Package gov.nih.mipav.model.algorithms

Class AlgorithmTalairachTransform

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTalairachTransform

All Implemented Interfaces:

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

public class AlgorithmTalairachTransform
extends AlgorithmBase

Performs original to ACPC, original to Talairach, ACPC to original, ACPC to Talairach, Talairach to original, or Talairach to ACPC transformation.

Version:

May 26, 2005

Author:

Pilou Bazin

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
static int	ACPC_TO_ORIG	DOCUMENT ME!
static int	ACPC_TO_TLRC	DOCUMENT ME!
static int	BILINEAR	Biilinear interpolation.
private AlgorithmBSpline	Bspline	DOCUMENT ME!
static int	BSPLINE3	Cubic bspline interpolation.
static int	BSPLINE4	Quadratic bspline interpolation.
private AlgorithmCubicLagrangian	CLag	DOCUMENT ME!
static int	CUBIC_LAGRANGIAN	Cubic lagrangian interpolation.
(package private) boolean	doClip	DOCUMENT ME!
(package private) boolean	doVOI	DOCUMENT ME!
static int	HEPTIC_LAGRANGIAN	Heptic lagrangian interpolation.
private AlgorithmHepticLagrangian	HLag	DOCUMENT ME!
(package private) int	interpolation	DOCUMENT ME!
private int[]	inVolExtents	DOCUMENT ME!
static int	NEAREST_NEIGHBOR	Nearest neighbor interpolation.
private int	nix	DOCUMENT ME!
private int	niy	DOCUMENT ME!
private int	niz	DOCUMENT ME!
private int	nrx	DOCUMENT ME!
private int	nry	DOCUMENT ME!
private int	nrz	DOCUMENT ME!
static int	ORIG_TO_ACPC	DOCUMENT ME!
static int	ORIG_TO_TLRC	DOCUMENT ME!
private AlgorithmQuinticLagrangian	QLag	DOCUMENT ME!
static int	QUINTIC_LAGRANGIAN	Quintic lagrangian interpolation.
(package private) java.lang.String	suffix	DOCUMENT ME!
private TalairachTransformInfo	tInfo	DOCUMENT ME!
static int	TLRC_TO_ACPC	DOCUMENT ME!
static int	TLRC_TO_ORIG	DOCUMENT ME!
(package private) int	transformType	DOCUMENT ME!
(package private) java.lang.String	transformTypeName	DOCUMENT ME!
static int	TRILINEAR	Trilinear interpolation.
private AlgorithmWSinc	WSinc	DOCUMENT ME!
static int	WSINC	Windowed sinc interpolation.

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
AlgorithmTalairachTransform(ModelImage destImage, ModelImage srcImage, TalairachTransformInfo tInfo, int transformType, int interpolation, boolean doClip, boolean doVOI)	Creates a new AlgorithmTalairachTransform object.

Method Summary

Modifier and Type	Method	Description
private void	computeBSplineImage(float xi, float yi, float zi, float[] result, int xr, int yr, int zr)	DOCUMENT ME!
private void	computeCubicLagrangian(float xi, float yi, float zi, float[] result, int xr, int yr, int zr)	DOCUMENT ME!
private void	computeHepticLagrangian(float xi, float yi, float zi, float[] result, int xr, int yr, int zr)	DOCUMENT ME!
private void	computeNearestImage(double[] img, float xi, float yi, float zi, float[] result, int xr, int yr, int zr)	Transforms and resamples volume using nearest neighbor interpolation.
private void	computeQuinticLagrangian(float xi, float yi, float zi, float[] result, int xr, int yr, int zr)	DOCUMENT ME!
private void	computeTrilinearImage(double[] img, float xi, float yi, float zi, float[] result, int xr, int yr, int zr)	Transforms and resamples volume using trilinear interpolation.
private void	computeWSincImage(float xi, float yi, float zi, float[] result, int xr, int yr, int zr)	DOCUMENT ME!
void	disposeLocal()	Dispose of local variables that may be taking up lots of room.
private VOI	generateVOI(VOI obj, java.util.BitSet mask)	extract a VOI from a binary mask image.
void	runAlgorithm()	DOCUMENT ME!
private void	transformTalairachVolume(double[] img, float[] result)	computes the selected Talairach transform.

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

TRILINEAR

public static final int TRILINEAR

Trilinear interpolation.

See Also:

Constant Field Values

BILINEAR

public static final int BILINEAR

Biilinear interpolation.

See Also:

Constant Field Values

NEAREST_NEIGHBOR

public static final int NEAREST_NEIGHBOR

Nearest neighbor interpolation.

See Also:

Constant Field Values

BSPLINE3

public static final int BSPLINE3

Cubic bspline interpolation.

See Also:

Constant Field Values

BSPLINE4

public static final int BSPLINE4

Quadratic bspline interpolation.

See Also:

Constant Field Values

CUBIC_LAGRANGIAN

public static final int CUBIC_LAGRANGIAN

Cubic lagrangian interpolation.

See Also:

Constant Field Values

QUINTIC_LAGRANGIAN

public static final int QUINTIC_LAGRANGIAN

Quintic lagrangian interpolation.

See Also:

Constant Field Values

HEPTIC_LAGRANGIAN

public static final int HEPTIC_LAGRANGIAN

Heptic lagrangian interpolation.

See Also:

Constant Field Values

WSINC

public static final int WSINC

Windowed sinc interpolation.

See Also:

Constant Field Values

ORIG_TO_ACPC

public static final int ORIG_TO_ACPC

DOCUMENT ME!

See Also:

Constant Field Values

ORIG_TO_TLRC

public static final int ORIG_TO_TLRC

DOCUMENT ME!

See Also:

Constant Field Values

ACPC_TO_TLRC

public static final int ACPC_TO_TLRC

DOCUMENT ME!

See Also:

Constant Field Values

TLRC_TO_ACPC

public static final int TLRC_TO_ACPC

DOCUMENT ME!

See Also:

Constant Field Values

TLRC_TO_ORIG

public static final int TLRC_TO_ORIG

DOCUMENT ME!

See Also:

Constant Field Values

ACPC_TO_ORIG

public static final int ACPC_TO_ORIG

DOCUMENT ME!

See Also:

Constant Field Values

doClip

boolean doClip

DOCUMENT ME!

doVOI

boolean doVOI

DOCUMENT ME!

interpolation

int interpolation

DOCUMENT ME!

suffix

java.lang.String suffix

DOCUMENT ME!

transformType

int transformType

DOCUMENT ME!

transformTypeName

java.lang.String transformTypeName

DOCUMENT ME!

Bspline

private AlgorithmBSpline Bspline

DOCUMENT ME!

CLag

private AlgorithmCubicLagrangian CLag

DOCUMENT ME!

HLag

private AlgorithmHepticLagrangian HLag

DOCUMENT ME!

inVolExtents

private int[] inVolExtents

DOCUMENT ME!

nix

private int nix

DOCUMENT ME!

niy

private int niy

DOCUMENT ME!

niz

private int niz

DOCUMENT ME!

nrx

private int nrx

DOCUMENT ME!

nry

private int nry

DOCUMENT ME!

nrz

private int nrz

DOCUMENT ME!

QLag

private AlgorithmQuinticLagrangian QLag

DOCUMENT ME!

tInfo

private TalairachTransformInfo tInfo

DOCUMENT ME!

WSinc

private AlgorithmWSinc WSinc

DOCUMENT ME!

Constructor Detail

AlgorithmTalairachTransform

public AlgorithmTalairachTransform(ModelImage destImage,
                                   ModelImage srcImage,
                                   TalairachTransformInfo tInfo,
                                   int transformType,
                                   int interpolation,
                                   boolean doClip,
                                   boolean doVOI)

Creates a new AlgorithmTalairachTransform object.

Parameters:

destImage - DOCUMENT ME!

srcImage - DOCUMENT ME!

tInfo - DOCUMENT ME!

transformType - DOCUMENT ME!

interpolation - DOCUMENT ME!

doClip - DOCUMENT ME!

doVOI - DOCUMENT ME!

Method Detail

disposeLocal

public void disposeLocal()

Dispose of local variables that may be taking up lots of room.

runAlgorithm

public void runAlgorithm()

DOCUMENT ME!

Specified by:

runAlgorithm in class AlgorithmBase

computeBSplineImage

private void computeBSplineImage(float xi,
                                 float yi,
                                 float zi,
                                 float[] result,
                                 int xr,
                                 int yr,
                                 int zr)

DOCUMENT ME!

Parameters:

xi - DOCUMENT ME!

yi - DOCUMENT ME!

zi - DOCUMENT ME!

result - DOCUMENT ME!

xr - DOCUMENT ME!

yr - DOCUMENT ME!

zr - DOCUMENT ME!

computeCubicLagrangian

private void computeCubicLagrangian(float xi,
                                    float yi,
                                    float zi,
                                    float[] result,
                                    int xr,
                                    int yr,
                                    int zr)

DOCUMENT ME!

Parameters:

xi - DOCUMENT ME!

yi - DOCUMENT ME!

zi - DOCUMENT ME!

result - DOCUMENT ME!

xr - DOCUMENT ME!

yr - DOCUMENT ME!

zr - DOCUMENT ME!

computeHepticLagrangian

private void computeHepticLagrangian(float xi,
                                     float yi,
                                     float zi,
                                     float[] result,
                                     int xr,
                                     int yr,
                                     int zr)

DOCUMENT ME!

Parameters:

xi - DOCUMENT ME!

yi - DOCUMENT ME!

zi - DOCUMENT ME!

result - DOCUMENT ME!

xr - DOCUMENT ME!

yr - DOCUMENT ME!

zr - DOCUMENT ME!

computeNearestImage

private void computeNearestImage(double[] img,
                                 float xi,
                                 float yi,
                                 float zi,
                                 float[] result,
                                 int xr,
                                 int yr,
                                 int zr)

Transforms and resamples volume using nearest neighbor interpolation.

Parameters:

img - DOCUMENT ME!

xi - DOCUMENT ME!

yi - DOCUMENT ME!

zi - DOCUMENT ME!

result - DOCUMENT ME!

xr - DOCUMENT ME!

yr - DOCUMENT ME!

zr - DOCUMENT ME!

computeQuinticLagrangian

private void computeQuinticLagrangian(float xi,
                                      float yi,
                                      float zi,
                                      float[] result,
                                      int xr,
                                      int yr,
                                      int zr)

DOCUMENT ME!

Parameters:

xi - DOCUMENT ME!

yi - DOCUMENT ME!

zi - DOCUMENT ME!

result - DOCUMENT ME!

xr - DOCUMENT ME!

yr - DOCUMENT ME!

zr - DOCUMENT ME!

computeTrilinearImage

private void computeTrilinearImage(double[] img,
                                   float xi,
                                   float yi,
                                   float zi,
                                   float[] result,
                                   int xr,
                                   int yr,
                                   int zr)

Transforms and resamples volume using trilinear interpolation.

Parameters:

img - DOCUMENT ME!

xi - DOCUMENT ME!

yi - DOCUMENT ME!

zi - DOCUMENT ME!

result - DOCUMENT ME!

xr - DOCUMENT ME!

yr - DOCUMENT ME!

zr - DOCUMENT ME!

computeWSincImage

private void computeWSincImage(float xi,
                               float yi,
                               float zi,
                               float[] result,
                               int xr,
                               int yr,
                               int zr)

DOCUMENT ME!

Parameters:

xi - DOCUMENT ME!

yi - DOCUMENT ME!

zi - DOCUMENT ME!

result - DOCUMENT ME!

xr - DOCUMENT ME!

yr - DOCUMENT ME!

zr - DOCUMENT ME!

generateVOI

private VOI generateVOI(VOI obj,
                        java.util.BitSet mask)

extract a VOI from a binary mask image.

Parameters:

obj - DOCUMENT ME!

mask - DOCUMENT ME!

Returns:

DOCUMENT ME!

transformTalairachVolume

private void transformTalairachVolume(double[] img,
                                      float[] result)

computes the selected Talairach transform.

Parameters:

img - the original image

result - the transformed image