Example usage for org.apache.commons.math3.random Well19937a Well19937a

List of usage examples for org.apache.commons.math3.random Well19937a Well19937a

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Introduction

In this page you can find the example usage for org.apache.commons.math3.random Well19937a Well19937a.

Prototype

public Well19937a()

Source Link

Document

Creates a new random number generator.

Usage

From source file:com.milaboratory.core.io.util.IOUtilTest.java

@Test
public void test1() throws Exception {
    RandomGenerator rg = new Well19937a();

    int count = 1000;
    int[] values = new int[count];

    for (int n = 0; n < 10; ++n) {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        for (int i = 0; i < count; ++i) {
            final int d = rg.nextInt(31);
            values[i] = (rg.nextInt(Integer.MAX_VALUE) >>> d);
            IOUtil.writeRawVarint32(bos, values[i]);
        }/*from w  w w. j a  va 2  s .  c  o  m*/

        byte[] data = bos.toByteArray();

        ByteArrayInputStream bis = new ByteArrayInputStream(data);
        int g;
        for (int i = 0; i < count; ++i) {
            Assert.assertEquals(values[i], IOUtil.readRawVarint32(bis, -1));
        }
        Assert.assertEquals(-1, IOUtil.readRawVarint32(bis, -1));
    }
}

From source file:com.milaboratory.core.io.util.IOUtilTest.java

@Test
public void test3() throws Exception {
    RandomGenerator rg = new Well19937a();

    int count = 1000;
    int[] values = new int[count];

    for (int n = 0; n < 10; ++n) {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        for (int i = 0; i < count; ++i) {
            final int d = rg.nextInt(31) + 1;
            values[i] = (rg.nextInt(Integer.MAX_VALUE) >>> d);
            if (rg.nextBoolean())
                values[i] *= -1;/*  ww  w  .j a  v  a  2 s . co  m*/
            final int encoded = IOUtil.encodeZigZag32(values[i]);
            Assert.assertTrue(-1 != encoded);
            IOUtil.writeRawVarint32(bos, encoded);
        }

        byte[] data = bos.toByteArray();

        ByteArrayInputStream bis = new ByteArrayInputStream(data);
        int g;
        for (int i = 0; i < count; ++i) {
            Assert.assertEquals(values[i], IOUtil.decodeZigZag32(IOUtil.readRawVarint32(bis, -1)));
        }
        Assert.assertEquals(-1, IOUtil.readRawVarint32(bis, -1));
    }
}

From source file:com.milaboratory.core.io.util.IOUtilTest.java

@Test
public void test2() throws Exception {
    RandomGenerator rg = new Well19937a();

    int count = 1000;
    long[] values = new long[count];

    for (int n = 0; n < 10; ++n) {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        for (int i = 0; i < count; ++i) {
            final int d = rg.nextInt(63) + 1;
            values[i] = (rg.nextLong() >>> d);
            IOUtil.writeRawVarint64(bos, values[i]);
        }//  w w  w .ja v a 2s  .c om

        byte[] data = bos.toByteArray();

        ByteArrayInputStream bis = new ByteArrayInputStream(data);
        int g;
        for (int i = 0; i < count; ++i) {
            Assert.assertEquals(values[i], IOUtil.readRawVarint64(bis, -1));
        }
        Assert.assertEquals(-1L, IOUtil.readRawVarint64(bis, -1));
    }
}

From source file:com.milaboratory.core.io.util.IOUtilTest.java

@Test
public void test4() throws Exception {
    RandomGenerator rg = new Well19937a();

    int count = 1000;
    long[] values = new long[count];

    for (int n = 0; n < 10; ++n) {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        for (int i = 0; i < count; ++i) {
            final int d = rg.nextInt(63) + 1;

            values[i] = (rg.nextLong() >>> d);

            if (rg.nextBoolean())
                values[i] *= -1;//from  ww  w.  ja  v  a 2  s .  c om

            final long encoded = IOUtil.encodeZigZag64(values[i]);
            Assert.assertTrue(-1L != encoded);
            IOUtil.writeRawVarint64(bos, encoded);
        }

        byte[] data = bos.toByteArray();

        ByteArrayInputStream bis = new ByteArrayInputStream(data);
        int g;
        for (int i = 0; i < count; ++i) {
            Assert.assertEquals(values[i], IOUtil.decodeZigZag64(IOUtil.readRawVarint64(bis, -1)));
        }
        Assert.assertEquals(-1L, IOUtil.readRawVarint64(bis, -1));
    }
}

From source file:com.milaboratory.core.clustering.ClusteringTest.java

@Test
public void testRandom1() throws Exception {
    int out = TestUtil.its(3, 30);
    Well19937a rand = new Well19937a();
    for (int x = 0; x < out; ++x) {
        int N = TestUtil.its(40, 300);
        Cluster<TestObject>[] clusters = new Cluster[N];
        Well19937a rand1 = new Well19937a(rand.nextLong());

        TestStrategy strategy = new TestStrategy(5, new TreeSearchParameters(1, 1, 1, 1));
        for (int i = 0; i < N; ++i)
            clusters[i] = getRandomTestCluster(
                    TestUtil.randomSequence(NucleotideSequence.ALPHABET, rand1, 45, 55), strategy.depth, 5,
                    10000 + rand1.nextInt(10000), 5 + rand1.nextInt(900), rand1.nextLong());

        assertClusters(false, strategy, clusters);
    }//  ww w.  j a  va 2 s  .  c o  m
}

From source file:com.milaboratory.core.clustering.ClusteringTest.java

@Test
public void testRandom2WithColor() {
    int out = TestUtil.its(3, 30);
    Well19937a rand = new Well19937a();
    int colors = 3;
    for (int x = 0; x < out; ++x) {
        int N = TestUtil.its(16, 100);
        Cluster<TestObject>[] clusters = new Cluster[N * colors];
        Well19937a rand1 = new Well19937a(rand.nextLong());

        TestStrategy strategy = new TestStrategy(5, new TreeSearchParameters(1, 1, 1, 1));
        int c = 0;
        for (int i = 0; i < N; ++i) {
            long seed = rand1.nextLong();
            NucleotideSequence sequence = TestUtil.randomSequence(NucleotideSequence.ALPHABET, rand1, 45, 55);
            for (int color = 0; color < colors; ++color) {
                clusters[c++] = getRandomTestCluster(sequence, color, strategy.depth, 5,
                        10000 + rand1.nextInt(10000), 5 + rand1.nextInt(900), seed);
            }/*from   w w w  .ja  va 2s.  c o m*/
        }

        assertDiffSizeClusters(strategy.getDummy(), clusters);
        assertClusters(false, strategy, clusters);
    }
}

From source file:com.milaboratory.core.tree.SequenceTreeMapTest.java

@Test
public void testRemoveTest() throws Exception {
    RandomGenerator gen = new Well19937a();
    RandomDataGenerator data = new RandomDataGenerator(gen);
    for (int k = 0; k < 100; ++k) {
        Set<NucleotideSequence> seqSet = new HashSet<>();

        for (int i = 0; i < 1000; ++i)
            seqSet.add(randomSequence(NucleotideSequence.ALPHABET, data, 4, 30));

        SequenceTreeMap<NucleotideSequence, NucleotideSequence> seqTree = new SequenceTreeMap<>(
                NucleotideSequence.ALPHABET);

        for (NucleotideSequence seq : seqSet)
            seqTree.put(seq, seq);// www . j av  a  2  s. c om

        int n = 0;

        for (NucleotideSequence seq : seqTree.values()) {
            assertTrue(seqSet.contains(seq));
            ++n;
        }

        assertEquals(seqSet.size(), n);

        for (NucleotideSequence seq : seqSet)
            assertEquals(seq, seqTree.remove(seq));

        for (int i = 0; i < 4; ++i)
            assertNull(seqTree.root.links[i]);

        n = 0;

        for (NucleotideSequence seq : seqTree.values())
            ++n;

        assertEquals(0, n);
    }
}

From source file:org.dawnsci.plotting.tools.diffraction.BeamCenterRefinement.java

/**
 * Run optimisation of sector region position in a separate job. 
 * //from   w  w w .j ava 2s  .  c  om
 * @param startPosition Initial position of sector region
 */
public void optimize(final double[] startPosition) {
    final int cmaesLambda = this.cmaesLambda;
    final double[] cmaesInputSigma = this.cmaesInputSigma;
    final int cmaesMaxIterations = this.cmaesMaxIterations;
    final int cmaesCheckFeasableCount = this.cmaesCheckFeasableCount;
    final ConvergenceChecker<PointValuePair> cmaesChecker = this.cmaesChecker;
    final BeamCenterRefinement function = this;
    Job job = new Job("Beam Position Refinement") {
        @Override
        protected IStatus run(IProgressMonitor monitor) {

            function.setInitPeaks(initPeaks);
            function.setMonitor(monitor);

            final double[] lB = new double[] { startPosition[0] - 20, startPosition[1] - 20 };
            final double[] uB = new double[] { startPosition[0] + 20, startPosition[1] + 20 };
            CMAESOptimizer beamPosOptimizer = new CMAESOptimizer(cmaesMaxIterations, 0.0, true, 0,
                    cmaesCheckFeasableCount, new Well19937a(), false, cmaesChecker);
            final PointValuePair result = beamPosOptimizer.optimize(new MaxEval(cmaesMaxIterations),
                    new ObjectiveFunction(function), GoalType.MAXIMIZE,
                    new CMAESOptimizer.PopulationSize(cmaesLambda), new CMAESOptimizer.Sigma(cmaesInputSigma),
                    new SimpleBounds(lB, uB), new InitialGuess(startPosition));

            final double[] newBeamPosition = result.getPoint();
            logger.info("Optimiser terminated at beam position ({}, {}) with the value {}",
                    new Object[] { newBeamPosition[0], newBeamPosition[1], result.getValue() });
            Display.getDefault().syncExec(new Runnable() {
                @Override
                public void run() {
                    ((IDiffractionMetadata) dataset.getMetadata()).getDetector2DProperties()
                            .setBeamCentreCoords(newBeamPosition);
                }
            });

            return Status.OK_STATUS;
        }
    };
    job.schedule();
}

From source file:org.optaplanner.core.impl.solver.random.DefaultRandomFactory.java

@Override
public Random createRandom() {
    switch (randomType) {
    case JDK://  w ww .  j  a v  a 2  s.c om
        return randomSeed == null ? new Random() : new Random(randomSeed);
    case MERSENNE_TWISTER:
        return new RandomAdaptor(randomSeed == null ? new MersenneTwister() : new MersenneTwister(randomSeed));
    case WELL512A:
        return new RandomAdaptor(randomSeed == null ? new Well512a() : new Well512a(randomSeed));
    case WELL1024A:
        return new RandomAdaptor(randomSeed == null ? new Well1024a() : new Well1024a(randomSeed));
    case WELL19937A:
        return new RandomAdaptor(randomSeed == null ? new Well19937a() : new Well19937a(randomSeed));
    case WELL19937C:
        return new RandomAdaptor(randomSeed == null ? new Well19937c() : new Well19937c(randomSeed));
    case WELL44497A:
        return new RandomAdaptor(randomSeed == null ? new Well44497a() : new Well44497a(randomSeed));
    case WELL44497B:
        return new RandomAdaptor(randomSeed == null ? new Well44497b() : new Well44497b(randomSeed));
    default:
        throw new IllegalStateException("The randomType (" + randomType + ") is not implemented.");
    }
}

From source file:uk.ac.diamond.scisoft.ncd.calibration.rcp.views.MultivariateFunctionWithMonitor.java

public void optimize(final double[] startPosition) {
    final int cmaesLambda = this.cmaesLambda;
    final double[] cmaesInputSigma = this.cmaesInputSigma;
    final int cmaesMaxIterations = this.cmaesMaxIterations;
    final int cmaesCheckFeasableCount = this.cmaesCheckFeasableCount;
    final ConvergenceChecker<PointValuePair> cmaesChecker = this.cmaesChecker;
    final MultivariateFunctionWithMonitor function = this;
    Job job = new Job(jobName) {
        @Override//from  ww  w .j  a va  2 s  .  c om
        protected IStatus run(IProgressMonitor monitor) {

            function.setInitPeaks(initPeaks);
            function.setMonitor(monitor);

            CMAESOptimizer beamPosOptimizer = new CMAESOptimizer(cmaesMaxIterations, 0.0, true, 0,
                    cmaesCheckFeasableCount, new Well19937a(), false, cmaesChecker);
            final PointValuePair res = beamPosOptimizer.optimize(new MaxEval(cmaesMaxIterations),
                    new ObjectiveFunction(function), GoalType.MAXIMIZE,
                    new CMAESOptimizer.PopulationSize(cmaesLambda), new CMAESOptimizer.Sigma(cmaesInputSigma),
                    SimpleBounds.unbounded(2), new InitialGuess(startPosition));
            final double[] newBeamPos = res.getPoint();
            logger.info("Optimiser terminated at beam position ({}, {}) with the value {}",
                    new Object[] { newBeamPos[0], newBeamPos[1], res.getValue() });
            // Run calculation with optimised beam center to update UI 
            function.value(newBeamPos);

            return Status.OK_STATUS;
        }
    };
    job.schedule();
}