build.gradle.kts

@@ -2,7 +2,7 @@ plugins {
     id("scientifik.publish") apply false
 }
 
-val kmathVersion by extra("0.1.4-dev-7")
+val kmathVersion by extra("0.1.4-dev-8")
 
 val bintrayRepo by extra("scientifik")
 val githubProject by extra("kmath")

examples/build.gradle.kts

@@ -4,8 +4,8 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 plugins {
     java
     kotlin("jvm")
-    kotlin("plugin.allopen") version "1.3.71"
-    id("kotlinx.benchmark") version "0.2.0-dev-7"
+    kotlin("plugin.allopen") version "1.3.72"
+    id("kotlinx.benchmark") version "0.2.0-dev-8"
 }
 
 configure<AllOpenExtension> {
@@ -33,8 +33,8 @@ dependencies {
     implementation(project(":kmath-dimensions"))
     implementation("com.kyonifer:koma-core-ejml:0.12")
     implementation("org.jetbrains.kotlinx:kotlinx-io-jvm:0.2.0-npm-dev-6")
-    implementation("org.jetbrains.kotlinx:kotlinx.benchmark.runtime:0.2.0-dev-7")
-    "benchmarksCompile"(sourceSets.main.get().compileClasspath)
+    implementation("org.jetbrains.kotlinx:kotlinx.benchmark.runtime:0.2.0-dev-8")
+    "benchmarksCompile"(sourceSets.main.get().output + sourceSets.main.get().compileClasspath) //sourceSets.main.output + sourceSets.main.runtimeClasspath
 }
 
 // Configure benchmark

examples/src/benchmarks/kotlin/scientifik/kmath/structures/ViktorBenchmark.kt

@@ -20,7 +20,7 @@ class ViktorBenchmark {
     final val viktorField = ViktorNDField(intArrayOf(dim, dim))
 
     @Benchmark
-    fun `Automatic field addition`() {
+    fun automaticFieldAddition() {
         autoField.run {
             var res = one
             repeat(n) {
@@ -30,7 +30,7 @@ class ViktorBenchmark {
     }
 
     @Benchmark
-    fun `Viktor field addition`() {
+    fun viktorFieldAddition() {
         viktorField.run {
             var res = one
             repeat(n) {
@@ -40,7 +40,7 @@ class ViktorBenchmark {
     }
 
     @Benchmark
-    fun `Raw Viktor`() {
+    fun rawViktor() {
         val one = F64Array.full(init = 1.0, shape = *intArrayOf(dim, dim))
         var res = one
         repeat(n) {
@@ -49,7 +49,7 @@ class ViktorBenchmark {
     }
 
     @Benchmark
-    fun `Real field log`() {
+    fun realdFieldLog() {
         realField.run {
             val fortyTwo = produce { 42.0 }
             var res = one
@@ -61,7 +61,7 @@ class ViktorBenchmark {
     }
 
     @Benchmark
-    fun `Raw Viktor log`() {
+    fun rawViktorLog() {
         val fortyTwo = F64Array.full(dim, dim, init = 42.0)
         var res: F64Array
         repeat(n) {

kmath-commons/src/main/kotlin/scientifik/kmath/commons/random/CMRandomGeneratorWrapper.kt

@@ -0,0 +1,38 @@
+package scientifik.kmath.commons.random
+
+import scientifik.kmath.prob.RandomGenerator
+
+class CMRandomGeneratorWrapper(val factory: (IntArray) -> RandomGenerator) :
+    org.apache.commons.math3.random.RandomGenerator {
+    private var generator = factory(intArrayOf())
+
+    override fun nextBoolean(): Boolean = generator.nextBoolean()
+
+    override fun nextFloat(): Float = generator.nextDouble().toFloat()
+
+    override fun setSeed(seed: Int) {
+        generator = factory(intArrayOf(seed))
+    }
+
+    override fun setSeed(seed: IntArray) {
+        generator = factory(seed)
+    }
+
+    override fun setSeed(seed: Long) {
+        setSeed(seed.toInt())
+    }
+
+    override fun nextBytes(bytes: ByteArray) {
+        generator.fillBytes(bytes)
+    }
+
+    override fun nextInt(): Int = generator.nextInt()
+
+    override fun nextInt(n: Int): Int = generator.nextInt(n)
+
+    override fun nextGaussian(): Double = TODO()
+
+    override fun nextDouble(): Double = generator.nextDouble()
+
+    override fun nextLong(): Long = generator.nextLong()
+}

kmath-core/src/commonMain/kotlin/scientifik/kmath/domains/Domain.kt

@@ -0,0 +1,15 @@
+package scientifik.kmath.domains
+
+import scientifik.kmath.linear.Point
+
+/**
+ * A simple geometric domain
+ */
+interface Domain<T : Any> {
+    operator fun contains(point: Point<T>): Boolean
+
+    /**
+     * Number of hyperspace dimensions
+     */
+    val dimension: Int
+}

kmath-core/src/commonMain/kotlin/scientifik/kmath/domains/HyperSquareDomain.kt

@@ -0,0 +1,67 @@
+/* 
+ * Copyright 2015 Alexander Nozik.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package scientifik.kmath.domains
+
+import scientifik.kmath.linear.Point
+import scientifik.kmath.structures.DoubleBuffer
+import scientifik.kmath.structures.indices
+
+/**
+ *
+ * HyperSquareDomain class.
+ *
+ * @author Alexander Nozik
+ */
+class HyperSquareDomain(private val lower: DoubleBuffer, private val upper: DoubleBuffer) : RealDomain {
+
+    override operator fun contains(point: Point<Double>): Boolean = point.indices.all { i ->
+        point[i] in lower[i]..upper[i]
+    }
+
+    override val dimension: Int get() = lower.size
+
+    override fun getLowerBound(num: Int, point: Point<Double>): Double? = lower[num]
+
+    override fun getLowerBound(num: Int): Double? = lower[num]
+
+    override fun getUpperBound(num: Int, point: Point<Double>): Double? = upper[num]
+
+    override fun getUpperBound(num: Int): Double? = upper[num]
+
+    override fun nearestInDomain(point: Point<Double>): Point<Double> {
+        val res: DoubleArray = DoubleArray(point.size) { i ->
+            when {
+                point[i] < lower[i] -> lower[i]
+                point[i] > upper[i] -> upper[i]
+                else -> point[i]
+            }
+        }
+        return DoubleBuffer(*res)
+    }
+
+    override fun volume(): Double {
+        var res = 1.0
+        for (i in 0 until dimension) {
+            if (lower[i].isInfinite() || upper[i].isInfinite()) {
+                return Double.POSITIVE_INFINITY
+            }
+            if (upper[i] > lower[i]) {
+                res *= upper[i] - lower[i]
+            }
+        }
+        return res
+    }
+}

kmath-core/src/commonMain/kotlin/scientifik/kmath/domains/RealDomain.kt

@@ -0,0 +1,65 @@
+/* 
+ * Copyright 2015 Alexander Nozik.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package scientifik.kmath.domains
+
+import scientifik.kmath.linear.Point
+
+/**
+ * n-dimensional volume
+ *
+ * @author Alexander Nozik
+ */
+interface RealDomain: Domain<Double> {
+
+    fun nearestInDomain(point: Point<Double>): Point<Double>
+
+    /**
+     * The lower edge for the domain going down from point
+     * @param num
+     * @param point
+     * @return
+     */
+    fun getLowerBound(num: Int, point: Point<Double>): Double?
+
+    /**
+     * The upper edge of the domain going up from point
+     * @param num
+     * @param point
+     * @return
+     */
+    fun getUpperBound(num: Int, point: Point<Double>): Double?
+
+    /**
+     * Global lower edge
+     * @param num
+     * @return
+     */
+    fun getLowerBound(num: Int): Double?
+
+    /**
+     * Global upper edge
+     * @param num
+     * @return
+     */
+    fun getUpperBound(num: Int): Double?
+
+    /**
+     * Hyper volume
+     * @return
+     */
+    fun volume(): Double
+
+}

kmath-core/src/commonMain/kotlin/scientifik/kmath/domains/UnconstrainedDomain.kt

@@ -0,0 +1,36 @@
+/* 
+ * Copyright 2015 Alexander Nozik.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package scientifik.kmath.domains
+
+import scientifik.kmath.linear.Point
+
+class UnconstrainedDomain(override val dimension: Int) : RealDomain {
+
+    override operator fun contains(point: Point<Double>): Boolean = true
+
+    override fun getLowerBound(num: Int, point: Point<Double>): Double? = Double.NEGATIVE_INFINITY
+
+    override fun getLowerBound(num: Int): Double? = Double.NEGATIVE_INFINITY
+
+    override fun getUpperBound(num: Int, point: Point<Double>): Double? = Double.POSITIVE_INFINITY
+
+    override fun getUpperBound(num: Int): Double? = Double.POSITIVE_INFINITY
+
+    override fun nearestInDomain(point: Point<Double>): Point<Double> = point
+
+    override fun volume(): Double = Double.POSITIVE_INFINITY
+
+}

kmath-core/src/commonMain/kotlin/scientifik/kmath/domains/UnivariateDomain.kt

@@ -0,0 +1,48 @@
+package scientifik.kmath.domains
+
+import scientifik.kmath.linear.Point
+import scientifik.kmath.structures.asBuffer
+
+inline class UnivariateDomain(val range: ClosedFloatingPointRange<Double>) : RealDomain {
+
+    operator fun contains(d: Double): Boolean = range.contains(d)
+
+    override operator fun contains(point: Point<Double>): Boolean {
+        require(point.size == 0)
+        return contains(point[0])
+    }
+
+    override fun nearestInDomain(point: Point<Double>): Point<Double> {
+        require(point.size == 1)
+        val value = point[0]
+        return when{
+            value in range -> point
+            value >= range.endInclusive -> doubleArrayOf(range.endInclusive).asBuffer()
+            else ->  doubleArrayOf(range.start).asBuffer()
+        }
+    }
+
+    override fun getLowerBound(num: Int, point: Point<Double>): Double? {
+        require(num == 0)
+        return range.start
+    }
+
+    override fun getUpperBound(num: Int, point: Point<Double>): Double? {
+        require(num == 0)
+        return range.endInclusive
+    }
+
+    override fun getLowerBound(num: Int): Double? {
+        require(num == 0)
+        return range.start
+    }
+
+    override fun getUpperBound(num: Int): Double? {
+        require(num == 0)
+        return range.endInclusive
+    }
+
+    override fun volume(): Double = range.endInclusive - range.start
+
+    override val dimension: Int get() = 1
+}

kmath-for-real/src/commonMain/kotlin/scientifik/kmath/real/RealVector.kt

@@ -12,26 +12,23 @@ import scientifik.kmath.structures.asBuffer
 import scientifik.kmath.structures.asIterable
 import kotlin.math.sqrt
 
+typealias RealPoint = Point<Double>
+
 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> {
+    SpaceElement<RealPoint, RealVector, VectorSpace<Double, RealField>>, RealPoint {
 
-    override val context: VectorSpace<Double, RealField>
-        get() = space(
-            point.size
-        )
+    override val context: VectorSpace<Double, RealField> get() = space(point.size)
 
-    override fun unwrap(): Point<Double> = point
+    override fun unwrap(): RealPoint = point
 
-    override fun Point<Double>.wrap(): RealVector =
-        RealVector(this)
+    override fun RealPoint.wrap(): RealVector = RealVector(this)
 
     override val size: Int get() = point.size
 
@@ -48,12 +45,8 @@ inline class RealVector(private val point: Point<Double>) :
 
         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) }
+        fun space(dim: Int): BufferVectorSpace<Double, RealField> = spaceCache.getOrPut(dim) {
+            BufferVectorSpace(dim, RealField) { size, init -> Buffer.real(size, init) }
         }
     }
 }

kmath-for-real/src/commonMain/kotlin/scientifik/kmath/real/realMatrix.kt

@@ -27,6 +27,10 @@ typealias RealMatrix = Matrix<Double>
 fun realMatrix(rowNum: Int, colNum: Int, initializer: (i: Int, j: Int) -> Double): RealMatrix =
     MatrixContext.real.produce(rowNum, colNum, initializer)
 
+fun Array<DoubleArray>.toMatrix(): RealMatrix{
+    return MatrixContext.real.produce(size, this[0].size) { row, col -> this[row][col] }
+}
+
 fun Sequence<DoubleArray>.toMatrix(): RealMatrix = toList().let {
     MatrixContext.real.produce(it.size, it[0].size) { row, col -> it[row][col] }
 }

kmath-histograms/src/commonMain/kotlin/scientifik/kmath/histogram/Histogram.kt

@@ -1,18 +1,10 @@
 package scientifik.kmath.histogram
 
+import scientifik.kmath.domains.Domain
 import scientifik.kmath.linear.Point
 import scientifik.kmath.structures.ArrayBuffer
 import scientifik.kmath.structures.DoubleBuffer
 
-/**
- * A simple geometric domain
- * TODO move to geometry module
- */
-interface Domain<T : Any> {
-    operator fun contains(vector: Point<out T>): Boolean
-    val dimension: Int
-}
-
 /**
  * The bin in the histogram. The histogram is by definition always done in the real space
  */

kmath-memory/src/commonMain/kotlin/scientifik/memory/MemorySpec.kt

@@ -10,6 +10,7 @@ interface MemorySpec<T : Any> {
     val objectSize: Int
 
     fun MemoryReader.read(offset: Int): T
+    //TODO consider thread safety
     fun MemoryWriter.write(offset: Int, value: T)
 }