double[] treFAPhase0,
                      double[] treFAPhase180,
                      java.lang.String[] ssfpImageNamesPhase0,
                      java.lang.String[] ssfpImageNamesPhase180,
                      java.lang.String t1ImageName,
                      java.lang.String b1ImageName,
                      double[] simplexLineValues,
                      double[] simplexResiduals,
                      double[] simplexCentre,
                      double[] reflection,
                      double[] expansion,
                      double[] contraction,
                      double[] shrink,
                      double[][] simplex,
                      double[] twoPSimplexLineValues,
                      double[] twoPSimplexResiduals,
                      double[] twoPSimplexCentre,
                      double[] twoPReflection,
                      double[] twoPExpansion,
                      double[] twoPContraction,
                      double[] twoPShrink,
                      double[][] twoPSimplex,
                      int[] bestToWorst,
                      java.lang.String[] wList)

AlgorithmTreT2

public AlgorithmTreT2(ModelImage destImage,
                      ModelImage srcImage,
                      JDialogTreT2 dialog,
                      double[] treFAPhase0,
                      double[] treFAPhase180,
                      java.lang.String[] ssfpImageNamesPhase0,
                      java.lang.String[] ssfpImageNamesPhase180,
                      java.lang.String t1ImageName,
                      java.lang.String b1ImageName,
                      double[] simplexLineValues,
                      double[] simplexResiduals,
                      double[] simplexCentre,
                      double[] reflection,
                      double[] expansion,
                      double[] contraction,
                      double[] shrink,
                      double[][] simplex,
                      double[] twoPSimplexLineValues,
                      double[] twoPSimplexResiduals,
                      double[] twoPSimplexCentre,
                      double[] twoPReflection,
                      double[] twoPExpansion,
                      double[] twoPContraction,
                      double[] twoPShrink,
                      double[][] twoPSimplex,
                      int[] bestToWorst,
                      java.lang.String[] wList)

Method Detail

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

calculateT2with0Phase

public void calculateT2with0Phase()

calculateT2with180Phase

public void calculateT2with180Phase()

calculateT2withApproximateModeling

public void calculateT2withApproximateModeling()

calculateT2withFullModeling

public void calculateT2withFullModeling()

twoPDownHillSimplex

public void twoPDownHillSimplex(double[] optimization,
                                double[] initialGuess,
                                double b0,
                                double t1,
                                double tr,
                                double[] ssfpSampleData,
                                double[] sina,
                                double[] cosa,
                                double[] phaseIncrements,
                                int N)

threePDownHillSimplex

public void threePDownHillSimplex(double[] optimization,
                                  double[] initialGuess,
                                  double t1,
                                  double tr,
                                  double[] ssfpSampleData,
                                  double[] sina,
                                  double[] cosa,
                                  double[] phaseIncrements,
                                  int N)

calculateTwoPResiduals

public double calculateTwoPResiduals(double[] simplexLineValues,
                                     double b0,
                                     double t1,
                                     double tr,
                                     double[] Signal,
                                     double[] sina,
                                     double[] cosa,
                                     double[] phaseIncrements,
                                     int N)

calculateResiduals

public double calculateResiduals(double[] simplexLineValues,
                                 double t1,
                                 double tr,
                                 double[] Signal,
                                 double[] sina,
                                 double[] cosa,
                                 double[] phaseIncrements,
                                 int N)

calculate2PResiduals

public double calculate2PResiduals(double[] simplexLineValues,
                                   double b0,
                                   double t1,
                                   double tr,
                                   double[] Signal,
                                   double[] sina,
                                   double[] cosa,
                                   double[] phaseIncrements,
                                   int N)

calculateBestToWorst

public void calculateBestToWorst(double[] simplexResiduals,
                                 int[] bestToWorst,
                                 int numVertices)

reduceB0Field

public void reduceB0Field(double[][] b0Field,
                          double resonancePeriod,
                          int width,
                          int height)

smoothField

public void smoothField(double[][] field,
                        float[][] fieldValues,
                        int width,
                        int height,
                        int k)

smoothFieldB

public void smoothFieldB(double[][] field,
                         int width,
                         int height)

resetSliceToZero

public void resetSliceToZero(double[][] field,
                             int width,
                             int height)

swapMatrixForVector

public void swapMatrixForVector(double[][] fieldField,
                                float[][] fieldValues,
                                int k,
                                int width,
                                int height)

swapMatrixForVectorB

public void swapMatrixForVectorB(double[][] fieldField,
                                 float[][] fieldValues,
                                 int k,
                                 int width,
                                 int height)

getT2ResultStack

public ModelImage getT2ResultStack()

getM0ResultStack

public ModelImage getM0ResultStack()

getR2ResultStack

public ModelImage getR2ResultStack()

getB0ResultStack

public ModelImage getB0ResultStack()

computeProcessors

protected void computeProcessors()

Specified by:

computeProcessors in class AlgorithmTProcess

displayImages

protected void displayImages()

Specified by:

displayImages in class AlgorithmTProcess