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0.4 WIP

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This commit is contained in:
Alexander Nozik 2023-11-18 22:29:59 +03:00
parent 2f2f552648
commit 5c82a5e1fa
54 changed files with 541 additions and 433 deletions
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3
CHANGELOG.md
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@ -3,7 +3,7 @@
## Unreleased
### Added
- Explicit `SafeType` for algebras and buffers.
- Reification. Explicit `SafeType` for algebras and buffers.
- Integer division algebras.
- Float32 geometries.
- New Attributes-kt module that could be used as stand-alone. It declares. type-safe attributes containers.
@ -16,6 +16,7 @@
- kmath-geometry is split into `euclidean2d` and `euclidean3d`
- Features replaced with Attributes.
- Transposed refactored.
- Kmath-memory is moved on top of core.
### Deprecated

11
attributes-kt/src/commonMain/kotlin/space/kscience/attributes/Attribute.kt
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@ -24,14 +24,3 @@ public interface AttributeWithDefault<T> : Attribute<T> {
*/
public interface SetAttribute<V> : Attribute<Set<V>>
/**
* An attribute that has a type parameter for value
* @param type parameter-type
*/
public abstract class PolymorphicAttribute<T>(public val type: SafeType<T>) : Attribute<T> {
override fun equals(other: Any?): Boolean = other != null &&
(this::class == other::class) &&
(other as? PolymorphicAttribute<*>)?.type == this.type
override fun hashCode(): Int = this::class.hashCode() + type.hashCode()
}

8
attributes-kt/src/commonMain/kotlin/space/kscience/attributes/AttributeContainer.kt
View File

@ -6,8 +6,14 @@
package space.kscience.attributes
/**
* A container for attributes. [attributes] could be made mutable by implementation
* A container for [Attributes]
*/
public interface AttributeContainer {
public val attributes: Attributes
}
/**
* A scope, where attribute keys could be resolved
*/
public interface AttributeScope<O>

42
attributes-kt/src/commonMain/kotlin/space/kscience/attributes/Attributes.kt
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@ -7,21 +7,27 @@ package space.kscience.attributes
import kotlin.jvm.JvmInline
@JvmInline
public value class Attributes internal constructor(public val content: Map<out Attribute<*>, Any?>) {
/**
* A set of attributes. The implementation must guarantee that [content] keys correspond to its value types.
*/
public interface Attributes {
public val content: Map<out Attribute<*>, Any?>
public val keys: Set<Attribute<*>> get() = content.keys
@Suppress("UNCHECKED_CAST")
public operator fun <T> get(attribute: Attribute<T>): T? = content[attribute] as? T
override fun toString(): String = "Attributes(value=${content.entries})"
public companion object {
public val EMPTY: Attributes = Attributes(emptyMap())
public val EMPTY: Attributes = AttributesImpl(emptyMap())
}
}
@JvmInline
internal value class AttributesImpl(override val content: Map<out Attribute<*>, Any?>) : Attributes {
override fun toString(): String = "Attributes(value=${content.entries})"
}
public fun Attributes.isEmpty(): Boolean = content.isEmpty()
/**
@ -33,19 +39,19 @@ public fun <T> Attributes.getOrDefault(attribute: AttributeWithDefault<T>): T =
* Check if there is an attribute that matches given key by type and adheres to [predicate].
*/
@Suppress("UNCHECKED_CAST")
public inline fun <T, reified A : Attribute<T>> Attributes.any(predicate: (value: T) -> Boolean): Boolean =
public inline fun <T, reified A : Attribute<T>> Attributes.hasAny(predicate: (value: T) -> Boolean): Boolean =
content.any { (mapKey, mapValue) -> mapKey is A && predicate(mapValue as T) }
/**
* Check if there is an attribute of given type (subtypes included)
*/
public inline fun <T, reified A : Attribute<T>> Attributes.any(): Boolean =
public inline fun <reified A : Attribute<*>> Attributes.hasAny(): Boolean =
content.any { (mapKey, _) -> mapKey is A }
/**
* Check if [Attributes] contains a flag. Multiple keys that are instances of a flag could be present
*/
public inline fun <reified A : FlagAttribute> Attributes.has(): Boolean =
public inline fun <reified A : FlagAttribute> Attributes.hasFlag(): Boolean =
content.keys.any { it is A }
/**
@ -54,7 +60,7 @@ public inline fun <reified A : FlagAttribute> Attributes.has(): Boolean =
public fun <T, A : Attribute<T>> Attributes.withAttribute(
attribute: A,
attrValue: T,
): Attributes = Attributes(content + (attribute to attrValue))
): Attributes = AttributesImpl(content + (attribute to attrValue))
public fun <A : Attribute<Unit>> Attributes.withAttribute(attribute: A): Attributes =
withAttribute(attribute, Unit)
@ -62,7 +68,7 @@ public fun <A : Attribute<Unit>> Attributes.withAttribute(attribute: A): Attribu
/**
* Create a new [Attributes] by modifying the current one
*/
public fun Attributes.modify(block: AttributesBuilder.() -> Unit): Attributes = Attributes {
public fun <T> Attributes.modify(block: AttributesBuilder<T>.() -> Unit): Attributes = Attributes<T> {
from(this@modify)
block()
}
@ -70,7 +76,7 @@ public fun Attributes.modify(block: AttributesBuilder.() -> Unit): Attributes =
/**
* Create new [Attributes] by removing [attribute] key
*/
public fun Attributes.withoutAttribute(attribute: Attribute<*>): Attributes = Attributes(content.minus(attribute))
public fun Attributes.withoutAttribute(attribute: Attribute<*>): Attributes = AttributesImpl(content.minus(attribute))
/**
* Add an element to a [SetAttribute]
@ -80,7 +86,7 @@ public fun <T, A : SetAttribute<T>> Attributes.withAttributeElement(
attrValue: T,
): Attributes {
val currentSet: Set<T> = get(attribute) ?: emptySet()
return Attributes(
return AttributesImpl(
content + (attribute to (currentSet + attrValue))
)
}
@ -93,9 +99,7 @@ public fun <T, A : SetAttribute<T>> Attributes.withoutAttributeElement(
attrValue: T,
): Attributes {
val currentSet: Set<T> = get(attribute) ?: emptySet()
return Attributes(
content + (attribute to (currentSet - attrValue))
)
return AttributesImpl(content + (attribute to (currentSet - attrValue)))
}
/**
@ -104,13 +108,13 @@ public fun <T, A : SetAttribute<T>> Attributes.withoutAttributeElement(
public fun <T, A : Attribute<T>> Attributes(
attribute: A,
attrValue: T,
): Attributes = Attributes(mapOf(attribute to attrValue))
): Attributes = AttributesImpl(mapOf(attribute to attrValue))
/**
* Create Attributes with a single [Unit] valued attribute
*/
public fun <A : Attribute<Unit>> Attributes(
attribute: A
): Attributes = Attributes(mapOf(attribute to Unit))
attribute: A,
): Attributes = AttributesImpl(mapOf(attribute to Unit))
public operator fun Attributes.plus(other: Attributes): Attributes = Attributes(content + other.content)
public operator fun Attributes.plus(other: Attributes): Attributes = AttributesImpl(content + other.content)

33
attributes-kt/src/commonMain/kotlin/space/kscience/attributes/AttributesBuilder.kt
View File

@ -10,19 +10,24 @@ package space.kscience.attributes
*
* @param O type marker of an owner object, for which these attributes are made
*/
public class TypedAttributesBuilder<in O> internal constructor(private val map: MutableMap<Attribute<*>, Any?>) {
public class AttributesBuilder<out O> internal constructor(
private val map: MutableMap<Attribute<*>, Any?>,
) : Attributes {
public constructor() : this(mutableMapOf())
@Suppress("UNCHECKED_CAST")
public operator fun <T> get(attribute: Attribute<T>): T? = map[attribute] as? T
override val content: Map<out Attribute<*>, Any?> get() = map
public operator fun <T> set(attribute: Attribute<T>, value: T?) {
if (value == null) {
map.remove(attribute)
} else {
map[attribute] = value
}
}
public operator fun <V> Attribute<V>.invoke(value: V?) {
if (value == null) {
map.remove(this)
} else {
map[this] = value
}
set(this, value)
}
public fun from(attributes: Attributes) {
@ -46,14 +51,8 @@ public class TypedAttributesBuilder<in O> internal constructor(private val map:
map[this] = currentSet - attrValue
}
public fun build(): Attributes = Attributes(map)
public fun build(): Attributes = AttributesImpl(map)
}
public typealias AttributesBuilder = TypedAttributesBuilder<Any?>
public fun AttributesBuilder(
attributes: Attributes,
): AttributesBuilder = AttributesBuilder(attributes.content.toMutableMap())
public inline fun Attributes(builder: AttributesBuilder.() -> Unit): Attributes =
AttributesBuilder().apply(builder).build()
public inline fun <O> Attributes(builder: AttributesBuilder<O>.() -> Unit): Attributes =
AttributesBuilder<O>().apply(builder).build()

31
attributes-kt/src/commonMain/kotlin/space/kscience/attributes/PolymorphicAttribute.kt Normal file
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@ -0,0 +1,31 @@
/*
* Copyright 2018-2023 KMath contributors.
* Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/
package space.kscience.attributes
/**
* An attribute that has a type parameter for value
* @param type parameter-type
*/
public abstract class PolymorphicAttribute<T>(public val type: SafeType<T>) : Attribute<T> {
override fun equals(other: Any?): Boolean = other != null &&
(this::class == other::class) &&
(other as? PolymorphicAttribute<*>)?.type == this.type
override fun hashCode(): Int = this::class.hashCode() + type.hashCode()
}
/**
* Get a polymorphic attribute using attribute factory
*/
public operator fun <T> Attributes.get(attributeKeyBuilder: () -> PolymorphicAttribute<T>): T? = get(attributeKeyBuilder())
/**
* Set a polymorphic attribute using its factory
*/
public operator fun <O, T> AttributesBuilder<O>.set(attributeKeyBuilder: () -> PolymorphicAttribute<T>, value: T) {
set(attributeKeyBuilder(), value)
}

12
buildSrc/src/main/kotlin/space/kscience/kmath/ejml/codegen/ejmlCodegen.kt
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@ -19,6 +19,8 @@ public class Ejml${type}Vector<out M : $ejmlMatrixType>(override val origin: M)
require(origin.numRows == 1) { "The origin matrix must have only one row to form a vector" }
}
override val type: SafeType<${type}> get() = safeTypeOf()
override operator fun get(index: Int): $type = origin[0, index]
}"""
appendLine(text)
@ -30,6 +32,8 @@ private fun Appendable.appendEjmlMatrix(type: String, ejmlMatrixType: String) {
* [EjmlMatrix] specialization for [$type].
*/
public class Ejml${type}Matrix<out M : $ejmlMatrixType>(override val origin: M) : EjmlMatrix<$type, M>(origin) {
override val type: SafeType<${type}> get() = safeTypeOf()
override operator fun get(i: Int, j: Int): $type = origin[i, j]
}"""
appendLine(text)
@ -46,7 +50,9 @@ private fun Appendable.appendEjmlLinearSpace(
denseOps: String,
isDense: Boolean,
) {
@Language("kotlin") val text = """/**
@Language("kotlin") val text = """
/**
* [EjmlLinearSpace] implementation based on [CommonOps_$ops], [DecompositionFactory_${ops}] operations and
* [${ejmlMatrixType}] matrices.
*/
@ -56,7 +62,7 @@ public object EjmlLinearSpace${ops} : EjmlLinearSpace<${type}, ${kmathAlgebra},
*/
override val elementAlgebra: $kmathAlgebra get() = $kmathAlgebra
override val elementType: KType get() = typeOf<$type>()
override val type: SafeType<${type}> get() = safeTypeOf()
@Suppress("UNCHECKED_CAST")
override fun Matrix<${type}>.toEjml(): Ejml${type}Matrix<${ejmlMatrixType}> = when {
@ -385,6 +391,8 @@ import org.ejml.sparse.csc.factory.DecompositionFactory_DSCC
import org.ejml.sparse.csc.factory.DecompositionFactory_FSCC
import org.ejml.sparse.csc.factory.LinearSolverFactory_DSCC
import org.ejml.sparse.csc.factory.LinearSolverFactory_FSCC
import space.kscience.attributes.SafeType
import space.kscience.attributes.safeTypeOf
import space.kscience.kmath.linear.*
import space.kscience.kmath.linear.Matrix
import space.kscience.kmath.UnstableKMathAPI

4
examples/src/main/kotlin/space/kscience/kmath/fit/chiSquared.kt
View File

@ -15,7 +15,7 @@ import space.kscience.kmath.operations.asIterable
import space.kscience.kmath.operations.toList
import space.kscience.kmath.optimization.FunctionOptimizationTarget
import space.kscience.kmath.optimization.optimizeWith
import space.kscience.kmath.optimization.resultPoint
import space.kscience.kmath.optimization.result
import space.kscience.kmath.optimization.resultValue
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.real.DoubleVector
@ -98,7 +98,7 @@ suspend fun main() {
scatter {
mode = ScatterMode.lines
x(x)
y(x.map { result.resultPoint[a]!! * it.pow(2) + result.resultPoint[b]!! * it + 1 })
y(x.map { result.result[a]!! * it.pow(2) + result.result[b]!! * it + 1 })
name = "fit"
}
}

4
examples/src/main/kotlin/space/kscience/kmath/fit/qowFit.kt
View File

@ -94,13 +94,13 @@ suspend fun main() {
scatter {
mode = ScatterMode.lines
x(x)
y(x.map { result.model(result.startPoint + result.resultPoint + (Symbol.x to it)) })
y(x.map { result.model(result.startPoint + result.result + (Symbol.x to it)) })
name = "fit"
}
}
br()
h3 {
+"Fit result: ${result.resultPoint}"
+"Fit result: ${result.result}"
}
h3 {
+"Chi2/dof = ${result.chiSquaredOrNull!! / result.dof}"

36
kmath-ast/src/commonMain/kotlin/space/kscience/kmath/ast/TypedMst.kt
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@ -5,6 +5,8 @@
package space.kscience.kmath.ast
import space.kscience.attributes.SafeType
import space.kscience.attributes.WithType
import space.kscience.kmath.expressions.Expression
import space.kscience.kmath.expressions.Symbol
import space.kscience.kmath.operations.Algebra
@ -15,7 +17,7 @@ import space.kscience.kmath.operations.NumericAlgebra
*
* @param T the type.
*/
public sealed interface TypedMst<T> {
public sealed interface TypedMst<T> : WithType<T> {
/**
* A node containing a unary operation.
*
@ -24,8 +26,13 @@ public sealed interface TypedMst<T> {
* @property function The function implementing this operation.
* @property value The argument of this operation.
*/
public class Unary<T>(public val operation: String, public val function: (T) -> T, public val value: TypedMst<T>) :
TypedMst<T> {
public class Unary<T>(
public val operation: String,
public val function: (T) -> T,
public val value: TypedMst<T>,
) : TypedMst<T> {
override val type: SafeType<T> get() = value.type
override fun equals(other: Any?): Boolean {
if (this === other) return true
if (other == null || this::class != other::class) return false
@ -59,6 +66,13 @@ public sealed interface TypedMst<T> {
public val left: TypedMst<T>,
public val right: TypedMst<T>,
) : TypedMst<T> {
init {
require(left.type==right.type){"Left and right expressions must be of the same type"}
}
override val type: SafeType<T> get() = left.type
override fun equals(other: Any?): Boolean {
if (this === other) return true
if (other == null || this::class != other::class) return false
@ -89,7 +103,12 @@ public sealed interface TypedMst<T> {
* @property value The held value.
* @property number The number this value corresponds.
*/
public class Constant<T>(public val value: T, public val number: Number?) : TypedMst<T> {
public class Constant<T>(
override val type: SafeType<T>,
public val value: T,
public val number: Number?,
) : TypedMst<T> {
override fun equals(other: Any?): Boolean {
if (this === other) return true
if (other == null || this::class != other::class) return false
@ -114,7 +133,7 @@ public sealed interface TypedMst<T> {
* @param T the type.
* @property symbol The symbol of the variable.
*/
public class Variable<T>(public val symbol: Symbol) : TypedMst<T> {
public class Variable<T>(override val type: SafeType<T>, public val symbol: Symbol) : TypedMst<T> {
override fun equals(other: Any?): Boolean {
if (this === other) return true
if (other == null || this::class != other::class) return false
@ -167,6 +186,7 @@ public fun <T> TypedMst<T>.interpret(algebra: Algebra<T>, vararg arguments: Pair
/**
* Interpret this [TypedMst] node as expression.
*/
public fun <T : Any> TypedMst<T>.toExpression(algebra: Algebra<T>): Expression<T> = Expression { arguments ->
interpret(algebra, arguments)
}
public fun <T : Any> TypedMst<T>.toExpression(algebra: Algebra<T>): Expression<T> =
Expression(algebra.type) { arguments ->
interpret(algebra, arguments)
}

9
kmath-ast/src/commonMain/kotlin/space/kscience/kmath/ast/evaluateConstants.kt
View File

@ -16,6 +16,7 @@ import space.kscience.kmath.operations.bindSymbolOrNull
*/
public fun <T> MST.evaluateConstants(algebra: Algebra<T>): TypedMst<T> = when (this) {
is MST.Numeric -> TypedMst.Constant(
algebra.type,
(algebra as? NumericAlgebra<T>)?.number(value) ?: error("Numeric nodes are not supported by $algebra"),
value,
)
@ -27,7 +28,7 @@ public fun <T> MST.evaluateConstants(algebra: Algebra<T>): TypedMst<T> = when (t
arg.value,
)
TypedMst.Constant(value, if (value is Number) value else null)
TypedMst.Constant(algebra.type, value, if (value is Number) value else null)
}
else -> TypedMst.Unary(operation, algebra.unaryOperationFunction(operation), arg)
@ -59,7 +60,7 @@ public fun <T> MST.evaluateConstants(algebra: Algebra<T>): TypedMst<T> = when (t
)
}
TypedMst.Constant(value, if (value is Number) value else null)
TypedMst.Constant(algebra.type, value, if (value is Number) value else null)
}
algebra is NumericAlgebra && left is TypedMst.Constant && left.number != null -> TypedMst.Binary(
@ -84,8 +85,8 @@ public fun <T> MST.evaluateConstants(algebra: Algebra<T>): TypedMst<T> = when (t
val boundSymbol = algebra.bindSymbolOrNull(this)
if (boundSymbol != null)
TypedMst.Constant(boundSymbol, if (boundSymbol is Number) boundSymbol else null)
TypedMst.Constant(algebra.type, boundSymbol, if (boundSymbol is Number) boundSymbol else null)
else
TypedMst.Variable(this)
TypedMst.Variable(algebra.type, this)
}
}

4
kmath-ast/src/jsMain/kotlin/space/kscience/kmath/estree/estree.kt
View File

@ -22,7 +22,7 @@ import space.kscience.kmath.operations.Algebra
@OptIn(UnstableKMathAPI::class)
public fun <T : Any> MST.compileToExpression(algebra: Algebra<T>): Expression<T> {
val typed = evaluateConstants(algebra)
if (typed is TypedMst.Constant<T>) return Expression { typed.value }
if (typed is TypedMst.Constant<T>) return Expression(algebra.type) { typed.value }
fun ESTreeBuilder<T>.visit(node: TypedMst<T>): BaseExpression = when (node) {
is TypedMst.Constant -> constant(node.value)
@ -36,7 +36,7 @@ public fun <T : Any> MST.compileToExpression(algebra: Algebra<T>): Expression<T>
)
}
return ESTreeBuilder { visit(typed) }.instance
return ESTreeBuilder(algebra.type) { visit(typed) }.instance
}
/**

15
kmath-ast/src/jsMain/kotlin/space/kscience/kmath/estree/internal/ESTreeBuilder.kt
View File

@ -5,13 +5,22 @@
package space.kscience.kmath.estree.internal
import space.kscience.attributes.SafeType
import space.kscience.attributes.WithType
import space.kscience.kmath.expressions.Expression
import space.kscience.kmath.expressions.Symbol
import space.kscience.kmath.internal.astring.generate
import space.kscience.kmath.internal.estree.*
internal class ESTreeBuilder<T>(val bodyCallback: ESTreeBuilder<T>.() -> BaseExpression) {
private class GeneratedExpression<T>(val executable: dynamic, val constants: Array<dynamic>) : Expression<T> {
internal class ESTreeBuilder<T>(
override val type: SafeType<T>,
val bodyCallback: ESTreeBuilder<T>.() -> BaseExpression,
) : WithType<T> {
private class GeneratedExpression<T>(
override val type: SafeType<T>,
val executable: dynamic,
val constants: Array<dynamic>,
) : Expression<T> {
@Suppress("UNUSED_VARIABLE")
override fun invoke(arguments: Map<Symbol, T>): T {
val e = executable
@ -30,7 +39,7 @@ internal class ESTreeBuilder<T>(val bodyCallback: ESTreeBuilder<T>.() -> BaseExp
)
val code = generate(node)
GeneratedExpression(js("new Function('constants', 'arguments_0', code)"), constants.toTypedArray())
GeneratedExpression(type, js("new Function('constants', 'arguments_0', code)"), constants.toTypedArray())
}
private val constants = mutableListOf<Any>()

2
kmath-ast/src/jvmMain/kotlin/space/kscience/kmath/asm/asm.kt
View File

@ -29,7 +29,7 @@ import space.kscience.kmath.operations.Int64Ring
@PublishedApi
internal fun <T : Any> MST.compileWith(type: Class<T>, algebra: Algebra<T>): Expression<T> {
val typed = evaluateConstants(algebra)
if (typed is TypedMst.Constant<T>) return Expression { typed.value }
if (typed is TypedMst.Constant<T>) return Expression(algebra.type) { typed.value }
fun GenericAsmBuilder<T>.variablesVisitor(node: TypedMst<T>): Unit = when (node) {
is TypedMst.Unary -> variablesVisitor(node.value)

19
kmath-commons/src/jvmMain/kotlin/space/kscience/kmath/commons/expressions/CmDsExpression.kt
View File

@ -8,10 +8,13 @@
package space.kscience.kmath.commons.expressions
import org.apache.commons.math3.analysis.differentiation.DerivativeStructure
import space.kscience.attributes.SafeType
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.expressions.*
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.ExtendedField
import space.kscience.kmath.operations.NumbersAddOps
import space.kscience.kmath.structures.MutableBufferFactory
/**
* A field over commons-math [DerivativeStructure].
@ -26,6 +29,9 @@ public class CmDsField(
bindings: Map<Symbol, Double>,
) : ExtendedField<DerivativeStructure>, ExpressionAlgebra<Double, DerivativeStructure>,
NumbersAddOps<DerivativeStructure> {
override val bufferFactory: MutableBufferFactory<DerivativeStructure> = MutableBufferFactory()
public val numberOfVariables: Int = bindings.size
override val zero: DerivativeStructure by lazy { DerivativeStructure(numberOfVariables, order) }
@ -77,7 +83,9 @@ public class CmDsField(
override fun scale(a: DerivativeStructure, value: Double): DerivativeStructure = a.multiply(value)
override fun multiply(left: DerivativeStructure, right: DerivativeStructure): DerivativeStructure = left.multiply(right)
override fun multiply(left: DerivativeStructure, right: DerivativeStructure): DerivativeStructure =
left.multiply(right)
override fun divide(left: DerivativeStructure, right: DerivativeStructure): DerivativeStructure = left.divide(right)
override fun sin(arg: DerivativeStructure): DerivativeStructure = arg.sin()
override fun cos(arg: DerivativeStructure): DerivativeStructure = arg.cos()
@ -113,8 +121,8 @@ public class CmDsField(
*/
@Deprecated("Use generic DSAlgebra from the core")
public object CmDsProcessor : AutoDiffProcessor<Double, DerivativeStructure, CmDsField> {
override fun differentiate(
function: CmDsField.() -> DerivativeStructure,
override fun differentiate(
function: CmDsField.() -> DerivativeStructure,
): CmDsExpression = CmDsExpression(function)
}
@ -125,13 +133,16 @@ public object CmDsProcessor : AutoDiffProcessor<Double, DerivativeStructure, CmD
public class CmDsExpression(
public val function: CmDsField.() -> DerivativeStructure,
) : DifferentiableExpression<Double> {
override val type: SafeType<Double> get() = DoubleField.type
override operator fun invoke(arguments: Map<Symbol, Double>): Double =
CmDsField(0, arguments).function().value
/**
* Get the derivative expression with given orders
*/
override fun derivativeOrNull(symbols: List<Symbol>): Expression<Double> = Expression { arguments ->
override fun derivativeOrNull(symbols: List<Symbol>): Expression<Double> = Expression(type) { arguments ->
with(CmDsField(symbols.size, arguments)) { function().derivative(symbols) }
}
}

4
kmath-commons/src/jvmMain/kotlin/space/kscience/kmath/commons/integration/CMGaussRuleIntegrator.kt
View File

@ -16,7 +16,7 @@ public class CMGaussRuleIntegrator(
private var type: GaussRule = GaussRule.LEGENDRE,
) : UnivariateIntegrator<Double> {
override fun process(integrand: UnivariateIntegrand<Double>): UnivariateIntegrand<Double> {
override fun integrate(integrand: UnivariateIntegrand<Double>): UnivariateIntegrand<Double> {
val range = integrand[IntegrationRange]
?: error("Integration range is not provided")
val integrator: GaussIntegrator = getIntegrator(range)
@ -79,7 +79,7 @@ public class CMGaussRuleIntegrator(
numPoints: Int = 100,
type: GaussRule = GaussRule.LEGENDRE,
function: (Double) -> Double,
): Double = CMGaussRuleIntegrator(numPoints, type).process(
): Double = CMGaussRuleIntegrator(numPoints, type).integrate(
UnivariateIntegrand({IntegrationRange(range)},function)
).value
}

17
kmath-commons/src/jvmMain/kotlin/space/kscience/kmath/commons/integration/CMIntegrator.kt
View File

@ -7,6 +7,7 @@ package space.kscience.kmath.commons.integration
import org.apache.commons.math3.analysis.integration.IterativeLegendreGaussIntegrator
import org.apache.commons.math3.analysis.integration.SimpsonIntegrator
import space.kscience.attributes.Attributes
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.integration.*
import org.apache.commons.math3.analysis.integration.UnivariateIntegrator as CMUnivariateIntegrator
@ -19,7 +20,7 @@ public class CMIntegrator(
public val integratorBuilder: (Integrand<Double>) -> CMUnivariateIntegrator,
) : UnivariateIntegrator<Double> {
override fun process(integrand: UnivariateIntegrand<Double>): UnivariateIntegrand<Double> {
override fun integrate(integrand: UnivariateIntegrand<Double>): UnivariateIntegrand<Double> {
val integrator = integratorBuilder(integrand)
val maxCalls = integrand[IntegrandMaxCalls] ?: defaultMaxCalls
val remainingCalls = maxCalls - integrand.calls
@ -73,15 +74,9 @@ public class CMIntegrator(
}
@UnstableKMathAPI
public var MutableList<IntegrandFeature>.targetAbsoluteAccuracy: Double?
get() = filterIsInstance<IntegrandAbsoluteAccuracy>().lastOrNull()?.accuracy
set(value) {
value?.let { add(IntegrandAbsoluteAccuracy(value)) }
}
public val Attributes.targetAbsoluteAccuracy: Double?
get() = get(IntegrandAbsoluteAccuracy)
@UnstableKMathAPI
public var MutableList<IntegrandFeature>.targetRelativeAccuracy: Double?
get() = filterIsInstance<IntegrandRelativeAccuracy>().lastOrNull()?.accuracy
set(value) {
value?.let { add(IntegrandRelativeAccuracy(value)) }
}
public val Attributes.targetRelativeAccuracy: Double?
get() = get(IntegrandRelativeAccuracy)

38
kmath-commons/src/jvmMain/kotlin/space/kscience/kmath/commons/linear/CMMatrix.kt
View File

@ -6,18 +6,20 @@
package space.kscience.kmath.commons.linear
import org.apache.commons.math3.linear.*
import org.apache.commons.math3.linear.LUDecomposition
import space.kscience.attributes.SafeType
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.linear.*
import space.kscience.kmath.nd.Structure2D
import space.kscience.kmath.nd.StructureAttribute
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.Float64Field
import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.structures.Float64Buffer
import kotlin.reflect.KClass
import kotlin.reflect.KType
import kotlin.reflect.cast
import kotlin.reflect.typeOf
public class CMMatrix(public val origin: RealMatrix) : Matrix<Double> {
override val type: SafeType<Double> get() = DoubleField.type
override val rowNum: Int get() = origin.rowDimension
override val colNum: Int get() = origin.columnDimension
@ -26,6 +28,7 @@ public class CMMatrix(public val origin: RealMatrix) : Matrix<Double> {
@JvmInline
public value class CMVector(public val origin: RealVector) : Point<Double> {
override val type: SafeType<Double> get() = DoubleField.type
override val size: Int get() = origin.dimension
override operator fun get(index: Int): Double = origin.getEntry(index)
@ -40,7 +43,7 @@ public fun RealVector.toPoint(): CMVector = CMVector(this)
public object CMLinearSpace : LinearSpace<Double, Float64Field> {
override val elementAlgebra: Float64Field get() = Float64Field
override val elementType: KType = typeOf<Double>()
override val type: SafeType<Double> get() = DoubleField.type
override fun buildMatrix(
rows: Int,
@ -102,19 +105,14 @@ public object CMLinearSpace : LinearSpace<Double, Float64Field> {
override fun Double.times(v: Point<Double>): CMVector =
v * this
@UnstableKMathAPI
override fun <F : StructureAttribute> computeFeature(structure: Matrix<Double>, type: KClass<out F>): F? {
//Return the feature if it is intrinsic to the structure
structure.getFeature(type)?.let { return it }
override fun <V, A : StructureAttribute<V>> computeAttribute(structure: Structure2D<Double>, attribute: A): V? {
val origin = structure.toCM().origin
return when (type) {
IsDiagonal::class -> if (origin is DiagonalMatrix) IsDiagonal else null
Determinant::class, LupDecompositionAttribute::class -> object :
Determinant<Double>,
LupDecompositionAttribute<Double> {
return when (attribute) {
IsDiagonal -> if (origin is DiagonalMatrix) IsDiagonal else null
Determinant -> LUDecomposition(origin).determinant
LUP -> GenericLupDecomposition {
private val lup by lazy { LUDecomposition(origin) }
override val determinant: Double by lazy { lup.determinant }
override val l: Matrix<Double> by lazy<Matrix<Double>> { CMMatrix(lup.l).withAttribute(LowerTriangular) }
@ -122,20 +120,24 @@ public object CMLinearSpace : LinearSpace<Double, Float64Field> {
override val p: Matrix<Double> by lazy { CMMatrix(lup.p) }
}
CholeskyDecompositionAttribute::class -> object : CholeskyDecompositionAttribute<Double> {
CholeskyDecompositionAttribute -> object : CholeskyDecompositionAttribute<Double> {
override val l: Matrix<Double> by lazy<Matrix<Double>> {
val cholesky = CholeskyDecomposition(origin)
CMMatrix(cholesky.l).withAttribute(LowerTriangular)
}
}
QRDecompositionAttribute::class -> object : QRDecompositionAttribute<Double> {
QRDecompositionAttribute -> object : QRDecompositionAttribute<Double> {
private val qr by lazy { QRDecomposition(origin) }
override val q: Matrix<Double> by lazy<Matrix<Double>> { CMMatrix(qr.q).withAttribute(OrthogonalAttribute) }
override val q: Matrix<Double> by lazy<Matrix<Double>> {
CMMatrix(qr.q).withAttribute(
OrthogonalAttribute
)
}
override val r: Matrix<Double> by lazy<Matrix<Double>> { CMMatrix(qr.r).withAttribute(UpperTriangular) }
}
SVDAttribute::class -> object : SVDAttribute<Double> {
SVDAttribute -> object : SVDAttribute<Double> {
private val sv by lazy { SingularValueDecomposition(origin) }
override val u: Matrix<Double> by lazy { CMMatrix(sv.u) }
override val s: Matrix<Double> by lazy { CMMatrix(sv.s) }

35
kmath-commons/src/jvmMain/kotlin/space/kscience/kmath/commons/optimization/CMOptimizer.kt
View File

@ -13,6 +13,8 @@ import org.apache.commons.math3.optim.nonlinear.scalar.ObjectiveFunctionGradient
import org.apache.commons.math3.optim.nonlinear.scalar.gradient.NonLinearConjugateGradientOptimizer
import org.apache.commons.math3.optim.nonlinear.scalar.noderiv.NelderMeadSimplex
import org.apache.commons.math3.optim.nonlinear.scalar.noderiv.SimplexOptimizer
import space.kscience.attributes.AttributesBuilder
import space.kscience.attributes.SetAttribute
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.expressions.Symbol
import space.kscience.kmath.expressions.SymbolIndexer
@ -26,34 +28,25 @@ import kotlin.reflect.KClass
public operator fun PointValuePair.component1(): DoubleArray = point
public operator fun PointValuePair.component2(): Double = value
public class CMOptimizerEngine(public val optimizerBuilder: () -> MultivariateOptimizer) : OptimizationFeature {
override fun toString(): String = "CMOptimizer($optimizerBuilder)"
}
public object CMOptimizerEngine: OptimizationAttribute<() -> MultivariateOptimizer>
/**
* Specify a Commons-maths optimization engine
*/
public fun FunctionOptimizationBuilder<Double>.cmEngine(optimizerBuilder: () -> MultivariateOptimizer) {
addFeature(CMOptimizerEngine(optimizerBuilder))
public fun AttributesBuilder<FunctionOptimization<Double>>.cmEngine(optimizerBuilder: () -> MultivariateOptimizer) {
set(CMOptimizerEngine, optimizerBuilder)
}
public class CMOptimizerData(public val data: List<SymbolIndexer.() -> OptimizationData>) : OptimizationFeature {
public constructor(vararg data: (SymbolIndexer.() -> OptimizationData)) : this(data.toList())
override fun toString(): String = "CMOptimizerData($data)"
}
public object CMOptimizerData: SetAttribute<SymbolIndexer.() -> OptimizationData>
/**
* Specify Commons-maths optimization data.
*/
public fun FunctionOptimizationBuilder<Double>.cmOptimizationData(data: SymbolIndexer.() -> OptimizationData) {
updateFeature<CMOptimizerData> {
val newData = (it?.data ?: emptyList()) + data
CMOptimizerData(newData)
}
public fun AttributesBuilder<FunctionOptimization<Double>>.cmOptimizationData(data: SymbolIndexer.() -> OptimizationData) {
CMOptimizerData.add(data)
}
public fun FunctionOptimizationBuilder<Double>.simplexSteps(vararg steps: Pair<Symbol, Double>) {
public fun AttributesBuilder<FunctionOptimization<Double>>.simplexSteps(vararg steps: Pair<Symbol, Double>) {
//TODO use convergence checker from features
cmEngine { SimplexOptimizer(CMOptimizer.defaultConvergenceChecker) }
cmOptimizationData { NelderMeadSimplex(mapOf(*steps).toDoubleArray()) }
@ -78,8 +71,8 @@ public object CMOptimizer : Optimizer<Double, FunctionOptimization<Double>> {
): FunctionOptimization<Double> {
val startPoint = problem.startPoint
val parameters = problem.getFeature<OptimizationParameters>()?.symbols
?: problem.getFeature<OptimizationStartPoint<Double>>()?.point?.keys
val parameters = problem.attributes[OptimizationParameters]
?: problem.attributes[OptimizationStartPoint<Double>()]?.keys
?: startPoint.keys
@ -90,7 +83,7 @@ public object CMOptimizer : Optimizer<Double, FunctionOptimization<Double>> {
DEFAULT_MAX_ITER
)
val cmOptimizer: MultivariateOptimizer = problem.getFeature<CMOptimizerEngine>()?.optimizerBuilder?.invoke()
val cmOptimizer: MultivariateOptimizer = problem.attributes[CMOptimizerEngine]?.invoke()
?: NonLinearConjugateGradientOptimizer(
NonLinearConjugateGradientOptimizer.Formula.FLETCHER_REEVES,
convergenceChecker
@ -123,7 +116,7 @@ public object CMOptimizer : Optimizer<Double, FunctionOptimization<Double>> {
}
addOptimizationData(gradientFunction)
val logger = problem.getFeature<OptimizationLog>()
val logger = problem.attributes[OptimizationLog]
for (feature in problem.attributes) {
when (feature) {
@ -139,7 +132,7 @@ public object CMOptimizer : Optimizer<Double, FunctionOptimization<Double>> {
}
val (point, value) = cmOptimizer.optimize(*optimizationData.values.toTypedArray())
return problem.withFeatures(OptimizationResult(point.toMap()), OptimizationValue(value))
return problem.withAttributes(OptimizationResult(point.toMap()), OptimizationValue(value))
}
}
}

4
kmath-commons/src/jvmTest/kotlin/space/kscience/kmath/commons/optimization/OptimizeTest.kt
View File

@ -31,7 +31,7 @@ internal class OptimizeTest {
@Test
fun testGradientOptimization() = runBlocking {
val result = normal.optimizeWith(CMOptimizer, x to 1.0, y to 1.0)
println(result.resultPoint)
println(result.result)
println(result.resultValue)
}
@ -42,7 +42,7 @@ internal class OptimizeTest {
//this sets simplex optimizer
}
println(result.resultPoint)
println(result.result)
println(result.resultValue)
}

11
kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/DSAlgebra.kt
View File

@ -5,6 +5,7 @@
package space.kscience.kmath.expressions
import space.kscience.attributes.SafeType
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.operations.*
import space.kscience.kmath.structures.Buffer
@ -331,10 +332,13 @@ public class DerivativeStructureRingExpression<T, A>(
public val elementBufferFactory: MutableBufferFactory<T> = algebra.bufferFactory,
public val function: DSRing<T, A>.() -> DS<T, A>,
) : DifferentiableExpression<T> where A : Ring<T>, A : ScaleOperations<T>, A : NumericAlgebra<T> {
override val type: SafeType<T> get() = elementBufferFactory.type
override operator fun invoke(arguments: Map<Symbol, T>): T =
DSRing(algebra, 0, arguments).function().value
override fun derivativeOrNull(symbols: List<Symbol>): Expression<T> = Expression { arguments ->
override fun derivativeOrNull(symbols: List<Symbol>): Expression<T> = Expression(type) { arguments ->
with(
DSRing(
algebra,
@ -443,10 +447,13 @@ public class DSFieldExpression<T, A : ExtendedField<T>>(
public val algebra: A,
public val function: DSField<T, A>.() -> DS<T, A>,
) : DifferentiableExpression<T> {
override val type: SafeType<T> get() = algebra.type
override operator fun invoke(arguments: Map<Symbol, T>): T =
DSField(algebra, 0, arguments).function().value
override fun derivativeOrNull(symbols: List<Symbol>): Expression<T> = Expression { arguments ->
override fun derivativeOrNull(symbols: List<Symbol>): Expression<T> = Expression(type) { arguments ->
DSField(
algebra,
symbols.size,

29
kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/Expression.kt
View File

@ -5,8 +5,13 @@
package space.kscience.kmath.expressions
import space.kscience.attributes.SafeType
import space.kscience.attributes.WithType
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.operations.Algebra
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.IntRing
import space.kscience.kmath.operations.LongRing
import kotlin.jvm.JvmName
import kotlin.properties.ReadOnlyProperty
@ -15,7 +20,7 @@ import kotlin.properties.ReadOnlyProperty
*
* @param T the type this expression takes as argument and returns.
*/
public fun interface Expression<T> {
public interface Expression<T> : WithType<T> {
/**
* Calls this expression from arguments.
*
@ -25,11 +30,20 @@ public fun interface Expression<T> {
public operator fun invoke(arguments: Map<Symbol, T>): T
}
public fun <T> Expression(type: SafeType<T>, block: (Map<Symbol, T>) -> T): Expression<T> = object : Expression<T> {
override fun invoke(arguments: Map<Symbol, T>): T = block(arguments)
override val type: SafeType<T> = type
}
/**
* Specialization of [Expression] for [Double] allowing better performance because of using array.
*/
@UnstableKMathAPI
public interface DoubleExpression : Expression<Double> {
override val type: SafeType<Double> get() = DoubleField.type
/**
* The indexer of this expression's arguments that should be used to build array for [invoke].
*
@ -49,7 +63,7 @@ public interface DoubleExpression : Expression<Double> {
*/
public operator fun invoke(arguments: DoubleArray): Double
public companion object{
public companion object {
internal val EMPTY_DOUBLE_ARRAY = DoubleArray(0)
}
}
@ -59,6 +73,9 @@ public interface DoubleExpression : Expression<Double> {
*/
@UnstableKMathAPI
public interface IntExpression : Expression<Int> {
override val type: SafeType<Int> get() = IntRing.type
/**
* The indexer of this expression's arguments that should be used to build array for [invoke].
*
@ -78,7 +95,7 @@ public interface IntExpression : Expression<Int> {
*/
public operator fun invoke(arguments: IntArray): Int
public companion object{
public companion object {
internal val EMPTY_INT_ARRAY = IntArray(0)
}
}
@ -88,6 +105,9 @@ public interface IntExpression : Expression<Int> {
*/
@UnstableKMathAPI
public interface LongExpression : Expression<Long> {
override val type: SafeType<Long> get() = LongRing.type
/**
* The indexer of this expression's arguments that should be used to build array for [invoke].
*
@ -107,7 +127,7 @@ public interface LongExpression : Expression<Long> {
*/
public operator fun invoke(arguments: LongArray): Long
public companion object{
public companion object {
internal val EMPTY_LONG_ARRAY = LongArray(0)
}
}
@ -158,7 +178,6 @@ public operator fun <T> Expression<T>.invoke(vararg pairs: Pair<String, T>): T =
)
/**
* Calls this expression without providing any arguments.
*

8
kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/ExpressionWithDefault.kt
View File

@ -5,10 +5,15 @@
package space.kscience.kmath.expressions
import space.kscience.attributes.SafeType
public class ExpressionWithDefault<T>(
private val origin: Expression<T>,
private val defaultArgs: Map<Symbol, T>,
) : Expression<T> {
override val type: SafeType<T>
get() = origin.type
override fun invoke(arguments: Map<Symbol, T>): T = origin.invoke(defaultArgs + arguments)
}
@ -21,6 +26,9 @@ public class DiffExpressionWithDefault<T>(
private val defaultArgs: Map<Symbol, T>,
) : DifferentiableExpression<T> {
override val type: SafeType<T>
get() = origin.type
override fun invoke(arguments: Map<Symbol, T>): T = origin.invoke(defaultArgs + arguments)
override fun derivativeOrNull(symbols: List<Symbol>): Expression<T>? =

19
kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/FunctionalExpressionAlgebra.kt
View File

@ -23,26 +23,27 @@ public abstract class FunctionalExpressionAlgebra<T, out A : Algebra<T>>(
/**
* Builds an Expression of constant expression that does not depend on arguments.
*/
override fun const(value: T): Expression<T> = Expression { value }
override fun const(value: T): Expression<T> = Expression(algebra.type) { value }
/**
* Builds an Expression to access a variable.
*/
override fun bindSymbolOrNull(value: String): Expression<T>? = Expression { arguments ->
override fun bindSymbolOrNull(value: String): Expression<T>? = Expression(algebra.type) { arguments ->
algebra.bindSymbolOrNull(value)
?: arguments[StringSymbol(value)]
?: error("Symbol '$value' is not supported in $this")
}
override fun binaryOperationFunction(operation: String): (left: Expression<T>, right: Expression<T>) -> Expression<T> =
{ left, right ->
Expression { arguments ->
algebra.binaryOperationFunction(operation)(left(arguments), right(arguments))
}
override fun binaryOperationFunction(
operation: String,
): (left: Expression<T>, right: Expression<T>) -> Expression<T> = { left, right ->
Expression(algebra.type) { arguments ->
algebra.binaryOperationFunction(operation)(left(arguments), right(arguments))
}
}
override fun unaryOperationFunction(operation: String): (arg: Expression<T>) -> Expression<T> = { arg ->
Expression { arguments -> algebra.unaryOperation(operation, arg(arguments)) }
Expression(algebra.type) { arguments -> algebra.unaryOperation(operation, arg(arguments)) }
}
}
@ -124,7 +125,7 @@ public open class FunctionalExpressionField<T, out A : Field<T>>(
super<FunctionalExpressionRing>.binaryOperationFunction(operation)
override fun scale(a: Expression<T>, value: Double): Expression<T> = algebra {
Expression { args -> a(args) * value }
Expression(algebra.type) { args -> a(args) * value }
}
override fun bindSymbolOrNull(value: String): Expression<T>? =

2
kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/MST.kt
View File

@ -108,4 +108,4 @@ public fun <T> MST.interpret(algebra: Algebra<T>, vararg arguments: Pair<Symbol,
* Interpret this [MST] as expression.
*/
public fun <T : Any> MST.toExpression(algebra: Algebra<T>): Expression<T> =
Expression { arguments -> interpret(algebra, arguments) }
Expression(algebra.type) { arguments -> interpret(algebra, arguments) }

5
kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/SimpleAutoDiff.kt
View File

@ -243,12 +243,15 @@ public class SimpleAutoDiffExpression<T : Any, F : Field<T>>(
public val field: F,
public val function: SimpleAutoDiffField<T, F>.() -> AutoDiffValue<T>,
) : FirstDerivativeExpression<T>() {
override val type: SafeType<T> get() = this.field.type
override operator fun invoke(arguments: Map<Symbol, T>): T {
//val bindings = arguments.entries.map { it.key.bind(it.value) }
return SimpleAutoDiffField(field, arguments).function().value
}
override fun derivativeOrNull(symbol: Symbol): Expression<T> = Expression { arguments ->
override fun derivativeOrNull(symbol: Symbol): Expression<T> = Expression(type) { arguments ->
//val bindings = arguments.entries.map { it.key.bind(it.value) }
val derivationResult = SimpleAutoDiffField(field, arguments).differentiate(function)
derivationResult.derivative(symbol)

2
kmath-core/src/commonMain/kotlin/space/kscience/kmath/linear/LinearSolver.kt
View File

@ -11,7 +11,7 @@ package space.kscience.kmath.linear
*
* @param T the type of items.
*/
public interface LinearSolver<T : Any> {
public interface LinearSolver<T> {
/**
* Solve a dot x = b matrix equation and return x
*/

21
kmath-core/src/commonMain/kotlin/space/kscience/kmath/linear/LinearSpace.kt
View File

@ -5,10 +5,7 @@
package space.kscience.kmath.linear
import space.kscience.attributes.Attributes
import space.kscience.attributes.SafeType
import space.kscience.attributes.WithType
import space.kscience.attributes.withAttribute
import space.kscience.attributes.*
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.nd.*
import space.kscience.kmath.operations.BufferRingOps
@ -31,19 +28,13 @@ public typealias MutableMatrix<T> = MutableStructure2D<T>
*/
public typealias Point<T> = Buffer<T>
/**
* A marker interface for algebras that operate on matrices
* @param T type of matrix element
*/
public interface MatrixOperations<T> : WithType<T>
/**
* Basic operations on matrices and vectors.
*
* @param T the type of items in the matrices.
* @param A the type of ring over [T].
*/
public interface LinearSpace<T, out A : Ring<T>> : MatrixOperations<T> {
public interface LinearSpace<T, out A : Ring<T>> : MatrixScope<T> {
public val elementAlgebra: A
override val type: SafeType<T> get() = elementAlgebra.type
@ -177,10 +168,10 @@ public interface LinearSpace<T, out A : Ring<T>> : MatrixOperations<T> {
/**
* Compute an [attribute] value for given [structure]. Return null if the attribute could not be computed.
*/
public fun <V, A : StructureAttribute<V>> computeAttribute(structure: StructureND<*>, attribute: A): V? = null
public fun <V, A : StructureAttribute<V>> computeAttribute(structure: Structure2D<T>, attribute: A): V? = null
@UnstableKMathAPI
public fun <V, A : StructureAttribute<V>> StructureND<*>.getOrComputeAttribute(attribute: A): V? {
public fun <V, A : StructureAttribute<V>> Structure2D<T>.getOrComputeAttribute(attribute: A): V? {
return attributes[attribute] ?: computeAttribute(this, attribute)
}
@ -225,7 +216,7 @@ public inline operator fun <LS : LinearSpace<*, *>, R> LS.invoke(block: LS.() ->
/**
* Convert matrix to vector if it is possible.
*/
public fun <T : Any> Matrix<T>.asVector(): Point<T> =
public fun <T> Matrix<T>.asVector(): Point<T> =
if (this.colNum == 1) as1D()
else error("Can't convert matrix with more than one column to vector")
@ -236,4 +227,4 @@ public fun <T : Any> Matrix<T>.asVector(): Point<T> =
* @receiver a buffer.
* @return the new matrix.
*/
public fun <T : Any> Point<T>.asMatrix(): VirtualMatrix<T> = VirtualMatrix(type, size, 1) { i, _ -> get(i) }
public fun <T> Point<T>.asMatrix(): VirtualMatrix<T> = VirtualMatrix(type, size, 1) { i, _ -> get(i) }

41
kmath-core/src/commonMain/kotlin/space/kscience/kmath/linear/LupDecomposition.kt
View File

@ -9,12 +9,20 @@ package space.kscience.kmath.linear
import space.kscience.attributes.Attributes
import space.kscience.attributes.PolymorphicAttribute
import space.kscience.attributes.SafeType
import space.kscience.attributes.safeTypeOf
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.operations.*
import space.kscience.kmath.structures.*
public interface LupDecomposition<T> {
public val linearSpace: LinearSpace<T, Field<T>>
public val elementAlgebra: Field<T> get() = linearSpace.elementAlgebra
public val pivot: IntBuffer
public val l: Matrix<T>
public val u: Matrix<T>
}
/**
* Matrices with this feature support LU factorization with partial pivoting: *[p] &middot; a = [l] &middot; [u]* where
* *a* is the owning matrix.
@ -22,15 +30,14 @@ import space.kscience.kmath.structures.*
* @param T the type of matrices' items.
* @param lu combined L and U matrix
*/
public class LupDecomposition<T>(
public val linearSpace: LinearSpace<T, Ring<T>>,
public class GenericLupDecomposition<T>(
override val linearSpace: LinearSpace<T, Field<T>>,
private val lu: Matrix<T>,
public val pivot: IntBuffer,
override val pivot: IntBuffer,
private val even: Boolean,
) {
public val elementAlgebra: Ring<T> get() = linearSpace.elementAlgebra
) : LupDecomposition<T> {
public val l: Matrix<T>
override val l: Matrix<T>
get() = VirtualMatrix(lu.type, lu.rowNum, lu.colNum, attributes = Attributes(LowerTriangular)) { i, j ->
when {
j < i -> lu[i, j]
@ -39,7 +46,7 @@ public class LupDecomposition<T>(
}
}
public val u: Matrix<T>
override val u: Matrix<T>
get() = VirtualMatrix(lu.type, lu.rowNum, lu.colNum, attributes = Attributes(UpperTriangular)) { i, j ->
if (j >= i) lu[i, j] else elementAlgebra.zero
}
@ -55,13 +62,12 @@ public class LupDecomposition<T>(
}
public class LupDecompositionAttribute<T>(type: SafeType<LupDecomposition<T>>) :
PolymorphicAttribute<LupDecomposition<T>>(type),
public class LupDecompositionAttribute<T> :
PolymorphicAttribute<LupDecomposition<T>>(safeTypeOf()),
MatrixAttribute<LupDecomposition<T>>
public val <T> MatrixOperations<T>.LUP: LupDecompositionAttribute<T>
get() = LupDecompositionAttribute(safeTypeOf())
public val <T> MatrixScope<T>.LUP: LupDecompositionAttribute<T>
get() = LupDecompositionAttribute()
@PublishedApi
internal fun <T : Comparable<T>> LinearSpace<T, Ring<T>>.abs(value: T): T =
@ -79,7 +85,7 @@ public fun <T : Comparable<T>> LinearSpace<T, Field<T>>.lup(
val pivot = IntArray(matrix.rowNum)
//TODO just waits for multi-receivers
with(BufferAccessor2D(matrix.rowNum, matrix.colNum, elementAlgebra.bufferFactory)){
with(BufferAccessor2D(matrix.rowNum, matrix.colNum, elementAlgebra.bufferFactory)) {
val lu = create(matrix)
@ -142,18 +148,17 @@ public fun <T : Comparable<T>> LinearSpace<T, Field<T>>.lup(
for (row in col + 1 until m) lu[row, col] /= luDiag
}
return LupDecomposition(this@lup, lu.toStructure2D(), pivot.asBuffer(), even)
return GenericLupDecomposition(this@lup, lu.toStructure2D(), pivot.asBuffer(), even)
}
}
public fun LinearSpace<Double, Float64Field>.lup(
matrix: Matrix<Double>,
singularityThreshold: Double = 1e-11,
): LupDecomposition<Double> = lup(matrix) { it < singularityThreshold }
internal fun <T : Any, A : Field<T>> LinearSpace<T, A>.solve(
internal fun <T> LinearSpace<T, Field<T>>.solve(
lup: LupDecomposition<T>,
matrix: Matrix<T>,
): Matrix<T> {
@ -205,7 +210,7 @@ internal fun <T : Any, A : Field<T>> LinearSpace<T, A>.solve(
* Produce a generic solver based on LUP decomposition
*/
@OptIn(UnstableKMathAPI::class)
public fun <T : Comparable<T>, F : Field<T>> LinearSpace<T, F>.lupSolver(
public fun <T : Comparable<T>> LinearSpace<T, Field<T>>.lupSolver(
singularityCheck: (T) -> Boolean,
): LinearSolver<T> = object : LinearSolver<T> {
override fun solve(a: Matrix<T>, b: Matrix<T>): Matrix<T> {

10
kmath-core/src/commonMain/kotlin/space/kscience/kmath/linear/MatrixWrapper.kt
View File

@ -35,7 +35,7 @@ public val <T : Any> Matrix<T>.origin: Matrix<T>
/**
* Add a single feature to a [Matrix]
*/
public fun <T : Any, A : Attribute<T>> Matrix<T>.withAttribute(
public fun <T, A : Attribute<T>> Matrix<T>.withAttribute(
attribute: A,
attrValue: T,
): MatrixWrapper<T> = if (this is MatrixWrapper) {
@ -44,7 +44,7 @@ public fun <T : Any, A : Attribute<T>> Matrix<T>.withAttribute(
MatrixWrapper(this, Attributes(attribute, attrValue))
}
public fun <T : Any, A : Attribute<Unit>> Matrix<T>.withAttribute(
public fun <T, A : Attribute<Unit>> Matrix<T>.withAttribute(
attribute: A,
): MatrixWrapper<T> = if (this is MatrixWrapper) {
MatrixWrapper(origin, attributes.withAttribute(attribute))
@ -55,7 +55,7 @@ public fun <T : Any, A : Attribute<Unit>> Matrix<T>.withAttribute(
/**
* Modify matrix attributes
*/
public fun <T : Any> Matrix<T>.modifyAttributes(modifier: (Attributes) -> Attributes): MatrixWrapper<T> =
public fun <T> Matrix<T>.modifyAttributes(modifier: (Attributes) -> Attributes): MatrixWrapper<T> =
if (this is MatrixWrapper) {
MatrixWrapper(origin, modifier(attributes))
} else {
@ -65,7 +65,7 @@ public fun <T : Any> Matrix<T>.modifyAttributes(modifier: (Attributes) -> Attrib
/**
* Diagonal matrix of ones. The matrix is virtual, no actual matrix is created.
*/
public fun <T : Any> LinearSpace<T, Ring<T>>.one(
public fun <T> LinearSpace<T, Ring<T>>.one(
rows: Int,
columns: Int,
): MatrixWrapper<T> = VirtualMatrix(type, rows, columns) { i, j ->
@ -76,7 +76,7 @@ public fun <T : Any> LinearSpace<T, Ring<T>>.one(
/**
* A virtual matrix of zeroes
*/
public fun <T : Any> LinearSpace<T, Ring<T>>.zero(
public fun <T> LinearSpace<T, Ring<T>>.zero(
rows: Int,
columns: Int,
): MatrixWrapper<T> = VirtualMatrix(type, rows, columns) { _, _ ->

44
kmath-core/src/commonMain/kotlin/space/kscience/kmath/linear/matrixAttributes.kt
View File

@ -10,6 +10,13 @@ package space.kscience.kmath.linear
import space.kscience.attributes.*
import space.kscience.kmath.nd.StructureAttribute
/**
* A marker interface for algebras that operate on matrices
* @param T type of matrix element
*/
public interface MatrixScope<T> : AttributeScope<Matrix<T>>, WithType<T>
/**
* A marker interface representing some properties of matrices or additional transformations of them. Features are used
* to optimize matrix operations performance in some cases or retrieve the APIs.
@ -38,11 +45,11 @@ public object IsUnit : IsDiagonal
*
* @param T the type of matrices' items.
*/
public class Inverted<T>(type: SafeType<Matrix<T>>) :
PolymorphicAttribute<Matrix<T>>(type),
public class Inverted<T>() :
PolymorphicAttribute<Matrix<T>>(safeTypeOf()),
MatrixAttribute<Matrix<T>>
public val <T> MatrixOperations<T>.Inverted: Inverted<T> get() = Inverted(safeTypeOf())
public val <T> MatrixScope<T>.Inverted: Inverted<T> get() = Inverted()
/**
* Matrices with this feature can compute their determinant.
@ -53,7 +60,7 @@ public class Determinant<T>(type: SafeType<T>) :
PolymorphicAttribute<T>(type),
MatrixAttribute<T>
public val <T> MatrixOperations<T>.Determinant: Determinant<T> get() = Determinant(type)
public val <T> MatrixScope<T>.Determinant: Determinant<T> get() = Determinant(type)
/**
* Matrices with this feature are lower triangular ones.
@ -77,11 +84,11 @@ public data class LUDecomposition<T>(val l: Matrix<T>, val u: Matrix<T>)
*
* @param T the type of matrices' items.
*/
public class LuDecompositionAttribute<T>(type: SafeType<LUDecomposition<T>>) :
PolymorphicAttribute<LUDecomposition<T>>(type),
public class LuDecompositionAttribute<T> :
PolymorphicAttribute<LUDecomposition<T>>(safeTypeOf()),
MatrixAttribute<LUDecomposition<T>>
public val <T> MatrixOperations<T>.LU: LuDecompositionAttribute<T> get() = LuDecompositionAttribute(safeTypeOf())
public val <T> MatrixScope<T>.LU: LuDecompositionAttribute<T> get() = LuDecompositionAttribute()
/**
@ -108,12 +115,12 @@ public interface QRDecomposition<out T> {
*
* @param T the type of matrices' items.
*/
public class QRDecompositionAttribute<T>(type: SafeType<QRDecomposition<T>>) :
PolymorphicAttribute<QRDecomposition<T>>(type),
public class QRDecompositionAttribute<T>() :
PolymorphicAttribute<QRDecomposition<T>>(safeTypeOf()),
MatrixAttribute<QRDecomposition<T>>
public val <T> MatrixOperations<T>.QR: QRDecompositionAttribute<T>
get() = QRDecompositionAttribute(safeTypeOf())
public val <T> MatrixScope<T>.QR: QRDecompositionAttribute<T>
get() = QRDecompositionAttribute()
public interface CholeskyDecomposition<T> {
/**
@ -128,12 +135,12 @@ public interface CholeskyDecomposition<T> {
*
* @param T the type of matrices' items.
*/
public class CholeskyDecompositionAttribute<T>(type: SafeType<CholeskyDecomposition<T>>) :
PolymorphicAttribute<CholeskyDecomposition<T>>(type),
public class CholeskyDecompositionAttribute<T> :
PolymorphicAttribute<CholeskyDecomposition<T>>(safeTypeOf()),
MatrixAttribute<CholeskyDecomposition<T>>
public val <T> MatrixOperations<T>.Cholesky: CholeskyDecompositionAttribute<T>
get() = CholeskyDecompositionAttribute(safeTypeOf())
public val <T> MatrixScope<T>.Cholesky: CholeskyDecompositionAttribute<T>
get() = CholeskyDecompositionAttribute()
public interface SingularValueDecomposition<T> {
/**
@ -163,12 +170,11 @@ public interface SingularValueDecomposition<T> {
*
* @param T the type of matrices' items.
*/
public class SVDAttribute<T>(type: SafeType<SingularValueDecomposition<T>>) :
PolymorphicAttribute<SingularValueDecomposition<T>>(type),
public class SVDAttribute<T>() :
PolymorphicAttribute<SingularValueDecomposition<T>>(safeTypeOf()),
MatrixAttribute<SingularValueDecomposition<T>>
public val <T> MatrixOperations<T>.SVD: SVDAttribute<T>
get() = SVDAttribute(safeTypeOf())
public val <T> MatrixScope<T>.SVD: SVDAttribute<T> get() = SVDAttribute()
//TODO add sparse matrix feature

2
kmath-ejml/src/main/kotlin/space/kscience/kmath/ejml/EjmlLinearSpace.kt
View File

@ -39,5 +39,5 @@ public abstract class EjmlLinearSpace<T : Any, out A : Ring<T>, out M : org.ejml
@UnstableKMathAPI
public fun EjmlMatrix<T, *>.inverted(): Matrix<Double> =
attributeForOrNull(this, Float64Field.linearSpace.Inverted)
computeAttribute(this, Float64Field.linearSpace.Inverted)!!
}

39
kmath-ejml/src/main/kotlin/space/kscience/kmath/ejml/_generated.kt
View File

@ -19,9 +19,13 @@ import org.ejml.sparse.csc.factory.DecompositionFactory_DSCC
import org.ejml.sparse.csc.factory.DecompositionFactory_FSCC
import org.ejml.sparse.csc.factory.LinearSolverFactory_DSCC
import org.ejml.sparse.csc.factory.LinearSolverFactory_FSCC
import space.kscience.attributes.SafeType
import space.kscience.attributes.safeTypeOf
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.linear.*
import space.kscience.kmath.linear.Matrix
import space.kscience.kmath.nd.Structure2D
import space.kscience.kmath.nd.StructureAttribute
import space.kscience.kmath.nd.StructureFeature
import space.kscience.kmath.operations.Float32Field
import space.kscience.kmath.operations.Float64Field
@ -39,6 +43,8 @@ public class EjmlDoubleVector<out M : DMatrix>(override val origin: M) : EjmlVec
require(origin.numRows == 1) { "The origin matrix must have only one row to form a vector" }
}
override val type: SafeType<Double> get() = safeTypeOf()
override operator fun get(index: Int): Double = origin[0, index]
}
@ -50,6 +56,8 @@ public class EjmlFloatVector<out M : FMatrix>(override val origin: M) : EjmlVect
require(origin.numRows == 1) { "The origin matrix must have only one row to form a vector" }
}
override val type: SafeType<Float> get() = safeTypeOf()
override operator fun get(index: Int): Float = origin[0, index]
}
@ -57,6 +65,8 @@ public class EjmlFloatVector<out M : FMatrix>(override val origin: M) : EjmlVect
* [EjmlMatrix] specialization for [Double].
*/
public class EjmlDoubleMatrix<out M : DMatrix>(override val origin: M) : EjmlMatrix<Double, M>(origin) {
override val type: SafeType<Double> get() = safeTypeOf()
override operator fun get(i: Int, j: Int): Double = origin[i, j]
}
@ -64,9 +74,12 @@ public class EjmlDoubleMatrix<out M : DMatrix>(override val origin: M) : EjmlMat
* [EjmlMatrix] specialization for [Float].
*/
public class EjmlFloatMatrix<out M : FMatrix>(override val origin: M) : EjmlMatrix<Float, M>(origin) {
override val type: SafeType<Float> get() = safeTypeOf()
override operator fun get(i: Int, j: Int): Float = origin[i, j]
}
/**
* [EjmlLinearSpace] implementation based on [CommonOps_DDRM], [DecompositionFactory_DDRM] operations and
* [DMatrixRMaj] matrices.
@ -77,7 +90,7 @@ public object EjmlLinearSpaceDDRM : EjmlLinearSpace<Double, Float64Field, DMatri
*/
override val elementAlgebra: Float64Field get() = Float64Field
override val elementType: KType get() = typeOf<Double>()
override val type: SafeType<Double> get() = safeTypeOf()
@Suppress("UNCHECKED_CAST")
override fun Matrix<Double>.toEjml(): EjmlDoubleMatrix<DMatrixRMaj> = when {
@ -205,6 +218,18 @@ public object EjmlLinearSpaceDDRM : EjmlLinearSpace<Double, Float64Field, DMatri
override fun Double.times(v: Point<Double>): EjmlDoubleVector<DMatrixRMaj> = v * this
override fun <V, A : StructureAttribute<V>> computeAttribute(structure: Structure2D<Double>, attribute: A): V? {
val origin = structure.toEjml().origin
return when(attribute){
Inverted -> {
val res = origin.copy()
CommonOps_DDRM.invert(res)
res.wrapMatrix()
}
else->
}
}
@UnstableKMathAPI
override fun <F : StructureFeature> computeFeature(structure: Matrix<Double>, type: KClass<out F>): F? {
structure.getFeature(type)?.let { return it }
@ -305,6 +330,8 @@ public object EjmlLinearSpaceDDRM : EjmlLinearSpace<Double, Float64Field, DMatri
}
}
import org.checkerframework.checker.guieffect.qual.SafeType
/**
* [EjmlLinearSpace] implementation based on [CommonOps_FDRM], [DecompositionFactory_FDRM] operations and
* [FMatrixRMaj] matrices.
@ -315,7 +342,7 @@ public object EjmlLinearSpaceFDRM : EjmlLinearSpace<Float, Float32Field, FMatrix
*/
override val elementAlgebra: Float32Field get() = Float32Field
override val elementType: KType get() = typeOf<Float>()
override val type: SafeType<Float> get() = safeTypeOf()
@Suppress("UNCHECKED_CAST")
override fun Matrix<Float>.toEjml(): EjmlFloatMatrix<FMatrixRMaj> = when {
@ -543,6 +570,8 @@ public object EjmlLinearSpaceFDRM : EjmlLinearSpace<Float, Float32Field, FMatrix
}
}
import org.checkerframework.checker.guieffect.qual.SafeType
/**
* [EjmlLinearSpace] implementation based on [CommonOps_DSCC], [DecompositionFactory_DSCC] operations and
* [DMatrixSparseCSC] matrices.
@ -553,7 +582,7 @@ public object EjmlLinearSpaceDSCC : EjmlLinearSpace<Double, Float64Field, DMatri
*/
override val elementAlgebra: Float64Field get() = Float64Field
override val elementType: KType get() = typeOf<Double>()
override val type: SafeType<Double> get() = safeTypeOf()
@Suppress("UNCHECKED_CAST")
override fun Matrix<Double>.toEjml(): EjmlDoubleMatrix<DMatrixSparseCSC> = when {
@ -776,6 +805,8 @@ public object EjmlLinearSpaceDSCC : EjmlLinearSpace<Double, Float64Field, DMatri
}
}
import org.checkerframework.checker.guieffect.qual.SafeType
/**
* [EjmlLinearSpace] implementation based on [CommonOps_FSCC], [DecompositionFactory_FSCC] operations and
* [FMatrixSparseCSC] matrices.
@ -786,7 +817,7 @@ public object EjmlLinearSpaceFSCC : EjmlLinearSpace<Float, Float32Field, FMatrix
*/
override val elementAlgebra: Float32Field get() = Float32Field
override val elementType: KType get() = typeOf<Float>()
override val type: SafeType<Float> get() = safeTypeOf()
@Suppress("UNCHECKED_CAST")
override fun Matrix<Float>.toEjml(): EjmlFloatMatrix<FMatrixSparseCSC> = when {

4
kmath-functions/src/commonMain/kotlin/space/kscience/kmath/integration/GaussIntegrator.kt
View File

@ -4,7 +4,7 @@
*/
package space.kscience.kmath.integration
import space.kscience.attributes.TypedAttributesBuilder
import space.kscience.attributes.AttributesBuilder
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.operations.Field
import space.kscience.kmath.structures.Buffer
@ -92,7 +92,7 @@ public inline fun <reified T : Any> GaussIntegrator<T>.integrate(
range: ClosedRange<Double>,
order: Int = 10,
intervals: Int = 10,
attributesBuilder: TypedAttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
attributesBuilder: AttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
noinline function: (Double) -> T,
): UnivariateIntegrand<T> {
require(range.endInclusive > range.start) { "The range upper bound should be higher than lower bound" }

2
kmath-functions/src/commonMain/kotlin/space/kscience/kmath/integration/Integrand.kt
View File

@ -30,7 +30,7 @@ public sealed class IntegrandValue<T> private constructor(): IntegrandAttribute<
}
}
public fun <T> TypedAttributesBuilder<Integrand<T>>.value(value: T) {
public fun <T> AttributesBuilder<Integrand<T>>.value(value: T) {
IntegrandValue.forType<T>().invoke(value)
}

4
kmath-functions/src/commonMain/kotlin/space/kscience/kmath/integration/MultivariateIntegrand.kt
View File

@ -25,10 +25,10 @@ public fun <T, A : Any> MultivariateIntegrand<T>.withAttribute(
): MultivariateIntegrand<T> = withAttributes(attributes.withAttribute(attribute, value))
public fun <T> MultivariateIntegrand<T>.withAttributes(
block: TypedAttributesBuilder<MultivariateIntegrand<T>>.() -> Unit,
block: AttributesBuilder<MultivariateIntegrand<T>>.() -> Unit,
): MultivariateIntegrand<T> = withAttributes(attributes.modify(block))
public inline fun <reified T : Any> MultivariateIntegrand(
attributeBuilder: TypedAttributesBuilder<MultivariateIntegrand<T>>.() -> Unit,
attributeBuilder: AttributesBuilder<MultivariateIntegrand<T>>.() -> Unit,
noinline function: (Point<T>) -> T,
): MultivariateIntegrand<T> = MultivariateIntegrand(safeTypeOf<T>(), Attributes(attributeBuilder), function)

10
kmath-functions/src/commonMain/kotlin/space/kscience/kmath/integration/UnivariateIntegrand.kt
View File

@ -26,11 +26,11 @@ public fun <T, A : Any> UnivariateIntegrand<T>.withAttribute(
): UnivariateIntegrand<T> = withAttributes(attributes.withAttribute(attribute, value))
public fun <T> UnivariateIntegrand<T>.withAttributes(
block: TypedAttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
block: AttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
): UnivariateIntegrand<T> = withAttributes(attributes.modify(block))
public inline fun <reified T : Any> UnivariateIntegrand(
attributeBuilder: TypedAttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
attributeBuilder: AttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
noinline function: (Double) -> T,
): UnivariateIntegrand<T> = UnivariateIntegrand(safeTypeOf(), Attributes(attributeBuilder), function)
@ -58,7 +58,7 @@ public class UnivariateIntegrandRanges(public val ranges: List<Pair<ClosedRange<
public object UnivariateIntegrationNodes : IntegrandAttribute<Buffer<Double>>
public fun TypedAttributesBuilder<UnivariateIntegrand<*>>.integrationNodes(vararg nodes: Double) {
public fun AttributesBuilder<UnivariateIntegrand<*>>.integrationNodes(vararg nodes: Double) {
UnivariateIntegrationNodes(Float64Buffer(nodes))
}
@ -68,7 +68,7 @@ public fun TypedAttributesBuilder<UnivariateIntegrand<*>>.integrationNodes(varar
*/
@UnstableKMathAPI
public inline fun <reified T : Any> UnivariateIntegrator<T>.integrate(
attributesBuilder: TypedAttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
attributesBuilder: AttributesBuilder<UnivariateIntegrand<T>>.() -> Unit,
noinline function: (Double) -> T,
): UnivariateIntegrand<T> = integrate(UnivariateIntegrand(attributesBuilder, function))
@ -79,7 +79,7 @@ public inline fun <reified T : Any> UnivariateIntegrator<T>.integrate(
@UnstableKMathAPI
public inline fun <reified T : Any> UnivariateIntegrator<T>.integrate(
range: ClosedRange<Double>,
attributeBuilder: TypedAttributesBuilder<UnivariateIntegrand<T>>.() -> Unit = {},
attributeBuilder: AttributesBuilder<UnivariateIntegrand<T>>.() -> Unit = {},
noinline function: (Double) -> T,
): UnivariateIntegrand<T> {

2
kmath-jafama/build.gradle.kts
View File

@ -14,7 +14,7 @@ repositories {
}
readme {
maturity = space.kscience.gradle.Maturity.PROTOTYPE
maturity = space.kscience.gradle.Maturity.DEPRECATED
propertyByTemplate("artifact", rootProject.file("docs/templates/ARTIFACT-TEMPLATE.md"))
feature("jafama-double", "src/main/kotlin/space/kscience/kmath/jafama/") {

12
kmath-jafama/src/main/kotlin/space/kscience/kmath/jafama/KMathJafama.kt
View File

@ -7,16 +7,17 @@ package space.kscience.kmath.jafama
import net.jafama.FastMath
import net.jafama.StrictFastMath
import space.kscience.kmath.operations.ExtendedField
import space.kscience.kmath.operations.Norm
import space.kscience.kmath.operations.PowerOperations
import space.kscience.kmath.operations.ScaleOperations
import space.kscience.kmath.operations.*
import space.kscience.kmath.structures.MutableBufferFactory
/**
* A field for [Double] (using FastMath) without boxing. Does not produce appropriate field element.
*/
@Suppress("EXTENSION_SHADOWED_BY_MEMBER", "OVERRIDE_BY_INLINE", "NOTHING_TO_INLINE")
public object JafamaDoubleField : ExtendedField<Double>, Norm<Double, Double>, ScaleOperations<Double> {
override val bufferFactory: MutableBufferFactory<Double> get() = DoubleField.bufferFactory
override inline val zero: Double get() = 0.0
override inline val one: Double get() = 1.0
@ -68,6 +69,9 @@ public object JafamaDoubleField : ExtendedField<Double>, Norm<Double, Double>, S
*/
@Suppress("EXTENSION_SHADOWED_BY_MEMBER", "OVERRIDE_BY_INLINE", "NOTHING_TO_INLINE")
public object StrictJafamaDoubleField : ExtendedField<Double>, Norm<Double, Double>, ScaleOperations<Double> {
override val bufferFactory: MutableBufferFactory<Double> get() = DoubleField.bufferFactory
override inline val zero: Double get() = 0.0
override inline val one: Double get() = 1.0

2
kmath-multik/src/commonMain/kotlin/space/kscience/kmath/multik/MultikDoubleAlgebra.kt
View File

@ -20,7 +20,7 @@ public class MultikDoubleAlgebra(
) : MultikDivisionTensorAlgebra<Double, Float64Field>(multikEngine),
TrigonometricOperations<StructureND<Double>>, ExponentialOperations<StructureND<Double>> {
override val elementAlgebra: Float64Field get() = Float64Field
override val type: DataType get() = DataType.DoubleDataType
override val dataType: DataType get() = DataType.DoubleDataType
override fun sin(arg: StructureND<Double>): MultikTensor<Double> = multikMath.mathEx.sin(arg.asMultik().array).wrap()

2
kmath-multik/src/commonMain/kotlin/space/kscience/kmath/multik/MultikFloatAlgebra.kt
View File

@ -15,7 +15,7 @@ public class MultikFloatAlgebra(
multikEngine: Engine
) : MultikDivisionTensorAlgebra<Float, Float32Field>(multikEngine) {
override val elementAlgebra: Float32Field get() = Float32Field
override val type: DataType get() = DataType.FloatDataType
override val dataType: DataType get() = DataType.FloatDataType
override fun scalar(value: Float): MultikTensor<Float> = Multik.ndarrayOf(value).wrap()
}

2
kmath-multik/src/commonMain/kotlin/space/kscience/kmath/multik/MultikIntAlgebra.kt
View File

@ -15,7 +15,7 @@ public class MultikIntAlgebra(
multikEngine: Engine
) : MultikTensorAlgebra<Int, Int32Ring>(multikEngine) {
override val elementAlgebra: Int32Ring get() = Int32Ring
override val type: DataType get() = DataType.IntDataType
override val dataType: DataType get() = DataType.IntDataType
override fun scalar(value: Int): MultikTensor<Int> = Multik.ndarrayOf(value).wrap()
}

2
kmath-multik/src/commonMain/kotlin/space/kscience/kmath/multik/MultikLongAlgebra.kt
View File

@ -15,7 +15,7 @@ public class MultikLongAlgebra(
multikEngine: Engine
) : MultikTensorAlgebra<Long, Int64Ring>(multikEngine) {
override val elementAlgebra: Int64Ring get() = Int64Ring
override val type: DataType get() = DataType.LongDataType
override val dataType: DataType get() = DataType.LongDataType
override fun scalar(value: Long): MultikTensor<Long> = Multik.ndarrayOf(value).wrap()
}

2
kmath-multik/src/commonMain/kotlin/space/kscience/kmath/multik/MultikShortAlgebra.kt
View File

@ -15,7 +15,7 @@ public class MultikShortAlgebra(
multikEngine: Engine
) : MultikTensorAlgebra<Short, Int16Ring>(multikEngine) {
override val elementAlgebra: Int16Ring get() = Int16Ring
override val type: DataType get() = DataType.ShortDataType
override val dataType: DataType get() = DataType.ShortDataType
override fun scalar(value: Short): MultikTensor<Short> = Multik.ndarrayOf(value).wrap()
}

20
kmath-multik/src/commonMain/kotlin/space/kscience/kmath/multik/MultikTensor.kt
View File

@ -6,13 +6,33 @@
package space.kscience.kmath.multik
import org.jetbrains.kotlinx.multik.ndarray.data.*
import space.kscience.attributes.SafeType
import space.kscience.attributes.safeTypeOf
import space.kscience.kmath.PerformancePitfall
import space.kscience.kmath.complex.ComplexField
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.operations.*
import space.kscience.kmath.tensors.api.Tensor
import kotlin.jvm.JvmInline
public val DataType.type: SafeType<*>
get() = when (this) {
DataType.ByteDataType -> ByteRing.type
DataType.ShortDataType -> ShortRing.type
DataType.IntDataType -> IntRing.type
DataType.LongDataType -> LongRing.type
DataType.FloatDataType -> Float32Field.type
DataType.DoubleDataType -> Float64Field.type
DataType.ComplexFloatDataType -> safeTypeOf<Pair<Float, Float>>()
DataType.ComplexDoubleDataType -> ComplexField.type
}
@JvmInline
public value class MultikTensor<T>(public val array: MutableMultiArray<T, DN>) : Tensor<T> {
@Suppress("UNCHECKED_CAST")
override val type: SafeType<T> get() = array.dtype.type as SafeType<T>
override val shape: ShapeND get() = ShapeND(array.shape)
@PerformancePitfall

14
kmath-multik/src/commonMain/kotlin/space/kscience/kmath/multik/MultikTensorAlgebra.kt
View File

@ -26,7 +26,7 @@ public abstract class MultikTensorAlgebra<T, A : Ring<T>>(
private val multikEngine: Engine,
) : TensorAlgebra<T, A> where T : Number, T : Comparable<T> {
public abstract val type: DataType
public abstract val dataType: DataType
protected val multikMath: Math = multikEngine.getMath()
protected val multikLinAl: LinAlg = multikEngine.getLinAlg()
@ -35,7 +35,7 @@ public abstract class MultikTensorAlgebra<T, A : Ring<T>>(
@OptIn(UnsafeKMathAPI::class)
override fun mutableStructureND(shape: ShapeND, initializer: A.(IntArray) -> T): MultikTensor<T> {
val strides = ColumnStrides(shape)
val memoryView = initMemoryView<T>(strides.linearSize, type)
val memoryView = initMemoryView<T>(strides.linearSize, dataType)
strides.asSequence().forEachIndexed { linearIndex, tensorIndex ->
memoryView[linearIndex] = elementAlgebra.initializer(tensorIndex)
}
@ -44,7 +44,7 @@ public abstract class MultikTensorAlgebra<T, A : Ring<T>>(
@OptIn(PerformancePitfall::class, UnsafeKMathAPI::class)
override fun StructureND<T>.map(transform: A.(T) -> T): MultikTensor<T> = if (this is MultikTensor) {
val data = initMemoryView<T>(array.size, type)
val data = initMemoryView<T>(array.size, dataType)
var count = 0
for (el in array) data[count++] = elementAlgebra.transform(el)
NDArray(data, shape = shape.asArray(), dim = array.dim).wrap()
@ -58,7 +58,7 @@ public abstract class MultikTensorAlgebra<T, A : Ring<T>>(
override fun StructureND<T>.mapIndexed(transform: A.(index: IntArray, T) -> T): MultikTensor<T> =
if (this is MultikTensor) {
val array = asMultik().array
val data = initMemoryView<T>(array.size, type)
val data = initMemoryView<T>(array.size, dataType)
val indexIter = array.multiIndices.iterator()
var index = 0
for (item in array) {
@ -95,7 +95,7 @@ public abstract class MultikTensorAlgebra<T, A : Ring<T>>(
require(left.shape.contentEquals(right.shape)) { "ND array shape mismatch" } //TODO replace by ShapeMismatchException
val leftArray = left.asMultik().array
val rightArray = right.asMultik().array
val data = initMemoryView<T>(leftArray.size, type)
val data = initMemoryView<T>(leftArray.size, dataType)
var counter = 0
val leftIterator = leftArray.iterator()
val rightIterator = rightArray.iterator()
@ -114,7 +114,7 @@ public abstract class MultikTensorAlgebra<T, A : Ring<T>>(
public fun StructureND<T>.asMultik(): MultikTensor<T> = if (this is MultikTensor) {
this
} else {
val res = mk.zeros<T, DN>(shape.asArray(), type).asDNArray()
val res = mk.zeros<T, DN>(shape.asArray(), dataType).asDNArray()
for (index in res.multiIndices) {
res[index] = this[index]
}
@ -296,7 +296,7 @@ public abstract class MultikDivisionTensorAlgebra<T, A : Field<T>>(
@OptIn(UnsafeKMathAPI::class)
override fun T.div(arg: StructureND<T>): MultikTensor<T> =
Multik.ones<T, DN>(arg.shape.asArray(), type).apply { divAssign(arg.asMultik().array) }.wrap()
Multik.ones<T, DN>(arg.shape.asArray(), dataType).apply { divAssign(arg.asMultik().array) }.wrap()
override fun StructureND<T>.div(arg: T): MultikTensor<T> =
asMultik().array.div(arg).wrap()

51
kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/FunctionOptimization.kt
View File

@ -9,20 +9,21 @@ import space.kscience.attributes.*
import space.kscience.kmath.expressions.DifferentiableExpression
import space.kscience.kmath.expressions.Symbol
public class OptimizationValue<T>(public val value: T) : OptimizationFeature {
override fun toString(): String = "Value($value)"
}
public class OptimizationValue<V>(type: SafeType<V>) : PolymorphicAttribute<V>(type)
public enum class FunctionOptimizationTarget {
public enum class OptimizationDirection {
MAXIMIZE,
MINIMIZE
}
public object FunctionOptimizationTarget: OptimizationAttribute<OptimizationDirection>
public class FunctionOptimization<T>(
override val attributes: Attributes,
public val expression: DifferentiableExpression<T>,
override val attributes: Attributes,
) : OptimizationProblem<T> {
override val type: SafeType<T> get() = expression.type
override fun equals(other: Any?): Boolean {
if (this === other) return true
@ -47,36 +48,52 @@ public class FunctionOptimization<T>(
public companion object
}
public fun <T> FunctionOptimization(
expression: DifferentiableExpression<T>,
attributeBuilder: AttributesBuilder<FunctionOptimization<T>>.() -> Unit,
): FunctionOptimization<T> = FunctionOptimization(expression, Attributes(attributeBuilder))
public class OptimizationPrior<T>(type: SafeType<T>):
public class OptimizationPrior<T> :
PolymorphicAttribute<DifferentiableExpression<T>>(safeTypeOf()),
Attribute<DifferentiableExpression<T>>
//public val <T> FunctionOptimization.Companion.Optimization get() =
public fun <T> FunctionOptimization<T>.withFeatures(
vararg newFeature: OptimizationFeature,
public fun <T> FunctionOptimization<T>.withAttributes(
modifier: AttributesBuilder<FunctionOptimization<T>>.() -> Unit,
): FunctionOptimization<T> = FunctionOptimization(
attributes.with(*newFeature),
expression,
attributes.modify(modifier),
)
/**
* Optimizes differentiable expression using specific [optimizer] form given [startingPoint].
*/
public suspend fun <T : Any> DifferentiableExpression<T>.optimizeWith(
public suspend fun <T> DifferentiableExpression<T>.optimizeWith(
optimizer: Optimizer<T, FunctionOptimization<T>>,
startingPoint: Map<Symbol, T>,
vararg features: OptimizationFeature,
modifier: AttributesBuilder<FunctionOptimization<T>>.() -> Unit = {},
): FunctionOptimization<T> {
val problem = FunctionOptimization<T>(FeatureSet.of(OptimizationStartPoint(startingPoint), *features), this)
val problem = FunctionOptimization(this){
startAt(startingPoint)
modifier()
}
return optimizer.optimize(problem)
}
public val <T> FunctionOptimization<T>.resultValueOrNull: T?
get() = getFeature<OptimizationResult<T>>()?.point?.let { expression(it) }
get() = attributes[OptimizationResult<T>()]?.let { expression(it) }
public val <T> FunctionOptimization<T>.resultValue: T
get() = resultValueOrNull ?: error("Result is not present in $this")
public suspend fun <T> DifferentiableExpression<T>.optimizeWith(
optimizer: Optimizer<T, FunctionOptimization<T>>,
vararg startingPoint: Pair<Symbol, T>,
builder: AttributesBuilder<FunctionOptimization<T>>.() -> Unit = {},
): FunctionOptimization<T> {
val problem = FunctionOptimization<T>(this) {
startAt(mapOf(*startingPoint))
builder()
}
return optimizer.optimize(problem)
}

96
kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/OptimizationBuilder.kt
View File

@ -1,96 +0,0 @@
/*
* Copyright 2018-2022 KMath contributors.
* Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/
package space.kscience.kmath.optimization
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.data.XYColumnarData
import space.kscience.kmath.expressions.DifferentiableExpression
import space.kscience.kmath.expressions.Symbol
import space.kscience.kmath.misc.FeatureSet
public abstract class OptimizationBuilder<T, R : OptimizationProblem<T>> {
public val features: MutableList<OptimizationFeature> = ArrayList()
public fun addFeature(feature: OptimizationFeature) {
features.add(feature)
}
public inline fun <reified T : OptimizationFeature> updateFeature(update: (T?) -> T) {
val existing = features.find { it.key == T::class } as? T
val new = update(existing)
if (existing != null) {
features.remove(existing)
}
addFeature(new)
}
public abstract fun build(): R
}
public fun <T> OptimizationBuilder<T, *>.startAt(startingPoint: Map<Symbol, T>) {
addFeature(OptimizationStartPoint(startingPoint))
}
public class FunctionOptimizationBuilder<T>(
private val expression: DifferentiableExpression<T>,
) : OptimizationBuilder<T, FunctionOptimization<T>>() {
override fun build(): FunctionOptimization<T> = FunctionOptimization(FeatureSet.of(features), expression)
}
public fun <T> FunctionOptimization(
expression: DifferentiableExpression<T>,
builder: FunctionOptimizationBuilder<T>.() -> Unit,
): FunctionOptimization<T> = FunctionOptimizationBuilder(expression).apply(builder).build()
public suspend fun <T> DifferentiableExpression<T>.optimizeWith(
optimizer: Optimizer<T, FunctionOptimization<T>>,
startingPoint: Map<Symbol, T>,
builder: FunctionOptimizationBuilder<T>.() -> Unit = {},
): FunctionOptimization<T> {
val problem = FunctionOptimization<T>(this) {
startAt(startingPoint)
builder()
}
return optimizer.optimize(problem)
}
public suspend fun <T> DifferentiableExpression<T>.optimizeWith(
optimizer: Optimizer<T, FunctionOptimization<T>>,
vararg startingPoint: Pair<Symbol, T>,
builder: FunctionOptimizationBuilder<T>.() -> Unit = {},
): FunctionOptimization<T> {
val problem = FunctionOptimization<T>(this) {
startAt(mapOf(*startingPoint))
builder()
}
return optimizer.optimize(problem)
}
@OptIn(UnstableKMathAPI::class)
public class XYOptimizationBuilder(
public val data: XYColumnarData<Double, Double, Double>,
public val model: DifferentiableExpression<Double>,
) : OptimizationBuilder<Double, XYFit>() {
public var pointToCurveDistance: PointToCurveDistance = PointToCurveDistance.byY
public var pointWeight: PointWeight = PointWeight.byYSigma
override fun build(): XYFit = XYFit(
data,
model,
FeatureSet.of(features),
pointToCurveDistance,
pointWeight
)
}
@OptIn(UnstableKMathAPI::class)
public fun XYOptimization(
data: XYColumnarData<Double, Double, Double>,
model: DifferentiableExpression<Double>,
builder: XYOptimizationBuilder.() -> Unit,
): XYFit = XYOptimizationBuilder(data, model).apply(builder).build()

61
kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/OptimizationProblem.kt
View File

@ -6,64 +6,53 @@
package space.kscience.kmath.optimization
import space.kscience.attributes.*
import space.kscience.kmath.expressions.DifferentiableExpression
import space.kscience.kmath.expressions.NamedMatrix
import space.kscience.kmath.expressions.Symbol
import space.kscience.kmath.misc.*
import kotlin.reflect.KClass
import space.kscience.kmath.misc.Loggable
public interface OptimizationAttribute<T>: Attribute<T>
public interface OptimizationAttribute<T> : Attribute<T>
public interface OptimizationProblem<T> : AttributeContainer
public interface OptimizationProblem<T> : AttributeContainer, WithType<T>
public inline fun <reified F : OptimizationFeature> OptimizationProblem<*>.getFeature(): F? = getFeature(F::class)
public open class OptimizationStartPoint<T>(public val point: Map<Symbol, T>) : OptimizationFeature {
override fun toString(): String = "StartPoint($point)"
}
/**
* Covariance matrix for
*/
public class OptimizationCovariance<T>(public val covariance: NamedMatrix<T>) : OptimizationFeature {
override fun toString(): String = "Covariance($covariance)"
}
public class OptimizationStartPoint<T> : OptimizationAttribute<Map<Symbol, T>>,
PolymorphicAttribute<Map<Symbol, T>>(safeTypeOf())
/**
* Get the starting point for optimization. Throws error if not defined.
*/
public val <T> OptimizationProblem<T>.startPoint: Map<Symbol, T>
get() = getFeature<OptimizationStartPoint<T>>()?.point
?: error("Starting point not defined in $this")
get() = attributes[OptimizationStartPoint()] ?: error("Starting point not defined in $this")
public open class OptimizationResult<T>(public val point: Map<Symbol, T>) : OptimizationFeature {
override fun toString(): String = "Result($point)"
public fun <T> AttributesBuilder<OptimizationProblem<T>>.startAt(startingPoint: Map<Symbol, T>) {
set(::OptimizationStartPoint, startingPoint)
}
public val <T> OptimizationProblem<T>.resultPointOrNull: Map<Symbol, T>?
get() = getFeature<OptimizationResult<T>>()?.point
public val <T> OptimizationProblem<T>.resultPoint: Map<Symbol, T>
get() = resultPointOrNull ?: error("Result is not present in $this")
/**
* Covariance matrix for optimization
*/
public class OptimizationCovariance<T> : OptimizationAttribute<NamedMatrix<T>>,
PolymorphicAttribute<NamedMatrix<T>>(safeTypeOf())
public class OptimizationLog(private val loggable: Loggable) : Loggable by loggable, OptimizationFeature {
override fun toString(): String = "Log($loggable)"
}
public class OptimizationResult<T>() : OptimizationAttribute<Map<Symbol, T>>,
PolymorphicAttribute<Map<Symbol, T>>(safeTypeOf())
public val <T> OptimizationProblem<T>.resultOrNull: Map<Symbol, T>? get() = attributes[OptimizationResult()]
public val <T> OptimizationProblem<T>.result: Map<Symbol, T>
get() = resultOrNull ?: error("Result is not present in $this")
public object OptimizationLog : OptimizationAttribute<Loggable>
/**
* Free parameters of the optimization
*/
public class OptimizationParameters(public val symbols: List<Symbol>) : OptimizationFeature {
public constructor(vararg symbols: Symbol) : this(listOf(*symbols))
override fun toString(): String = "Parameters($symbols)"
}
public object OptimizationParameters : OptimizationAttribute<List<Symbol>>
/**
* Maximum allowed number of iterations
*/
public class OptimizationIterations(public val maxIterations: Int) : OptimizationFeature {
override fun toString(): String = "Iterations($maxIterations)"
}
public object OptimizationIterations : OptimizationAttribute<Int>

27
kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/QowOptimizer.kt
View File

@ -16,13 +16,7 @@ import space.kscience.kmath.structures.Float64Buffer
import kotlin.math.abs
public class QowRuns(public val runs: Int) : OptimizationFeature {
init {
require(runs >= 1) { "Number of runs must be more than zero" }
}
override fun toString(): String = "QowRuns(runs=$runs)"
}
public object QowRuns: OptimizationAttribute<Int>
/**
@ -69,7 +63,7 @@ public object QowOptimizer : Optimizer<Double, XYFit> {
}
val prior: DifferentiableExpression<Double>?
get() = problem.getFeature<OptimizationPrior<Double>>()?.withDefaultArgs(allParameters)
get() = problem.attributes[OptimizationPrior<Double>()]?.withDefaultArgs(allParameters)
override fun toString(): String = freeParameters.toString()
}
@ -176,7 +170,7 @@ public object QowOptimizer : Optimizer<Double, XYFit> {
fast: Boolean = false,
): QoWeight {
val logger = problem.getFeature<OptimizationLog>()
val logger = problem.attributes[OptimizationLog]
var dis: Double //discrepancy value
@ -231,7 +225,7 @@ public object QowOptimizer : Optimizer<Double, XYFit> {
}
private fun QoWeight.covariance(): NamedMatrix<Double> {
val logger = problem.getFeature<OptimizationLog>()
val logger = problem.attributes[OptimizationLog]
logger?.log {
"""
@ -257,11 +251,11 @@ public object QowOptimizer : Optimizer<Double, XYFit> {
}
override suspend fun optimize(problem: XYFit): XYFit {
val qowRuns = problem.getFeature<QowRuns>()?.runs ?: 2
val iterations = problem.getFeature<OptimizationIterations>()?.maxIterations ?: 50
val qowRuns = problem.attributes[QowRuns] ?: 2
val iterations = problem.attributes[OptimizationIterations] ?: 50
val freeParameters: Map<Symbol, Double> = problem.getFeature<OptimizationParameters>()?.let { op ->
problem.startPoint.filterKeys { it in op.symbols }
val freeParameters: Map<Symbol, Double> = problem.attributes[OptimizationParameters]?.let { symbols ->
problem.startPoint.filterKeys { it in symbols }
} ?: problem.startPoint
var qow = QoWeight(problem, freeParameters)
@ -271,6 +265,9 @@ public object QowOptimizer : Optimizer<Double, XYFit> {
res = qow.newtonianRun(maxSteps = iterations)
}
val covariance = res.covariance()
return res.problem.withFeature(OptimizationResult(res.freeParameters), OptimizationCovariance(covariance))
return res.problem.withAttributes {
set(OptimizationResult(), res.freeParameters)
set(OptimizationCovariance(), covariance)
}
}
}

64
kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/XYFit.kt
View File

@ -2,37 +2,41 @@
* Copyright 2018-2022 KMath contributors.
* Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/
@file:OptIn(UnstableKMathAPI::class)
@file:OptIn(UnstableKMathAPI::class, UnstableKMathAPI::class)
package space.kscience.kmath.optimization
import space.kscience.attributes.*
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.data.XYColumnarData
import space.kscience.kmath.data.indices
import space.kscience.kmath.expressions.*
import space.kscience.kmath.misc.FeatureSet
import space.kscience.kmath.misc.Loggable
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.ExtendedField
import space.kscience.kmath.operations.Float64Field
import space.kscience.kmath.operations.bindSymbol
import kotlin.math.pow
/**
* Specify the way to compute distance from point to the curve as DifferentiableExpression
*/
public interface PointToCurveDistance : OptimizationFeature {
public interface PointToCurveDistance {
public fun distance(problem: XYFit, index: Int): DifferentiableExpression<Double>
public companion object {
public companion object : OptimizationAttribute<PointToCurveDistance> {
public val byY: PointToCurveDistance = object : PointToCurveDistance {
override fun distance(problem: XYFit, index: Int): DifferentiableExpression<Double> {
val x = problem.data.x[index]
val y = problem.data.y[index]
return object : DifferentiableExpression<Double> {
override val type: SafeType<Double> get() = DoubleField.type
override fun derivativeOrNull(
symbols: List<Symbol>,
): Expression<Double>? = problem.model.derivativeOrNull(symbols)?.let { derivExpression ->
Expression { arguments ->
Expression(DoubleField.type) { arguments ->
derivExpression.invoke(arguments + (Symbol.x to x))
}
}
@ -51,18 +55,21 @@ public interface PointToCurveDistance : OptimizationFeature {
* Compute a wight of the point. The more the weight, the more impact this point will have on the fit.
* By default, uses Dispersion^-1
*/
public interface PointWeight : OptimizationFeature {
public interface PointWeight {
public fun weight(problem: XYFit, index: Int): DifferentiableExpression<Double>
public companion object {
public companion object : OptimizationAttribute<PointWeight> {
public fun bySigma(sigmaSymbol: Symbol): PointWeight = object : PointWeight {
override fun weight(problem: XYFit, index: Int): DifferentiableExpression<Double> =
object : DifferentiableExpression<Double> {
override val type: SafeType<Double> get() = DoubleField.type
override fun invoke(arguments: Map<Symbol, Double>): Double {
return problem.data[sigmaSymbol]?.get(index)?.pow(-2) ?: 1.0
}
override fun derivativeOrNull(symbols: List<Symbol>): Expression<Double> = Expression { 0.0 }
override fun derivativeOrNull(symbols: List<Symbol>): Expression<Double> =
Expression(DoubleField.type) { 0.0 }
}
override fun toString(): String = "PointWeightBySigma($sigmaSymbol)"
@ -79,41 +86,52 @@ public interface PointWeight : OptimizationFeature {
public class XYFit(
public val data: XYColumnarData<Double, Double, Double>,
public val model: DifferentiableExpression<Double>,
override val attributes: FeatureSet<OptimizationFeature>,
override val attributes: Attributes,
internal val pointToCurveDistance: PointToCurveDistance = PointToCurveDistance.byY,
internal val pointWeight: PointWeight = PointWeight.byYSigma,
public val xSymbol: Symbol = Symbol.x,
) : OptimizationProblem<Double> {
override val type: SafeType<Double> get() = Float64Field.type
public fun distance(index: Int): DifferentiableExpression<Double> = pointToCurveDistance.distance(this, index)
public fun weight(index: Int): DifferentiableExpression<Double> = pointWeight.weight(this, index)
}
public fun XYFit.withFeature(vararg features: OptimizationFeature): XYFit {
return XYFit(data, model, this.attributes.with(*features), pointToCurveDistance, pointWeight)
}
public fun XYOptimization(
data: XYColumnarData<Double, Double, Double>,
model: DifferentiableExpression<Double>,
builder: AttributesBuilder<XYFit>.() -> Unit,
): XYFit = XYFit(data, model, Attributes(builder))
public fun XYFit.withAttributes(
modifier: AttributesBuilder<XYFit>.() -> Unit,
): XYFit = XYFit(data, model, attributes.modify(modifier), pointToCurveDistance, pointWeight, xSymbol)
public suspend fun XYColumnarData<Double, Double, Double>.fitWith(
optimizer: Optimizer<Double, XYFit>,
modelExpression: DifferentiableExpression<Double>,
startingPoint: Map<Symbol, Double>,
vararg features: OptimizationFeature = emptyArray(),
attributes: Attributes = Attributes.EMPTY,
xSymbol: Symbol = Symbol.x,
pointToCurveDistance: PointToCurveDistance = PointToCurveDistance.byY,
pointWeight: PointWeight = PointWeight.byYSigma,
): XYFit {
var actualFeatures = FeatureSet.of(*features, OptimizationStartPoint(startingPoint))
if (actualFeatures.getFeature<OptimizationLog>() == null) {
actualFeatures = actualFeatures.with(OptimizationLog(Loggable.console))
}
val problem = XYFit(
this,
modelExpression,
actualFeatures,
attributes.modify<XYFit> {
set(::OptimizationStartPoint, startingPoint)
if (!hasAny<OptimizationLog>()) {
set(OptimizationLog, Loggable.console)
}
},
pointToCurveDistance,
pointWeight,
xSymbol
xSymbol,
)
return optimizer.optimize(problem)
}
@ -125,7 +143,7 @@ public suspend fun <I : Any, A> XYColumnarData<Double, Double, Double>.fitWith(
optimizer: Optimizer<Double, XYFit>,
processor: AutoDiffProcessor<Double, I, A>,
startingPoint: Map<Symbol, Double>,
vararg features: OptimizationFeature = emptyArray(),
attributes: Attributes = Attributes.EMPTY,
xSymbol: Symbol = Symbol.x,
pointToCurveDistance: PointToCurveDistance = PointToCurveDistance.byY,
pointWeight: PointWeight = PointWeight.byYSigma,
@ -140,7 +158,7 @@ public suspend fun <I : Any, A> XYColumnarData<Double, Double, Double>.fitWith(
optimizer = optimizer,
modelExpression = modelExpression,
startingPoint = startingPoint,
features = features,
attributes = attributes,
xSymbol = xSymbol,
pointToCurveDistance = pointToCurveDistance,
pointWeight = pointWeight
@ -152,7 +170,7 @@ public suspend fun <I : Any, A> XYColumnarData<Double, Double, Double>.fitWith(
*/
public val XYFit.chiSquaredOrNull: Double?
get() {
val result = startPoint + (resultPointOrNull ?: return null)
val result = startPoint + (resultOrNull ?: return null)
return data.indices.sumOf { index ->
@ -167,4 +185,4 @@ public val XYFit.chiSquaredOrNull: Double?
}
public val XYFit.dof: Int
get() = data.size - (getFeature<OptimizationParameters>()?.symbols?.size ?: startPoint.size)
get() = data.size - (attributes[OptimizationParameters]?.size ?: startPoint.size)

19
kmath-optimization/src/commonMain/kotlin/space/kscience/kmath/optimization/logLikelihood.kt
View File

@ -5,6 +5,8 @@
package space.kscience.kmath.optimization
import space.kscience.attributes.AttributesBuilder
import space.kscience.attributes.SafeType
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.data.XYColumnarData
import space.kscience.kmath.data.indices
@ -12,6 +14,7 @@ import space.kscience.kmath.expressions.DifferentiableExpression
import space.kscience.kmath.expressions.Expression
import space.kscience.kmath.expressions.Symbol
import space.kscience.kmath.expressions.derivative
import space.kscience.kmath.operations.Float64Field
import kotlin.math.PI
import kotlin.math.ln
import kotlin.math.pow
@ -22,7 +25,9 @@ private val oneOver2Pi = 1.0 / sqrt(2 * PI)
@UnstableKMathAPI
internal fun XYFit.logLikelihood(): DifferentiableExpression<Double> = object : DifferentiableExpression<Double> {
override fun derivativeOrNull(symbols: List<Symbol>): Expression<Double> = Expression { arguments ->
override val type: SafeType<Double> get() = Float64Field.type
override fun derivativeOrNull(symbols: List<Symbol>): Expression<Double> = Expression(type) { arguments ->
data.indices.sumOf { index ->
val d = distance(index)(arguments)
val weight = weight(index)(arguments)
@ -53,14 +58,18 @@ internal fun XYFit.logLikelihood(): DifferentiableExpression<Double> = object :
*/
@UnstableKMathAPI
public suspend fun Optimizer<Double, FunctionOptimization<Double>>.maximumLogLikelihood(problem: XYFit): XYFit {
val functionOptimization = FunctionOptimization(problem.attributes, problem.logLikelihood())
val result = optimize(functionOptimization.withFeatures(FunctionOptimizationTarget.MAXIMIZE))
return XYFit(problem.data, problem.model, result.attributes)
val functionOptimization = FunctionOptimization(problem.logLikelihood(), problem.attributes)
val result = optimize(
functionOptimization.withAttributes {
FunctionOptimizationTarget(OptimizationDirection.MAXIMIZE)
}
)
return XYFit(problem.data,problem.model, result.attributes)
}
@UnstableKMathAPI
public suspend fun Optimizer<Double, FunctionOptimization<Double>>.maximumLogLikelihood(
data: XYColumnarData<Double, Double, Double>,
model: DifferentiableExpression<Double>,
builder: XYOptimizationBuilder.() -> Unit,
builder: AttributesBuilder<XYFit>.() -> Unit,
): XYFit = maximumLogLikelihood(XYOptimization(data, model, builder))

4
kmath-tensors/src/commonMain/kotlin/space/kscience/kmath/tensors/core/DoubleTensor.kt
View File

@ -5,10 +5,12 @@
package space.kscience.kmath.tensors.core
import space.kscience.attributes.SafeType
import space.kscience.kmath.PerformancePitfall
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.nd.MutableStructureNDOfDouble
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.structures.*
import space.kscience.kmath.tensors.core.internal.toPrettyString
@ -88,6 +90,8 @@ public open class DoubleTensor(
final override val source: OffsetDoubleBuffer,
) : BufferedTensor<Double>(shape), MutableStructureNDOfDouble {
override val type: SafeType<Double> get() = DoubleField.type
init {
require(linearSize == source.size) { "Source buffer size must be equal tensor size" }
}

6
kmath-tensors/src/commonMain/kotlin/space/kscience/kmath/tensors/core/IntTensor.kt
View File

@ -5,8 +5,10 @@
package space.kscience.kmath.tensors.core
import space.kscience.attributes.SafeType
import space.kscience.kmath.PerformancePitfall
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.operations.IntRing
import space.kscience.kmath.structures.*
/**
@ -24,6 +26,8 @@ public class OffsetIntBuffer(
require(offset + size <= source.size) { "Maximum index must be inside source dimension" }
}
override val type: SafeType<Int> get() = IntRing.type
override fun set(index: Int, value: Int) {
require(index in 0 until size) { "Index must be in [0, size)" }
source[index + offset] = value
@ -83,6 +87,8 @@ public class IntTensor(
require(linearSize == source.size) { "Source buffer size must be equal tensor size" }
}
override val type: SafeType<Int> get() = IntRing.type
public constructor(shape: ShapeND, buffer: Int32Buffer) : this(shape, OffsetIntBuffer(buffer, 0, buffer.size))
@OptIn(PerformancePitfall::class)