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

All Methods Instance Methods Concrete Methods
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()
```

Class AlgorithmSeparableConvolver

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

cFactor

colorImage

curPercent

incIndex

outputBuffer

entireImage

inputBuffer

inputMask

imgExtents

kernelExtents

kernelBuffer

red

green

blue

Constructor Detail

AlgorithmSeparableConvolver

AlgorithmSeparableConvolver

Method Detail

finalize

convolve

convolveNoColor

performMT

perform

convolveX

convolveY

convolveZ

beforeExecute

execute

afterExecute

runAlgorithm

setColorChannels

setMask

getOutputBuffer