forked from kscience/kmath
Refactor, remove unused files, remove BasicSampler
This commit is contained in:
parent
d4aa4587a9
commit
612f6f0082
@ -31,4 +31,4 @@ fun main() {
|
|||||||
strides.indices().forEach { res = array[strides.offset(it)] }
|
strides.indices().forEach { res = array[strides.offset(it)] }
|
||||||
}
|
}
|
||||||
println("Array reading finished in $time3 millis")
|
println("Array reading finished in $time3 millis")
|
||||||
}
|
}
|
||||||
|
@ -1,3 +1,5 @@
|
|||||||
|
import ru.mipt.npm.gradle.Maturity
|
||||||
|
|
||||||
plugins {
|
plugins {
|
||||||
id("ru.mipt.npm.mpp")
|
id("ru.mipt.npm.mpp")
|
||||||
id("ru.mipt.npm.native")
|
id("ru.mipt.npm.native")
|
||||||
@ -11,36 +13,42 @@ kotlin.sourceSets.commonMain {
|
|||||||
|
|
||||||
readme {
|
readme {
|
||||||
description = "Core classes, algebra definitions, basic linear algebra"
|
description = "Core classes, algebra definitions, basic linear algebra"
|
||||||
maturity = ru.mipt.npm.gradle.Maturity.DEVELOPMENT
|
maturity = Maturity.DEVELOPMENT
|
||||||
propertyByTemplate("artifact", rootProject.file("docs/templates/ARTIFACT-TEMPLATE.md"))
|
propertyByTemplate("artifact", rootProject.file("docs/templates/ARTIFACT-TEMPLATE.md"))
|
||||||
|
|
||||||
feature(
|
feature(
|
||||||
id = "algebras",
|
id = "algebras",
|
||||||
description = "Algebraic structures: contexts and elements",
|
description = "Algebraic structures: contexts and elements",
|
||||||
ref = "src/commonMain/kotlin/kscience/kmath/operations/Algebra.kt"
|
ref = "src/commonMain/kotlin/kscience/kmath/operations/Algebra.kt"
|
||||||
)
|
)
|
||||||
|
|
||||||
feature(
|
feature(
|
||||||
id = "nd",
|
id = "nd",
|
||||||
description = "Many-dimensional structures",
|
description = "Many-dimensional structures",
|
||||||
ref = "src/commonMain/kotlin/kscience/kmath/structures/NDStructure.kt"
|
ref = "src/commonMain/kotlin/kscience/kmath/structures/NDStructure.kt"
|
||||||
)
|
)
|
||||||
|
|
||||||
feature(
|
feature(
|
||||||
id = "buffers",
|
id = "buffers",
|
||||||
description = "One-dimensional structure",
|
description = "One-dimensional structure",
|
||||||
ref = "src/commonMain/kotlin/kscience/kmath/structures/Buffers.kt"
|
ref = "src/commonMain/kotlin/kscience/kmath/structures/Buffers.kt"
|
||||||
)
|
)
|
||||||
|
|
||||||
feature(
|
feature(
|
||||||
id = "expressions",
|
id = "expressions",
|
||||||
description = "Functional Expressions",
|
description = "Functional Expressions",
|
||||||
ref = "src/commonMain/kotlin/kscience/kmath/expressions"
|
ref = "src/commonMain/kotlin/kscience/kmath/expressions"
|
||||||
)
|
)
|
||||||
|
|
||||||
feature(
|
feature(
|
||||||
id = "domains",
|
id = "domains",
|
||||||
description = "Domains",
|
description = "Domains",
|
||||||
ref = "src/commonMain/kotlin/kscience/kmath/domains"
|
ref = "src/commonMain/kotlin/kscience/kmath/domains"
|
||||||
)
|
)
|
||||||
|
|
||||||
feature(
|
feature(
|
||||||
id = "autodif",
|
id = "autodif",
|
||||||
description = "Automatic differentiation",
|
description = "Automatic differentiation",
|
||||||
ref = "src/commonMain/kotlin/kscience/kmath/misc/AutoDiff.kt"
|
ref = "src/commonMain/kotlin/kscience/kmath/misc/AutoDiff.kt"
|
||||||
)
|
)
|
||||||
}
|
}
|
||||||
|
@ -237,18 +237,18 @@ public class BigInt internal constructor(
|
|||||||
)
|
)
|
||||||
|
|
||||||
private fun compareMagnitudes(mag1: Magnitude, mag2: Magnitude): Int {
|
private fun compareMagnitudes(mag1: Magnitude, mag2: Magnitude): Int {
|
||||||
when {
|
return when {
|
||||||
mag1.size > mag2.size -> return 1
|
mag1.size > mag2.size -> 1
|
||||||
mag1.size < mag2.size -> return -1
|
mag1.size < mag2.size -> -1
|
||||||
|
|
||||||
else -> {
|
else -> {
|
||||||
for (i in mag1.size - 1 downTo 0) {
|
for (i in mag1.size - 1 downTo 0) return when {
|
||||||
if (mag1[i] > mag2[i]) {
|
mag1[i] > mag2[i] -> 1
|
||||||
return 1
|
mag1[i] < mag2[i] -> -1
|
||||||
} else if (mag1[i] < mag2[i]) {
|
else -> continue
|
||||||
return -1
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
return 0
|
|
||||||
|
0
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -298,10 +298,11 @@ public class BigInt internal constructor(
|
|||||||
var carry = 0uL
|
var carry = 0uL
|
||||||
|
|
||||||
for (i in mag.indices) {
|
for (i in mag.indices) {
|
||||||
val cur: ULong = carry + mag[i].toULong() * x.toULong()
|
val cur = carry + mag[i].toULong() * x.toULong()
|
||||||
result[i] = (cur and BASE).toUInt()
|
result[i] = (cur and BASE).toUInt()
|
||||||
carry = cur shr BASE_SIZE
|
carry = cur shr BASE_SIZE
|
||||||
}
|
}
|
||||||
|
|
||||||
result[resultLength - 1] = (carry and BASE).toUInt()
|
result[resultLength - 1] = (carry and BASE).toUInt()
|
||||||
|
|
||||||
return stripLeadingZeros(result)
|
return stripLeadingZeros(result)
|
||||||
|
@ -71,7 +71,7 @@ public interface Buffer<T> {
|
|||||||
@Suppress("UNCHECKED_CAST")
|
@Suppress("UNCHECKED_CAST")
|
||||||
public inline fun <T : Any> auto(type: KClass<T>, size: Int, initializer: (Int) -> T): Buffer<T> =
|
public inline fun <T : Any> auto(type: KClass<T>, size: Int, initializer: (Int) -> T): Buffer<T> =
|
||||||
when (type) {
|
when (type) {
|
||||||
Double::class -> RealBuffer(size) { initializer(it) as Double } as Buffer<T>
|
Double::class -> real(size) { initializer(it) as Double } as Buffer<T>
|
||||||
Short::class -> ShortBuffer(size) { initializer(it) as Short } as Buffer<T>
|
Short::class -> ShortBuffer(size) { initializer(it) as Short } as Buffer<T>
|
||||||
Int::class -> IntBuffer(size) { initializer(it) as Int } as Buffer<T>
|
Int::class -> IntBuffer(size) { initializer(it) as Int } as Buffer<T>
|
||||||
Long::class -> LongBuffer(size) { initializer(it) as Long } as Buffer<T>
|
Long::class -> LongBuffer(size) { initializer(it) as Long } as Buffer<T>
|
||||||
|
@ -22,7 +22,7 @@ public interface Structure2D<T> : NDStructure<T> {
|
|||||||
|
|
||||||
override fun elements(): Sequence<Pair<IntArray, T>> = sequence {
|
override fun elements(): Sequence<Pair<IntArray, T>> = sequence {
|
||||||
for (i in (0 until rowNum))
|
for (i in (0 until rowNum))
|
||||||
for (j in (0 until colNum)) yield(intArrayOf(i, j) to get(i, j))
|
for (j in (0 until colNum)) yield(intArrayOf(i, j) to this@Structure2D[i, j])
|
||||||
}
|
}
|
||||||
|
|
||||||
public companion object
|
public companion object
|
||||||
@ -35,7 +35,6 @@ private inline class Structure2DWrapper<T>(val structure: NDStructure<T>) : Stru
|
|||||||
override val shape: IntArray get() = structure.shape
|
override val shape: IntArray get() = structure.shape
|
||||||
|
|
||||||
override operator fun get(i: Int, j: Int): T = structure[i, j]
|
override operator fun get(i: Int, j: Int): T = structure[i, j]
|
||||||
|
|
||||||
override fun elements(): Sequence<Pair<IntArray, T>> = structure.elements()
|
override fun elements(): Sequence<Pair<IntArray, T>> = structure.elements()
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -29,12 +29,11 @@ class NumberNDFieldTest {
|
|||||||
|
|
||||||
val array = real2D(3, 3) { i, j -> (i * 10 + j).toDouble() }
|
val array = real2D(3, 3) { i, j -> (i * 10 + j).toDouble() }
|
||||||
|
|
||||||
for (i in 0..2) {
|
for (i in 0..2)
|
||||||
for (j in 0..2) {
|
for (j in 0..2) {
|
||||||
val expected = (i * 10 + j).toDouble()
|
val expected = (i * 10 + j).toDouble()
|
||||||
assertEquals(expected, array[i, j], "Error at index [$i, $j]")
|
assertEquals(expected, array[i, j], "Error at index [$i, $j]")
|
||||||
}
|
}
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
|
@ -63,12 +63,10 @@ public class MarkovChain<out R : Any>(private val seed: suspend () -> R, private
|
|||||||
|
|
||||||
public fun value(): R? = value
|
public fun value(): R? = value
|
||||||
|
|
||||||
public override suspend fun next(): R {
|
public override suspend fun next(): R = mutex.withLock {
|
||||||
mutex.withLock {
|
val newValue = gen(value ?: seed())
|
||||||
val newValue = gen(value ?: seed())
|
value = newValue
|
||||||
value = newValue
|
newValue
|
||||||
return newValue
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
public override fun fork(): Chain<R> = MarkovChain(seed = { value ?: seed() }, gen = gen)
|
public override fun fork(): Chain<R> = MarkovChain(seed = { value ?: seed() }, gen = gen)
|
||||||
@ -90,12 +88,10 @@ public class StatefulChain<S, out R>(
|
|||||||
|
|
||||||
public fun value(): R? = value
|
public fun value(): R? = value
|
||||||
|
|
||||||
public override suspend fun next(): R {
|
public override suspend fun next(): R = mutex.withLock {
|
||||||
mutex.withLock {
|
val newValue = state.gen(value ?: state.seed())
|
||||||
val newValue = state.gen(value ?: state.seed())
|
value = newValue
|
||||||
value = newValue
|
newValue
|
||||||
return newValue
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
public override fun fork(): Chain<R> = StatefulChain(forkState(state), seed, forkState, gen)
|
public override fun fork(): Chain<R> = StatefulChain(forkState(state), seed, forkState, gen)
|
||||||
|
@ -28,7 +28,7 @@ public fun <T> Flow<T>.chunked(bufferSize: Int, bufferFactory: BufferFactory<T>)
|
|||||||
var counter = 0
|
var counter = 0
|
||||||
|
|
||||||
this@chunked.collect { element ->
|
this@chunked.collect { element ->
|
||||||
list.add(element)
|
list += element
|
||||||
counter++
|
counter++
|
||||||
|
|
||||||
if (counter == bufferSize) {
|
if (counter == bufferSize) {
|
||||||
|
@ -48,11 +48,9 @@ public class RingBuffer<T>(
|
|||||||
/**
|
/**
|
||||||
* A safe snapshot operation
|
* A safe snapshot operation
|
||||||
*/
|
*/
|
||||||
public suspend fun snapshot(): Buffer<T> {
|
public suspend fun snapshot(): Buffer<T> = mutex.withLock {
|
||||||
mutex.withLock {
|
val copy = buffer.copy()
|
||||||
val copy = buffer.copy()
|
VirtualBuffer(size) { i -> copy[startIndex.forward(i)] as T }
|
||||||
return VirtualBuffer(size) { i -> copy[startIndex.forward(i)] as T }
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
public suspend fun push(element: T) {
|
public suspend fun push(element: T) {
|
||||||
|
@ -23,8 +23,8 @@ public class OrderedPiecewisePolynomial<T : Comparable<T>>(delimiter: T) :
|
|||||||
*/
|
*/
|
||||||
public fun putRight(right: T, piece: Polynomial<T>) {
|
public fun putRight(right: T, piece: Polynomial<T>) {
|
||||||
require(right > delimiters.last()) { "New delimiter should be to the right of old one" }
|
require(right > delimiters.last()) { "New delimiter should be to the right of old one" }
|
||||||
delimiters.add(right)
|
delimiters += right
|
||||||
pieces.add(piece)
|
pieces += piece
|
||||||
}
|
}
|
||||||
|
|
||||||
public fun putLeft(left: T, piece: Polynomial<T>) {
|
public fun putLeft(left: T, piece: Polynomial<T>) {
|
||||||
@ -52,4 +52,4 @@ public class OrderedPiecewisePolynomial<T : Comparable<T>>(delimiter: T) :
|
|||||||
public fun <T : Comparable<T>, C : Ring<T>> PiecewisePolynomial<T>.value(ring: C, arg: T): T? =
|
public fun <T : Comparable<T>, C : Ring<T>> PiecewisePolynomial<T>.value(ring: C, arg: T): T? =
|
||||||
findPiece(arg)?.value(ring, arg)
|
findPiece(arg)?.value(ring, arg)
|
||||||
|
|
||||||
public fun <T : Comparable<T>, C : Ring<T>> PiecewisePolynomial<T>.asFunction(ring: C): (T) -> T? = { value(ring, it) }
|
public fun <T : Comparable<T>, C : Ring<T>> PiecewisePolynomial<T>.asFunction(ring: C): (T) -> T? = { value(ring, it) }
|
||||||
|
@ -5,8 +5,18 @@ import kscience.kmath.chains.Chain
|
|||||||
import kscience.kmath.chains.collect
|
import kscience.kmath.chains.collect
|
||||||
import kscience.kmath.structures.Buffer
|
import kscience.kmath.structures.Buffer
|
||||||
import kscience.kmath.structures.BufferFactory
|
import kscience.kmath.structures.BufferFactory
|
||||||
|
import kscience.kmath.structures.IntBuffer
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Sampler that generates chains of values of type [T].
|
||||||
|
*/
|
||||||
public fun interface Sampler<T : Any> {
|
public fun interface Sampler<T : Any> {
|
||||||
|
/**
|
||||||
|
* Generates a chain of samples.
|
||||||
|
*
|
||||||
|
* @param generator the randomness provider.
|
||||||
|
* @return the new chain.
|
||||||
|
*/
|
||||||
public fun sample(generator: RandomGenerator): Chain<T>
|
public fun sample(generator: RandomGenerator): Chain<T>
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -59,16 +69,25 @@ public fun <T : Any> Sampler<T>.sampleBuffer(
|
|||||||
//clear list from previous run
|
//clear list from previous run
|
||||||
tmp.clear()
|
tmp.clear()
|
||||||
//Fill list
|
//Fill list
|
||||||
repeat(size) { tmp.add(chain.next()) }
|
repeat(size) { tmp += chain.next() }
|
||||||
//return new buffer with elements from tmp
|
//return new buffer with elements from tmp
|
||||||
bufferFactory(size) { tmp[it] }
|
bufferFactory(size) { tmp[it] }
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Samples one value from this [Sampler].
|
||||||
|
*/
|
||||||
public suspend fun <T : Any> Sampler<T>.next(generator: RandomGenerator): T = sample(generator).first()
|
public suspend fun <T : Any> Sampler<T>.next(generator: RandomGenerator): T = sample(generator).first()
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Generate a bunch of samples from real distributions
|
* Generates [size] real samples and chunks them into some buffers.
|
||||||
*/
|
*/
|
||||||
public fun Sampler<Double>.sampleBuffer(generator: RandomGenerator, size: Int): Chain<Buffer<Double>> =
|
public fun Sampler<Double>.sampleBuffer(generator: RandomGenerator, size: Int): Chain<Buffer<Double>> =
|
||||||
sampleBuffer(generator, size, Buffer.Companion::real)
|
sampleBuffer(generator, size, Buffer.Companion::real)
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates [size] integer samples and chunks them into some buffers.
|
||||||
|
*/
|
||||||
|
public fun Sampler<Int>.sampleBuffer(generator: RandomGenerator, size: Int): Chain<Buffer<Int>> =
|
||||||
|
sampleBuffer(generator, size, ::IntBuffer)
|
||||||
|
@ -38,6 +38,6 @@ public class DistributionBuilder<T : Any> {
|
|||||||
private val distributions = ArrayList<NamedDistribution<T>>()
|
private val distributions = ArrayList<NamedDistribution<T>>()
|
||||||
|
|
||||||
public infix fun String.to(distribution: Distribution<T>) {
|
public infix fun String.to(distribution: Distribution<T>) {
|
||||||
distributions.add(NamedDistributionWrapper(this, distribution))
|
distributions += NamedDistributionWrapper(this, distribution)
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
@ -82,6 +82,8 @@ public interface RandomGenerator {
|
|||||||
|
|
||||||
/**
|
/**
|
||||||
* Implements [RandomGenerator] by delegating all operations to [Random].
|
* Implements [RandomGenerator] by delegating all operations to [Random].
|
||||||
|
*
|
||||||
|
* @property random the underlying [Random] object.
|
||||||
*/
|
*/
|
||||||
public inline class DefaultGenerator(public val random: Random = Random) : RandomGenerator {
|
public inline class DefaultGenerator(public val random: Random = Random) : RandomGenerator {
|
||||||
public override fun nextBoolean(): Boolean = random.nextBoolean()
|
public override fun nextBoolean(): Boolean = random.nextBoolean()
|
||||||
|
@ -7,25 +7,28 @@ import kscience.kmath.chains.zip
|
|||||||
import kscience.kmath.operations.Space
|
import kscience.kmath.operations.Space
|
||||||
import kscience.kmath.operations.invoke
|
import kscience.kmath.operations.invoke
|
||||||
|
|
||||||
public class BasicSampler<T : Any>(public val chainBuilder: (RandomGenerator) -> Chain<T>) : Sampler<T> {
|
/**
|
||||||
public override fun sample(generator: RandomGenerator): Chain<T> = chainBuilder(generator)
|
* Implements [Sampler] by sampling only certain [value].
|
||||||
}
|
*
|
||||||
|
* @property value the value to sample.
|
||||||
|
*/
|
||||||
public class ConstantSampler<T : Any>(public val value: T) : Sampler<T> {
|
public class ConstantSampler<T : Any>(public val value: T) : Sampler<T> {
|
||||||
public override fun sample(generator: RandomGenerator): Chain<T> = ConstantChain(value)
|
public override fun sample(generator: RandomGenerator): Chain<T> = ConstantChain(value)
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* A space for samplers. Allows to perform simple operations on distributions
|
* A space of samplers. Allows to perform simple operations on distributions.
|
||||||
|
*
|
||||||
|
* @property space the space to provide addition and scalar multiplication for [T].
|
||||||
*/
|
*/
|
||||||
public class SamplerSpace<T : Any>(public val space: Space<T>) : Space<Sampler<T>> {
|
public class SamplerSpace<T : Any>(public val space: Space<T>) : Space<Sampler<T>> {
|
||||||
public override val zero: Sampler<T> = ConstantSampler(space.zero)
|
public override val zero: Sampler<T> = ConstantSampler(space.zero)
|
||||||
|
|
||||||
public override fun add(a: Sampler<T>, b: Sampler<T>): Sampler<T> = BasicSampler { generator ->
|
public override fun add(a: Sampler<T>, b: Sampler<T>): Sampler<T> = Sampler { generator ->
|
||||||
a.sample(generator).zip(b.sample(generator)) { aValue, bValue -> space { aValue + bValue } }
|
a.sample(generator).zip(b.sample(generator)) { aValue, bValue -> space { aValue + bValue } }
|
||||||
}
|
}
|
||||||
|
|
||||||
public override fun multiply(a: Sampler<T>, k: Number): Sampler<T> = BasicSampler { generator ->
|
public override fun multiply(a: Sampler<T>, k: Number): Sampler<T> = Sampler { generator ->
|
||||||
a.sample(generator).map { space { it * k.toDouble() } }
|
a.sample(generator).map { space { it * k.toDouble() } }
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
@ -98,28 +98,21 @@ internal object InternalGamma {
|
|||||||
private const val INV_GAMMA1P_M1_C12 = .113302723198169588237412962033074E-05
|
private const val INV_GAMMA1P_M1_C12 = .113302723198169588237412962033074E-05
|
||||||
private const val INV_GAMMA1P_M1_C13 = -.205633841697760710345015413002057E-06
|
private const val INV_GAMMA1P_M1_C13 = -.205633841697760710345015413002057E-06
|
||||||
|
|
||||||
fun logGamma(x: Double): Double {
|
fun logGamma(x: Double): Double = when {
|
||||||
val ret: Double
|
x.isNaN() || x <= 0.0 -> Double.NaN
|
||||||
|
x < 0.5 -> logGamma1p(x) - ln(x)
|
||||||
|
x <= 2.5 -> logGamma1p(x - 0.5 - 0.5)
|
||||||
|
|
||||||
when {
|
x <= 8.0 -> {
|
||||||
x.isNaN() || x <= 0.0 -> ret = Double.NaN
|
val n = floor(x - 1.5).toInt()
|
||||||
x < 0.5 -> return logGamma1p(x) - ln(x)
|
val prod = (1..n).fold(1.0, { prod, i -> prod * (x - i) })
|
||||||
x <= 2.5 -> return logGamma1p(x - 0.5 - 0.5)
|
logGamma1p(x - (n + 1)) + ln(prod)
|
||||||
|
|
||||||
x <= 8.0 -> {
|
|
||||||
val n = floor(x - 1.5).toInt()
|
|
||||||
var prod = 1.0
|
|
||||||
(1..n).forEach { i -> prod *= x - i }
|
|
||||||
return logGamma1p(x - (n + 1)) + ln(prod)
|
|
||||||
}
|
|
||||||
|
|
||||||
else -> {
|
|
||||||
val tmp = x + LANCZOS_G + .5
|
|
||||||
ret = (x + .5) * ln(tmp) - tmp + HALF_LOG_2_PI + ln(lanczos(x) / x)
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
return ret
|
else -> {
|
||||||
|
val tmp = x + LANCZOS_G + .5
|
||||||
|
(x + .5) * ln(tmp) - tmp + HALF_LOG_2_PI + ln(lanczos(x) / x)
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun regularizedGammaP(
|
private fun regularizedGammaP(
|
||||||
|
@ -20,24 +20,17 @@ internal object InternalUtils {
|
|||||||
|
|
||||||
fun validateProbabilities(probabilities: DoubleArray?): Double {
|
fun validateProbabilities(probabilities: DoubleArray?): Double {
|
||||||
require(!(probabilities == null || probabilities.isEmpty())) { "Probabilities must not be empty." }
|
require(!(probabilities == null || probabilities.isEmpty())) { "Probabilities must not be empty." }
|
||||||
var sumProb = 0.0
|
|
||||||
|
|
||||||
probabilities.forEach { prob ->
|
val sumProb = probabilities.sumByDouble { prob ->
|
||||||
validateProbability(prob)
|
require(!(prob < 0 || prob.isInfinite() || prob.isNaN())) { "Invalid probability: $prob" }
|
||||||
sumProb += prob
|
prob
|
||||||
}
|
}
|
||||||
|
|
||||||
require(!(sumProb.isInfinite() || sumProb <= 0)) { "Invalid sum of probabilities: $sumProb" }
|
require(!(sumProb.isInfinite() || sumProb <= 0)) { "Invalid sum of probabilities: $sumProb" }
|
||||||
return sumProb
|
return sumProb
|
||||||
}
|
}
|
||||||
|
|
||||||
private fun validateProbability(probability: Double): Unit =
|
class FactorialLog private constructor(numValues: Int, cache: DoubleArray?) {
|
||||||
require(!(probability < 0 || probability.isInfinite() || probability.isNaN())) { "Invalid probability: $probability" }
|
|
||||||
|
|
||||||
class FactorialLog private constructor(
|
|
||||||
numValues: Int,
|
|
||||||
cache: DoubleArray?
|
|
||||||
) {
|
|
||||||
private val logFactorials: DoubleArray = DoubleArray(numValues)
|
private val logFactorials: DoubleArray = DoubleArray(numValues)
|
||||||
|
|
||||||
init {
|
init {
|
||||||
@ -46,14 +39,15 @@ internal object InternalUtils {
|
|||||||
if (cache != null && cache.size > BEGIN_LOG_FACTORIALS) {
|
if (cache != null && cache.size > BEGIN_LOG_FACTORIALS) {
|
||||||
// Copy available values.
|
// Copy available values.
|
||||||
endCopy = min(cache.size, numValues)
|
endCopy = min(cache.size, numValues)
|
||||||
|
|
||||||
cache.copyInto(
|
cache.copyInto(
|
||||||
logFactorials,
|
logFactorials,
|
||||||
BEGIN_LOG_FACTORIALS,
|
BEGIN_LOG_FACTORIALS,
|
||||||
BEGIN_LOG_FACTORIALS, endCopy
|
BEGIN_LOG_FACTORIALS, endCopy
|
||||||
)
|
)
|
||||||
}
|
} else
|
||||||
// All values to be computed
|
// All values to be computed
|
||||||
else endCopy = BEGIN_LOG_FACTORIALS
|
endCopy = BEGIN_LOG_FACTORIALS
|
||||||
|
|
||||||
// Compute remaining values.
|
// Compute remaining values.
|
||||||
(endCopy until numValues).forEach { i ->
|
(endCopy until numValues).forEach { i ->
|
||||||
@ -65,9 +59,7 @@ internal object InternalUtils {
|
|||||||
}
|
}
|
||||||
|
|
||||||
fun value(n: Int): Double {
|
fun value(n: Int): Double {
|
||||||
if (n < logFactorials.size)
|
if (n < logFactorials.size) return logFactorials[n]
|
||||||
return logFactorials[n]
|
|
||||||
|
|
||||||
return if (n < FACTORIALS.size) ln(FACTORIALS[n].toDouble()) else InternalGamma.logGamma(n + 1.0)
|
return if (n < FACTORIALS.size) ln(FACTORIALS[n].toDouble()) else InternalGamma.logGamma(n + 1.0)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -42,7 +42,7 @@ public open class AliasMethodDiscreteSampler private constructor(
|
|||||||
protected val alias: IntArray
|
protected val alias: IntArray
|
||||||
) : Sampler<Int> {
|
) : Sampler<Int> {
|
||||||
|
|
||||||
private class SmallTableAliasMethodDiscreteSampler internal constructor(
|
private class SmallTableAliasMethodDiscreteSampler(
|
||||||
probability: LongArray,
|
probability: LongArray,
|
||||||
alias: IntArray
|
alias: IntArray
|
||||||
) : AliasMethodDiscreteSampler(probability, alias) {
|
) : AliasMethodDiscreteSampler(probability, alias) {
|
||||||
@ -71,7 +71,7 @@ public open class AliasMethodDiscreteSampler private constructor(
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
override fun sample(generator: RandomGenerator): Chain<Int> = generator.chain {
|
public override fun sample(generator: RandomGenerator): Chain<Int> = generator.chain {
|
||||||
// This implements the algorithm as per Vose (1991):
|
// This implements the algorithm as per Vose (1991):
|
||||||
// v = uniform() in [0, 1)
|
// v = uniform() in [0, 1)
|
||||||
// j = uniform(n) in [0, n)
|
// j = uniform(n) in [0, n)
|
||||||
|
@ -1,2 +0,0 @@
|
|||||||
package kscience.kmath.prob.samplers
|
|
||||||
|
|
@ -1,2 +0,0 @@
|
|||||||
package kscience.kmath.prob.samplers
|
|
||||||
|
|
@ -26,35 +26,24 @@ public class ZigguratNormalizedGaussianSampler private constructor() :
|
|||||||
public override fun sample(generator: RandomGenerator): Chain<Double> = generator.chain { sampleOne(this) }
|
public override fun sample(generator: RandomGenerator): Chain<Double> = generator.chain { sampleOne(this) }
|
||||||
public override fun toString(): String = "Ziggurat normalized Gaussian deviate"
|
public override fun toString(): String = "Ziggurat normalized Gaussian deviate"
|
||||||
|
|
||||||
private fun fix(
|
private fun fix(generator: RandomGenerator, hz: Long, iz: Int): Double {
|
||||||
generator: RandomGenerator,
|
var x = hz * W[iz]
|
||||||
hz: Long,
|
|
||||||
iz: Int
|
|
||||||
): Double {
|
|
||||||
var x: Double
|
|
||||||
var y: Double
|
|
||||||
x = hz * W[iz]
|
|
||||||
|
|
||||||
return if (iz == 0) {
|
return when {
|
||||||
// Base strip.
|
iz == 0 -> {
|
||||||
// This branch is called about 5.7624515E-4 times per sample.
|
var y: Double
|
||||||
do {
|
|
||||||
y = -ln(generator.nextDouble())
|
|
||||||
x = -ln(generator.nextDouble()) * ONE_OVER_R
|
|
||||||
} while (y + y < x * x)
|
|
||||||
|
|
||||||
val out = R + x
|
do {
|
||||||
if (hz > 0) out else -out
|
y = -ln(generator.nextDouble())
|
||||||
} else {
|
x = -ln(generator.nextDouble()) * ONE_OVER_R
|
||||||
// Wedge of other strips.
|
} while (y + y < x * x)
|
||||||
// This branch is called about 0.027323 times per sample.
|
|
||||||
// else
|
val out = R + x
|
||||||
// Try again.
|
if (hz > 0) out else -out
|
||||||
// This branch is called about 0.012362 times per sample.
|
}
|
||||||
if (F[iz] + generator.nextDouble() * (F[iz - 1] - F[iz]) < gauss(
|
|
||||||
x
|
F[iz] + generator.nextDouble() * (F[iz - 1] - F[iz]) < gauss(x) -> x
|
||||||
)
|
else -> sampleOne(generator)
|
||||||
) x else sampleOne(generator)
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -3,10 +3,14 @@ package kscience.kmath.prob
|
|||||||
import org.apache.commons.rng.UniformRandomProvider
|
import org.apache.commons.rng.UniformRandomProvider
|
||||||
import org.apache.commons.rng.simple.RandomSource
|
import org.apache.commons.rng.simple.RandomSource
|
||||||
|
|
||||||
public class RandomSourceGenerator(public val source: RandomSource, seed: Long?) : RandomGenerator {
|
/**
|
||||||
internal val random: UniformRandomProvider = seed?.let {
|
* Implements [RandomGenerator] by delegating all operations to [RandomSource].
|
||||||
RandomSource.create(source, seed)
|
*
|
||||||
} ?: RandomSource.create(source)
|
* @property source the underlying [RandomSource] object.
|
||||||
|
*/
|
||||||
|
public class RandomSourceGenerator internal constructor(public val source: RandomSource, seed: Long?) : RandomGenerator {
|
||||||
|
internal val random: UniformRandomProvider = seed?.let { RandomSource.create(source, seed) }
|
||||||
|
?: RandomSource.create(source)
|
||||||
|
|
||||||
public override fun nextBoolean(): Boolean = random.nextBoolean()
|
public override fun nextBoolean(): Boolean = random.nextBoolean()
|
||||||
public override fun nextDouble(): Double = random.nextDouble()
|
public override fun nextDouble(): Double = random.nextDouble()
|
||||||
@ -23,19 +27,84 @@ public class RandomSourceGenerator(public val source: RandomSource, seed: Long?)
|
|||||||
public override fun fork(): RandomGenerator = RandomSourceGenerator(source, nextLong())
|
public override fun fork(): RandomGenerator = RandomSourceGenerator(source, nextLong())
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Implements [UniformRandomProvider] by delegating all operations to [RandomGenerator].
|
||||||
|
*
|
||||||
|
* @property generator the underlying [RandomGenerator] object.
|
||||||
|
*/
|
||||||
public inline class RandomGeneratorProvider(public val generator: RandomGenerator) : UniformRandomProvider {
|
public inline class RandomGeneratorProvider(public val generator: RandomGenerator) : UniformRandomProvider {
|
||||||
|
/**
|
||||||
|
* Generates a [Boolean] value.
|
||||||
|
*
|
||||||
|
* @return the next random value.
|
||||||
|
*/
|
||||||
public override fun nextBoolean(): Boolean = generator.nextBoolean()
|
public override fun nextBoolean(): Boolean = generator.nextBoolean()
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates a [Float] value between 0 and 1.
|
||||||
|
*
|
||||||
|
* @return the next random value between 0 and 1.
|
||||||
|
*/
|
||||||
public override fun nextFloat(): Float = generator.nextDouble().toFloat()
|
public override fun nextFloat(): Float = generator.nextDouble().toFloat()
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates [Byte] values and places them into a user-supplied array.
|
||||||
|
*
|
||||||
|
* The number of random bytes produced is equal to the length of the the byte array.
|
||||||
|
*
|
||||||
|
* @param bytes byte array in which to put the random bytes.
|
||||||
|
*/
|
||||||
public override fun nextBytes(bytes: ByteArray): Unit = generator.fillBytes(bytes)
|
public override fun nextBytes(bytes: ByteArray): Unit = generator.fillBytes(bytes)
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates [Byte] values and places them into a user-supplied array.
|
||||||
|
*
|
||||||
|
* The array is filled with bytes extracted from random integers. This implies that the number of random bytes
|
||||||
|
* generated may be larger than the length of the byte array.
|
||||||
|
*
|
||||||
|
* @param bytes the array in which to put the generated bytes.
|
||||||
|
* @param start the index at which to start inserting the generated bytes.
|
||||||
|
* @param len the number of bytes to insert.
|
||||||
|
*/
|
||||||
public override fun nextBytes(bytes: ByteArray, start: Int, len: Int) {
|
public override fun nextBytes(bytes: ByteArray, start: Int, len: Int) {
|
||||||
generator.fillBytes(bytes, start, start + len)
|
generator.fillBytes(bytes, start, start + len)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates an [Int] value.
|
||||||
|
*
|
||||||
|
* @return the next random value.
|
||||||
|
*/
|
||||||
public override fun nextInt(): Int = generator.nextInt()
|
public override fun nextInt(): Int = generator.nextInt()
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates an [Int] value between 0 (inclusive) and the specified value (exclusive).
|
||||||
|
*
|
||||||
|
* @param n the bound on the random number to be returned. Must be positive.
|
||||||
|
* @return a random integer between 0 (inclusive) and [n] (exclusive).
|
||||||
|
*/
|
||||||
public override fun nextInt(n: Int): Int = generator.nextInt(n)
|
public override fun nextInt(n: Int): Int = generator.nextInt(n)
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates a [Double] value between 0 and 1.
|
||||||
|
*
|
||||||
|
* @return the next random value between 0 and 1.
|
||||||
|
*/
|
||||||
public override fun nextDouble(): Double = generator.nextDouble()
|
public override fun nextDouble(): Double = generator.nextDouble()
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates a [Long] value.
|
||||||
|
*
|
||||||
|
* @return the next random value.
|
||||||
|
*/
|
||||||
public override fun nextLong(): Long = generator.nextLong()
|
public override fun nextLong(): Long = generator.nextLong()
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates a [Long] value between 0 (inclusive) and the specified value (exclusive).
|
||||||
|
*
|
||||||
|
* @param n Bound on the random number to be returned. Must be positive.
|
||||||
|
* @return a random long value between 0 (inclusive) and [n] (exclusive).
|
||||||
|
*/
|
||||||
public override fun nextLong(n: Long): Long = generator.nextLong(n)
|
public override fun nextLong(n: Long): Long = generator.nextLong(n)
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -48,8 +117,14 @@ public fun RandomGenerator.asUniformRandomProvider(): UniformRandomProvider = if
|
|||||||
else
|
else
|
||||||
RandomGeneratorProvider(this)
|
RandomGeneratorProvider(this)
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns [RandomSourceGenerator] with given [RandomSource] and [seed].
|
||||||
|
*/
|
||||||
public fun RandomGenerator.Companion.fromSource(source: RandomSource, seed: Long? = null): RandomSourceGenerator =
|
public fun RandomGenerator.Companion.fromSource(source: RandomSource, seed: Long? = null): RandomSourceGenerator =
|
||||||
RandomSourceGenerator(source, seed)
|
RandomSourceGenerator(source, seed)
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Returns [RandomSourceGenerator] with [RandomSource.MT] algorithm and given [seed].
|
||||||
|
*/
|
||||||
public fun RandomGenerator.Companion.mersenneTwister(seed: Long? = null): RandomSourceGenerator =
|
public fun RandomGenerator.Companion.mersenneTwister(seed: Long? = null): RandomSourceGenerator =
|
||||||
fromSource(RandomSource.MT, seed)
|
fromSource(RandomSource.MT, seed)
|
||||||
|
@ -7,11 +7,8 @@ class SamplerTest {
|
|||||||
|
|
||||||
@Test
|
@Test
|
||||||
fun bufferSamplerTest() {
|
fun bufferSamplerTest() {
|
||||||
val sampler: Sampler<Double> =
|
val sampler = Sampler { it.chain { nextDouble() } }
|
||||||
BasicSampler { it.chain { nextDouble() } }
|
|
||||||
val data = sampler.sampleBuffer(RandomGenerator.default, 100)
|
val data = sampler.sampleBuffer(RandomGenerator.default, 100)
|
||||||
runBlocking {
|
runBlocking { println(data.next()) }
|
||||||
println(data.next())
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
}
|
}
|
Loading…
Reference in New Issue
Block a user