Package gov.nih.mipav.model.algorithms.DiffusionTensorImaging

Class AlgorithmDTITract

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.DiffusionTensorImaging.AlgorithmDTITract

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, 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

Thread.Builder, Thread.State, 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 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, 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, String kFile, boolean bNegX, boolean bNegY, boolean bNegZ)	Initialize the Algorithm with the input DTI Image:

Method Summary

Modifier and Type	Method	Description
void	disposeLocal()	Clean up memory.
private void	outputTract(Vector<Integer> kTract, int iDimX, int iDimY, int iDimZ, 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(Vector<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, 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

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 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 Details

AlgorithmDTITract

public AlgorithmDTITract(ModelImage kDTI,
 ModelImage kEigenVectorImage,
 ModelImage kEigenValueImage,
 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,
 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 Details

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(Vector<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.

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).

DTI - Diffusion Tensor image used to calculate next direction of tract.

outputTract

private void outputTract(Vector<Integer> kTract,
 int iDimX,
 int iDimY,
 int iDimZ,
 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.