Re: Handle multiple bit depths

Posted by Reinhard Mayr aka Czerwinski on Oct 10, 2008; 4:20pm
URL: http://imagej.273.s1.nabble.com/Handle-multiple-bit-depths-tp3694774p3694778.html

Hi Mike,

I once did some extentions to the AVI Reader plugin, and I remember that  
in that case there are also different depths are handled. Maybe you find a  
hint for your problem in the source. see  
http://rsbweb.nih.gov/ij/plugins/avi-reader.html

hth,

Reinhard.

On Fri, 10 Oct 2008 18:11:35 +0200, Michael Doube <[hidden email]>  
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");
> }
> }

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