Package gov.nih.mipav.model.algorithms.utilities

Class AlgorithmReslice

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmReslice

All Implemented Interfaces:

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

public class AlgorithmReslice
extends AlgorithmBase

Reslices 3D image into (isotropic)cubic voxels. This class assumes that the the X and Y dimensions are equal and that the Z dimension is of lower resolution than of X and Y. However, it does not assume equal spacing in the input image between all slices (sometimes common in CT and MR images). Note that since this class only adds images between slices it reduces to a 1D problem. For example, we only need the pixel above and below for linear interp since there isn't any change in X or change in Y.

Version:

0.1 Sept 14, 1998

Author:

Matthew J. McAuliffe, Ph.D.

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
static int	CUBIC	Cubic interpolation mode.
static int	CUBIC_BSPLINE	Cubic b-spline interpolation mode.
private int	interpMode	Interpolation mode (Linear, Cubic Bspline, Cubic Convolution).
static int	LINEAR	Linear interpolation mode.

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
AlgorithmReslice(ModelImage srcImg, int _interpMode)	Creates new algorithm for reslicing to isotropic voxels.

Method Summary

Modifier and Type	Method	Description
private float	calcRBSpline(float u)	Reslice data is Cubic Bspline where.
private float	calcRCUBIC(float u)	Reslice using cubic convolution reslice where.
private void	cubicReslice()	Reslices the data into isotropic voxels using one of two interpolation methods (cubic Bspline or cubic convolution).
void	finalize()	Prepares this class for destruction.
ModelImage	getResultImage()	Accessor to get interpolated image.
private void	linearReslice()	Reslices the data into isotropic voxels using linear interpolation.
void	runAlgorithm()	Starts the program.

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

LINEAR

public static final int LINEAR

Linear interpolation mode.

See Also:

Constant Field Values

CUBIC_BSPLINE

public static final int CUBIC_BSPLINE

Cubic b-spline interpolation mode.

See Also:

Constant Field Values

CUBIC

public static final int CUBIC

Cubic interpolation mode.

See Also:

Constant Field Values

interpMode

private int interpMode

Interpolation mode (Linear, Cubic Bspline, Cubic Convolution).

Constructor Detail

AlgorithmReslice

public AlgorithmReslice(ModelImage srcImg,
                        int _interpMode)

Creates new algorithm for reslicing to isotropic voxels.

Parameters:

srcImg - source image model

_interpMode - interpolation mode supported by the class.

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getResultImage

public ModelImage getResultImage()

Accessor to get interpolated image.

Returns:

the interpolated image

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

calcRBSpline

private float calcRBSpline(float u)

Reslice data is Cubic Bspline where.

R(u) = 2/3 + 0.5*|u|^3 - u^2 for 0 <= |u| < 1

R(u) = 1/6 * (2 - |u|)^3 for 1 <= |u| < 2

Parameters:

u - is the position to be interpolated

Returns:

DOCUMENT ME!

calcRCUBIC

private float calcRCUBIC(float u)

Reslice using cubic convolution reslice where.

R(u) = 3/2*|u|^3 - 5/2*u^2 + 1 for 0 <= |u| < 1

R(u) = -1/2*|u|^3 + 5/2*u^2 - 4*|u| + 2 for 1 <= |u| <= 2

Parameters:

u - is the position to be interpolated

Returns:

the interpolated value

cubicReslice

private void cubicReslice()

Reslices the data into isotropic voxels using one of two interpolation methods (cubic Bspline or cubic convolution). Positions between the first and second image, and the last two images are interpolated using terminal slices in 2 of the buffers instead of only in 1 buffer because traditional usage of the interpolation function in these positions would exceed the bounds of the input data.

linearReslice

private void linearReslice()

Reslices the data into isotropic voxels using linear interpolation.