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

Initial Mercurial check in.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/samer/mds/CorrelationTask.java	Tue Jan 17 17:50:20 2012 +0000
@@ -0,0 +1,40 @@
+package samer.mds;
+
+// import samer.core.*;
+import samer.maths.*;
+import samer.tools.*;
+
+/**
+	Transfer correlation matrix to MDS distances. Assumes 1s
+	down the main diagonal and a symmetric matrix.
+  */
+public class CorrelationTask extends AnonymousTask
+{
+	int		N;
+	double [] d;				// linear array of distances
+	double [][] _R;			// matrix of correlation coefficients
+		
+	/** link each object to all the others using distances in matrix, returns a task
+		that can be used to refresh distances from original matrix */
+	public CorrelationTask(MDSBase mds, Matrix R) {
+		N = R.getRowDimension();
+		
+		d=new double[N*(N - 1)/2];
+		_R=R.getArray();
+		
+		mds.clearLinks(d);
+		for (int k=0, i=0; i<N; i++) 
+			for (int j=0; j<i; j++) mds.setLink(k++,i,j);
+		
+		run();
+	}
+
+	public Vec getDistances() { return new Vec.ForArray(d); }
+	public void run() {
+		for (int k=0, i=0; i<N; i++) {
+			double [] Ri=_R[i];
+			for (int j=0; j<i; j++)
+				d[k++]=Math.sqrt(-Math.log(Math.abs(Ri[j])));
+		}
+	}
+}