jurls.core.becca.Daisychain.java Source code

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Here is the source code for jurls.core.becca.Daisychain.java

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/*
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package jurls.core.becca;

import org.apache.commons.math3.linear.Array2DRowRealMatrix;

/**
 * 
 * @author me
 */
public class Daisychain {
    private double[] cable, cablePre;

    /** transition probability matrix: chain(i,j) = [cable i,cable j] */
    private Array2DRowRealMatrix tp;
    private double[] chainVector;
    double updateRate = 0.5;

    public int getNumChains() {
        return cable.length * cable.length;
    }

    public double[] in(double[] cable) {
        this.cable = cable;

        double min = Double.POSITIVE_INFINITY, max = Double.NEGATIVE_INFINITY;

        if ((tp == null) || (tp.getRowDimension() != cable.length)) {
            tp = new Array2DRowRealMatrix(cable.length, cable.length);
            // TODO transfer old probability to the new instance
        }

        if (cablePre != null) {
            for (int i = 0; i < cablePre.length; i++) {
                for (int j = 0; j < cable.length; j++) {
                    double c = cablePre[i] * cable[j];

                    double prevProb = tp.getEntry(i, j);
                    if (Double.isNaN(prevProb))
                        prevProb = 0;

                    double newProb = c * (updateRate) + prevProb * (1.0 - updateRate);

                    if (newProb < min)
                        min = newProb;
                    if (newProb > max)
                        max = newProb;

                    tp.setEntry(i, j, newProb);
                }
            }
        }

        if ((cablePre == null) || (cablePre.length != cable.length))
            cablePre = new double[cable.length];

        System.arraycopy(cable, 0, cablePre, 0, cable.length);

        return ravel(tp, chainVector, 0, max);
    }

    public static double[] ravel(Array2DRowRealMatrix t, double[] x, double min, double max) {
        int size = t.getRowDimension() * t.getColumnDimension();
        if ((x == null) || (x.length != size))
            x = new double[size];

        double[][] xd = t.getDataRef();
        int p = 0;

        double factor = min != max ? (1.0 / (max - min)) : 1.0;

        for (double[] row : xd) {
            for (int i = 0; i < row.length; i++)
                row[i] = (row[i] - min) * factor;

            System.arraycopy(row, 0, x, p, row.length);
            p += row.length;
        }

        return x;
    }
}