thick-section-stack.bsh

import java.util.*;

n = 10;

void makeAverage( average, weightedParts) { 
  weights = new ArrayList(weightedParts.keySet()); 
  Collections.sort(weights); 
  int s = 0; 
  for (int w : weights) { 
    s += w; 
    average.multiply(1.0-(double)w/s); 
    fp = weightedParts.get(w).duplicate(); 
    fp.multiply((double)w/s);
    average.copyBits(fp,0,0,Blitter.ADD); 
  } 
}

ImageProcessor averageStack(stack) {
	HashMap images = new HashMap();
	ip = new FloatProcessor(w, h);
	for (int i = 0; i < stack.getSize();) {
		a = imp.getType() == ImagePlus.GRAY32 ?
			stack.getProcessor(++i).duplicate() :
			stack.getProcessor(++i).convertToFloat();
		int w = 1;
		FloatProcessor b = images.remove(w);
		while (b != null) {
			w *= 2;
			a.copyBits(b, 0, 0, Blitter.ADD);
			a.multiply(0.5);
			b = images.remove(w);
		}
		images.put(w, a);
	}
	makeAverage(ip, images);
	switch (IJ.getImage().getType()) {
	case ImagePlus.GRAY16:
	  ip = ip.convertToShort(false);
	  break;
	case ImagePlus.GRAY8:
	case ImagePlus.COLOR_256:
	  ip = ip.convertToByte(false);
	  break;
	case ImagePlus.COLOR_RGB:
	  ip = ip.convertToRGB();
	  break;
	}
	return ip;
}

imp = IJ.getImage();
stack = imp.getStack(); 
w = imp.getWidth();
h = imp.getHeight();

stack2 = new ImageStack(w, h);
imp2;
stack3 = new ImageStack(w, h);
for (int i = 0; i < stack.getSize();) {
	stack3.addSlice("",stack.getProcessor(++i));
	if (i % n == 0) {
		stack2.addSlice("",averageStack(stack3));
		stack3 = new ImageStack(w, h);
		if (i == n) {
			imp2 = new ImagePlus("10", stack2);
			imp2.show();
		}
		imp2.setStack(stack2);
		imp2.updateAndDraw();
	}
	IJ.showProgress(i, stack.getSize());
}