java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.registration.AlgorithmRegPatientPos

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.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) java.lang.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

All Methods Instance Methods Concrete Methods
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, 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
  - name
```
java.lang.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 Detail
  - 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 Detail
  - 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 & 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.

Class AlgorithmRegPatientPos

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

name

alignmentXfrm

axisDirA

axisDirB

coordA

coordB

dimB

resB

doMatch

imageA

imageB

orientedImgB

shiftedImgB

resultImg

index2Axial

index2ImgA

sign2Axial

sign2ImgA

orientA

orientB

orientA_inv

orientB_inv

orientMatrixA

orientMatrixB

xOrientA

yOrientA

zOrientA

xOrientB

yOrientB

zOrientB

Constructor Detail

AlgorithmRegPatientPos

Method Detail

finalize

getPatientOrientation

getPatientPosition

getResultImage

runAlgorithm

vectorCrossProduct

getIndices

getTransform

matchOrigin

reOrient