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

Class AlgorithmRegPatientPos

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.registration.AlgorithmRegPatientPos

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmRegPatientPos
extends AlgorithmBase

Use origin and image orientations to align images based on patient position.

Version:

1.0 Sept 2000

Author:

Delia McGarry, Zohara Cohen

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 TransMatrix	alignmentXfrm	DOCUMENT ME!
private int[]	axisDirA	DOCUMENT ME!
private int[]	axisDirB	DOCUMENT ME!
private double[]	coordA	DOCUMENT ME!
private double[]	coordB	DOCUMENT ME!
private double[]	dimB	private double dimA[], resA[];.
private boolean	doMatch	DOCUMENT ME!
private ModelImage	imageA	DOCUMENT ME!
private ModelImage	imageB	DOCUMENT ME!
private int[]	index2Axial	DOCUMENT ME!
private int[]	index2ImgA	DOCUMENT ME!
(package private) String	name	DOCUMENT ME!
private TransMatrix	orientA	DOCUMENT ME!
private TransMatrix	orientA_inv	DOCUMENT ME!
private TransMatrix	orientB	DOCUMENT ME!
private TransMatrix	orientB_inv	DOCUMENT ME!
private ModelImage	orientedImgB	DOCUMENT ME!
private double[][]	orientMatrixA	DOCUMENT ME!
private double[][]	orientMatrixB	DOCUMENT ME!
private double[]	resB	private double dimA[], resA[];.
private ModelImage	resultImg	DOCUMENT ME!
private ModelImage	shiftedImgB	DOCUMENT ME!
private int[]	sign2Axial	DOCUMENT ME!
private int[]	sign2ImgA	DOCUMENT ME!
private double[]	xOrientA	DOCUMENT ME!
private double[]	xOrientB	DOCUMENT ME!
private double[]	yOrientA	DOCUMENT ME!
private double[]	yOrientB	DOCUMENT ME!
private double[]	zOrientA	DOCUMENT ME!
private double[]	zOrientB	DOCUMENT ME!

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
AlgorithmRegPatientPos(ModelImage imageA, ModelImage imageB, boolean doMatch)	Creates new algorithm.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for destruction.
private void	getIndices()	Get indices for reordering data from Image B to the Axial coordinate system (LPS) and to the coordinate system of Image A.
void	getPatientOrientation(double[] xOrient, double[] yOrient, ModelImage image)	Extract orientation info from file header.
void	getPatientPosition(double[] coord, ModelImage image)	Extracts the origin from image file info.
ModelImage	getResultImage()	Accessor that returns the result image.
private void	getTransform()	Get transformation matrix from Image B to Image A.
private void	matchOrigin()	Add image margins to image B, or crop to match Image A.
private void	reOrient()	Reorient ImageB so that directions will coincide with ImageA.
void	runAlgorithm()	Starts the program.
(package private) double[]	vectorCrossProduct(double[] a, double[] b)	Returns orgthogonal vector.

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, 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

name

String name

DOCUMENT ME!

alignmentXfrm

private TransMatrix alignmentXfrm

DOCUMENT ME!

axisDirA

private int[] axisDirA

DOCUMENT ME!

axisDirB

private int[] axisDirB

DOCUMENT ME!

coordA

private double[] coordA

DOCUMENT ME!

coordB

private double[] coordB

DOCUMENT ME!

dimB

private double[] dimB

private double dimA[], resA[];.

resB

private double[] resB

private double dimA[], resA[];.

doMatch

private boolean doMatch

DOCUMENT ME!

imageA

private ModelImage imageA

DOCUMENT ME!

imageB

private ModelImage imageB

DOCUMENT ME!

orientedImgB

private ModelImage orientedImgB

DOCUMENT ME!

shiftedImgB

private ModelImage shiftedImgB

DOCUMENT ME!

resultImg

private ModelImage resultImg

DOCUMENT ME!

index2Axial

private int[] index2Axial

DOCUMENT ME!

index2ImgA

private int[] index2ImgA

DOCUMENT ME!

sign2Axial

private int[] sign2Axial

DOCUMENT ME!

sign2ImgA

private int[] sign2ImgA

DOCUMENT ME!

orientA

private TransMatrix orientA

DOCUMENT ME!

orientB

private TransMatrix orientB

DOCUMENT ME!

orientA_inv

private TransMatrix orientA_inv

DOCUMENT ME!

orientB_inv

private TransMatrix orientB_inv

DOCUMENT ME!

orientMatrixA

private double[][] orientMatrixA

DOCUMENT ME!

orientMatrixB

private double[][] orientMatrixB

DOCUMENT ME!

xOrientA

private double[] xOrientA

DOCUMENT ME!

yOrientA

private double[] yOrientA

DOCUMENT ME!

zOrientA

private double[] zOrientA

DOCUMENT ME!

xOrientB

private double[] xOrientB

DOCUMENT ME!

yOrientB

private double[] yOrientB

DOCUMENT ME!

zOrientB

private double[] zOrientB

DOCUMENT ME!

Constructor Details

AlgorithmRegPatientPos

public AlgorithmRegPatientPos(ModelImage imageA,
 ModelImage imageB,
 boolean doMatch)

Creates new algorithm.

Parameters:

imageA - image A

imageB - image B, to be registered to imageA

doMatch - whether to match the image origins

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getPatientOrientation

public void getPatientOrientation(double[] xOrient,
 double[] yOrient,
 ModelImage image)

Extract orientation info from file header.

Parameters:

xOrient - 3D array of directional cosines in x

yOrient - 3D array of directional cosines in y

image - image

getPatientPosition

public void getPatientPosition(double[] coord,
 ModelImage image)

Extracts the origin from image file info.

Parameters:

coord - 3D array of patient position x,y,z *

image - image

getResultImage

public ModelImage getResultImage()

Accessor that returns the result image.

Returns:

result image

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

vectorCrossProduct

double[] vectorCrossProduct(double[] a,
 double[] b)

Returns orgthogonal vector.

Parameters:

a - vector

b - vector

Returns:

vector orthogonal to a invalid input: '&' b

getIndices

private void getIndices()

Get indices for reordering data from Image B to the Axial coordinate system (LPS) and to the coordinate system of Image A.

getTransform

private void getTransform()

Get transformation matrix from Image B to Image A.

matchOrigin

private void matchOrigin()

Add image margins to image B, or crop to match Image A.

reOrient

private void reOrient()

Reorient ImageB so that directions will coincide with ImageA.