Re: Handle multiple bit depths

Posted by Michael Doube on Oct 14, 2008; 7:00pm
URL: http://imagej.273.s1.nabble.com/Handle-multiple-bit-depths-tp3694774p3694775.html

Thanks everyone for your creative suggestions.  The winner was Wayne's
suggestion to use a method, getPixel(x,y), that handles multiple
bit depths so I don't have to worry about those sorts of details.

In the end, the code just iterates through all pixels in the usual way,
compares ipSlice.getPixel(x,y) to the thresholds and conditionally
increments the counter.  What could be simpler?

http://doube.org/plugins.html#volfrac

Cheers

Mike


Michael Doube wrote:

> 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");
>     }
> }