Examples with Distribution cbit.vcell.math.Distribution used on opensource projects

Example 1 with Distribution

use of cbit.vcell.math.Distribution in project vcell by virtualcell.

the class FiniteVolumeFileWriter method generateRandomNumbers.

private double[] generateRandomNumbers(RandomVariable rv, int numRandomNumbers) throws ExpressionException {
    VariableDomain variableDomain = (rv instanceof VolumeRandomVariable) ? VariableDomain.VARIABLEDOMAIN_VOLUME : VariableDomain.VARIABLEDOMAIN_MEMBRANE;
    Expression seedExpr = subsituteExpression(rv.getSeed(), variableDomain);
    if (!seedExpr.isNumeric()) {
        throw new ExpressionException("Seed for RandomVariable '" + rv.getName() + " is not Constant!");
    }
    int seed = (int) rv.getSeed().evaluateConstant();
    Distribution distribution = rv.getDistribution();
    double[] randomNumbers = new double[numRandomNumbers];
    Random random = new Random(seed);
    if (distribution instanceof UniformDistribution) {
        UniformDistribution ud = (UniformDistribution) distribution;
        Expression minFlattened = subsituteExpression(ud.getMinimum(), variableDomain);
        Expression maxFlattened = subsituteExpression(ud.getMaximum(), variableDomain);
        if (!minFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', minimum for UniformDistribution is not Constant!");
        }
        if (!maxFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', maximum for UniformDistribution is not Constant!");
        }
        double minVal = minFlattened.evaluateConstant();
        double maxVal = maxFlattened.evaluateConstant();
        for (int i = 0; i < numRandomNumbers; i++) {
            double r = random.nextDouble();
            randomNumbers[i] = (maxVal - minVal) * r + minVal;
        }
    } else if (distribution instanceof GaussianDistribution) {
        GaussianDistribution gd = (GaussianDistribution) distribution;
        Expression meanFlattened = subsituteExpression(gd.getMean(), variableDomain);
        Expression sdFlattened = subsituteExpression(gd.getStandardDeviation(), variableDomain);
        if (!meanFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', mean for GaussianDistribution is not Constant!");
        }
        if (!sdFlattened.isNumeric()) {
            throw new ExpressionException("For RandomVariable '" + rv.getName() + "', standard deviation for GaussianDistribution is not Constant!");
        }
        double muVal = meanFlattened.evaluateConstant();
        double sigmaVal = sdFlattened.evaluateConstant();
        for (int i = 0; i < numRandomNumbers; i++) {
            double r = random.nextGaussian();
            randomNumbers[i] = sigmaVal * r + muVal;
        }
    }
    return randomNumbers;
}

Example 2 with Distribution

use of cbit.vcell.math.Distribution in project vcell by virtualcell.

the class XmlReader method getRandomVariable.

private RandomVariable getRandomVariable(Element param) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Element element = param.getChild(XMLTags.RandomVariableSeedTag, vcNamespace);
    Expression seed = null;
    if (element != null) {
        seed = unMangleExpression(element.getText());
    }
    Distribution dist = null;
    element = param.getChild(XMLTags.UniformDistributionTag, vcNamespace);
    if (element != null) {
        dist = getUniformDistribution(element);
    }
    element = param.getChild(XMLTags.GaussianDistributionTag, vcNamespace);
    if (element != null) {
        dist = getGaussianDistribution(element);
    }
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    RandomVariable var = null;
    if (param.getName().equals(XMLTags.VolumeRandomVariableTag)) {
        var = new VolumeRandomVariable(name, seed, dist, domain);
    } else if (param.getName().equals(XMLTags.MembraneRandomVariableTag)) {
        var = new MembraneRandomVariable(name, seed, dist, domain);
    } else {
        throw new XmlParseException(param.getName() + " is not supported!");
    }
    transcribeComments(param, var);
    return var;
}