Package gov.nih.mipav.model.algorithms

Class AlgorithmVesselEnhancement

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmVesselEnhancement

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmVesselEnhancement
extends AlgorithmBase

Author:

ilb This is a port of MATLAB code vesselnessv2d.m by Boguslaw Obara. multiscale vessel enhancement filtering with vectors Ported under: Apache License Version 2.0, January 2004 Reference:

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 double	alpha
private double	beta
int	BORDER_CONSTANT
int	BORDER_DEFAULT
int	BORDER_REFLECT
int	BORDER_REFLECT_101
int	BORDER_REPLICATE
int	BORDER_WRAP
private double	c
private int	dimlenx
private int	dimleny
private int	dimlenz
private double	epsilon
private double	gamma
private double[][]	sigma
private boolean	wb

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
AlgorithmVesselEnhancement(ModelImage destImg, ModelImage srcImg, double[][] sigma, double gamma, double alpha, double beta, double c, boolean wb)

Method Summary

Modifier and Type	Method	Description
private double[][]	copyMakeBorder2D(double[][] src, int top, int bottom, int left, int right, int borderType, double borderValue)
private void	eigen_sort3d_m(double[][][] l1, double[][][] l2, double[][][] l3)
private void	eigen2d_m(double[][] l1, double[][] l2, double[][] a, double[][] b, double[][] c, double[][] d)
private void	eigen3d_m(double[][][] l1, double[][][] l2, double[][][] l3, double[][][] x1, double[][][] x2, double[][][] x3, double[][][] x4, double[][][] x5, double[][][] x6, double[][][] x7, double[][][] x8, double[][][] x9)
private void	filter2Same(double[][] result, double[][] img, double[][] win)
private void	filter3Same(double[][][] result, double[][][] img, double[][][] win)
private void	gaussian2nd2d(double[][] gxx, double[][] gxy, double[][] gyy, double[] s)
private void	gaussian2nd3d(double[][][] gxx, double[][][] gyy, double[][][] gzz, double[][][] gxy, double[][][] gxz, double[][][] gyz, double[] s)
private void	hessian2d(double[][] hxx, double[][] hxy, double[][] hyy, double[][] im, double[] s)
private void	hessian3D(double[][][] hxx, double[][][] hyy, double[][][] hzz, double[][][] hxy, double[][][] hxz, double[][][] hyz, double[][][] im, double[] s)
private double[][][]	replicateBorder3d(double[][][] src, int front, int back, int top, int bottom, int left, int right)
void	runAlgorithm()	Actually runs the algorithm.
void	vesselnessv2d()
void	vesselnessv3d()

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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

sigma

private double[][] sigma

gamma

private double gamma

alpha

private double alpha

beta

private double beta

c

private double c

wb

private boolean wb

dimlenx

private int dimlenx

dimleny

private int dimleny

dimlenz

private int dimlenz

epsilon

private final double epsilon

See Also:

Constant Field Values

BORDER_CONSTANT

public final int BORDER_CONSTANT

See Also:

Constant Field Values

BORDER_REPLICATE

public final int BORDER_REPLICATE

See Also:

Constant Field Values

BORDER_REFLECT

public final int BORDER_REFLECT

See Also:

Constant Field Values

BORDER_WRAP

public final int BORDER_WRAP

See Also:

Constant Field Values

BORDER_REFLECT_101

public final int BORDER_REFLECT_101

See Also:

Constant Field Values

BORDER_DEFAULT

public final int BORDER_DEFAULT

See Also:

Constant Field Values

Constructor Detail

AlgorithmVesselEnhancement

public AlgorithmVesselEnhancement(ModelImage destImg,
                                  ModelImage srcImg,
                                  double[][] sigma,
                                  double gamma,
                                  double alpha,
                                  double beta,
                                  double c,
                                  boolean wb)

Method Detail

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

vesselnessv2d

public void vesselnessv2d()

gaussian2nd2d

private void gaussian2nd2d(double[][] gxx,
                           double[][] gxy,
                           double[][] gyy,
                           double[] s)

replicateBorder3d

private double[][][] replicateBorder3d(double[][][] src,
                                       int front,
                                       int back,
                                       int top,
                                       int bottom,
                                       int left,
                                       int right)

copyMakeBorder2D

private double[][] copyMakeBorder2D(double[][] src,
                                    int top,
                                    int bottom,
                                    int left,
                                    int right,
                                    int borderType,
                                    double borderValue)

filter2Same

private void filter2Same(double[][] result,
                         double[][] img,
                         double[][] win)

filter3Same

private void filter3Same(double[][][] result,
                         double[][][] img,
                         double[][][] win)

hessian2d

private void hessian2d(double[][] hxx,
                       double[][] hxy,
                       double[][] hyy,
                       double[][] im,
                       double[] s)

eigen2d_m

private void eigen2d_m(double[][] l1,
                       double[][] l2,
                       double[][] a,
                       double[][] b,
                       double[][] c,
                       double[][] d)

vesselnessv3d

public void vesselnessv3d()

hessian3D

private void hessian3D(double[][][] hxx,
                       double[][][] hyy,
                       double[][][] hzz,
                       double[][][] hxy,
                       double[][][] hxz,
                       double[][][] hyz,
                       double[][][] im,
                       double[] s)

gaussian2nd3d

private void gaussian2nd3d(double[][][] gxx,
                           double[][][] gyy,
                           double[][][] gzz,
                           double[][][] gxy,
                           double[][][] gxz,
                           double[][][] gyz,
                           double[] s)

eigen3d_m

private void eigen3d_m(double[][][] l1,
                       double[][][] l2,
                       double[][][] l3,
                       double[][][] x1,
                       double[][][] x2,
                       double[][][] x3,
                       double[][][] x4,
                       double[][][] x5,
                       double[][][] x6,
                       double[][][] x7,
                       double[][][] x8,
                       double[][][] x9)

eigen_sort3d_m

private void eigen_sort3d_m(double[][][] l1,
                            double[][][] l2,
                            double[][][] l3)