gov.nih.mipav.model.algorithms.registration.AlgorithmRegChamfer

All Implemented Interfaces:: de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables, ActionListener, WindowListener, Runnable, 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
Thread.Builder, Thread.State, 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

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, 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
- 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 Details
- 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 Details
- 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 Details

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 Details

AlgorithmRegChamfer

AlgorithmRegChamfer

Method Details

SQR

finalize

getTransformMatchtoBase

getTransformMatchtoBase

runAlgorithm

concatenateMatrix

distanceTransform

distanceTransform25D

generateCoordList

generateCoordList25D

getNumberMatchPts

getNumberMatchPts25D

getTransformFromX

initializeNelderMead

min

search

transform25DMatchSlice

eval

getNumberOfVariables