annotate src/samer/mds/MDSBase.java @ 8:5e3cbbf173aa tip

Reorganise some more

package samer.mds;

import samer.core.*;
import samer.core.types.*;
import samer.maths.*;
import samer.tools.*;

/**
	MDS base class. Manages a NxE matrix of object positions,
	an array of links (end point object indices and a distance per link),
	a stress value and a learning rate, and a buffer which for
	accumulating the "force" on each object.

	Client code or subclass must set up link array and implement
	the actual adaptation algorithm.
*/

public class MDSBase extends Viewable implements Task
{
	int			N, M, E;		// points, links, dimensions
	Matrix		P;			// object positions
	VDouble		S, rate;	// stress, learning rate
	double[]		D;			// input distances
	short []		l1, l2;		// arrays of link end points
	double [][]	F;			// object 'forces'
	double []	f; 		// force buffer

	public MDSBase(Matrix p)
	{
		super("mds");

		P=p;
		Shell.push(node);
		N = p.getRowDimension();
		E = p.getColumnDimension();
		Shell.print("MDS: "+N+" objects");
		Shell.print("MDS: space is "+E+" dimensional");
		rate = new VDouble("rate",0.001);
		S = new VDouble("stress");
		Shell.pop();
		F = new double[N][P.getColumnDimension()];
		f = new double[P.getColumnDimension()];
		M=0;
		D = new double[M];
	}

	/** optimises only first E columns of P
		E must be less than width of original P */
	public void setDimensionality(int e) { E=e; }

	/** link each object to all the others , returns distance array */
	public void clearLinks(double [] D) {
		M=D.length;
		Shell.print("MDS: creating "+M+" links.");

		l1 = new short[M];
		l2 = new short[M];
		this.D = D;
	}

	/** the kth link joint objects i and j */
	public void setLink(int k, int i, int j) { l1[k]=(short)i; l2[k]=(short)j; }
	public double [] getLinkArray() { return D; }

	public void dispose() { S.dispose(); rate.dispose(); }
	public void starting() {}
	public void stopping() {}
	public void run() {}
}