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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmStandardDeviationThreshold
extends AlgorithmBase
```
The Standard Deviation Threshold works by first having an active VOI in which the standard deviation and other statistics are calculated. The dialog allows the user to enter the number of standard deviations and the values outside the range for the thersholding process. The theresholding can be done on the whole image or alternatively, on other VOIS that are not active that might be on the image. The destination can either be a new image or paint in existing image except if the src image is a color image.

Author:

pandyan

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 java.util.BitSet`	`bitset`	bitset for src image
`private boolean`	`inverseThreshold`	flags for destination, threshold, inverse, and color image
`private boolean`	`isColorImage`	flags for destination, threshold, inverse, and color image
`private int`	`length`	dimensions and length
`private java.util.BitSet`	`mask`	bitset of vois mask
`private float`	`maxIntensity`	max intensities for threshold
`private float`	`maxIntensityB`	max intensities for threshold
`private float`	`maxIntensityG`	max intensities for threshold
`private float`	`maxIntensityR`	max intensities for threshold
`private float`	`minIntensity`	min intensities for threshold
`private float`	`minIntensityB`	min intensities for threshold
`private float`	`minIntensityG`	min intensities for threshold
`private float`	`minIntensityR`	min intensities for threshold
`private boolean`	`newImageDestination`	flags for destination, threshold, inverse, and color image
`private int`	`numPixels`	num pixels in threshold
`private int`	`numPixelsB`	num pixels in threshold
`private int`	`numPixelsG`	num pixels in threshold
`private int`	`numPixelsR`	num pixels in threshold
`private ModelImage`	`resultImage`	src image, result image
`private ModelImage`	`srcImage`	src image, result image
`private float`	`sumIntensities`	total volume in threshold
`private float`	`sumIntensitiesB`	total volume in threshold
`private float`	`sumIntensitiesG`	total volume in threshold
`private float`	`sumIntensitiesR`	total volume in threshold
`private float`	`totalArea`	total volume in threshold
`private float`	`totalAreaB`	total volume in threshold
`private float`	`totalAreaG`	total volume in threshold
`private float`	`totalAreaR`	total volume in threshold
`private float`	`totalVolume`	total volume in threshold
`private float`	`totalVolumeB`	total volume in threshold
`private float`	`totalVolumeG`	total volume in threshold
`private float`	`totalVolumeR`	total volume in threshold
`private float`	`valuesOutside`	values outside intensities for threshold
`private float`	`valuesOutsideB`	values outside intensities for threshold
`private float`	`valuesOutsideG`	values outside intensities for threshold
`private float`	`valuesOutsideR`	values outside intensities for threshold
`private boolean`	`wholeImageThreshold`	flags for destination, threshold, inverse, and color image
`private int`	`xDim`	dimensions and length
`private float`	`xRes`	resolutions
`private int`	`yDim`	dimensions and length
`private float`	`yRes`	resolutions
`private int`	`zDim`	dimensions and length
`private float`	`zRes`	resolutions

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmStandardDeviationThreshold(ModelImage srcImage, float minIntensity, float maxIntensity, float valuesOutside, boolean newImageDestination, boolean wholeImageThreshold, boolean inverseThreshold)`	constructor for grey scale image
`AlgorithmStandardDeviationThreshold(ModelImage srcImage, float minIntensityR, float minIntensityG, float minIntensityB, float maxIntensityR, float maxIntensityG, float maxIntensityB, float valuesOutsideR, float valuesOutsideG, float valuesOutsideB, boolean newImageDestination, boolean wholeImageThreshold, boolean inverseThreshold)`	constructor for color image

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getNumPixels()`	getNumPixels
`int`	`getNumPixelsB()`	getNumPixelsB
`int`	`getNumPixelsG()`	getNumPixelsG
`int`	`getNumPixelsR()`	getNumPixelsR
`ModelImage`	`getResultImage()`	getResultImage
`float`	`getSumIntensities()`	get sum intensities
`float`	`getSumIntensitiesB()`	get sum intensities B
`float`	`getSumIntensitiesG()`	get sum intensities G
`float`	`getSumIntensitiesR()`	get sum intensities R
`float`	`getTotalArea()`	getTotalArea
`float`	`getTotalAreaB()`	getTotalAreaB
`float`	`getTotalAreaG()`	getTotalAreaG
`float`	`getTotalAreaR()`	getTotalAreaR
`float`	`getTotalVolume()`	getTotalVolume
`float`	`getTotalVolumeB()`	getTotalVolumeB
`float`	`getTotalVolumeG()`	getTotalVolumeG
`float`	`getTotalVolumeR()`	getTotalVolumeR
`void`	`runAlgorithm()`	run algorithm

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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
- maxIntensity
```
private float maxIntensity
```
  max intensities for threshold
- maxIntensityR
```
private float maxIntensityR
```
  max intensities for threshold
- maxIntensityG
```
private float maxIntensityG
```
  max intensities for threshold
- maxIntensityB
```
private float maxIntensityB
```
  max intensities for threshold
- minIntensity
```
private float minIntensity
```
  min intensities for threshold
- minIntensityR
```
private float minIntensityR
```
  min intensities for threshold
- minIntensityG
```
private float minIntensityG
```
  min intensities for threshold
- minIntensityB
```
private float minIntensityB
```
  min intensities for threshold
- srcImage
```
private ModelImage srcImage
```
  src image, result image
- resultImage
```
private ModelImage resultImage
```
  src image, result image
- valuesOutside
```
private float valuesOutside
```
  values outside intensities for threshold
- valuesOutsideR
```
private float valuesOutsideR
```
  values outside intensities for threshold
- valuesOutsideG
```
private float valuesOutsideG
```
  values outside intensities for threshold
- valuesOutsideB
```
private float valuesOutsideB
```
  values outside intensities for threshold
- xDim
```
private int xDim
```
  dimensions and length
- yDim
```
private int yDim
```
  dimensions and length
- zDim
```
private int zDim
```
  dimensions and length
- length
```
private int length
```
  dimensions and length
- numPixels
```
private int numPixels
```
  num pixels in threshold
- numPixelsR
```
private int numPixelsR
```
  num pixels in threshold
- numPixelsG
```
private int numPixelsG
```
  num pixels in threshold
- numPixelsB
```
private int numPixelsB
```
  num pixels in threshold
- totalVolume
```
private float totalVolume
```
  total volume in threshold
- totalArea
```
private float totalArea
```
  total volume in threshold
- totalVolumeR
```
private float totalVolumeR
```
  total volume in threshold
- totalVolumeG
```
private float totalVolumeG
```
  total volume in threshold
- totalVolumeB
```
private float totalVolumeB
```
  total volume in threshold
- totalAreaR
```
private float totalAreaR
```
  total volume in threshold
- totalAreaG
```
private float totalAreaG
```
  total volume in threshold
- totalAreaB
```
private float totalAreaB
```
  total volume in threshold
- sumIntensities
```
private float sumIntensities
```
  total volume in threshold
- sumIntensitiesR
```
private float sumIntensitiesR
```
  total volume in threshold
- sumIntensitiesG
```
private float sumIntensitiesG
```
  total volume in threshold
- sumIntensitiesB
```
private float sumIntensitiesB
```
  total volume in threshold
- xRes
```
private float xRes
```
  resolutions
- yRes
```
private float yRes
```
  resolutions
- zRes
```
private float zRes
```
  resolutions
- bitset
```
private java.util.BitSet bitset
```
  bitset for src image
- newImageDestination
```
private boolean newImageDestination
```
  flags for destination, threshold, inverse, and color image
- wholeImageThreshold
```
private boolean wholeImageThreshold
```
  flags for destination, threshold, inverse, and color image
- inverseThreshold
```
private boolean inverseThreshold
```
  flags for destination, threshold, inverse, and color image
- isColorImage
```
private boolean isColorImage
```
  flags for destination, threshold, inverse, and color image
- mask
```
private java.util.BitSet mask
```
  bitset of vois mask

Constructor Detail

AlgorithmStandardDeviationThreshold

public AlgorithmStandardDeviationThreshold(ModelImage srcImage,
                                           float minIntensity,
                                           float maxIntensity,
                                           float valuesOutside,
                                           boolean newImageDestination,
                                           boolean wholeImageThreshold,
                                           boolean inverseThreshold)

constructor for grey scale image

Parameters:: srcImage -; minIntensity -; maxIntensity -; valuesOutside -; newImageDestination -; wholeImageThreshold -; inverseThreshold -

AlgorithmStandardDeviationThreshold

public AlgorithmStandardDeviationThreshold(ModelImage srcImage,
                                           float minIntensityR,
                                           float minIntensityG,
                                           float minIntensityB,
                                           float maxIntensityR,
                                           float maxIntensityG,
                                           float maxIntensityB,
                                           float valuesOutsideR,
                                           float valuesOutsideG,
                                           float valuesOutsideB,
                                           boolean newImageDestination,
                                           boolean wholeImageThreshold,
                                           boolean inverseThreshold)

constructor for color image

Parameters:: srcImage -; minIntensityR -; minIntensityG -; minIntensityB -; maxIntensityR -; maxIntensityG -; maxIntensityB -; valuesOutsideR -; valuesOutsideG -; valuesOutsideB -; newImageDestination -; wholeImageThreshold -; inverseThreshold -

Method Detail
- runAlgorithm
```
public void runAlgorithm()
```
  run algorithm
  
  Specified by:
  
  runAlgorithm in class AlgorithmBase
- getResultImage
```
public ModelImage getResultImage()
```
  getResultImage
  
  Returns:
- getTotalArea
```
public float getTotalArea()
```
  getTotalArea
  
  Returns:
- getTotalVolume
```
public float getTotalVolume()
```
  getTotalVolume
  
  Returns:
- getNumPixels
```
public int getNumPixels()
```
  getNumPixels
  
  Returns:
- getNumPixelsB
```
public int getNumPixelsB()
```
  getNumPixelsB
  
  Returns:
- getNumPixelsG
```
public int getNumPixelsG()
```
  getNumPixelsG
  
  Returns:
- getNumPixelsR
```
public int getNumPixelsR()
```
  getNumPixelsR
  
  Returns:
- getTotalAreaB
```
public float getTotalAreaB()
```
  getTotalAreaB
  
  Returns:
- getTotalAreaG
```
public float getTotalAreaG()
```
  getTotalAreaG
  
  Returns:
- getTotalAreaR
```
public float getTotalAreaR()
```
  getTotalAreaR
  
  Returns:
- getTotalVolumeB
```
public float getTotalVolumeB()
```
  getTotalVolumeB
  
  Returns:
- getTotalVolumeG
```
public float getTotalVolumeG()
```
  getTotalVolumeG
  
  Returns:
- getTotalVolumeR
```
public float getTotalVolumeR()
```
  getTotalVolumeR
  
  Returns:
- getSumIntensities
```
public float getSumIntensities()
```
  get sum intensities
  
  Returns:
- getSumIntensitiesB
```
public float getSumIntensitiesB()
```
  get sum intensities B
  
  Returns:
- getSumIntensitiesG
```
public float getSumIntensitiesG()
```
  get sum intensities G
  
  Returns:
- getSumIntensitiesR
```
public float getSumIntensitiesR()
```
  get sum intensities R
  
  Returns:

Class AlgorithmStandardDeviationThreshold

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

maxIntensity

maxIntensityR

maxIntensityG

maxIntensityB

minIntensity

minIntensityR

minIntensityG

minIntensityB

srcImage

resultImage

valuesOutside

valuesOutsideR

valuesOutsideG

valuesOutsideB

xDim

yDim

zDim

length

numPixels

numPixelsR

numPixelsG

numPixelsB

totalVolume

totalArea

totalVolumeR

totalVolumeG

totalVolumeB

totalAreaR

totalAreaG

totalAreaB

sumIntensities

sumIntensitiesR

sumIntensitiesG

sumIntensitiesB

xRes

yRes

zRes

bitset

newImageDestination

wholeImageThreshold

inverseThreshold

isColorImage

mask

Constructor Detail

AlgorithmStandardDeviationThreshold

AlgorithmStandardDeviationThreshold

Method Detail

runAlgorithm

getResultImage

getTotalArea

getTotalVolume

getNumPixels

getNumPixelsB

getNumPixelsG

getNumPixelsR

getTotalAreaB

getTotalAreaG

getTotalAreaR

getTotalVolumeB

getTotalVolumeG

getTotalVolumeR

getSumIntensities

getSumIntensitiesB

getSumIntensitiesG

getSumIntensitiesR