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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmAutoCovariance
extends AlgorithmBase
```
let deli(x,y) = (i(x,y) - )/ where the angle brackets are used to denote a spatial average. Then the two-dimensional autocovariance function, g(e,n) is defined as g(e,n) = which for a M by P discrete data set is calculated as g(e,n) = (num/denom) - 1 where num = (1/(M - e)(P - n))sum from j = 1 to M-e sum from k = 1 to P-n for: i(j,k)*i(j+e,k+n) denom = [(1/(2(M-e)(P-n))) sum from j = 1 to M sum from k = 1 to P of i(j,k) + i(j+e,k+n)]**2 Note that while some medical literature refers to this as a autocorrelation, it is actually an autocovariance since means are subtracted. 3 articles in which this formula are used: 1.) "Two-photon image correlation spectroscopy and image cross-correlation spectroscopy" by P. W. Wiseman, J.A. Squier, M.H. Ellisman, and K.R. Wilson, Journal of Microscopy, Vol. 200. Pt. 1, October 2000, pp. 14-25. 2.) "Quantitation of Membrane Receptor Distributions by Image Correlation Spectroscopy: Concept and Application" by Nils O. Petersen, Pia L. Hoddelius, Paul W. Wiseman, Olle Seger, and Karl-Eric Magnusson, Biophysical Journal, Volume 65, September, 1993, pp. 1135-1146. 3.) "Image cross-correlation spectroscopy: A new experimental bipohysical approach to measurement of slow diffusion of fluorescent molecules" by Mamta Srivastava & Nils O. Petersen, Methods in Cell Science, Vol 18, March, 1996, pp. 47-54.
The autocovariance fits to a function of the form a0 + a1*exp(-(x**2 + y**2)/w**2) = a0 + a1*exp(a2*distSqr), where a2 < 0. The fitting is performed to determine the full width at half maximum of the autocovariance. For color images the full width at half maximum is considered to be the minimum of the red, green, and blue values.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

(package private) class AlgorithmAutoCovariance.FitCovarianceModel
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 autocovariance.
`private int`	`fwhmB`	DOCUMENT ME!
`private int`	`fwhmG`	DOCUMENT ME!
`private int`	`fwhmR`	DOCUMENT ME!

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
`AlgorithmAutoCovariance(ModelImage destImg, ModelImage srcImg)`	Constructor for black and white image in which covariance coefficients are placed in a predetermined destination image.
`AlgorithmAutoCovariance(ModelImage destImageR, ModelImage destImageG, ModelImage destImageB, ModelImage srcImg)`	Constructor for color image in which covariance 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 autocovariance coefficients and places them in the destination image for black and white images.
`private void`	`calcStoreInDest2DC()`	This function calculates the autocovariance coefficients and places them in the destination images for color images.
`private void`	`calcStoreInDest3D()`	This function calculates the autocovariance coefficients and places them in the destination image for black and white images.
`private void`	`calcStoreInDest3DC()`	This function calculates the autocovariance coefficients and places them in the destination images for color images.
`private void`	`calcStoreInDest4D()`	This function calculates the autocovariance coefficients and places them in the destination image for black and white images.
`private void`	`calcStoreInDest4DC()`	This function calculates the autocovariance coefficients and places them in the destination images for color images.
`void`	`finalize()`	Prepares this class for destruction.
`int`	`getFWHM()`	returns the full width at half maximum of the autocovariance.
`int`	`getFWHMB()`	returns the full width at half maximum of the blue autocovariance.
`int`	`getFWHMG()`	returns the full width at half maximum of the green autocovariance.
`int`	`getFWHMR()`	returns the full width at half maximum of the red autocovariance.
`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 autocovariance.
  - fwhmB
```
private int fwhmB
```
    DOCUMENT ME!
  - fwhmG
```
private int fwhmG
```
    DOCUMENT ME!
  - fwhmR
```
private int fwhmR
```
    DOCUMENT ME!
- Constructor Detail
  - AlgorithmAutoCovariance
```
public AlgorithmAutoCovariance(ModelImage destImg,
                               ModelImage srcImg)
```
    Constructor for black and white image in which covariance coefficients are placed in a predetermined destination image.
    
    Parameters:
    
    destImg - Image model where result image is stored.
    
    srcImg - Source image model.
  - AlgorithmAutoCovariance
```
public AlgorithmAutoCovariance(ModelImage destImageR,
                               ModelImage destImageG,
                               ModelImage destImageB,
                               ModelImage srcImg)
```
    Constructor for color image in which covariance 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 autocovariance.
    
    Returns:
    
    fwhm
  - getFWHMB
```
public int getFWHMB()
```
    returns the full width at half maximum of the blue autocovariance.
    
    Returns:
    
    fwhmB
  - getFWHMG
```
public int getFWHMG()
```
    returns the full width at half maximum of the green autocovariance.
    
    Returns:
    
    fwhmG
  - getFWHMR
```
public int getFWHMR()
```
    returns the full width at half maximum of the red autocovariance.
    
    Returns:
    
    fwhmR
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - calcStoreInDest2D
```
private void calcStoreInDest2D()
```
    This function calculates the autocovariance coefficients and places them in the destination image for black and white images.
  - calcStoreInDest2DC
```
private void calcStoreInDest2DC()
```
    This function calculates the autocovariance coefficients and places them in the destination images for color images.
  - calcStoreInDest3D
```
private void calcStoreInDest3D()
```
    This function calculates the autocovariance coefficients and places them in the destination image for black and white images.
  - calcStoreInDest3DC
```
private void calcStoreInDest3DC()
```
    This function calculates the autocovariance coefficients and places them in the destination images for color images.
  - calcStoreInDest4D
```
private void calcStoreInDest4D()
```
    This function calculates the autocovariance coefficients and places them in the destination image for black and white images.
  - calcStoreInDest4DC
```
private void calcStoreInDest4DC()
```
    This function calculates the autocovariance coefficients and places them in the destination images for color images.

Class AlgorithmAutoCovariance

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

fwhmB

fwhmG

fwhmR

Constructor Detail

AlgorithmAutoCovariance

AlgorithmAutoCovariance

Method Detail

finalize

getFWHM

getFWHMB

getFWHMG

getFWHMR

runAlgorithm

calcStoreInDest2D

calcStoreInDest2DC

calcStoreInDest3D

calcStoreInDest3DC

calcStoreInDest4D

calcStoreInDest4DC