Package gov.nih.mipav.model.algorithms

Class AlgorithmSeparableConvolver

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmSeparableConvolver

All Implemented Interfaces:

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

public class AlgorithmSeparableConvolver
extends AlgorithmBase

Convolves an image with a separable (symmetric) kernel and returns the result. The Gaussian and its derivatives are separable.

Faster than the regualar convolver -- reg 2D: n^d*m^d, sep 2D: d*n^d*m ; d = img dimension, n = img size, m = kern size -- but requires more memory -- ~2 times more for 2D, ~3 times for 3D (plus significant extra memory required for algorithms which use this class (2 or 3 times more, depending on the dimension)).

Also note that this convolver has a different interface which must be used than the static point convolution functions which most algorithms use from the AlgorithmConvolver.

Color and voi mask code not tested (although the voi code is pretty straight-forward).

Author:

Evan McCreedy

See Also:

AlgorithmConvolver

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 boolean	blue	Flags to indicate which color channels to process.
private int	cFactor	Buffer size adjustment for color images.
private boolean	colorImage	Flag to indicate if the source image is color.
(package private) int	curPercent
private boolean	entireImage	Whether to convolve the whole image or just pixels inside a mask.
private boolean	green	Flags to indicate which color channels to process.
private int[]	imgExtents	The dimensions of the both source and destination images.
(package private) int	incIndex
private double[]	inputBuffer	Holds the original image data.
private boolean[]	inputMask	Holds the original image mask data.
private float[][]	kernelBuffer
private int[]	kernelExtents	The dimensions of the kernel.
private double[]	outputBuffer	Holds the result image data.
private boolean	red	Flags to indicate which color channels to process.

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
AlgorithmSeparableConvolver(float[] srcBuffer, int[] iExtents, float[][] kernBuffer, boolean colorImage)	Sets destination, source, and kernel buffers.
AlgorithmSeparableConvolver(float[] srcBuffer, int[] iExtents, float[] kernBuffers, int[] kExtents, boolean colorImage)

Method Summary

Modifier and Type	Method	Description
void	afterExecute()
void	beforeExecute()
private void	convolve(double[] imageBuffer, float[] kernelBuffer, double[] resultBuffer)	Perform one-dimension convolution.
private void	convolveNoColor(double[] imageBuffer, float[] kernelBuffer, double[] resultBuffer, boolean[] maskBuffer)	Perform one-dimension convolution.
private void	convolveX(int from, int to)
private void	convolveY(int from, int to)
private void	convolveZ(int from, int to)
void	execute()
void	finalize()	Prepares this class for destruction.
float[]	getOutputBuffer()
void	perform()	Begins the excution of the 3D convolver.
void	performMT()
void	runAlgorithm()	Starts the convolution of the source image with the provided kernel.
void	setColorChannels(boolean _red, boolean _green, boolean _blue)	Sets what color channels to convolve and tells the convolver that it is working on a color image.
void	setMask(java.util.BitSet newMask)	Sets the mask to convolve within.

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, 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

cFactor

private int cFactor

Buffer size adjustment for color images.

colorImage

private boolean colorImage

Flag to indicate if the source image is color.

curPercent

int curPercent

incIndex

int incIndex

outputBuffer

private double[] outputBuffer

Holds the result image data.

entireImage

private boolean entireImage

Whether to convolve the whole image or just pixels inside a mask.

inputBuffer

private double[] inputBuffer

Holds the original image data.

inputMask

private boolean[] inputMask

Holds the original image mask data.

imgExtents

private int[] imgExtents

The dimensions of the both source and destination images.

kernelExtents

private int[] kernelExtents

The dimensions of the kernel.

kernelBuffer

private float[][] kernelBuffer

red

private boolean red

Flags to indicate which color channels to process.

green

private boolean green

Flags to indicate which color channels to process.

blue

private boolean blue

Flags to indicate which color channels to process.

Constructor Detail

AlgorithmSeparableConvolver

public AlgorithmSeparableConvolver(float[] srcBuffer,
                                   int[] iExtents,
                                   float[][] kernBuffer,
                                   boolean colorImage)

Sets destination, source, and kernel buffers. Call run() to convolve image.

Parameters:

srcBuffer - source image data buffer

iExtents - source and destination image dimensions

kernBuffer - kernel image data buffer (kernel must be symmetric)

kExtents - kernel dimensions

color - whether the image is color

minProgressValue - the minimum progress value.

maxProgressValue - the maximum progress value.

AlgorithmSeparableConvolver

public AlgorithmSeparableConvolver(float[] srcBuffer,
                                   int[] iExtents,
                                   float[] kernBuffers,
                                   int[] kExtents,
                                   boolean colorImage)

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

convolve

private void convolve(double[] imageBuffer,
                      float[] kernelBuffer,
                      double[] resultBuffer)

Perform one-dimension convolution.

Parameters:

imageBuffer -

kernelBuffer -

resultBuffer -

convolveNoColor

private void convolveNoColor(double[] imageBuffer,
                             float[] kernelBuffer,
                             double[] resultBuffer,
                             boolean[] maskBuffer)

Perform one-dimension convolution.

Parameters:

imageBuffer -

kernelBuffer -

resultBuffer -

performMT

public void performMT()

perform

public void perform()

Begins the excution of the 3D convolver.

convolveX

private void convolveX(int from,
                       int to)

convolveY

private void convolveY(int from,
                       int to)

convolveZ

private void convolveZ(int from,
                       int to)

beforeExecute

public void beforeExecute()

execute

public void execute()

afterExecute

public void afterExecute()

runAlgorithm

public void runAlgorithm()

Starts the convolution of the source image with the provided kernel.

Specified by:

runAlgorithm in class AlgorithmBase

setColorChannels

public void setColorChannels(boolean _red,
                             boolean _green,
                             boolean _blue)

Sets what color channels to convolve and tells the convolver that it is working on a color image.

Parameters:

_red - process the red channel

_green - process the green channel

_blue - process the blue channel

setMask

public void setMask(java.util.BitSet newMask)

Sets the mask to convolve within.

Overrides:

setMask in class AlgorithmBase

Parameters:

newMask - mask to convolve within

getOutputBuffer

public float[] getOutputBuffer()