Refactor/histograms #203
@ -41,6 +41,7 @@
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- Refactor histograms. They are marked as prototype
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- Refactor histograms. They are marked as prototype
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- `Complex` and related features moved to a separate module `kmath-complex`
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- `Complex` and related features moved to a separate module `kmath-complex`
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- Refactor AlgebraElement
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- Refactor AlgebraElement
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- Add `out` projection to `Buffer` generic
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### Deprecated
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### Deprecated
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@ -76,6 +76,14 @@ benchmark {
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iterationTimeUnit = "ms" // time unity for iterationTime, default is seconds
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iterationTimeUnit = "ms" // time unity for iterationTime, default is seconds
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include("DotBenchmark")
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include("DotBenchmark")
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}
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}
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configurations.register("expressions") {
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warmups = 1 // number of warmup iterations
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iterations = 3 // number of iterations
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iterationTime = 500 // time in seconds per iteration
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iterationTimeUnit = "ms" // time unity for iterationTime, default is seconds
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include("ExpressionsInterpretersBenchmark")
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}
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}
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}
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kotlin.sourceSets.all {
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kotlin.sourceSets.all {
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@ -21,8 +21,17 @@ public class MstExpression<T, out A : Algebra<T>>(public val algebra: A, public
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null
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null
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} ?: arguments.getValue(StringSymbol(value))
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} ?: arguments.getValue(StringSymbol(value))
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override fun unaryOperationFunction(operation: String): (arg: T) -> T = algebra.unaryOperationFunction(operation)
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override fun unaryOperation(operation: String, arg: T): T =
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override fun binaryOperationFunction(operation: String): (left: T, right: T) -> T = algebra.binaryOperationFunction(operation)
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algebra.unaryOperation(operation, arg)
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override fun binaryOperation(operation: String, left: T, right: T): T =
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algebra.binaryOperation(operation, left, right)
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override fun unaryOperationFunction(operation: String): (arg: T) -> T =
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algebra.unaryOperationFunction(operation)
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override fun binaryOperationFunction(operation: String): (left: T, right: T) -> T =
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algebra.binaryOperationFunction(operation)
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@Suppress("UNCHECKED_CAST")
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@Suppress("UNCHECKED_CAST")
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override fun number(value: Number): T = if (algebra is NumericAlgebra<*>)
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override fun number(value: Number): T = if (algebra is NumericAlgebra<*>)
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@ -4,7 +4,7 @@ public abstract interface class kscience/kmath/domains/Domain {
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}
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}
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public final class kscience/kmath/domains/HyperSquareDomain : kscience/kmath/domains/RealDomain {
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public final class kscience/kmath/domains/HyperSquareDomain : kscience/kmath/domains/RealDomain {
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public synthetic fun <init> ([D[DLkotlin/jvm/internal/DefaultConstructorMarker;)V
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public fun <init> (Lkscience/kmath/structures/Buffer;Lkscience/kmath/structures/Buffer;)V
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public fun contains (Lkscience/kmath/structures/Buffer;)Z
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public fun contains (Lkscience/kmath/structures/Buffer;)Z
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public fun getDimension ()I
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public fun getDimension ()I
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public fun getLowerBound (I)Ljava/lang/Double;
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public fun getLowerBound (I)Ljava/lang/Double;
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@ -16,6 +16,7 @@
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package kscience.kmath.domains
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package kscience.kmath.domains
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import kscience.kmath.linear.Point
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import kscience.kmath.linear.Point
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import kscience.kmath.structures.Buffer
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import kscience.kmath.structures.RealBuffer
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import kscience.kmath.structures.RealBuffer
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import kscience.kmath.structures.indices
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import kscience.kmath.structures.indices
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@ -25,20 +26,20 @@ import kscience.kmath.structures.indices
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*
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*
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* @author Alexander Nozik
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* @author Alexander Nozik
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*/
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*/
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public class HyperSquareDomain(private val lower: RealBuffer, private val upper: RealBuffer) : RealDomain {
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public class HyperSquareDomain(private val lower: Buffer<Double>, private val upper: Buffer<Double>) : RealDomain {
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public override val dimension: Int get() = lower.size
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public override val dimension: Int get() = lower.size
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public override operator fun contains(point: Point<Double>): Boolean = point.indices.all { i ->
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public override operator fun contains(point: Point<Double>): Boolean = point.indices.all { i ->
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point[i] in lower[i]..upper[i]
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point[i] in lower[i]..upper[i]
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}
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}
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public override fun getLowerBound(num: Int, point: Point<Double>): Double? = lower[num]
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public override fun getLowerBound(num: Int, point: Point<Double>): Double = lower[num]
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public override fun getLowerBound(num: Int): Double? = lower[num]
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public override fun getLowerBound(num: Int): Double = lower[num]
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public override fun getUpperBound(num: Int, point: Point<Double>): Double? = upper[num]
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public override fun getUpperBound(num: Int, point: Point<Double>): Double = upper[num]
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public override fun getUpperBound(num: Int): Double? = upper[num]
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public override fun getUpperBound(num: Int): Double = upper[num]
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public override fun nearestInDomain(point: Point<Double>): Point<Double> {
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public override fun nearestInDomain(point: Point<Double>): Point<Double> {
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val res = DoubleArray(point.size) { i ->
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val res = DoubleArray(point.size) { i ->
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@ -78,8 +78,7 @@ public interface NDStructure<T> {
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strides: Strides,
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strides: Strides,
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bufferFactory: BufferFactory<T> = Buffer.Companion::boxing,
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bufferFactory: BufferFactory<T> = Buffer.Companion::boxing,
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initializer: (IntArray) -> T,
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initializer: (IntArray) -> T,
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): NDBuffer<T> =
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): NDBuffer<T> = NDBuffer(strides, bufferFactory(strides.linearSize) { i -> initializer(strides.index(i)) })
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NDBuffer(strides, bufferFactory(strides.linearSize) { i -> initializer(strides.index(i)) })
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/**
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/**
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* Inline create NDStructure with non-boxing buffer implementation if it is possible
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* Inline create NDStructure with non-boxing buffer implementation if it is possible
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@ -87,15 +86,13 @@ public interface NDStructure<T> {
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public inline fun <reified T : Any> auto(
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public inline fun <reified T : Any> auto(
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strides: Strides,
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strides: Strides,
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crossinline initializer: (IntArray) -> T,
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crossinline initializer: (IntArray) -> T,
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): NDBuffer<T> =
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): NDBuffer<T> = NDBuffer(strides, Buffer.auto(strides.linearSize) { i -> initializer(strides.index(i)) })
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NDBuffer(strides, Buffer.auto(strides.linearSize) { i -> initializer(strides.index(i)) })
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public inline fun <T : Any> auto(
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public inline fun <T : Any> auto(
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type: KClass<T>,
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type: KClass<T>,
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strides: Strides,
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strides: Strides,
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crossinline initializer: (IntArray) -> T,
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crossinline initializer: (IntArray) -> T,
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): NDBuffer<T> =
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): NDBuffer<T> = NDBuffer(strides, Buffer.auto(type, strides.linearSize) { i -> initializer(strides.index(i)) })
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NDBuffer(strides, Buffer.auto(type, strides.linearSize) { i -> initializer(strides.index(i)) })
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public fun <T> build(
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public fun <T> build(
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shape: IntArray,
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shape: IntArray,
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@ -106,8 +103,7 @@ public interface NDStructure<T> {
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public inline fun <reified T : Any> auto(
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public inline fun <reified T : Any> auto(
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shape: IntArray,
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shape: IntArray,
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crossinline initializer: (IntArray) -> T,
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crossinline initializer: (IntArray) -> T,
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): NDBuffer<T> =
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): NDBuffer<T> = auto(DefaultStrides(shape), initializer)
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auto(DefaultStrides(shape), initializer)
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@JvmName("autoVarArg")
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@JvmName("autoVarArg")
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public inline fun <reified T : Any> auto(
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public inline fun <reified T : Any> auto(
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@ -120,8 +116,7 @@ public interface NDStructure<T> {
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type: KClass<T>,
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type: KClass<T>,
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vararg shape: Int,
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vararg shape: Int,
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crossinline initializer: (IntArray) -> T,
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crossinline initializer: (IntArray) -> T,
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): NDBuffer<T> =
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): NDBuffer<T> = auto(type, DefaultStrides(shape), initializer)
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auto(type, DefaultStrides(shape), initializer)
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}
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}
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}
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}
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@ -21,7 +21,7 @@ public typealias MutableBufferFactory<T> = (Int, (Int) -> T) -> MutableBuffer<T>
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*
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*
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* @param T the type of elements contained in the buffer.
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* @param T the type of elements contained in the buffer.
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*/
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*/
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public interface Buffer<T> {
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public interface Buffer<out T> {
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/**
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/**
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* The size of this buffer.
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* The size of this buffer.
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*/
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*/
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@ -2,16 +2,18 @@ package kscience.kmath.histogram
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import kotlinx.atomicfu.atomic
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import kotlinx.atomicfu.atomic
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import kotlinx.atomicfu.getAndUpdate
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import kotlinx.atomicfu.getAndUpdate
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import kscience.kmath.operations.RealField
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import kscience.kmath.operations.Space
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import kscience.kmath.operations.Space
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/*
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/**
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* Common representation for atomic counters
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* Common representation for atomic counters
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* TODO replace with atomics
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*/
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*/
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public interface Counter<T : Any> {
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public interface Counter<T : Any> {
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public fun add(delta: T)
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public fun add(delta: T)
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public val value: T
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public val value: T
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public companion object{
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public fun real(): ObjectCounter<Double> = ObjectCounter(RealField)
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}
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}
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}
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public class IntCounter : Counter<Int> {
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public class IntCounter : Counter<Int> {
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@ -13,8 +13,6 @@ public interface Bin<T : Any> : Domain<T> {
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* The value of this bin.
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* The value of this bin.
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*/
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*/
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public val value: Number
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public val value: Number
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public val center: Point<T>
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}
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}
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public interface Histogram<T : Any, out B : Bin<T>> {
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public interface Histogram<T : Any, out B : Bin<T>> {
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@ -28,29 +26,30 @@ public interface Histogram<T : Any, out B : Bin<T>> {
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*/
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*/
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public val dimension: Int
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public val dimension: Int
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public val bins: Collection<B>
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public val bins: Iterable<B>
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}
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}
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public interface HistogramBuilder<T : Any, out B : Bin<T>> : Histogram<T, B> {
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public fun interface HistogramBuilder<T : Any> {
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/**
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/**
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* Increment appropriate bin
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* Increment appropriate bin
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*/
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*/
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public fun putWithWeight(point: Point<out T>, weight: Double)
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public fun putValue(point: Point<out T>, value: Number)
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public fun put(point: Point<out T>): Unit = putWithWeight(point, 1.0)
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}
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}
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public fun <T : Any> HistogramBuilder<T, *>.put(vararg point: T): Unit = put(ArrayBuffer(point))
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public fun <T : Any, B : Bin<T>> HistogramBuilder<T>.put(point: Point<out T>): Unit = putValue(point, 1.0)
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public fun HistogramBuilder<Double, *>.put(vararg point: Number): Unit =
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public fun <T : Any> HistogramBuilder<T>.put(vararg point: T): Unit = put(ArrayBuffer(point))
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public fun HistogramBuilder<Double>.put(vararg point: Number): Unit =
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put(RealBuffer(point.map { it.toDouble() }.toDoubleArray()))
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put(RealBuffer(point.map { it.toDouble() }.toDoubleArray()))
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public fun HistogramBuilder<Double, *>.put(vararg point: Double): Unit = put(RealBuffer(point))
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public fun HistogramBuilder<Double>.put(vararg point: Double): Unit = put(RealBuffer(point))
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public fun <T : Any> HistogramBuilder<T, *>.fill(sequence: Iterable<Point<T>>): Unit = sequence.forEach { put(it) }
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public fun <T : Any> HistogramBuilder<T>.fill(sequence: Iterable<Point<T>>): Unit = sequence.forEach { put(it) }
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/**
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/**
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* Pass a sequence builder into histogram
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* Pass a sequence builder into histogram
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*/
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*/
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public fun <T : Any> HistogramBuilder<T, *>.fill(block: suspend SequenceScope<Point<T>>.() -> Unit): Unit =
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public fun <T : Any> HistogramBuilder<T>.fill(block: suspend SequenceScope<Point<T>>.() -> Unit): Unit =
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fill(sequence(block).asIterable())
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fill(sequence(block).asIterable())
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@ -0,0 +1,76 @@
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package kscience.kmath.histogram
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import kscience.kmath.domains.Domain
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import kscience.kmath.linear.Point
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import kscience.kmath.misc.UnstableKMathAPI
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import kscience.kmath.nd.NDSpace
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import kscience.kmath.nd.NDStructure
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import kscience.kmath.nd.Strides
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import kscience.kmath.operations.Space
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import kscience.kmath.operations.SpaceElement
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import kscience.kmath.operations.invoke
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/**
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* A simple histogram bin based on domain
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*/
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public data class DomainBin<T : Comparable<T>>(
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public val domain: Domain<T>,
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public override val value: Number,
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) : Bin<T>, Domain<T> by domain
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@OptIn(UnstableKMathAPI::class)
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public class IndexedHistogram<T : Comparable<T>, V : Any>(
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override val context: IndexedHistogramSpace<T, V>,
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public val values: NDStructure<V>,
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) : Histogram<T, Bin<T>>, SpaceElement<IndexedHistogram<T, V>, IndexedHistogramSpace<T, V>> {
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override fun get(point: Point<T>): Bin<T>? {
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val index = context.getIndex(point) ?: return null
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return context.produceBin(index, values[index])
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}
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override val dimension: Int get() = context.strides.shape.size
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override val bins: Iterable<Bin<T>>
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get() = context.strides.indices().map {
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context.produceBin(it, values[it])
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|
}.asIterable()
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}
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/**
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* A space for producing histograms with values in a NDStructure
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|
*/
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public interface IndexedHistogramSpace<T : Comparable<T>, V : Any> : Space<IndexedHistogram<T, V>> {
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//public val valueSpace: Space<V>
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|
public val strides: Strides
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|
public val histogramValueSpace: NDSpace<V, *> //= NDAlgebra.space(valueSpace, Buffer.Companion::boxing, *shape),
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|
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|
/**
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|
* Resolve index of the bin including given [point]
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|
*/
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public fun getIndex(point: Point<T>): IntArray?
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|
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|
/**
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|
* Get a bin domain represented by given index
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|
*/
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|
public fun getDomain(index: IntArray): Domain<T>?
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|
|
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|
public fun produceBin(index: IntArray, value: V): Bin<T>
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|
|
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|
public fun produce(builder: HistogramBuilder<T>.() -> Unit): IndexedHistogram<T, V>
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|
|
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|
override fun add(a: IndexedHistogram<T, V>, b: IndexedHistogram<T, V>): IndexedHistogram<T, V> {
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|
require(a.context == this) { "Can't operate on a histogram produced by external space" }
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|
require(b.context == this) { "Can't operate on a histogram produced by external space" }
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|
return IndexedHistogram(this, histogramValueSpace.invoke { a.values + b.values })
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|
}
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|
|
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|
override fun multiply(a: IndexedHistogram<T, V>, k: Number): IndexedHistogram<T, V> {
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|
require(a.context == this) { "Can't operate on a histogram produced by external space" }
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|
return IndexedHistogram(this, histogramValueSpace.invoke { a.values * k })
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|
}
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|
|
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|
override val zero: IndexedHistogram<T, V> get() = produce { }
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||||||
|
}
|
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|
|
@ -1,166 +0,0 @@
|
|||||||
package kscience.kmath.histogram
|
|
||||||
|
|
||||||
import kscience.kmath.linear.Point
|
|
||||||
import kscience.kmath.nd.DefaultStrides
|
|
||||||
import kscience.kmath.nd.NDStructure
|
|
||||||
import kscience.kmath.operations.SpaceOperations
|
|
||||||
import kscience.kmath.operations.invoke
|
|
||||||
import kscience.kmath.structures.*
|
|
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import kotlin.math.floor
|
|
||||||
|
|
||||||
public data class MultivariateBinDefinition<T : Comparable<T>>(
|
|
||||||
public val space: SpaceOperations<Point<T>>,
|
|
||||||
public val center: Point<T>,
|
|
||||||
public val sizes: Point<T>,
|
|
||||||
) {
|
|
||||||
public fun contains(vector: Point<out T>): Boolean {
|
|
||||||
require(vector.size == center.size) { "Dimension mismatch for input vector. Expected ${center.size}, but found ${vector.size}" }
|
|
||||||
val upper = space { center + sizes / 2.0 }
|
|
||||||
val lower = space { center - sizes / 2.0 }
|
|
||||||
return vector.asSequence().mapIndexed { i, value -> value in lower[i]..upper[i] }.all { it }
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
public class MultivariateBin<T : Comparable<T>>(
|
|
||||||
public val definition: MultivariateBinDefinition<T>,
|
|
||||||
public val count: Long,
|
|
||||||
public override val value: Double,
|
|
||||||
) : Bin<T> {
|
|
||||||
public override val dimension: Int
|
|
||||||
get() = definition.center.size
|
|
||||||
|
|
||||||
public override val center: Point<T>
|
|
||||||
get() = definition.center
|
|
||||||
|
|
||||||
public override operator fun contains(point: Point<T>): Boolean = definition.contains(point)
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Uniform multivariate histogram with fixed borders. Based on NDStructure implementation with complexity of m for bin search, where m is the number of dimensions.
|
|
||||||
*/
|
|
||||||
public class RealHistogram(
|
|
||||||
private val lower: Buffer<Double>,
|
|
||||||
private val upper: Buffer<Double>,
|
|
||||||
private val binNums: IntArray = IntArray(lower.size) { 20 },
|
|
||||||
) : HistogramBuilder<Double, MultivariateBin<Double>> {
|
|
||||||
private val strides = DefaultStrides(IntArray(binNums.size) { binNums[it] + 2 })
|
|
||||||
private val counts: NDStructure<LongCounter> = NDStructure.auto(strides) { LongCounter() }
|
|
||||||
private val values: NDStructure<DoubleCounter> = NDStructure.auto(strides) { DoubleCounter() }
|
|
||||||
public override val dimension: Int get() = lower.size
|
|
||||||
private val binSize = RealBuffer(dimension) { (upper[it] - lower[it]) / binNums[it] }
|
|
||||||
|
|
||||||
init {
|
|
||||||
// argument checks
|
|
||||||
require(lower.size == upper.size) { "Dimension mismatch in histogram lower and upper limits." }
|
|
||||||
require(lower.size == binNums.size) { "Dimension mismatch in bin count." }
|
|
||||||
require(!(0 until dimension).any { upper[it] - lower[it] < 0 }) { "Range for one of axis is not strictly positive" }
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Get internal [NDStructure] bin index for given axis
|
|
||||||
*/
|
|
||||||
private fun getIndex(axis: Int, value: Double): Int = when {
|
|
||||||
value >= upper[axis] -> binNums[axis] + 1 // overflow
|
|
||||||
value < lower[axis] -> 0 // underflow
|
|
||||||
else -> floor((value - lower[axis]) / binSize[axis]).toInt() + 1
|
|
||||||
}
|
|
||||||
|
|
||||||
private fun getIndex(point: Buffer<out Double>): IntArray = IntArray(dimension) { getIndex(it, point[it]) }
|
|
||||||
|
|
||||||
private fun getCount(index: IntArray): Long = counts[index].sum()
|
|
||||||
|
|
||||||
public fun getCount(point: Buffer<out Double>): Long = getCount(getIndex(point))
|
|
||||||
|
|
||||||
private fun getValue(index: IntArray): Double = values[index].sum()
|
|
||||||
|
|
||||||
public fun getValue(point: Buffer<out Double>): Double = getValue(getIndex(point))
|
|
||||||
|
|
||||||
private fun getBinDefinition(index: IntArray): MultivariateBinDefinition<Double> {
|
|
||||||
val center = index.mapIndexed { axis, i ->
|
|
||||||
when (i) {
|
|
||||||
0 -> Double.NEGATIVE_INFINITY
|
|
||||||
strides.shape[axis] - 1 -> Double.POSITIVE_INFINITY
|
|
||||||
else -> lower[axis] + (i.toDouble() - 0.5) * binSize[axis]
|
|
||||||
}
|
|
||||||
}.asBuffer()
|
|
||||||
|
|
||||||
return MultivariateBinDefinition(RealBufferFieldOperations, center, binSize)
|
|
||||||
}
|
|
||||||
|
|
||||||
public fun getBinDefinition(point: Buffer<out Double>): MultivariateBinDefinition<Double> =
|
|
||||||
getBinDefinition(getIndex(point))
|
|
||||||
|
|
||||||
public override operator fun get(point: Buffer<out Double>): MultivariateBin<Double>? {
|
|
||||||
val index = getIndex(point)
|
|
||||||
return MultivariateBin(getBinDefinition(index), getCount(index), getValue(index))
|
|
||||||
}
|
|
||||||
|
|
||||||
// fun put(point: Point<out Double>){
|
|
||||||
// val index = getIndex(point)
|
|
||||||
// values[index].increment()
|
|
||||||
// }
|
|
||||||
|
|
||||||
public override fun putWithWeight(point: Buffer<out Double>, weight: Double) {
|
|
||||||
val index = getIndex(point)
|
|
||||||
counts[index].increment()
|
|
||||||
values[index].add(weight)
|
|
||||||
}
|
|
||||||
|
|
||||||
override val bins: Collection<MultivariateBin<Double>>
|
|
||||||
get() = strides.indices().map { index ->
|
|
||||||
MultivariateBin(getBinDefinition(index), counts[index].sum(), values[index].sum())
|
|
||||||
}.toList()
|
|
||||||
|
|
||||||
/**
|
|
||||||
* NDStructure containing number of events in bins without weights
|
|
||||||
*/
|
|
||||||
public fun counts(): NDStructure<Long> = NDStructure.auto(counts.shape) { counts[it].sum() }
|
|
||||||
|
|
||||||
/**
|
|
||||||
* NDStructure containing values of bins including weights
|
|
||||||
*/
|
|
||||||
public fun values(): NDStructure<Double> = NDStructure.auto(values.shape) { values[it].sum() }
|
|
||||||
|
|
||||||
public companion object {
|
|
||||||
/**
|
|
||||||
* Use it like
|
|
||||||
* ```
|
|
||||||
*FastHistogram.fromRanges(
|
|
||||||
* (-1.0..1.0),
|
|
||||||
* (-1.0..1.0)
|
|
||||||
*)
|
|
||||||
*```
|
|
||||||
*/
|
|
||||||
public fun fromRanges(vararg ranges: ClosedFloatingPointRange<Double>): RealHistogram = RealHistogram(
|
|
||||||
ranges.map(ClosedFloatingPointRange<Double>::start).asBuffer(),
|
|
||||||
ranges.map(ClosedFloatingPointRange<Double>::endInclusive).asBuffer()
|
|
||||||
)
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Use it like
|
|
||||||
* ```
|
|
||||||
*FastHistogram.fromRanges(
|
|
||||||
* (-1.0..1.0) to 50,
|
|
||||||
* (-1.0..1.0) to 32
|
|
||||||
*)
|
|
||||||
*```
|
|
||||||
*/
|
|
||||||
public fun fromRanges(vararg ranges: Pair<ClosedFloatingPointRange<Double>, Int>): RealHistogram =
|
|
||||||
RealHistogram(
|
|
||||||
ListBuffer(
|
|
||||||
ranges
|
|
||||||
.map(Pair<ClosedFloatingPointRange<Double>, Int>::first)
|
|
||||||
.map(ClosedFloatingPointRange<Double>::start)
|
|
||||||
),
|
|
||||||
|
|
||||||
ListBuffer(
|
|
||||||
ranges
|
|
||||||
.map(Pair<ClosedFloatingPointRange<Double>, Int>::first)
|
|
||||||
.map(ClosedFloatingPointRange<Double>::endInclusive)
|
|
||||||
),
|
|
||||||
|
|
||||||
ranges.map(Pair<ClosedFloatingPointRange<Double>, Int>::second).toIntArray()
|
|
||||||
)
|
|
||||||
}
|
|
||||||
}
|
|
@ -0,0 +1,121 @@
|
|||||||
|
package kscience.kmath.histogram
|
||||||
|
|
||||||
|
import kscience.kmath.domains.Domain
|
||||||
|
import kscience.kmath.domains.HyperSquareDomain
|
||||||
|
import kscience.kmath.nd.*
|
||||||
|
import kscience.kmath.structures.*
|
||||||
|
import kotlin.math.floor
|
||||||
|
|
||||||
|
public class RealHistogramSpace(
|
||||||
|
private val lower: Buffer<Double>,
|
||||||
|
private val upper: Buffer<Double>,
|
||||||
|
private val binNums: IntArray = IntArray(lower.size) { 20 },
|
||||||
|
) : IndexedHistogramSpace<Double, Double> {
|
||||||
|
|
||||||
|
init {
|
||||||
|
// argument checks
|
||||||
|
require(lower.size == upper.size) { "Dimension mismatch in histogram lower and upper limits." }
|
||||||
|
require(lower.size == binNums.size) { "Dimension mismatch in bin count." }
|
||||||
|
require(!lower.indices.any { upper[it] - lower[it] < 0 }) { "Range for one of axis is not strictly positive" }
|
||||||
|
}
|
||||||
|
|
||||||
|
public val dimension: Int get() = lower.size
|
||||||
|
|
||||||
|
private val shape = IntArray(binNums.size) { binNums[it] + 2 }
|
||||||
|
override val histogramValueSpace: RealNDField = NDAlgebra.real(*shape)
|
||||||
|
|
||||||
|
override val strides: Strides get() = histogramValueSpace.strides
|
||||||
|
private val binSize = RealBuffer(dimension) { (upper[it] - lower[it]) / binNums[it] }
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Get internal [NDStructure] bin index for given axis
|
||||||
|
*/
|
||||||
|
private fun getIndex(axis: Int, value: Double): Int = when {
|
||||||
|
value >= upper[axis] -> binNums[axis] + 1 // overflow
|
||||||
|
value < lower[axis] -> 0 // underflow
|
||||||
|
else -> floor((value - lower[axis]) / binSize[axis]).toInt()
|
||||||
|
}
|
||||||
|
|
||||||
|
override fun getIndex(point: Buffer<Double>): IntArray = IntArray(dimension) {
|
||||||
|
getIndex(it, point[it])
|
||||||
|
}
|
||||||
|
|
||||||
|
override fun getDomain(index: IntArray): Domain<Double> {
|
||||||
|
val lowerBoundary = index.mapIndexed { axis, i ->
|
||||||
|
when (i) {
|
||||||
|
0 -> Double.NEGATIVE_INFINITY
|
||||||
|
strides.shape[axis] - 1 -> upper[axis]
|
||||||
|
else -> lower[axis] + (i.toDouble()) * binSize[axis]
|
||||||
|
}
|
||||||
|
}.asBuffer()
|
||||||
|
|
||||||
|
val upperBoundary = index.mapIndexed { axis, i ->
|
||||||
|
when (i) {
|
||||||
|
0 -> lower[axis]
|
||||||
|
strides.shape[axis] - 1 -> Double.POSITIVE_INFINITY
|
||||||
|
else -> lower[axis] + (i.toDouble() + 1) * binSize[axis]
|
||||||
|
}
|
||||||
|
}.asBuffer()
|
||||||
|
|
||||||
|
return HyperSquareDomain(lowerBoundary, upperBoundary)
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
override fun produceBin(index: IntArray, value: Double): Bin<Double> {
|
||||||
|
val domain = getDomain(index)
|
||||||
|
return DomainBin(domain, value)
|
||||||
|
}
|
||||||
|
|
||||||
|
override fun produce(builder: HistogramBuilder<Double>.() -> Unit): IndexedHistogram<Double, Double> {
|
||||||
|
val ndCounter = NDStructure.auto(strides) { Counter.real() }
|
||||||
|
val hBuilder = HistogramBuilder<Double> { point, value ->
|
||||||
|
val index = getIndex(point)
|
||||||
|
ndCounter[index].add(1.0)
|
||||||
|
}
|
||||||
|
hBuilder.apply(builder)
|
||||||
|
val values: NDBuffer<Double> = ndCounter.mapToBuffer { it.value }
|
||||||
|
return IndexedHistogram(this, values)
|
||||||
|
}
|
||||||
|
|
||||||
|
public companion object{
|
||||||
|
/**
|
||||||
|
* Use it like
|
||||||
|
* ```
|
||||||
|
*FastHistogram.fromRanges(
|
||||||
|
* (-1.0..1.0),
|
||||||
|
* (-1.0..1.0)
|
||||||
|
*)
|
||||||
|
*```
|
||||||
|
*/
|
||||||
|
public fun fromRanges(vararg ranges: ClosedFloatingPointRange<Double>): RealHistogramSpace = RealHistogramSpace(
|
||||||
|
ranges.map(ClosedFloatingPointRange<Double>::start).asBuffer(),
|
||||||
|
ranges.map(ClosedFloatingPointRange<Double>::endInclusive).asBuffer()
|
||||||
|
)
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Use it like
|
||||||
|
* ```
|
||||||
|
*FastHistogram.fromRanges(
|
||||||
|
* (-1.0..1.0) to 50,
|
||||||
|
* (-1.0..1.0) to 32
|
||||||
|
*)
|
||||||
|
*```
|
||||||
|
*/
|
||||||
|
public fun fromRanges(vararg ranges: Pair<ClosedFloatingPointRange<Double>, Int>): RealHistogramSpace =
|
||||||
|
RealHistogramSpace(
|
||||||
|
ListBuffer(
|
||||||
|
ranges
|
||||||
|
.map(Pair<ClosedFloatingPointRange<Double>, Int>::first)
|
||||||
|
.map(ClosedFloatingPointRange<Double>::start)
|
||||||
|
),
|
||||||
|
|
||||||
|
ListBuffer(
|
||||||
|
ranges
|
||||||
|
.map(Pair<ClosedFloatingPointRange<Double>, Int>::first)
|
||||||
|
.map(ClosedFloatingPointRange<Double>::endInclusive)
|
||||||
|
),
|
||||||
|
|
||||||
|
ranges.map(Pair<ClosedFloatingPointRange<Double>, Int>::second).toIntArray()
|
||||||
|
)
|
||||||
|
}
|
||||||
|
}
|
@ -1,6 +1,6 @@
|
|||||||
package scietifik.kmath.histogram
|
package scietifik.kmath.histogram
|
||||||
|
|
||||||
import kscience.kmath.histogram.RealHistogram
|
import kscience.kmath.histogram.RealHistogramSpace
|
||||||
import kscience.kmath.histogram.fill
|
import kscience.kmath.histogram.fill
|
||||||
import kscience.kmath.histogram.put
|
import kscience.kmath.histogram.put
|
||||||
import kscience.kmath.real.RealVector
|
import kscience.kmath.real.RealVector
|
||||||
@ -11,11 +11,13 @@ import kotlin.test.*
|
|||||||
internal class MultivariateHistogramTest {
|
internal class MultivariateHistogramTest {
|
||||||
@Test
|
@Test
|
||||||
fun testSinglePutHistogram() {
|
fun testSinglePutHistogram() {
|
||||||
val histogram = RealHistogram.fromRanges(
|
val hSpace = RealHistogramSpace.fromRanges(
|
||||||
(-1.0..1.0),
|
(-1.0..1.0),
|
||||||
(-1.0..1.0)
|
(-1.0..1.0)
|
||||||
)
|
)
|
||||||
histogram.put(0.55, 0.55)
|
val histogram = hSpace.produce {
|
||||||
|
put(0.55, 0.55)
|
||||||
|
}
|
||||||
val bin = histogram.bins.find { it.value.toInt() > 0 } ?: fail()
|
val bin = histogram.bins.find { it.value.toInt() > 0 } ?: fail()
|
||||||
assertTrue { bin.contains(RealVector(0.55, 0.55)) }
|
assertTrue { bin.contains(RealVector(0.55, 0.55)) }
|
||||||
assertTrue { bin.contains(RealVector(0.6, 0.5)) }
|
assertTrue { bin.contains(RealVector(0.6, 0.5)) }
|
||||||
@ -24,7 +26,7 @@ internal class MultivariateHistogramTest {
|
|||||||
|
|
||||||
@Test
|
@Test
|
||||||
fun testSequentialPut() {
|
fun testSequentialPut() {
|
||||||
val histogram = RealHistogram.fromRanges(
|
val hSpace = RealHistogramSpace.fromRanges(
|
||||||
(-1.0..1.0),
|
(-1.0..1.0),
|
||||||
(-1.0..1.0),
|
(-1.0..1.0),
|
||||||
(-1.0..1.0)
|
(-1.0..1.0)
|
||||||
@ -34,12 +36,13 @@ internal class MultivariateHistogramTest {
|
|||||||
fun nextDouble() = random.nextDouble(-1.0, 1.0)
|
fun nextDouble() = random.nextDouble(-1.0, 1.0)
|
||||||
|
|
||||||
val n = 10000
|
val n = 10000
|
||||||
|
val histogram = hSpace.produce {
|
||||||
histogram.fill {
|
fill {
|
||||||
repeat(n) {
|
repeat(n) {
|
||||||
yield(RealVector(nextDouble(), nextDouble(), nextDouble()))
|
yield(RealVector(nextDouble(), nextDouble(), nextDouble()))
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
assertEquals(n, histogram.bins.sumBy { it.value.toInt() })
|
assertEquals(n, histogram.bins.sumBy { it.value.toInt() })
|
||||||
}
|
}
|
||||||
}
|
}
|
@ -30,7 +30,7 @@ public interface UnivariateBin : Bin<Double> {
|
|||||||
*/
|
*/
|
||||||
public val standardDeviation: Double
|
public val standardDeviation: Double
|
||||||
|
|
||||||
public override val center: Point<Double> get() = doubleArrayOf(position).asBuffer()
|
public val center: Point<Double> get() = doubleArrayOf(position).asBuffer()
|
||||||
|
|
||||||
public override val dimension: Int get() = 1
|
public override val dimension: Int get() = 1
|
||||||
|
|
||||||
@ -44,7 +44,7 @@ public operator fun UnivariateBin.contains(value: Double): Boolean =
|
|||||||
public interface UnivariateHistogram : Histogram<Double, UnivariateBin>,
|
public interface UnivariateHistogram : Histogram<Double, UnivariateBin>,
|
||||||
SpaceElement<UnivariateHistogram, UnivariateHistogramSpace> {
|
SpaceElement<UnivariateHistogram, UnivariateHistogramSpace> {
|
||||||
public operator fun get(value: Double): UnivariateBin?
|
public operator fun get(value: Double): UnivariateBin?
|
||||||
public override operator fun get(point: Buffer<out Double>): UnivariateBin? = get(point[0])
|
public override operator fun get(point: Buffer<Double>): UnivariateBin? = get(point[0])
|
||||||
|
|
||||||
public companion object {
|
public companion object {
|
||||||
/**
|
/**
|
||||||
@ -67,12 +67,14 @@ public interface UnivariateHistogram : Histogram<Double, UnivariateBin>,
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
public interface UnivariateHistogramBuilder {
|
public interface UnivariateHistogramBuilder: HistogramBuilder<Double> {
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Thread safe put operation
|
* Thread safe put operation
|
||||||
*/
|
*/
|
||||||
public fun put(value: Double, weight: Double = 1.0)
|
public fun put(value: Double, weight: Double = 1.0)
|
||||||
public fun putWithWeight(point: Buffer<out Double>, weight: Double)
|
|
||||||
|
override fun putValue(point: Buffer<Double>, value: Number)
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Put several items into a single bin
|
* Put several items into a single bin
|
||||||
|
@ -31,19 +31,19 @@ private class UnivariateBinCounter(
|
|||||||
override val def: UnivariateHistogramBinDefinition,
|
override val def: UnivariateHistogramBinDefinition,
|
||||||
) : UnivariateBin {
|
) : UnivariateBin {
|
||||||
val counter: LongCounter = LongCounter()
|
val counter: LongCounter = LongCounter()
|
||||||
val valueCounter: DoubleCounter = DoubleCounter()
|
val valueCounter: ObjectCounter<Double> = Counter.real()
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* The precise number of events ignoring weighting
|
* The precise number of events ignoring weighting
|
||||||
*/
|
*/
|
||||||
val count: Long get() = counter.sum()
|
val count: Long get() = counter.value
|
||||||
|
|
||||||
override val standardDeviation: Double get() = sqrt(count.toDouble()) / count * value
|
override val standardDeviation: Double get() = sqrt(count.toDouble()) / count * value
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* The value of histogram including weighting
|
* The value of histogram including weighting
|
||||||
*/
|
*/
|
||||||
override val value: Double get() = valueCounter.sum()
|
override val value: Double get() = valueCounter.value
|
||||||
|
|
||||||
public fun increment(count: Long, value: Double) {
|
public fun increment(count: Long, value: Double) {
|
||||||
counter.add(count)
|
counter.add(count)
|
||||||
@ -83,8 +83,8 @@ public class UnivariateHistogramSpace(
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
override fun putWithWeight(point: Buffer<out Double>, weight: Double) {
|
override fun putValue(point: Buffer<Double>, value: Number) {
|
||||||
put(point[0], weight)
|
put(point[0], value.toDouble())
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
Loading…
Reference in New Issue
Block a user