Document memory module and several ND objects

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/BoxingNDField.kt

@@ -3,7 +3,6 @@ package scientifik.kmath.structures
 import scientifik.kmath.operations.Field
 import scientifik.kmath.operations.FieldElement
 
-
 class BoxingNDField<T, F : Field<T>>(
     override val shape: IntArray,
     override val elementContext: F,

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/BufferedNDAlgebra.kt

@@ -11,7 +11,8 @@ interface BufferedNDAlgebra<T, C> : NDAlgebra<T, C, NDBuffer<T>> {
 
     /**
      * Convert any [NDStructure] to buffered structure using strides from this context.
-     * If the structure is already [NDBuffer], conversion is free. If not, it could be expensive because iteration over indexes
+     * If the structure is already [NDBuffer], conversion is free. If not, it could be expensive because iteration over
+     * indices.
      *
      * If the argument is [NDBuffer] with different strides structure, the new element will be produced.
      */

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/ComplexNDField.kt

@@ -98,13 +98,13 @@ inline fun BufferedNDField<Complex, ComplexField>.produceInline(crossinline init
 }
 
 /**
- * Map one [ComplexNDElement] using function with indexes
+ * Map one [ComplexNDElement] using function with indices.
  */
 inline fun ComplexNDElement.mapIndexed(crossinline transform: ComplexField.(index: IntArray, Complex) -> Complex): ComplexNDElement =
     context.produceInline { offset -> transform(strides.index(offset), buffer[offset]) }
 
 /**
- * Map one [ComplexNDElement] using function without indexes
+ * Map one [ComplexNDElement] using function without indices.
  */
 inline fun ComplexNDElement.map(crossinline transform: ComplexField.(Complex) -> Complex): ComplexNDElement {
     val buffer = Buffer.complex(strides.linearSize) { offset -> ComplexField.transform(buffer[offset]) }

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/ExtendedNDField.kt

@@ -2,6 +2,13 @@ package scientifik.kmath.structures
 
 import scientifik.kmath.operations.ExtendedField
 
+/**
+ * [ExtendedField] over [NDStructure].
+ *
+ * @param T the type of the element contained in ND structure.
+ * @param N the type of ND structure.
+ * @param F the extended field of structure elements.
+ */
 interface ExtendedNDField<T : Any, F : ExtendedField<T>, N : NDStructure<T>> : NDField<T, F, N>, ExtendedField<N>
 
 ///**

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/MemoryBuffer.kt

@@ -10,7 +10,6 @@ import scientifik.memory.*
  * @property spec the spec of [T] type.
  */
 open class MemoryBuffer<T : Any>(protected val memory: Memory, protected val spec: MemorySpec<T>) : Buffer<T> {
-
     override val size: Int get() = memory.size / spec.objectSize
 
     private val reader: MemoryReader = memory.reader()

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/NDAlgebra.kt

@@ -105,10 +105,11 @@ interface NDRing<T, R : Ring<T>, N : NDStructure<T>> : Ring<N>, NDSpace<T, R, N>
 }
 
 /**
- * Field for n-dimensional structures.
+ * Field of [NDStructure].
  *
- * @param T the type of the element contained in ND structure
+ * @param T the type of the element contained in ND structure.
- * @param F field of structure elements
+ * @param N the type of ND structure.
+ * @param F field of structure elements.
  */
 interface NDField<T, F : Field<T>, N : NDStructure<T>> : Field<N>, NDRing<T, F, N> {
 

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/NDStructure.kt

@@ -3,15 +3,38 @@ package scientifik.kmath.structures
 import kotlin.jvm.JvmName
 import kotlin.reflect.KClass
 
-
+/**
+ * Represents n-dimensional structure, i.e. multidimensional container of items of the same type and size. The number
+ * of dimensions and items in an array is defined by its shape, which is a sequence of non-negative integers that
+ * specify the sizes of each dimension.
+ *
+ * @param T the type of items.
+ */
 interface NDStructure<T> {
-
+    /**
+     * The shape of structure, i.e. non-empty sequence of non-negative integers that specify sizes of dimensions of
+     * this structure.
+     */
     val shape: IntArray
 
+    /**
+     * The count of dimensions in this structure. It should be equal to size of [shape].
+     */
     val dimension: Int get() = shape.size
 
+    /**
+     * Returns the value at the specified indices.
+     *
+     * @param index the indices.
+     * @return the value.
+     */
     operator fun get(index: IntArray): T
 
+    /**
+     * Returns the sequence of all the elements associated by their indices.
+     *
+     * @return the lazy sequence of pairs of indices to values.
+     */
     fun elements(): Sequence<Pair<IntArray, T>>
 
     override fun equals(other: Any?): Boolean
@@ -19,6 +42,9 @@ interface NDStructure<T> {
     override fun hashCode(): Int
 
     companion object {
+        /**
+         * Indicates whether some [NDStructure] is equal to another one.
+         */
         fun equals(st1: NDStructure<*>, st2: NDStructure<*>): Boolean {
             if (st1 === st2) return true
 
@@ -36,9 +62,9 @@ interface NDStructure<T> {
         }
 
         /**
-         * Create a NDStructure with explicit buffer factory
+         * Creates a NDStructure with explicit buffer factory.
          *
-         * Strides should be reused if possible
+         * Strides should be reused if possible.
          */
         fun <T> build(
             strides: Strides,
@@ -91,9 +117,24 @@ interface NDStructure<T> {
     }
 }
 
+/**
+ * Returns the value at the specified indices.
+ *
+ * @param index the indices.
+ * @return the value.
+ */
 operator fun <T> NDStructure<T>.get(vararg index: Int): T = get(index)
 
+/**
+ * Represents mutable [NDStructure].
+ */
 interface MutableNDStructure<T> : NDStructure<T> {
+    /**
+     * Inserts an item at the specified indices.
+     *
+     * @param index the indices.
+     * @param value the value.
+     */
     operator fun set(index: IntArray, value: T)
 }
 
@@ -104,7 +145,7 @@ inline fun <T> MutableNDStructure<T>.mapInPlace(action: (IntArray, T) -> T) {
 }
 
 /**
- * A way to convert ND index to linear one and back
+ * A way to convert ND index to linear one and back.
  */
 interface Strides {
     /**
@@ -141,6 +182,9 @@ interface Strides {
     }
 }
 
+/**
+ * Simple implementation of [Strides].
+ */
 class DefaultStrides private constructor(override val shape: IntArray) : Strides {
     /**
      * Strides for memory access
@@ -180,19 +224,14 @@ class DefaultStrides private constructor(override val shape: IntArray) : Strides
     override val linearSize: Int
         get() = strides[shape.size]
 
-
     override fun equals(other: Any?): Boolean {
         if (this === other) return true
         if (other !is DefaultStrides) return false
-
         if (!shape.contentEquals(other.shape)) return false
-
         return true
     }
 
-    override fun hashCode(): Int {
+    override fun hashCode(): Int = shape.contentHashCode()
-        return shape.contentHashCode()
-    }
 
     companion object {
         private val defaultStridesCache = HashMap<IntArray, Strides>()
@@ -204,8 +243,20 @@ class DefaultStrides private constructor(override val shape: IntArray) : Strides
     }
 }
 
+/**
+ * Represents [NDStructure] over [Buffer].
+ *
+ * @param T the type of items.
+ */
 abstract class NDBuffer<T> : NDStructure<T> {
+    /**
+     * The underlying buffer.
+     */
     abstract val buffer: Buffer<T>
+
+    /**
+     * The strides to access elements of [Buffer] by linear indices.
+     */
     abstract val strides: Strides
 
     override fun get(index: IntArray): T = buffer[strides.offset(index)]
@@ -263,8 +314,8 @@ class MutableBufferNDStructure<T>(
 ) : NDBuffer<T>(), MutableNDStructure<T> {
 
     init {
-        if (strides.linearSize != buffer.size) {
+        require(strides.linearSize == buffer.size) {
-            error("Expected buffer side of ${strides.linearSize}, but found ${buffer.size}")
+            "Expected buffer side of ${strides.linearSize}, but found ${buffer.size}"
         }
     }
 

kmath-core/src/commonMain/kotlin/scientifik/kmath/structures/RealNDField.kt

@@ -93,13 +93,13 @@ inline fun BufferedNDField<Double, RealField>.produceInline(crossinline initiali
 }
 
 /**
- * Map one [RealNDElement] using function with indexes
+ * Map one [RealNDElement] using function with indices.
  */
 inline fun RealNDElement.mapIndexed(crossinline transform: RealField.(index: IntArray, Double) -> Double): RealNDElement =
     context.produceInline { offset -> transform(strides.index(offset), buffer[offset]) }
 
 /**
- * Map one [RealNDElement] using function without indexes
+ * Map one [RealNDElement] using function without indices.
  */
 inline fun RealNDElement.map(crossinline transform: RealField.(Double) -> Double): RealNDElement {
     val array = DoubleArray(strides.linearSize) { offset -> RealField.transform(buffer[offset]) }

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

@@ -1,77 +1,148 @@
 package scientifik.memory
 
+/**
+ * Represents a display of certain memory structure.
+ */
 interface Memory {
+    /**
+     * The length of this memory in bytes.
+     */
     val size: Int
 
     /**
-     * Get a projection of this memory (it reflects the changes in the parent memory block)
+     * Get a projection of this memory (it reflects the changes in the parent memory block).
      */
     fun view(offset: Int, length: Int): Memory
 
     /**
-     * Create a copy of this memory, which does not know anything about this memory
+     * Creates an independent copy of this memory.
      */
     fun copy(): Memory
 
     /**
-     * Create and possibly register a new reader
+     * Gets or creates a reader of this memory.
      */
     fun reader(): MemoryReader
 
+    /**
+     * Gets or creates a writer of this memory.
+     */
     fun writer(): MemoryWriter
 
-    companion object {
+    companion object
-
-    }
 }
 
+/**
+ * The interface to read primitive types in this memory.
+ */
 interface MemoryReader {
+    /**
+     * The underlying memory.
+     */
     val memory: Memory
 
+    /**
+     * Reads [Double] at certain [offset].
+     */
     fun readDouble(offset: Int): Double
+
+    /**
+     * Reads [Float] at certain [offset].
+     */
     fun readFloat(offset: Int): Float
+
+    /**
+     * Reads [Byte] at certain [offset].
+     */
     fun readByte(offset: Int): Byte
+
+    /**
+     * Reads [Short] at certain [offset].
+     */
     fun readShort(offset: Int): Short
+
+    /**
+     * Reads [Int] at certain [offset].
+     */
     fun readInt(offset: Int): Int
+
+    /**
+     * Reads [Long] at certain [offset].
+     */
     fun readLong(offset: Int): Long
 
+    /**
+     * Disposes this reader if needed.
+     */
     fun release()
 }
 
 /**
- * Use the memory for read then release the reader
+ * Uses the memory for read then releases the reader.
  */
 inline fun Memory.read(block: MemoryReader.() -> Unit) {
-    reader().apply(block).apply { release() }
+    reader().apply(block).release()
 }
 
+/**
+ * The interface to write primitive types into this memory.
+ */
 interface MemoryWriter {
+    /**
+     * The underlying memory.
+     */
     val memory: Memory
 
+    /**
+     * Writes [Double] at certain [offset].
+     */
     fun writeDouble(offset: Int, value: Double)
+
+    /**
+     * Writes [Float] at certain [offset].
+     */
     fun writeFloat(offset: Int, value: Float)
+
+    /**
+     * Writes [Byte] at certain [offset].
+     */
     fun writeByte(offset: Int, value: Byte)
+
+    /**
+     * Writes [Short] at certain [offset].
+     */
     fun writeShort(offset: Int, value: Short)
+
+    /**
+     * Writes [Int] at certain [offset].
+     */
     fun writeInt(offset: Int, value: Int)
+
+    /**
+     * Writes [Long] at certain [offset].
+     */
     fun writeLong(offset: Int, value: Long)
 
+    /**
+     * Disposes this writer if needed.
+     */
     fun release()
 }
 
 /**
- * Use the memory for write then release the writer
+ * Uses the memory for write then releases the writer.
  */
 inline fun Memory.write(block: MemoryWriter.() -> Unit) {
-    writer().apply(block).apply { release() }
+    writer().apply(block).release()
 }
 
 /**
- * Allocate the most effective platform-specific memory
+ * Allocates the most effective platform-specific memory.
  */
 expect fun Memory.Companion.allocate(length: Int): Memory
 
 /**
- * Wrap a [Memory] around existing [ByteArray]. This operation is unsafe since the array is not copied
+ * Wraps a [Memory] around existing [ByteArray]. This operation is unsafe since the array is not copied
- * and could be mutated independently from the resulting [Memory]
+ * and could be mutated independently from the resulting [Memory].
  */
 expect fun Memory.Companion.wrap(array: ByteArray): Memory

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

@@ -7,7 +7,7 @@ package scientifik.memory
  */
 interface MemorySpec<T : Any> {
     /**
-     * Size of [T] in bytes after serialization
+     * Size of [T] in bytes after serialization.
      */
     val objectSize: Int
 
@@ -24,9 +24,19 @@ interface MemorySpec<T : Any> {
     fun MemoryWriter.write(offset: Int, value: T)
 }
 
+/**
+ * Reads the object with [spec] starting from [offset].
+ */
 fun <T : Any> MemoryReader.read(spec: MemorySpec<T>, offset: Int): T = with(spec) { read(offset) }
+
+/**
+ * Writes the object [value] with [spec] starting from [offset].
+ */
 fun <T : Any> MemoryWriter.write(spec: MemorySpec<T>, offset: Int, value: T): Unit = with(spec) { write(offset, value) }
 
+/**
+ * Reads array of [size] objects mapped by [spec] at certain [offset].
+ */
 inline fun <reified T : Any> MemoryReader.readArray(spec: MemorySpec<T>, offset: Int, size: Int): Array<T> =
     Array(size) { i ->
         spec.run {
@@ -34,7 +44,10 @@ inline fun <reified T : Any> MemoryReader.readArray(spec: MemorySpec<T>, offset:
         }
     }
 
+/**
+ * Writes [array] of objects mapped by [spec] at certain [offset].
+ */
 fun <T : Any> MemoryWriter.writeArray(spec: MemorySpec<T>, offset: Int, array: Array<T>): Unit =
     with(spec) { array.indices.forEach { i -> write(offset + i * objectSize, array[i]) } }
 
-//TODO It is possible to add elastic MemorySpec with unknown object size
+// TODO It is possible to add elastic MemorySpec with unknown object size

kmath-memory/src/jsMain/kotlin/scientifik/memory/DataViewMemory.kt

@@ -4,13 +4,13 @@ import org.khronos.webgl.ArrayBuffer
 import org.khronos.webgl.DataView
 import org.khronos.webgl.Int8Array
 
-class DataViewMemory(val view: DataView) : Memory {
+private class DataViewMemory(val view: DataView) : Memory {
-
     override val size: Int get() = view.byteLength
 
     override fun view(offset: Int, length: Int): Memory {
         require(offset >= 0) { "offset shouldn't be negative: $offset" }
         require(length >= 0) { "length shouldn't be negative: $length" }
+        require(offset + length <= size) { "Can't view memory outside the parent region." }
 
         if (offset + length > size)
             throw IndexOutOfBoundsException("offset + length > size: $offset + $length > $size")
@@ -33,11 +33,11 @@ class DataViewMemory(val view: DataView) : Memory {
 
         override fun readInt(offset: Int): Int = view.getInt32(offset, false)
 
-        override fun readLong(offset: Int): Long = (view.getInt32(offset, false).toLong() shl 32) or
+        override fun readLong(offset: Int): Long =
-                view.getInt32(offset + 4, false).toLong()
+            view.getInt32(offset, false).toLong() shl 32 or view.getInt32(offset + 4, false).toLong()
 
         override fun release() {
-            // does nothing on JS because of GC
+            // does nothing on JS
         }
     }
 
@@ -72,7 +72,7 @@ class DataViewMemory(val view: DataView) : Memory {
         }
 
         override fun release() {
-            //does nothing on JS
+            // does nothing on JS
         }
     }
 
@@ -81,13 +81,17 @@ class DataViewMemory(val view: DataView) : Memory {
 }
 
 /**
- * Allocate the most effective platform-specific memory
+ * Allocates memory based on a [DataView].
  */
 actual fun Memory.Companion.allocate(length: Int): Memory {
     val buffer = ArrayBuffer(length)
     return DataViewMemory(DataView(buffer, 0, length))
 }
 
+/**
+ * Wraps a [Memory] around existing [ByteArray]. This operation is unsafe since the array is not copied
+ * and could be mutated independently from the resulting [Memory].
+ */
 actual fun Memory.Companion.wrap(array: ByteArray): Memory {
     @Suppress("CAST_NEVER_SUCCEEDS") val int8Array = array as Int8Array
     return DataViewMemory(DataView(int8Array.buffer, int8Array.byteOffset, int8Array.length))

kmath-memory/src/jvmMain/kotlin/scientifik/memory/ByteBufferMemory.kt

@@ -6,19 +6,18 @@ import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.StandardOpenOption
 
-
 private class ByteBufferMemory(
     val buffer: ByteBuffer,
     val startOffset: Int = 0,
     override val size: Int = buffer.limit()
 ) : Memory {
-
-
     @Suppress("NOTHING_TO_INLINE")
     private inline fun position(o: Int): Int = startOffset + o
 
     override fun view(offset: Int, length: Int): Memory {
-        if (offset + length > size) error("Selecting a Memory view outside of memory range")
+        require(offset >= 0) { "offset shouldn't be negative: $offset" }
+        require(length >= 0) { "length shouldn't be negative: $length" }
+        require(offset + length <= size) { "Can't view memory outside the parent region." }
         return ByteBufferMemory(buffer, position(offset), length)
     }
 
@@ -28,10 +27,9 @@ private class ByteBufferMemory(
         copy.put(buffer)
         copy.flip()
         return ByteBufferMemory(copy)
-
     }
 
-    private val reader = object : MemoryReader {
+    private val reader: MemoryReader = object : MemoryReader {
         override val memory: Memory get() = this@ByteBufferMemory
 
         override fun readDouble(offset: Int) = buffer.getDouble(position(offset))
@@ -47,13 +45,13 @@ private class ByteBufferMemory(
         override fun readLong(offset: Int) = buffer.getLong(position(offset))
 
         override fun release() {
-            //does nothing on JVM
+            // does nothing on JVM
         }
     }
 
     override fun reader(): MemoryReader = reader
 
-    private val writer = object : MemoryWriter {
+    private val writer: MemoryWriter = object : MemoryWriter {
         override val memory: Memory get() = this@ByteBufferMemory
 
         override fun writeDouble(offset: Int, value: Double) {
@@ -81,7 +79,7 @@ private class ByteBufferMemory(
         }
 
         override fun release() {
-            //does nothing on JVM
+            // does nothing on JVM
         }
     }
 
@@ -89,26 +87,32 @@ private class ByteBufferMemory(
 }
 
 /**
- * Allocate the most effective platform-specific memory
+ * Allocates memory based on a [ByteBuffer].
  */
-actual fun Memory.Companion.allocate(length: Int): Memory {
+actual fun Memory.Companion.allocate(length: Int): Memory =
-    val buffer = ByteBuffer.allocate(length)
+    ByteBufferMemory(checkNotNull(ByteBuffer.allocate(length)))
-    return ByteBufferMemory(buffer)
-}
 
-actual fun Memory.Companion.wrap(array: ByteArray): Memory {
+/**
-    val buffer = ByteBuffer.wrap(array)
+ * Wraps a [Memory] around existing [ByteArray]. This operation is unsafe since the array is not copied
-    return ByteBufferMemory(buffer)
+ * and could be mutated independently from the resulting [Memory].
-}
+ */
+actual fun Memory.Companion.wrap(array: ByteArray): Memory = ByteBufferMemory(checkNotNull(ByteBuffer.wrap(array)))
 
+/**
+ * Wraps this [ByteBuffer] to [Memory] object.
+ *
+ * @receiver the byte buffer.
+ * @param startOffset the start offset.
+ * @param size the size of memory to map.
+ * @return the [Memory] object.
+ */
 fun ByteBuffer.asMemory(startOffset: Int = 0, size: Int = limit()): Memory =
     ByteBufferMemory(this, startOffset, size)
 
 /**
- * Use direct memory-mapped buffer from file to read something and close it afterwards.
+ * Uses direct memory-mapped buffer from file to read something and close it afterwards.
  */
-fun <R> Path.readAsMemory(position: Long = 0, size: Long = Files.size(this), block: Memory.() -> R): R {
+fun <R> Path.readAsMemory(position: Long = 0, size: Long = Files.size(this), block: Memory.() -> R): R =
-    return FileChannel.open(this, StandardOpenOption.READ).use {
+    FileChannel.open(this, StandardOpenOption.READ).use {
         ByteBufferMemory(it.map(FileChannel.MapMode.READ_ONLY, position, size)).block()
     }
-}