samer@0: package samer.mds;
samer@0: 
samer@0: import samer.core.*;
samer@0: import samer.core.types.*;
samer@0: import samer.maths.*;
samer@0: import samer.tools.*;
samer@0: 
samer@0: /**
samer@0: 	MDS base class. Manages a NxE matrix of object positions,
samer@0: 	an array of links (end point object indices and a distance per link),
samer@0: 	a stress value and a learning rate, and a buffer which for
samer@0: 	accumulating the "force" on each object.
samer@0: 
samer@0: 	Client code or subclass must set up link array and implement
samer@0: 	the actual adaptation algorithm.
samer@0: */
samer@0: 
samer@0: public class MDSBase extends Viewable implements Task
samer@0: {
samer@0: 	int			N, M, E;		// points, links, dimensions
samer@0: 	Matrix		P;			// object positions
samer@0: 	VDouble		S, rate;	// stress, learning rate
samer@0: 	double[]		D;			// input distances
samer@0: 	short []		l1, l2;		// arrays of link end points
samer@0: 	double [][]	F;			// object 'forces'
samer@0: 	double []	f; 		// force buffer
samer@0: 
samer@0: 	public MDSBase(Matrix p)
samer@0: 	{
samer@0: 		super("mds");
samer@0: 
samer@0: 		P=p;
samer@0: 		Shell.push(node);
samer@0: 		N = p.getRowDimension();
samer@0: 		E = p.getColumnDimension();
samer@0: 		Shell.print("MDS: "+N+" objects");
samer@0: 		Shell.print("MDS: space is "+E+" dimensional");
samer@0: 		rate = new VDouble("rate",0.001);
samer@0: 		S = new VDouble("stress");
samer@0: 		Shell.pop();
samer@0: 		F = new double[N][P.getColumnDimension()];
samer@0: 		f = new double[P.getColumnDimension()];
samer@0: 		M=0;
samer@0: 		D = new double[M];
samer@0: 	}
samer@0: 
samer@0: 	/** optimises only first E columns of P
samer@0: 		E must be less than width of original P */
samer@0: 	public void setDimensionality(int e) { E=e; }
samer@0: 
samer@0: 	/** link each object to all the others , returns distance array */
samer@0: 	public void clearLinks(double [] D) {
samer@0: 		M=D.length;
samer@0: 		Shell.print("MDS: creating "+M+" links.");
samer@0: 
samer@0: 		l1 = new short[M];
samer@0: 		l2 = new short[M];
samer@0: 		this.D = D;
samer@0: 	}
samer@0: 
samer@0: 	/** the kth link joint objects i and j */
samer@0: 	public void setLink(int k, int i, int j) { l1[k]=(short)i; l2[k]=(short)j; }
samer@0: 	public double [] getLinkArray() { return D; }
samer@0: 
samer@0: 	public void dispose() { S.dispose(); rate.dispose(); }
samer@0: 	public void starting() {}
samer@0: 	public void stopping() {}
samer@0: 	public void run() {}
samer@0: }