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