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

All Methods Instance Methods Concrete Methods
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

Class AlgorithmTalairachTransform

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

TRILINEAR

BILINEAR

NEAREST_NEIGHBOR

BSPLINE3

BSPLINE4

CUBIC_LAGRANGIAN

QUINTIC_LAGRANGIAN

HEPTIC_LAGRANGIAN

WSINC

ORIG_TO_ACPC

ORIG_TO_TLRC

ACPC_TO_TLRC

TLRC_TO_ACPC

TLRC_TO_ORIG

ACPC_TO_ORIG

doClip

doVOI

interpolation

suffix

transformType

transformTypeName

Bspline

CLag

HLag

inVolExtents

nix

niy

niz

nrx

nry

nrz

QLag

tInfo

WSinc

Constructor Detail

AlgorithmTalairachTransform

Method Detail

disposeLocal

runAlgorithm

computeBSplineImage

computeCubicLagrangian

computeHepticLagrangian

computeNearestImage

computeQuinticLagrangian

computeTrilinearImage

computeWSincImage

generateVOI

transformTalairachVolume