package org.doube.bone.geometry;
/* Volume fraction of Bone
 * Plugin to calculate volume fraction in stacks and single slices
 * (C) Michael Doube 2008
 * Imperial College London
 * GPL v3 or any earlier version.
 */

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;
	boolean showMask = true;
	
	public int setup(String arg, ImagePlus imp) {
	    stack = imp.getStack();
	    this.imp = imp;
	    return DOES_8G + DOES_16 + DOES_32;
	}
	
	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();
        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();
		ImageProcessor mask = ip.getMask();
		boolean hasMask = (mask != null);
		if (hasMask && showMask) {
			(new ImagePlus("The Mask", mask)).show();
		}
		
		int rLeft = r.x;
		int rTop = r.y;
		int rRight = rLeft + r.width;
		int rBottom = rTop + r.height;

		int volTotal = 0;
    	int volBone = 0;
        for (int s = startSlice; s <= endSlice; s++) {
        	ImageProcessor ipSlice = stack.getProcessor(s);	
    		for (int v = rTop; v < rBottom; v++){
    			for (int u = rLeft; u < rRight; u++){
    				if (!hasMask || mask.getPixel(u-rLeft, v-rTop)>0){
    					volTotal++;
    		            if (ipSlice.getPixel(u,v) >= minT && ipSlice.getPixel(u,v) <= maxT){
    		            	volBone++;
    		            }
    				}
    			}
    		}        	
	    }
	    double p = (double) volBone / volTotal; 
		rt.incrementCounter();
		rt.addLabel("Label", title);
		rt.addValue("VfB", p);
		rt.show("Results");
	}
}