List of usage examples for org.apache.commons.math3.random RandomGenerator nextLong
long nextLong();
long value from this random number generator's sequence. From source file:com.github.rinde.rinsim.util.StochasticSuppliersTest.java
@Test public void testUniform() { final RandomGenerator rng = new MersenneTwister(123L); final StochasticSupplier<Integer> sup = uniformInt(2, 10); final IntegerDistribution id = new UniformIntegerDistribution(2, 10); final Multiset<Integer> ms = TreeMultiset.create(); for (int i = 0; i < 1000; i++) { ms.add(sup.get(rng.nextLong())); }//from w w w . j ava2 s .co m final List<Integer> observations = newArrayList(); final List<Double> expectations = newArrayList(); for (final Multiset.Entry<Integer> entry : ms.entrySet()) { observations.add(entry.getCount()); expectations.add(id.probability(entry.getElement())); } assertTrue(chiSquare(expectations, observations, .01)); }
From source file:com.github.rinde.rinsim.scenario.generator.TimeWindowsTest.java
/** * Tests the generated time windows on two properties: * <ul>//from www .j ava2s.co m * <li>The distance between pickupTW.begin and deliveryTW.begin</li> * <li>The distance between pickupTW.end and deliveryTW.end</li> * </ul> */ @Test public void overlapTest() { final RandomGenerator rng = new MersenneTwister(123L); for (final TravelTimes tt : DistanceTT.values()) { for (final Parcel.Builder parcelBuilder : parcelBuilders()) { for (int i = 0; i < 10; i++) { timeWindowGenerator.generate(rng.nextLong(), parcelBuilder, tt, END_TIME); final long pickDelTT = tt.getShortestTravelTime(parcelBuilder.getPickupLocation(), parcelBuilder.getDeliveryLocation()); final long toDepotTT = tt.getTravelTimeToNearestDepot(parcelBuilder.getDeliveryLocation()); final TimeWindow pickTW = parcelBuilder.getPickupTimeWindow(); final TimeWindow delTW = parcelBuilder.getDeliveryTimeWindow(); final long pickDur = parcelBuilder.getPickupDuration(); assertTrue(pickTW.begin() >= 0); assertTrue(i + " " + tt + " " + pickTW + " " + delTW, pickTW.end() <= delTW.end() + pickDelTT + pickDur); // FIXME update and re-enable this test // assertTrue(i + " " + tt + " " + pickTW + " " + delTW + " " // + pickDelTT + " " + pickDur, // delTW.begin >= pickTW.begin + pickDelTT + pickDur); } } } }
From source file:com.github.rinde.rinsim.scenario.generator.PoissonIntensityTest.java
/** * Tests whether the Poisson process (crudely) approximates the intensity * function when a large number of runs is done. *//*from w w w.ja v a 2 s.com*/ @Test public void intensityApproximationPoissonProcessTest() { final RandomGenerator rng = new MersenneTwister(123); final TimeSeriesGenerator pp = TimeSeries.nonHomogenousPoisson(100d, intensityFunction); final Multiset<Double> ms = TreeMultiset.create(); final int repetitions = 10000; for (int i = 0; i < repetitions; i++) { final List<Double> times = pp.generate(rng.nextLong()); for (final Double d : times) { ms.add(new Double(Math.ceil(d))); } } for (final Multiset.Entry<Double> entry : ms.entrySet()) { final double exp = IntensityFunctions.areaByIntegration(intensityFunction, entry.getElement() - 1d, entry.getElement()); final double observation = entry.getCount() / (double) repetitions; assertEquals(exp, observation, 0.05); } }
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]); }/*from w w w. jav a2 s. co m*/ 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;/* ww w . ja va2s . c o m*/ 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:it.unimi.dsi.sux4j.mph.ZFastTrieDistributorMonotoneMinimalPerfectHashFunction.java
/** Creates a new monotone minimal perfect hash function based on a z-fast trie distributor using the given * keys, transformation strategy and bucket size. * //www. j av a2s . c o m * @param keys the keys among which the trie must be able to rank. * @param transform a transformation strategy that must turn the keys into a list of * distinct, prefix-free, lexicographically increasing (in iteration order) bit vectors. * @param log2BucketSize the logarithm of the bucket size, or -1 for the default value. * @param signatureWidth a signature width, or 0 for no signature. * @param tempDir a temporary directory for the store files, or {@code null} for the standard temporary directory. */ protected ZFastTrieDistributorMonotoneMinimalPerfectHashFunction(final Iterable<? extends T> keys, final TransformationStrategy<? super T> transform, final int log2BucketSize, final int signatureWidth, final File tempDir) throws IOException { this.transform = transform; defRetValue = -1; // For the very few cases in which we can decide long maxLength = 0; long totalLength = 0; RandomGenerator r = new XorShift1024StarRandomGenerator(); final ChunkedHashStore<BitVector> chunkedHashStore = new ChunkedHashStore<BitVector>( TransformationStrategies.identity(), tempDir); chunkedHashStore.reset(r.nextLong()); final Iterable<BitVector> bitVectors = TransformationStrategies.wrap(keys, transform); final ProgressLogger pl = new ProgressLogger(LOGGER); pl.displayLocalSpeed = true; pl.displayFreeMemory = true; pl.itemsName = "keys"; pl.start("Scanning collection..."); for (BitVector bv : bitVectors) { maxLength = Math.max(maxLength, bv.length()); totalLength += bv.length(); chunkedHashStore.add(bv); pl.lightUpdate(); } pl.done(); chunkedHashStore.checkAndRetry(bitVectors); size = chunkedHashStore.size(); if (size == 0) { this.log2BucketSize = -1; distributor = null; offset = null; signatureMask = 0; signatures = null; chunkedHashStore.close(); return; } final long averageLength = (totalLength + size - 1) / size; final long forecastBucketSize = (long) Math.ceil( 10.5 + 4.05 * log(averageLength) + 2.43 * log(log(size) + 1) + 2.43 * log(log(averageLength) + 1)); this.log2BucketSize = log2BucketSize == -1 ? Fast.mostSignificantBit(forecastBucketSize) : log2BucketSize; LOGGER.debug("Average length: " + averageLength); LOGGER.debug("Max length: " + maxLength); LOGGER.debug("Bucket size: " + (1L << this.log2BucketSize)); LOGGER.info("Computing z-fast trie distributor..."); distributor = new ZFastTrieDistributor<BitVector>(bitVectors, this.log2BucketSize, TransformationStrategies.identity(), chunkedHashStore); LOGGER.info("Computing offsets..."); offset = new GOV3Function.Builder<BitVector>().store(chunkedHashStore).values(new AbstractLongBigList() { final long bucketSizeMask = (1L << ZFastTrieDistributorMonotoneMinimalPerfectHashFunction.this.log2BucketSize) - 1; public long getLong(long index) { return index & bucketSizeMask; } public long size64() { return size; } }, this.log2BucketSize).indirect().build(); seed = chunkedHashStore.seed(); double logU = averageLength * log(2); LOGGER.info("Forecast bit cost per element: " + 1.0 / forecastBucketSize * (-6 * log2(log(2)) + 5 * log2(logU) + 2 * log2(forecastBucketSize) + log2(log(logU) - log(log(2))) + 6 * GOV3Function.C + 3 * log2(E) + 3 * log2(log(3.0 * size)) + 3 + GOV3Function.C * forecastBucketSize + GOV3Function.C * forecastBucketSize * log2(forecastBucketSize))); LOGGER.info("Actual bit cost per element: " + (double) numBits() / size); if (signatureWidth != 0) { signatureMask = -1L >>> Long.SIZE - signatureWidth; signatures = chunkedHashStore.signatures(signatureWidth, pl); } else { signatureMask = 0; signatures = null; } chunkedHashStore.close(); }
From source file:com.github.rinde.rinsim.scenario.generator.ScenarioGenerator.java
/** * Generates a new {@link Scenario} instance. * @param rng The random number generator used for drawing random numbers. * @param id The id of this specific scenario. * @return A new instance.//w w w . java 2s .c om */ // TODO change rng to seed? public Scenario generate(RandomGenerator rng, String id) { final ImmutableList.Builder<TimedEvent> b = ImmutableList.builder(); // depots final Iterable<? extends AddDepotEvent> depots = depotGenerator.generate(rng.nextLong(), parcelGenerator.getCenter()); b.addAll(depots); // vehicles final ImmutableList<AddVehicleEvent> vehicles = vehicleGenerator.generate(rng.nextLong(), parcelGenerator.getCenter(), builder.getTimeWindow().end()); b.addAll(vehicles); final TravelTimes tm = createTravelTimes(modelBuilders, getTimeUnit(), depots, vehicles); // parcels b.addAll(parcelGenerator.generate(rng.nextLong(), tm, builder.getTimeWindow().end())); // time out b.add(TimeOutEvent.create(builder.getTimeWindow().end())); // create return Scenario.builder(builder, builder.problemClass).addModels(modelBuilders).addEvents(b.build()) .instanceId(id).build(); }
From source file:it.unimi.dsi.sux4j.mph.PaCoTrieDistributorMonotoneMinimalPerfectHashFunction.java
/** Creates a new PaCo-trie-based monotone minimal perfect hash function using the given * elements and transformation strategy. * /*from w w w . j ava2 s . c o m*/ * @param elements the elements among which the trie must be able to rank. * @param transform a transformation strategy that must turn the elements in <code>elements</code> into a list of * distinct, prefix-free, lexicographically increasing (in iteration order) bit vectors. */ public PaCoTrieDistributorMonotoneMinimalPerfectHashFunction(final Iterable<? extends T> elements, final TransformationStrategy<? super T> transform) throws IOException { this.transform = transform; defRetValue = -1; // For the very few cases in which we can decide long maxLength = 0; long totalLength = 0; BitVector bv; final RandomGenerator random = new XorShift1024StarRandomGenerator(); ProgressLogger pl = new ProgressLogger(LOGGER); pl.displayLocalSpeed = true; pl.displayFreeMemory = true; pl.itemsName = "keys"; pl.start("Creating chunked hash store..."); final ChunkedHashStore<BitVector> chunkedHashStore = new ChunkedHashStore<BitVector>( TransformationStrategies.identity()); chunkedHashStore.reset(random.nextLong()); for (T s : elements) { bv = transform.toBitVector(s); chunkedHashStore.add(bv); maxLength = Math.max(maxLength, bv.length()); totalLength += bv.length(); pl.lightUpdate(); } pl.done(); LOGGER.debug("Maximum length: " + maxLength); LOGGER.debug("Average length: " + totalLength / (double) chunkedHashStore.size()); size = chunkedHashStore.size(); if (size == 0) { bucketSize = log2BucketSize = 0; distributor = null; offset = null; chunkedHashStore.close(); return; } final long averageLength = (totalLength + size - 1) / size; int t = Fast.mostSignificantBit( (int) Math.floor(averageLength - Math.log(size) - Math.log(averageLength - Math.log(size)) - 1)); final int firstbucketSize = 1 << t; LOGGER.debug("First bucket size estimate: " + firstbucketSize); final Iterable<BitVector> bitVectors = TransformationStrategies.wrap(elements, transform); LOGGER.info("Creating distributor..."); PaCoTrieDistributor<BitVector> firstDistributor = new PaCoTrieDistributor<BitVector>(bitVectors, t, TransformationStrategies.identity()); if (firstDistributor.numBits() == 0 || firstbucketSize >= size) log2BucketSize = t; else { // Reassign bucket size based on empirical estimation log2BucketSize = t - Fast.mostSignificantBit((int) Math.ceil(size / (firstDistributor.numBits() * Math.log(2)))); } bucketSize = 1 << log2BucketSize; LOGGER.debug("Second bucket size estimate: " + bucketSize); if (firstbucketSize == bucketSize) distributor = firstDistributor; else { firstDistributor = null; distributor = new PaCoTrieDistributor<BitVector>(bitVectors, log2BucketSize, TransformationStrategies.identity()); } LOGGER.debug("Bucket size: " + bucketSize); final int bucketSizeMask = bucketSize - 1; LOGGER.info("Generating offset function..."); offset = new GOV3Function.Builder<BitVector>().keys(bitVectors) .transform(TransformationStrategies.identity()).store(chunkedHashStore) .values(new AbstractLongBigList() { public long getLong(long index) { return index & bucketSizeMask; } public long size64() { return size; } }, log2BucketSize).indirect().build(); chunkedHashStore.close(); LOGGER.debug("Forecast distributor bit cost: " + (size / bucketSize) * (maxLength + log2BucketSize - Math.log(size))); LOGGER.debug("Actual distributor bit cost: " + distributor.numBits()); LOGGER.debug("Forecast bit cost per element: " + (GOV3Function.C + Fast.log2(Math.E) - Fast.log2(Fast.log2(Math.E)) + Fast.log2(maxLength - Fast.log2(size)))); LOGGER.info("Actual bit cost per element: " + (double) numBits() / size); }
From source file:it.unimi.dsi.sux4j.mph.VLPaCoTrieDistributorMonotoneMinimalPerfectHashFunction.java
/** Creates a new PaCo-trie-based monotone minimal perfect hash function using the given * elements and transformation strategy. * //from www.j a v a2s .c o m * @param elements the elements among which the trie must be able to rank. * @param transform a transformation strategy that must turn the elements in <code>elements</code> into a list of * distinct, prefix-free, lexicographically increasing (in iteration order) bit vectors. */ public VLPaCoTrieDistributorMonotoneMinimalPerfectHashFunction(final Iterable<? extends T> elements, final TransformationStrategy<? super T> transform) throws IOException { this.transform = transform; defRetValue = -1; // For the very few cases in which we can decide long maxLength = 0; long totalLength = 0; BitVector bv; final RandomGenerator random = new XorShift1024StarRandomGenerator(); ProgressLogger pl = new ProgressLogger(LOGGER); pl.displayLocalSpeed = true; pl.displayFreeMemory = true; pl.itemsName = "keys"; pl.start("Creating chunked hash store..."); final ChunkedHashStore<BitVector> chunkedHashStore = new ChunkedHashStore<BitVector>( TransformationStrategies.identity()); chunkedHashStore.reset(random.nextLong()); for (T s : elements) { bv = transform.toBitVector(s); chunkedHashStore.add(bv); maxLength = Math.max(maxLength, bv.length()); totalLength += bv.length(); pl.lightUpdate(); } pl.done(); size = chunkedHashStore.size(); if (size == 0) { bucketSize = log2BucketSize = 0; distributor = null; offset = null; chunkedHashStore.close(); return; } final long averageLength = (totalLength + size - 1) / size; int t = Fast.mostSignificantBit( (int) Math.floor(averageLength - Math.log(size) - Math.log(averageLength - Math.log(size)) - 1)); final int firstbucketSize = 1 << t; LOGGER.debug("First bucket size estimate: " + firstbucketSize); final Iterable<BitVector> bitVectors = TransformationStrategies.wrap(elements, transform); VLPaCoTrieDistributor<BitVector> firstDistributor = new VLPaCoTrieDistributor<BitVector>(bitVectors, size, firstbucketSize, TransformationStrategies.identity()); if (firstDistributor.numBits() == 0 || firstbucketSize >= size) log2BucketSize = t; else { // Reassign bucket size based on empirical estimation log2BucketSize = t - Fast.mostSignificantBit((int) Math.ceil(size / (firstDistributor.numBits() * Math.log(2)))); } bucketSize = 1 << log2BucketSize; LOGGER.debug("Second bucket size estimate: " + bucketSize); if (firstbucketSize == bucketSize) distributor = firstDistributor; else { firstDistributor = null; distributor = new VLPaCoTrieDistributor<BitVector>(bitVectors, size, bucketSize, TransformationStrategies.identity()); } LOGGER.info("Bucket size: " + bucketSize); final SparseRank sparseRank; if (size > 2 * bucketSize) { sparseRank = new SparseRank(distributor.offset.getLong(distributor.offset.size64() - 1) + 1, distributor.offset.size64(), distributor.offset.iterator()); if (ASSERTS) { long i = 0; for (BitVector b : bitVectors) { final long d = distributor.getLong(b); assert sparseRank.rank(i) == d : "At " + i + ": " + sparseRank.rank(i) + " != " + d; i++; } } select = sparseRank.getSelect(); } else { sparseRank = null; select = null; } if (size > 0) { offset = new GOV3Function.Builder<BitVector>().keys(bitVectors) .transform(TransformationStrategies.identity()).store(chunkedHashStore) .values(new AbstractLongBigList() { public long getLong(long index) { final long rank = sparseRank == null ? 0 : sparseRank.rank(index); if (ASSERTS) { assert rank == 0 || distributor.offset.getLong(rank - 1) <= index : distributor.offset .getLong(rank - 1) + " >= " + index + "(rank=" + rank + ")"; assert rank == 0 && index < bucketSize * 2 || rank > 0 && index - distributor.offset.getLong(rank - 1) < bucketSize * 2; } return rank == 0 ? index : index - distributor.offset.getLong(rank - 1); } public long size64() { return size; } }, log2BucketSize + 1).indirect().build(); } else offset = null; chunkedHashStore.close(); LOGGER.debug("Forecast distributor bit cost: " + (size / bucketSize) * (maxLength + log2BucketSize - Math.log(size))); LOGGER.debug("Actual distributor bit cost: " + distributor.numBits()); LOGGER.debug("Forecast bit cost per element: " + (GOV3Function.C + Fast.log2(Math.E) - Fast.log2(Fast.log2(Math.E)) + Fast.log2(maxLength - Fast.log2(size)))); LOGGER.info("Actual bit cost per element: " + (double) numBits() / size); }
From source file:com.milaboratory.core.motif.MotifTest.java
@Test public void testRandom1() throws Exception { RandomGenerator rg = new Well19937c(); for (WildcardSymbol wildcardSymbol : NucleotideSequence.ALPHABET.getAllWildcards()) { int seqLength = 20 + rg.nextInt(100); int motifSize = rg.nextInt(20); StringBuilder builder = new StringBuilder(motifSize); for (int i = 0; i < motifSize; ++i) builder.append(wildcardSymbol.getSymbol()); Motif<NucleotideSequence> motif = new Motif<>(NucleotideSequence.ALPHABET, builder.toString()); NucleotideSequenceBuilder seqBuilder = new NucleotideSequenceBuilder().ensureCapacity(seqLength); for (int i = 0; i < seqLength; ++i) seqBuilder.append(wildcardSymbol.getUniformlyDistributedSymbol(rg.nextLong())); NucleotideSequence seq = seqBuilder.createAndDestroy(); for (int i = 0; i < seq.size() - motif.size(); ++i) assertTrue(motif.matches(seq, i)); }// w w w . jav a2s . c o m }