Dev #280

Merged
altavir merged 99 commits from dev into master 2021-04-16 19:45:55 +03:00
22 changed files with 194 additions and 127 deletions
Showing only changes of commit 612f6f0082 - Show all commits

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@ -31,4 +31,4 @@ fun main() {
strides.indices().forEach { res = array[strides.offset(it)] }
}
println("Array reading finished in $time3 millis")
}
}

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@ -1,3 +1,5 @@
import ru.mipt.npm.gradle.Maturity
plugins {
id("ru.mipt.npm.mpp")
id("ru.mipt.npm.native")
@ -11,36 +13,42 @@ kotlin.sourceSets.commonMain {
readme {
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"))
feature(
id = "algebras",
description = "Algebraic structures: contexts and elements",
ref = "src/commonMain/kotlin/kscience/kmath/operations/Algebra.kt"
)
feature(
id = "nd",
description = "Many-dimensional structures",
ref = "src/commonMain/kotlin/kscience/kmath/structures/NDStructure.kt"
)
feature(
id = "buffers",
description = "One-dimensional structure",
ref = "src/commonMain/kotlin/kscience/kmath/structures/Buffers.kt"
)
feature(
id = "expressions",
description = "Functional Expressions",
ref = "src/commonMain/kotlin/kscience/kmath/expressions"
)
feature(
id = "domains",
description = "Domains",
ref = "src/commonMain/kotlin/kscience/kmath/domains"
)
feature(
id = "autodif",
description = "Automatic differentiation",
ref = "src/commonMain/kotlin/kscience/kmath/misc/AutoDiff.kt"
)
}
}

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@ -237,18 +237,18 @@ public class BigInt internal constructor(
)
private fun compareMagnitudes(mag1: Magnitude, mag2: Magnitude): Int {
when {
mag1.size > mag2.size -> return 1
mag1.size < mag2.size -> return -1
return when {
mag1.size > mag2.size -> 1
mag1.size < mag2.size -> -1
else -> {
for (i in mag1.size - 1 downTo 0) {
if (mag1[i] > mag2[i]) {
return 1
} else if (mag1[i] < mag2[i]) {
return -1
}
for (i in mag1.size - 1 downTo 0) return when {
mag1[i] > mag2[i] -> 1
mag1[i] < mag2[i] -> -1
else -> continue
}
return 0
0
}
}
}
@ -298,10 +298,11 @@ public class BigInt internal constructor(
var carry = 0uL
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()
carry = cur shr BASE_SIZE
}
result[resultLength - 1] = (carry and BASE).toUInt()
return stripLeadingZeros(result)

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@ -71,7 +71,7 @@ public interface Buffer<T> {
@Suppress("UNCHECKED_CAST")
public inline fun <T : Any> auto(type: KClass<T>, size: Int, initializer: (Int) -> T): Buffer<T> =
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>
Int::class -> IntBuffer(size) { initializer(it) as Int } as Buffer<T>
Long::class -> LongBuffer(size) { initializer(it) as Long } as Buffer<T>

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@ -22,7 +22,7 @@ public interface Structure2D<T> : NDStructure<T> {
override fun elements(): Sequence<Pair<IntArray, T>> = sequence {
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
@ -35,7 +35,6 @@ private inline class Structure2DWrapper<T>(val structure: NDStructure<T>) : Stru
override val shape: IntArray get() = structure.shape
override operator fun get(i: Int, j: Int): T = structure[i, j]
override fun elements(): Sequence<Pair<IntArray, T>> = structure.elements()
}

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@ -29,12 +29,11 @@ class NumberNDFieldTest {
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) {
val expected = (i * 10 + j).toDouble()
assertEquals(expected, array[i, j], "Error at index [$i, $j]")
}
}
}
@Test

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@ -63,12 +63,10 @@ public class MarkovChain<out R : Any>(private val seed: suspend () -> R, private
public fun value(): R? = value
public override suspend fun next(): R {
mutex.withLock {
val newValue = gen(value ?: seed())
value = newValue
return newValue
}
public override suspend fun next(): R = mutex.withLock {
val newValue = gen(value ?: seed())
value = newValue
newValue
}
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 override suspend fun next(): R {
mutex.withLock {
val newValue = state.gen(value ?: state.seed())
value = newValue
return newValue
}
public override suspend fun next(): R = mutex.withLock {
val newValue = state.gen(value ?: state.seed())
value = newValue
newValue
}
public override fun fork(): Chain<R> = StatefulChain(forkState(state), seed, forkState, gen)

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@ -28,7 +28,7 @@ public fun <T> Flow<T>.chunked(bufferSize: Int, bufferFactory: BufferFactory<T>)
var counter = 0
this@chunked.collect { element ->
list.add(element)
list += element
counter++
if (counter == bufferSize) {

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@ -48,11 +48,9 @@ public class RingBuffer<T>(
/**
* A safe snapshot operation
*/
public suspend fun snapshot(): Buffer<T> {
mutex.withLock {
val copy = buffer.copy()
return VirtualBuffer(size) { i -> copy[startIndex.forward(i)] as T }
}
public suspend fun snapshot(): Buffer<T> = mutex.withLock {
val copy = buffer.copy()
VirtualBuffer(size) { i -> copy[startIndex.forward(i)] as T }
}
public suspend fun push(element: T) {

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@ -23,8 +23,8 @@ public class OrderedPiecewisePolynomial<T : Comparable<T>>(delimiter: T) :
*/
public fun putRight(right: T, piece: Polynomial<T>) {
require(right > delimiters.last()) { "New delimiter should be to the right of old one" }
delimiters.add(right)
pieces.add(piece)
delimiters += right
pieces += piece
}
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? =
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) }

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@ -5,8 +5,18 @@ import kscience.kmath.chains.Chain
import kscience.kmath.chains.collect
import kscience.kmath.structures.Buffer
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> {
/**
* Generates a chain of samples.
*
* @param generator the randomness provider.
* @return the new chain.
*/
public fun sample(generator: RandomGenerator): Chain<T>
}
@ -59,16 +69,25 @@ public fun <T : Any> Sampler<T>.sampleBuffer(
//clear list from previous run
tmp.clear()
//Fill list
repeat(size) { tmp.add(chain.next()) }
repeat(size) { tmp += chain.next() }
//return new buffer with elements from tmp
bufferFactory(size) { tmp[it] }
}
}
/**
* Samples one value from this [Sampler].
*/
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>> =
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)

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@ -38,6 +38,6 @@ public class DistributionBuilder<T : Any> {
private val distributions = ArrayList<NamedDistribution<T>>()
public infix fun String.to(distribution: Distribution<T>) {
distributions.add(NamedDistributionWrapper(this, distribution))
distributions += NamedDistributionWrapper(this, distribution)
}
}

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@ -82,6 +82,8 @@ public interface RandomGenerator {
/**
* 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 override fun nextBoolean(): Boolean = random.nextBoolean()

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@ -7,25 +7,28 @@ import kscience.kmath.chains.zip
import kscience.kmath.operations.Space
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 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 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 } }
}
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() } }
}
}

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@ -98,28 +98,21 @@ internal object InternalGamma {
private const val INV_GAMMA1P_M1_C12 = .113302723198169588237412962033074E-05
private const val INV_GAMMA1P_M1_C13 = -.205633841697760710345015413002057E-06
fun logGamma(x: Double): Double {
val ret: Double
fun logGamma(x: Double): Double = when {
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.isNaN() || x <= 0.0 -> ret = Double.NaN
x < 0.5 -> return logGamma1p(x) - ln(x)
x <= 2.5 -> return logGamma1p(x - 0.5 - 0.5)
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)
}
x <= 8.0 -> {
val n = floor(x - 1.5).toInt()
val prod = (1..n).fold(1.0, { prod, i -> prod * (x - i) })
logGamma1p(x - (n + 1)) + ln(prod)
}
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(

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@ -20,24 +20,17 @@ internal object InternalUtils {
fun validateProbabilities(probabilities: DoubleArray?): Double {
require(!(probabilities == null || probabilities.isEmpty())) { "Probabilities must not be empty." }
var sumProb = 0.0
probabilities.forEach { prob ->
validateProbability(prob)
sumProb += prob
val sumProb = probabilities.sumByDouble { prob ->
require(!(prob < 0 || prob.isInfinite() || prob.isNaN())) { "Invalid probability: $prob" }
prob
}
require(!(sumProb.isInfinite() || sumProb <= 0)) { "Invalid sum of probabilities: $sumProb" }
return sumProb
}
private fun validateProbability(probability: Double): Unit =
require(!(probability < 0 || probability.isInfinite() || probability.isNaN())) { "Invalid probability: $probability" }
class FactorialLog private constructor(
numValues: Int,
cache: DoubleArray?
) {
class FactorialLog private constructor(numValues: Int, cache: DoubleArray?) {
private val logFactorials: DoubleArray = DoubleArray(numValues)
init {
@ -46,14 +39,15 @@ internal object InternalUtils {
if (cache != null && cache.size > BEGIN_LOG_FACTORIALS) {
// Copy available values.
endCopy = min(cache.size, numValues)
cache.copyInto(
logFactorials,
BEGIN_LOG_FACTORIALS,
BEGIN_LOG_FACTORIALS, endCopy
)
}
} else
// All values to be computed
else endCopy = BEGIN_LOG_FACTORIALS
endCopy = BEGIN_LOG_FACTORIALS
// Compute remaining values.
(endCopy until numValues).forEach { i ->
@ -65,9 +59,7 @@ internal object InternalUtils {
}
fun value(n: Int): Double {
if (n < logFactorials.size)
return logFactorials[n]
if (n < logFactorials.size) return logFactorials[n]
return if (n < FACTORIALS.size) ln(FACTORIALS[n].toDouble()) else InternalGamma.logGamma(n + 1.0)
}

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@ -42,7 +42,7 @@ public open class AliasMethodDiscreteSampler private constructor(
protected val alias: IntArray
) : Sampler<Int> {
private class SmallTableAliasMethodDiscreteSampler internal constructor(
private class SmallTableAliasMethodDiscreteSampler(
probability: LongArray,
alias: IntArray
) : 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):
// v = uniform() in [0, 1)
// j = uniform(n) in [0, n)

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@ -1,2 +0,0 @@
package kscience.kmath.prob.samplers

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@ -1,2 +0,0 @@
package kscience.kmath.prob.samplers

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@ -26,35 +26,24 @@ public class ZigguratNormalizedGaussianSampler private constructor() :
public override fun sample(generator: RandomGenerator): Chain<Double> = generator.chain { sampleOne(this) }
public override fun toString(): String = "Ziggurat normalized Gaussian deviate"
private fun fix(
generator: RandomGenerator,
hz: Long,
iz: Int
): Double {
var x: Double
var y: Double
x = hz * W[iz]
private fun fix(generator: RandomGenerator, hz: Long, iz: Int): Double {
var x = hz * W[iz]
return if (iz == 0) {
// Base strip.
// This branch is called about 5.7624515E-4 times per sample.
do {
y = -ln(generator.nextDouble())
x = -ln(generator.nextDouble()) * ONE_OVER_R
} while (y + y < x * x)
return when {
iz == 0 -> {
var y: Double
val out = R + x
if (hz > 0) out else -out
} else {
// Wedge of other strips.
// This branch is called about 0.027323 times per sample.
// else
// Try again.
// This branch is called about 0.012362 times per sample.
if (F[iz] + generator.nextDouble() * (F[iz - 1] - F[iz]) < gauss(
x
)
) x else sampleOne(generator)
do {
y = -ln(generator.nextDouble())
x = -ln(generator.nextDouble()) * ONE_OVER_R
} while (y + y < x * x)
val out = R + x
if (hz > 0) out else -out
}
F[iz] + generator.nextDouble() * (F[iz - 1] - F[iz]) < gauss(x) -> x
else -> sampleOne(generator)
}
}

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@ -3,10 +3,14 @@ package kscience.kmath.prob
import org.apache.commons.rng.UniformRandomProvider
import org.apache.commons.rng.simple.RandomSource
public class RandomSourceGenerator(public val source: RandomSource, seed: Long?) : RandomGenerator {
internal val random: UniformRandomProvider = seed?.let {
RandomSource.create(source, seed)
} ?: RandomSource.create(source)
/**
* Implements [RandomGenerator] by delegating all operations to [RandomSource].
*
* @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 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())
}
/**
* Implements [UniformRandomProvider] by delegating all operations to [RandomGenerator].
*
* @property generator the underlying [RandomGenerator] object.
*/
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()
/**
* 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()
/**
* 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)
/**
* 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) {
generator.fillBytes(bytes, start, start + len)
}
/**
* Generates an [Int] value.
*
* @return the next random value.
*/
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)
/**
* Generates a [Double] value between 0 and 1.
*
* @return the next random value between 0 and 1.
*/
public override fun nextDouble(): Double = generator.nextDouble()
/**
* Generates a [Long] value.
*
* @return the next random value.
*/
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)
}
@ -48,8 +117,14 @@ public fun RandomGenerator.asUniformRandomProvider(): UniformRandomProvider = if
else
RandomGeneratorProvider(this)
/**
* Returns [RandomSourceGenerator] with given [RandomSource] and [seed].
*/
public fun RandomGenerator.Companion.fromSource(source: RandomSource, seed: Long? = null): RandomSourceGenerator =
RandomSourceGenerator(source, seed)
/**
* Returns [RandomSourceGenerator] with [RandomSource.MT] algorithm and given [seed].
*/
public fun RandomGenerator.Companion.mersenneTwister(seed: Long? = null): RandomSourceGenerator =
fromSource(RandomSource.MT, seed)

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@ -7,11 +7,8 @@ class SamplerTest {
@Test
fun bufferSamplerTest() {
val sampler: Sampler<Double> =
BasicSampler { it.chain { nextDouble() } }
val sampler = Sampler { it.chain { nextDouble() } }
val data = sampler.sampleBuffer(RandomGenerator.default, 100)
runBlocking {
println(data.next())
}
runBlocking { println(data.next()) }
}
}