/* * Otsu Thresholding algorithm * * Copyright (c) 2003 by Christopher Mei (christopher.mei@sophia.inria.fr) *                    and Maxime Dauphin * * This plugin is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License version 2  * as published by the Free Software Foundation. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this plugin; if not, write to the Free Software * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. */import ij.*;import ij.plugin.filter.PlugInFilter;import ij.process.*;import ij.gui.*;import ij.plugin.frame.PlugInFrame;import java.awt.*;import java.util.*;import java.lang.*;/** *  This algorithm is an implementation of Otsu thresholding technique  *  based on the minimization of inter-class variance [otsu79]. * *  @Article{otsu79, *    author =       "N. Otsu", *    title =        "A threshold selection method from gray level *                    histograms", *    journal =      "{IEEE} Trans. Systems, Man and Cybernetics", *    year =         "1979", *    volume =       "9", *    pages =        "62--66", *    month =        mar, *    keywords =     "threshold selection", *    note =         "minimize inter class variance", *  } *   **/public class OtsuThresholding_ implements PlugInFilter {    private int threshold;    final static int HMIN = 0;    final static int HMAX = 256;    public int setup(String arg, ImagePlus imp) {	if (arg.equals("about"))	    {showAbout(); return DONE;}	return DOES_8G+DOES_STACKS+SUPPORTS_MASKING+NO_CHANGES;    }        public void run(ImageProcessor ip) {	boolean debug = false;	int width =  ip.getWidth();	int height = ip.getHeight();	GrayLevelClass.N = width*height;	GrayLevelClass.probabilityHistogramDone = false;	GrayLevelClass C1 = new GrayLevelClass((ByteProcessor) ip, true);	GrayLevelClass C2 = new GrayLevelClass((ByteProcessor) ip, false);	//IJ.showStatus("Iterating...");		float fullMu = C1.getOmega()*C1.getMu()+C2.getOmega()*C2.getMu();	//IJ.write("Full Omega : "+fullMu);	double sigmaMax = 0;	int threshold = 0;	/** Start  **/	for(int i=0 ; i<255 ; i++) {	    //IJ.showStatus("Iteration "+i+"/"+256+"...");	    //IJ.showProgress(i/256);	    double sigma = C1.getOmega()*(Math.pow(C1.getMu()-fullMu,2))+C2.getOmega()*(Math.pow(C2.getMu()-fullMu,2));	    	    if(sigma>sigmaMax) {		sigmaMax = sigma;		threshold = C1.getThreshold();	    }	    C1.addToEnd();	    C2.removeFromBeginning();	}		ImagePlus imp = NewImage.createByteImage ("Threshold", width, height, 1, NewImage.FILL_WHITE);	ImageProcessor nip = imp.getProcessor();	byte[] pixels = (byte[]) ((ByteProcessor) ip).getPixels();	int offset = 0;	for (int y=0; y<height; y++) {	    offset = y*width;	    for (int x=0; x<width; x++) {		if ((pixels[offset + x] & 0xff) <= threshold)		    nip.putPixel(x, y, 0);	    }        }	imp.show();	IJ.showMessage("Found threshold : "+threshold);    }        void showAbout() {	IJ.showMessage("About OtsuThresholding_...",		       "This plug-in filter calculates the OtsuThresholding of a 8-bit image.\n"		       );    }}