Package gov.nih.mipav.model.algorithms.registration

Class AlgorithmRegBSpline25D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline

gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline25D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmRegBSpline25D
extends AlgorithmRegBSpline

BSpline based registration of 2.5D images.

Nested Class Summary

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

AlgorithmRegBSpline.Options

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
protected int	m_iSliceTarget	Index of the slice in the input source image to use as the target.

Fields inherited from class gov.nih.mipav.model.algorithms.registration.AlgorithmRegBSpline

m_kImageDeformation, m_kImageResult, m_kImageSource, m_kImageTarget, m_kOptionsPass1, m_kOptionsPass2, m_kRegMeasure

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
AlgorithmRegBSpline25D(ModelImage kImageResult, ModelImage kImageSource, int iSliceTarget, ModelImage kImageDeformation, RegistrationMeasure kRegMeasure, AlgorithmRegBSpline.Options kOptionsPass1, AlgorithmRegBSpline.Options kOptionsPass2)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	disposeLocal()	Prepares this class for destruction.
void	finalize()	Override of Object method called by garbage collection.
void	runAlgorithm()	AlgorithmBase abstract method implementation which performs the registration.
protected BSplineRegistration2Df	runPass(ModelSimpleImage kSource, ModelSimpleImage kTarget, AlgorithmRegBSpline.Options kOptions, BSplineRegistration2Df kRegPrev)	Perform a "pass" of BSpline based registration.
private void	transform2DVOI(ModelImage image, ModelImage destImage, float[] imgBuffer, float[] kImageMapX, float[] kImageMapY, int iSlice, int iNumSlices)
private void	writeResults(BSplineRegistration2Df[] akReg)	Save the registration information to a file.

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

m_iSliceTarget

protected final int m_iSliceTarget

Index of the slice in the input source image to use as the target. If the value is -1, then each slice is registered to its adjacent one.

Constructor Detail

AlgorithmRegBSpline25D

public AlgorithmRegBSpline25D(ModelImage kImageResult,
                              ModelImage kImageSource,
                              int iSliceTarget,
                              ModelImage kImageDeformation,
                              RegistrationMeasure kRegMeasure,
                              AlgorithmRegBSpline.Options kOptionsPass1,
                              AlgorithmRegBSpline.Options kOptionsPass2)

Constructor.

Parameters:

kImageResult - ModelImage Reference to an image to store the registered source image. This image must have the same dimensions as the input source image.

kImageSource - ModelImage Reference to the original input image to use as the registration source.

iSliceTarget - int Index of the slice in the input source image that is to be used as the reference. If this index is -1, then each slice is registered to the one before it

kImageDeformation - ModelImage Reference to an image to store the computed deformation. This may be a null reference to indicate that the deformation is not to be computed. If this reference is not null, then the image must have the same dimensions as the input source image.

kRegMeasure - RegistrationMeasure Reference to the particular cost measure to use for this registration. The cost measure is the same for all passes.

kOptionsPass1 - Options Options to use for a first pass of registration. This may *not* be a null reference.

kOptionsPass2 - Options Options to use for a second pass of registration. This may be null to indicate that only a single pass of registration is to be performed.

Method Detail

disposeLocal

public void disposeLocal()

Prepares this class for destruction.

Overrides:

disposeLocal in class AlgorithmRegBSpline

finalize

public void finalize()

Override of Object method called by garbage collection.

Overrides:

finalize in class AlgorithmRegBSpline

runAlgorithm

public void runAlgorithm()

AlgorithmBase abstract method implementation which performs the registration.

Specified by:

runAlgorithm in class AlgorithmBase

Throws:

java.lang.RuntimeException - DOCUMENT ME!

transform2DVOI

private void transform2DVOI(ModelImage image,
                            ModelImage destImage,
                            float[] imgBuffer,
                            float[] kImageMapX,
                            float[] kImageMapY,
                            int iSlice,
                            int iNumSlices)

runPass

protected BSplineRegistration2Df runPass(ModelSimpleImage kSource,
                                         ModelSimpleImage kTarget,
                                         AlgorithmRegBSpline.Options kOptions,
                                         BSplineRegistration2Df kRegPrev)

Perform a "pass" of BSpline based registration. A "pass" is defined to be one or more iterations using the BSpline basis parameters, gradient descent parameters, and convergence parameters.

Parameters:

kSource - ModelSimpleImage Reference to the original input image to use as the registration source. This image does not have to have the same dimensions as the image to be used as the registration target.

kTarget - ModelSimpleImage Reference to the original input image to use as the registration target.

kOptions - Options Options to use for a this registration pass. This may *not* be a null reference.

kRegPrev - BSplineRegistration2Df Reference to a previous registration which can be used to initialize this registration. This may be a null reference meaning that the this registration uses the default "identity" initialization. If this it not a null reference, then this registration is initialized to provide the a close approximation to the same BSpline mapping as determined by the input registration. The main property of a registration is the position of its control points.

Returns:

BSplineRegistration2Df Registration instance resulting from this pass. This may be needed to provide for the initialization of subsequent passes or to compute the deformation image.

writeResults

private void writeResults(BSplineRegistration2Df[] akReg)

Save the registration information to a file. This information includes the BSpline parameters; in particular, the coordinates for the lattice of control points.

Parameters:

akReg - BSplineRegistration2Df[] Contains the parameters which define the BSpline for registering each slice of the source image to the particular reference slice.