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Dev #127

Merged
altavir merged 214 commits from dev into master 2020-08-11 08:33:21 +03:00
Conversation 0 Commits 214 Files Changed 149 +172 -138
19 changed files with 172 additions and 138 deletions
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4
build.gradle.kts
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@ -1,8 +1,8 @@
plugins {
id("scientifik.publish") version "0.4.2" apply false
id("scientifik.publish") apply false
}
val kmathVersion by extra("0.1.4-dev-4")
val kmathVersion by extra("0.1.4-dev-5")
val bintrayRepo by extra("scientifik")
val githubProject by extra("kmath")

2
examples/build.gradle.kts
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@ -57,6 +57,6 @@ benchmark {
tasks.withType<KotlinCompile> {
kotlinOptions {
jvmTarget = Scientifik.JVM_VERSION
jvmTarget = Scientifik.JVM_TARGET.toString()
}
}

11
kmath-commons/src/main/kotlin/scientifik/kmath/commons/linear/CMMatrix.kt
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@ -5,6 +5,7 @@ import org.apache.commons.math3.linear.RealMatrix
import org.apache.commons.math3.linear.RealVector
import scientifik.kmath.linear.*
import scientifik.kmath.structures.Matrix
import scientifik.kmath.structures.NDStructure
class CMMatrix(val origin: RealMatrix, features: Set<MatrixFeature>? = null) :
FeaturedMatrix<Double> {
@ -19,6 +20,16 @@ class CMMatrix(val origin: RealMatrix, features: Set<MatrixFeature>? = null) :
CMMatrix(origin, this.features + features)
override fun get(i: Int, j: Int): Double = origin.getEntry(i, j)
override fun equals(other: Any?): Boolean {
return NDStructure.equals(this, other as? NDStructure<*> ?: return false)
}
override fun hashCode(): Int {
var result = origin.hashCode()
result = 31 * result + features.hashCode()
return result
}
}
fun Matrix<Double>.toCM(): CMMatrix = if (this is CMMatrix) {

16
kmath-core/src/commonMain/kotlin/scientifik/kmath/operations/BigInt.kt
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@ -2,6 +2,7 @@ package scientifik.kmath.operations
import scientifik.kmath.operations.BigInt.Companion.BASE
import scientifik.kmath.operations.BigInt.Companion.BASE_SIZE
import scientifik.kmath.structures.*
import kotlin.math.log2
import kotlin.math.max
import kotlin.math.min
@ -482,3 +483,18 @@ fun String.parseBigInteger(): BigInt? {
}
return res * sign
}
inline fun Buffer.Companion.bigInt(size: Int, initializer: (Int) -> BigInt): Buffer<BigInt> =
boxing(size, initializer)
inline fun MutableBuffer.Companion.bigInt(size: Int, initializer: (Int) -> BigInt): MutableBuffer<BigInt> =
boxing(size, initializer)
fun NDAlgebra.Companion.bigInt(vararg shape: Int): BoxingNDRing<BigInt, BigIntField> =
BoxingNDRing(shape, BigIntField, Buffer.Companion::bigInt)
fun NDElement.Companion.bigInt(
vararg shape: Int,
initializer: BigIntField.(IntArray) -> BigInt
): BufferedNDRingElement<BigInt, BigIntField> =
NDAlgebra.bigInt(*shape).produce(initializer)

12
kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/BufferedNDElement.kt
View File

@ -3,10 +3,10 @@ package scientifik.kmath.structures
import scientifik.kmath.operations.*
/**
* Base interface for an element with context, containing strides
* Base class for an element with context, containing strides
*/
interface BufferedNDElement<T, C> : NDBuffer<T>, NDElement<T, C, NDBuffer<T>> {
override val context: BufferedNDAlgebra<T, C>
abstract class BufferedNDElement<T, C> : NDBuffer<T>(), NDElement<T, C, NDBuffer<T>> {
abstract override val context: BufferedNDAlgebra<T, C>
override val strides get() = context.strides
@ -16,7 +16,7 @@ interface BufferedNDElement<T, C> : NDBuffer<T>, NDElement<T, C, NDBuffer<T>> {
class BufferedNDSpaceElement<T, S : Space<T>>(
override val context: BufferedNDSpace<T, S>,
override val buffer: Buffer<T>
) : BufferedNDElement<T, S>, SpaceElement<NDBuffer<T>, BufferedNDSpaceElement<T, S>, BufferedNDSpace<T, S>> {
) : BufferedNDElement<T, S>(), SpaceElement<NDBuffer<T>, BufferedNDSpaceElement<T, S>, BufferedNDSpace<T, S>> {
override fun unwrap(): NDBuffer<T> = this
@ -29,7 +29,7 @@ class BufferedNDSpaceElement<T, S : Space<T>>(
class BufferedNDRingElement<T, R : Ring<T>>(
override val context: BufferedNDRing<T, R>,
override val buffer: Buffer<T>
) : BufferedNDElement<T, R>, RingElement<NDBuffer<T>, BufferedNDRingElement<T, R>, BufferedNDRing<T, R>> {
) : BufferedNDElement<T, R>(), RingElement<NDBuffer<T>, BufferedNDRingElement<T, R>, BufferedNDRing<T, R>> {
override fun unwrap(): NDBuffer<T> = this
@ -42,7 +42,7 @@ class BufferedNDRingElement<T, R : Ring<T>>(
class BufferedNDFieldElement<T, F : Field<T>>(
override val context: BufferedNDField<T, F>,
override val buffer: Buffer<T>
) : BufferedNDElement<T, F>, FieldElement<NDBuffer<T>, BufferedNDFieldElement<T, F>, BufferedNDField<T, F>> {
) : BufferedNDElement<T, F>(), FieldElement<NDBuffer<T>, BufferedNDFieldElement<T, F>, BufferedNDField<T, F>> {
override fun unwrap(): NDBuffer<T> = this

2
kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/Buffers.kt
View File

@ -71,7 +71,7 @@ interface Buffer<T> {
fun <T> Buffer<T>.asSequence(): Sequence<T> = Sequence(::iterator)
fun <T> Buffer<T>.asIterable(): Iterable<T> = asSequence().asIterable()
fun <T> Buffer<T>.asIterable(): Iterable<T> = Iterable(::iterator)
val Buffer<*>.indices: IntRange get() = IntRange(0, size - 1)

62
kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/NDStructure.kt
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@ -14,15 +14,21 @@ interface NDStructure<T> {
fun elements(): Sequence<Pair<IntArray, T>>
override fun equals(other: Any?): Boolean
override fun hashCode(): Int
companion object {
fun equals(st1: NDStructure<*>, st2: NDStructure<*>): Boolean {
return when {
st1 === st2 -> true
st1 is BufferNDStructure<*> && st2 is BufferNDStructure<*> && st1.strides == st2.strides -> st1.buffer.contentEquals(
st2.buffer
)
else -> st1.elements().all { (index, value) -> value == st2[index] }
if(st1===st2) return true
// fast comparison of buffers if possible
if(st1 is NDBuffer && st2 is NDBuffer && st1.strides == st2.strides){
return st1.buffer.contentEquals(st2.buffer)
}
//element by element comparison if it could not be avoided
return st1.elements().all { (index, value) -> value == st2[index] }
}
/**
@ -177,15 +183,25 @@ class DefaultStrides private constructor(override val shape: IntArray) : Strides
}
}
interface NDBuffer<T> : NDStructure<T> {
val buffer: Buffer<T>
val strides: Strides
abstract class NDBuffer<T> : NDStructure<T> {
abstract val buffer: Buffer<T>
abstract val strides: Strides
override fun get(index: IntArray): T = buffer[strides.offset(index)]
override val shape: IntArray get() = strides.shape
override fun elements() = strides.indices().map { it to this[it] }
override fun elements(): Sequence<Pair<IntArray, T>> = strides.indices().map { it to this[it] }
override fun equals(other: Any?): Boolean {
return NDStructure.equals(this, other as? NDStructure<*> ?: return false)
}
override fun hashCode(): Int {
var result = strides.hashCode()
result = 31 * result + buffer.hashCode()
return result
}
}
/**
@ -194,34 +210,12 @@ interface NDBuffer<T> : NDStructure<T> {
class BufferNDStructure<T>(
override val strides: Strides,
override val buffer: Buffer<T>
) : NDBuffer<T> {
) : NDBuffer<T>(){
init {
if (strides.linearSize != buffer.size) {
error("Expected buffer side of ${strides.linearSize}, but found ${buffer.size}")
}
}
override fun get(index: IntArray): T = buffer[strides.offset(index)]
override val shape: IntArray get() = strides.shape
override fun elements() = strides.indices().map { it to this[it] }
override fun equals(other: Any?): Boolean {
return when {
this === other -> true
other is BufferNDStructure<*> && this.strides == other.strides -> this.buffer.contentEquals(other.buffer)
other is NDStructure<*> -> elements().all { (index, value) -> value == other[index] }
else -> false
}
}
override fun hashCode(): Int {
var result = strides.hashCode()
result = 31 * result + buffer.hashCode()
return result
}
}
/**
@ -245,7 +239,7 @@ inline fun <T, reified R : Any> NDStructure<T>.mapToBuffer(
class MutableBufferNDStructure<T>(
override val strides: Strides,
override val buffer: MutableBuffer<T>
) : NDBuffer<T>, MutableNDStructure<T> {
) : NDBuffer<T>(), MutableNDStructure<T> {
init {
if (strides.linearSize != buffer.size) {

19
kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/Structure2D.kt
View File

@ -14,7 +14,6 @@ interface Structure2D<T> : NDStructure<T> {
return get(index[0], index[1])
}
val rows: Buffer<Buffer<T>>
get() = VirtualBuffer(rowNum) { i ->
VirtualBuffer(colNum) { j -> get(i, j) }
@ -58,22 +57,4 @@ fun <T> NDStructure<T>.as2D(): Structure2D<T> = if (shape.size == 2) {
error("Can't create 2d-structure from ${shape.size}d-structure")
}
/**
* Represent this 2D structure as 1D if it has exactly one column. Throw error otherwise.
*/
fun <T> Structure2D<T>.as1D() = if (colNum == 1) {
object : Structure1D<T> {
override fun get(index: Int): T = get(index, 0)
override val shape: IntArray get() = intArrayOf(rowNum)
override fun elements(): Sequence<Pair<IntArray, T>> = elements()
override val size: Int get() = rowNum
}
} else {
error("Can't convert matrix with more than one column to vector")
}
typealias Matrix<T> = Structure2D<T>

21
kmath-core/src/jvmMain/kotlin/scientifik/kmath/operations/BigNumbers.kt → kmath-core/src/jvmMain/kotlin/scientifik/kmath/operations/bigNumbers.kt
View File

@ -5,7 +5,7 @@ import java.math.BigDecimal
import java.math.BigInteger
import java.math.MathContext
object BigIntegerRing : Ring<BigInteger> {
object JBigIntegerField : Field<BigInteger> {
override val zero: BigInteger = BigInteger.ZERO
override val one: BigInteger = BigInteger.ONE
@ -14,9 +14,11 @@ object BigIntegerRing : Ring<BigInteger> {
override fun multiply(a: BigInteger, k: Number): BigInteger = a.multiply(k.toInt().toBigInteger())
override fun multiply(a: BigInteger, b: BigInteger): BigInteger = a.multiply(b)
override fun divide(a: BigInteger, b: BigInteger): BigInteger = a.div(b)
}
class BigDecimalField(val mathContext: MathContext = MathContext.DECIMAL64) : Field<BigDecimal> {
class JBigDecimalField(val mathContext: MathContext = MathContext.DECIMAL64) : Field<BigDecimal> {
override val zero: BigDecimal = BigDecimal.ZERO
override val one: BigDecimal = BigDecimal.ONE
@ -28,18 +30,3 @@ class BigDecimalField(val mathContext: MathContext = MathContext.DECIMAL64) : Fi
override fun multiply(a: BigDecimal, b: BigDecimal): BigDecimal = a.multiply(b, mathContext)
override fun divide(a: BigDecimal, b: BigDecimal): BigDecimal = a.divide(b, mathContext)
}
inline fun Buffer.Companion.bigInt(size: Int, initializer: (Int) -> BigInteger): Buffer<BigInteger> =
boxing(size, initializer)
inline fun MutableBuffer.Companion.bigInt(size: Int, initializer: (Int) -> BigInteger): MutableBuffer<BigInteger> =
boxing(size, initializer)
fun NDAlgebra.Companion.bigInt(vararg shape: Int): BoxingNDRing<BigInteger, BigIntegerRing> =
BoxingNDRing(shape, BigIntegerRing, Buffer.Companion::bigInt)
fun NDElement.Companion.bigInt(
vararg shape: Int,
initializer: BigIntegerRing.(IntArray) -> BigInteger
): BufferedNDRingElement<BigInteger, BigIntegerRing> =
NDAlgebra.bigInt(*shape).produce(initializer)

4
kmath-coroutines/src/commonMain/kotlin/scientifik/kmath/chains/Chain.kt
View File

@ -68,6 +68,8 @@ class MarkovChain<out R : Any>(private val seed: suspend () -> R, private val ge
private var value: R? = null
fun value() = value
override suspend fun next(): R {
mutex.withLock {
val newValue = gen(value ?: seed())
@ -97,6 +99,8 @@ class StatefulChain<S, out R>(
private var value: R? = null
fun value() = value
override suspend fun next(): R {
mutex.withLock {
val newValue = state.gen(value ?: state.seed())

14
kmath-coroutines/src/jvmMain/kotlin/scientifik/kmath/structures/LazyNDStructure.kt
View File

@ -30,6 +30,20 @@ class LazyNDStructure<T>(
}
return res.asSequence()
}
override fun equals(other: Any?): Boolean {
return NDStructure.equals(this, other as? NDStructure<*> ?: return false)
}
override fun hashCode(): Int {
var result = scope.hashCode()
result = 31 * result + shape.contentHashCode()
result = 31 * result + function.hashCode()
result = 31 * result + cache.hashCode()
return result
}
}
fun <T> NDStructure<T>.deferred(index: IntArray) =

48
kmath-for-real/src/commonMain/kotlin/scientifik/kmath/linear/RealVector.kt
View File

@ -1,48 +0,0 @@
package scientifik.kmath.linear
import scientifik.kmath.operations.Field
import scientifik.kmath.operations.Norm
import scientifik.kmath.operations.RealField
import scientifik.kmath.operations.SpaceElement
import scientifik.kmath.structures.Buffer
import scientifik.kmath.structures.DoubleBuffer
import scientifik.kmath.structures.asBuffer
import scientifik.kmath.structures.asSequence
fun DoubleArray.asVector() = RealVector(this.asBuffer())
fun List<Double>.asVector() = RealVector(this.asBuffer())
object VectorL2Norm : Norm<Point<out Number>, Double> {
override fun norm(arg: Point<out Number>): Double =
kotlin.math.sqrt(arg.asSequence().sumByDouble { it.toDouble() })
}
inline class RealVector(val point: Point<Double>) :
SpaceElement<Point<Double>, RealVector, VectorSpace<Double, RealField>>, Point<Double> {
override val context: VectorSpace<Double, RealField> get() = space(point.size)
override fun unwrap(): Point<Double> = point
override fun Point<Double>.wrap(): RealVector = RealVector(this)
override val size: Int get() = point.size
override fun get(index: Int): Double = point[index]
override fun iterator(): Iterator<Double> = point.iterator()
companion object {
private val spaceCache = HashMap<Int, BufferVectorSpace<Double, RealField>>()
inline operator fun invoke(dim:Int, initalizer: (Int)-> Double) = RealVector(DoubleBuffer(dim, initalizer))
operator fun invoke(vararg values: Double) = values.asVector()
fun space(dim: Int) =
spaceCache.getOrPut(dim) {
BufferVectorSpace(dim, RealField) { size, init -> Buffer.real(size, init) }
}
}
}

59
kmath-for-real/src/commonMain/kotlin/scientifik/kmath/real/RealVector.kt Normal file
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@ -0,0 +1,59 @@
package scientifik.kmath.real
import scientifik.kmath.linear.BufferVectorSpace
import scientifik.kmath.linear.Point
import scientifik.kmath.linear.VectorSpace
import scientifik.kmath.operations.Norm
import scientifik.kmath.operations.RealField
import scientifik.kmath.operations.SpaceElement
import scientifik.kmath.structures.Buffer
import scientifik.kmath.structures.DoubleBuffer
import scientifik.kmath.structures.asBuffer
import scientifik.kmath.structures.asIterable
import kotlin.math.sqrt
fun DoubleArray.asVector() = RealVector(this.asBuffer())
fun List<Double>.asVector() = RealVector(this.asBuffer())
object VectorL2Norm : Norm<Point<out Number>, Double> {
override fun norm(arg: Point<out Number>): Double = sqrt(arg.asIterable().sumByDouble { it.toDouble() })
}
inline class RealVector(private val point: Point<Double>) :
SpaceElement<Point<Double>, RealVector, VectorSpace<Double, RealField>>, Point<Double> {
override val context: VectorSpace<Double, RealField>
get() = space(
point.size
)
override fun unwrap(): Point<Double> = point
override fun Point<Double>.wrap(): RealVector =
RealVector(this)
override val size: Int get() = point.size
override fun get(index: Int): Double = point[index]
override fun iterator(): Iterator<Double> = point.iterator()
companion object {
private val spaceCache = HashMap<Int, BufferVectorSpace<Double, RealField>>()
inline operator fun invoke(dim: Int, initializer: (Int) -> Double) =
RealVector(DoubleBuffer(dim, initializer))
operator fun invoke(vararg values: Double): RealVector = values.asVector()
fun space(dim: Int): BufferVectorSpace<Double, RealField> =
spaceCache.getOrPut(dim) {
BufferVectorSpace(
dim,
RealField
) { size, init -> Buffer.real(size, init) }
}
}
}

1
kmath-for-real/src/commonTest/kotlin/scientifik/kmath/linear/VectorTest.kt
View File

@ -1,5 +1,6 @@
package scientifik.kmath.linear
import scientifik.kmath.real.RealVector
import kotlin.test.Test
import kotlin.test.assertEquals

2
kmath-histograms/src/commonMain/kotlin/scientifik/kmath/histogram/RealHistogram.kt
View File

@ -1,7 +1,7 @@
package scientifik.kmath.histogram
import scientifik.kmath.linear.Point
import scientifik.kmath.linear.asVector
import scientifik.kmath.real.asVector
import scientifik.kmath.operations.SpaceOperations
import scientifik.kmath.structures.*
import kotlin.math.floor

2
kmath-histograms/src/commonTest/kotlin/scietifik/kmath/histogram/MultivariateHistogramTest.kt
View File

@ -3,7 +3,7 @@ package scietifik.kmath.histogram
import scientifik.kmath.histogram.RealHistogram
import scientifik.kmath.histogram.fill
import scientifik.kmath.histogram.put
import scientifik.kmath.linear.RealVector
import scientifik.kmath.real.RealVector
import kotlin.random.Random
import kotlin.test.Test
import kotlin.test.assertEquals

4
kmath-histograms/src/jvmMain/kotlin/scientifik/kmath/histogram/UnivariateHistogram.kt
View File

@ -1,7 +1,7 @@
package scientifik.kmath.histogram
import scientifik.kmath.linear.RealVector
import scientifik.kmath.linear.asVector
import scientifik.kmath.real.RealVector
import scientifik.kmath.real.asVector
import scientifik.kmath.structures.Buffer
import java.util.*
import kotlin.math.floor

13
kmath-koma/src/commonMain/kotlin/scientifik.kmath.linear/KomaMatrix.kt
View File

@ -4,6 +4,7 @@ import koma.extensions.fill
import koma.matrix.MatrixFactory
import scientifik.kmath.operations.Space
import scientifik.kmath.structures.Matrix
import scientifik.kmath.structures.NDStructure
class KomaMatrixContext<T : Any>(
private val factory: MatrixFactory<koma.matrix.Matrix<T>>,
@ -85,6 +86,18 @@ class KomaMatrix<T : Any>(val origin: koma.matrix.Matrix<T>, features: Set<Matri
KomaMatrix(this.origin, this.features + features)
override fun get(i: Int, j: Int): T = origin.getGeneric(i, j)
override fun equals(other: Any?): Boolean {
return NDStructure.equals(this, other as? NDStructure<*> ?: return false)
}
override fun hashCode(): Int {
var result = origin.hashCode()
result = 31 * result + features.hashCode()
return result
}
}
class KomaVector<T : Any> internal constructor(val origin: koma.matrix.Matrix<T>) : Point<T> {

12
settings.gradle.kts
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@ -1,10 +1,12 @@
pluginManagement {
val toolsVersion = "0.5.0"
plugins {
id("scientifik.mpp") version "0.4.1"
id("scientifik.jvm") version "0.4.1"
id("scientifik.atomic") version "0.4.1"
id("scientifik.publish") version "0.4.1"
id("scientifik.mpp") version toolsVersion
id("scientifik.jvm") version toolsVersion
id("scientifik.atomic") version toolsVersion
id("scientifik.publish") version toolsVersion
}
repositories {
@ -20,7 +22,7 @@ pluginManagement {
resolutionStrategy {
eachPlugin {
when (requested.id.id) {
"scientifik.mpp", "scientifik.jvm", "scientifik.publish" -> useModule("scientifik:gradle-tools:${requested.version}")
"scientifik.mpp", "scientifik.jvm", "scientifik.publish" -> useModule("scientifik:gradle-tools:$toolsVersion")
}
}
}