Package gov.nih.mipav.model.algorithms

Class TVL1FLOW

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.TVL1FLOW

All Implemented Interfaces:

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

public class TVL1FLOW
extends AlgorithmBase

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
(package private) int	BOUNDARY_CONDITION
(package private) int	BOUNDARY_CONDITION_DIRICHLET
(package private) int	BOUNDARY_CONDITION_PERIODIC
(package private) int	BOUNDARY_CONDITION_REFLECTING
(package private) int	DEFAULT_BOUNDARY_CONDITION
(package private) int	DEFAULT_GAUSSIAN_WINDOW_SIZE
private ModelImage	destuImage
private ModelImage	destvImage
private double	epsilon
(package private) double	GRAD_IS_ZERO
private double	lambda
(package private) int	MAX_ITERATIONS
(package private) int	Neumann
private int	nscales
private int	nwarps
(package private) double	PAR_DEFAULT_EPSILON
(package private) double	PAR_DEFAULT_LAMBDA
(package private) int	PAR_DEFAULT_NSCALES
(package private) int	PAR_DEFAULT_NWARPS
(package private) double	PAR_DEFAULT_TAU
(package private) double	PAR_DEFAULT_THETA
(package private) int	PAR_DEFAULT_VERBOSE
(package private) double	PAR_DEFAULT_ZFACTOR
(package private) int	Periodic
(package private) double	PRESMOOTHING_SIGMA
private ModelImage	srcImage1
private ModelImage	srcImage2
(package private) int	Symmetric
private double	tau
private double	theta
private boolean	verbose
private double	zfactor
(package private) double	ZOOM_SIGMA_ZERO

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
TVL1FLOW()
TVL1FLOW(ModelImage destuImg, ModelImage destvImg, ModelImage srcImg1, ModelImage srcImg2, double tau, double lambda, double theta, int nscales, double zfactor, int nwarps, double epsilon, boolean verbose)

Method Summary

Modifier and Type	Method	Description
double	bicubic_interpolation_at(double[] input, double uu, double vv, int nx, int ny, boolean border_out)	Compute the bicubic interpolation of a point in an image.
double	bicubic_interpolation_cell(double[][] p, double x, double y)	Bicubic interpolation in two dimensions
void	bicubic_interpolation_warp(double[] input, double[] u, double[] v, double[] output, int nx, int ny, boolean border_out)	Compute the bicubic interpolation of an image.
void	centered_gradient(double[] input, double[] dx, double[] dy, int nx, int ny)	Function to compute the gradient with centered differences
double	cubic_interpolation_cell(double[] v, double x)	Cubic interpolation in one dimension
void	divergence(double[] v1, double[] v2, double[] div, int nx, int ny)	Function to compute the divergence with backward differences (see [2] for details)
void	Dual_TVL1_optic_flow(double[] I0, double[] I1, double[] u1, double[] u2, int nx, int ny, double tau, double lambda, double theta, int warps, double epsilon, boolean verbose)	Function to compute the optical flow in one scale
void	Dual_TVL1_optic_flow_multiscale(double[] I0, double[] I1, double[] u1, double[] u2, int nxx, int nyy, double tau, double lambda, double theta, int nscales, double zfactor, int warps, double epsilon, boolean verbose)	Function to compute the optical flow using multiple scales
void	forward_gradient(double[] f, double[] fx, double[] fy, int nx, int ny)	Function to compute the gradient with forward differences (see [2] for details)
void	gaussian(double[] I, int xdim, int ydim, double sigma)	In-place Gaussian smoothing of an image
void	getminmax(double[] min, double[] max, double[] x, int n)	Compute the max and min of an array
private double	hypot(double x, double y)
void	image_normalization(double[] I0, double[] I1, double[] I0n, double[] I1n, int size)	Function to normalize the images between 0 and 255
int	neumann_bc(int x, int nx, boolean[] out)	Neumann boundary condition test
int	periodic_bc(int x, int nx, boolean[] out)	Periodic boundary condition test
void	runAlgorithm()	Actually runs the algorithm.
int	symmetric_bc(int x, int nx, boolean[] out)	Symmetric boundary condition test
void	zoom_in(double[] I, double[] Iout, int nx, int ny, int nxx, int nyy)	Function to upsample the image
void	zoom_out(double[] I, double[] Iout, int nx, int ny, double factor)	Downsample an image
void	zoom_size(int nx, int ny, int[] nxx, int[] nyy, double factor)	Compute the size of a zoomed image from the zoom factor

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

Neumann

final int Neumann

See Also:

Constant Field Values

Periodic

final int Periodic

See Also:

Constant Field Values

Symmetric

final int Symmetric

See Also:

Constant Field Values

BOUNDARY_CONDITION

int BOUNDARY_CONDITION

PAR_DEFAULT_TAU

final double PAR_DEFAULT_TAU

See Also:

Constant Field Values

PAR_DEFAULT_LAMBDA

final double PAR_DEFAULT_LAMBDA

See Also:

Constant Field Values

PAR_DEFAULT_THETA

final double PAR_DEFAULT_THETA

See Also:

Constant Field Values

PAR_DEFAULT_NSCALES

final int PAR_DEFAULT_NSCALES

See Also:

Constant Field Values

PAR_DEFAULT_ZFACTOR

final double PAR_DEFAULT_ZFACTOR

See Also:

Constant Field Values

PAR_DEFAULT_NWARPS

final int PAR_DEFAULT_NWARPS

See Also:

Constant Field Values

PAR_DEFAULT_EPSILON

final double PAR_DEFAULT_EPSILON

See Also:

Constant Field Values

PAR_DEFAULT_VERBOSE

final int PAR_DEFAULT_VERBOSE

See Also:

Constant Field Values

srcImage1

private ModelImage srcImage1

srcImage2

private ModelImage srcImage2

destuImage

private ModelImage destuImage

destvImage

private ModelImage destvImage

tau

private double tau

lambda

private double lambda

theta

private double theta

nscales

private int nscales

zfactor

private double zfactor

nwarps

private int nwarps

epsilon

private double epsilon

verbose

private boolean verbose

BOUNDARY_CONDITION_DIRICHLET

final int BOUNDARY_CONDITION_DIRICHLET

See Also:

Constant Field Values

BOUNDARY_CONDITION_REFLECTING

final int BOUNDARY_CONDITION_REFLECTING

See Also:

Constant Field Values

BOUNDARY_CONDITION_PERIODIC

final int BOUNDARY_CONDITION_PERIODIC

See Also:

Constant Field Values

DEFAULT_GAUSSIAN_WINDOW_SIZE

final int DEFAULT_GAUSSIAN_WINDOW_SIZE

See Also:

Constant Field Values

DEFAULT_BOUNDARY_CONDITION

final int DEFAULT_BOUNDARY_CONDITION

See Also:

Constant Field Values

ZOOM_SIGMA_ZERO

final double ZOOM_SIGMA_ZERO

See Also:

Constant Field Values

MAX_ITERATIONS

final int MAX_ITERATIONS

See Also:

Constant Field Values

PRESMOOTHING_SIGMA

final double PRESMOOTHING_SIGMA

See Also:

Constant Field Values

GRAD_IS_ZERO

final double GRAD_IS_ZERO

See Also:

Constant Field Values

Constructor Detail

TVL1FLOW

public TVL1FLOW()

TVL1FLOW

public TVL1FLOW(ModelImage destuImg,
                ModelImage destvImg,
                ModelImage srcImg1,
                ModelImage srcImg2,
                double tau,
                double lambda,
                double theta,
                int nscales,
                double zfactor,
                int nwarps,
                double epsilon,
                boolean verbose)

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

hypot

private double hypot(double x,
                     double y)

neumann_bc

public int neumann_bc(int x,
                      int nx,
                      boolean[] out)

Neumann boundary condition test

periodic_bc

public int periodic_bc(int x,
                       int nx,
                       boolean[] out)

Periodic boundary condition test

symmetric_bc

public int symmetric_bc(int x,
                        int nx,
                        boolean[] out)

Symmetric boundary condition test

cubic_interpolation_cell

public double cubic_interpolation_cell(double[] v,
                                       double x)

Cubic interpolation in one dimension

bicubic_interpolation_cell

public double bicubic_interpolation_cell(double[][] p,
                                         double x,
                                         double y)

Bicubic interpolation in two dimensions

bicubic_interpolation_at

public double bicubic_interpolation_at(double[] input,
                                       double uu,
                                       double vv,
                                       int nx,
                                       int ny,
                                       boolean border_out)

Compute the bicubic interpolation of a point in an image. Detect if the point goes outside the image domain.

bicubic_interpolation_warp

public void bicubic_interpolation_warp(double[] input,
                                       double[] u,
                                       double[] v,
                                       double[] output,
                                       int nx,
                                       int ny,
                                       boolean border_out)

Compute the bicubic interpolation of an image.

divergence

public void divergence(double[] v1,
                       double[] v2,
                       double[] div,
                       int nx,
                       int ny)

Function to compute the divergence with backward differences (see [2] for details)

forward_gradient

public void forward_gradient(double[] f,
                             double[] fx,
                             double[] fy,
                             int nx,
                             int ny)

Function to compute the gradient with forward differences (see [2] for details)

centered_gradient

public void centered_gradient(double[] input,
                              double[] dx,
                              double[] dy,
                              int nx,
                              int ny)

Function to compute the gradient with centered differences

gaussian

public void gaussian(double[] I,
                     int xdim,
                     int ydim,
                     double sigma)

In-place Gaussian smoothing of an image

zoom_size

public void zoom_size(int nx,
                      int ny,
                      int[] nxx,
                      int[] nyy,
                      double factor)

Compute the size of a zoomed image from the zoom factor

zoom_out

public void zoom_out(double[] I,
                     double[] Iout,
                     int nx,
                     int ny,
                     double factor)

Downsample an image

zoom_in

public void zoom_in(double[] I,
                    double[] Iout,
                    int nx,
                    int ny,
                    int nxx,
                    int nyy)

Function to upsample the image

Dual_TVL1_optic_flow

public void Dual_TVL1_optic_flow(double[] I0,
                                 double[] I1,
                                 double[] u1,
                                 double[] u2,
                                 int nx,
                                 int ny,
                                 double tau,
                                 double lambda,
                                 double theta,
                                 int warps,
                                 double epsilon,
                                 boolean verbose)

Function to compute the optical flow in one scale

getminmax

public void getminmax(double[] min,
                      double[] max,
                      double[] x,
                      int n)

Compute the max and min of an array

image_normalization

public void image_normalization(double[] I0,
                                double[] I1,
                                double[] I0n,
                                double[] I1n,
                                int size)

Function to normalize the images between 0 and 255

Dual_TVL1_optic_flow_multiscale

public void Dual_TVL1_optic_flow_multiscale(double[] I0,
                                            double[] I1,
                                            double[] u1,
                                            double[] u2,
                                            int nxx,
                                            int nyy,
                                            double tau,
                                            double lambda,
                                            double theta,
                                            int nscales,
                                            double zfactor,
                                            int warps,
                                            double epsilon,
                                            boolean verbose)

Function to compute the optical flow using multiple scales