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Refactoring

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This commit is contained in:
Alexander Nozik 2021-11-09 13:42:22 +03:00
parent f6b576071d
commit d62bc66d4a
32 changed files with 86 additions and 55 deletions
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21
benchmarks/src/jvmMain/kotlin/space/kscience/kmath/benchmarks/BufferBenchmark.kt
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@ -6,31 +6,38 @@
package space.kscience.kmath.benchmarks package space.kscience.kmath.benchmarks
import kotlinx.benchmark.Benchmark import kotlinx.benchmark.Benchmark
import kotlinx.benchmark.Blackhole
import kotlinx.benchmark.Scope import kotlinx.benchmark.Scope
import kotlinx.benchmark.State import kotlinx.benchmark.State
import space.kscience.kmath.complex.Complex import space.kscience.kmath.complex.Complex
import space.kscience.kmath.complex.ComplexField
import space.kscience.kmath.complex.complex import space.kscience.kmath.complex.complex
import space.kscience.kmath.operations.invoke
import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.structures.DoubleBuffer import space.kscience.kmath.structures.DoubleBuffer
import space.kscience.kmath.structures.MutableBuffer
@State(Scope.Benchmark) @State(Scope.Benchmark)
internal class BufferBenchmark { internal class BufferBenchmark {
@Benchmark @Benchmark
fun genericDoubleBufferReadWrite() { fun genericDoubleBufferReadWrite(blackhole: Blackhole) {
val buffer = DoubleBuffer(size) { it.toDouble() } val buffer = DoubleBuffer(size) { it.toDouble() }
var res = 0.0
(0 until size).forEach { (0 until size).forEach {
buffer[it] res += buffer[it]
} }
blackhole.consume(res)
} }
@Benchmark @Benchmark
fun complexBufferReadWrite() { fun complexBufferReadWrite(blackhole: Blackhole) = ComplexField {
val buffer = MutableBuffer.complex(size / 2) { Complex(it.toDouble(), -it.toDouble()) } val buffer = Buffer.complex(size / 2) { Complex(it.toDouble(), -it.toDouble()) }
var res = zero
(0 until size / 2).forEach { (0 until size / 2).forEach {
buffer[it] res += buffer[it]
} }
blackhole.consume(res)
} }
private companion object { private companion object {

2
examples/src/main/kotlin/space/kscience/kmath/fit/chiSquared.kt
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@ -16,10 +16,10 @@ import space.kscience.kmath.optimization.FunctionOptimizationTarget
import space.kscience.kmath.optimization.optimizeWith import space.kscience.kmath.optimization.optimizeWith
import space.kscience.kmath.optimization.resultPoint import space.kscience.kmath.optimization.resultPoint
import space.kscience.kmath.optimization.resultValue import space.kscience.kmath.optimization.resultValue
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.real.DoubleVector import space.kscience.kmath.real.DoubleVector
import space.kscience.kmath.real.map import space.kscience.kmath.real.map
import space.kscience.kmath.real.step import space.kscience.kmath.real.step
import space.kscience.kmath.stat.RandomGenerator
import space.kscience.kmath.structures.asIterable import space.kscience.kmath.structures.asIterable
import space.kscience.kmath.structures.toList import space.kscience.kmath.structures.toList
import space.kscience.plotly.* import space.kscience.plotly.*

2
examples/src/main/kotlin/space/kscience/kmath/fit/qowFit.kt
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@ -17,9 +17,9 @@ import space.kscience.kmath.optimization.QowOptimizer
import space.kscience.kmath.optimization.chiSquaredOrNull import space.kscience.kmath.optimization.chiSquaredOrNull
import space.kscience.kmath.optimization.fitWith import space.kscience.kmath.optimization.fitWith
import space.kscience.kmath.optimization.resultPoint import space.kscience.kmath.optimization.resultPoint
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.real.map import space.kscience.kmath.real.map
import space.kscience.kmath.real.step import space.kscience.kmath.real.step
import space.kscience.kmath.stat.RandomGenerator
import space.kscience.kmath.structures.asIterable import space.kscience.kmath.structures.asIterable
import space.kscience.kmath.structures.toList import space.kscience.kmath.structures.toList
import space.kscience.plotly.* import space.kscience.plotly.*

1
examples/src/main/kotlin/space/kscience/kmath/stat/DistributionBenchmark.kt
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@ -10,6 +10,7 @@ import kotlinx.coroutines.async
import kotlinx.coroutines.runBlocking import kotlinx.coroutines.runBlocking
import org.apache.commons.rng.sampling.distribution.BoxMullerNormalizedGaussianSampler import org.apache.commons.rng.sampling.distribution.BoxMullerNormalizedGaussianSampler
import org.apache.commons.rng.simple.RandomSource import org.apache.commons.rng.simple.RandomSource
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.samplers.GaussianSampler import space.kscience.kmath.samplers.GaussianSampler
import java.time.Duration import java.time.Duration
import java.time.Instant import java.time.Instant

1
examples/src/main/kotlin/space/kscience/kmath/stat/DistributionDemo.kt
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@ -9,6 +9,7 @@ import kotlinx.coroutines.runBlocking
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.chains.collectWithState import space.kscience.kmath.chains.collectWithState
import space.kscience.kmath.distributions.NormalDistribution import space.kscience.kmath.distributions.NormalDistribution
import space.kscience.kmath.random.RandomGenerator
private data class AveragingChainState(var num: Int = 0, var value: Double = 0.0) private data class AveragingChainState(var num: Int = 0, var value: Double = 0.0)

2
kmath-commons/src/main/kotlin/space/kscience/kmath/commons/random/CMRandomGeneratorWrapper.kt
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@ -8,9 +8,9 @@ package space.kscience.kmath.commons.random
import kotlinx.coroutines.runBlocking import kotlinx.coroutines.runBlocking
import space.kscience.kmath.misc.PerformancePitfall import space.kscience.kmath.misc.PerformancePitfall
import space.kscience.kmath.misc.toIntExact import space.kscience.kmath.misc.toIntExact
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.samplers.GaussianSampler import space.kscience.kmath.samplers.GaussianSampler
import space.kscience.kmath.samplers.next import space.kscience.kmath.samplers.next
import space.kscience.kmath.stat.RandomGenerator
public class CMRandomGeneratorWrapper( public class CMRandomGeneratorWrapper(

2
kmath-commons/src/test/kotlin/space/kscience/kmath/commons/optimization/OptimizeTest.kt
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@ -14,7 +14,7 @@ import space.kscience.kmath.expressions.Symbol.Companion.y
import space.kscience.kmath.expressions.chiSquaredExpression import space.kscience.kmath.expressions.chiSquaredExpression
import space.kscience.kmath.expressions.symbol import space.kscience.kmath.expressions.symbol
import space.kscience.kmath.optimization.* import space.kscience.kmath.optimization.*
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.DoubleBuffer import space.kscience.kmath.structures.DoubleBuffer
import space.kscience.kmath.structures.asBuffer import space.kscience.kmath.structures.asBuffer
import space.kscience.kmath.structures.map import space.kscience.kmath.structures.map

27
kmath-core/src/commonMain/kotlin/space/kscience/kmath/operations/BufferAlgebra.kt
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@ -21,11 +21,6 @@ public interface BufferAlgebra<T, out A : Algebra<T>> : Algebra<Buffer<T>> {
public val elementAlgebra: A public val elementAlgebra: A
public val bufferFactory: BufferFactory<T> public val bufferFactory: BufferFactory<T>
public fun buffer(size: Int, vararg elements: T): Buffer<T> {
require(elements.size == size) { "Expected $size elements but found ${elements.size}" }
return bufferFactory(size) { elements[it] }
}
//TODO move to multi-receiver inline extension //TODO move to multi-receiver inline extension
public fun Buffer<T>.map(block: A.(T) -> T): Buffer<T> = mapInline(this, block) public fun Buffer<T>.map(block: A.(T) -> T): Buffer<T> = mapInline(this, block)
@ -49,12 +44,15 @@ public interface BufferAlgebra<T, out A : Algebra<T>> : Algebra<Buffer<T>> {
} }
} }
public fun <T, A : Algebra<T>> BufferAlgebra<T, A>.buffer(vararg elements: T): Buffer<T> =
bufferFactory(elements.size) { elements[it] }
/** /**
* Inline map * Inline map
*/ */
private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.mapInline( private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.mapInline(
buffer: Buffer<T>, buffer: Buffer<T>,
crossinline block: A.(T) -> T crossinline block: A.(T) -> T,
): Buffer<T> = bufferFactory(buffer.size) { elementAlgebra.block(buffer[it]) } ): Buffer<T> = bufferFactory(buffer.size) { elementAlgebra.block(buffer[it]) }
/** /**
@ -62,7 +60,7 @@ private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.mapInline(
*/ */
private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.mapIndexedInline( private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.mapIndexedInline(
buffer: Buffer<T>, buffer: Buffer<T>,
crossinline block: A.(index: Int, arg: T) -> T crossinline block: A.(index: Int, arg: T) -> T,
): Buffer<T> = bufferFactory(buffer.size) { elementAlgebra.block(it, buffer[it]) } ): Buffer<T> = bufferFactory(buffer.size) { elementAlgebra.block(it, buffer[it]) }
/** /**
@ -71,7 +69,7 @@ private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.mapIndexedInline(
private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.zipInline( private inline fun <T, A : Algebra<T>> BufferAlgebra<T, A>.zipInline(
l: Buffer<T>, l: Buffer<T>,
r: Buffer<T>, r: Buffer<T>,
crossinline block: A.(l: T, r: T) -> T crossinline block: A.(l: T, r: T) -> T,
): Buffer<T> { ): Buffer<T> {
require(l.size == r.size) { "Incompatible buffer sizes. left: ${l.size}, right: ${r.size}" } require(l.size == r.size) { "Incompatible buffer sizes. left: ${l.size}, right: ${r.size}" }
return bufferFactory(l.size) { elementAlgebra.block(l[it], r[it]) } return bufferFactory(l.size) { elementAlgebra.block(l[it], r[it]) }
@ -128,13 +126,13 @@ public fun <T, A : ExponentialOperations<T>> BufferAlgebra<T, A>.atanh(arg: Buff
mapInline(arg) { atanh(it) } mapInline(arg) { atanh(it) }
public fun <T, A : PowerOperations<T>> BufferAlgebra<T, A>.pow(arg: Buffer<T>, pow: Number): Buffer<T> = public fun <T, A : PowerOperations<T>> BufferAlgebra<T, A>.pow(arg: Buffer<T>, pow: Number): Buffer<T> =
mapInline(arg) {it.pow(pow) } mapInline(arg) { it.pow(pow) }
public open class BufferRingOps<T, A: Ring<T>>( public open class BufferRingOps<T, A : Ring<T>>(
override val elementAlgebra: A, override val elementAlgebra: A,
override val bufferFactory: BufferFactory<T>, override val bufferFactory: BufferFactory<T>,
) : BufferAlgebra<T, A>, RingOps<Buffer<T>>{ ) : BufferAlgebra<T, A>, RingOps<Buffer<T>> {
override fun add(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l + r } override fun add(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l + r }
override fun multiply(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l * r } override fun multiply(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l * r }
@ -155,7 +153,8 @@ public val ShortRing.bufferAlgebra: BufferRingOps<Short, ShortRing>
public open class BufferFieldOps<T, A : Field<T>>( public open class BufferFieldOps<T, A : Field<T>>(
elementAlgebra: A, elementAlgebra: A,
bufferFactory: BufferFactory<T>, bufferFactory: BufferFactory<T>,
) : BufferRingOps<T, A>(elementAlgebra, bufferFactory), BufferAlgebra<T, A>, FieldOps<Buffer<T>>, ScaleOperations<Buffer<T>> { ) : BufferRingOps<T, A>(elementAlgebra, bufferFactory), BufferAlgebra<T, A>, FieldOps<Buffer<T>>,
ScaleOperations<Buffer<T>> {
override fun add(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l + r } override fun add(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l + r }
override fun multiply(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l * r } override fun multiply(left: Buffer<T>, right: Buffer<T>): Buffer<T> = zipInline(left, right) { l, r -> l * r }
@ -172,7 +171,7 @@ public open class BufferFieldOps<T, A : Field<T>>(
public class BufferField<T, A : Field<T>>( public class BufferField<T, A : Field<T>>(
elementAlgebra: A, elementAlgebra: A,
bufferFactory: BufferFactory<T>, bufferFactory: BufferFactory<T>,
override val size: Int override val size: Int,
) : BufferFieldOps<T, A>(elementAlgebra, bufferFactory), Field<Buffer<T>>, WithSize { ) : BufferFieldOps<T, A>(elementAlgebra, bufferFactory), Field<Buffer<T>>, WithSize {
override val zero: Buffer<T> = bufferFactory(size) { elementAlgebra.zero } override val zero: Buffer<T> = bufferFactory(size) { elementAlgebra.zero }
@ -195,4 +194,4 @@ public fun BufferField<Double, *>.buffer(vararg elements: Number): Buffer<Double
public fun <T, A : Field<T>> A.bufferAlgebra(bufferFactory: BufferFactory<T>): BufferFieldOps<T, A> = public fun <T, A : Field<T>> A.bufferAlgebra(bufferFactory: BufferFactory<T>): BufferFieldOps<T, A> =
BufferFieldOps(this, bufferFactory) BufferFieldOps(this, bufferFactory)
public val DoubleField.bufferAlgebra: DoubleBufferOps get() = DoubleBufferOps public val DoubleField.bufferAlgebra: DoubleBufferOps get() = DoubleBufferOps

9
kmath-core/src/commonMain/kotlin/space/kscience/kmath/operations/DoubleBufferOps.kt
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@ -135,6 +135,7 @@ public abstract class DoubleBufferOps : BufferAlgebra<Double, DoubleField>, Exte
override fun scale(a: Buffer<Double>, value: Double): DoubleBuffer = a.mapInline { it * value } override fun scale(a: Buffer<Double>, value: Double): DoubleBuffer = a.mapInline { it * value }
public companion object : DoubleBufferOps() { public companion object : DoubleBufferOps() {
public inline fun Buffer<Double>.mapInline(block: (Double) -> Double): DoubleBuffer = public inline fun Buffer<Double>.mapInline(block: (Double) -> Double): DoubleBuffer =
if (this is DoubleBuffer) { if (this is DoubleBuffer) {
DoubleArray(size) { block(array[it]) }.asBuffer() DoubleArray(size) { block(array[it]) }.asBuffer()
@ -144,6 +145,14 @@ public abstract class DoubleBufferOps : BufferAlgebra<Double, DoubleField>, Exte
} }
} }
public inline fun BufferAlgebra<Double, DoubleField>.buffer(size: Int, init: (Int) -> Double): DoubleBuffer {
val res = DoubleArray(size)
for (i in 0 until size) {
res[i] = init(i)
}
return res.asBuffer()
}
public object DoubleL2Norm : Norm<Point<Double>, Double> { public object DoubleL2Norm : Norm<Point<Double>, Double> {
override fun norm(arg: Point<Double>): Double = sqrt(arg.fold(0.0) { acc: Double, d: Double -> acc + d.pow(2) }) override fun norm(arg: Point<Double>): Double = sqrt(arg.fold(0.0) { acc: Double, d: Double -> acc + d.pow(2) })
} }

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/distributions/Distribution.kt
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@ -6,8 +6,8 @@
package space.kscience.kmath.distributions package space.kscience.kmath.distributions
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.samplers.Sampler import space.kscience.kmath.samplers.Sampler
import space.kscience.kmath.stat.RandomGenerator
/** /**
* A distribution of typed objects. * A distribution of typed objects.

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/distributions/FactorizedDistribution.kt
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@ -7,7 +7,7 @@ package space.kscience.kmath.distributions
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.chains.SimpleChain import space.kscience.kmath.chains.SimpleChain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
/** /**
* A multivariate distribution that takes a map of parameters. * A multivariate distribution that takes a map of parameters.

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/distributions/NormalDistribution.kt
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@ -6,11 +6,11 @@
package space.kscience.kmath.distributions package space.kscience.kmath.distributions
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.samplers.GaussianSampler import space.kscience.kmath.samplers.GaussianSampler
import space.kscience.kmath.samplers.InternalErf import space.kscience.kmath.samplers.InternalErf
import space.kscience.kmath.samplers.NormalizedGaussianSampler import space.kscience.kmath.samplers.NormalizedGaussianSampler
import space.kscience.kmath.samplers.ZigguratNormalizedGaussianSampler import space.kscience.kmath.samplers.ZigguratNormalizedGaussianSampler
import space.kscience.kmath.stat.RandomGenerator
import kotlin.math.* import kotlin.math.*
/** /**

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/distributions/UniformDistribution.kt
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@ -7,7 +7,7 @@ package space.kscience.kmath.distributions
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.chains.SimpleChain import space.kscience.kmath.chains.SimpleChain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
public class UniformDistribution(public val range: ClosedFloatingPointRange<Double>) : UnivariateDistribution<Double> { public class UniformDistribution(public val range: ClosedFloatingPointRange<Double>) : UnivariateDistribution<Double> {
private val length: Double = range.endInclusive - range.start private val length: Double = range.endInclusive - range.start

4
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/random/MCScope.kt
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@ -22,6 +22,10 @@ public class MCScope(
public val random: RandomGenerator, public val random: RandomGenerator,
) )
public fun MCScope.asCoroutineScope(): CoroutineScope = object : CoroutineScope {
override val coroutineContext: CoroutineContext get() = this@asCoroutineScope.coroutineContext
}
/** /**
* Launches a supervised Monte-Carlo scope * Launches a supervised Monte-Carlo scope
*/ */

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/AhrensDieterExponentialSampler.kt
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@ -6,7 +6,7 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingDoubleChain import space.kscience.kmath.chains.BlockingDoubleChain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.DoubleBuffer import space.kscience.kmath.structures.DoubleBuffer
import kotlin.math.ln import kotlin.math.ln
import kotlin.math.pow import kotlin.math.pow

10
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/AhrensDieterMarsagliaTsangGammaSampler.kt
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@ -6,8 +6,8 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.stat.chain import space.kscience.kmath.random.chain
import kotlin.math.* import kotlin.math.*
/** /**
@ -23,14 +23,14 @@ import kotlin.math.*
*/ */
public class AhrensDieterMarsagliaTsangGammaSampler private constructor( public class AhrensDieterMarsagliaTsangGammaSampler private constructor(
alpha: Double, alpha: Double,
theta: Double theta: Double,
) : Sampler<Double> { ) : Sampler<Double> {
private val delegate: BaseGammaSampler = private val delegate: BaseGammaSampler =
if (alpha < 1) AhrensDieterGammaSampler(alpha, theta) else MarsagliaTsangGammaSampler(alpha, theta) if (alpha < 1) AhrensDieterGammaSampler(alpha, theta) else MarsagliaTsangGammaSampler(alpha, theta)
private abstract class BaseGammaSampler internal constructor( private abstract class BaseGammaSampler internal constructor(
protected val alpha: Double, protected val alpha: Double,
protected val theta: Double protected val theta: Double,
) : Sampler<Double> { ) : Sampler<Double> {
init { init {
require(alpha > 0) { "alpha is not strictly positive: $alpha" } require(alpha > 0) { "alpha is not strictly positive: $alpha" }
@ -117,7 +117,7 @@ public class AhrensDieterMarsagliaTsangGammaSampler private constructor(
public companion object { public companion object {
public fun of( public fun of(
alpha: Double, alpha: Double,
theta: Double theta: Double,
): Sampler<Double> = AhrensDieterMarsagliaTsangGammaSampler(alpha, theta) ): Sampler<Double> = AhrensDieterMarsagliaTsangGammaSampler(alpha, theta)
} }
} }

4
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/AliasMethodDiscreteSampler.kt
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@ -6,8 +6,8 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.stat.chain import space.kscience.kmath.random.chain
import kotlin.math.ceil import kotlin.math.ceil
import kotlin.math.max import kotlin.math.max
import kotlin.math.min import kotlin.math.min

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/BoxMullerSampler.kt
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@ -6,7 +6,7 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingDoubleChain import space.kscience.kmath.chains.BlockingDoubleChain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.DoubleBuffer import space.kscience.kmath.structures.DoubleBuffer
import kotlin.math.* import kotlin.math.*

4
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/GaussianSampler.kt
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@ -7,7 +7,7 @@ package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingDoubleChain import space.kscience.kmath.chains.BlockingDoubleChain
import space.kscience.kmath.chains.map import space.kscience.kmath.chains.map
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
/** /**
* Sampling from a Gaussian distribution with given mean and standard deviation. * Sampling from a Gaussian distribution with given mean and standard deviation.
@ -21,7 +21,7 @@ import space.kscience.kmath.stat.RandomGenerator
public class GaussianSampler( public class GaussianSampler(
public val mean: Double, public val mean: Double,
public val standardDeviation: Double, public val standardDeviation: Double,
private val normalized: NormalizedGaussianSampler = BoxMullerSampler private val normalized: NormalizedGaussianSampler = BoxMullerSampler,
) : BlockingDoubleSampler { ) : BlockingDoubleSampler {
init { init {

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/KempSmallMeanPoissonSampler.kt
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@ -6,7 +6,7 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingIntChain import space.kscience.kmath.chains.BlockingIntChain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.IntBuffer import space.kscience.kmath.structures.IntBuffer
import kotlin.math.exp import kotlin.math.exp

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/MarsagliaNormalizedGaussianSampler.kt
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@ -6,7 +6,7 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingDoubleChain import space.kscience.kmath.chains.BlockingDoubleChain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.DoubleBuffer import space.kscience.kmath.structures.DoubleBuffer
import kotlin.math.ln import kotlin.math.ln
import kotlin.math.sqrt import kotlin.math.sqrt

6
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/NormalizedGaussianSampler.kt
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@ -6,9 +6,9 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingDoubleChain import space.kscience.kmath.chains.BlockingDoubleChain
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
public interface BlockingDoubleSampler: Sampler<Double>{ public interface BlockingDoubleSampler : Sampler<Double> {
override fun sample(generator: RandomGenerator): BlockingDoubleChain override fun sample(generator: RandomGenerator): BlockingDoubleChain
} }
@ -17,6 +17,6 @@ public interface BlockingDoubleSampler: Sampler<Double>{
* Marker interface for a sampler that generates values from an N(0,1) * Marker interface for a sampler that generates values from an N(0,1)
* [Gaussian distribution](https://en.wikipedia.org/wiki/Normal_distribution). * [Gaussian distribution](https://en.wikipedia.org/wiki/Normal_distribution).
*/ */
public fun interface NormalizedGaussianSampler : BlockingDoubleSampler{ public fun interface NormalizedGaussianSampler : BlockingDoubleSampler {
public companion object public companion object
} }

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/PoissonSampler.kt
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@ -7,7 +7,7 @@ package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingIntChain import space.kscience.kmath.chains.BlockingIntChain
import space.kscience.kmath.misc.toIntExact import space.kscience.kmath.misc.toIntExact
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.IntBuffer import space.kscience.kmath.structures.IntBuffer
import kotlin.math.* import kotlin.math.*

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/Sampler.kt
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@ -8,7 +8,7 @@ package space.kscience.kmath.samplers
import kotlinx.coroutines.flow.first import kotlinx.coroutines.flow.first
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.chains.collect import space.kscience.kmath.chains.collect
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.Buffer import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.structures.BufferFactory import space.kscience.kmath.structures.BufferFactory
import space.kscience.kmath.structures.DoubleBuffer import space.kscience.kmath.structures.DoubleBuffer

2
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/SamplerAlgebra.kt
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@ -12,7 +12,7 @@ import space.kscience.kmath.chains.zip
import space.kscience.kmath.operations.Group import space.kscience.kmath.operations.Group
import space.kscience.kmath.operations.ScaleOperations import space.kscience.kmath.operations.ScaleOperations
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
import space.kscience.kmath.stat.RandomGenerator import space.kscience.kmath.random.RandomGenerator
/** /**
* Implements [Sampler] by sampling only certain [value]. * Implements [Sampler] by sampling only certain [value].

3
kmath-stat/src/commonMain/kotlin/space/kscience/kmath/samplers/ZigguratNormalizedGaussianSampler.kt
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@ -6,8 +6,7 @@
package space.kscience.kmath.samplers package space.kscience.kmath.samplers
import space.kscience.kmath.chains.BlockingDoubleChain import space.kscience.kmath.chains.BlockingDoubleChain
import space.kscience.kmath.misc.toIntExact import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.stat.RandomGenerator
import space.kscience.kmath.structures.DoubleBuffer import space.kscience.kmath.structures.DoubleBuffer
import kotlin.math.* import kotlin.math.*

6
kmath-stat/src/jvmMain/kotlin/space/kscience/kmath/stat/RandomSourceGenerator.kt
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@ -7,13 +7,17 @@ package space.kscience.kmath.stat
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
import space.kscience.kmath.random.RandomGenerator
/** /**
* Implements [RandomGenerator] by delegating all operations to [RandomSource]. * Implements [RandomGenerator] by delegating all operations to [RandomSource].
* *
* @property source the underlying [RandomSource] object. * @property source the underlying [RandomSource] object.
*/ */
public class RandomSourceGenerator internal constructor(public val source: RandomSource, seed: Long?) : RandomGenerator { public class RandomSourceGenerator internal constructor(
public val source: RandomSource,
seed: Long?,
) : RandomGenerator {
internal val random: UniformRandomProvider = seed?.let { RandomSource.create(source, seed) } internal val random: UniformRandomProvider = seed?.let { RandomSource.create(source, seed) }
?: RandomSource.create(source) ?: RandomSource.create(source)

1
kmath-stat/src/jvmTest/kotlin/space/kscience/kmath/stat/CommonsDistributionsTest.kt
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@ -8,6 +8,7 @@ package space.kscience.kmath.stat
import kotlinx.coroutines.runBlocking import kotlinx.coroutines.runBlocking
import org.junit.jupiter.api.Assertions import org.junit.jupiter.api.Assertions
import org.junit.jupiter.api.Test import org.junit.jupiter.api.Test
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.samplers.GaussianSampler import space.kscience.kmath.samplers.GaussianSampler
internal class CommonsDistributionsTest { internal class CommonsDistributionsTest {

8
kmath-stat/src/jvmTest/kotlin/space/kscience/kmath/stat/MCScopeTest.kt
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@ -6,20 +6,22 @@
package space.kscience.kmath.stat package space.kscience.kmath.stat
import kotlinx.coroutines.* import kotlinx.coroutines.*
import space.kscience.kmath.random.launch
import space.kscience.kmath.random.mcScope
import java.util.* import java.util.*
import kotlin.test.Test import kotlin.test.Test
import kotlin.test.assertEquals import kotlin.test.assertEquals
data class RandomResult(val branch: String, val order: Int, val value: Int) data class RandomResult(val branch: String, val order: Int, val value: Int)
typealias ATest = suspend CoroutineScope.() -> Set<RandomResult> internal typealias ATest = suspend () -> Set<RandomResult>
class MCScopeTest { internal class MCScopeTest {
val simpleTest: ATest = { val simpleTest: ATest = {
mcScope(1111) { mcScope(1111) {
val res = Collections.synchronizedSet(HashSet<RandomResult>()) val res = Collections.synchronizedSet(HashSet<RandomResult>())
launch { launch{
//println(random) //println(random)
repeat(10) { repeat(10) {
delay(10) delay(10)

2
kmath-stat/src/jvmTest/kotlin/space/kscience/kmath/stat/SamplerTest.kt
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@ -6,6 +6,8 @@
package space.kscience.kmath.stat package space.kscience.kmath.stat
import kotlinx.coroutines.runBlocking import kotlinx.coroutines.runBlocking
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.random.chain
import space.kscience.kmath.samplers.Sampler import space.kscience.kmath.samplers.Sampler
import space.kscience.kmath.samplers.sampleBuffer import space.kscience.kmath.samplers.sampleBuffer
import kotlin.test.Test import kotlin.test.Test

2
kmath-stat/src/jvmTest/kotlin/space/kscience/kmath/stat/StatisticTest.kt
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@ -9,6 +9,8 @@ import kotlinx.coroutines.flow.first
import kotlinx.coroutines.flow.last import kotlinx.coroutines.flow.last
import kotlinx.coroutines.flow.take import kotlinx.coroutines.flow.take
import kotlinx.coroutines.runBlocking import kotlinx.coroutines.runBlocking
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.random.chain
import space.kscience.kmath.streaming.chunked import space.kscience.kmath.streaming.chunked
import kotlin.test.Test import kotlin.test.Test
import kotlin.test.assertEquals import kotlin.test.assertEquals

2
kmath-tensors/src/commonMain/kotlin/space/kscience/kmath/tensors/core/internal/utils.kt
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@ -6,8 +6,8 @@
package space.kscience.kmath.tensors.core.internal package space.kscience.kmath.tensors.core.internal
import space.kscience.kmath.nd.as1D import space.kscience.kmath.nd.as1D
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.samplers.GaussianSampler import space.kscience.kmath.samplers.GaussianSampler
import space.kscience.kmath.stat.RandomGenerator
import space.kscience.kmath.structures.* import space.kscience.kmath.structures.*
import space.kscience.kmath.tensors.core.BufferedTensor import space.kscience.kmath.tensors.core.BufferedTensor
import space.kscience.kmath.tensors.core.DoubleTensor import space.kscience.kmath.tensors.core.DoubleTensor