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

All Implemented Interfaces:

de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmRegChamfer
extends AlgorithmBase
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
```
AlgorithmRegChamfer First slice is template (base image) to which match image is registered. Minimize cost, measures distance between surfaces in base image and match image.

Version:

1.0 April, 2000

Author:

Delia McGarry

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmRegChamfer.CostFunction
Class for specifying optimization function for AlgorithmSimplexOpt.
- 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 float[]`	`baseBuffer`	DOCUMENT ME!
`private int`	`DIM`	DOCUMENT ME!
`private ModelImage`	`edgeImg`	DOCUMENT ME!
`private boolean`	`entireImage`	DOCUMENT ME!
`private AlgorithmRegChamfer.CostFunction`	`func`
`private boolean`	`image25D`	DOCUMENT ME!
`private ModelImage`	`match`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f[]`	`matchPts`	DOCUMENT ME!
`private int`	`N`	DOCUMENT ME!
`private int`	`simplexDim`	DOCUMENT ME!
`private int`	`sliceSize`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f[]`	`TmatchPts`	DOCUMENT ME!
`private TransMatrix[]`	`tMatrixMatchtoBase`	DOCUMENT ME!
`private TransMatrix`	`tmpXfrm`	DOCUMENT ME!
`private int`	`volLength`	DOCUMENT ME!
`private ModelImage`	`volume25D`	DOCUMENT ME!
`private int`	`xdimB`	DOCUMENT ME!
`private int`	`xdimM`	DOCUMENT ME!
`private float`	`xresB`	DOCUMENT ME!
`private float`	`xresM`	DOCUMENT ME!
`private int`	`ydimB`	DOCUMENT ME!
`private int`	`ydimM`	DOCUMENT ME!
`private float`	`yresB`	DOCUMENT ME!
`private int`	`zdimB`	DOCUMENT ME!
`private int`	`zdimM`	DOCUMENT ME!
`private float`	`zresB`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, 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
`AlgorithmRegChamfer(ModelImage base, ModelImage matchImage, boolean maskFlag)`	Constructs a new registration algorithm.
`AlgorithmRegChamfer(ModelImage volume25D, ModelImage edgeImg, boolean maskFlag, boolean image25D)`	Constructs new registration algorithm.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`concatenateMatrix(TransMatrix[] tMatrixMatchtoBase, int matchSlice)`	Concatenates the matrices.
`private void`	`distanceTransform()`	Chamfer matching: Distance transformation coverts binary surface image into grey-level image where each pixel's intensity = distance to nearest surface pixel.
`private void`	`distanceTransform25D()`	Chamfer matching: Distance transformation coverts binary surface image into grey-level image where each pixel's intensity = distance to nearest surface pixel.
`double`	`eval(double[] x)`
`void`	`finalize()`	Prepares this class for destruction.
`private void`	`generateCoordList()`	Generates the coordinate list.
`private void`	`generateCoordList25D(int matchSlice)`	Generates the coordinate list 2.5 D.
`private int`	`getNumberMatchPts()`	Gets the number of match points.
`private int`	`getNumberMatchPts25D(int matchSlice)`	Get number of match points 2.5 D.
`int`	`getNumberOfVariables()`
`private void`	`getTransformFromX(double[] x, TransMatrix xfrm)`	Converts row of p into 3x3 matrix.
`TransMatrix`	`getTransformMatchtoBase()`	Accessor that returns the transformation from match to base.
`TransMatrix`	`getTransformMatchtoBase(int sliceNum)`	Accessor that returns the transformation from match to base.
`private void`	`initializeNelderMead(double[][] xi, double[] initialPoint)`
`private float`	`min(float[] x)`	Finds minimum sum under mask.
`void`	`runAlgorithm()`	Starts the algorithm.
`private void`	`search(TransMatrix xfrm)`	Search.
`static double`	`SQR(double x)`	SQR = x^2.
`private void`	`transform25DMatchSlice(int matchSlice, TransMatrix xfrm, float[] imgBuf, float[] tImgBuf)`	Transforms 2.5 D match slice.

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
  - baseBuffer
```
private float[] baseBuffer
```
    DOCUMENT ME!
  - DIM
```
private int DIM
```
    DOCUMENT ME!
  - entireImage
```
private boolean entireImage
```
    DOCUMENT ME!
  - image25D
```
private boolean image25D
```
    DOCUMENT ME!
  - match
```
private ModelImage match
```
    DOCUMENT ME!
  - volume25D
```
private ModelImage volume25D
```
    DOCUMENT ME!
  - edgeImg
```
private ModelImage edgeImg
```
    DOCUMENT ME!
  - matchPts
```
private WildMagic.LibFoundation.Mathematics.Vector3f[] matchPts
```
    DOCUMENT ME!
  - N
```
private int N
```
    DOCUMENT ME!
  - simplexDim
```
private int simplexDim
```
    DOCUMENT ME!
  - TmatchPts
```
private WildMagic.LibFoundation.Mathematics.Vector3f[] TmatchPts
```
    DOCUMENT ME!
  - tMatrixMatchtoBase
```
private TransMatrix[] tMatrixMatchtoBase
```
    DOCUMENT ME!
  - tmpXfrm
```
private TransMatrix tmpXfrm
```
    DOCUMENT ME!
  - volLength
```
private int volLength
```
    DOCUMENT ME!
  - sliceSize
```
private int sliceSize
```
    DOCUMENT ME!
  - xdimB
```
private int xdimB
```
    DOCUMENT ME!
  - ydimB
```
private int ydimB
```
    DOCUMENT ME!
  - zdimB
```
private int zdimB
```
    DOCUMENT ME!
  - xdimM
```
private int xdimM
```
    DOCUMENT ME!
  - ydimM
```
private int ydimM
```
    DOCUMENT ME!
  - zdimM
```
private int zdimM
```
    DOCUMENT ME!
  - xresB
```
private float xresB
```
    DOCUMENT ME!
  - yresB
```
private float yresB
```
    DOCUMENT ME!
  - zresB
```
private float zresB
```
    DOCUMENT ME!
  - xresM
```
private float xresM
```
    DOCUMENT ME!
  - func
```
private AlgorithmRegChamfer.CostFunction func
```
- Constructor Detail
  - AlgorithmRegChamfer
```
public AlgorithmRegChamfer(ModelImage base,
                           ModelImage matchImage,
                           boolean maskFlag)
```
    Constructs a new registration algorithm.
    
    Parameters:
    
    base - binary, edge-extracted base image
    
    matchImage - binary edge-extracted image to be transformed
    
    maskFlag - flag indicating if the whole image should be processed
  - AlgorithmRegChamfer
```
public AlgorithmRegChamfer(ModelImage volume25D,
                           ModelImage edgeImg,
                           boolean maskFlag,
                           boolean image25D)
```
    Constructs new registration algorithm.
    
    Parameters:
    
    volume25D - volume to be registered
    
    edgeImg - binary, edge-extracted version of volume25D
    
    maskFlag - flag indicating whether to mask to image or not
    
    image25D - volume processed as 2.5D, slices registered to adjacent slice
- Method Detail
  - SQR
```
public static double SQR(double x)
```
    SQR = x^2.
    
    Parameters:
    
    x - Number to square.
    
    Returns:
    
    DOCUMENT ME!
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getTransformMatchtoBase
```
public TransMatrix getTransformMatchtoBase()
```
    Accessor that returns the transformation from match to base. For 2D or 3D.
    
    Returns:
    
    Transformation.
  - getTransformMatchtoBase
```
public TransMatrix getTransformMatchtoBase(int sliceNum)
```
    Accessor that returns the transformation from match to base. For 2.5D.
    
    Parameters:
    
    sliceNum - Match slice.
    
    Returns:
    
    Transformation.
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - concatenateMatrix
```
private void concatenateMatrix(TransMatrix[] tMatrixMatchtoBase,
                               int matchSlice)
```
    Concatenates the matrices.
    
    Parameters:
    
    tMatrixMatchtoBase - Array of matrices to concatenate
    
    matchSlice - Last slice to concatenate
  - distanceTransform
```
private void distanceTransform()
```
    Chamfer matching: Distance transformation coverts binary surface image into grey-level image where each pixel's intensity = distance to nearest surface pixel.
  - distanceTransform25D
```
private void distanceTransform25D()
```
    Chamfer matching: Distance transformation coverts binary surface image into grey-level image where each pixel's intensity = distance to nearest surface pixel.
  - generateCoordList
```
private void generateCoordList()
```
    Generates the coordinate list.
  - generateCoordList25D
```
private void generateCoordList25D(int matchSlice)
```
    Generates the coordinate list 2.5 D.
    
    Parameters:
    
    matchSlice - Slice to match.
  - getNumberMatchPts
```
private int getNumberMatchPts()
```
    Gets the number of match points.
    
    Returns:
    
    The number of match points.
  - getNumberMatchPts25D
```
private int getNumberMatchPts25D(int matchSlice)
```
    Get number of match points 2.5 D.
    
    Parameters:
    
    matchSlice - Slice to match.
    
    Returns:
    
    Number of match points.
  - getTransformFromX
```
private void getTransformFromX(double[] x,
                               TransMatrix xfrm)
```
    Converts row of p into 3x3 matrix.
    
    Parameters:
    
    x - row of p[][]
    
    xfrm - transformation matrix.
  - initializeNelderMead
```
private void initializeNelderMead(double[][] xi,
                                  double[] initialPoint)
```
  - min
```
private float min(float[] x)
```
    Finds minimum sum under mask.
    
    Parameters:
    
    x - Array to find minimum of.
    
    Returns:
    
    DOCUMENT ME!
  - search
```
private void search(TransMatrix xfrm)
```
    Search.
    
    Parameters:
    
    xfrm - Transformation matrix.
  - transform25DMatchSlice
```
private void transform25DMatchSlice(int matchSlice,
                                    TransMatrix xfrm,
                                    float[] imgBuf,
                                    float[] tImgBuf)
```
    Transforms 2.5 D match slice.
    
    Parameters:
    
    matchSlice - Slice to match
    
    xfrm - Transformation matrix
    
    imgBuf - Image buffer
    
    tImgBuf - Transformed image buffer
  - eval
```
public double eval(double[] x)
```
    Specified by:
    
    eval in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
  - getNumberOfVariables
```
public int getNumberOfVariables()
```
    Specified by:
    
    getNumberOfVariables in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables

Class AlgorithmRegChamfer

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

baseBuffer

DIM

entireImage

image25D

match

volume25D

edgeImg

matchPts

N

simplexDim

TmatchPts

tMatrixMatchtoBase

tmpXfrm

volLength

sliceSize

xdimB

ydimB

zdimB

xdimM

ydimM

zdimM

xresB

yresB

zresB

xresM

func

Constructor Detail

AlgorithmRegChamfer

AlgorithmRegChamfer

Method Detail

SQR

finalize

getTransformMatchtoBase

getTransformMatchtoBase

runAlgorithm

concatenateMatrix

distanceTransform

distanceTransform25D

generateCoordList

generateCoordList25D

getNumberMatchPts

getNumberMatchPts25D

getTransformFromX

initializeNelderMead

min

search

transform25DMatchSlice

eval

getNumberOfVariables