java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.filters.AlgorithmGradientMagnitudeSep

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmGradientMagnitudeSep
extends AlgorithmBase
```
Calculates the gradient magnitude of an image at a scale defined by the user (using separable convolutions). Adapted from AlgorithmGradientMagnitude. This version should be faster but uses significantly more memory.
Produces equivalent result images to AlgorithmGradientMagnitude (aside from some rounding error that seems to be at most 10^-4)

Version:

0.1 July 31, 2003

Author:

Evan McCreedy

See Also:

AlgorithmGradientMagnitude

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`	DOCUMENT ME!
`private boolean`	`directionNeeded`
`private boolean`	`doEndSlices`
`private boolean`	`entireImage`	Flag, if true, indicates that the whole image should be processed.
`private Kernel`	`gaussianKernel`
`private boolean`	`green`	DOCUMENT ME!
`private int[]`	`kExtents`
`private boolean`	`normalized`
`private float[]`	`outputBuffer`
`private boolean`	`red`	Flags indicate which color channel to process.
`private float[]`	`sigmas`	Standard deviations of the gaussian used to calculate the kernels.
`private float[]`	`xDerivativeDirections`
`private float[]`	`yDerivativeDirections`
`private int`	`zEnd`

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
`AlgorithmGradientMagnitudeSep(ModelImage srcImg, float[] sigmas, boolean maskFlag, boolean img25D)`	Creates a new AlgorithmGradientMagnitudeSep object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`afterExecute()`
`void`	`beforeExecute()`
`private float[]`	`calculateDerivativeImage(float[] imgData, int[] imgExtents, boolean color, float[][] kernelData, int progressFrom, int progressTo)`
`int`	`calculateValidEndZIndex()`
`int`	`calculateValidStartZIndex()`
`void`	`execute()`
`void`	`finalize()`	Prepares this class for destruction.
`int[]`	`getKExtents()`
`float[]`	`getResultBuffer()`
`float[]`	`getXDerivativeDirections()`
`float[]`	`getYDerivativeDirections()`
`private boolean`	`is3DKernel()`
`boolean`	`isDirectionNeeded()`
`boolean`	`isNormalized()`
`private float[]`	`magnitude(float[] buffer, int cFactor, float[] xDerivatives, float[] yDerivatives, float[] zDerivatives, int progressFrom, int progressTo)`
`void`	`runAlgorithm()`	Starts the program.
`void`	`setBlue(boolean flag)`	Sets the flag for the blue channel.
`void`	`setDirectionNeeded(boolean directionNeeded)`
`void`	`setGreen(boolean flag)`	Sets the flag for the green channel.
`void`	`setNormalized(boolean normalized)`
`void`	`setRed(boolean flag)`	Sets the flag for the red channel.

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
- blue
```
private boolean blue
```
  DOCUMENT ME!
- entireImage
```
private boolean entireImage
```
  Flag, if true, indicates that the whole image should be processed. If false only process the image over the mask areas.
- green
```
private boolean green
```
  DOCUMENT ME!
- gaussianKernel
```
private Kernel gaussianKernel
```
- red
```
private boolean red
```
  Flags indicate which color channel to process. True indicates the channel should be processed.
- sigmas
```
private float[] sigmas
```
  Standard deviations of the gaussian used to calculate the kernels.
- outputBuffer
```
private float[] outputBuffer
```
- normalized
```
private boolean normalized
```
- directionNeeded
```
private boolean directionNeeded
```
- xDerivativeDirections
```
private float[] xDerivativeDirections
```
- yDerivativeDirections
```
private float[] yDerivativeDirections
```
- zEnd
```
private int zEnd
```
- doEndSlices
```
private boolean doEndSlices
```
- kExtents
```
private int[] kExtents
```

Constructor Detail
- AlgorithmGradientMagnitudeSep
```
public AlgorithmGradientMagnitudeSep(ModelImage srcImg,
                                     float[] sigmas,
                                     boolean maskFlag,
                                     boolean img25D)
```
  Creates a new AlgorithmGradientMagnitudeSep object.
  
  Parameters:
  
  srcImg - source image model
  
  sigmas - Gaussian standard deviations in each dimension
  
  maskFlag - Flag, if true, indicates that the gradient magnitude will be calculated for the whole image
  
  img25D - Flag, if true, indicates that each slice of the 3D volume should be processed independently. 2D images disregard this flag.

Method Detail

beforeExecute
```
public void beforeExecute()
```

execute
```
public void execute()
```

afterExecute
```
public void afterExecute()
```

calculateDerivativeImage

private float[] calculateDerivativeImage(float[] imgData,
                                         int[] imgExtents,
                                         boolean color,
                                         float[][] kernelData,
                                         int progressFrom,
                                         int progressTo)

magnitude

private float[] magnitude(float[] buffer,
                          int cFactor,
                          float[] xDerivatives,
                          float[] yDerivatives,
                          float[] zDerivatives,
                          int progressFrom,
                          int progressTo)

finalize
```
public void finalize()
```
Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm
```
public void runAlgorithm()
```
Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

setBlue
```
public void setBlue(boolean flag)
```
Sets the flag for the blue channel.

Parameters:

flag - if set to true then the blue channel is processed.

setGreen
```
public void setGreen(boolean flag)
```
Sets the flag for the green channel.

Parameters:

flag - if set to true then the green channel is processed.

setRed
```
public void setRed(boolean flag)
```
Sets the flag for the red channel.

Parameters:

flag - if set to true then the red channel is processed.

getResultBuffer
```
public float[] getResultBuffer()
```

getXDerivativeDirections

public float[] getXDerivativeDirections()

getYDerivativeDirections

public float[] getYDerivativeDirections()

isNormalized
```
public boolean isNormalized()
```

setNormalized

public void setNormalized(boolean normalized)

isDirectionNeeded
```
public boolean isDirectionNeeded()
```

setDirectionNeeded

public void setDirectionNeeded(boolean directionNeeded)

is3DKernel
```
private boolean is3DKernel()
```

calculateValidStartZIndex

public int calculateValidStartZIndex()

calculateValidEndZIndex
```
public int calculateValidEndZIndex()
```

getKExtents
```
public int[] getKExtents()
```

Class AlgorithmGradientMagnitudeSep

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

blue

entireImage

green

gaussianKernel

red

sigmas

outputBuffer

normalized

directionNeeded

xDerivativeDirections

yDerivativeDirections

zEnd

doEndSlices

kExtents

Constructor Detail

AlgorithmGradientMagnitudeSep

Method Detail

beforeExecute

execute

afterExecute

calculateDerivativeImage

magnitude

finalize

runAlgorithm

setBlue

setGreen

setRed

getResultBuffer

getXDerivativeDirections

getYDerivativeDirections

isNormalized

setNormalized

isDirectionNeeded

setDirectionNeeded

is3DKernel

calculateValidStartZIndex

calculateValidEndZIndex

getKExtents