Package gov.nih.mipav.model.algorithms

Class AlgorithmTPSpline

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTPSpline

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmTPSpline
extends AlgorithmBase

Thin plate spline Warning: If the supplied (x,y) data set in setupTPSpline2D is nearly collinear, singular matrices will result and a matrix inversion will fail. This code calculating the function f at interpolated points is a port of software from Geometric Tools at www.geometrictools.com. Reference: Thin Plate Splines by David Eberly of Geometric Tools at http://www.geometrictools.com/SampleMathematics/ThinPlateSplines/ThinPlateSplines.html.

The Eberly Thin plate splines 2D is a physically based 2D interpolation scheme for arbitrarily spaced tabulated data (xi,yi,f(xi,yi)). These splines are the generalization of the natural cubic splines in 1D. The spline surface represents a thin metal sheet that is constrained not to move at the grid points. The Eberly Thin plate spines 3D operates on data of the form (xi,yi,zi,f(xi,yi,zi).

Also given is thin plate spline code for warping from one x,y source set to another x',y' target set. This code is based on the paper Principal Warps: Thin-Plate Splines and the Decompositions of Deformations by Fred L. BookStein, IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 11, No. 6, June, 1989, pp. 567 - 585.

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 ModelImage	baseImage	DOCUMENT ME!
private float[][]	C	DOCUMENT ME!
private boolean	doSetupOnly
private float[]	mA	DOCUMENT ME!
private ModelImage	matchImage	DOCUMENT ME!
private float[]	mB	DOCUMENT ME!
private float[]	mX	DOCUMENT ME!
private float[]	mY	DOCUMENT ME!
private float[]	mZ	DOCUMENT ME!
private int	N	DOCUMENT ME!
private ModelImage	resultImage	DOCUMENT ME!
private boolean	run2D
private boolean	setupRequired
private float	smooth	DOCUMENT ME!
private double[]	x	DOCUMENT ME!
private int	xDimA
private float	xInvRange	DOCUMENT ME!
private float	xMin	DOCUMENT ME!
private double[]	xTar	DOCUMENT ME!
private double[]	y	DOCUMENT ME!
private int	yDimA
private float	yInvRange	DOCUMENT ME!
private float	yMin	DOCUMENT ME!
private double[]	yTar	DOCUMENT ME!
private double[]	z	DOCUMENT ME!
private int	zDimA
private float	zInvRange	DOCUMENT ME!
private float	zMin	DOCUMENT ME!
private double[]	zTar	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
AlgorithmTPSpline()	AlgorithmTPSpline - default constructor.
AlgorithmTPSpline(double[] xSource, double[] ySource, double[] zSource, double[] xTar, double[] yTar, double[] zTar, float smooth, ModelImage baseImage, ModelImage matchImage)	AlgorithmTPSpline - constructor for 3D case.
AlgorithmTPSpline(double[] xSource, double[] ySource, double[] zSource, double[] xTar, double[] yTar, double[] zTar, float smooth, ModelImage baseImage, ModelImage matchImage, boolean doSetupOnly)	AlgorithmTPSpline - constructor for 3D case.
AlgorithmTPSpline(double[] xSource, double[] ySource, double[] xTar, double[] yTar, float smooth, ModelImage baseImage, ModelImage matchImage)	AlgorithmTPSpline - constructor for 2D case.
AlgorithmTPSpline(ModelImage matchImage)	Constructor used when N, xDimA, yDimA, zDimA, x[], y[], z[], and C[][] are read from a file

Method Summary

Modifier and Type	Method	Description
void	finalize()	finalize -
final float[]	getCorrespondingPoint(float xTar, float yTar, float zTar)
float[]	getCorrespondingPoint(int xTar, int yTar, int zTar)
ModelImage	getResultImage()	DOCUMENT ME!
final double	kernel(double fT)	DOCUMENT ME!
void	readMatrix(RandomAccessFile raFile)	Reads: 1.)
void	runAlgorithm()	run - starts the program.
void	saveMatrix(String fileName, String message)	Saves: 1.)
void	setupTPSpline2D()	setupTPSpline2D - computes the thin plate spline coefficients.
void	setupTPSpline2D(double[] xSource, double[] ySource, double[] xTar, double[] yTar, float smooth)	setupTPSpline2D computes the thin plate spline coefficients.
void	setupTPSpline2D(float[] x, float[] y, float[] f, float smooth)	setupTPSpline2D computes the thin plate spline coefficients.
void	setupTPSpline3D()	setupTPSpline3D - computes the thin plate spline coefficients.
void	setupTPSpline3D(double[] xSource, double[] ySource, double[] zSource, double[] xTar, double[] yTar, double[] zTar, float smooth)	setupTPSpline3D computes the thin plate spline coefficients.
void	setupTPSpline3D(float[] x, float[] y, float[] z, float[] f, float smooth)	setupTPSpline3D computes the thin plate spline coefficients.
private void	tpSpline2D()	DOCUMENT ME!
float[][]	tpSpline2D(float[] xWarp, float[] yWarp)	DOCUMENT ME!
private void	tpSpline3D()	DOCUMENT ME!
private void	transform25DVOI(ModelImage image, ModelImage destImage, float[] imgBuffer)
private void	transform3DVOI(ModelImage image, ModelImage destImage, float[] imgBuffer)
void	updateFileInfo()	Copy important file information to resultant image structure.

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

baseImage

private ModelImage baseImage

DOCUMENT ME!

C

private float[][] C

DOCUMENT ME!

mA

private float[] mA

DOCUMENT ME!

matchImage

private ModelImage matchImage

DOCUMENT ME!

mB

private float[] mB

DOCUMENT ME!

mX

private float[] mX

DOCUMENT ME!

mY

private float[] mY

DOCUMENT ME!

mZ

private float[] mZ

DOCUMENT ME!

N

private int N

DOCUMENT ME!

resultImage

private ModelImage resultImage

DOCUMENT ME!

smooth

private float smooth

DOCUMENT ME!

x

private double[] x

DOCUMENT ME!

xInvRange

private float xInvRange

DOCUMENT ME!

xMin

private float xMin

DOCUMENT ME!

xTar

private double[] xTar

DOCUMENT ME!

y

private double[] y

DOCUMENT ME!

yInvRange

private float yInvRange

DOCUMENT ME!

yMin

private float yMin

DOCUMENT ME!

yTar

private double[] yTar

DOCUMENT ME!

z

private double[] z

DOCUMENT ME!

zInvRange

private float zInvRange

DOCUMENT ME!

zMin

private float zMin

DOCUMENT ME!

zTar

private double[] zTar

DOCUMENT ME!

setupRequired

private boolean setupRequired

run2D

private boolean run2D

xDimA

private int xDimA

yDimA

private int yDimA

zDimA

private int zDimA

doSetupOnly

private boolean doSetupOnly

Constructor Details

AlgorithmTPSpline

public AlgorithmTPSpline()

AlgorithmTPSpline - default constructor.

AlgorithmTPSpline

public AlgorithmTPSpline(double[] xSource,
 double[] ySource,
 double[] xTar,
 double[] yTar,
 float smooth,
 ModelImage baseImage,
 ModelImage matchImage)

AlgorithmTPSpline - constructor for 2D case.

Parameters:

xSource - array with x coordinates of source data

ySource - array with y coordinates of source data

xTar - array with x coordinates of target data

yTar - array with y coordinates of target data

smooth - cannot be negative. If the smoothing term is nonzero, the interpolation is not exact

baseImage - DOCUMENT ME!

matchImage - DOCUMENT ME!

AlgorithmTPSpline

public AlgorithmTPSpline(double[] xSource,
 double[] ySource,
 double[] zSource,
 double[] xTar,
 double[] yTar,
 double[] zTar,
 float smooth,
 ModelImage baseImage,
 ModelImage matchImage)

AlgorithmTPSpline - constructor for 3D case.

Parameters:

xSource - array with x coordinates of source data

ySource - array with y coordinates of source data

zSource - array with z coordinates of source data

xTar - array with x coordinates of target data

yTar - array with y coordinates of target data

zTar - array with z coordinates of target data

smooth - cannot be negative. * If the smoothing term is nonzero, the interpolation is not exact

baseImage - DOCUMENT ME!

matchImage - DOCUMENT ME!

AlgorithmTPSpline

public AlgorithmTPSpline(double[] xSource,
 double[] ySource,
 double[] zSource,
 double[] xTar,
 double[] yTar,
 double[] zTar,
 float smooth,
 ModelImage baseImage,
 ModelImage matchImage,
 boolean doSetupOnly)

AlgorithmTPSpline - constructor for 3D case.

Parameters:

xSource - array with x coordinates of source data

ySource - array with y coordinates of source data

zSource - array with z coordinates of source data

xTar - array with x coordinates of target data

yTar - array with y coordinates of target data

zTar - array with z coordinates of target data

smooth - cannot be negative. * If the smoothing term is nonzero, the interpolation is not exact

baseImage - DOCUMENT ME!

matchImage - DOCUMENT ME!

AlgorithmTPSpline

public AlgorithmTPSpline(ModelImage matchImage)

Constructor used when N, xDimA, yDimA, zDimA, x[], y[], z[], and C[][] are read from a file

Parameters:

matchImage -

Method Details

finalize

public void finalize()

finalize -

Overrides:

finalize in class AlgorithmBase

getResultImage

public ModelImage getResultImage()

DOCUMENT ME!

Returns:

resultImage

kernel

public final double kernel(double fT)

DOCUMENT ME!

Parameters:

fT - DOCUMENT ME!

Returns:

DOCUMENT ME!

runAlgorithm

public void runAlgorithm()

run - starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

setupTPSpline2D

public void setupTPSpline2D()

setupTPSpline2D - computes the thin plate spline coefficients.

setupTPSpline2D

public void setupTPSpline2D(float[] x,
 float[] y,
 float[] f,
 float smooth)

setupTPSpline2D computes the thin plate spline coefficients.

Parameters:

x - array with x coordinates of data

y - array with y coordinates of data

f - array with values of data at (x,y) locations

smooth - nonnegative smoothing parameter

setupTPSpline2D

public void setupTPSpline2D(double[] xSource,
 double[] ySource,
 double[] xTar,
 double[] yTar,
 float smooth)

setupTPSpline2D computes the thin plate spline coefficients.

Parameters:

xSource - array with x coordinates of source data

ySource - array with y coordinates of source data

xTar - array with x coordinates of target data

yTar - array with y coordinates of target data

smooth - cannot be negative If the smoothing term is nonzero, the interpolation is not exact

setupTPSpline3D

public void setupTPSpline3D()

setupTPSpline3D - computes the thin plate spline coefficients.

setupTPSpline3D

public void setupTPSpline3D(float[] x,
 float[] y,
 float[] z,
 float[] f,
 float smooth)

setupTPSpline3D computes the thin plate spline coefficients.

Parameters:

x - array with x coordinates of data

y - array with y coordinates of data

z - array with z coordinates of data

f - array with values of data at (x,y,z) locations

smooth - nonnegative smoothing parameter

setupTPSpline3D

public void setupTPSpline3D(double[] xSource,
 double[] ySource,
 double[] zSource,
 double[] xTar,
 double[] yTar,
 double[] zTar,
 float smooth)

setupTPSpline3D computes the thin plate spline coefficients.

Parameters:

xSource - array with x coordinates of source data

ySource - array with y coordinates of source data

zSource - array with z coordinates of source data

xTar - array with x coordinates of target data

yTar - array with y coordinates of target data

zTar - array with z coordinates of target data

smooth - cannot be negative If the smoothing term is nonzero, the interpolation is not exact

tpSpline2D

public float[][] tpSpline2D(float[] xWarp,
 float[] yWarp)

DOCUMENT ME!

Parameters:

xWarp - DOCUMENT ME!

yWarp - DOCUMENT ME!

Returns:

DOCUMENT ME!

updateFileInfo

public void updateFileInfo()

Copy important file information to resultant image structure.

tpSpline2D

private void tpSpline2D()

DOCUMENT ME!

transform25DVOI

private void transform25DVOI(ModelImage image,
 ModelImage destImage,
 float[] imgBuffer)

getCorrespondingPoint

public float[] getCorrespondingPoint(int xTar,
 int yTar,
 int zTar)

getCorrespondingPoint

public final float[] getCorrespondingPoint(float xTar,
 float yTar,
 float zTar)

tpSpline3D

private void tpSpline3D()

DOCUMENT ME!

transform3DVOI

private void transform3DVOI(ModelImage image,
 ModelImage destImage,
 float[] imgBuffer)

saveMatrix

public void saveMatrix(String fileName,
 String message)

Saves: 1.) N, the number of matching control points in baseImage and matchImage 2.) Number of rows in C matrix 3.) Number of columns in C matrix 4.) xDim of baseImage 5.) yDim of baseImage 6.) If noncoplanar 3D thin plate spline is used, saves zDim of baseImage 7.) x coordinates of baseImage control points 8.) y coordinates of baseImage control points 9.) If noncoplanar 3D thin plate spline is used, saves z coordinates of baseImage control points 10.) If 2D or coplanar 3D, saves n+3 by 2 C[][] float matrix from setupTPSpline2D If noncoplanar 3D, saves n+4 by 3 C[][] float matrix from setupTPSpline3D 11.) Saves optional message.

Parameters:

fileName - - file name, including the path

message - optionally write a message at the file end

readMatrix

public void readMatrix(RandomAccessFile raFile)

Reads: 1.) N, the number of matching control points in baseImage and matchImage 2.) Number of rows in C matrix 3.) Number of columns in C matrix 4.) xDim of baseImage 5.) yDim of baseImage 6.) If noncoplanar 3D thin plate spline is used, reads zDim of baseImage 7.) x coordinates of baseImage control points 8.) y coordinates of baseImage control points 9.) If noncoplanar 3D thin plate spline is used, reads z coordinates of baseImage control points 10.) If 2D or coplanar 3D, reads n+3 by 2 C[][] float matrix from setupTPSpline2D If noncoplanar 3D, reads n+4 by 3 C[][] float matrix from setupTPSpline3D Does not read optional message at end of file.

Parameters:

raFile - file to be read