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:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
java.lang.Thread.State, java.lang.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 java.lang.String[]`	`titles`
`private double[]`	`treFA`
`private double`	`treTR`
`private boolean`	`uniformAngleSpacing`
`private boolean`	`useWeights`
`private java.lang.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, java.lang.String[] wList, java.lang.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, java.lang.String[] wList, java.lang.String[] titles)

Method Summary

All Methods Instance Methods Concrete Methods
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, 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

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 java.lang.String[] wList
```

titles
```
private java.lang.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 Detail

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,
                      java.lang.String[] wList,
                      java.lang.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,
                      java.lang.String[] wList,
                      java.lang.String[] titles)

Method Detail

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)

Class AlgorithmTreT1

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

t1ResultStack

m0ResultStack

r1ResultStack

b1ResultStack

t1ResultData

m0ResultData

r1ResultData

b1ResultData

largestImage

treTR

irspgrTR

irspgrKy

irspgrFA

maxT1

maxM0

treFA

irspgrTr

irspgrTI

spgrData

irspgrData

scale

pointScale

scaleIncrement

estimates

residuals

direction

spgrImageIndex

irspgrImageIndex

b1ImageIndex

angleIncrement

Nsa

Nti

maxAngle

smoothB1Field

performStraightTreT1

performTreT1withPreCalculatedB1Map

performTreT1HIFI

doubleInversion

singleInversion

geScanner

siemensScanner

threeTField

onefiveTField

calculateT1

showB1Map

calculateM0

invertT1toR1

useWeights

uniformAngleSpacing

wList

titles

completed

t1ResultWindow

m0ResultWindow

r1ResultWindow

b1ResultWindow

Constructor Detail

AlgorithmTreT1

AlgorithmTreT1

Method Detail

init

computeProcessors

displayImages

calculateT1UsingTreT1HIFI

calculateT1UsingConventionalTreT1