Examples with Variance org.apache.commons.math3.stat.descriptive.moment.Variance used on opensource projects

Example 61 with Variance

use of org.apache.commons.math3.stat.descriptive.moment.Variance in project vcell by virtualcell.

the class BrownianDynamics2DSolver method bleachGuassian0.

private long bleachGuassian0(double muX, double muY, double psfVar, double bleachFactor_K, double deltaT) {
    // 
    // distribute each particle using a normalized Gaussian point spread function with variance psfVar.
    // we add the fluorescence to the image (can be called multiple times to accumulate fluorescence).
    // 
    long bleachCount = 0;
    double DISTANCE_6_SIGMA = Math.sqrt(psfVar) * 6;
    for (int p = 0; p < numParticles; p++) {
        if (bFluorescent[p]) {
            double pX = particleX[p] - muX;
            double pY = particleY[p] - muY;
            double radius2 = pX * pX + pY * pY;
            if (radius2 < DISTANCE_6_SIGMA) {
                double particleFluorRate = bleachFactor_K * deltaT * FastMath.exp(-radius2 / psfVar);
                PoissonDistribution poisson = new PoissonDistribution(simulationRng, particleFluorRate, PoissonDistribution.DEFAULT_EPSILON, PoissonDistribution.DEFAULT_MAX_ITERATIONS);
                if (poisson.sample() >= 1) {
                    // if bleaching event happened
                    bFluorescent[p] = false;
                    bleachCount++;
                }
            }
        }
    }
    return bleachCount;
}

Example 62 with Variance

use of org.apache.commons.math3.stat.descriptive.moment.Variance in project metron by apache.

the class StellarStatisticsFunctionsTest method run.

/**
 * Runs a Stellar expression.
 * @param expr The expression to run.
 * @param variables The variables available to the expression.
 */
private static Object run(String expr, Map<String, Object> variables) {
    StellarProcessor processor = new StellarProcessor();
    Object ret = processor.parse(expr, new DefaultVariableResolver(x -> variables.get(x), x -> variables.containsKey(x)), StellarFunctions.FUNCTION_RESOLVER(), Context.EMPTY_CONTEXT());
    byte[] raw = SerDeUtils.toBytes(ret);
    Object actual = SerDeUtils.fromBytes(raw, Object.class);
    if (ret instanceof StatisticsProvider) {
        StatisticsProvider left = (StatisticsProvider) ret;
        StatisticsProvider right = (StatisticsProvider) actual;
        // N
        tolerantAssertEquals(prov -> prov.getCount(), left, right);
        // sum
        tolerantAssertEquals(prov -> prov.getSum(), left, right, 1e-3);
        // sum of squares
        tolerantAssertEquals(prov -> prov.getSumSquares(), left, right, 1e-3);
        // sum of squares
        tolerantAssertEquals(prov -> prov.getSumLogs(), left, right, 1e-3);
        // Mean
        tolerantAssertEquals(prov -> prov.getMean(), left, right, 1e-3);
        // Quadratic Mean
        tolerantAssertEquals(prov -> prov.getQuadraticMean(), left, right, 1e-3);
        // SD
        tolerantAssertEquals(prov -> prov.getStandardDeviation(), left, right, 1e-3);
        // Variance
        tolerantAssertEquals(prov -> prov.getVariance(), left, right, 1e-3);
        // Min
        tolerantAssertEquals(prov -> prov.getMin(), left, right, 1e-3);
        // Max
        tolerantAssertEquals(prov -> prov.getMax(), left, right, 1e-3);
        // Kurtosis
        tolerantAssertEquals(prov -> prov.getKurtosis(), left, right, 1e-3);
        // Skewness
        tolerantAssertEquals(prov -> prov.getSkewness(), left, right, 1e-3);
        for (double d = 10.0; d < 100.0; d += 10) {
            final double pctile = d;
            // This is a sketch, so we're a bit more forgiving here in our choice of \epsilon.
            tolerantAssertEquals(prov -> prov.getPercentile(pctile), left, right, 1e-2);
        }
    }
    return ret;
}