Moved probability distributions to commons-rng and to prob module

build.gradle.kts

@@ -2,7 +2,7 @@ plugins {
     id("scientifik.publish") apply false
 }
 
-val kmathVersion by extra("0.1.4-dev-6")
+val kmathVersion by extra("0.1.4-dev-7")
 
 val bintrayRepo by extra("scientifik")
 val githubProject by extra("kmath")

kmath-commons/src/main/kotlin/scientifik/kmath/commons/prob/CMRandomGeneratorWrapper.kt

@@ -1,32 +0,0 @@
-package scientifik.kmath.commons.prob
-
-import org.apache.commons.math3.random.JDKRandomGenerator
-import scientifik.kmath.prob.RandomGenerator
-import org.apache.commons.math3.random.RandomGenerator as CMRandom
-
-inline class CMRandomGeneratorWrapper(val generator: CMRandom) : RandomGenerator {
-    override fun nextDouble(): Double = generator.nextDouble()
-
-    override fun nextInt(): Int = generator.nextInt()
-
-    override fun nextLong(): Long = generator.nextLong()
-
-    override fun nextBlock(size: Int): ByteArray = ByteArray(size).apply { generator.nextBytes(this) }
-
-    override fun fork(): RandomGenerator {
-        TODO("not implemented") //To change body of created functions use File | Settings | File Templates.
-    }
-}
-
-fun CMRandom.asKmathGenerator(): RandomGenerator = CMRandomGeneratorWrapper(this)
-
-fun RandomGenerator.asCMGenerator(): CMRandom =
-    (this as? CMRandomGeneratorWrapper)?.generator ?: TODO("Implement reverse CM wrapper")
-
-val RandomGenerator.Companion.default: RandomGenerator by lazy { JDKRandomGenerator().asKmathGenerator() }
-
-fun RandomGenerator.Companion.jdk(seed: Int? = null): RandomGenerator = if (seed == null) {
-    JDKRandomGenerator()
-} else {
-    JDKRandomGenerator(seed)
-}.asKmathGenerator()

kmath-commons/src/main/kotlin/scientifik/kmath/commons/prob/CommonsDistribution.kt

@@ -1,82 +0,0 @@
-package scientifik.kmath.commons.prob
-
-import org.apache.commons.math3.distribution.*
-import scientifik.kmath.prob.Distribution
-import scientifik.kmath.prob.RandomChain
-import scientifik.kmath.prob.RandomGenerator
-import scientifik.kmath.prob.UnivariateDistribution
-import org.apache.commons.math3.random.RandomGenerator as CMRandom
-
-class CMRealDistributionWrapper(val builder: (CMRandom?) -> RealDistribution) : UnivariateDistribution<Double> {
-
-    private val defaultDistribution by lazy { builder(null) }
-
-    override fun probability(arg: Double): Double = defaultDistribution.probability(arg)
-
-    override fun cumulative(arg: Double): Double = defaultDistribution.cumulativeProbability(arg)
-
-    override fun sample(generator: RandomGenerator): RandomChain<Double> {
-        val distribution = builder(generator.asCMGenerator())
-        return RandomChain(generator) { distribution.sample() }
-    }
-}
-
-class CMIntDistributionWrapper(val builder: (CMRandom?) -> IntegerDistribution) : UnivariateDistribution<Int> {
-
-    private val defaultDistribution by lazy { builder(null) }
-
-    override fun probability(arg: Int): Double = defaultDistribution.probability(arg)
-
-    override fun cumulative(arg: Int): Double = defaultDistribution.cumulativeProbability(arg)
-
-    override fun sample(generator: RandomGenerator): RandomChain<Int> {
-        val distribution = builder(generator.asCMGenerator())
-        return RandomChain(generator) { distribution.sample() }
-    }
-}
-
-
-fun Distribution.Companion.normal(mean: Double = 0.0, sigma: Double = 1.0): UnivariateDistribution<Double> =
-    CMRealDistributionWrapper { generator -> NormalDistribution(generator, mean, sigma) }
-
-fun Distribution.Companion.poisson(mean: Double): UnivariateDistribution<Int> = CMIntDistributionWrapper { generator ->
-    PoissonDistribution(
-        generator,
-        mean,
-        PoissonDistribution.DEFAULT_EPSILON,
-        PoissonDistribution.DEFAULT_MAX_ITERATIONS
-    )
-}
-
-fun Distribution.Companion.binomial(trials: Int, p: Double): UnivariateDistribution<Int> =
-    CMIntDistributionWrapper { generator ->
-        BinomialDistribution(generator, trials, p)
-    }
-
-fun Distribution.Companion.student(degreesOfFreedom: Double): UnivariateDistribution<Double> =
-    CMRealDistributionWrapper { generator ->
-        TDistribution(generator, degreesOfFreedom, TDistribution.DEFAULT_INVERSE_ABSOLUTE_ACCURACY)
-    }
-
-fun Distribution.Companion.chi2(degreesOfFreedom: Double): UnivariateDistribution<Double> =
-    CMRealDistributionWrapper { generator ->
-        ChiSquaredDistribution(generator, degreesOfFreedom)
-    }
-
-fun Distribution.Companion.fisher(
-    numeratorDegreesOfFreedom: Double,
-    denominatorDegreesOfFreedom: Double
-): UnivariateDistribution<Double> =
-    CMRealDistributionWrapper { generator ->
-        FDistribution(generator, numeratorDegreesOfFreedom, denominatorDegreesOfFreedom)
-    }
-
-fun Distribution.Companion.exponential(mean: Double): UnivariateDistribution<Double> =
-    CMRealDistributionWrapper { generator ->
-        ExponentialDistribution(generator, mean)
-    }
-
-fun Distribution.Companion.uniform(a: Double, b: Double): UnivariateDistribution<Double> =
-    CMRealDistributionWrapper { generator ->
-        UniformRealDistribution(generator, a, b)
-    }

kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/chains/Chain.kt

@@ -38,9 +38,13 @@ interface Chain<out R>: Flow<R> {
      */
     fun fork(): Chain<R>
 
-    @InternalCoroutinesApi
+    @OptIn(InternalCoroutinesApi::class)
     override suspend fun collect(collector: FlowCollector<R>) {
-        kotlinx.coroutines.flow.flow { while (true) emit(next()) }.collect(collector)
+        kotlinx.coroutines.flow.flow {
+            while (true){
+                emit(next())
+            }
+        }.collect(collector)
     }
 
     companion object

kmath-memory/src/commonMain/kotlin/scientifik/memory/Memory.kt

@@ -69,3 +69,9 @@ inline fun Memory.write(block: MemoryWriter.() -> Unit) {
  * Allocate the most effective platform-specific memory
  */
 expect fun Memory.Companion.allocate(length: Int): Memory
+
+/**
+ * Wrap a [Memory] around existing [ByteArray]. This operation is unsafe since the array is not copied
+ * and could be mutated independently from the resulting [Memory]
+ */
+expect fun Memory.Companion.wrap(array: ByteArray): Memory

kmath-memory/src/jsMain/kotlin/scientifik/memory/DataViewMemory.kt

@@ -2,14 +2,7 @@ package scientifik.memory
 
 import org.khronos.webgl.ArrayBuffer
 import org.khronos.webgl.DataView
-
+import org.khronos.webgl.Int8Array
-/**
- * Allocate the most effective platform-specific memory
- */
-actual fun Memory.Companion.allocate(length: Int): Memory {
-    val buffer = ArrayBuffer(length)
-    return DataViewMemory(DataView(buffer, 0, length))
-}
 
 class DataViewMemory(val view: DataView) : Memory {
 
@@ -89,3 +82,16 @@ class DataViewMemory(val view: DataView) : Memory {
     override fun writer(): MemoryWriter = writer
 
 }
+
+/**
+ * Allocate the most effective platform-specific memory
+ */
+actual fun Memory.Companion.allocate(length: Int): Memory {
+    val buffer = ArrayBuffer(length)
+    return DataViewMemory(DataView(buffer, 0, length))
+}
+
+actual fun Memory.Companion.wrap(array: ByteArray): Memory {
+    @Suppress("CAST_NEVER_SUCCEEDS") val int8Array = array as Int8Array
+    return DataViewMemory(DataView(int8Array.buffer, int8Array.byteOffset, int8Array.length))
+}

kmath-memory/src/jvmMain/kotlin/scientifik/memory/ByteBufferMemory.kt

@@ -7,14 +7,6 @@ import java.nio.file.Path
 import java.nio.file.StandardOpenOption
 
 
-/**
- * Allocate the most effective platform-specific memory
- */
-actual fun Memory.Companion.allocate(length: Int): Memory {
-    val buffer = ByteBuffer.allocate(length)
-    return ByteBufferMemory(buffer)
-}
-
 private class ByteBufferMemory(
     val buffer: ByteBuffer,
     val startOffset: Int = 0,
@@ -96,6 +88,22 @@ private class ByteBufferMemory(
     override fun writer(): MemoryWriter = writer
 }
 
+/**
+ * Allocate the most effective platform-specific memory
+ */
+actual fun Memory.Companion.allocate(length: Int): Memory {
+    val buffer = ByteBuffer.allocate(length)
+    return ByteBufferMemory(buffer)
+}
+
+actual fun Memory.Companion.wrap(array: ByteArray): Memory {
+    val buffer = ByteBuffer.wrap(array)
+    return ByteBufferMemory(buffer)
+}
+
+fun ByteBuffer.asMemory(startOffset: Int = 0, size: Int = limit()): Memory =
+    ByteBufferMemory(this, startOffset, size)
+
 /**
  * Use direct memory-mapped buffer from file to read something and close it afterwards.
  */

kmath-prob/build.gradle.kts

@@ -8,4 +8,10 @@ kotlin.sourceSets {
             api(project(":kmath-coroutines"))
         }
     }
+    jvmMain{
+        dependencies{
+            api("org.apache.commons:commons-rng-sampling:1.3")
+            api("org.apache.commons:commons-rng-simple:1.3")
+        }
+    }
 }

kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/RandomGenerator.kt

@@ -6,10 +6,16 @@ import kotlin.random.Random
  * A basic generator
  */
 interface RandomGenerator {
+    fun nextBoolean(): Boolean
+
     fun nextDouble(): Double
     fun nextInt(): Int
+    fun nextInt(until: Int): Int
     fun nextLong(): Long
-    fun nextBlock(size: Int): ByteArray
+    fun nextLong(until: Long): Long
+
+    fun fillBytes(array: ByteArray, fromIndex: Int = 0, toIndex: Int = array.size)
+    fun nextBytes(size: Int): ByteArray = ByteArray(size).also { fillBytes(it) }
 
     /**
      * Create a new generator which is independent from current generator (operations on new generator do not affect this one
@@ -21,21 +27,29 @@ interface RandomGenerator {
     fun fork(): RandomGenerator
 
     companion object {
-        val default by lazy { DefaultGenerator(Random.nextLong()) }
+        val default by lazy { DefaultGenerator() }
+
+        fun default(seed: Long) = DefaultGenerator(Random(seed))
     }
 }
 
-class DefaultGenerator(seed: Long?) : RandomGenerator {
+inline class DefaultGenerator(val random: Random = Random) : RandomGenerator {
-    private val random = seed?.let { Random(it) } ?: Random
+    override fun nextBoolean(): Boolean = random.nextBoolean()
 
     override fun nextDouble(): Double = random.nextDouble()
 
     override fun nextInt(): Int = random.nextInt()
+    override fun nextInt(until: Int): Int = random.nextInt(until)
 
     override fun nextLong(): Long = random.nextLong()
 
-    override fun nextBlock(size: Int): ByteArray = random.nextBytes(size)
+    override fun nextLong(until: Long): Long = random.nextLong(until)
 
-    override fun fork(): RandomGenerator = DefaultGenerator(nextLong())
+    override fun fillBytes(array: ByteArray, fromIndex: Int, toIndex: Int) {
+        random.nextBytes(array, fromIndex, toIndex)
+    }
 
+    override fun nextBytes(size: Int): ByteArray = random.nextBytes(size)
+
+    override fun fork(): RandomGenerator = RandomGenerator.default(random.nextLong())
 }

kmath-prob/src/commonMain/kotlin/scientifik/kmath/prob/UniformDistribution.kt

@@ -29,3 +29,6 @@ class UniformDistribution(val range: ClosedFloatingPointRange<Double>) : Univari
         }
     }
 }
+
+fun Distribution.Companion.uniform(range: ClosedFloatingPointRange<Double>): UniformDistribution =
+    UniformDistribution(range)

kmath-prob/src/jvmMain/kotlin/scientifik/kmath/prob/RandomSourceGenerator.kt

@@ -0,0 +1,61 @@
+package scientifik.kmath.prob
+
+import org.apache.commons.rng.UniformRandomProvider
+import org.apache.commons.rng.simple.RandomSource
+
+class RandomSourceGenerator(val source: RandomSource, seed: Long?) : RandomGenerator {
+    internal val random: UniformRandomProvider = seed?.let {
+        RandomSource.create(source, seed, null)
+    } ?: RandomSource.create(source)
+
+    override fun nextBoolean(): Boolean = random.nextBoolean()
+
+    override fun nextDouble(): Double = random.nextDouble()
+
+    override fun nextInt(): Int = random.nextInt()
+    override fun nextInt(until: Int): Int = random.nextInt(until)
+
+    override fun nextLong(): Long = random.nextLong()
+    override fun nextLong(until: Long): Long = random.nextLong(until)
+
+    override fun fillBytes(array: ByteArray, fromIndex: Int, toIndex: Int) {
+        require(toIndex > fromIndex)
+        random.nextBytes(array, fromIndex, toIndex - fromIndex)
+    }
+
+    override fun fork(): RandomGenerator = RandomSourceGenerator(source, nextLong())
+}
+
+inline class RandomGeneratorProvider(val generator: RandomGenerator) : UniformRandomProvider {
+    override fun nextBoolean(): Boolean = generator.nextBoolean()
+
+    override fun nextFloat(): Float = generator.nextDouble().toFloat()
+
+    override fun nextBytes(bytes: ByteArray) {
+        generator.fillBytes(bytes)
+    }
+
+    override fun nextBytes(bytes: ByteArray, start: Int, len: Int) {
+        generator.fillBytes(bytes, start, start + len)
+    }
+
+    override fun nextInt(): Int = generator.nextInt()
+
+    override fun nextInt(n: Int): Int = generator.nextInt(n)
+
+    override fun nextDouble(): Double = generator.nextDouble()
+
+    override fun nextLong(): Long = generator.nextLong()
+
+    override fun nextLong(n: Long): Long = generator.nextLong(n)
+}
+
+/**
+ * Represent this [RandomGenerator] as commons-rng [UniformRandomProvider] preserving and mirroring its current state.
+ * Getting new value from one of those changes the state of another.
+ */
+fun RandomGenerator.asUniformRandomProvider(): UniformRandomProvider = if (this is RandomSourceGenerator) {
+    random
+} else {
+    RandomGeneratorProvider(this)
+}

kmath-prob/src/jvmMain/kotlin/scientifik/kmath/prob/distributions.kt

@@ -0,0 +1,107 @@
+package scientifik.kmath.prob
+
+import org.apache.commons.rng.UniformRandomProvider
+import org.apache.commons.rng.sampling.distribution.*
+import scientifik.kmath.chains.Chain
+import java.util.*
+import kotlin.math.PI
+import kotlin.math.exp
+import kotlin.math.pow
+import kotlin.math.sqrt
+
+abstract class ContinuousSamplerDistribution : Distribution<Double> {
+
+    private inner class ContinuousSamplerChain(val generator: RandomGenerator) : Chain<Double> {
+        private val sampler = buildSampler(generator)
+
+        override suspend fun next(): Double = sampler.sample()
+
+        override fun fork(): Chain<Double> = ContinuousSamplerChain(generator.fork())
+    }
+
+    protected abstract fun buildSampler(generator: RandomGenerator): ContinuousSampler
+
+    override fun sample(generator: RandomGenerator): Chain<Double> = ContinuousSamplerChain(generator)
+}
+
+abstract class DiscreteSamplerDistribution : Distribution<Int> {
+
+    private inner class ContinuousSamplerChain(val generator: RandomGenerator) : Chain<Int> {
+        private val sampler = buildSampler(generator)
+
+        override suspend fun next(): Int = sampler.sample()
+
+        override fun fork(): Chain<Int> = ContinuousSamplerChain(generator.fork())
+    }
+
+    protected abstract fun buildSampler(generator: RandomGenerator): DiscreteSampler
+
+    override fun sample(generator: RandomGenerator): Chain<Int> = ContinuousSamplerChain(generator)
+}
+
+enum class NormalSamplerMethod {
+    BoxMuller,
+    Marsaglia,
+    Ziggurat
+}
+
+private fun normalSampler(method: NormalSamplerMethod, provider: UniformRandomProvider): NormalizedGaussianSampler =
+    when (method) {
+        NormalSamplerMethod.BoxMuller -> BoxMullerNormalizedGaussianSampler(provider)
+        NormalSamplerMethod.Marsaglia -> MarsagliaNormalizedGaussianSampler(provider)
+        NormalSamplerMethod.Ziggurat -> ZigguratNormalizedGaussianSampler(provider)
+    }
+
+fun Distribution.Companion.normal(
+    method: NormalSamplerMethod = NormalSamplerMethod.Ziggurat
+): Distribution<Double> = object : ContinuousSamplerDistribution() {
+    override fun buildSampler(generator: RandomGenerator): ContinuousSampler {
+        val provider: UniformRandomProvider = generator.asUniformRandomProvider()
+        return normalSampler(method, provider)
+    }
+
+    override fun probability(arg: Double): Double {
+        return exp(-arg.pow(2) / 2) / sqrt(PI * 2)
+    }
+}
+
+fun Distribution.Companion.normal(
+    mean: Double,
+    sigma: Double,
+    method: NormalSamplerMethod = NormalSamplerMethod.Ziggurat
+): Distribution<Double> = object : ContinuousSamplerDistribution() {
+    private val sigma2 = sigma.pow(2)
+    private val norm = sigma * sqrt(PI * 2)
+
+    override fun buildSampler(generator: RandomGenerator): ContinuousSampler {
+        val provider: UniformRandomProvider = generator.asUniformRandomProvider()
+        val normalizedSampler = normalSampler(method, provider)
+        return GaussianSampler(normalizedSampler, mean, sigma)
+    }
+
+    override fun probability(arg: Double): Double {
+        return exp(-(arg - mean).pow(2) / 2 / sigma2) / norm
+    }
+}
+
+fun Distribution.Companion.poisson(
+    lambda: Double
+): Distribution<Int> = object : DiscreteSamplerDistribution() {
+
+    override fun buildSampler(generator: RandomGenerator): DiscreteSampler {
+        return PoissonSampler.of(generator.asUniformRandomProvider(), lambda)
+    }
+
+    private val computedProb: HashMap<Int, Double> = hashMapOf(0 to exp(-lambda))
+
+    override fun probability(arg: Int): Double {
+        require(arg >= 0) { "The argument must be >= 0" }
+        return if (arg > 40) {
+            exp(-(arg - lambda).pow(2) / 2 / lambda) / sqrt(2 * PI * lambda)
+        } else {
+            computedProb.getOrPut(arg) {
+                probability(arg - 1) * lambda / arg
+            }
+        }
+    }
+}

kmath-prob/src/jvmTest/kotlin/scientifik/kmath/prob/CommonsDistributionsTest.kt

@@ -0,0 +1,19 @@
+package scientifik.kmath.prob
+
+import kotlinx.coroutines.flow.take
+import kotlinx.coroutines.flow.toList
+import kotlinx.coroutines.runBlocking
+import org.junit.jupiter.api.Assertions
+import org.junit.jupiter.api.Test
+
+class CommonsDistributionsTest {
+    @Test
+    fun testNormalDistribution(){
+        val distribution = Distribution.normal(7.0,2.0)
+        val generator = RandomGenerator.default(1)
+        val sample = runBlocking {
+            distribution.sample(generator).take(1000).toList()
+        }
+        Assertions.assertEquals(7.0, sample.average(), 0.1)
+    }
+}

kmath-prob/src/jvmTest/kotlin/scientifik/kmath/prob/StatisticTest.kt

@@ -9,7 +9,7 @@ import kotlin.test.Test
 
 class StatisticTest {
     //create a random number generator.
-    val generator = DefaultGenerator(1)
+    val generator = RandomGenerator.default(1)
     //Create a stateless chain from generator.
     val data = generator.chain { nextDouble() }
     //Convert a chaint to Flow and break it into chunks.