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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmAutoCorrelation
extends AlgorithmBase
```
Reference: Digital Image Processing, Second Edition by Rafael C. Gonzalez and Richard C. Woods, Prentice-Hall, Inc., 2002, pp. 205 - 208 and pp. 414-417. The autocorrelation coefficient = A(deltaX, deltaY)/A(0,0) where A(deltaX,deltaY) = num/denom with num = sum from X = 0 to X = xDim - 1 - deltaX sum from Y = 0 to Y = yDim - 1 - deltaY f(x,y)*f(x+deltaX,y+deltaY) denom = (xDim - deltaX)*(yDim - deltaY) Autocorrelation does not subtract out the means while autocovariance does subtract out the means.
The autocorrelation coefficeints are fitted to a function of the form (1 - a0) + a0*exp(-(x**2 + y**2)/w**2) = (1 - a0) + a0*exp(a1*distSqr), where 1 >= a0 > 0, a1

Nested Class Summary

Nested Classes
Modifier and Type Class Description

(package private) class AlgorithmAutoCorrelation.FitCorrelationModel
DOCUMENT ME!
- 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 ModelImage`	`destImageB`	DOCUMENT ME!
`private ModelImage`	`destImageG`	DOCUMENT ME!
`private ModelImage`	`destImageR`	DOCUMENT ME!
`private int`	`fwhm`	Full width at half maximum of the autocorrelation.

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
`AlgorithmAutoCorrelation(ModelImage destImg, ModelImage srcImg)`	Constructor for black and white image in which correlation coefficients are placed in a predetermined destination image.
`AlgorithmAutoCorrelation(ModelImage destImageR, ModelImage destImageG, ModelImage destImageB, ModelImage srcImg)`	Constructor for color image in which correlation coefficients are placed in predetermined destination images.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcStoreInDest2D()`	This function calculates the autocorrelation coefficients and places them in the destination image for black and white images.
`private void`	`calcStoreInDest2DC()`	This function calculates the autocorrelation coefficients and places them in the destination image for color images.
`private void`	`calcStoreInDest3D()`	This function calculates the autocorrelation coefficients and places them in the destination image for black and white images.
`private void`	`calcStoreInDest3DC()`	This function calculates the autocorrelation coefficients and places them in the destination image for color images.
`private void`	`calcStoreInDest4D()`	This function calculates the autocorrelation coefficients and places them in the destination image for black and white images.
`private void`	`calcStoreInDest4DC()`	This function calculates the autocorrelation coefficients and places them in the destination image for color images.
`void`	`finalize()`	Prepares this class for destruction.
`int`	`getFWHM()`	Returns the full width at half maximum of the autocorrelation.
`void`	`runAlgorithm()`	Starts 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
  - destImageB
```
private ModelImage destImageB
```
    DOCUMENT ME!
  - destImageG
```
private ModelImage destImageG
```
    DOCUMENT ME!
  - destImageR
```
private ModelImage destImageR
```
    DOCUMENT ME!
  - fwhm
```
private int fwhm
```
    Full width at half maximum of the autocorrelation.
- Constructor Detail
  - AlgorithmAutoCorrelation
```
public AlgorithmAutoCorrelation(ModelImage destImg,
                                ModelImage srcImg)
```
    Constructor for black and white image in which correlation coefficients are placed in a predetermined destination image.
    
    Parameters:
    
    destImg - Image model where result image is stored.
    
    srcImg - Source image model.
  - AlgorithmAutoCorrelation
```
public AlgorithmAutoCorrelation(ModelImage destImageR,
                                ModelImage destImageG,
                                ModelImage destImageB,
                                ModelImage srcImg)
```
    Constructor for color image in which correlation coefficients are placed in predetermined destination images.
    
    Parameters:
    
    destImageR - Image model where red result is stored.
    
    destImageG - Image model where green result is stored.
    
    destImageB - Image model where blue result is stored.
    
    srcImg - Source image model.
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getFWHM
```
public int getFWHM()
```
    Returns the full width at half maximum of the autocorrelation.
    
    Returns:
    
    fwhm
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - calcStoreInDest2D
```
private void calcStoreInDest2D()
```
    This function calculates the autocorrelation coefficients and places them in the destination image for black and white images.
  - calcStoreInDest2DC
```
private void calcStoreInDest2DC()
```
    This function calculates the autocorrelation coefficients and places them in the destination image for color images.
  - calcStoreInDest3D
```
private void calcStoreInDest3D()
```
    This function calculates the autocorrelation coefficients and places them in the destination image for black and white images.
  - calcStoreInDest3DC
```
private void calcStoreInDest3DC()
```
    This function calculates the autocorrelation coefficients and places them in the destination image for color images.
  - calcStoreInDest4D
```
private void calcStoreInDest4D()
```
    This function calculates the autocorrelation coefficients and places them in the destination image for black and white images.
  - calcStoreInDest4DC
```
private void calcStoreInDest4DC()
```
    This function calculates the autocorrelation coefficients and places them in the destination image for color images.

Class AlgorithmAutoCorrelation

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

destImageB

destImageG

destImageR

fwhm

Constructor Detail

AlgorithmAutoCorrelation

AlgorithmAutoCorrelation

Method Detail

finalize

getFWHM

runAlgorithm

calcStoreInDest2D

calcStoreInDest2DC

calcStoreInDest3D

calcStoreInDest3DC

calcStoreInDest4D

calcStoreInDest4DC