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

Class AlgorithmDTI2EGFA

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.DiffusionTensorImaging.AlgorithmDTI2EGFA

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmDTI2EGFA
extends AlgorithmBase

Algorithm requires input of a Diffusion Tensor Image to calculate an Apparent Diffusion Coefficient Image, Functional Anisotropy Image, Color Image, Eigen Value Image, Eigen Vector Image, Relative Anisotropy Image, Trace Image, and Volume Ratio Image This algorithm works in conjunction with AlgorithmDTITract 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 ModelImage	m_kADCImage	Output Trace (ADC) Image (before diagonalization of diffusion tensor):
private ModelImage	m_kColorImage	Output Color mapped Image:
private ModelImage	m_kDTI	Input Diffusion Tensor Image:
private ModelImage	m_kEigenValueImage	Output EigenValue Image:
private ModelImage	m_kEigenVectorImage	Output EigenVector Image:
private ModelImage	m_kFAImage	Output Functional Anisotropy Image:
private ModelImage	m_kRAImage	Output RA (Relative Anisotropy) Image:
private ModelImage	m_kTraceImage	Output Trace Image (before diagonalization of diffusion tensor):
private ModelImage	m_kVRImage	Output VR (Volume Radio) Image:

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
AlgorithmDTI2EGFA(ModelImage kDTI)	Initialize the Algorithm with the input DTI Image:

Method Summary

Modifier and Type	Method	Description
private void	calcEigenVectorFA()	Calculates the eigen vector data from the DTI.
void	disposeLocal()	Clean up memory.
ModelImage	getADCImage()	Returns the Apparent Diffusion Coefficient Image.
ModelImage	getColorImage()	Returns the Color Map Image.
ModelImage	getEigenValueImage()	Returns the Eigen Value Image.
ModelImage	getEigenVectorImage()	Returns the Eigen Vector Image.
ModelImage	getFAImage()	Returns the Functional Anisotropy Image.
ModelImage	getRAImage()	Returns the Relative Anisotropy Image.
ModelImage	getTraceImage()	Returns the Trace Image.
ModelImage	getVRImage()	Returns the Volume Ratio Image.
void	runAlgorithm()	Run the DTI -> EigenVector Functional Anisotropy algorithm.

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_kEigenVectorImage

private ModelImage m_kEigenVectorImage

Output EigenVector Image:

m_kEigenValueImage

private ModelImage m_kEigenValueImage

Output EigenValue Image:

m_kFAImage

private ModelImage m_kFAImage

Output Functional Anisotropy Image:

m_kADCImage

private ModelImage m_kADCImage

Output Trace (ADC) Image (before diagonalization of diffusion tensor):

m_kTraceImage

private ModelImage m_kTraceImage

Output Trace Image (before diagonalization of diffusion tensor):

m_kRAImage

private ModelImage m_kRAImage

Output RA (Relative Anisotropy) Image:

m_kVRImage

private ModelImage m_kVRImage

Output VR (Volume Radio) Image:

m_kColorImage

private ModelImage m_kColorImage

Output Color mapped Image:

Constructor Details

AlgorithmDTI2EGFA

public AlgorithmDTI2EGFA(ModelImage kDTI)

Initialize the Algorithm with the input DTI Image:

Parameters:

kDTI - input DTI Image.

Method Details

disposeLocal

public void disposeLocal()

Clean up memory.

getColorImage

public ModelImage getColorImage()

Returns the Color Map Image.

Returns:

the Color Map Image.

getADCImage

public ModelImage getADCImage()

Returns the Apparent Diffusion Coefficient Image.

Returns:

the Apparent Diffusion Coefficient Image.

getEigenVectorImage

public ModelImage getEigenVectorImage()

Returns the Eigen Vector Image.

Returns:

the Eigen Vector Image.

getEigenValueImage

public ModelImage getEigenValueImage()

Returns the Eigen Value Image.

Returns:

the Eigen Value Image.

getFAImage

public ModelImage getFAImage()

Returns the Functional Anisotropy Image.

Returns:

the Functional Anisotropy Image.

getRAImage

public ModelImage getRAImage()

Returns the Relative Anisotropy Image.

Returns:

the Relative Anisotropy Image.

getTraceImage

public ModelImage getTraceImage()

Returns the Trace Image.

Returns:

the Trace Image.

getVRImage

public ModelImage getVRImage()

Returns the Volume Ratio Image.

Returns:

the Volume Ratio Image.

runAlgorithm

public void runAlgorithm()

Run the DTI -> EigenVector Functional Anisotropy algorithm.

Specified by:

runAlgorithm in class AlgorithmBase

calcEigenVectorFA

private void calcEigenVectorFA()

Calculates the eigen vector data from the DTI.