Examples with RandomGenerator org.apache.commons.math3.random.RandomGenerator used on opensource projects

Example 66 with RandomGenerator

use of org.apache.commons.math3.random.RandomGenerator in project GDSC-SMLM by aherbert.

the class JumpDistanceAnalysis method createCMAESOptimizer.

private CMAESOptimizer createCMAESOptimizer() {
    double rel = 1e-8;
    double abs = 1e-10;
    int maxIterations = 2000;
    //Double.NEGATIVE_INFINITY;
    double stopFitness = 0;
    boolean isActiveCMA = true;
    int diagonalOnly = 20;
    int checkFeasableCount = 1;
    RandomGenerator random = new Well19937c();
    boolean generateStatistics = false;
    ConvergenceChecker<PointValuePair> checker = new SimpleValueChecker(rel, abs);
    // Iterate this for stability in the initial guess
    return new CMAESOptimizer(maxIterations, stopFitness, isActiveCMA, diagonalOnly, checkFeasableCount, random, generateStatistics, checker);
}

Example 67 with RandomGenerator

use of org.apache.commons.math3.random.RandomGenerator in project GDSC-SMLM by aherbert.

the class FilterTest method canCompareMultiFilter.

@Test
public void canCompareMultiFilter() {
    RandomGenerator randomGenerator = new Well19937c(System.currentTimeMillis() + System.identityHashCode(this));
    MultiFilter f = new MultiFilter(0, 0, 0, 0, 0, 0, 0);
    for (int i = 1000; i-- > 0; ) {
        MultiFilter f1 = (MultiFilter) f.create(random(f.getNumberOfParameters(), randomGenerator));
        MultiFilter f2 = (MultiFilter) f.create(random(f.getNumberOfParameters(), randomGenerator));
        int e = f1.weakest((Filter) f2);
        int o = f1.weakest(f2);
        Assert.assertEquals(e, o);
    }
}

Example 68 with RandomGenerator

use of org.apache.commons.math3.random.RandomGenerator in project gatk by broadinstitute.

the class AlleleFractionSegmenterUnitTest method testChromosomesOnDifferentSegments.

@Test
public void testChromosomesOnDifferentSegments() {
    final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(563));
    final double[] trueMinorAlleleFractions = new double[] { 0.12, 0.32, 0.5 };
    final double trueMemoryLength = 1e5;
    final AlleleFractionGlobalParameters trueParams = new AlleleFractionGlobalParameters(1.0, 0.01, 0.01);
    // randomly set positions
    final int chainLength = 100;
    final List<SimpleInterval> positions = CopyRatioSegmenterUnitTest.randomPositions("chr1", chainLength, rng, trueMemoryLength / 4);
    positions.addAll(CopyRatioSegmenterUnitTest.randomPositions("chr2", chainLength, rng, trueMemoryLength / 4));
    positions.addAll(CopyRatioSegmenterUnitTest.randomPositions("chr3", chainLength, rng, trueMemoryLength / 4));
    //fix everything to the same state 2
    final int trueState = 2;
    final List<Double> minorAlleleFractionSequence = Collections.nCopies(positions.size(), trueMinorAlleleFractions[trueState]);
    final AllelicCountCollection counts = generateCounts(minorAlleleFractionSequence, positions, rng, trueParams);
    final AlleleFractionSegmenter segmenter = new AlleleFractionSegmenter(10, counts, AllelicPanelOfNormals.EMPTY_PON);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    //check that each chromosome has at least one segment
    final int numDifferentContigsInSegments = (int) segments.stream().map(ModeledSegment::getContig).distinct().count();
    Assert.assertEquals(numDifferentContigsInSegments, 3);
}

Example 69 with RandomGenerator

use of org.apache.commons.math3.random.RandomGenerator in project gatk by broadinstitute.

the class AlleleFractionSegmenterUnitTest method testSegmentation.

@Test
public void testSegmentation() {
    final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(563));
    final List<Double> trueWeights = Arrays.asList(0.2, 0.5, 0.3);
    final List<Double> trueMinorAlleleFractions = Arrays.asList(0.12, 0.32, 0.5);
    final double trueMemoryLength = 1e5;
    final AlleleFractionGlobalParameters trueParams = new AlleleFractionGlobalParameters(1.0, 0.01, 0.01);
    final AlleleFractionHMM trueModel = new AlleleFractionHMM(trueMinorAlleleFractions, trueWeights, trueMemoryLength, AllelicPanelOfNormals.EMPTY_PON, trueParams);
    // randomly set positions
    final int chainLength = 10000;
    final List<SimpleInterval> positions = CopyRatioSegmenterUnitTest.randomPositions("chr1", chainLength, rng, trueMemoryLength / 4);
    final List<Integer> trueStates = trueModel.generateHiddenStateChain(positions);
    final List<Double> truthMinorFractions = trueStates.stream().map(trueModel::getMinorAlleleFraction).collect(Collectors.toList());
    final AllelicCountCollection counts = generateCounts(truthMinorFractions, positions, rng, trueParams);
    final AlleleFractionSegmenter segmenter = new AlleleFractionSegmenter(10, counts, AllelicPanelOfNormals.EMPTY_PON);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    final double[] segmentMinorFractions = segments.stream().flatMap(s -> Collections.nCopies((int) s.getTargetCount(), s.getSegmentMean()).stream()).mapToDouble(x -> x).toArray();
    final double averageMinorFractionError = IntStream.range(0, truthMinorFractions.size()).mapToDouble(n -> Math.abs(segmentMinorFractions[n] - truthMinorFractions.get(n))).average().getAsDouble();
    Assert.assertEquals(averageMinorFractionError, 0, 0.01);
}

Example 70 with RandomGenerator

use of org.apache.commons.math3.random.RandomGenerator in project gatk by broadinstitute.

the class CopyRatioSegmenterUnitTest method testChromosomesOnDifferentSegments.

@Test
public void testChromosomesOnDifferentSegments() {
    final RandomGenerator rng = RandomGeneratorFactory.createRandomGenerator(new Random(563));
    final double[] trueLog2CopyRatios = new double[] { -2.0, 0.0, 1.7 };
    final double trueMemoryLength = 1e5;
    final double trueStandardDeviation = 0.2;
    // randomly set positions
    final int chainLength = 100;
    final List<SimpleInterval> positions = randomPositions("chr1", chainLength, rng, trueMemoryLength / 4);
    positions.addAll(randomPositions("chr2", chainLength, rng, trueMemoryLength / 4));
    positions.addAll(randomPositions("chr3", chainLength, rng, trueMemoryLength / 4));
    //fix everything to the same state 2
    final int trueState = 2;
    final List<Double> data = new ArrayList<>();
    for (int n = 0; n < positions.size(); n++) {
        final double copyRatio = trueLog2CopyRatios[trueState];
        final double observed = generateData(trueStandardDeviation, copyRatio, rng);
        data.add(observed);
    }
    final List<Target> targets = positions.stream().map(Target::new).collect(Collectors.toList());
    final ReadCountCollection rcc = new ReadCountCollection(targets, Arrays.asList("SAMPLE"), new Array2DRowRealMatrix(data.stream().mapToDouble(x -> x).toArray()));
    final CopyRatioSegmenter segmenter = new CopyRatioSegmenter(10, rcc);
    final List<ModeledSegment> segments = segmenter.getModeledSegments();
    //check that each chromosome has at least one segment
    final int numDifferentContigsInSegments = (int) segments.stream().map(ModeledSegment::getContig).distinct().count();
    Assert.assertEquals(numDifferentContigsInSegments, 3);
}