scale-z-stack.bsh

/**
 * Compress a stack by averaging ranges of slices.  Averaging
 * minimizes error accumulation by a pyramid of equal-n sums.
 * 
 * Export is 8-bit grayscale.
 * 
 * Doesn't work for RGB or indexed color.
 * 
 * @author Stephan Saalfeld <saalfeld@mpi-cbg.de>
 */
import java.util.*;

/* number of slices to be averaged into one */
step = 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 averageRange(imp, first, length) {
	stack = imp.getStack();
	images = new HashMap();
	for (int i = first; i < first + length && i < stack.getSize(); /* i incremented inside loop */) {
  		a = imp.getType() == ImagePlus.GRAY32 ?
      			stack.getProcessor(++i).duplicate() :
      			stack.getProcessor(++i).convertToFloat();
  		int w = 1;
  		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);
	}
	ip = new FloatProcessor(imp.getWidth(), imp.getHeight());
	makeAverage(ip, images);
	switch (imp.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();
min = imp.getProcessor().getMin();
max = imp.getProcessor().getMax();
stack = imp.getStack(); 
w = imp.getWidth();
h = imp.getHeight();
stackScaled = new ImageStack(w, h);
impScaled;

for (int i = 0; i < stack.getSize(); i += step) {
	ip = averageRange(imp, i, step);
	ip.setMinAndMax(min, max);
	ip = ip.convertToByte(true);
	stackScaled.addSlice(ip);
	IJ.showProgress(i, stack.getSize());
	if (stackScaled.getSize() == 1) {
		impScaled = new ImagePlus(imp.getTitle() + "scaled", stackScaled);
		impScaled.show();
	}
	else
	{
		impScaled.setStack(stackScaled);
		impScaled.updateAndDraw();
	}
}