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

All Implemented Interfaces:

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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	finalize -
`float[]`	`getCorrespondingPoint(float xTar, float yTar, float zTar)`
`float[]`	`getCorrespondingPoint(int xTar, int yTar, int zTar)`
`ModelImage`	`getResultImage()`	DOCUMENT ME!
`double`	`kernel(double fT)`	DOCUMENT ME!
`void`	`readMatrix(java.io.RandomAccessFile raFile)`	Reads: 1.)
`void`	`runAlgorithm()`	run - starts the program.
`void`	`saveMatrix(java.lang.String fileName, java.lang.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, 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
  - 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 Detail
  - 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 Detail
  - 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(java.lang.String fileName,
                       java.lang.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(java.io.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

Class AlgorithmTPSpline

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

baseImage

C

mA

matchImage

mB

mX

mY

mZ

N

resultImage

smooth

x

xInvRange

xMin

xTar

y

yInvRange

yMin

yTar

z

zInvRange

zMin

zTar

setupRequired

run2D

xDimA

yDimA

zDimA

doSetupOnly

Constructor Detail

AlgorithmTPSpline

AlgorithmTPSpline

AlgorithmTPSpline

AlgorithmTPSpline

AlgorithmTPSpline

Method Detail

finalize

getResultImage

kernel

runAlgorithm

setupTPSpline2D

setupTPSpline2D

setupTPSpline2D

setupTPSpline3D

setupTPSpline3D

setupTPSpline3D

tpSpline2D

updateFileInfo

tpSpline2D

transform25DVOI

getCorrespondingPoint

getCorrespondingPoint

tpSpline3D

transform3DVOI

saveMatrix

readMatrix