java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.DiffusionTensorImaging.AlgorithmDTITract

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmDTITract
extends AlgorithmBase
```
Algorithm requires input of previous calculated FA, EigenVector and EigenValue images from AlgorithmDTI2EGFA to calculate fiber bundle tracts This algorithm works in conjunction with AlgorithmDTI2EGFA to create the MIPAV DTI Fiber Tracking/ Statistics Dialog See:Introduction to Diffusion Tensor Imaging, by Susumu Mori

Nested Class Summary
- 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 boolean[]`	`m_abVisited`	Which tensor nodes are already on the fiber bundle tract
`private boolean`	`m_bFirstWrite`	When saving the fiber bundle tracts.
`private boolean`	`m_bNegX`
`private boolean`	`m_bNegY`
`private boolean`	`m_bNegZ`
`private float`	`m_fAngleMax`
`private float`	`m_fFAMax`
`private float`	`m_fFAMin`
`private int`	`m_iMinLength`
`private ModelImage`	`m_kDTI`	Input Diffusion Tensor Image:
`private ModelImage`	`m_kEigenValueImage`	Input EigenValue Image:
`private ModelImage`	`m_kEigenVectorImage`	Input EigenVector Image:
`private ModelImage`	`m_kFAImage`	Input FA Image:
`private java.lang.String`	`m_kOutputFile`	The name of the tract output file, specified by the user.

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
`AlgorithmDTITract(ModelImage kDTI, ModelImage kFAImage, ModelImage kEigenVectorImage, ModelImage kEigenValueImage, java.lang.String kFile, boolean bNegX, boolean bNegY, boolean bNegZ, float fFAMin, float fFAMax, float fMaxAngle, int iMinLength)`	Initialize the Algorithm with the input DTI Image:
`AlgorithmDTITract(ModelImage kDTI, ModelImage kEigenVectorImage, ModelImage kEigenValueImage, java.lang.String kFile, boolean bNegX, boolean bNegY, boolean bNegZ)`	Initialize the Algorithm with the input DTI Image:

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`disposeLocal()`	Clean up memory.
`private void`	`outputTract(java.util.Vector<java.lang.Integer> kTract, int iDimX, int iDimY, int iDimZ, java.io.FileOutputStream kFileWriter)`	Writes the fiber bundle tract to disk.
`private void`	`reconstructTracts()`	Constructs the Fiber Bundle Tracts from the DTI and the EigenVectorImage parameters.
`void`	`runAlgorithm()`	Run the DTI -> EigenVector Functional Anisotropy algorithm.
`private void`	`traceTract2(java.util.Vector<java.lang.Integer> kTract, WildMagic.LibFoundation.Mathematics.Vector3f kStart, WildMagic.LibFoundation.Mathematics.Vector3f kDir, ModelImage EigenVectorImage, ModelImage eigenValueImage, ModelImage kFAImage, boolean bDir)`	Traces a single fiber bundle tract starting at the input position and following the input direction.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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

m_kDTI
```
private ModelImage m_kDTI
```
Input Diffusion Tensor Image:

m_kFAImage
```
private ModelImage m_kFAImage
```
Input FA Image:

m_kEigenVectorImage
```
private ModelImage m_kEigenVectorImage
```
Input EigenVector Image:

m_kEigenValueImage
```
private ModelImage m_kEigenValueImage
```
Input EigenValue Image:

m_kOutputFile
```
private java.lang.String m_kOutputFile
```
The name of the tract output file, specified by the user.

m_abVisited
```
private boolean[] m_abVisited
```
Which tensor nodes are already on the fiber bundle tract

m_bFirstWrite
```
private boolean m_bFirstWrite
```
When saving the fiber bundle tracts.

m_bNegX
```
private boolean m_bNegX
```

m_bNegY
```
private boolean m_bNegY
```

m_bNegZ
```
private boolean m_bNegZ
```

m_fFAMin
```
private float m_fFAMin
```

m_fFAMax
```
private float m_fFAMax
```

m_fAngleMax
```
private float m_fAngleMax
```

m_iMinLength
```
private int m_iMinLength
```

Constructor Detail

AlgorithmDTITract

public AlgorithmDTITract(ModelImage kDTI,
                         ModelImage kEigenVectorImage,
                         ModelImage kEigenValueImage,
                         java.lang.String kFile,
                         boolean bNegX,
                         boolean bNegY,
                         boolean bNegZ)

Initialize the Algorithm with the input DTI Image:

Parameters:: kDTI - input DTI Image.

AlgorithmDTITract

public AlgorithmDTITract(ModelImage kDTI,
                         ModelImage kFAImage,
                         ModelImage kEigenVectorImage,
                         ModelImage kEigenValueImage,
                         java.lang.String kFile,
                         boolean bNegX,
                         boolean bNegY,
                         boolean bNegZ,
                         float fFAMin,
                         float fFAMax,
                         float fMaxAngle,
                         int iMinLength)

Initialize the Algorithm with the input DTI Image:

Parameters:: kDTI - input DTI Image.

Method Detail
- disposeLocal
```
public void disposeLocal()
```
  Clean up memory.
- runAlgorithm
```
public void runAlgorithm()
```
  Run the DTI -> EigenVector Functional Anisotropy algorithm.
  
  Specified by:
  
  runAlgorithm in class AlgorithmBase
- reconstructTracts
```
private void reconstructTracts()
```
  Constructs the Fiber Bundle Tracts from the DTI and the EigenVectorImage parameters. The fiber bundles are output to a file specified by the user.
  
  Parameters:
  
  DTI - Diffusion Tensor Image.
  
  EigenVectorImage - EigenVector Image.
- traceTract2
```
private void traceTract2(java.util.Vector<java.lang.Integer> kTract,
                         WildMagic.LibFoundation.Mathematics.Vector3f kStart,
                         WildMagic.LibFoundation.Mathematics.Vector3f kDir,
                         ModelImage EigenVectorImage,
                         ModelImage eigenValueImage,
                         ModelImage kFAImage,
                         boolean bDir)
```
  Traces a single fiber bundle tract starting at the input position and following the input direction.
  
  Parameters:
  
  kTract - fiber bundle tract, new positions are stored in this tract as the fiber is traced.
  
  kStart - starting position of the tract.
  
  kDir - direction from the position.
  
  DTI - Diffusion Tensor image used to calculate next direction of tract.
  
  bDir - boolean when true the positions are added to the end of the tract (positive direction). When false the positions are added to the beginning of the tract (negative direction).
- outputTract
```
private void outputTract(java.util.Vector<java.lang.Integer> kTract,
                         int iDimX,
                         int iDimY,
                         int iDimZ,
                         java.io.FileOutputStream kFileWriter)
```
  Writes the fiber bundle tract to disk.
  
  Parameters:
  
  kTract - the fiber bundle tract.
  
  iDimX - x-dimension of the diffusion tensor image.
  
  iDimY - y-dimension of the diffusion tensor image.
  
  iDimZ - z-dimension of the diffusion tensor image.
  
  kFileWrite - FileOutputStream.

Class AlgorithmDTITract

Nested Class Summary

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

Field Summary

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.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

m_kDTI

m_kFAImage

m_kEigenVectorImage

m_kEigenValueImage

m_kOutputFile

m_abVisited

m_bFirstWrite

m_bNegX

m_bNegY

m_bNegZ

m_fFAMin

m_fFAMax

m_fAngleMax

m_iMinLength

Constructor Detail

AlgorithmDTITract

AlgorithmDTITract

Method Detail

disposeLocal

runAlgorithm

reconstructTracts

traceTract2

outputTract