Histograms for jvm are in working order.
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package scientifik.kmath.histogram
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/*
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* Common representation for atomic counters
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*/
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expect class LongCounter(){
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fun decrement()
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fun increment()
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fun reset()
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fun sum(): Long
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fun add(l:Long)
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}
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expect class DoubleCounter(){
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fun reset()
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fun sum(): Double
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fun add(d: Double)
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}
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@ -1,12 +1,22 @@
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package scientifik.kmath.histogram
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import scientifik.kmath.linear.RealVector
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import scientifik.kmath.linear.toVector
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import scientifik.kmath.operations.Space
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/**
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* A simple geometric domain
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* TODO move to geometry module
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*/
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interface Domain {
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operator fun contains(vector: RealVector): Boolean
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val dimension: Int
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}
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/**
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* The bin in the histogram. The histogram is by definition always done in the real space
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*/
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interface Bin {
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interface Bin : Domain {
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/**
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* The value of this bin
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*/
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@ -14,26 +24,36 @@ interface Bin {
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val center: RealVector
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}
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/**
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* Creates a new bin with zero count corresponding to given point
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*/
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interface BinFactory<out B : Bin> {
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fun createBin(point: RealVector): B
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}
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interface Histogram<out B : Bin> : Iterable<B> {
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/**
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* Find existing bin, corresponding to given coordinates
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*/
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fun findBin(point: RealVector): B?
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operator fun get(point: RealVector): B?
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/**
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* Dimension of the histogram
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*/
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val dimension: Int
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/**
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* Increment appropriate bin
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*/
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fun put(point: RealVector)
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}
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fun Histogram<*>.put(vararg point: Double) = put(point.toVector())
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fun Histogram<*>.fill(sequence: Iterable<RealVector>) = sequence.forEach { put(it) }
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/**
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* Pass a sequence builder into histogram
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*/
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fun Histogram<*>.fill(buider: suspend SequenceScope<RealVector>.() -> Unit) = fill(sequence(buider).asIterable())
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/**
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* A space to perform arithmetic operations on histograms
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*/
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interface HistogramSpace<B : Bin, H : Histogram<B>> : Space<H> {
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/**
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* Rules for performing operations on bins
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@ -162,9 +162,8 @@ abstract class VectorSpace<T : Any>(val size: Int, val field: Field<T>) : Space<
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}
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interface Vector<T : Any> : SpaceElement<Vector<T>, VectorSpace<T>> {
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val size: Int
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get() = context.size
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interface Vector<T : Any> : SpaceElement<Vector<T>, VectorSpace<T>>, Iterable<T> {
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val size: Int get() = context.size
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operator fun get(i: Int): T
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@ -181,6 +180,8 @@ interface Vector<T : Any> : SpaceElement<Vector<T>, VectorSpace<T>> {
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fun ofReal(size: Int, initializer: (Int) -> Double) =
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ArrayVector(ArrayVectorSpace(size, DoubleField, realNDFieldFactory), initializer)
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fun ofReal(vararg point: Double) = point.toVector()
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fun equals(v1: Vector<*>, v2: Vector<*>): Boolean {
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if (v1 === v2) return true
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if (v1.context != v2.context) return false
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@ -265,6 +266,10 @@ class ArrayVector<T : Any> internal constructor(override val context: ArrayVecto
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}
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override val self: ArrayVector<T> get() = this
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override fun iterator(): Iterator<T> = (0 until size).map { array[it] }.iterator()
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override fun toString(): String = this.joinToString(prefix = "[",postfix = "]", separator = ", "){it.toString()}
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}
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typealias RealVector = Vector<Double>
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@ -284,6 +289,7 @@ interface LinearSolver<T : Any> {
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fun <T : Any> Array<T>.toVector(field: Field<T>) = Vector.of(size, field) { this[it] }
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fun DoubleArray.toVector() = Vector.ofReal(this.size) { this[it] }
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fun List<Double>.toVector() = Vector.ofReal(this.size) { this[it] }
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/**
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* Convert matrix to vector if it is possible
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@ -105,9 +105,12 @@ abstract class NDField<T>(val shape: IntArray, val field: Field<T>) : Field<NDAr
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}
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/**
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* NDStructure coupled to the context. Emulates Python ndarray
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* Immutable [NDStructure] coupled to the context. Emulates Python ndarray
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*/
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data class NDArray<T>(override val context: NDField<T>, private val structure: NDStructure<T>) : FieldElement<NDArray<T>, NDField<T>>, NDStructure<T> by structure {
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//TODO ensure structure is immutable
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override val self: NDArray<T>
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get() = this
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@ -76,7 +76,7 @@ class DefaultStrides(override val shape: IntArray) : Strides {
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override fun offset(index: IntArray): Int {
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return index.mapIndexed { i, value ->
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if (value < 0 || value >= shape[i]) {
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throw RuntimeException("Index out of shape bounds: ($i,$value)")
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throw RuntimeException("Index $value out of shape bounds: (0,${shape[i]})")
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}
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value * strides[i]
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}.sum()
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package scientifik.kmath.histogram
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actual class LongCounter{
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private var sum: Long = 0
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actual fun decrement() {sum--}
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actual fun increment() {sum++}
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actual fun reset() {sum = 0}
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actual fun sum(): Long = sum
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actual fun add(l: Long) {sum+=l}
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}
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actual class DoubleCounter{
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private var sum: Double = 0.0
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actual fun reset() {sum = 0.0}
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actual fun sum(): Double = sum
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actual fun add(d: Double) {sum+=d}
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}
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package scientifik.kmath.histogram
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import java.util.concurrent.atomic.DoubleAdder
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import java.util.concurrent.atomic.LongAdder
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actual typealias LongCounter = LongAdder
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actual typealias DoubleCounter = DoubleAdder
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package scientifik.kmath.histogram
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import scientifik.kmath.linear.RealVector
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import scientifik.kmath.linear.toVector
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import scientifik.kmath.structures.NDStructure
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import scientifik.kmath.structures.ndStructure
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import kotlin.math.floor
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class MultivariateBin(override val center: RealVector, val sizes: RealVector, val counter: LongCounter = LongCounter()) : Bin {
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init {
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if (center.size != sizes.size) error("Dimension mismatch in bin creation. Expected ${center.size}, but found ${sizes.size}")
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}
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override fun contains(vector: RealVector): Boolean {
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assert(vector.size == center.size)
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return vector.asSequence().mapIndexed { i, value -> value in (center[i] - sizes[i] / 2)..(center[i] + sizes[i] / 2) }.all { it }
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}
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override val value: Number get() = counter.sum()
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internal operator fun inc() = this.also { counter.increment() }
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override val dimension: Int get() = center.size
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}
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/**
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* Uniform multivariate histogram with fixed borders. Based on NDStructure implementation with complexity of m for bin search, where m is the number of dimensions
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*/
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class FastHistogram(
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private val lower: RealVector,
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private val upper: RealVector,
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private val binNums: IntArray = IntArray(lower.size) { 100 }
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) : Histogram<MultivariateBin> {
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init {
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// argument checks
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if (lower.size != upper.size) error("Dimension mismatch in histogram lower and upper limits.")
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if (lower.size != binNums.size) error("Dimension mismatch in bin count.")
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if ((upper - lower).any { it <= 0 }) error("Range for one of axis is not strictly positive")
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}
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override val dimension: Int get() = lower.size
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//TODO optimize binSize performance if needed
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private val binSize = (upper - lower).mapIndexed { index, value -> value / binNums[index] }.toVector()
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private val bins: NDStructure<MultivariateBin> by lazy {
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val actualSizes = IntArray(binNums.size) { binNums[it] + 2 }
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ndStructure(actualSizes) { indexArray ->
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val center = indexArray.mapIndexed { axis, index ->
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when (index) {
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0 -> Double.NEGATIVE_INFINITY
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actualSizes[axis] -> Double.POSITIVE_INFINITY
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else -> lower[axis] + (index - 1) * binSize[axis]
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}
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}.toVector()
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MultivariateBin(center, binSize)
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}
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}
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/**
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* Get internal [NDStructure] bin index for given axis
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*/
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private fun getIndex(axis: Int, value: Double): Int {
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return when {
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value >= upper[axis] -> binNums[axis] + 1 // overflow
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value < lower[axis] -> 0 // underflow
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else -> floor((value - lower[axis]) / binSize[axis]).toInt() + 1
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}
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}
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override fun get(point: RealVector): MultivariateBin? {
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val index = IntArray(dimension) { getIndex(it, point[it]) }
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return bins[index]
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}
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override fun put(point: RealVector) {
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this[point]?.inc() ?: error("Could not find appropriate bin (should not be possible)")
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}
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override fun iterator(): Iterator<MultivariateBin> = bins.asSequence().map { it.second }.iterator()
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companion object {
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/**
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* Use it like
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* ```
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*FastHistogram.fromRanges(
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* (-1.0..1.0),
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* (-1.0..1.0)
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*)
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*```
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*/
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fun fromRanges(vararg ranges: ClosedFloatingPointRange<Double>): FastHistogram {
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return FastHistogram(ranges.map { it.start }.toVector(), ranges.map { it.endInclusive }.toVector())
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}
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/**
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* Use it like
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* ```
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*FastHistogram.fromRanges(
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* (-1.0..1.0) to 50,
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* (-1.0..1.0) to 32
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*)
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*```
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*/
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fun fromRanges(vararg ranges: Pair<ClosedFloatingPointRange<Double>,Int>): FastHistogram {
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return FastHistogram(
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ranges.map { it.first.start }.toVector(),
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ranges.map { it.first.endInclusive }.toVector(),
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ranges.map { it.second }.toIntArray()
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)
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}
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}
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}
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package scientifik.kmath.histogram
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import scientifik.kmath.linear.RealVector
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import scientifik.kmath.linear.toVector
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import java.util.*
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import kotlin.math.floor
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//TODO move to common
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class UnivariateBin(val position: Double, val size: Double, val counter: LongCounter = LongCounter()) : Bin {
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//TODO add weighting
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override val value: Number get() = counter.sum()
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override val center: RealVector get() = doubleArrayOf(position).toVector()
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operator fun contains(value: Double): Boolean = value in (position - size / 2)..(position + size / 2)
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override fun contains(vector: RealVector): Boolean = contains(vector[0])
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internal operator fun inc() = this.also { counter.increment()}
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override val dimension: Int get() = 1
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}
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/**
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* Univariate histogram with log(n) bin search speed
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*/
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class UnivariateHistogram private constructor(private val factory: (Double) -> UnivariateBin) : Histogram<UnivariateBin> {
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private val bins: TreeMap<Double, UnivariateBin> = TreeMap()
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private operator fun get(value: Double): UnivariateBin? {
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// check ceiling entry and return it if it is what needed
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val ceil = bins.ceilingEntry(value)?.value
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if (ceil != null && value in ceil) return ceil
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//check floor entry
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val floor = bins.floorEntry(value)?.value
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if (floor != null && value in floor) return floor
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//neither is valid, not found
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return null
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}
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private fun createBin(value: Double): UnivariateBin = factory(value).also {
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synchronized(this) { bins.put(it.position, it) }
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}
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override fun get(point: RealVector): UnivariateBin? = get(point[0])
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override val dimension: Int get() = 1
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override fun iterator(): Iterator<UnivariateBin> = bins.values.iterator()
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/**
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* Thread safe put operation
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*/
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fun put(value: Double) {
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(get(value) ?: createBin(value)).inc()
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}
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override fun put(point: RealVector) = put(point[0])
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companion object {
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fun uniform(binSize: Double, start: Double = 0.0): UnivariateHistogram {
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return UnivariateHistogram { value ->
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val center = start + binSize * floor((value - start) / binSize + 0.5)
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UnivariateBin(center, binSize)
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}
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}
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fun custom(borders: DoubleArray): UnivariateHistogram {
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val sorted = borders.sortedArray()
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return UnivariateHistogram { value ->
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if (value < sorted.first()) {
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UnivariateBin(Double.NEGATIVE_INFINITY, Double.MAX_VALUE)
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} else if (value > sorted.last()) {
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UnivariateBin(Double.POSITIVE_INFINITY, Double.MAX_VALUE)
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} else {
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val index = (0 until sorted.size).first { value > sorted[it] }
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val left = sorted[index]
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val right = sorted[index + 1]
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UnivariateBin((left + right) / 2, (right - left))
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}
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}
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}
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}
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}
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fun UnivariateHistogram.fill(sequence: Iterable<Double>) = sequence.forEach { put(it) }
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package scientifik.kmath.histogram
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import org.junit.Test
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import scientifik.kmath.linear.Vector
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import kotlin.random.Random
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import kotlin.test.assertEquals
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import kotlin.test.assertFalse
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import kotlin.test.assertTrue
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class MultivariateHistogramTest {
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@Test
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fun testSinglePutHistogram() {
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val histogram = FastHistogram.fromRanges(
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(-1.0..1.0),
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(-1.0..1.0)
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)
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histogram.put(0.6, 0.6)
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val bin = histogram.find { it.value.toInt() > 0 }!!
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assertTrue { bin.contains(Vector.ofReal(0.6, 0.6)) }
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assertFalse { bin.contains(Vector.ofReal(-0.6, 0.6)) }
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}
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@Test
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fun testSequentialPut(){
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val histogram = FastHistogram.fromRanges(
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(-1.0..1.0),
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(-1.0..1.0),
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(-1.0..1.0)
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)
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val random = Random(1234)
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fun nextDouble() = random.nextDouble(-1.0,1.0)
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val n = 10000
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histogram.fill {
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repeat(n){
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yield(Vector.ofReal(nextDouble(),nextDouble(),nextDouble()))
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}
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}
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assertEquals(n, histogram.sumBy { it.value.toInt() })
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}
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}
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