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

All Methods Instance Methods Concrete Methods
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

Class AlgorithmTreT2

Nested Class Summary

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

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

Field Summary

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

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

treFA_phase0

treFA_phase180

simplexLineValues

simplexResiduals

simplexCentre

reflection

expansion

contraction

shrink

simplex

twoPSimplexLineValues

twoPSimplexResiduals

twoPSimplexCentre

twoPReflection

twoPExpansion

twoPContraction

twoPShrink

twoPSimplex

bestToWorst

hardInterrupt

t2ResultStack

m0ResultStack

r2ResultStack

b0ResultStack

t2ResultWindow

m0ResultWindow

r2ResultWindow

b0ResultWindow

ssfpImageNames_phase0

ssfpImageNames_phase180

t1ImageName

b1ImageName

dialog

Constructor Detail

AlgorithmTreT2

AlgorithmTreT2

Method Detail

finalize

runAlgorithm

calculateT2with0Phase

calculateT2with180Phase

calculateT2withApproximateModeling

calculateT2withFullModeling

twoPDownHillSimplex

threePDownHillSimplex

calculateTwoPResiduals

calculateResiduals

calculate2PResiduals

calculateBestToWorst

reduceB0Field

smoothField

smoothFieldB

resetSliceToZero

swapMatrixForVector

swapMatrixForVectorB

getT2ResultStack

getM0ResultStack

getR2ResultStack

getB0ResultStack

computeProcessors

displayImages