Handle multiple bit depths

Posted by Michael Doube on Oct 10, 2008; 4:11pm
URL: http://imagej.273.s1.nabble.com/Handle-multiple-bit-depths-tp3694774.html

Hi all

How do I handle multiple bit depths in a plugin?  I am writing a
super-simple plugin to calculate volume fraction, which is just the
ratio of thresholded pixels to all pixels in a selected volume.  I've
tried a few things, but always get caught out by declaring the pixels[]
array in an if statement like:

if (imp.getBitDepth == 8){byte[] pixels = (byte[])stack.getPixels(s)};

or by casting in a wrong way.  I've looked around for examples but
haven't come up with much.

Cheers

Mike
---------------
/*Volume fraction of Bone
  * Plugin to calculate volume fraction in stacks
  */

import java.awt.Rectangle;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.ImageProcessor;
import ij.plugin.filter.PlugInFilter;
import ij.measure.ResultsTable;
import ij.gui.*;

public class Volume_Fraction implements PlugInFilter {
        ImagePlus imp;
        protected ImageStack stack;
       
        public int setup(String arg, ImagePlus imp) {
            stack = imp.getStack();
            this.imp = imp;
            return DOES_8G + DOES_16 + DOES_32 + STACK_REQUIRED;
        }
        public void run(ImageProcessor ip) {
                ResultsTable rt = ResultsTable.getResultsTable();
                rt.reset();
                String title = imp.getTitle();
      IJ.run("Threshold...");
      new WaitForUserDialog("Set the threshold, then click OK.").show();
      short minT = (short)ip.getMinThreshold();
      short maxT = (short)ip.getMaxThreshold();
            int startSlice = 1;
            int endSlice = stack.getSize();
                int w = stack.getWidth();
         GenericDialog gd = new GenericDialog("Limit Slices");
         gd.addNumericField("Start Slice:",startSlice,0);
         gd.addNumericField("End Slice:",endSlice,0);
         gd.showDialog();
         if (gd.wasCanceled()) {
             IJ.error("PlugIn canceled!");
             return;
         }
         startSlice = (int)gd.getNextNumber();
         endSlice = (int)gd.getNextNumber();
                Rectangle r = ip.getRoi();
                int volTotal = r.height * r.width * (endSlice - startSlice + 1);
            int offset, i;
      int volBone = 0;
         for (int s=startSlice;s<=endSlice;s++) {
          double[] pixels = (double[])stack.getPixels(s);
            for (int y=r.y; y<(r.y+r.height); y++) {
                        offset = y*w;
                        for (int x=r.x; x<(r.x+r.width); x++) {
                            i = offset + x;
                            if (pixels[i] >= minT && pixels[i] <= maxT){
                            volBone++;
                            }
                        }
                    }
            }
            double p = (double) volBone / volTotal;
                rt.incrementCounter();
                rt.addLabel("Label", title);
                rt.addValue("VfB", p);
                rt.show("Results");
        }
}