====== Auto Correlation ======

**A macro to determine image focal quality image-wide (not ROI-wide)**

<code java>

// A macro to determine image focal quality image-wide (not ROI-wide)
// Based on algorithm F-12 "AutoCorrelation"
// In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149.
// 
// Version: 0.1
// Date: 14/07/2006
// Author: Andy Weller

macro "Auto_Correlation" {
W = getWidth();
H = getHeight();
b = 0;
c = 0;
autoCorr = 0; // Set to 0 which is out of focus
for (j=0; j<H; j++) {
   for (i=0; i<W; i++) {
      p = getPixel(i,j);
      p1 = getPixel(i+1,j);
      p2 = getPixel(i+2,j);
      s = p*p1;
      t = p*p2;
      b += s;
      c += t;
      }
   }
autoCorr = b-c; // Maximum value is best-focused, decreasing as defocus increases
print(autoCorr); // This can also (should) be changed to return(autoCorr)
}

</code>

by Andy Weller — last modified 2006-07-14 20:44