OrientationKMeans.java
48ddf8ee5334master

OrientationKMeans.java
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			//==============================================================================
			//
			// Project: Directional Image Analysis - OrientationJ plugin
			//
			// Author: Daniel Sage
			//
			// Organization: Biomedical Imaging Group (BIG)
			// Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
			//
			// Information:
			// OrientationJ: http://bigwww.epfl.ch/demo/orientation/
			// MonogenicJ: http://bigwww.epfl.ch/demo/monogenic/
			//
			//
			// Reference on methods and plugin
			// Z. Püspöki, M. Storath, D. Sage, M. Unser
			// "Transforms and Operators for Directional Bioimage Analysis: A Survey,"
			// Advances in Anatomy, Embryology and Cell Biology, vol. 219, Focus on Bio-Image Informatics,
			// Springer International Publishing, ch. 3, pp. 69-93, May 21, 2016.
			//
			// Reference on applications
			// E. Fonck, G.G. Feigl, J. Fasel, D. Sage, M. Unser, D.A. Ruefenacht, N. Stergiopulos
			// "Effect of Aging on Elastin Functionality in Human Cerebral Arteries,"
			// Stroke, vol. 40, no. 7, pp. 2552-2556, July 2009.
			//
			// R. Rezakhaniha, A. Agianniotis, J.T.C. Schrauwen, A. Griffa, D. Sage, C.V.C. Bouten, F.N. van de Vosse, M. Unser, N. Stergiopulos
			// "Experimental Investigation of Collagen Waviness and Orientation in the Arterial Adventitia Using Confocal Laser Scanning Microscopy,"
			// Biomechanics and Modeling in Mechanobiology, vol. 11, no. 3-4, pp. 461-473, 2012.

			// Conditions of use: You'll be free to use this software for research purposes,
			// but you should not redistribute it without our consent. In addition, we
			// expect you to include a citation or acknowledgment whenever you present or
			// publish results that are based on it.
			//
			// History:
			// - Updated (Daniel Sage, 24 January 2011)
			// - Added the Vector field (Daniel Sage, 1 March 2017)
			//
			//==============================================================================

			package orientation;

			import ij.IJ;
			import imageware.Builder;
			import imageware.ImageWare;

			public class OrientationKMeans {
			private boolean valueChanged;
			private int[] regions;

			private double[] osin;
			private double[] ocos;
			private double[] classSin;
			private double[] classCos;

			public ImageWare run(ImageWare orientation, int nbClasses, int maxIterations) {
			int ny = orientation.getHeight();
			int nx = orientation.getWidth();
			int size = nx*ny;
			float angles[] = orientation.getSliceFloat(0);
			osin = new double[size];
			ocos = new double[size];
			for(int i=0; i<size; i++) {
			osin[i] = Math.sin(angles[i]);
			ocos[i] = Math.cos(angles[i]);
			}

			float classAngle[] = new float[nbClasses];
			classSin = new double[nbClasses];
			classCos = new double[nbClasses];
			double max = orientation.getMaximum();
			double min = orientation.getMinimum();

			for(int i = 0; i < nbClasses; i++) {
			classAngle[i] =(float)( i*(max-min)/nbClasses + min);
			classSin[i] = Math.sin(classAngle[i]);
			classCos[i] = Math.cos(classAngle[i]);
			IJ.log(" class:" + i + " " + classAngle[i]);
			}

			regions = new int[size];
			int iterations = 0;
			do {
			iterate();
			update(classAngle);
			iterations++;
			} while(valueChanged && iterations < maxIterations);

			ImageWare out = Builder.create(nx, ny, 1, ImageWare.FLOAT);
			float[] pixout = out.getSliceFloat(0);
			for(int i=0; i<size; i++) {
			pixout[i] = classAngle[regions[i]];
			}

			IJ.log("iterations: "+iterations);
			for(int k=0; k<nbClasses; k++) {
			IJ.log(" class:" + k + " " + classAngle[k]);
			}
			return out;
			}

			private void iterate(){
			int size = osin.length;
			int nbClasses = classSin.length;
			valueChanged = false;
			double current, distance;
			for(int i=0; i<size; i++) {
			current = cost(i, regions[i]);
			for(int k=0; k<nbClasses; k++) {
			distance = cost(i, k);
			if((distance > current)) {
			current = distance;
			regions[i] = k;
			valueChanged = true;
			}
			}
			}
			}

			private double cost(int p, int m) {
			return Math.abs(ocos[p] * classCos[m] + osin[p]*classSin[m]);
			}

			private void update(float classAngle[]) {
			int nbClasses = classAngle.length;
			for(int k=0; k<nbClasses; k++) {
			double dx = 0.0;
			double dy = 0.0;
			for(int j=0; j<regions.length; j++) {
			if(regions[j] == k) {
			dx += ocos[j];
			dy += osin[j];
			}
			}
			double angle = Math.atan2(dy, dx);
			if (angle > Math.PI/2)
			angle -= Math.PI/2;
			if (angle < -Math.PI/2)
			angle += Math.PI/2;
			classAngle[k] = (float)angle;
			classSin[k] = Math.sin(angle);
			classCos[k] = Math.cos(angle);
			}
			}
			}

OrientationJ/src/orientation/OrientationKMeans.java48ddf8ee5334master

OrientationKMeans.javaView Options

OrientationJ/src/orientation/OrientationKMeans.java
48ddf8ee5334master

OrientationKMeans.java
View Options