Example usage for org.apache.commons.math3.random HaltonSequenceGenerator skipTo

Introduction

In this page you can find the example usage for org.apache.commons.math3.random HaltonSequenceGenerator skipTo.

Prototype

public double[] skipTo(final int index) throws NotPositiveException 

Source Link

Document

Skip to the i-th point in the Halton sequence.

Usage

From source file:gdsc.smlm.model.UniformDistribution.java

/**
 * Create a new uniform distribution using a Halton sequence
 * // ww w. j  a v a  2s  . c o m
 * @param min
 *            The minimum bounds for the distribution
 * @param max
 *            The maximum bounds for the distribution
 * @param seed
 *            Start at the i-th point in the Halton sequence
 */
public UniformDistribution(double[] min, double[] max, int seed) {
    //HaltonSequenceGenerator randomVectorGenerator = new HaltonSequenceGenerator(3);
    // The Halton sequence based on the prime of 2 does not provide great variety in the
    // lesser significant digits when simulating a 512x512 pixel image. This is not suitable for
    // PSF fitting since we require variation to at least 3 decimal places.
    HaltonSequenceGenerator randomVectorGenerator = new HaltonSequenceGenerator(3, new int[] { 3, 5, 7 }, null);
    randomVectorGenerator.skipTo(Math.abs(seed));
    init(min, max, randomVectorGenerator);
}

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From source file:com.vmware.photon.controller.cloudstore.xenon.entity.SchedulingConstantGenerator.java

private void nextValue(State state) {
    if (state == null) {
        throw new RuntimeException("state == null");
    }/*w ww  .j a  v  a  2 s  .c om*/
    if (state.nextHaltonSequenceIndex == null) {
        throw new RuntimeException("state.nextHaltonSequenceIndex == null");
    }

    HaltonSequenceGenerator hsg = new HaltonSequenceGenerator(1);
    if (hsg == null) {
        throw new RuntimeException("hsg == null");
    }
    double[] nextValues = hsg.skipTo(state.nextHaltonSequenceIndex);

    state.nextHaltonSequenceIndex++;
    state.lastSchedulingConstant = (long) (nextValues[0] * HostService.MAX_SCHEDULING_CONSTANT);
}

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From source file:gdsc.smlm.ij.plugins.DensityImage.java

/**
 * Compute the Ripley's L-function for user selected radii and show it on a plot.
 * /*  ww w .  j a  va2  s  .  c  o m*/
 * @param results
 */
private void computeRipleysPlot(MemoryPeakResults results) {
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage("Compute Ripley's L(r) - r plot");
    gd.addNumericField("Min_radius", minR, 2);
    gd.addNumericField("Max_radius", maxR, 2);
    gd.addNumericField("Increment", incrementR, 2);
    gd.addCheckbox("Confidence_intervals", confidenceIntervals);

    gd.showDialog();
    if (gd.wasCanceled())
        return;
    minR = gd.getNextNumber();
    maxR = gd.getNextNumber();
    incrementR = gd.getNextNumber();
    confidenceIntervals = gd.getNextBoolean();

    if (minR > maxR || incrementR < 0 || gd.invalidNumber()) {
        IJ.error(TITLE, "Invalid radius parameters");
        return;
    }

    DensityManager dm = new DensityManager(results);
    double[][] values = calculateLScores(dm);

    // 99% confidence intervals
    final int iterations = (confidenceIntervals) ? 99 : 0;
    double[] upper = null;
    double[] lower = null;
    Rectangle bounds = results.getBounds();
    // Use a uniform distribution for the coordinates
    HaltonSequenceGenerator dist = new HaltonSequenceGenerator(2);
    dist.skipTo(new Well19937c(System.currentTimeMillis() + System.identityHashCode(this)).nextInt());
    for (int i = 0; i < iterations; i++) {
        IJ.showProgress(i, iterations);
        IJ.showStatus(String.format("L-score confidence interval %d / %d", i + 1, iterations));

        // Randomise coordinates
        float[] x = new float[results.size()];
        float[] y = new float[x.length];
        for (int j = x.length; j-- > 0;) {
            final double[] d = dist.nextVector();
            x[j] = (float) (d[0] * bounds.width);
            y[j] = (float) (d[1] * bounds.height);
        }
        double[][] values2 = calculateLScores(new DensityManager(x, y, bounds));
        if (upper == null) {
            upper = values2[1];
            lower = new double[upper.length];
            System.arraycopy(upper, 0, lower, 0, upper.length);
        } else {
            for (int m = upper.length; m-- > 0;) {
                if (upper[m] < values2[1][m])
                    upper[m] = values2[1][m];
                if (lower[m] > values2[1][m])
                    lower[m] = values2[1][m];
            }
        }
    }

    String title = results.getName() + " Ripley's (L(r) - r) / r";
    Plot2 plot = new Plot2(title, "Radius", "(L(r) - r) / r", values[0], values[1]);
    // Get the limits
    double yMin = min(0, values[1]);
    double yMax = max(0, values[1]);
    if (iterations > 0) {
        yMin = min(yMin, lower);
        yMax = max(yMax, upper);
    }
    plot.setLimits(0, values[0][values[0].length - 1], yMin, yMax);
    if (iterations > 0) {
        plot.setColor(Color.BLUE);
        plot.addPoints(values[0], upper, 1);
        plot.setColor(Color.RED);
        plot.addPoints(values[0], lower, 1);
        plot.setColor(Color.BLACK);
    }
    Utils.display(title, plot);
}

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