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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmBoundaryAttenuation
extends AlgorithmBase
```
Attenuate around the boundary of an object defined by a VOI in an image volume.

Author:

Evan McCreedy

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 float[]`	`attenuationBuffer`	The attenuated VOI mask buffer.
`private int`	`kDimXY`	The erosion kernel x and y dims.
`private int`	`kDimZ`	The erosion kernel z dimension.
`private java.util.BitSet`	`kernel`	The erosion kernel.
`private ModelImage`	`maskImage`	The mask image generated from the VOIs within the image.
`private float`	`maxAttenuation`	The maximum amount of attenuation to perform (between 0 and 1).
`private int`	`numErosions`	The number of erosions to perform (and the number of levels of attenuation to do).
`private int`	`xDim`	The image's x dimension.
`private float`	`xRes`	The image's x resolution.
`private int`	`yDim`	The image's y dimension.
`private int`	`zDim`	The image's z dimension.
`private float`	`zRes`	The image's z resolution.

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
`AlgorithmBoundaryAttenuation(ModelImage srcImg, int numErosions, float maxAttenuation)`	Set up the algorithm.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`erode(ModelImage img, int iterations)`	Erode an image and mark the pixels we erode for attenuation later.
`void`	`finalize()`	Clean up memory used by the algorithm.
`ModelImage`	`getResultImage()`	Return the attenuated image.
`private void`	`makeKernel(int kernelType)`	Generates a kernel of the indicated type.
`void`	`runAlgorithm()`	Start the algorithm.

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
  - attenuationBuffer
```
private float[] attenuationBuffer
```
    The attenuated VOI mask buffer.
  - kDimXY
```
private int kDimXY
```
    The erosion kernel x and y dims.
  - kDimZ
```
private int kDimZ
```
    The erosion kernel z dimension.
  - kernel
```
private java.util.BitSet kernel
```
    The erosion kernel.
  - maskImage
```
private ModelImage maskImage
```
    The mask image generated from the VOIs within the image.
  - maxAttenuation
```
private float maxAttenuation
```
    The maximum amount of attenuation to perform (between 0 and 1).
  - numErosions
```
private int numErosions
```
    The number of erosions to perform (and the number of levels of attenuation to do).
  - xDim
```
private int xDim
```
    The image's x dimension.
  - xRes
```
private float xRes
```
    The image's x resolution.
  - yDim
```
private int yDim
```
    The image's y dimension.
  - zDim
```
private int zDim
```
    The image's z dimension.
  - zRes
```
private float zRes
```
    The image's z resolution.
- Constructor Detail
  - AlgorithmBoundaryAttenuation
```
public AlgorithmBoundaryAttenuation(ModelImage srcImg,
                                    int numErosions,
                                    float maxAttenuation)
```
    Set up the algorithm. Extract a mask to use in the attenuation using VOIs within the image and set up the kernel.
    
    Parameters:
    
    srcImg - the image to attenuate (must have a VOI in it to define the area to attenuate)
    
    numErosions - the number of erosions to do
    
    maxAttenuation - the maximum amount to reduce the object intensity by (0,1)
- Method Detail
  - finalize
```
public void finalize()
```
    Clean up memory used by the algorithm.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getResultImage
```
public ModelImage getResultImage()
```
    Return the attenuated image.
    
    Returns:
    
    the attenuated image
  - runAlgorithm
```
public void runAlgorithm()
```
    Start the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - erode
```
private void erode(ModelImage img,
                   int iterations)
```
    Erode an image and mark the pixels we erode for attenuation later.
    
    Parameters:
    
    img - the image to erode
    
    iterations - the number of erosions to perform
  - makeKernel
```
private void makeKernel(int kernelType)
```
    Generates a kernel of the indicated type.
    
    Parameters:
    
    kernelType - type of kernel to be generated

Class AlgorithmBoundaryAttenuation

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

attenuationBuffer

kDimXY

kDimZ

kernel

maskImage

maxAttenuation

numErosions

xDim

xRes

yDim

zDim

zRes

Constructor Detail

AlgorithmBoundaryAttenuation

Method Detail

finalize

getResultImage

runAlgorithm

erode

makeKernel