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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmBSpline
extends AlgorithmBase
```
Modified code from Aaron Carass's Java implementation of Philippe Thevenaz's Cubic B-spline Interpolation. Code is simply wrapped to allow for calls consistent with MIPAV style as well as allow for 2D images. B-Spline interpolation.

Author:

Philippe Thevenaz, Aaron Carass Jet code is untouched from when the new code was implemented on June 24th, 2014. Fourth-order Bspline for 1-3D lines and 2D surface. This class is based on code from Dave Eberly's MAGIC C++ library.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmBSpline.ColorInterpolation
- 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 AlgorithmBSpline.ColorInterpolation`	`colorInter`
`private double`	`DBL_EPSILON`
`private int`	`degree`	DOCUMENT ME!
`private int`	`depth`	DOCUMENT ME!
`private double[]`	`dt`	DOCUMENT ME!
`private double[]`	`dt_double`	DOCUMENT ME!
`private double[]`	`geoms`	DOCUMENT ME!
`private double[]`	`geomx`	DOCUMENT ME!
`private double[]`	`geomy`	DOCUMENT ME!
`private double[]`	`geomz`	DOCUMENT ME!
`private int`	`height`	DOCUMENT ME!
`private double[][][]`	`imData`
`private static double[][]`	`mat4`	Blending matrix for a 4th degree Bspline.
`private int`	`width`	DOCUMENT ME!
`private int`	`xold_tbase`	DOCUMENT ME!
`private int`	`xyold_tbase`	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

AlgorithmBSpline()
default constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`bSpline2D(int orderDx, int orderDy, double x, double y)`	This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation.
`double[]`	`bSpline2DC(int orderDx, int orderDy, double x, double y)`	This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation.
`double`	`bSpline3D(int orderDx, int orderDy, int orderDz, double x, double y, double z)`	This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation.
`double[]`	`bSpline3DC(int orderDx, int orderDy, int orderDz, double x, double y, double z)`	This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation.
`float`	`bSplineJet1D(byte derivOrder, float t, float[] dataX)`	This method can also be used to calculate derivatives of the Bspline.
`WildMagic.LibFoundation.Mathematics.Vector2f`	`bSplineJetXY(int derivOrder, float t, float[] dataX, float[] dataY)`	This method can also be used to calculate derivatives of the Bspline.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`bSplineJetXYZ(int derivOrder, float t, float[] dataX, float[] dataY, float[] dataZ)`	This method can also be used to calculate derivatives of the Bspline.
`javax.vecmath.Vector3d`	`bSplineJetXYZ_double(int derivOrder, float t, float[] dataX, float[] dataY, float[] dataZ)`	This method can also be used to calculate derivatives of the Bspline.
`private void`	`ConvertToInterpolationCoefficients(double[] c, int DataLength, double[] z, int NbPoles, double Tolerance)`
`void`	`finalize()`	Clean up memeory.
`private double[]`	`GetColumn(int x, int z, double[][][] Image)`
`private double[]`	`GetRow(int y, int z, double[][][] Image, int width)`
`private double[]`	`GetVertical(int x, int y, double[][][] Image)`
`private double`	`InitialAntiCausalCoefficient(double[] c, int DataLength, double z)`
`private double`	`InitialCausalCoefficient(double[] c, int DataLength, double z, double Tolerance)`
`private double`	`interpolateBSpline(double[][][] image, double x, double y, double z, int SplineDegree)`	Do the B-Spline Interpolation
`private double`	`interpolateBSpline2D(double[][][] image, double x, double y, int SplineDegree)`
`private void`	`PutColumn(double[] Line, int x, int z, double[][][] Image)`
`private void`	`PutRow(double[] Line, int y, int z, double[][][] Image)`
`private void`	`PutVertical(double[] Line, int x, int y, double[][][] Image)`
`void`	`resetBspline()`	Resets parameters used by the Bsplines.
`void`	`runAlgorithm()`	Default method that is not really appropriate for this class but must be defined because this class extends AlgorithmBase.
`private int`	`SamplesToCoefficients(double[][][] Image, int SplineDegree)`
`private int`	`SamplesToCoefficients2D(double[][][] Image, int SplineDegree)`
`void`	`setup2DBSpline(double[] vol, int[] extents, int _degree)`	Allocates memory and constructs arrays needed for BSpline.
`void`	`setup2DBSplineC(double[] vol, int[] extents, int _degree)`	Allocates memory and constructs arrays needed for BSpline.
`void`	`setup3DBSpline(double[] vol, int[] extents, int _degree)`	setup3DBSpline - setup 3D Bspline for black and white.
`void`	`setup3DBSplineC(double[] vol, int[] extents, int _degree)`	Allocates memory and constructs arrays needed for BSpline.

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
  - mat4
```
private static double[][] mat4
```
    Blending matrix for a 4th degree Bspline.
  - DBL_EPSILON
```
private final double DBL_EPSILON
```
    See Also:
    
    Constant Field Values
  - degree
```
private int degree
```
    DOCUMENT ME!
  - dt
```
private double[] dt
```
    DOCUMENT ME!
  - dt_double
```
private double[] dt_double
```
    DOCUMENT ME!
  - geoms
```
private double[] geoms
```
    DOCUMENT ME!
  - geomx
```
private double[] geomx
```
    DOCUMENT ME!
  - geomy
```
private double[] geomy
```
    DOCUMENT ME!
  - geomz
```
private double[] geomz
```
    DOCUMENT ME!
  - width
```
private int width
```
    DOCUMENT ME!
  - height
```
private int height
```
    DOCUMENT ME!
  - depth
```
private int depth
```
    DOCUMENT ME!
  - xold_tbase
```
private int xold_tbase
```
    DOCUMENT ME!
  - xyold_tbase
```
private int xyold_tbase
```
    DOCUMENT ME!
  - colorInter
```
private AlgorithmBSpline.ColorInterpolation colorInter
```
  - imData
```
private double[][][] imData
```
- Constructor Detail
  - AlgorithmBSpline
```
public AlgorithmBSpline()
```
    default constructor.
- Method Detail
  - bSpline2D
```
public double bSpline2D(int orderDx,
                        int orderDy,
                        double x,
                        double y)
```
    This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation. For precise interpolation, use the analogous method in AlgorithmBSpline3D instead, as that provides true B-spline interpolation. This method can also be used to calculate derivatives of the Bspline.
    
    Parameters:
    
    orderDx - derivative order in x direction (n <= 4 )
    
    orderDy - derivative order in y direction (n <= 4 )
    
    x - double point index along the Bspline indicating point of interest
    
    y - double point index along the Bspline indicating point of interest
    
    Returns:
    
    the Bspline interpolated data point
  - bSpline2DC
```
public double[] bSpline2DC(int orderDx,
                           int orderDy,
                           double x,
                           double y)
```
    This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation. For precise interpolation, use the analogous method in AlgorithmBSpline3D instead, as that provides true B-spline interpolation. This method can also be used to calculate derivatives of the Bspline.
    
    Parameters:
    
    orderDx - derivative order in x direction (n <= 4 )
    
    orderDy - derivative order in y direction (n <= 4 )
    
    x - double point index along the Bspline indicating point of interest
    
    y - double point index along the Bspline indicating point of interest
    
    Returns:
    
    the Bspline interpolated data point
  - bSpline3D
```
public double bSpline3D(int orderDx,
                        int orderDy,
                        int orderDz,
                        double x,
                        double y,
                        double z)
```
    This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation. For precise interpolation, use the analogous method in AlgorithmBSpline3D instead, as that provides true B-spline interpolation. 3D graph Bspline for black and white. This method can also be used to calculate derivatives of the Bspline. WARNING - programmer must call setup3DBSpline before using this function!!!
    
    Parameters:
    
    orderDx - derivative order in x direction (n <= 4 )
    
    orderDy - derivative order in y direction (n <= 4 )
    
    orderDz - derivative order in z direction (n <= 4 )
    
    x - double point index along the Bspline indicating point of interest
    
    y - double point index along the Bspline indicating point of interest
    
    z - double point index along the Bspline indicating pointof interest
    
    Returns:
    
    the Bspline interpolated data point
  - bSpline3DC
```
public double[] bSpline3DC(int orderDx,
                           int orderDy,
                           int orderDz,
                           double x,
                           double y,
                           double z)
```
    This method is out of date, as it provides smoothed interpolation as opposed to precise interpolation. For precise interpolation, use the analogous method in AlgorithmBSpline3D instead, as that provides true B-spline interpolation. 3D graph Bspline for color. This method can also be used to calculate derivatives of the Bspline. WARNING - programmer must call setup3DBSpline before using this function!!!
    
    Parameters:
    
    orderDx - derivative order in x direction (n <= 4 )
    
    orderDy - derivative order in y direction (n <= 4 )
    
    orderDz - derivative order in z direction (n <= 4 )
    
    x - double point index along the Bspline indicating point of interest
    
    y - double point index along the Bspline indicating point of interest
    
    z - double point index along the Bspline indicating point of interest
    
    Returns:
    
    the Bspline interpolated data point
  - bSplineJet1D
```
public float bSplineJet1D(byte derivOrder,
                          float t,
                          float[] dataX)
```
    This method can also be used to calculate derivatives of the Bspline.
    
    Parameters:
    
    derivOrder - derivative order (n <= 4 )
    
    t - float point index along the Bspline indicating point of interest
    
    dataX - control points for the Bspline
    
    Returns:
    
    the Bspline interpolated data point
  - bSplineJetXY
```
public WildMagic.LibFoundation.Mathematics.Vector2f bSplineJetXY(int derivOrder,
                                                                 float t,
                                                                 float[] dataX,
                                                                 float[] dataY)
```
    This method can also be used to calculate derivatives of the Bspline. Used for smoothing VOI lines
    
    Parameters:
    
    derivOrder - derivative order (n <= 4 )
    
    t - float point index along the Bspline indicating point of interest
    
    dataX - control points for the Bspline
    
    dataY - control points for the Bspline
    
    Returns:
    
    the Bspline interpolated data point
  - bSplineJetXYZ
```
public WildMagic.LibFoundation.Mathematics.Vector3f bSplineJetXYZ(int derivOrder,
                                                                  float t,
                                                                  float[] dataX,
                                                                  float[] dataY,
                                                                  float[] dataZ)
```
    This method can also be used to calculate derivatives of the Bspline. Used for smoothing VOI lines
    
    Parameters:
    
    derivOrder - derivative order (n <= 4 )
    
    t - float point index along the Bspline indicating point of interest
    
    dataX - control points for the Bspline
    
    dataY - control points for the Bspline
    
    dataZ - control points for the Bspline
    
    Returns:
    
    the Bspline interpolated data point
  - bSplineJetXYZ_double
```
public javax.vecmath.Vector3d bSplineJetXYZ_double(int derivOrder,
                                                   float t,
                                                   float[] dataX,
                                                   float[] dataY,
                                                   float[] dataZ)
```
    This method can also be used to calculate derivatives of the Bspline.
    
    Parameters:
    
    derivOrder - derivative order (n <= 4 )
    
    t - float point index along the Bspline indicating point of interest
    
    dataX - control points for the Bspline
    
    dataY - control points for the Bspline
    
    dataZ - control points for the Bspline
    
    Returns:
    
    the Bspline interpolated data point
  - finalize
```
public void finalize()
```
    Clean up memeory.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - resetBspline
```
public void resetBspline()
```
    Resets parameters used by the Bsplines.
  - runAlgorithm
```
public void runAlgorithm()
```
    Default method that is not really appropriate for this class but must be defined because this class extends AlgorithmBase.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setup2DBSpline
```
public void setup2DBSpline(double[] vol,
                           int[] extents,
                           int _degree)
```
    Allocates memory and constructs arrays needed for BSpline.
    
    Parameters:
    
    vol - volume comprising control points for the Bspline
    
    extents - vol extents (xDim,yDim)
    
    _degree - degree of spline (3 or 4)
  - setup2DBSplineC
```
public void setup2DBSplineC(double[] vol,
                            int[] extents,
                            int _degree)
```
    Allocates memory and constructs arrays needed for BSpline.
    
    Parameters:
    
    vol - volume comprising control points for the Bspline
    
    extents - vol extents (xDim,yDim)
    
    _degree - degree of spline (3 or 4)
  - setup3DBSpline
```
public void setup3DBSpline(double[] vol,
                           int[] extents,
                           int _degree)
```
    setup3DBSpline - setup 3D Bspline for black and white. Allocates memory and constructs arrays needed for BSpline
    
    Parameters:
    
    vol - volume comprising control points for the Bspline
    
    extents - vol extents (xDim,yDim, zDim)
    
    _degree - degree of spline (3 or 4)
  - setup3DBSplineC
```
public void setup3DBSplineC(double[] vol,
                            int[] extents,
                            int _degree)
```
    Allocates memory and constructs arrays needed for BSpline.
    
    Parameters:
    
    vol - volume comprising control points for the Bspline
    
    extents - vol extents (xDim,yDim, zDim)
    
    _degree - degree of spline (3 or 4)
  - interpolateBSpline
```
private double interpolateBSpline(double[][][] image,
                                  double x,
                                  double y,
                                  double z,
                                  int SplineDegree)
```
    Do the B-Spline Interpolation
    
    Parameters:
    
    Bcoeff - B-spline array of coefficients
    
    Width - Width of the image
    
    Height - Height of the image
    
    Depth - Depth of the image
    
    x - x coordinate where to interpolate
    
    y - y coordinate where to interpolate
    
    z - z coordinate where to interpolate
    
    SplineDegree - Degree of the B-Spline
  - interpolateBSpline2D
```
private double interpolateBSpline2D(double[][][] image,
                                    double x,
                                    double y,
                                    int SplineDegree)
```
  - ConvertToInterpolationCoefficients
```
private void ConvertToInterpolationCoefficients(double[] c,
                                                int DataLength,
                                                double[] z,
                                                int NbPoles,
                                                double Tolerance)
```
    Parameters:
    
    c - Samples
    
    DataLength - Number of samples or coefficients
    
    z - Poles
    
    NbPoles - Number of poles
    
    Tolerance - Admissible relative error
  - InitialCausalCoefficient
```
private double InitialCausalCoefficient(double[] c,
                                        int DataLength,
                                        double z,
                                        double Tolerance)
```
  - InitialAntiCausalCoefficient
```
private double InitialAntiCausalCoefficient(double[] c,
                                            int DataLength,
                                            double z)
```
  - GetRow
```
private double[] GetRow(int y,
                        int z,
                        double[][][] Image,
                        int width)
```
  - PutRow
```
private void PutRow(double[] Line,
                    int y,
                    int z,
                    double[][][] Image)
```
  - GetColumn
```
private double[] GetColumn(int x,
                           int z,
                           double[][][] Image)
```
  - PutColumn
```
private void PutColumn(double[] Line,
                       int x,
                       int z,
                       double[][][] Image)
```
  - GetVertical
```
private double[] GetVertical(int x,
                             int y,
                             double[][][] Image)
```
  - PutVertical
```
private void PutVertical(double[] Line,
                         int x,
                         int y,
                         double[][][] Image)
```
  - SamplesToCoefficients
```
private int SamplesToCoefficients(double[][][] Image,
                                  int SplineDegree)
```
  - SamplesToCoefficients2D
```
private int SamplesToCoefficients2D(double[][][] Image,
                                    int SplineDegree)
```

Class AlgorithmBSpline

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

mat4

DBL_EPSILON

degree

dt

dt_double

geoms

geomx

geomy

geomz

width

height

depth

xold_tbase

xyold_tbase

colorInter

imData

Constructor Detail

AlgorithmBSpline

Method Detail

bSpline2D

bSpline2DC

bSpline3D

bSpline3DC

bSplineJet1D

bSplineJetXY

bSplineJetXYZ

bSplineJetXYZ_double

finalize

resetBspline

runAlgorithm

setup2DBSpline

setup2DBSplineC

setup3DBSpline

setup3DBSplineC

interpolateBSpline

interpolateBSpline2D

ConvertToInterpolationCoefficients

InitialCausalCoefficient

InitialAntiCausalCoefficient

GetRow

PutRow

GetColumn

PutColumn

GetVertical

PutVertical

SamplesToCoefficients

SamplesToCoefficients2D