diff src/samer/mds/MDS.java @ 0:bf79fb79ee13

Initial Mercurial check in.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/samer/mds/MDS.java	Tue Jan 17 17:50:20 2012 +0000
@@ -0,0 +1,90 @@
+package samer.mds;
+
+import samer.core.*;
+import samer.core.types.*;
+import samer.maths.*;
+import samer.tools.*;
+
+/**
+     This is an alternative version of MDS that uses less memory.
+     Rather than keep a record of the force in each link, it accumulates
+     the link forces on a per-object basis.
+ */
+public class MDS extends MDSBase
+{
+	Metric		metric;		// metric function
+	Stress		stress;		// stress function
+
+	public interface Metric {
+		/** return distance between x and y, put y-x in r */
+		double d(double [] x, double [] y, double [] r);
+	}
+
+	public interface Stress {
+		/** accumulate stress due to a link and return dStress/dcurrent */
+		double add( double target, double current);
+
+		/** return normalised stress and reset for next time */
+		double done();
+
+		/** return last value returned by done() */
+		double get();
+	}
+
+	public static class SamerStress implements Stress {
+		double S=0, a=0;
+		int			n=0;
+
+		public double add( double target, double current) {
+			a += sqr(current/target-1); n++;
+			return (current-target)/(target*target);
+		}
+		public double done() { S=a/n; a=0; n=0; return S; }
+		public double get() { return S; }
+		private final static double sqr(double t) {return t*t;}
+	}
+
+	public MDS(Matrix p)
+	{
+		super(p);
+
+		Shell.push(node);
+		metric=new Euclidean();
+		stress=new SamerStress();
+		Shell.pop();
+	}
+
+	public void setMetric(Metric m) { metric=m; }
+
+	public void run()
+	{
+		double [][] _P=P.getArray();
+		double	d, dS;
+		int 		i, j, k;
+
+		// accumulate all forces on a per object basis
+
+		for (k=0; k<N; k++) Mathx.zero(F[k]); // zero out object forces
+		for (k=0; k<M; k++) {			// for each link
+			i=l1[k]; j=l2[k]; 				// object indices
+			d=metric.d(_P[i],_P[j],f); 		// current distance, vector from i to j in f
+			dS=stress.add(D[k],d);
+
+			if (d>0) { // ignore if current distance is zero
+				// replace f with dS/dd * grad d
+				Mathx.mul(f,dS/d);
+
+				// f contains 'force' on j from i
+				// accumulate this force for both objects (only E dimensions used)
+				Mathx.add(E,F[i],f);
+				Mathx.sub(E,F[j],f);
+			}
+		}
+		S.set(stress.done());
+
+		// now move objects at the ends of each link,
+		// but only the first E dimensions
+		for (k=0; k<N; k++) Mathx.muladd(E,_P[k],F[k],rate.value);
+		P.changed();
+	}
+}