Package gov.nih.mipav.model.algorithms

Class AlgorithmAutoCovariance

java.lang.Object
java.lang.Thread
gov.nih.mipav.model.algorithms.AlgorithmBase
gov.nih.mipav.model.algorithms.AlgorithmAutoCovariance
All Implemented Interfaces:
ActionListener, WindowListener, Runnable, EventListener
public class AlgorithmAutoCovariance extends AlgorithmBase
let deli(x,y) = (i(x,y) - invalid input: '<'i(x,y)>)/invalid input: '<'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) = invalid input: '<'deli(x,y)deli(x + e, y + 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 invalid input: '&' 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 invalid input: '<' 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.

  • Field Details

    • 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 Details

    • 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 Details

    • 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.