Initial work on distributions

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

@@ -18,6 +18,7 @@ package scientifik.kmath.chains
 
 import kotlinx.atomicfu.atomic
 import kotlinx.coroutines.FlowPreview
+import kotlinx.coroutines.flow.Flow
 
 
 /**
@@ -28,7 +29,7 @@ interface Chain<out R> {
     /**
      * Last cached value of the chain. Returns null if [next] was not called
      */
-    val value: R?
+    fun peek(): R?
 
     /**
      * Generate next value, changing state if needed
@@ -46,13 +47,12 @@ interface Chain<out R> {
  * Chain as a coroutine flow. The flow emit affects chain state and vice versa
  */
 @FlowPreview
-val <R> Chain<R>.flow
+val <R> Chain<R>.flow: Flow<R>
     get() = kotlinx.coroutines.flow.flow { while (true) emit(next()) }
 
 fun <T> Iterator<T>.asChain(): Chain<T> = SimpleChain { next() }
 fun <T> Sequence<T>.asChain(): Chain<T> = iterator().asChain()
 
-
 /**
  * Map the chain result using suspended transformation. Initial chain result can no longer be safely consumed
  * since mapped chain consumes tokens. Accepts regular transformation function
@@ -60,7 +60,7 @@ fun <T> Sequence<T>.asChain(): Chain<T> = iterator().asChain()
 fun <T, R> Chain<T>.map(func: (T) -> R): Chain<R> {
     val parent = this;
     return object : Chain<R> {
-        override val value: R? get() = parent.value?.let(func)
+        override fun peek(): R? = parent.peek()?.let(func)
 
         override suspend fun next(): R {
             return func(parent.next())
@@ -77,7 +77,7 @@ fun <T, R> Chain<T>.map(func: (T) -> R): Chain<R> {
  */
 class SimpleChain<out R>(private val gen: suspend () -> R) : Chain<R> {
     private val atomicValue = atomic<R?>(null)
-    override val value: R? get() = atomicValue.value
+    override fun peek(): R? = atomicValue.value
 
     override suspend fun next(): R = gen().also { atomicValue.lazySet(it) }
 
@@ -95,16 +95,16 @@ class MarkovChain<out R : Any>(private val seed: () -> R, private val gen: suspe
     constructor(seed: R, gen: suspend (R) -> R) : this({ seed }, gen)
 
     private val atomicValue = atomic<R?>(null)
-    override val value: R get() = atomicValue.value ?: seed()
+    override fun peek(): R = atomicValue.value ?: seed()
 
     override suspend fun next(): R {
-        val newValue = gen(value)
+        val newValue = gen(peek())
         atomicValue.lazySet(newValue)
-        return value
+        return peek()
     }
 
     override fun fork(): Chain<R> {
-        return MarkovChain(value, gen)
+        return MarkovChain(peek(), gen)
     }
 }
 
@@ -121,12 +121,12 @@ class StatefulChain<S, out R>(
     constructor(state: S, seed: R, gen: suspend S.(R) -> R) : this(state, { seed }, gen)
 
     private val atomicValue = atomic<R?>(null)
-    override val value: R get() = atomicValue.value ?: seed(state)
+    override fun peek(): R = atomicValue.value ?: seed(state)
 
     override suspend fun next(): R {
-        val newValue = gen(state, value)
+        val newValue = gen(state, peek())
         atomicValue.lazySet(newValue)
-        return value
+        return peek()
     }
 
     override fun fork(): Chain<R> {
@@ -137,10 +137,10 @@ class StatefulChain<S, out R>(
 /**
  * A chain that repeats the same value
  */
-class ConstantChain<out T>(override val value: T) : Chain<T> {
+class ConstantChain<out T>(val value: T) : Chain<T> {
-    override suspend fun next(): T {
+    override fun peek(): T? = value
-        return value
+
-    }
+    override suspend fun next(): T = value
 
     override fun fork(): Chain<T> {
         return this

kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/coroutines/CoroutinesExtra.kt

@@ -1,4 +1,4 @@
-package scientifik.kmath
+package scientifik.kmath.coroutines
 
 import kotlinx.coroutines.*
 import kotlinx.coroutines.channels.produce
@@ -42,13 +42,14 @@ fun <T, R> Flow<T>.async(
 }
 
 @FlowPreview
-fun <T, R> AsyncFlow<T>.map(action: (T) -> R) = AsyncFlow(deferredFlow.map { input ->
+fun <T, R> AsyncFlow<T>.map(action: (T) -> R) =
+    AsyncFlow(deferredFlow.map { input ->
         //TODO add function composition
         LazyDeferred(input.dispatcher) {
             input.start(this)
             action(input.await())
         }
-})
+    })
 
 @ExperimentalCoroutinesApi
 @FlowPreview

kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/streaming/BufferFlow.kt

@@ -22,7 +22,7 @@ fun <T> Flow<Buffer<out T>>.spread(): Flow<T> = flatMapConcat { it.asFlow() }
  * Collect incoming flow into fixed size chunks
  */
 @FlowPreview
-fun <T> Flow<T>.chunked(bufferSize: Int, bufferFactory: BufferFactory<T>) = flow {
+fun <T> Flow<T>.chunked(bufferSize: Int, bufferFactory: BufferFactory<T>): Flow<Buffer<T>> = flow {
     require(bufferSize > 0) { "Resulting chunk size must be more than zero" }
     val list = ArrayList<T>(bufferSize)
     var counter = 0
@@ -46,7 +46,7 @@ fun <T> Flow<T>.chunked(bufferSize: Int, bufferFactory: BufferFactory<T>) = flow
  * Specialized flow chunker for real buffer
  */
 @FlowPreview
-fun Flow<Double>.chunked(bufferSize: Int) = flow {
+fun Flow<Double>.chunked(bufferSize: Int): Flow<DoubleBuffer> = flow {
     require(bufferSize > 0) { "Resulting chunk size must be more than zero" }
     val array = DoubleArray(bufferSize)
     var counter = 0

kmath-coroutines/src/jvmMain/kotlin/scientifik/kmath/chains/ChainExt.kt

@@ -27,7 +27,7 @@ fun <R> Chain<R>.asSequence(): Sequence<R> = object : Sequence<R> {
 fun <T, R> Chain<T>.map(func: suspend (T) -> R): Chain<R> {
     val parent = this;
     return object : Chain<R> {
-        override val value: R? get() = runBlocking { parent.value?.let { func(it) } }
+        override fun peek(): R? = runBlocking { parent.peek()?.let { func(it) } }
 
         override suspend fun next(): R {
             return func(parent.next())

kmath-coroutines/src/jvmMain/kotlin/scientifik/kmath/structures/LazyNDStructure.kt

@@ -1,7 +1,7 @@
 package scientifik.kmath.structures
 
 import kotlinx.coroutines.*
-import scientifik.kmath.Math
+import scientifik.kmath.coroutines.Math
 
 class LazyNDStructure<T>(
     val scope: CoroutineScope,

kmath-coroutines/src/jvmTest/kotlin/scientifik/kmath/streaming/BufferFlowTest.kt

@@ -4,9 +4,9 @@ import kotlinx.coroutines.*
 import kotlinx.coroutines.flow.asFlow
 import kotlinx.coroutines.flow.collect
 import org.junit.Test
-import scientifik.kmath.async
+import scientifik.kmath.coroutines.async
-import scientifik.kmath.collect
+import scientifik.kmath.coroutines.collect
-import scientifik.kmath.map
+import scientifik.kmath.coroutines.map
 import java.util.concurrent.Executors
 
 

kmath-prob/build.gradle.kts

@@ -6,13 +6,14 @@ plugins {
 kotlin.sourceSets {
     commonMain {
         dependencies {
-            api(project(":kmath-core"))
             api(project(":kmath-coroutines"))
             compileOnly("org.jetbrains.kotlinx:atomicfu-common:${Versions.atomicfuVersion}")
         }
     }
     jvmMain {
         dependencies {
+            // https://mvnrepository.com/artifact/org.apache.commons/commons-rng-simple
+            api("org.apache.commons:commons-rng-sampling:1.2")
             compileOnly("org.jetbrains.kotlinx:atomicfu:${Versions.atomicfuVersion}")
         }
     }

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

@@ -0,0 +1,28 @@
+package scientifik.kmath.prob
+
+import scientifik.kmath.chains.Chain
+
+/**
+ * A distribution of typed objects
+ */
+interface Distribution<T : Any> {
+    /**
+     * A probability value for given argument [arg].
+     * For continuous distributions returns PDF
+     */
+    fun probability(arg: T): Double
+
+    /**
+     * Create a chain of samples from this distribution.
+     * The chain is not guaranteed to be stateless.
+     */
+    fun sample(generator: RandomGenerator): Chain<T>
+    //TODO add sample bunch generator
+}
+
+interface UnivariateDistribution<T : Comparable<T>> : Distribution<T> {
+    /**
+     * Cumulative distribution for ordered parameter
+     */
+    fun cumulative(arg: T): Double
+}

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

@@ -0,0 +1,11 @@
+package scientifik.kmath.prob
+
+/**
+ * A basic generator
+ */
+interface RandomGenerator {
+    fun nextDouble(): Double
+    fun nextInt(): Int
+    fun nextLong(): Long
+    fun nextBlock(size: Int): ByteArray
+}

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

@@ -0,0 +1,53 @@
+package scientifik.kmath.prob
+
+import org.apache.commons.rng.sampling.distribution.*
+import scientifik.kmath.chains.Chain
+import scientifik.kmath.chains.SimpleChain
+import kotlin.math.PI
+import kotlin.math.exp
+import kotlin.math.sqrt
+
+class NormalDistribution(val mean: Double, val sigma: Double) : UnivariateDistribution<Double> {
+    enum class Sampler {
+        BoxMuller,
+        Marsaglia,
+        Ziggurat
+    }
+
+    override fun probability(arg: Double): Double {
+        val d = (arg - mean) / sigma
+        return 1.0 / sqrt(2.0 * PI * sigma) * exp(-d * d / 2)
+    }
+
+    override fun cumulative(arg: Double): Double {
+        TODO("not implemented") //To change body of created functions use File | Settings | File Templates.
+    }
+
+    fun sample(generator: RandomGenerator, sampler: Sampler): Chain<Double> {
+        val normalized = when (sampler) {
+            Sampler.BoxMuller -> BoxMullerNormalizedGaussianSampler(generator.asProvider())
+            Sampler.Marsaglia -> MarsagliaNormalizedGaussianSampler(generator.asProvider())
+            Sampler.Ziggurat -> ZigguratNormalizedGaussianSampler(generator.asProvider())
+        }
+        val gauss = GaussianSampler(normalized, mean, sigma)
+        //TODO add generator to chain state to allow stateful forks
+        return SimpleChain { gauss.sample() }
+    }
+
+    override fun sample(generator: RandomGenerator): Chain<Double> = sample(generator, Sampler.BoxMuller)
+}
+
+class PoissonDistribution(val mean: Double): UnivariateDistribution<Int>{
+    override fun probability(arg: Int): Double {
+        TODO("not implemented") //To change body of created functions use File | Settings | File Templates.
+    }
+
+    override fun cumulative(arg: Int): Double {
+        TODO("not implemented") //To change body of created functions use File | Settings | File Templates.
+    }
+
+    override fun sample(generator: RandomGenerator): Chain<Int> {
+        val sampler = PoissonSampler(generator.asProvider(), mean)
+        return SimpleChain{sampler.sample()}
+    }
+}

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

@@ -0,0 +1,18 @@
+package scientifik.kmath.prob
+
+import org.apache.commons.rng.UniformRandomProvider
+
+inline class CommonsRandomProviderWrapper(val provider: UniformRandomProvider) : RandomGenerator {
+    override fun nextDouble(): Double = provider.nextDouble()
+
+    override fun nextInt(): Int = provider.nextInt()
+
+    override fun nextLong(): Long = provider.nextLong()
+
+    override fun nextBlock(size: Int): ByteArray = ByteArray(size).also { provider.nextBytes(it) }
+}
+
+fun UniformRandomProvider.asGenerator(): RandomGenerator = CommonsRandomProviderWrapper(this)
+
+fun RandomGenerator.asProvider(): UniformRandomProvider =
+    (this as? CommonsRandomProviderWrapper)?.provider ?: TODO("implement reverse wrapper")