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1 Commits

Author SHA1 Message Date
Iaroslav Postovalov
86b8cd1c97
Clone some APIs from DoubleTensorAlgebra to Nd4j, fix #348 2022-04-10 13:53:50 +07:00
629 changed files with 10286 additions and 23953 deletions

3
.github/CODEOWNERS vendored
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@ -1,3 +0,0 @@
@altavir
/kmath-trajectory @ESchouten

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@ -7,18 +7,26 @@ on:
jobs: jobs:
build: build:
runs-on: windows-latest strategy:
timeout-minutes: 20 matrix:
os: [ macOS-latest, windows-latest ]
runs-on: ${{matrix.os}}
timeout-minutes: 40
steps: steps:
- uses: actions/checkout@v3 - uses: actions/checkout@v3.0.0
- uses: actions/setup-java@v3.5.1 - uses: actions/setup-java@v3.0.0
with: with:
java-version: '11' java-version: 11
distribution: 'liberica' distribution: liberica
cache: 'gradle' - name: Cache konan
uses: actions/cache@v3.0.1
with:
path: ~/.konan
key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }}
restore-keys: |
${{ runner.os }}-gradle-
- name: Gradle Wrapper Validation - name: Gradle Wrapper Validation
uses: gradle/wrapper-validation-action@v1.0.4 uses: gradle/wrapper-validation-action@v1.0.4
- name: Gradle Build - uses: gradle/gradle-build-action@v2.1.5
uses: gradle/gradle-build-action@v2.4.2
with: with:
arguments: test jvmTest arguments: build

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@ -1,9 +1,8 @@
name: Dokka publication name: Dokka publication
on: on:
workflow_dispatch: push:
release: branches: [ master ]
types: [ created ]
jobs: jobs:
build: build:
@ -22,10 +21,10 @@ jobs:
key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }} key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }}
restore-keys: | restore-keys: |
${{ runner.os }}-gradle- ${{ runner.os }}-gradle-
- uses: gradle/gradle-build-action@v2.4.2 - uses: gradle/gradle-build-action@v2.1.5
with: with:
arguments: dokkaHtmlMultiModule --no-parallel arguments: dokkaHtmlMultiModule --no-parallel
- uses: JamesIves/github-pages-deploy-action@v4.3.0 - uses: JamesIves/github-pages-deploy-action@4.2.5
with: with:
branch: gh-pages branch: gh-pages
folder: build/dokka/htmlMultiModule folder: build/dokka/htmlMultiModule

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@ -15,7 +15,7 @@ jobs:
runs-on: ${{matrix.os}} runs-on: ${{matrix.os}}
steps: steps:
- uses: actions/checkout@v3.0.0 - uses: actions/checkout@v3.0.0
- uses: actions/setup-java@v3.10.0 - uses: actions/setup-java@v3.0.0
with: with:
java-version: 11 java-version: 11
distribution: liberica distribution: liberica
@ -26,25 +26,24 @@ jobs:
key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }} key: ${{ runner.os }}-gradle-${{ hashFiles('*.gradle.kts') }}
restore-keys: | restore-keys: |
${{ runner.os }}-gradle- ${{ runner.os }}-gradle-
- uses: gradle/wrapper-validation-action@v1.0.4
- name: Publish Windows Artifacts - name: Publish Windows Artifacts
if: matrix.os == 'windows-latest' if: matrix.os == 'windows-latest'
uses: gradle/gradle-build-action@v2.4.2 uses: gradle/gradle-build-action@v2.1.5
with: with:
arguments: | arguments: |
publishAllPublicationsToSpaceRepository releaseAll
-Ppublishing.targets=all -Ppublishing.enabled=true
-Ppublishing.space.user=${{ secrets.SPACE_APP_ID }} -Ppublishing.space.user=${{ secrets.SPACE_APP_ID }}
-Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }} -Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }}
- name: Publish Mac Artifacts - name: Publish Mac Artifacts
if: matrix.os == 'macOS-latest' if: matrix.os == 'macOS-latest'
uses: gradle/gradle-build-action@v2.4.2 uses: gradle/gradle-build-action@v2.1.5
with: with:
arguments: | arguments: |
publishMacosX64PublicationToSpaceRepository releaseMacosX64
publishMacosArm64PublicationToSpaceRepository releaseIosArm64
publishIosX64PublicationToSpaceRepository releaseIosX64
publishIosArm64PublicationToSpaceRepository -Ppublishing.enabled=true
publishIosSimulatorArm64PublicationToSpaceRepository
-Ppublishing.targets=all
-Ppublishing.space.user=${{ secrets.SPACE_APP_ID }} -Ppublishing.space.user=${{ secrets.SPACE_APP_ID }}
-Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }} -Ppublishing.space.token=${{ secrets.SPACE_APP_SECRET }}

8
.gitignore vendored
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@ -3,11 +3,10 @@ build/
out/ out/
.idea/ .idea/
.vscode/
.fleet/
.kotlin/
.vscode/
# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored) # Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
!gradle-wrapper.jar !gradle-wrapper.jar
@ -20,5 +19,4 @@ out/
!/.idea/copyright/ !/.idea/copyright/
!/.idea/scopes/ !/.idea/scopes/
/gradle/yarn.lock /kotlin-js-store/yarn.lock

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@ -1,7 +1,6 @@
<component name="CopyrightManager"> <component name="CopyrightManager">
<copyright> <copyright>
<option name="allowReplaceRegexp" value="Copyright \d{4}-\d{4} KMath" /> <option name="notice" value="Copyright 2018-2021 KMath contributors.&#10;Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file." />
<option name="notice" value="Copyright 2018-&amp;#36;today.year KMath contributors.&#10;Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file." /> <option name="myName" value="kmath" />
<option name="myName" value="kmath" /> </copyright>
</copyright>
</component> </component>

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@ -1,5 +1,5 @@
<component name="CopyrightManager"> <component name="CopyrightManager">
<settings> <settings default="kmath">
<module2copyright> <module2copyright>
<element module="Apply copyright" copyright="kmath" /> <element module="Apply copyright" copyright="kmath" />
</module2copyright> </module2copyright>

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@ -1,48 +1,3 @@
import kotlin.io.path.readText
val projectName = "kmath"
job("Build") { job("Build") {
//Perform only jvm tests gradlew("openjdk:11", "build")
gradlew("spc.registry.jetbrains.space/p/sci/containers/kotlin-ci:1.0.3", "test", "jvmTest")
}
job("Publish") {
startOn {
gitPush { enabled = false }
}
container("spc.registry.jetbrains.space/p/sci/containers/kotlin-ci:1.0.3") {
env["SPACE_USER"] = "{{ project:space_user }}"
env["SPACE_TOKEN"] = "{{ project:space_token }}"
kotlinScript { api ->
val spaceUser = System.getenv("SPACE_USER")
val spaceToken = System.getenv("SPACE_TOKEN")
// write the version to the build directory
api.gradlew("version")
//read the version from build file
val version = java.nio.file.Path.of("build/project-version.txt").readText()
val revisionSuffix = if (version.endsWith("SNAPSHOT")) {
"-" + api.gitRevision().take(7)
} else {
""
}
api.space().projects.automation.deployments.start(
project = api.projectIdentifier(),
targetIdentifier = TargetIdentifier.Key(projectName),
version = version + revisionSuffix,
// automatically update deployment status based on the status of a job
syncWithAutomationJob = true
)
api.gradlew(
"publishAllPublicationsToSpaceRepository",
"-Ppublishing.space.user=\"$spaceUser\"",
"-Ppublishing.space.token=\"$spaceToken\"",
)
}
}
} }

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@ -1,96 +1,7 @@
# KMath # KMath
## Unreleased ## [Unreleased]
### Added ### Added
- Metropolis-Hastings sampler
### Changed
### Deprecated
### Removed
### Fixed
### Security
## 0.4.0-dev-3 - 2024-02-18
### Added
- Reification. Explicit `SafeType` for algebras.
- Integer division algebras.
- Float32 geometries.
- New Attributes-kt module that could be used as stand-alone. It declares. type-safe attributes containers.
- Explicit `mutableStructureND` builders for mutable structures.
- `Buffer.asList()` zero-copy transformation.
- Wasm support.
- Parallel implementation of `LinearSpace` for Float64
- Parallel buffer factories
### Changed
- Buffer copy removed from API (added as an extension).
- Default naming for algebra and buffers now uses IntXX/FloatXX notation instead of Java types.
- Remove unnecessary inlines in basic algebras.
- QuaternionField -> QuaternionAlgebra and does not implement `Field` anymore since it is non-commutative
- kmath-geometry is split into `euclidean2d` and `euclidean3d`
- Features replaced with Attributes.
- Transposed refactored.
- Kmath-memory is moved on top of core.
### Deprecated
- ND4J engine
### Removed
- `asPolynomial` function due to scope pollution
- Codegend for ejml (450 lines of codegen for 1000 lines of code is too much)
### Fixed
- Median statistics
- Complex power of negative real numbers
- Add proper mutability for MutableBufferND rows and columns
- Generic Float32 and Float64 vectors are used in geometry algebras.
## 0.3.1 - 2023-04-09
### Added
- Wasm support for `memory`, `core`, `complex` and `functions` modules.
- Generic builders for `BufferND` and `MutableBufferND`
- `NamedMatrix` - matrix with symbol-based indexing
- `Expression` with default arguments
- Type-aliases for numbers like `Float64`
- Autodiff for generic algebra elements in core!
- Algebra now has an obligatory `bufferFactory` (#477).
### Changed
- Removed marker `Vector` type for geometry
- Geometry uses type-safe angles
- Tensor operations switched to prefix notation
- Row-wise and column-wise ND shapes in the core
- Shape is read-only
- Major refactor of tensors (only minor API changes)
- Kotlin 1.8.20
- `LazyStructure` `deffered` -> `async` to comply with coroutines code style
- Default `dot` operation in tensor algebra no longer support broadcasting. Instead `matmul` operation is added
to `DoubleTensorAlgebra`.
- Multik went MPP
### Removed
- Trajectory moved to https://github.com/SciProgCentre/maps-kt
- Polynomials moved to https://github.com/SciProgCentre/kmath-polynomial
## 0.3.0
### Added
- `ScaleOperations` interface - `ScaleOperations` interface
- `Field` extends `ScaleOperations` - `Field` extends `ScaleOperations`
- Basic integration API - Basic integration API
@ -108,15 +19,8 @@
- Complex power - Complex power
- Separate methods for UInt, Int and Number powers. NaN safety. - Separate methods for UInt, Int and Number powers. NaN safety.
- Tensorflow prototype - Tensorflow prototype
- `ValueAndErrorField`
- MST compilation to WASM: #286
- Jafama integration: #176
- `contentEquals` with tolerance: #364
- Compilation to TeX for MST: #254
### Changed ### Changed
- Annotations moved to `space.kscience.kmath`
- Exponential operations merged with hyperbolic functions - Exponential operations merged with hyperbolic functions
- Space is replaced by Group. Space is reserved for vector spaces. - Space is replaced by Group. Space is reserved for vector spaces.
- VectorSpace is now a vector space - VectorSpace is now a vector space
@ -144,16 +48,11 @@
- Operations -> Ops - Operations -> Ops
- Default Buffer and ND algebras are now Ops and lack neutral elements (0, 1) as well as algebra-level shapes. - Default Buffer and ND algebras are now Ops and lack neutral elements (0, 1) as well as algebra-level shapes.
- Tensor algebra takes read-only structures as input and inherits AlgebraND - Tensor algebra takes read-only structures as input and inherits AlgebraND
- `UnivariateDistribution` renamed to `Distribution1D`
- Rework of histograms.
- `UnivariateFunction` -> `Function1D`, `MultivariateFunction` -> `FunctionND`
### Deprecated ### Deprecated
- Specialized `DoubleBufferAlgebra` - Specialized `DoubleBufferAlgebra`
### Removed ### Removed
- Nearest in Domain. To be implemented in geometry package. - Nearest in Domain. To be implemented in geometry package.
- Number multiplication and division in main Algebra chain - Number multiplication and division in main Algebra chain
- `contentEquals` from Buffer. It moved to the companion. - `contentEquals` from Buffer. It moved to the companion.
@ -164,14 +63,13 @@
- Algebra elements are completely removed. Use algebra contexts instead. - Algebra elements are completely removed. Use algebra contexts instead.
### Fixed ### Fixed
- Ring inherits RingOperations, not GroupOperations - Ring inherits RingOperations, not GroupOperations
- Univariate histogram filling - Univariate histogram filling
## 0.2.0 ### Security
## [0.2.0]
### Added ### Added
- `fun` annotation for SAM interfaces in library - `fun` annotation for SAM interfaces in library
- Explicit `public` visibility for all public APIs - Explicit `public` visibility for all public APIs
- Better trigonometric and hyperbolic functions for `AutoDiffField` (https://github.com/mipt-npm/kmath/pull/140) - Better trigonometric and hyperbolic functions for `AutoDiffField` (https://github.com/mipt-npm/kmath/pull/140)
@ -191,7 +89,6 @@
- Basic Quaternion vector support in `kmath-complex`. - Basic Quaternion vector support in `kmath-complex`.
### Changed ### Changed
- Package changed from `scientifik` to `space.kscience` - Package changed from `scientifik` to `space.kscience`
- Gradle version: 6.6 -> 6.8.2 - Gradle version: 6.6 -> 6.8.2
- Minor exceptions refactor (throwing `IllegalArgumentException` by argument checks instead of `IllegalStateException`) - Minor exceptions refactor (throwing `IllegalArgumentException` by argument checks instead of `IllegalStateException`)
@ -201,7 +98,7 @@
- Full autodiff refactoring based on `Symbol` - Full autodiff refactoring based on `Symbol`
- `kmath-prob` renamed to `kmath-stat` - `kmath-prob` renamed to `kmath-stat`
- Grid generators moved to `kmath-for-real` - Grid generators moved to `kmath-for-real`
- Use `Point<Float64>` instead of specialized type in `kmath-for-real` - Use `Point<Double>` instead of specialized type in `kmath-for-real`
- Optimized dot product for buffer matrices moved to `kmath-for-real` - Optimized dot product for buffer matrices moved to `kmath-for-real`
- EjmlMatrix context is an object - EjmlMatrix context is an object
- Matrix LUP `inverse` renamed to `inverseWithLup` - Matrix LUP `inverse` renamed to `inverseWithLup`
@ -215,8 +112,9 @@
- `symbol` method in `Algebra` renamed to `bindSymbol` to avoid ambiguity - `symbol` method in `Algebra` renamed to `bindSymbol` to avoid ambiguity
- Add `out` projection to `Buffer` generic - Add `out` projection to `Buffer` generic
### Removed ### Deprecated
### Removed
- `kmath-koma` module because it doesn't support Kotlin 1.4. - `kmath-koma` module because it doesn't support Kotlin 1.4.
- Support of `legacy` JS backend (we will support only IR) - Support of `legacy` JS backend (we will support only IR)
- `toGrid` method. - `toGrid` method.
@ -225,24 +123,22 @@
- StructureND identity and equals - StructureND identity and equals
### Fixed ### Fixed
- `symbol` method in `MstExtendedField` (https://github.com/mipt-npm/kmath/pull/140) - `symbol` method in `MstExtendedField` (https://github.com/mipt-npm/kmath/pull/140)
## 0.1.4 ### Security
## [0.1.4]
### Added ### Added
- Functional Expressions API - Functional Expressions API
- Mathematical Syntax Tree, its interpreter and API - Mathematical Syntax Tree, its interpreter and API
- String to MST parser (https://github.com/mipt-npm/kmath/pull/120) - String to MST parser (https://github.com/mipt-npm/kmath/pull/120)
- MST to JVM bytecode translator (https://github.com/mipt-npm/kmath/pull/94) - MST to JVM bytecode translator (https://github.com/mipt-npm/kmath/pull/94)
- FloatBuffer (specialized MutableBuffer over FloatArray) - FloatBuffer (specialized MutableBuffer over FloatArray)
- FlaggedBuffer to associate primitive numbers buffer with flags (to mark values infinite or missing, etc.) - FlaggedBuffer to associate primitive numbers buffer with flags (to mark values infinite or missing, etc.)
- Specialized builder functions for all primitive buffers - Specialized builder functions for all primitive buffers like `IntBuffer(25) { it + 1 }` (https://github.com/mipt-npm/kmath/pull/125)
like `IntBuffer(25) { it + 1 }` (https://github.com/mipt-npm/kmath/pull/125)
- Interface `NumericAlgebra` where `number` operation is available to convert numbers to algebraic elements - Interface `NumericAlgebra` where `number` operation is available to convert numbers to algebraic elements
- Inverse trigonometric functions support in - Inverse trigonometric functions support in ExtendedField (`asin`, `acos`, `atan`) (https://github.com/mipt-npm/kmath/pull/114)
ExtendedField (`asin`, `acos`, `atan`) (https://github.com/mipt-npm/kmath/pull/114)
- New space extensions: `average` and `averageWith` - New space extensions: `average` and `averageWith`
- Local coding conventions - Local coding conventions
- Geometric Domains API in `kmath-core` - Geometric Domains API in `kmath-core`
@ -251,12 +147,10 @@
- Norm support for `Complex` - Norm support for `Complex`
### Changed ### Changed
- `readAsMemory` now has `throws IOException` in JVM signature. - `readAsMemory` now has `throws IOException` in JVM signature.
- Several functions taking functional types were made `inline`. - Several functions taking functional types were made `inline`.
- Several functions taking functional types now have `callsInPlace` contracts. - Several functions taking functional types now have `callsInPlace` contracts.
- BigInteger and BigDecimal algebra: JBigDecimalField has companion object with default math context; minor - BigInteger and BigDecimal algebra: JBigDecimalField has companion object with default math context; minor optimizations
optimizations
- `power(T, Int)` extension function has preconditions and supports `Field<T>` - `power(T, Int)` extension function has preconditions and supports `Field<T>`
- Memory objects have more preconditions (overflow checking) - Memory objects have more preconditions (overflow checking)
- `tg` function is renamed to `tan` (https://github.com/mipt-npm/kmath/pull/114) - `tg` function is renamed to `tan` (https://github.com/mipt-npm/kmath/pull/114)
@ -264,7 +158,6 @@
- Moved probability distributions to commons-rng and to `kmath-prob` - Moved probability distributions to commons-rng and to `kmath-prob`
### Fixed ### Fixed
- Missing copy method in Memory implementation on JS (https://github.com/mipt-npm/kmath/pull/106) - Missing copy method in Memory implementation on JS (https://github.com/mipt-npm/kmath/pull/106)
- D3.dim value in `kmath-dimensions` - D3.dim value in `kmath-dimensions`
- Multiplication in integer rings in `kmath-core` (https://github.com/mipt-npm/kmath/pull/101) - Multiplication in integer rings in `kmath-core` (https://github.com/mipt-npm/kmath/pull/101)

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@ -1,6 +1,6 @@
[![JetBrains Research](https://jb.gg/badges/research.svg)](https://confluence.jetbrains.com/display/ALL/JetBrains+on+GitHub) [![JetBrains Research](https://jb.gg/badges/research.svg)](https://confluence.jetbrains.com/display/ALL/JetBrains+on+GitHub)
[![DOI](https://zenodo.org/badge/129486382.svg)](https://zenodo.org/badge/latestdoi/129486382) [![DOI](https://zenodo.org/badge/129486382.svg)](https://zenodo.org/badge/latestdoi/129486382)
![Gradle build](https://github.com/SciProgCentre/kmath/workflows/Gradle%20build/badge.svg) ![Gradle build](https://github.com/mipt-npm/kmath/workflows/Gradle%20build/badge.svg)
[![Maven Central](https://img.shields.io/maven-central/v/space.kscience/kmath-core.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22space.kscience%22) [![Maven Central](https://img.shields.io/maven-central/v/space.kscience/kmath-core.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22space.kscience%22)
[![Space](https://img.shields.io/badge/dynamic/xml?color=orange&label=Space&query=//metadata/versioning/latest&url=https%3A%2F%2Fmaven.pkg.jetbrains.space%2Fmipt-npm%2Fp%2Fsci%2Fmaven%2Fspace%2Fkscience%2Fkmath-core%2Fmaven-metadata.xml)](https://maven.pkg.jetbrains.space/mipt-npm/p/sci/maven/space/kscience/) [![Space](https://img.shields.io/badge/dynamic/xml?color=orange&label=Space&query=//metadata/versioning/latest&url=https%3A%2F%2Fmaven.pkg.jetbrains.space%2Fmipt-npm%2Fp%2Fsci%2Fmaven%2Fspace%2Fkscience%2Fkmath-core%2Fmaven-metadata.xml)](https://maven.pkg.jetbrains.space/mipt-npm/p/sci/maven/space/kscience/)
@ -11,22 +11,18 @@ analog to Python's NumPy library. Later we found that kotlin is much more flexib
architecture designs. In contrast to `numpy` and `scipy` it is modular and has a lightweight core. The `numpy`-like architecture designs. In contrast to `numpy` and `scipy` it is modular and has a lightweight core. The `numpy`-like
experience could be achieved with [kmath-for-real](/kmath-for-real) extension module. experience could be achieved with [kmath-for-real](/kmath-for-real) extension module.
[Documentation site](https://SciProgCentre.github.io/kmath/) [Documentation site (**WIP**)](https://mipt-npm.github.io/kmath/)
## Publications and talks ## Publications and talks
* [A conceptual article about context-oriented design](https://proandroiddev.com/an-introduction-context-oriented-programming-in-kotlin-2e79d316b0a2) * [A conceptual article about context-oriented design](https://proandroiddev.com/an-introduction-context-oriented-programming-in-kotlin-2e79d316b0a2)
* [Another article about context-oriented design](https://proandroiddev.com/diving-deeper-into-context-oriented-programming-in-kotlin-3ecb4ec38814) * [Another article about context-oriented design](https://proandroiddev.com/diving-deeper-into-context-oriented-programming-in-kotlin-3ecb4ec38814)
* [ACAT 2019 conference paper](https://aip.scitation.org/doi/abs/10.1063/1.5130103) * [ACAT 2019 conference paper](https://aip.scitation.org/doi/abs/10.1063/1.5130103)
* [A talk at KotlinConf 2019 about using kotlin for science](https://youtu.be/LI_5TZ7tnOE?si=4LknX41gl_YeUbIe)
* [A talk on architecture at Joker-2021 (in Russian)](https://youtu.be/1bZ2doHiRRM?si=9w953ro9yu98X_KJ)
* [The same talk in English](https://youtu.be/yP5DIc2fVwQ?si=louZzQ1dcXV6gP10)
* [A seminar on tensor API](https://youtu.be/0H99wUs0xTM?si=6c__04jrByFQtVpo)
# Goal # Goal
* Provide a flexible and powerful API to work with mathematics abstractions in Kotlin-multiplatform (JVM, JS, Native and * Provide a flexible and powerful API to work with mathematics abstractions in Kotlin-multiplatform (JVM, JS and Native)
Wasm). .
* Provide basic multiplatform implementations for those abstractions (without significant performance optimization). * Provide basic multiplatform implementations for those abstractions (without significant performance optimization).
* Provide bindings and wrappers with those abstractions for popular optimized platform libraries. * Provide bindings and wrappers with those abstractions for popular optimized platform libraries.
@ -48,7 +44,7 @@ module definitions below. The module stability could have the following levels:
* **PROTOTYPE**. On this level there are no compatibility guarantees. All methods and classes form those modules could * **PROTOTYPE**. On this level there are no compatibility guarantees. All methods and classes form those modules could
break any moment. You can still use it, but be sure to fix the specific version. break any moment. You can still use it, but be sure to fix the specific version.
* **EXPERIMENTAL**. The general API is decided, but some changes could be made. Volatile API is marked * **EXPERIMENTAL**. The general API is decided, but some changes could be made. Volatile API is marked
with `@UnstableKMathAPI` or other stability warning annotations. with `@UnstableKmathAPI` or other stability warning annotations.
* **DEVELOPMENT**. API breaking generally follows semantic versioning ideology. There could be changes in minor * **DEVELOPMENT**. API breaking generally follows semantic versioning ideology. There could be changes in minor
versions, but not in patch versions. API is protected versions, but not in patch versions. API is protected
with [binary-compatibility-validator](https://github.com/Kotlin/binary-compatibility-validator) tool. with [binary-compatibility-validator](https://github.com/Kotlin/binary-compatibility-validator) tool.
@ -57,21 +53,19 @@ module definitions below. The module stability could have the following levels:
## Modules ## Modules
### [attributes-kt](attributes-kt)
> An API and basic implementation for arranging objects in a continuous memory block.
>
> **Maturity**: DEVELOPMENT
### [benchmarks](benchmarks) ### [benchmarks](benchmarks)
> >
>
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
### [examples](examples) ### [examples](examples)
> >
>
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
### [kmath-ast](kmath-ast) ### [kmath-ast](kmath-ast)
> >
>
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
> >
> **Features:** > **Features:**
@ -82,7 +76,7 @@ module definitions below. The module stability could have the following levels:
### [kmath-commons](kmath-commons) ### [kmath-commons](kmath-commons)
> Commons math binding for kmath >
> >
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
@ -92,8 +86,8 @@ module definitions below. The module stability could have the following levels:
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
> >
> **Features:** > **Features:**
> - [complex](kmath-complex/src/commonMain/kotlin/space/kscience/kmath/complex/Complex.kt) : Complex numbers operations > - [complex](kmath-complex/src/commonMain/kotlin/space/kscience/kmath/complex/Complex.kt) : Complex Numbers
> - [quaternion](kmath-complex/src/commonMain/kotlin/space/kscience/kmath/complex/Quaternion.kt) : Quaternions and their composition > - [quaternion](kmath-complex/src/commonMain/kotlin/space/kscience/kmath/complex/Quaternion.kt) : Quaternions
### [kmath-core](kmath-core) ### [kmath-core](kmath-core)
@ -111,20 +105,21 @@ objects to the expression by providing a context. Expressions can be used for a
performance calculations to code generation. performance calculations to code generation.
> - [domains](kmath-core/src/commonMain/kotlin/space/kscience/kmath/domains) : Domains > - [domains](kmath-core/src/commonMain/kotlin/space/kscience/kmath/domains) : Domains
> - [autodiff](kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/SimpleAutoDiff.kt) : Automatic differentiation > - [autodiff](kmath-core/src/commonMain/kotlin/space/kscience/kmath/expressions/SimpleAutoDiff.kt) : Automatic differentiation
> - [Parallel linear algebra](kmath-core/#) : Parallel implementation for `LinearAlgebra`
### [kmath-coroutines](kmath-coroutines) ### [kmath-coroutines](kmath-coroutines)
> >
>
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
### [kmath-dimensions](kmath-dimensions) ### [kmath-dimensions](kmath-dimensions)
> A proof of concept module for adding type-safe dimensions to structures >
> >
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
### [kmath-ejml](kmath-ejml) ### [kmath-ejml](kmath-ejml)
> >
>
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
> >
> **Features:** > **Features:**
@ -147,7 +142,7 @@ One can still use generic algebras though.
### [kmath-functions](kmath-functions) ### [kmath-functions](kmath-functions)
> Functions, integration and interpolation >
> >
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
> >
@ -161,16 +156,18 @@ One can still use generic algebras though.
### [kmath-geometry](kmath-geometry) ### [kmath-geometry](kmath-geometry)
> >
>
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
### [kmath-histograms](kmath-histograms) ### [kmath-histograms](kmath-histograms)
> >
>
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
### [kmath-jafama](kmath-jafama) ### [kmath-jafama](kmath-jafama)
> Jafama integration module
> >
> **Maturity**: DEPRECATED >
> **Maturity**: PROTOTYPE
> >
> **Features:** > **Features:**
> - [jafama-double](kmath-jafama/src/main/kotlin/space/kscience/kmath/jafama/) : Double ExtendedField implementations based on Jafama > - [jafama-double](kmath-jafama/src/main/kotlin/space/kscience/kmath/jafama/) : Double ExtendedField implementations based on Jafama
@ -178,10 +175,11 @@ One can still use generic algebras though.
### [kmath-jupyter](kmath-jupyter) ### [kmath-jupyter](kmath-jupyter)
> >
>
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
### [kmath-kotlingrad](kmath-kotlingrad) ### [kmath-kotlingrad](kmath-kotlingrad)
> Kotlin∇ integration module >
> >
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
> >
@ -196,14 +194,14 @@ One can still use generic algebras though.
> **Maturity**: DEVELOPMENT > **Maturity**: DEVELOPMENT
### [kmath-multik](kmath-multik) ### [kmath-multik](kmath-multik)
> JetBrains Multik connector >
> >
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
### [kmath-nd4j](kmath-nd4j) ### [kmath-nd4j](kmath-nd4j)
> ND4J NDStructure implementation and according NDAlgebra classes
> >
> **Maturity**: DEPRECATED >
> **Maturity**: EXPERIMENTAL
> >
> **Features:** > **Features:**
> - [nd4jarraystructure](kmath-nd4j/#) : NDStructure wrapper for INDArray > - [nd4jarraystructure](kmath-nd4j/#) : NDStructure wrapper for INDArray
@ -213,24 +211,27 @@ One can still use generic algebras though.
### [kmath-optimization](kmath-optimization) ### [kmath-optimization](kmath-optimization)
> >
>
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
### [kmath-stat](kmath-stat) ### [kmath-stat](kmath-stat)
> >
>
> **Maturity**: EXPERIMENTAL > **Maturity**: EXPERIMENTAL
### [kmath-symja](kmath-symja) ### [kmath-symja](kmath-symja)
> Symja integration module >
> >
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
### [kmath-tensorflow](kmath-tensorflow) ### [kmath-tensorflow](kmath-tensorflow)
> Google tensorflow connector >
> >
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
### [kmath-tensors](kmath-tensors) ### [kmath-tensors](kmath-tensors)
> >
>
> **Maturity**: PROTOTYPE > **Maturity**: PROTOTYPE
> >
> **Features:** > **Features:**
@ -240,13 +241,9 @@ One can still use generic algebras though.
### [kmath-viktor](kmath-viktor) ### [kmath-viktor](kmath-viktor)
> Binding for https://github.com/JetBrains-Research/viktor
> >
> **Maturity**: DEPRECATED
### [test-utils](test-utils)
> >
> **Maturity**: EXPERIMENTAL > **Maturity**: DEVELOPMENT
## Multi-platform support ## Multi-platform support
@ -254,24 +251,23 @@ One can still use generic algebras though.
KMath is developed as a multi-platform library, which means that most of the interfaces are declared in the KMath is developed as a multi-platform library, which means that most of the interfaces are declared in the
[common source sets](/kmath-core/src/commonMain) and implemented there wherever it is possible. In some cases, features [common source sets](/kmath-core/src/commonMain) and implemented there wherever it is possible. In some cases, features
are delegated to platform-specific implementations even if they could be provided in the common module for performance are delegated to platform-specific implementations even if they could be provided in the common module for performance
reasons. Currently, Kotlin/JVM is the primary platform, however, Kotlin/Native and Kotlin/JS contributions and reasons. Currently, the Kotlin/JVM is the primary platform, however Kotlin/Native and Kotlin/JS contributions and
feedback are also welcome. feedback are also welcome.
## Performance ## Performance
Calculation of performance is one of the major goals of KMath in the future, but in some cases it is impossible to Calculation performance is one of major goals of KMath in the future, but in some cases it is impossible to achieve both
achieve both
performance and flexibility. performance and flexibility.
We expect to focus on creating a convenient universal API first and then work on increasing performance for specific We expect to focus on creating convenient universal API first and then work on increasing performance for specific
cases. We expect the worst KMath benchmarks will perform better than native Python, but worse than optimized cases. We expect the worst KMath benchmarks will perform better than native Python, but worse than optimized
native/SciPy (mostly due to boxing operations on primitive numbers). The best performance of optimized parts could be native/SciPy (mostly due to boxing operations on primitive numbers). The best performance of optimized parts could be
better than SciPy. better than SciPy.
## Requirements ## Requirements
KMath currently relies on JDK 11 for compilation and execution of Kotlin-JVM part. We recommend using GraalVM-CE or KMath currently relies on JDK 11 for compilation and execution of Kotlin-JVM part. We recommend to use GraalVM-CE 11 for
Oracle GraalVM for execution to get better performance. execution to get better performance.
### Repositories ### Repositories
@ -291,10 +287,11 @@ dependencies {
} }
``` ```
Gradle `6.0+` is required for multiplatform artifacts.
## Contributing ## Contributing
The project requires a lot of additional work. The most important thing we need is feedback about what features are The project requires a lot of additional work. The most important thing we need is a feedback about what features are
required the most. Feel free to create feature requests. We are also welcome to code contributions, especially in issues required the most. Feel free to create feature requests. We are also welcome to code contributions, especially in issues
marked marked with
with [good first issue](hhttps://github.com/SciProgCentre/kmath/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22) [waiting for a hero](https://github.com/mipt-npm/kmath/labels/waiting%20for%20a%20hero) label.
label.

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@ -1,21 +0,0 @@
# Module attributes-kt
## Usage
## Artifact:
The Maven coordinates of this project are `space.kscience:attributes-kt:0.1.0`.
**Gradle Kotlin DSL:**
```kotlin
repositories {
maven("https://repo.kotlin.link")
mavenCentral()
}
dependencies {
implementation("space.kscience:attributes-kt:0.1.0")
}
```

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@ -1,104 +0,0 @@
public abstract interface class space/kscience/attributes/Attribute {
}
public abstract interface class space/kscience/attributes/AttributeContainer {
public abstract fun getAttributes ()Lspace/kscience/attributes/Attributes;
}
public abstract interface class space/kscience/attributes/AttributeScope {
}
public abstract interface class space/kscience/attributes/AttributeWithDefault : space/kscience/attributes/Attribute {
public abstract fun getDefault ()Ljava/lang/Object;
}
public abstract interface class space/kscience/attributes/Attributes {
public static final field Companion Lspace/kscience/attributes/Attributes$Companion;
public abstract fun equals (Ljava/lang/Object;)Z
public fun get (Lspace/kscience/attributes/Attribute;)Ljava/lang/Object;
public abstract fun getContent ()Ljava/util/Map;
public fun getKeys ()Ljava/util/Set;
public abstract fun hashCode ()I
public abstract fun toString ()Ljava/lang/String;
}
public final class space/kscience/attributes/Attributes$Companion {
public final fun equals (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/Attributes;)Z
public final fun getEMPTY ()Lspace/kscience/attributes/Attributes;
}
public final class space/kscience/attributes/AttributesBuilder : space/kscience/attributes/Attributes {
public final fun add (Lspace/kscience/attributes/SetAttribute;Ljava/lang/Object;)V
public final fun build ()Lspace/kscience/attributes/Attributes;
public fun equals (Ljava/lang/Object;)Z
public fun getContent ()Ljava/util/Map;
public fun hashCode ()I
public final fun invoke (Lspace/kscience/attributes/Attribute;Ljava/lang/Object;)V
public final fun put (Lspace/kscience/attributes/Attribute;Ljava/lang/Object;)V
public final fun putAll (Lspace/kscience/attributes/Attributes;)V
public final fun remove (Lspace/kscience/attributes/SetAttribute;Ljava/lang/Object;)V
public final fun set (Lspace/kscience/attributes/Attribute;Ljava/lang/Object;)V
public fun toString ()Ljava/lang/String;
}
public final class space/kscience/attributes/AttributesBuilderKt {
public static final fun Attributes (Lkotlin/jvm/functions/Function1;)Lspace/kscience/attributes/Attributes;
}
public final class space/kscience/attributes/AttributesKt {
public static final fun Attributes (Lspace/kscience/attributes/Attribute;)Lspace/kscience/attributes/Attributes;
public static final fun Attributes (Lspace/kscience/attributes/Attribute;Ljava/lang/Object;)Lspace/kscience/attributes/Attributes;
public static final fun getOrDefault (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/AttributeWithDefault;)Ljava/lang/Object;
public static final fun isEmpty (Lspace/kscience/attributes/Attributes;)Z
public static final fun modified (Lspace/kscience/attributes/Attributes;Lkotlin/jvm/functions/Function1;)Lspace/kscience/attributes/Attributes;
public static final fun plus (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/Attributes;)Lspace/kscience/attributes/Attributes;
public static final fun withAttribute (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/Attribute;)Lspace/kscience/attributes/Attributes;
public static final fun withAttribute (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/Attribute;Ljava/lang/Object;)Lspace/kscience/attributes/Attributes;
public static final fun withAttributeElement (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/SetAttribute;Ljava/lang/Object;)Lspace/kscience/attributes/Attributes;
public static final fun withoutAttribute (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/Attribute;)Lspace/kscience/attributes/Attributes;
public static final fun withoutAttributeElement (Lspace/kscience/attributes/Attributes;Lspace/kscience/attributes/SetAttribute;Ljava/lang/Object;)Lspace/kscience/attributes/Attributes;
}
public abstract interface class space/kscience/attributes/FlagAttribute : space/kscience/attributes/Attribute {
}
public abstract class space/kscience/attributes/PolymorphicAttribute : space/kscience/attributes/Attribute {
public synthetic fun <init> (Lkotlin/reflect/KType;Lkotlin/jvm/internal/DefaultConstructorMarker;)V
public fun equals (Ljava/lang/Object;)Z
public final fun getType-V0oMfBY ()Lkotlin/reflect/KType;
public fun hashCode ()I
}
public final class space/kscience/attributes/PolymorphicAttributeKt {
public static final fun get (Lspace/kscience/attributes/Attributes;Lkotlin/jvm/functions/Function0;)Ljava/lang/Object;
public static final fun set (Lspace/kscience/attributes/AttributesBuilder;Lkotlin/jvm/functions/Function0;Ljava/lang/Object;)V
}
public final class space/kscience/attributes/SafeType {
public static final synthetic fun box-impl (Lkotlin/reflect/KType;)Lspace/kscience/attributes/SafeType;
public static fun constructor-impl (Lkotlin/reflect/KType;)Lkotlin/reflect/KType;
public fun equals (Ljava/lang/Object;)Z
public static fun equals-impl (Lkotlin/reflect/KType;Ljava/lang/Object;)Z
public static final fun equals-impl0 (Lkotlin/reflect/KType;Lkotlin/reflect/KType;)Z
public final fun getKType ()Lkotlin/reflect/KType;
public fun hashCode ()I
public static fun hashCode-impl (Lkotlin/reflect/KType;)I
public fun toString ()Ljava/lang/String;
public static fun toString-impl (Lkotlin/reflect/KType;)Ljava/lang/String;
public final synthetic fun unbox-impl ()Lkotlin/reflect/KType;
}
public final class space/kscience/attributes/SafeTypeKt {
public static final fun getKClass-X0YbwmU (Lkotlin/reflect/KType;)Lkotlin/reflect/KClass;
}
public abstract interface class space/kscience/attributes/SetAttribute : space/kscience/attributes/Attribute {
}
public abstract interface annotation class space/kscience/attributes/UnstableAttributesAPI : java/lang/annotation/Annotation {
}
public abstract interface class space/kscience/attributes/WithType {
public abstract fun getType-V0oMfBY ()Lkotlin/reflect/KType;
}

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@ -1,20 +0,0 @@
plugins {
id("space.kscience.gradle.mpp")
`maven-publish`
}
version = rootProject.extra.get("attributesVersion").toString()
kscience {
jvm()
js()
native()
wasm()
}
readme {
maturity = space.kscience.gradle.Maturity.DEVELOPMENT
description = """
An API and basic implementation for arranging objects in a continuous memory block.
""".trimIndent()
}

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@ -1,29 +0,0 @@
/*
* 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
/**
* A marker interface for an attribute. Attributes are used as keys to access contents of type [T] in the container.
*/
public interface Attribute<T>
/**
* An attribute that could be either present or absent
*/
public interface FlagAttribute : Attribute<Unit>
/**
* An attribute with a default value
*/
public interface AttributeWithDefault<T> : Attribute<T> {
public val default: T
}
/**
* Attribute containing a set of values
*/
public interface SetAttribute<V> : Attribute<Set<V>>

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@ -1,20 +0,0 @@
/*
* 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
/**
* A container for [Attributes]
*/
public interface AttributeContainer {
public val attributes: Attributes
}
/**
* A scope, where attribute keys could be resolved.
* [O] is used only to resolve types in compile-time.
*/
public interface AttributeScope<O>

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@ -1,157 +0,0 @@
/*
* 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
/**
* A set of attributes. The implementation must guarantee that [content] keys correspond to their value types.
*/
public interface Attributes {
/**
* Raw content for this [Attributes]
*/
public val content: Map<out Attribute<*>, Any?>
/**
* Attribute keys contained in this [Attributes]
*/
public val keys: Set<Attribute<*>> get() = content.keys
/**
* Provide an attribute value. Return null if attribute is not present or if its value is null.
*/
@Suppress("UNCHECKED_CAST")
public operator fun <T> get(attribute: Attribute<T>): T? = content[attribute] as? T
override fun toString(): String
override fun equals(other: Any?): Boolean
override fun hashCode(): Int
public companion object {
public val EMPTY: Attributes = object : Attributes {
override val content: Map<out Attribute<*>, Any?> get() = emptyMap()
override fun toString(): String = "Attributes.EMPTY"
override fun equals(other: Any?): Boolean = (other as? Attributes)?.isEmpty() ?: false
override fun hashCode(): Int = Unit.hashCode()
}
public fun equals(a1: Attributes, a2: Attributes): Boolean =
a1.keys == a2.keys && a1.keys.all { a1[it] == a2[it] }
}
}
internal class MapAttributes(override val content: Map<out Attribute<*>, Any?>) : Attributes {
override fun toString(): String = "Attributes(value=${content.entries})"
override fun equals(other: Any?): Boolean = other is Attributes && Attributes.equals(this, other)
override fun hashCode(): Int = content.hashCode()
}
public fun Attributes.isEmpty(): Boolean = keys.isEmpty()
/**
* Get attribute value or default
*/
public fun <T> Attributes.getOrDefault(attribute: AttributeWithDefault<T>): T = get(attribute) ?: attribute.default
/**
* 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.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 <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.hasFlag(): Boolean =
content.keys.any { it is A }
/**
* Create [Attributes] with an added or replaced attribute key.
*/
public fun <T, A : Attribute<T>> Attributes.withAttribute(
attribute: A,
attrValue: T,
): Attributes = MapAttributes(content + (attribute to attrValue))
public fun <A : Attribute<Unit>> Attributes.withAttribute(attribute: A): Attributes =
withAttribute(attribute, Unit)
/**
* Create a new [Attributes] by modifying the current one
*/
public fun <O> Attributes.modified(block: AttributesBuilder<O>.() -> Unit): Attributes = Attributes<O> {
putAll(this@modified)
block()
}
/**
* Create new [Attributes] by removing [attribute] key
*/
public fun Attributes.withoutAttribute(attribute: Attribute<*>): Attributes = MapAttributes(content.minus(attribute))
/**
* Add an element to a [SetAttribute]
*/
public fun <T, A : SetAttribute<T>> Attributes.withAttributeElement(
attribute: A,
attrValue: T,
): Attributes {
val currentSet: Set<T> = get(attribute) ?: emptySet()
return MapAttributes(
content + (attribute to (currentSet + attrValue))
)
}
/**
* Remove an element from [SetAttribute]
*/
public fun <T, A : SetAttribute<T>> Attributes.withoutAttributeElement(
attribute: A,
attrValue: T,
): Attributes {
val currentSet: Set<T> = get(attribute) ?: emptySet()
return MapAttributes(content + (attribute to (currentSet - attrValue)))
}
/**
* Create [Attributes] with a single key
*/
public fun <T, A : Attribute<T>> Attributes(
attribute: A,
attrValue: T,
): Attributes = MapAttributes(mapOf(attribute to attrValue))
/**
* Create Attributes with a single [Unit] valued attribute
*/
public fun <A : Attribute<Unit>> Attributes(
attribute: A,
): Attributes = MapAttributes(mapOf(attribute to Unit))
/**
* Create a new [Attributes] that overlays [other] on top of this set of attributes. New attributes are added.
* Existing attribute keys are replaced.
*/
public operator fun Attributes.plus(other: Attributes): Attributes = when {
isEmpty() -> other
other.isEmpty() -> this
else -> MapAttributes(content + other.content)
}
/**
* Create a new [Attributes] with removed [key] (if it is present).
*/
public operator fun Attributes.minus(key: Attribute<*>): Attributes =
if (content.contains(key)) MapAttributes(content.minus(key)) else this

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@ -1,68 +0,0 @@
/*
* 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
/**
* A builder for [Attributes].
* The builder is not thread safe
*
* @param O type marker of an owner object, for which these attributes are made
*/
public class AttributesBuilder<out O> internal constructor() : Attributes {
private val map = mutableMapOf<Attribute<*>, Any?>()
override fun toString(): String = "Attributes(value=${map.entries})"
override fun equals(other: Any?): Boolean = other is Attributes && Attributes.equals(this, other)
override fun hashCode(): Int = map.hashCode()
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?) {
set(this, value)
}
public infix fun <V> Attribute<V>.put(value: V?) {
set(this, value)
}
/**
* Put all attributes for given [attributes]
*/
public fun putAll(attributes: Attributes) {
map.putAll(attributes.content)
}
public infix fun <V> SetAttribute<V>.add(attrValue: V) {
val currentSet: Set<V> = get(this) ?: emptySet()
map[this] = currentSet + attrValue
}
/**
* Remove an element from [SetAttribute]
*/
public infix fun <V> SetAttribute<V>.remove(attrValue: V) {
val currentSet: Set<V> = get(this) ?: emptySet()
map[this] = currentSet - attrValue
}
public fun build(): Attributes = MapAttributes(map)
}
/**
* Create [Attributes] with a given [builder]
* @param O the type for which attributes are built. The type is used only during compilation phase for static extension dispatch
*/
public fun <O> Attributes(builder: AttributesBuilder<O>.() -> Unit): Attributes =
AttributesBuilder<O>().apply(builder).build()

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@ -1,34 +0,0 @@
/*
* 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
*/
@UnstableAttributesAPI
public operator fun <T> Attributes.get(attributeKeyBuilder: () -> PolymorphicAttribute<T>): T? =
get(attributeKeyBuilder())
/**
* Set a polymorphic attribute using its factory
*/
@UnstableAttributesAPI
public operator fun <O, T> AttributesBuilder<O>.set(attributeKeyBuilder: () -> PolymorphicAttribute<T>, value: T) {
set(attributeKeyBuilder(), value)
}

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@ -1,35 +0,0 @@
/*
* 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
import kotlin.jvm.JvmInline
import kotlin.reflect.KClass
import kotlin.reflect.KType
import kotlin.reflect.typeOf
/**
* Safe variant ok Kotlin [KType] that ensures that the type parameter is of the same type as [kType]
*
* @param kType raw [KType]
*/
@JvmInline
public value class SafeType<out T> @PublishedApi internal constructor(public val kType: KType)
public inline fun <reified T> safeTypeOf(): SafeType<T> = SafeType(typeOf<T>())
/**
* Derive Kotlin [KClass] from this type and fail if the type is not a class (should not happen)
*/
@Suppress("UNCHECKED_CAST")
@UnstableAttributesAPI
public val <T> SafeType<T>.kClass: KClass<T & Any> get() = kType.classifier as KClass<T & Any>
/**
* An interface containing [type] for dynamic type checking.
*/
public interface WithType<out T> {
public val type: SafeType<T>
}

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@ -1,17 +0,0 @@
/*
* 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
/**
* Marks declarations that are still experimental in the Attributes-kt APIs, which means that the design of the corresponding
* declarations has open issues that may (or may not) lead to their changes in the future. Roughly speaking, there is
* a chance of those declarations will be deprecated in the future or the semantics of their behavior may change
* in some way that may break some code.
*/
@MustBeDocumented
@Retention(value = AnnotationRetention.BINARY)
@RequiresOptIn("This API is unstable and could change in future", RequiresOptIn.Level.WARNING)
public annotation class UnstableAttributesAPI

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@ -1,119 +1,4 @@
# BenchmarksResult # Module benchmarks
## Report for benchmark configuration <code>main</code>
* Run on Java HotSpot(TM) 64-Bit Server VM (build 21.0.4+8-LTS-jvmci-23.1-b41) with Java process:
```
C:\Users\altavir\scoop\apps\graalvm-oracle-21jdk\current\bin\java.exe -XX:ThreadPriorityPolicy=1 -XX:+UnlockExperimentalVMOptions -XX:+EnableJVMCIProduct -XX:-UnlockExperimentalVMOptions -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant
```
* JMH 1.21 was used in `thrpt` mode with 5 warmup iterations by 10 s and 5 measurement iterations by 10 s.
### [ArrayBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/ArrayBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`benchmarkArrayRead`|1.9E+07 &plusmn; 2.3E+05 ops/s|
|`benchmarkBufferRead`|1.4E+07 &plusmn; 8.7E+05 ops/s|
|`nativeBufferRead`|1.4E+07 &plusmn; 1.3E+06 ops/s|
### [BigIntBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/BigIntBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`jvmAdd`|5.1E+07 &plusmn; 1.3E+06 ops/s|
|`jvmAddLarge`|5.1E+04 &plusmn; 8.2E+02 ops/s|
|`jvmMultiply`|8.5E+07 &plusmn; 9.7E+06 ops/s|
|`jvmMultiplyLarge`|2.5E+02 &plusmn; 15 ops/s|
|`jvmParsing10`|8.7E+06 &plusmn; 5.1E+05 ops/s|
|`jvmParsing16`|6.4E+06 &plusmn; 1.8E+05 ops/s|
|`jvmPower`|28 &plusmn; 0.79 ops/s|
|`jvmSmallAdd`|7.0E+07 &plusmn; 4.3E+06 ops/s|
|`kmAdd`|4.8E+07 &plusmn; 2.2E+06 ops/s|
|`kmAddLarge`|3.5E+04 &plusmn; 3.7E+03 ops/s|
|`kmMultiply`|6.7E+07 &plusmn; 1.5E+07 ops/s|
|`kmMultiplyLarge`|54 &plusmn; 4.2 ops/s|
|`kmParsing10`|4.5E+06 &plusmn; 8.3E+04 ops/s|
|`kmParsing16`|4.9E+06 &plusmn; 1.1E+05 ops/s|
|`kmPower`|10 &plusmn; 0.96 ops/s|
|`kmSmallAdd`|4.1E+07 &plusmn; 5.9E+05 ops/s|
### [BufferBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/BufferBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`bufferViewReadWrite`|5.8E+06 &plusmn; 1.6E+05 ops/s|
|`bufferViewReadWriteSpecialized`|5.6E+06 &plusmn; 2.6E+05 ops/s|
|`complexBufferReadWrite`|6.6E+06 &plusmn; 2.7E+05 ops/s|
|`doubleArrayReadWrite`|7.5E+06 &plusmn; 1.0E+06 ops/s|
|`doubleBufferReadWrite`|8.0E+06 &plusmn; 6.7E+05 ops/s|
### [DotBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/DotBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`bufferedDot`|1.3 &plusmn; 0.020 ops/s|
|`cmDot`|0.47 &plusmn; 0.42 ops/s|
|`cmDotWithConversion`|0.76 &plusmn; 0.13 ops/s|
|`ejmlDot`|6.7 &plusmn; 0.091 ops/s|
|`ejmlDotWithConversion`|6.4 &plusmn; 0.82 ops/s|
|`multikDot`|40 &plusmn; 6.7 ops/s|
|`parallelDot`|12 &plusmn; 1.8 ops/s|
|`tensorDot`|1.2 &plusmn; 0.041 ops/s|
|`tfDot`|5.9 &plusmn; 0.49 ops/s|
### [ExpressionsInterpretersBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/ExpressionsInterpretersBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`asmGenericExpression`|29 &plusmn; 1.2 ops/s|
|`asmPrimitiveExpression`|43 &plusmn; 1.3 ops/s|
|`asmPrimitiveExpressionArray`|71 &plusmn; 0.38 ops/s|
|`functionalExpression`|5.6 &plusmn; 0.11 ops/s|
|`justCalculate`|69 &plusmn; 9.0 ops/s|
|`mstExpression`|7.1 &plusmn; 0.020 ops/s|
|`rawExpression`|41 &plusmn; 1.5 ops/s|
### [IntegrationBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/IntegrationBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`complexIntegration`|3.6E+03 &plusmn; 1.9E+02 ops/s|
|`doubleIntegration`|3.7E+03 &plusmn; 12 ops/s|
### [JafamaBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/JafamaBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`core`|38 &plusmn; 0.64 ops/s|
|`jafama`|52 &plusmn; 0.36 ops/s|
|`strictJafama`|52 &plusmn; 4.0 ops/s|
### [MatrixInverseBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/MatrixInverseBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`cmLUPInversion`|2.2E+03 &plusmn; 76 ops/s|
|`ejmlInverse`|1.3E+03 &plusmn; 5.7 ops/s|
|`kmathLupInversion`|9.5E+02 &plusmn; 1.8E+02 ops/s|
|`kmathParallelLupInversion`|9.1E+02 &plusmn; 1.4E+02 ops/s|
### [NDFieldBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/NDFieldBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`boxingFieldAdd`|7.7 &plusmn; 0.79 ops/s|
|`multikAdd`|6.5 &plusmn; 0.33 ops/s|
|`multikInPlaceAdd`|64 &plusmn; 0.79 ops/s|
|`specializedFieldAdd`|8.0 &plusmn; 0.090 ops/s|
|`tensorAdd`|9.2 &plusmn; 0.053 ops/s|
|`tensorInPlaceAdd`|17 &plusmn; 10 ops/s|
|`viktorAdd`|7.6 &plusmn; 1.2 ops/s|
### [ViktorBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/ViktorBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`doubleFieldAddition`|7.7 &plusmn; 0.34 ops/s|
|`rawViktor`|5.9 &plusmn; 1.1 ops/s|
|`viktorFieldAddition`|7.3 &plusmn; 1.1 ops/s|
### [ViktorLogBenchmark](src/jvmMain/kotlin/space/kscience/kmath/benchmarks/ViktorLogBenchmark.kt)
| Benchmark | Score |
|:---------:|:-----:|
|`rawViktorLog`|1.4 &plusmn; 0.076 ops/s|
|`realFieldLog`|1.3 &plusmn; 0.069 ops/s|
|`viktorFieldLog`|1.3 &plusmn; 0.032 ops/s|

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@ -1,14 +1,11 @@
import com.fasterxml.jackson.module.kotlin.jacksonObjectMapper @file:Suppress("UNUSED_VARIABLE")
import com.fasterxml.jackson.module.kotlin.readValue
import kotlinx.benchmark.gradle.BenchmarksExtension import space.kscience.kmath.benchmarks.addBenchmarkProperties
import java.time.LocalDateTime
import java.time.ZoneId
import java.util.*
plugins { plugins {
kotlin("multiplatform") kotlin("multiplatform")
alias(spclibs.plugins.kotlin.plugin.allopen) kotlin("plugin.allopen")
alias(spclibs.plugins.kotlinx.benchmark) id("org.jetbrains.kotlinx.benchmark")
} }
allOpen.annotation("org.openjdk.jmh.annotations.State") allOpen.annotation("org.openjdk.jmh.annotations.State")
@ -29,9 +26,6 @@ kotlin {
all { all {
languageSettings { languageSettings {
progressiveMode = true progressiveMode = true
optIn("kotlin.contracts.ExperimentalContracts")
optIn("kotlin.ExperimentalUnsignedTypes")
optIn("space.kscience.kmath.UnstableKMathAPI")
} }
} }
@ -45,9 +39,7 @@ kotlin {
implementation(project(":kmath-dimensions")) implementation(project(":kmath-dimensions"))
implementation(project(":kmath-for-real")) implementation(project(":kmath-for-real"))
implementation(project(":kmath-tensors")) implementation(project(":kmath-tensors"))
implementation(project(":kmath-multik")) implementation("org.jetbrains.kotlinx:kotlinx-benchmark-runtime:0.4.2")
implementation(libs.multik.default)
implementation(spclibs.kotlinx.benchmark.runtime)
} }
} }
@ -59,6 +51,7 @@ kotlin {
implementation(project(":kmath-kotlingrad")) implementation(project(":kmath-kotlingrad"))
implementation(project(":kmath-viktor")) implementation(project(":kmath-viktor"))
implementation(project(":kmath-jafama")) implementation(project(":kmath-jafama"))
implementation(project(":kmath-multik"))
implementation(projects.kmath.kmathTensorflow) implementation(projects.kmath.kmathTensorflow)
implementation("org.tensorflow:tensorflow-core-platform:0.4.0") implementation("org.tensorflow:tensorflow-core-platform:0.4.0")
implementation("org.nd4j:nd4j-native:1.0.0-M1") implementation("org.nd4j:nd4j-native:1.0.0-M1")
@ -145,137 +138,32 @@ benchmark {
commonConfiguration() commonConfiguration()
include("ViktorLogBenchmark") include("ViktorLogBenchmark")
} }
}
configurations.register("integration") { // Fix kotlinx-benchmarks bug
commonConfiguration() afterEvaluate {
include("IntegrationBenchmark") val jvmBenchmarkJar by tasks.getting(org.gradle.jvm.tasks.Jar::class) {
duplicatesStrategy = DuplicatesStrategy.EXCLUDE
} }
} }
kotlin { kotlin.sourceSets.all {
jvmToolchain(11) with(languageSettings) {
compilerOptions { optIn("kotlin.contracts.ExperimentalContracts")
optIn.addAll( optIn("kotlin.ExperimentalUnsignedTypes")
"space.kscience.kmath.UnstableKMathAPI" optIn("space.kscience.kmath.misc.UnstableKMathAPI")
)
} }
} }
tasks.withType<org.jetbrains.kotlin.gradle.dsl.KotlinJvmCompile> {
private data class JmhReport( kotlinOptions {
val jmhVersion: String, jvmTarget = "11"
val benchmark: String, freeCompilerArgs = freeCompilerArgs + "-Xjvm-default=all" + "-Xlambdas=indy"
val mode: String,
val threads: Int,
val forks: Int,
val jvm: String,
val jvmArgs: List<String>,
val jdkVersion: String,
val vmName: String,
val vmVersion: String,
val warmupIterations: Int,
val warmupTime: String,
val warmupBatchSize: Int,
val measurementIterations: Int,
val measurementTime: String,
val measurementBatchSize: Int,
val params: Map<String, String> = emptyMap(),
val primaryMetric: PrimaryMetric,
val secondaryMetrics: Map<String, SecondaryMetric>,
) {
interface Metric {
val score: Double
val scoreError: Double
val scoreConfidence: List<Double>
val scorePercentiles: Map<Double, Double>
val scoreUnit: String
} }
data class PrimaryMetric(
override val score: Double,
override val scoreError: Double,
override val scoreConfidence: List<Double>,
override val scorePercentiles: Map<Double, Double>,
override val scoreUnit: String,
val rawDataHistogram: List<List<List<List<Double>>>>? = null,
val rawData: List<List<Double>>? = null,
) : Metric
data class SecondaryMetric(
override val score: Double,
override val scoreError: Double,
override val scoreConfidence: List<Double>,
override val scorePercentiles: Map<Double, Double>,
override val scoreUnit: String,
val rawData: List<List<Double>>,
) : Metric
} }
readme { readme {
maturity = space.kscience.gradle.Maturity.EXPERIMENTAL maturity = ru.mipt.npm.gradle.Maturity.EXPERIMENTAL
val jsonMapper = jacksonObjectMapper()
fun noun(number: Number, singular: String, plural: String) = if (number.toLong() == 1L) singular else plural
extensions.findByType(BenchmarksExtension::class.java)?.configurations?.forEach { cfg ->
val propertyName =
"benchmark${cfg.name.replaceFirstChar { if (it.isLowerCase()) it.titlecase(Locale.getDefault()) else it.toString() }}"
logger.info("Processing benchmark data from benchmark ${cfg.name} into readme property $propertyName")
val launches = layout.buildDirectory.dir("reports/benchmarks/${cfg.name}").get().asFile
if (!launches.exists()) return@forEach
property(propertyName) {
val resDirectory = launches.listFiles()?.maxByOrNull {
LocalDateTime.parse(it.name).atZone(ZoneId.systemDefault()).toInstant()
}
if (resDirectory == null || !(resDirectory.resolve("jvm.json")).exists()) {
"> **Can't find appropriate benchmark data. Try generating readme files after running benchmarks**."
} else {
val reports: List<JmhReport> =
jsonMapper.readValue<List<JmhReport>>(resDirectory.resolve("jvm.json"))
buildString {
appendLine("## Report for benchmark configuration <code>${cfg.name}</code>")
appendLine()
val first = reports.first()
appendLine("* Run on ${first.vmName} (build ${first.vmVersion}) with Java process:")
appendLine()
appendLine("```")
appendLine(
"${first.jvm} ${
first.jvmArgs.joinToString(" ")
}"
)
appendLine("```")
appendLine(
"* JMH ${first.jmhVersion} was used in `${first.mode}` mode with ${first.warmupIterations} warmup ${
noun(first.warmupIterations, "iteration", "iterations")
} by ${first.warmupTime} and ${first.measurementIterations} measurement ${
noun(first.measurementIterations, "iteration", "iterations")
} by ${first.measurementTime}."
)
reports.groupBy { it.benchmark.substringBeforeLast(".") }.forEach { (cl, compare) ->
appendLine("### [${cl.substringAfterLast(".")}](src/jvmMain/kotlin/${cl.replace(".","/")}.kt)")
appendLine()
appendLine("| Benchmark | Score |")
appendLine("|:---------:|:-----:|")
compare.forEach { report ->
val benchmarkName = report.benchmark.substringAfterLast(".")
val score = String.format("%.2G", report.primaryMetric.score)
val error = String.format("%.2G", report.primaryMetric.scoreError)
appendLine("|`$benchmarkName`|$score &plusmn; $error ${report.primaryMetric.scoreUnit}|")
}
}
}
}
}
}
} }
addBenchmarkProperties()

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@ -1,5 +0,0 @@
# BenchmarksResult
${benchmarkMain}

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -9,12 +9,11 @@ import kotlinx.benchmark.Benchmark
import kotlinx.benchmark.Blackhole import kotlinx.benchmark.Blackhole
import kotlinx.benchmark.Scope import kotlinx.benchmark.Scope
import kotlinx.benchmark.State import kotlinx.benchmark.State
import space.kscience.kmath.UnstableKMathAPI
import space.kscience.kmath.expressions.* import space.kscience.kmath.expressions.*
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.Algebra
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.bindSymbol import space.kscience.kmath.operations.bindSymbol
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
import space.kscience.kmath.structures.Float64
import kotlin.math.sin import kotlin.math.sin
import kotlin.random.Random import kotlin.random.Random
import space.kscience.kmath.estree.compileToExpression as estreeCompileToExpression import space.kscience.kmath.estree.compileToExpression as estreeCompileToExpression
@ -68,7 +67,7 @@ class ExpressionsInterpretersBenchmark {
blackhole.consume(sum) blackhole.consume(sum)
} }
private fun invokeAndSum(expr: Expression<Float64>, blackhole: Blackhole) { private fun invokeAndSum(expr: Expression<Double>, blackhole: Blackhole) {
val random = Random(0) val random = Random(0)
var sum = 0.0 var sum = 0.0
val m = HashMap<Symbol, Double>() val m = HashMap<Symbol, Double>()
@ -85,7 +84,7 @@ class ExpressionsInterpretersBenchmark {
private val x by symbol private val x by symbol
private const val times = 1_000_000 private const val times = 1_000_000
private val functional = Float64Field.expression { private val functional = DoubleField.expression {
val x = bindSymbol(Symbol.x) val x = bindSymbol(Symbol.x)
x * number(2.0) + 2.0 / x - 16.0 / sin(x) x * number(2.0) + 2.0 / x - 16.0 / sin(x)
} }
@ -94,14 +93,12 @@ class ExpressionsInterpretersBenchmark {
x * 2.0 + number(2.0) / x - number(16.0) / sin(x) x * 2.0 + number(2.0) / x - number(16.0) / sin(x)
} }
private val mst = node.toExpression(Float64Field) private val mst = node.toExpression(DoubleField)
private val wasm = node.wasmCompileToExpression(DoubleField)
private val estree = node.estreeCompileToExpression(DoubleField)
@OptIn(UnstableKMathAPI::class) private val raw = Expression<Double> { args ->
private val wasm = node.wasmCompileToExpression(Float64Field) val x = args[x]!!
private val estree = node.estreeCompileToExpression(Float64Field)
private val raw = Expression<Float64> { args ->
val x = args.getValue(x)
x * 2.0 + 2.0 / x - 16.0 / sin(x) x * 2.0 + 2.0 / x - 16.0 / sin(x)
} }
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -10,7 +10,7 @@ import kotlinx.benchmark.Blackhole
import org.openjdk.jmh.annotations.Benchmark import org.openjdk.jmh.annotations.Benchmark
import org.openjdk.jmh.annotations.Scope import org.openjdk.jmh.annotations.Scope
import org.openjdk.jmh.annotations.State import org.openjdk.jmh.annotations.State
import space.kscience.kmath.UnstableKMathAPI import space.kscience.kmath.misc.UnstableKMathAPI
import space.kscience.kmath.operations.BigIntField import space.kscience.kmath.operations.BigIntField
import space.kscience.kmath.operations.JBigIntegerField import space.kscience.kmath.operations.JBigIntegerField
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
@ -67,7 +67,7 @@ internal class BigIntBenchmark {
@Benchmark @Benchmark
fun kmMultiplyLarge(blackhole: Blackhole) = BigIntField { fun kmMultiplyLarge(blackhole: Blackhole) = BigIntField {
blackhole.consume(kmLargeNumber * kmLargeNumber) blackhole.consume(kmLargeNumber*kmLargeNumber)
} }
@Benchmark @Benchmark
@ -77,7 +77,7 @@ internal class BigIntBenchmark {
@Benchmark @Benchmark
fun jvmMultiplyLarge(blackhole: Blackhole) = JBigIntegerField { fun jvmMultiplyLarge(blackhole: Blackhole) = JBigIntegerField {
blackhole.consume(jvmLargeNumber * jvmLargeNumber) blackhole.consume(jvmLargeNumber*jvmLargeNumber)
} }
@Benchmark @Benchmark

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@ -1,80 +1,39 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.benchmarks package space.kscience.kmath.benchmarks
import kotlinx.benchmark.Benchmark import kotlinx.benchmark.Benchmark
import kotlinx.benchmark.Blackhole
import kotlinx.benchmark.Scope import kotlinx.benchmark.Scope
import kotlinx.benchmark.State import kotlinx.benchmark.State
import space.kscience.kmath.complex.Complex import space.kscience.kmath.complex.Complex
import space.kscience.kmath.complex.ComplexField
import space.kscience.kmath.complex.complex import space.kscience.kmath.complex.complex
import space.kscience.kmath.operations.invoke import space.kscience.kmath.structures.DoubleBuffer
import space.kscience.kmath.structures.Buffer import space.kscience.kmath.structures.MutableBuffer
import space.kscience.kmath.structures.Float64Buffer
import space.kscience.kmath.structures.getDouble
import space.kscience.kmath.structures.permute
@State(Scope.Benchmark) @State(Scope.Benchmark)
internal class BufferBenchmark { internal class BufferBenchmark {
@Benchmark @Benchmark
fun doubleArrayReadWrite(blackhole: Blackhole) { fun genericDoubleBufferReadWrite() {
val buffer = DoubleArray(size) { it.toDouble() } val buffer = DoubleBuffer(size) { it.toDouble() }
var res = 0.0
(0 until size).forEach { (0 until size).forEach {
res += buffer[it] buffer[it]
} }
blackhole.consume(res)
} }
@Benchmark @Benchmark
fun doubleBufferReadWrite(blackhole: Blackhole) { fun complexBufferReadWrite() {
val buffer = Float64Buffer(size) { it.toDouble() } val buffer = MutableBuffer.complex(size / 2) { Complex(it.toDouble(), -it.toDouble()) }
var res = 0.0
(0 until size).forEach {
res += buffer[it]
}
blackhole.consume(res)
}
@Benchmark
fun bufferViewReadWrite(blackhole: Blackhole) {
val buffer = Float64Buffer(size) { it.toDouble() }.permute(reversedIndices)
var res = 0.0
(0 until size).forEach {
res += buffer[it]
}
blackhole.consume(res)
}
@Benchmark
fun bufferViewReadWriteSpecialized(blackhole: Blackhole) {
val buffer = Float64Buffer(size) { it.toDouble() }.permute(reversedIndices)
var res = 0.0
(0 until size).forEach {
res += buffer.getDouble(it)
}
blackhole.consume(res)
}
@Benchmark
fun complexBufferReadWrite(blackhole: Blackhole) = ComplexField {
val buffer = Buffer.complex(size / 2) { Complex(it.toDouble(), -it.toDouble()) }
var res = zero
(0 until size / 2).forEach { (0 until size / 2).forEach {
res += buffer[it] buffer[it]
} }
blackhole.consume(res)
} }
private companion object { private companion object {
private const val size = 100 private const val size = 100
private val reversedIndices = IntArray(size) { it }.apply { reverse() }
} }
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -11,11 +11,14 @@ import kotlinx.benchmark.Scope
import kotlinx.benchmark.State import kotlinx.benchmark.State
import space.kscience.kmath.commons.linear.CMLinearSpace import space.kscience.kmath.commons.linear.CMLinearSpace
import space.kscience.kmath.ejml.EjmlLinearSpaceDDRM import space.kscience.kmath.ejml.EjmlLinearSpaceDDRM
import space.kscience.kmath.linear.Float64ParallelLinearSpace
import space.kscience.kmath.linear.invoke import space.kscience.kmath.linear.invoke
import space.kscience.kmath.linear.linearSpace import space.kscience.kmath.linear.linearSpace
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.multik.multikAlgebra
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.invoke
import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.tensorflow.produceWithTF import space.kscience.kmath.tensorflow.produceWithTF
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra
import space.kscience.kmath.tensors.core.tensorAlgebra import space.kscience.kmath.tensors.core.tensorAlgebra
import kotlin.random.Random import kotlin.random.Random
@ -26,10 +29,10 @@ internal class DotBenchmark {
const val dim = 1000 const val dim = 1000
//creating invertible matrix //creating invertible matrix
val matrix1 = Float64Field.linearSpace.buildMatrix(dim, dim) { _, _ -> val matrix1 = DoubleField.linearSpace.buildMatrix(dim, dim) { _, _ ->
random.nextDouble() random.nextDouble()
} }
val matrix2 = Float64Field.linearSpace.buildMatrix(dim, dim) { _, _ -> val matrix2 = DoubleField.linearSpace.buildMatrix(dim, dim) { _, _ ->
random.nextDouble() random.nextDouble()
} }
@ -44,7 +47,7 @@ internal class DotBenchmark {
@Benchmark @Benchmark
fun tfDot(blackhole: Blackhole) { fun tfDot(blackhole: Blackhole) {
blackhole.consume( blackhole.consume(
Float64Field.produceWithTF { DoubleField.produceWithTF {
matrix1 dot matrix1 matrix1 dot matrix1
} }
) )
@ -71,23 +74,27 @@ internal class DotBenchmark {
} }
@Benchmark @Benchmark
fun multikDot(blackhole: Blackhole) = with(multikAlgebra) { fun tensorDot(blackhole: Blackhole) = with(DoubleField.tensorAlgebra) {
blackhole.consume(matrix1 dot matrix2) blackhole.consume(matrix1 dot matrix2)
} }
@Benchmark @Benchmark
fun tensorDot(blackhole: Blackhole) = with(Float64Field.tensorAlgebra) { fun multikDot(blackhole: Blackhole) = with(DoubleField.multikAlgebra) {
blackhole.consume(matrix1 dot matrix2) blackhole.consume(matrix1 dot matrix2)
} }
@Benchmark @Benchmark
fun bufferedDot(blackhole: Blackhole) = with(Float64Field.linearSpace) { fun bufferedDot(blackhole: Blackhole) = with(DoubleField.linearSpace(Buffer.Companion::auto)) {
blackhole.consume(matrix1 dot matrix2) blackhole.consume(matrix1 dot matrix2)
} }
@Benchmark @Benchmark
fun parallelDot(blackhole: Blackhole) = with(Float64ParallelLinearSpace) { fun doubleDot(blackhole: Blackhole) = with(DoubleField.linearSpace) {
blackhole.consume(matrix1 dot matrix2) blackhole.consume(matrix1 dot matrix2)
} }
@Benchmark
fun doubleTensorDot(blackhole: Blackhole) = DoubleTensorAlgebra.invoke {
blackhole.consume(matrix1 dot matrix2)
}
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -12,10 +12,9 @@ import kotlinx.benchmark.State
import space.kscience.kmath.asm.compileToExpression import space.kscience.kmath.asm.compileToExpression
import space.kscience.kmath.expressions.* import space.kscience.kmath.expressions.*
import space.kscience.kmath.operations.Algebra import space.kscience.kmath.operations.Algebra
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.bindSymbol import space.kscience.kmath.operations.bindSymbol
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
import space.kscience.kmath.structures.Float64
import kotlin.math.sin import kotlin.math.sin
import kotlin.random.Random import kotlin.random.Random
@ -84,7 +83,7 @@ internal class ExpressionsInterpretersBenchmark {
blackhole.consume(sum) blackhole.consume(sum)
} }
private fun invokeAndSum(expr: Expression<Float64>, blackhole: Blackhole) { private fun invokeAndSum(expr: Expression<Double>, blackhole: Blackhole) {
val random = Random(0) val random = Random(0)
var sum = 0.0 var sum = 0.0
val m = HashMap<Symbol, Double>() val m = HashMap<Symbol, Double>()
@ -101,7 +100,7 @@ internal class ExpressionsInterpretersBenchmark {
private val x by symbol private val x by symbol
private const val times = 1_000_000 private const val times = 1_000_000
private val functional = Float64Field.expression { private val functional = DoubleField.expression {
val x = bindSymbol(Symbol.x) val x = bindSymbol(Symbol.x)
x * number(2.0) + 2.0 / x - 16.0 / sin(x) x * number(2.0) + 2.0 / x - 16.0 / sin(x)
} }
@ -110,14 +109,14 @@ internal class ExpressionsInterpretersBenchmark {
x * 2.0 + number(2.0) / x - number(16.0) / sin(x) x * 2.0 + number(2.0) / x - number(16.0) / sin(x)
} }
private val mst = node.toExpression(Float64Field) private val mst = node.toExpression(DoubleField)
private val asmPrimitive = node.compileToExpression(Float64Field) private val asmPrimitive = node.compileToExpression(DoubleField)
private val xIdx = asmPrimitive.indexer.indexOf(x) private val xIdx = asmPrimitive.indexer.indexOf(x)
private val asmGeneric = node.compileToExpression(Float64Field as Algebra<Float64>) private val asmGeneric = node.compileToExpression(DoubleField as Algebra<Double>)
private val raw = Expression<Float64> { args -> private val raw = Expression<Double> { args ->
val x = args[x]!! val x = args[x]!!
x * 2.0 + 2.0 / x - 16.0 / sin(x) x * 2.0 + 2.0 / x - 16.0 / sin(x)
} }

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@ -1,40 +0,0 @@
/*
* Copyright 2018-2024 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.benchmarks
import org.openjdk.jmh.annotations.Benchmark
import org.openjdk.jmh.annotations.Scope
import org.openjdk.jmh.annotations.State
import org.openjdk.jmh.infra.Blackhole
import space.kscience.kmath.complex.Complex
import space.kscience.kmath.complex.algebra
import space.kscience.kmath.integration.gaussIntegrator
import space.kscience.kmath.integration.integrate
import space.kscience.kmath.integration.value
import space.kscience.kmath.operations.algebra
@State(Scope.Benchmark)
internal class IntegrationBenchmark {
@Benchmark
fun doubleIntegration(blackhole: Blackhole) {
val res = Double.algebra.gaussIntegrator.integrate(0.0..1.0, intervals = 1000) { x: Double ->
//sin(1 / x)
1 / x
}.value
blackhole.consume(res)
}
@Benchmark
fun complexIntegration(blackhole: Blackhole) = with(Complex.algebra) {
val res = gaussIntegrator.integrate(0.0..1.0, intervals = 1000) { x: Double ->
// sin(1 / x) + i * cos(1 / x)
1 / x - i / x
}.value
blackhole.consume(res)
}
}

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -11,8 +11,10 @@ import org.openjdk.jmh.annotations.Scope
import org.openjdk.jmh.annotations.State import org.openjdk.jmh.annotations.State
import space.kscience.kmath.jafama.JafamaDoubleField import space.kscience.kmath.jafama.JafamaDoubleField
import space.kscience.kmath.jafama.StrictJafamaDoubleField import space.kscience.kmath.jafama.StrictJafamaDoubleField
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
import kotlin.contracts.InvocationKind
import kotlin.contracts.contract
import kotlin.random.Random import kotlin.random.Random
@State(Scope.Benchmark) @State(Scope.Benchmark)
@ -24,7 +26,7 @@ internal class JafamaBenchmark {
@Benchmark @Benchmark
fun core(blackhole: Blackhole) = invokeBenchmarks(blackhole) { x -> fun core(blackhole: Blackhole) = invokeBenchmarks(blackhole) { x ->
Float64Field { x * power(x, 4) * exp(x) / cos(x) + sin(x) } DoubleField { x * power(x, 4) * exp(x) / cos(x) + sin(x) }
} }
@Benchmark @Benchmark
@ -34,6 +36,7 @@ internal class JafamaBenchmark {
} }
private inline fun invokeBenchmarks(blackhole: Blackhole, expr: (Double) -> Double) { private inline fun invokeBenchmarks(blackhole: Blackhole, expr: (Double) -> Double) {
contract { callsInPlace(expr, InvocationKind.AT_LEAST_ONCE) }
val rng = Random(0) val rng = Random(0)
repeat(1000000) { blackhole.consume(expr(rng.nextDouble())) } repeat(1000000) { blackhole.consume(expr(rng.nextDouble())) }
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -15,7 +15,6 @@ import space.kscience.kmath.ejml.EjmlLinearSpaceDDRM
import space.kscience.kmath.linear.invoke import space.kscience.kmath.linear.invoke
import space.kscience.kmath.linear.linearSpace import space.kscience.kmath.linear.linearSpace
import space.kscience.kmath.linear.lupSolver import space.kscience.kmath.linear.lupSolver
import space.kscience.kmath.linear.parallel
import space.kscience.kmath.operations.algebra import space.kscience.kmath.operations.algebra
import kotlin.random.Random import kotlin.random.Random
@ -39,19 +38,16 @@ internal class MatrixInverseBenchmark {
} }
@Benchmark @Benchmark
fun kmathParallelLupInversion(blackhole: Blackhole) { fun cmLUPInversion(blackhole: Blackhole) {
blackhole.consume(Double.algebra.linearSpace.parallel.lupSolver().inverse(matrix)) CMLinearSpace {
blackhole.consume(lupSolver().inverse(matrix))
}
} }
@Benchmark @Benchmark
fun cmLUPInversion(blackhole: Blackhole) = CMLinearSpace { fun ejmlInverse(blackhole: Blackhole) {
blackhole.consume(lupSolver().inverse(matrix)) EjmlLinearSpaceDDRM {
blackhole.consume(matrix.toEjml().inverse())
}
} }
@Benchmark
fun ejmlInverse(blackhole: Blackhole) = EjmlLinearSpaceDDRM {
blackhole.consume(matrix.toEjml().inverted())
}
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -13,11 +13,14 @@ import org.jetbrains.kotlinx.multik.api.Multik
import org.jetbrains.kotlinx.multik.api.ones import org.jetbrains.kotlinx.multik.api.ones
import org.jetbrains.kotlinx.multik.ndarray.data.DN import org.jetbrains.kotlinx.multik.ndarray.data.DN
import org.jetbrains.kotlinx.multik.ndarray.data.DataType import org.jetbrains.kotlinx.multik.ndarray.data.DataType
import space.kscience.kmath.UnsafeKMathAPI import space.kscience.kmath.multik.multikAlgebra
import space.kscience.kmath.nd.* import space.kscience.kmath.nd.BufferedFieldOpsND
import space.kscience.kmath.nd.StructureND
import space.kscience.kmath.nd.ndAlgebra
import space.kscience.kmath.nd.one
import space.kscience.kmath.nd4j.nd4j import space.kscience.kmath.nd4j.nd4j
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.structures.Float64 import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.tensors.core.DoubleTensor import space.kscience.kmath.tensors.core.DoubleTensor
import space.kscience.kmath.tensors.core.one import space.kscience.kmath.tensors.core.one
import space.kscience.kmath.tensors.core.tensorAlgebra import space.kscience.kmath.tensors.core.tensorAlgebra
@ -25,41 +28,37 @@ import space.kscience.kmath.viktor.viktorAlgebra
@State(Scope.Benchmark) @State(Scope.Benchmark)
internal class NDFieldBenchmark { internal class NDFieldBenchmark {
@Benchmark
private companion object { fun autoFieldAdd(blackhole: Blackhole) = with(autoField) {
private const val dim = 1000 var res: StructureND<Double> = one(shape)
private const val n = 100 repeat(n) { res += 1.0 }
private val shape = ShapeND(dim, dim) blackhole.consume(res)
private val specializedField = Float64Field.ndAlgebra
private val genericField = BufferedFieldOpsND(Float64Field)
private val nd4jField = Float64Field.nd4j
private val viktorField = Float64Field.viktorAlgebra
} }
@Benchmark @Benchmark
fun specializedFieldAdd(blackhole: Blackhole) = with(specializedField) { fun specializedFieldAdd(blackhole: Blackhole) = with(specializedField) {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
blackhole.consume(res) blackhole.consume(res)
} }
@Benchmark @Benchmark
fun boxingFieldAdd(blackhole: Blackhole) = with(genericField) { fun boxingFieldAdd(blackhole: Blackhole) = with(genericField) {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
blackhole.consume(res) blackhole.consume(res)
} }
@Benchmark @Benchmark
fun multikAdd(blackhole: Blackhole) = with(multikAlgebra) { fun multikAdd(blackhole: Blackhole) = with(multikField) {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
blackhole.consume(res) blackhole.consume(res)
} }
@Benchmark @Benchmark
fun viktorAdd(blackhole: Blackhole) = with(viktorField) { fun viktorAdd(blackhole: Blackhole) = with(viktorField) {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
blackhole.consume(res) blackhole.consume(res)
} }
@ -78,20 +77,29 @@ internal class NDFieldBenchmark {
blackhole.consume(res) blackhole.consume(res)
} }
@OptIn(UnsafeKMathAPI::class)
@Benchmark @Benchmark
fun multikInPlaceAdd(blackhole: Blackhole) = with(multikAlgebra) { fun multikInPlaceAdd(blackhole: Blackhole) = with(DoubleField.multikAlgebra) {
val res = Multik.ones<Double, DN>(shape.asArray(), DataType.DoubleDataType).wrap() val res = Multik.ones<Double, DN>(shape, DataType.DoubleDataType).wrap()
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
blackhole.consume(res) blackhole.consume(res)
} }
// @Benchmark // @Benchmark
// fun nd4jAdd(blackhole: Blackhole) = with(nd4jField) { // fun nd4jAdd(blackhole: Blackhole) = with(nd4jField) {
// var res: StructureND<Float64> = one(dim, dim) // var res: StructureND<Double> = one(dim, dim)
// repeat(n) { res += 1.0 } // repeat(n) { res += 1.0 }
// blackhole.consume(res) // blackhole.consume(res)
// } // }
private companion object {
private const val dim = 1000
private const val n = 100
private val shape = intArrayOf(dim, dim)
private val autoField = BufferedFieldOpsND(DoubleField, Buffer.Companion::auto)
private val specializedField = DoubleField.ndAlgebra
private val genericField = BufferedFieldOpsND(DoubleField, Buffer.Companion::boxing)
private val nd4jField = DoubleField.nd4j
private val multikField = DoubleField.multikAlgebra
private val viktorField = DoubleField.viktorAlgebra
}
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -12,9 +12,7 @@ import kotlinx.benchmark.State
import space.kscience.kmath.linear.linearSpace import space.kscience.kmath.linear.linearSpace
import space.kscience.kmath.linear.matrix import space.kscience.kmath.linear.matrix
import space.kscience.kmath.linear.symmetric import space.kscience.kmath.linear.symmetric
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.tensors.core.symEigJacobi
import space.kscience.kmath.tensors.core.symEigSvd
import space.kscience.kmath.tensors.core.tensorAlgebra import space.kscience.kmath.tensors.core.tensorAlgebra
import kotlin.random.Random import kotlin.random.Random
@ -24,16 +22,16 @@ internal class TensorAlgebraBenchmark {
private val random = Random(12224) private val random = Random(12224)
private const val dim = 30 private const val dim = 30
private val matrix = Float64Field.linearSpace.matrix(dim, dim).symmetric { _, _ -> random.nextDouble() } private val matrix = DoubleField.linearSpace.matrix(dim, dim).symmetric { _, _ -> random.nextDouble() }
} }
@Benchmark @Benchmark
fun tensorSymEigSvd(blackhole: Blackhole) = with(Double.tensorAlgebra) { fun tensorSymEigSvd(blackhole: Blackhole) = with(Double.tensorAlgebra) {
blackhole.consume(symEigSvd(matrix, 1e-10)) blackhole.consume(matrix.symEigSvd(1e-10))
} }
@Benchmark @Benchmark
fun tensorSymEigJacobi(blackhole: Blackhole) = with(Double.tensorAlgebra) { fun tensorSymEigJacobi(blackhole: Blackhole) = with(Double.tensorAlgebra) {
blackhole.consume(symEigJacobi(matrix, 50, 1e-10)) blackhole.consume(matrix.symEigJacobi(50, 1e-10))
} }
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -10,21 +10,26 @@ import kotlinx.benchmark.Blackhole
import kotlinx.benchmark.Scope import kotlinx.benchmark.Scope
import kotlinx.benchmark.State import kotlinx.benchmark.State
import org.jetbrains.bio.viktor.F64Array import org.jetbrains.bio.viktor.F64Array
import space.kscience.kmath.nd.ShapeND import space.kscience.kmath.nd.*
import space.kscience.kmath.nd.StructureND import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.nd.ndAlgebra import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.nd.one
import space.kscience.kmath.operations.Float64Field
import space.kscience.kmath.structures.Float64
import space.kscience.kmath.viktor.ViktorFieldND import space.kscience.kmath.viktor.ViktorFieldND
@State(Scope.Benchmark) @State(Scope.Benchmark)
internal class ViktorBenchmark { internal class ViktorBenchmark {
@Benchmark
fun automaticFieldAddition(blackhole: Blackhole) {
with(autoField) {
var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 }
blackhole.consume(res)
}
}
@Benchmark @Benchmark
fun doubleFieldAddition(blackhole: Blackhole) { fun realFieldAddition(blackhole: Blackhole) {
with(doubleField) { with(realField) {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
blackhole.consume(res) blackhole.consume(res)
} }
@ -50,10 +55,11 @@ internal class ViktorBenchmark {
private companion object { private companion object {
private const val dim = 1000 private const val dim = 1000
private const val n = 100 private const val n = 100
private val shape = ShapeND(dim, dim) private val shape = Shape(dim, dim)
// automatically build context most suited for given type. // automatically build context most suited for given type.
private val doubleField = Float64Field.ndAlgebra private val autoField = BufferedFieldOpsND(DoubleField, Buffer.Companion::auto)
private val realField = DoubleField.ndAlgebra
private val viktorField = ViktorFieldND(dim, dim) private val viktorField = ViktorFieldND(dim, dim)
} }
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -10,17 +10,19 @@ import kotlinx.benchmark.Blackhole
import kotlinx.benchmark.Scope import kotlinx.benchmark.Scope
import kotlinx.benchmark.State import kotlinx.benchmark.State
import org.jetbrains.bio.viktor.F64Array import org.jetbrains.bio.viktor.F64Array
import space.kscience.kmath.nd.ShapeND import space.kscience.kmath.nd.BufferedFieldOpsND
import space.kscience.kmath.nd.Shape
import space.kscience.kmath.nd.ndAlgebra import space.kscience.kmath.nd.ndAlgebra
import space.kscience.kmath.nd.one import space.kscience.kmath.nd.one
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.viktor.ViktorFieldND import space.kscience.kmath.viktor.ViktorFieldND
@State(Scope.Benchmark) @State(Scope.Benchmark)
internal class ViktorLogBenchmark { internal class ViktorLogBenchmark {
@Benchmark @Benchmark
fun realFieldLog(blackhole: Blackhole) { fun realFieldLog(blackhole: Blackhole) {
with(doubleField) { with(realField) {
val fortyTwo = structureND(shape) { 42.0 } val fortyTwo = structureND(shape) { 42.0 }
var res = one(shape) var res = one(shape)
repeat(n) { res = ln(fortyTwo) } repeat(n) { res = ln(fortyTwo) }
@ -49,10 +51,11 @@ internal class ViktorLogBenchmark {
private companion object { private companion object {
private const val dim = 1000 private const val dim = 1000
private const val n = 100 private const val n = 100
private val shape = ShapeND(dim, dim) private val shape = Shape(dim, dim)
// automatically build context most suited for given type. // automatically build context most suited for given type.
private val doubleField = Float64Field.ndAlgebra private val autoField = BufferedFieldOpsND(DoubleField, Buffer.Companion::auto)
private val realField = DoubleField.ndAlgebra
private val viktorField = ViktorFieldND(dim, dim) private val viktorField = ViktorFieldND(dim, dim)
} }
} }

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@ -1,11 +0,0 @@
/*
* Copyright 2018-2024 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.benchmarks
import org.jetbrains.kotlinx.multik.default.DefaultEngine
import space.kscience.kmath.multik.MultikDoubleAlgebra
val multikAlgebra = MultikDoubleAlgebra(DefaultEngine())

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@ -1,13 +1,8 @@
import space.kscience.gradle.useApache2Licence
import space.kscience.gradle.useSPCTeam
plugins { plugins {
alias(spclibs.plugins.kscience.project) id("ru.mipt.npm.gradle.project")
alias(spclibs.plugins.kotlinx.kover) id("org.jetbrains.kotlinx.kover") version "0.5.0"
} }
val attributesVersion by extra("0.2.0")
allprojects { allprojects {
repositories { repositories {
maven("https://repo.kotlin.link") maven("https://repo.kotlin.link")
@ -16,13 +11,13 @@ allprojects {
} }
group = "space.kscience" group = "space.kscience"
version = "0.4.1-dev" version = "0.3.0-dev-20"
} }
subprojects { subprojects {
if (name.startsWith("kmath")) apply<MavenPublishPlugin>() if (name.startsWith("kmath")) apply<MavenPublishPlugin>()
plugins.withId("org.jetbrains.dokka") { plugins.withId("org.jetbrains.dokka"){
tasks.withType<org.jetbrains.dokka.gradle.DokkaTaskPartial> { tasks.withType<org.jetbrains.dokka.gradle.DokkaTaskPartial> {
dependsOn(tasks["assemble"]) dependsOn(tasks["assemble"])
@ -36,7 +31,7 @@ subprojects {
localDirectory.set(kotlinDir) localDirectory.set(kotlinDir)
remoteUrl.set( remoteUrl.set(
uri("https://github.com/SciProgCentre/kmath/tree/master/${this@subprojects.name}/$kotlinDirPath").toURL() java.net.URL("https://github.com/mipt-npm/kmath/tree/master/${this@subprojects.name}/$kotlinDirPath")
) )
} }
@ -61,12 +56,9 @@ subprojects {
readme.readmeTemplate = file("docs/templates/README-TEMPLATE.md") readme.readmeTemplate = file("docs/templates/README-TEMPLATE.md")
ksciencePublish { ksciencePublish {
pom("https://github.com/SciProgCentre/kmath") { github("kmath", addToRelease = false)
useApache2Licence() space()
useSPCTeam() sonatype()
}
repository("spc", "https://maven.sciprog.center/kscience")
sonatype("https://oss.sonatype.org")
} }
apiValidation.nonPublicMarkers.add("space.kscience.kmath.UnstableKMathAPI") apiValidation.nonPublicMarkers.add("space.kscience.kmath.misc.UnstableKMathAPI")

31
buildSrc/build.gradle.kts Normal file
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@ -0,0 +1,31 @@
plugins {
`kotlin-dsl`
`version-catalog`
alias(miptNpmLibs.plugins.kotlin.plugin.serialization)
}
java.targetCompatibility = JavaVersion.VERSION_11
repositories {
mavenLocal()
maven("https://repo.kotlin.link")
mavenCentral()
gradlePluginPortal()
}
val toolsVersion: String by extra
val kotlinVersion = miptNpmLibs.versions.kotlin.asProvider().get()
val benchmarksVersion = miptNpmLibs.versions.kotlinx.benchmark.get()
dependencies {
api("ru.mipt.npm:gradle-tools:$toolsVersion")
//plugins form benchmarks
api("org.jetbrains.kotlinx:kotlinx-benchmark-plugin:$benchmarksVersion")
api("org.jetbrains.kotlin:kotlin-allopen:$kotlinVersion")
//to be used inside build-script only
implementation(miptNpmLibs.kotlinx.serialization.json)
}
kotlin.sourceSets.all {
languageSettings.optIn("kotlin.OptIn")
}

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@ -0,0 +1,7 @@
#
# Copyright 2018-2021 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.
#
kotlin.code.style=official
toolsVersion=0.11.2-kotlin-1.6.10

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@ -0,0 +1,23 @@
/*
* Copyright 2018-2021 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.
*/
enableFeaturePreview("TYPESAFE_PROJECT_ACCESSORS")
dependencyResolutionManagement {
val toolsVersion: String by extra
repositories {
mavenLocal()
maven("https://repo.kotlin.link")
mavenCentral()
gradlePluginPortal()
}
versionCatalogs {
create("miptNpmLibs") {
from("ru.mipt.npm:version-catalog:$toolsVersion")
}
}
}

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@ -0,0 +1,60 @@
/*
* Copyright 2018-2021 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.benchmarks
import kotlinx.serialization.Serializable
@Serializable
data class JmhReport(
val jmhVersion: String,
val benchmark: String,
val mode: String,
val threads: Int,
val forks: Int,
val jvm: String,
val jvmArgs: List<String>,
val jdkVersion: String,
val vmName: String,
val vmVersion: String,
val warmupIterations: Int,
val warmupTime: String,
val warmupBatchSize: Int,
val measurementIterations: Int,
val measurementTime: String,
val measurementBatchSize: Int,
val params: Map<String, String> = emptyMap(),
val primaryMetric: PrimaryMetric,
val secondaryMetrics: Map<String, SecondaryMetric>,
) {
interface Metric {
val score: Double
val scoreError: Double
val scoreConfidence: List<Double>
val scorePercentiles: Map<Double, Double>
val scoreUnit: String
}
@Serializable
data class PrimaryMetric(
override val score: Double,
override val scoreError: Double,
override val scoreConfidence: List<Double>,
override val scorePercentiles: Map<Double, Double>,
override val scoreUnit: String,
val rawDataHistogram: List<List<List<List<Double>>>>? = null,
val rawData: List<List<Double>>? = null,
) : Metric
@Serializable
data class SecondaryMetric(
override val score: Double,
override val scoreError: Double,
override val scoreConfidence: List<Double>,
override val scorePercentiles: Map<Double, Double>,
override val scoreUnit: String,
val rawData: List<List<Double>>,
) : Metric
}

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@ -0,0 +1,103 @@
/*
* Copyright 2018-2021 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.benchmarks
import kotlinx.benchmark.gradle.BenchmarksExtension
import kotlinx.serialization.decodeFromString
import kotlinx.serialization.json.Json
import org.gradle.api.Project
import ru.mipt.npm.gradle.KScienceReadmeExtension
import java.time.LocalDateTime
import java.time.ZoneId
import java.time.format.DateTimeFormatter
import java.time.format.DateTimeFormatterBuilder
import java.time.format.SignStyle
import java.time.temporal.ChronoField.*
private val ISO_DATE_TIME: DateTimeFormatter = DateTimeFormatterBuilder().run {
parseCaseInsensitive()
appendValue(YEAR, 4, 10, SignStyle.EXCEEDS_PAD)
appendLiteral('-')
appendValue(MONTH_OF_YEAR, 2)
appendLiteral('-')
appendValue(DAY_OF_MONTH, 2)
appendLiteral('T')
appendValue(HOUR_OF_DAY, 2)
appendLiteral('.')
appendValue(MINUTE_OF_HOUR, 2)
optionalStart()
appendLiteral('.')
appendValue(SECOND_OF_MINUTE, 2)
optionalStart()
appendFraction(NANO_OF_SECOND, 0, 9, true)
optionalStart()
appendOffsetId()
optionalStart()
appendLiteral('[')
parseCaseSensitive()
appendZoneRegionId()
appendLiteral(']')
toFormatter()
}
private fun noun(number: Number, singular: String, plural: String) = if (number.toLong() == 1L) singular else plural
fun Project.addBenchmarkProperties() {
val benchmarksProject = this
rootProject.subprojects.forEach { p ->
p.extensions.findByType(KScienceReadmeExtension::class.java)?.run {
benchmarksProject.extensions.findByType(BenchmarksExtension::class.java)?.configurations?.forEach { cfg ->
property("benchmark${cfg.name.capitalize()}") {
val launches = benchmarksProject.buildDir.resolve("reports/benchmarks/${cfg.name}")
val resDirectory = launches.listFiles()?.maxByOrNull {
LocalDateTime.parse(it.name, ISO_DATE_TIME).atZone(ZoneId.systemDefault()).toInstant()
}
if (resDirectory == null || !(resDirectory.resolve("jvm.json")).exists()) {
"> **Can't find appropriate benchmark data. Try generating readme files after running benchmarks**."
} else {
val reports =
Json.decodeFromString<List<JmhReport>>(resDirectory.resolve("jvm.json").readText())
buildString {
appendLine("<details>")
appendLine("<summary>")
appendLine("Report for benchmark configuration <code>${cfg.name}</code>")
appendLine("</summary>")
appendLine()
val first = reports.first()
appendLine("* Run on ${first.vmName} (build ${first.vmVersion}) with Java process:")
appendLine()
appendLine("```")
appendLine("${first.jvm} ${
first.jvmArgs.joinToString(" ")
}")
appendLine("```")
appendLine("* JMH ${first.jmhVersion} was used in `${first.mode}` mode with ${first.warmupIterations} warmup ${
noun(first.warmupIterations, "iteration", "iterations")
} by ${first.warmupTime} and ${first.measurementIterations} measurement ${
noun(first.measurementIterations, "iteration", "iterations")
} by ${first.measurementTime}.")
appendLine()
appendLine("| Benchmark | Score |")
appendLine("|:---------:|:-----:|")
reports.forEach { report ->
appendLine("|`${report.benchmark}`|${report.primaryMetric.score} &plusmn; ${report.primaryMetric.scoreError} ${report.primaryMetric.scoreUnit}|")
}
appendLine("</details>")
}
}
}
}
}
}
}

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@ -0,0 +1,425 @@
/*
* Copyright 2018-2021 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:Suppress("KDocUnresolvedReference")
package space.kscience.kmath.ejml.codegen
import org.intellij.lang.annotations.Language
import java.io.File
private fun Appendable.appendEjmlVector(type: String, ejmlMatrixType: String) {
@Language("kotlin") val text = """/**
* [EjmlVector] specialization for [$type].
*/
public class Ejml${type}Vector<out M : $ejmlMatrixType>(override val origin: M) : EjmlVector<$type, M>(origin) {
init {
require(origin.numRows == 1) { "The origin matrix must have only one row to form a vector" }
}
override operator fun get(index: Int): $type = origin[0, index]
}"""
appendLine(text)
appendLine()
}
private fun Appendable.appendEjmlMatrix(type: String, ejmlMatrixType: String) {
val text = """/**
* [EjmlMatrix] specialization for [$type].
*/
public class Ejml${type}Matrix<out M : $ejmlMatrixType>(override val origin: M) : EjmlMatrix<$type, M>(origin) {
override operator fun get(i: Int, j: Int): $type = origin[i, j]
}"""
appendLine(text)
appendLine()
}
private fun Appendable.appendEjmlLinearSpace(
type: String,
kmathAlgebra: String,
ejmlMatrixParentTypeMatrix: String,
ejmlMatrixType: String,
ejmlMatrixDenseType: String,
ops: String,
denseOps: String,
isDense: Boolean,
) {
@Language("kotlin") val text = """/**
* [EjmlLinearSpace] implementation based on [CommonOps_$ops], [DecompositionFactory_${ops}] operations and
* [${ejmlMatrixType}] matrices.
*/
public object EjmlLinearSpace${ops} : EjmlLinearSpace<${type}, ${kmathAlgebra}, $ejmlMatrixType>() {
/**
* The [${kmathAlgebra}] reference.
*/
override val elementAlgebra: $kmathAlgebra get() = $kmathAlgebra
@Suppress("UNCHECKED_CAST")
override fun Matrix<${type}>.toEjml(): Ejml${type}Matrix<${ejmlMatrixType}> = when {
this is Ejml${type}Matrix<*> && origin is $ejmlMatrixType -> this as Ejml${type}Matrix<${ejmlMatrixType}>
else -> buildMatrix(rowNum, colNum) { i, j -> get(i, j) }
}
@Suppress("UNCHECKED_CAST")
override fun Point<${type}>.toEjml(): Ejml${type}Vector<${ejmlMatrixType}> = when {
this is Ejml${type}Vector<*> && origin is $ejmlMatrixType -> this as Ejml${type}Vector<${ejmlMatrixType}>
else -> Ejml${type}Vector(${ejmlMatrixType}(size, 1).also {
(0 until it.numRows).forEach { row -> it[row, 0] = get(row) }
})
}
override fun buildMatrix(
rows: Int,
columns: Int,
initializer: ${kmathAlgebra}.(i: Int, j: Int) -> ${type},
): Ejml${type}Matrix<${ejmlMatrixType}> = ${ejmlMatrixType}(rows, columns).also {
(0 until rows).forEach { row ->
(0 until columns).forEach { col -> it[row, col] = elementAlgebra.initializer(row, col) }
}
}.wrapMatrix()
override fun buildVector(
size: Int,
initializer: ${kmathAlgebra}.(Int) -> ${type},
): Ejml${type}Vector<${ejmlMatrixType}> = Ejml${type}Vector(${ejmlMatrixType}(size, 1).also {
(0 until it.numRows).forEach { row -> it[row, 0] = elementAlgebra.initializer(row) }
})
private fun <T : ${ejmlMatrixParentTypeMatrix}> T.wrapMatrix() = Ejml${type}Matrix(this)
private fun <T : ${ejmlMatrixParentTypeMatrix}> T.wrapVector() = Ejml${type}Vector(this)
override fun Matrix<${type}>.unaryMinus(): Matrix<${type}> = this * elementAlgebra { -one }
override fun Matrix<${type}>.dot(other: Matrix<${type}>): Ejml${type}Matrix<${ejmlMatrixType}> {
val out = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.mult(toEjml().origin, other.toEjml().origin, out)
return out.wrapMatrix()
}
override fun Matrix<${type}>.dot(vector: Point<${type}>): Ejml${type}Vector<${ejmlMatrixType}> {
val out = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.mult(toEjml().origin, vector.toEjml().origin, out)
return out.wrapVector()
}
override operator fun Matrix<${type}>.minus(other: Matrix<${type}>): Ejml${type}Matrix<${ejmlMatrixType}> {
val out = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.add(
elementAlgebra.one,
toEjml().origin,
elementAlgebra { -one },
other.toEjml().origin,
out,${
if (isDense) "" else
"""
null,
null,"""
}
)
return out.wrapMatrix()
}
override operator fun Matrix<${type}>.times(value: ${type}): Ejml${type}Matrix<${ejmlMatrixType}> {
val res = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.scale(value, toEjml().origin, res)
return res.wrapMatrix()
}
override fun Point<${type}>.unaryMinus(): Ejml${type}Vector<${ejmlMatrixType}> {
val res = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.changeSign(toEjml().origin, res)
return res.wrapVector()
}
override fun Matrix<${type}>.plus(other: Matrix<${type}>): Ejml${type}Matrix<${ejmlMatrixType}> {
val out = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.add(
elementAlgebra.one,
toEjml().origin,
elementAlgebra.one,
other.toEjml().origin,
out,${
if (isDense) "" else
"""
null,
null,"""
}
)
return out.wrapMatrix()
}
override fun Point<${type}>.plus(other: Point<${type}>): Ejml${type}Vector<${ejmlMatrixType}> {
val out = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.add(
elementAlgebra.one,
toEjml().origin,
elementAlgebra.one,
other.toEjml().origin,
out,${
if (isDense) "" else
"""
null,
null,"""
}
)
return out.wrapVector()
}
override fun Point<${type}>.minus(other: Point<${type}>): Ejml${type}Vector<${ejmlMatrixType}> {
val out = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.add(
elementAlgebra.one,
toEjml().origin,
elementAlgebra { -one },
other.toEjml().origin,
out,${
if (isDense) "" else
"""
null,
null,"""
}
)
return out.wrapVector()
}
override fun ${type}.times(m: Matrix<${type}>): Ejml${type}Matrix<${ejmlMatrixType}> = m * this
override fun Point<${type}>.times(value: ${type}): Ejml${type}Vector<${ejmlMatrixType}> {
val res = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.scale(value, toEjml().origin, res)
return res.wrapVector()
}
override fun ${type}.times(v: Point<${type}>): Ejml${type}Vector<${ejmlMatrixType}> = v * this
@UnstableKMathAPI
override fun <F : StructureFeature> computeFeature(structure: Matrix<${type}>, type: KClass<out F>): F? {
structure.getFeature(type)?.let { return it }
val origin = structure.toEjml().origin
return when (type) {
${
if (isDense)
""" InverseMatrixFeature::class -> object : InverseMatrixFeature<${type}> {
override val inverse: Matrix<${type}> by lazy {
val res = origin.copy()
CommonOps_${ops}.invert(res)
res.wrapMatrix()
}
}
DeterminantFeature::class -> object : DeterminantFeature<${type}> {
override val determinant: $type by lazy { CommonOps_${ops}.det(origin) }
}
SingularValueDecompositionFeature::class -> object : SingularValueDecompositionFeature<${type}> {
private val svd by lazy {
DecompositionFactory_${ops}.svd(origin.numRows, origin.numCols, true, true, false)
.apply { decompose(origin.copy()) }
}
override val u: Matrix<${type}> by lazy { svd.getU(null, false).wrapMatrix() }
override val s: Matrix<${type}> by lazy { svd.getW(null).wrapMatrix() }
override val v: Matrix<${type}> by lazy { svd.getV(null, false).wrapMatrix() }
override val singularValues: Point<${type}> by lazy { ${type}Buffer(svd.singularValues) }
}
QRDecompositionFeature::class -> object : QRDecompositionFeature<${type}> {
private val qr by lazy {
DecompositionFactory_${ops}.qr().apply { decompose(origin.copy()) }
}
override val q: Matrix<${type}> by lazy {
qr.getQ(null, false).wrapMatrix().withFeature(OrthogonalFeature)
}
override val r: Matrix<${type}> by lazy { qr.getR(null, false).wrapMatrix().withFeature(UFeature) }
}
CholeskyDecompositionFeature::class -> object : CholeskyDecompositionFeature<${type}> {
override val l: Matrix<${type}> by lazy {
val cholesky =
DecompositionFactory_${ops}.chol(structure.rowNum, true).apply { decompose(origin.copy()) }
cholesky.getT(null).wrapMatrix().withFeature(LFeature)
}
}
LupDecompositionFeature::class -> object : LupDecompositionFeature<${type}> {
private val lup by lazy {
DecompositionFactory_${ops}.lu(origin.numRows, origin.numCols).apply { decompose(origin.copy()) }
}
override val l: Matrix<${type}> by lazy {
lup.getLower(null).wrapMatrix().withFeature(LFeature)
}
override val u: Matrix<${type}> by lazy {
lup.getUpper(null).wrapMatrix().withFeature(UFeature)
}
override val p: Matrix<${type}> by lazy { lup.getRowPivot(null).wrapMatrix() }
}""" else """ QRDecompositionFeature::class -> object : QRDecompositionFeature<$type> {
private val qr by lazy {
DecompositionFactory_${ops}.qr(FillReducing.NONE).apply { decompose(origin.copy()) }
}
override val q: Matrix<${type}> by lazy {
qr.getQ(null, false).wrapMatrix().withFeature(OrthogonalFeature)
}
override val r: Matrix<${type}> by lazy { qr.getR(null, false).wrapMatrix().withFeature(UFeature) }
}
CholeskyDecompositionFeature::class -> object : CholeskyDecompositionFeature<${type}> {
override val l: Matrix<${type}> by lazy {
val cholesky =
DecompositionFactory_${ops}.cholesky().apply { decompose(origin.copy()) }
(cholesky.getT(null) as ${ejmlMatrixParentTypeMatrix}).wrapMatrix().withFeature(LFeature)
}
}
LUDecompositionFeature::class, DeterminantFeature::class, InverseMatrixFeature::class -> object :
LUDecompositionFeature<${type}>, DeterminantFeature<${type}>, InverseMatrixFeature<${type}> {
private val lu by lazy {
DecompositionFactory_${ops}.lu(FillReducing.NONE).apply { decompose(origin.copy()) }
}
override val l: Matrix<${type}> by lazy {
lu.getLower(null).wrapMatrix().withFeature(LFeature)
}
override val u: Matrix<${type}> by lazy {
lu.getUpper(null).wrapMatrix().withFeature(UFeature)
}
override val inverse: Matrix<${type}> by lazy {
var a = origin
val inverse = ${ejmlMatrixDenseType}(1, 1)
val solver = LinearSolverFactory_${ops}.lu(FillReducing.NONE)
if (solver.modifiesA()) a = a.copy()
val i = CommonOps_${denseOps}.identity(a.numRows)
solver.solve(i, inverse)
inverse.wrapMatrix()
}
override val determinant: $type by lazy { elementAlgebra.number(lu.computeDeterminant().real) }
}"""
}
else -> null
}?.let(type::cast)
}
/**
* Solves for *x* in the following equation: *x = [a] <sup>-1</sup> &middot; [b]*.
*
* @param a the base matrix.
* @param b n by p matrix.
* @return the solution for *x* that is n by p.
*/
public fun solve(a: Matrix<${type}>, b: Matrix<${type}>): Ejml${type}Matrix<${ejmlMatrixType}> {
val res = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.solve(${ejmlMatrixType}(a.toEjml().origin), ${ejmlMatrixType}(b.toEjml().origin), res)
return res.wrapMatrix()
}
/**
* Solves for *x* in the following equation: *x = [a] <sup>-1</sup> &middot; [b]*.
*
* @param a the base matrix.
* @param b n by p vector.
* @return the solution for *x* that is n by p.
*/
public fun solve(a: Matrix<${type}>, b: Point<${type}>): Ejml${type}Vector<${ejmlMatrixType}> {
val res = ${ejmlMatrixType}(1, 1)
CommonOps_${ops}.solve(${ejmlMatrixType}(a.toEjml().origin), ${ejmlMatrixType}(b.toEjml().origin), res)
return Ejml${type}Vector(res)
}
}"""
appendLine(text)
appendLine()
}
/**
* Generates routine EJML classes.
*/
fun ejmlCodegen(outputFile: String): Unit = File(outputFile).run {
parentFile.mkdirs()
writer().use {
it.appendLine("/*")
it.appendLine(" * Copyright 2018-2021 KMath contributors.")
it.appendLine(" * Use of this source code is governed by the Apache 2.0 license that can be found in the LICENSE file.")
it.appendLine(" */")
it.appendLine()
it.appendLine("/* This file is generated with buildSrc/src/main/kotlin/space/kscience/kmath/ejml/codegen/ejmlCodegen.kt */")
it.appendLine()
it.appendLine("package space.kscience.kmath.ejml")
it.appendLine()
it.appendLine("""import org.ejml.data.*
import org.ejml.dense.row.CommonOps_DDRM
import org.ejml.dense.row.CommonOps_FDRM
import org.ejml.dense.row.factory.DecompositionFactory_DDRM
import org.ejml.dense.row.factory.DecompositionFactory_FDRM
import org.ejml.sparse.FillReducing
import org.ejml.sparse.csc.CommonOps_DSCC
import org.ejml.sparse.csc.CommonOps_FSCC
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.kmath.linear.*
import space.kscience.kmath.linear.Matrix
import space.kscience.kmath.misc.UnstableKMathAPI
import space.kscience.kmath.nd.StructureFeature
import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.FloatField
import space.kscience.kmath.operations.invoke
import space.kscience.kmath.structures.DoubleBuffer
import space.kscience.kmath.structures.FloatBuffer
import kotlin.reflect.KClass
import kotlin.reflect.cast""")
it.appendLine()
it.appendEjmlVector("Double", "DMatrix")
it.appendEjmlVector("Float", "FMatrix")
it.appendEjmlMatrix("Double", "DMatrix")
it.appendEjmlMatrix("Float", "FMatrix")
it.appendEjmlLinearSpace("Double", "DoubleField", "DMatrix", "DMatrixRMaj", "DMatrixRMaj", "DDRM", "DDRM", true)
it.appendEjmlLinearSpace("Float", "FloatField", "FMatrix", "FMatrixRMaj", "FMatrixRMaj", "FDRM", "FDRM", true)
it.appendEjmlLinearSpace(
type = "Double",
kmathAlgebra = "DoubleField",
ejmlMatrixParentTypeMatrix = "DMatrix",
ejmlMatrixType = "DMatrixSparseCSC",
ejmlMatrixDenseType = "DMatrixRMaj",
ops = "DSCC",
denseOps = "DDRM",
isDense = false,
)
it.appendEjmlLinearSpace(
type = "Float",
kmathAlgebra = "FloatField",
ejmlMatrixParentTypeMatrix = "FMatrix",
ejmlMatrixType = "FMatrixSparseCSC",
ejmlMatrixDenseType = "FMatrixRMaj",
ops = "FSCC",
denseOps = "FDRM",
isDense = false,
)
}
}

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@ -17,4 +17,4 @@ own `MemoryBuffer.create()` factory).
## Buffer performance ## Buffer performance
One should avoid using default boxing buffer wherever it is possible. Try to use primitive buffers or memory buffers One should avoid using default boxing buffer wherever it is possible. Try to use primitive buffers or memory buffers
instead. instead .

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@ -1,27 +1,20 @@
# Coding Conventions # Coding Conventions
Generally, KMath code follows Generally, KMath code follows general [Kotlin coding conventions](https://kotlinlang.org/docs/reference/coding-conventions.html), but with a number of small changes and clarifications.
general [Kotlin coding conventions](https://kotlinlang.org/docs/reference/coding-conventions.html), but with a number of
small changes and clarifications.
## Utility Class Naming ## Utility Class Naming
Filename should coincide with a name of one of the classes contained in the file or start with small letter and describe Filename should coincide with a name of one of the classes contained in the file or start with small letter and describe its contents.
its contents.
The code convention [here](https://kotlinlang.org/docs/reference/coding-conventions.html#source-file-names) says that The code convention [here](https://kotlinlang.org/docs/reference/coding-conventions.html#source-file-names) says that file names should start with a capital letter even if file does not contain classes. Yet starting utility classes and aggregators with a small letter seems to be a good way to visually separate those files.
file names should start with a capital letter even if file does not contain classes. Yet starting utility classes and
aggregators with a small letter seems to be a good way to visually separate those files.
This convention could be changed in future in a non-breaking way. This convention could be changed in future in a non-breaking way.
## Private Variable Naming ## Private Variable Naming
Private variables' names may start with underscore `_` for of the private mutable variable is shadowed by the public Private variables' names may start with underscore `_` for of the private mutable variable is shadowed by the public read-only value with the same meaning.
read-only value with the same meaning.
This rule does not permit underscores in names, but it is sometimes useful to "underscore" the fact that public and This rule does not permit underscores in names, but it is sometimes useful to "underscore" the fact that public and private versions draw up the same entity. It is allowed only for private variables.
private versions draw up the same entity. It is allowed only for private variables.
This convention could be changed in future in a non-breaking way. This convention could be changed in future in a non-breaking way.
@ -31,5 +24,4 @@ Use one-liners when they occupy single code window line both for functions and p
`val b: String get() = "fff"`. The same should be performed with multiline expressions when they could be `val b: String get() = "fff"`. The same should be performed with multiline expressions when they could be
cleanly separated. cleanly separated.
There is no universal consensus whenever use `fun a() = ...` or `fun a() { return ... }`. Yet from reader outlook There is no universal consensus whenever use `fun a() = ...` or `fun a() { return ... }`. Yet from reader outlook one-lines seem to better show that the property or function is easily calculated.
one-lines seem to better show that the property or function is easily calculated.

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@ -1,19 +1,16 @@
# Expressions # Expressions
Expressions is a feature, which allows constructing lazily or immediately calculated parametric mathematical Expressions is a feature, which allows constructing lazily or immediately calculated parametric mathematical expressions.
expressions.
The potential use-cases for it (so far) are following: The potential use-cases for it (so far) are following:
* lazy evaluation (in general simple lambda is better, but there are some border cases); * lazy evaluation (in general simple lambda is better, but there are some border cases);
* automatic differentiation in single-dimension and in multiple dimensions; * automatic differentiation in single-dimension and in multiple dimensions;
* generation of mathematical syntax trees with subsequent code generation for other languages; * generation of mathematical syntax trees with subsequent code generation for other languages;
* symbolic computations, especially differentiation (and some other actions with `kmath-symja` integration with * symbolic computations, especially differentiation (and some other actions with `kmath-symja` integration with Symja's `IExpr`&mdash;integration, simplification, and more);
Symja's `IExpr`&mdash;integration, simplification, and more);
* visualization with `kmath-jupyter`. * visualization with `kmath-jupyter`.
The workhorse of this API is `Expression` interface, which exposes The workhorse of this API is `Expression` interface, which exposes single `operator fun invoke(arguments: Map<Symbol, T>): T`
single `operator fun invoke(arguments: Map<Symbol, T>): T`
method. `ExpressionAlgebra` is used to generate expressions and introduce variables. method. `ExpressionAlgebra` is used to generate expressions and introduce variables.
Currently there are two implementations: Currently there are two implementations:
@ -21,4 +18,4 @@ Currently there are two implementations:
* Generic `ExpressionField` in `kmath-core` which allows construction of custom lazy expressions * Generic `ExpressionField` in `kmath-core` which allows construction of custom lazy expressions
* Auto-differentiation expression in `kmath-commons` module allows using full power of `DerivativeStructure` * Auto-differentiation expression in `kmath-commons` module allows using full power of `DerivativeStructure`
from commons-math. **TODO: add example** from commons-math. **TODO: add example**

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@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- <!--
- Copyright 2018-2024 KMath contributors. - Copyright 2018-2021 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. - Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
--> -->

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<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- <!--
- Copyright 2018-2024 KMath contributors. - Copyright 2018-2021 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. - Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
--> -->

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<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- <!--
- Copyright 2018-2024 KMath contributors. - Copyright 2018-2021 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. - Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
--> -->

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<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- <!--
- Copyright 2018-2024 KMath contributors. - Copyright 2018-2021 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. - Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
--> -->

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@ -1,12 +1,8 @@
## Basic linear algebra layout ## Basic linear algebra layout
KMath support for linear algebra organized in a context-oriented way, which means that operations are in most cases KMath support for linear algebra organized in a context-oriented way, which means that operations are in most cases declared in context classes, and are not the members of classes that store data. This allows more flexible approach to maintain multiple back-ends. The new operations added as extensions to contexts instead of being member functions of data structures.
declared in context classes, and are not the members of classes that store data. This allows more flexible approach to
maintain multiple back-ends. The new operations added as extensions to contexts instead of being member functions of
data structures.
The main context for linear algebra over matrices and vectors is `LinearSpace`, which defines addition and dot products The main context for linear algebra over matrices and vectors is `LinearSpace`, which defines addition and dot products of matrices and vectors:
of matrices and vectors:
```kotlin ```kotlin
import space.kscience.kmath.linear.* import space.kscience.kmath.linear.*
@ -32,5 +28,4 @@ LinearSpace.Companion.real {
## Backends overview ## Backends overview
### EJML ### EJML
### Commons Math ### Commons Math

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@ -8,7 +8,6 @@ One of the most sought after features of mathematical libraries is the high-perf
structures. In `kmath` performance depends on which particular context was used for operation. structures. In `kmath` performance depends on which particular context was used for operation.
Let us consider following contexts: Let us consider following contexts:
```kotlin ```kotlin
// automatically build context most suited for given type. // automatically build context most suited for given type.
val autoField = NDField.auto(DoubleField, dim, dim) val autoField = NDField.auto(DoubleField, dim, dim)
@ -17,7 +16,6 @@ Let us consider following contexts:
//A generic boxing field. It should be used for objects, not primitives. //A generic boxing field. It should be used for objects, not primitives.
val genericField = NDField.buffered(DoubleField, dim, dim) val genericField = NDField.buffered(DoubleField, dim, dim)
``` ```
Now let us perform several tests and see, which implementation is best suited for each case: Now let us perform several tests and see, which implementation is best suited for each case:
## Test case ## Test case
@ -26,27 +24,22 @@ To test performance we will take 2d-structures with `dim = 1000` and add a struc
to it `n = 1000` times. to it `n = 1000` times.
## Specialized ## Specialized
The code to run this looks like: The code to run this looks like:
```kotlin ```kotlin
specializedField.run { specializedField.run {
var res: NDBuffer<Float64> = one var res: NDBuffer<Double> = one
repeat(n) { repeat(n) {
res += 1.0 res += 1.0
} }
} }
``` ```
The performance of this code is the best of all tests since it inlines all operations and is specialized for operation The performance of this code is the best of all tests since it inlines all operations and is specialized for operation
with doubles. We will measure everything else relative to this one, so time for this test will be `1x` (real time with doubles. We will measure everything else relative to this one, so time for this test will be `1x` (real time
on my computer is about 4.5 seconds). The only problem with this approach is that it requires specifying type on my computer is about 4.5 seconds). The only problem with this approach is that it requires specifying type
from the beginning. Everyone does so anyway, so it is the recommended approach. from the beginning. Everyone does so anyway, so it is the recommended approach.
## Automatic ## Automatic
Let's do the same with automatic field inference: Let's do the same with automatic field inference:
```kotlin ```kotlin
autoField.run { autoField.run {
var res = one var res = one
@ -55,16 +48,13 @@ Let's do the same with automatic field inference:
} }
} }
``` ```
Ths speed of this operation is approximately the same as for specialized case since `NDField.auto` just Ths speed of this operation is approximately the same as for specialized case since `NDField.auto` just
returns the same `RealNDField` in this case. Of course, it is usually better to use specialized method to be sure. returns the same `RealNDField` in this case. Of course, it is usually better to use specialized method to be sure.
## Lazy ## Lazy
Lazy field does not produce a structure when asked, instead it generates an empty structure and fills it on-demand Lazy field does not produce a structure when asked, instead it generates an empty structure and fills it on-demand
using coroutines to parallelize computations. using coroutines to parallelize computations.
When one calls When one calls
```kotlin ```kotlin
lazyField.run { lazyField.run {
var res = one var res = one
@ -73,14 +63,12 @@ When one calls
} }
} }
``` ```
The result will be calculated almost immediately but the result will be empty. To get the full result The result will be calculated almost immediately but the result will be empty. To get the full result
structure one needs to call all its elements. In this case computation overhead will be huge. So this field never structure one needs to call all its elements. In this case computation overhead will be huge. So this field never
should be used if one expects to use the full result structure. Though if one wants only small fraction, it could should be used if one expects to use the full result structure. Though if one wants only small fraction, it could
save a lot of time. save a lot of time.
This field still could be used with reasonable performance if call code is changed: This field still could be used with reasonable performance if call code is changed:
```kotlin ```kotlin
lazyField.run { lazyField.run {
val res = one.map { val res = one.map {
@ -94,37 +82,30 @@ This field still could be used with reasonable performance if call code is chang
res.elements().forEach { it.second } res.elements().forEach { it.second }
} }
``` ```
In this case it completes in about `4x-5x` time due to boxing. In this case it completes in about `4x-5x` time due to boxing.
## Boxing ## Boxing
The boxing field produced by The boxing field produced by
```kotlin ```kotlin
genericField.run { genericField.run {
var res: NDBuffer<Float64> = one var res: NDBuffer<Double> = one
repeat(n) { repeat(n) {
res += 1.0 res += 1.0
} }
} }
``` ```
is the slowest one, because it requires boxing and unboxing the `double` on each operation. It takes about is the slowest one, because it requires boxing and unboxing the `double` on each operation. It takes about
`15x` time (**TODO: there seems to be a problem here, it should be slow, but not that slow**). This field should `15x` time (**TODO: there seems to be a problem here, it should be slow, but not that slow**). This field should
never be used for primitives. never be used for primitives.
## Element operation ## Element operation
Let us also check the speed for direct operations on elements: Let us also check the speed for direct operations on elements:
```kotlin ```kotlin
var res = genericField.one var res = genericField.one
repeat(n) { repeat(n) {
res += 1.0 res += 1.0
} }
``` ```
One would expect to be at least as slow as field operation, but in fact, this one takes only `2x` time to complete. One would expect to be at least as slow as field operation, but in fact, this one takes only `2x` time to complete.
It happens, because in this particular case it does not use actual `NDField` but instead calculated directly It happens, because in this particular case it does not use actual `NDField` but instead calculated directly
via extension function. via extension function.
@ -133,7 +114,6 @@ via extension function.
Usually it is bad idea to compare the direct numerical operation performance in different languages, but it hard to Usually it is bad idea to compare the direct numerical operation performance in different languages, but it hard to
work completely without frame of reference. In this case, simple numpy code: work completely without frame of reference. In this case, simple numpy code:
```python ```python
import numpy as np import numpy as np
@ -141,9 +121,7 @@ res = np.ones((1000,1000))
for i in range(1000): for i in range(1000):
res = res + 1.0 res = res + 1.0
``` ```
gives the completion time of about `1.1x`, which means that specialized kotlin code in fact is working faster (I think it is
gives the completion time of about `1.1x`, which means that specialized kotlin code in fact is working faster (I think
it is
because better memory management). Of course if one writes `res += 1.0`, the performance will be different, because better memory management). Of course if one writes `res += 1.0`, the performance will be different,
but it would be different case, because numpy overrides `+=` with in-place operations. In-place operations are but it would be different case, because numpy overrides `+=` with in-place operations. In-place operations are
available in `kmath` with `MutableNDStructure` but there is no field for it (one can still work with mapping available in `kmath` with `MutableNDStructure` but there is no field for it (one can still work with mapping

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@ -1,223 +0,0 @@
# Polynomials and Rational Functions
KMath provides a way to work with uni- and multivariate polynomials and rational functions. It includes full support of
arithmetic operations of integers, **constants** (elements of ring polynomials are build over), variables (for certain
multivariate implementations), polynomials and rational functions encapsulated in so-called **polynomial space** and *
*rational function space** and some other utilities such as algebraic differentiation and substitution.
## Concrete realizations
There are 3 approaches to represent polynomials:
1. For univariate polynomials one can represent and store polynomial as a list of coefficients for each power of the
variable. I.e. polynomial $a_0 + \dots + a_n x^n $ can be represented as a finite sequence $(a_0; \dots; a_n)$. (
Compare to sequential definition of polynomials.)
2. For multivariate polynomials one can represent and store polynomial as a matching (in programming it is called "map"
or "dictionary", in math it is
called [functional relation](https://en.wikipedia.org/wiki/Binary_relation#Special_types_of_binary_relations)) of
each "**term signature**" (that describes what variables and in what powers appear in the term) with corresponding
coefficient of the term. But there are 2 possible approaches of term signature representation:
1. One can number all the variables, so term signature can be represented as a sequence describing powers of the
variables. I.e. signature of term $c \\; x_0^{d_0} \dots x_n^{d_n} $ (for natural or zero $d_i $) can be
represented as a finite sequence $(d_0; \dots; d_n)$.
2. One can represent variables as objects ("**labels**"), so term signature can be also represented as a matching of
each appeared variable with its power in the term. I.e. signature of term $c \\; x_0^{d_0} \dots x_n^{d_n} $ (for
natural non-zero $d_i $) can be represented as a finite matching $(x_0 \to d_1; \dots; x_n \to d_n)$.
All that three approaches are implemented by "list", "numbered", and "labeled" versions of polynomials and polynomial
spaces respectively. Whereas all rational functions are represented as fractions with corresponding polynomial numerator
and denominator, and rational functions' spaces are implemented in the same way as usual field of rational numbers (or
more precisely, as any field of fractions over integral domain) should be implemented.
So here are a bit of details. Let `C` by type of constants. Then:
1. `ListPolynomial`, `ListPolynomialSpace`, `ListRationalFunction` and `ListRationalFunctionSpace` implement the first
scenario. `ListPolynomial` stores polynomial $a_0 + \dots + a_n x^n $ as a coefficients
list `listOf(a_0, ..., a_n)` (of type `List<C>`).
They also have variation `ScalableListPolynomialSpace` that replaces former polynomials and
implements `ScaleOperations`.
2. `NumberedPolynomial`, `NumberedPolynomialSpace`, `NumberedRationalFunction` and `NumberedRationalFunctionSpace`
implement second scenario. `NumberedPolynomial` stores polynomials as structures of type `Map<List<UInt>, C>`.
Signatures are stored as `List<UInt>`. To prevent ambiguity signatures should not end with zeros.
3. `LabeledPolynomial`, `LabeledPolynomialSpace`, `LabeledRationalFunction` and `LabeledRationalFunctionSpace` implement
third scenario using common `Symbol` as variable type. `LabeledPolynomial` stores polynomials as structures of
type `Map<Map<Symbol, UInt>, C>`. Signatures are stored as `Map<Symbol, UInt>`. To prevent ambiguity each signature
should not map any variable to zero.
### Example: `ListPolynomial`
For example, polynomial $2 - 3x + x^2 $ (with `Int` coefficients) is represented
```kotlin
val polynomial: ListPolynomial<Int> = ListPolynomial(listOf(2, -3, 1))
// or
val polynomial: ListPolynomial<Int> = ListPolynomial(2, -3, 1)
```
All algebraic operations can be used in corresponding space:
```kotlin
val computationResult = Int.algebra.listPolynomialSpace {
ListPolynomial(2, -3, 1) + ListPolynomial(0, 6) == ListPolynomial(2, 3, 1)
}
println(computationResult) // true
```
For more see [examples](../examples/src/main/kotlin/space/kscience/kmath/functions/polynomials.kt).
### Example: `NumberedPolynomial`
For example, polynomial $3 + 5 x_1 - 7 x_0^2 x_2 $ (with `Int` coefficients) is represented
```kotlin
val polynomial: NumberedPolynomial<Int> = NumberedPolynomial(
mapOf(
listOf<UInt>() to 3,
listOf(0u, 1u) to 5,
listOf(2u, 0u, 1u) to -7,
)
)
// or
val polynomial: NumberedPolynomial<Int> = NumberedPolynomial(
listOf<UInt>() to 3,
listOf(0u, 1u) to 5,
listOf(2u, 0u, 1u) to -7,
)
```
All algebraic operations can be used in corresponding space:
```kotlin
val computationResult = Int.algebra.numberedPolynomialSpace {
NumberedPolynomial(
listOf<UInt>() to 3,
listOf(0u, 1u) to 5,
listOf(2u, 0u, 1u) to -7,
) + NumberedPolynomial(
listOf(0u, 1u) to -5,
listOf(0u, 0u, 0u, 4u) to 4,
) == NumberedPolynomial(
listOf<UInt>() to 3,
listOf(0u, 1u) to 0,
listOf(2u, 0u, 1u) to -7,
listOf(0u, 0u, 0u, 4u) to 4,
)
}
println(computationResult) // true
```
For more see [examples](../examples/src/main/kotlin/space/kscience/kmath/functions/polynomials.kt).
### Example: `LabeledPolynomial`
For example, polynomial $3 + 5 y - 7 x^2 z $ (with `Int` coefficients) is represented
```kotlin
val polynomial: LabeledPolynomial<Int> = LabeledPolynomial(
mapOf(
mapOf<Symbol, UInt>() to 3,
mapOf(y to 1u) to 5,
mapOf(x to 2u, z to 1u) to -7,
)
)
// or
val polynomial: LabeledPolynomial<Int> = LabeledPolynomial(
mapOf<Symbol, UInt>() to 3,
mapOf(y to 1u) to 5,
mapOf(x to 2u, z to 1u) to -7,
)
```
All algebraic operations can be used in corresponding space:
```kotlin
val computationResult = Int.algebra.labeledPolynomialSpace {
LabeledPolynomial(
listOf<UInt>() to 3,
listOf(0u, 1u) to 5,
listOf(2u, 0u, 1u) to -7,
) + LabeledPolynomial(
listOf(0u, 1u) to -5,
listOf(0u, 0u, 0u, 4u) to 4,
) == LabeledPolynomial(
listOf<UInt>() to 3,
listOf(0u, 1u) to 0,
listOf(2u, 0u, 1u) to -7,
listOf(0u, 0u, 0u, 4u) to 4,
)
}
println(computationResult) // true
```
For more see [examples](../examples/src/main/kotlin/space/kscience/kmath/functions/polynomials.kt).
## Abstract entities (interfaces and abstract classes)
```mermaid
classDiagram
Polynomial <|-- ListPolynomial
Polynomial <|-- NumberedPolynomial
Polynomial <|-- LabeledPolynomial
RationalFunction <|-- ListRationalFunction
RationalFunction <|-- NumberedRationalFunction
RationalFunction <|-- LabeledRationalFunction
Ring <|-- PolynomialSpace
PolynomialSpace <|-- MultivariatePolynomialSpace
PolynomialSpace <|-- PolynomialSpaceOverRing
Ring <|-- RationalFunctionSpace
RationalFunctionSpace <|-- MultivariateRationalFunctionSpace
RationalFunctionSpace <|-- RationalFunctionSpaceOverRing
RationalFunctionSpace <|-- RationalFunctionSpaceOverPolynomialSpace
RationalFunctionSpace <|-- PolynomialSpaceOfFractions
RationalFunctionSpaceOverPolynomialSpace <|-- MultivariateRationalFunctionSpaceOverMultivariatePolynomialSpace
MultivariateRationalFunctionSpace <|-- MultivariateRationalFunctionSpaceOverMultivariatePolynomialSpace
MultivariateRationalFunctionSpace <|-- MultivariatePolynomialSpaceOfFractions
PolynomialSpaceOfFractions <|-- MultivariatePolynomialSpaceOfFractions
```
There are implemented `Polynomial` and `RationalFunction` interfaces as abstractions of polynomials and rational
functions respectively (although, there is not a lot of logic in them) and `PolynomialSpace`
and `RationalFunctionSpace` (that implement `Ring` interface) as abstractions of polynomials' and rational functions'
spaces respectively. More precisely, that means they allow to declare common logic of interaction with such objects and
spaces:
- `Polynomial` does not provide any logic. It is marker interface.
- `RationalFunction` provides numerator and denominator of rational function and destructuring declaration for them.
- `PolynomialSpace` provides all possible arithmetic interactions of integers, constants (of type `C`), and
polynomials (of type `P`) like addition, subtraction, multiplication, and some others and common properties like
degree of polynomial.
- `RationalFunctionSpace` provides the same as `PolynomialSpace` but also for rational functions: all possible
arithmetic interactions of integers, constants (of type `C`), polynomials (of type `P`), and rational functions (of
type `R`) like addition, subtraction, multiplication, division (in some cases), and some others and common properties
like degree of polynomial.
Then to add abstraction of similar behaviour with variables (in multivariate case) there are
implemented `MultivariatePolynomialSpace` and `MultivariateRationalFunctionSpace`. They just include variables (of
type `V`) in the interactions of the entities.
Also, to remove boilerplates there were provided helping subinterfaces and abstract subclasses:
- `PolynomialSpaceOverRing` allows to replace implementation of interactions of integers and constants with
implementations from provided ring over constants (of type `A: Ring<C>`).
- `RationalFunctionSpaceOverRing` &mdash; the same but for `RationalFunctionSpace`.
- `RationalFunctionSpaceOverPolynomialSpace` &mdash; the same but "the inheritance" includes interactions with
polynomials from provided `PolynomialSpace`.
- `PolynomialSpaceOfFractions` is actually abstract subclass of `RationalFunctionSpace` that implements all fractions
boilerplates with provided (`protected`) constructor of rational functions by polynomial numerator and denominator.
- `MultivariateRationalFunctionSpaceOverMultivariatePolynomialSpace` and `MultivariatePolynomialSpaceOfFractions`
&mdash; the same stories of operators inheritance and fractions boilerplates respectively but in multivariate case.
## Utilities
For all kinds of polynomials there are provided (implementation details depend on kind of polynomials) such common
utilities as:
1. differentiation and anti-differentiation,
2. substitution, invocation and functional representation.

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@ -3,7 +3,17 @@
The Maven coordinates of this project are `${group}:${name}:${version}`. The Maven coordinates of this project are `${group}:${name}:${version}`.
**Gradle:** **Gradle:**
```gradle
repositories {
maven { url 'https://repo.kotlin.link' }
mavenCentral()
}
dependencies {
implementation '${group}:${name}:${version}'
}
```
**Gradle Kotlin DSL:**
```kotlin ```kotlin
repositories { repositories {
maven("https://repo.kotlin.link") maven("https://repo.kotlin.link")

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@ -1,6 +1,6 @@
[![JetBrains Research](https://jb.gg/badges/research.svg)](https://confluence.jetbrains.com/display/ALL/JetBrains+on+GitHub) [![JetBrains Research](https://jb.gg/badges/research.svg)](https://confluence.jetbrains.com/display/ALL/JetBrains+on+GitHub)
[![DOI](https://zenodo.org/badge/129486382.svg)](https://zenodo.org/badge/latestdoi/129486382) [![DOI](https://zenodo.org/badge/129486382.svg)](https://zenodo.org/badge/latestdoi/129486382)
![Gradle build](https://github.com/SciProgCentre/kmath/workflows/Gradle%20build/badge.svg) ![Gradle build](https://github.com/mipt-npm/kmath/workflows/Gradle%20build/badge.svg)
[![Maven Central](https://img.shields.io/maven-central/v/space.kscience/kmath-core.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22space.kscience%22) [![Maven Central](https://img.shields.io/maven-central/v/space.kscience/kmath-core.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22space.kscience%22)
[![Space](https://img.shields.io/badge/dynamic/xml?color=orange&label=Space&query=//metadata/versioning/latest&url=https%3A%2F%2Fmaven.pkg.jetbrains.space%2Fmipt-npm%2Fp%2Fsci%2Fmaven%2Fspace%2Fkscience%2Fkmath-core%2Fmaven-metadata.xml)](https://maven.pkg.jetbrains.space/mipt-npm/p/sci/maven/space/kscience/) [![Space](https://img.shields.io/badge/dynamic/xml?color=orange&label=Space&query=//metadata/versioning/latest&url=https%3A%2F%2Fmaven.pkg.jetbrains.space%2Fmipt-npm%2Fp%2Fsci%2Fmaven%2Fspace%2Fkscience%2Fkmath-core%2Fmaven-metadata.xml)](https://maven.pkg.jetbrains.space/mipt-npm/p/sci/maven/space/kscience/)
@ -11,22 +11,18 @@ analog to Python's NumPy library. Later we found that kotlin is much more flexib
architecture designs. In contrast to `numpy` and `scipy` it is modular and has a lightweight core. The `numpy`-like architecture designs. In contrast to `numpy` and `scipy` it is modular and has a lightweight core. The `numpy`-like
experience could be achieved with [kmath-for-real](/kmath-for-real) extension module. experience could be achieved with [kmath-for-real](/kmath-for-real) extension module.
[Documentation site](https://SciProgCentre.github.io/kmath/) [Documentation site (**WIP**)](https://mipt-npm.github.io/kmath/)
## Publications and talks ## Publications and talks
* [A conceptual article about context-oriented design](https://proandroiddev.com/an-introduction-context-oriented-programming-in-kotlin-2e79d316b0a2) * [A conceptual article about context-oriented design](https://proandroiddev.com/an-introduction-context-oriented-programming-in-kotlin-2e79d316b0a2)
* [Another article about context-oriented design](https://proandroiddev.com/diving-deeper-into-context-oriented-programming-in-kotlin-3ecb4ec38814) * [Another article about context-oriented design](https://proandroiddev.com/diving-deeper-into-context-oriented-programming-in-kotlin-3ecb4ec38814)
* [ACAT 2019 conference paper](https://aip.scitation.org/doi/abs/10.1063/1.5130103) * [ACAT 2019 conference paper](https://aip.scitation.org/doi/abs/10.1063/1.5130103)
* [A talk at KotlinConf 2019 about using kotlin for science](https://youtu.be/LI_5TZ7tnOE?si=4LknX41gl_YeUbIe)
* [A talk on architecture at Joker-2021 (in Russian)](https://youtu.be/1bZ2doHiRRM?si=9w953ro9yu98X_KJ)
* [The same talk in English](https://youtu.be/yP5DIc2fVwQ?si=louZzQ1dcXV6gP10)
* [A seminar on tensor API](https://youtu.be/0H99wUs0xTM?si=6c__04jrByFQtVpo)
# Goal # Goal
* Provide a flexible and powerful API to work with mathematics abstractions in Kotlin-multiplatform (JVM, JS, Native and * Provide a flexible and powerful API to work with mathematics abstractions in Kotlin-multiplatform (JVM, JS and Native)
Wasm). .
* Provide basic multiplatform implementations for those abstractions (without significant performance optimization). * Provide basic multiplatform implementations for those abstractions (without significant performance optimization).
* Provide bindings and wrappers with those abstractions for popular optimized platform libraries. * Provide bindings and wrappers with those abstractions for popular optimized platform libraries.
@ -48,7 +44,7 @@ module definitions below. The module stability could have the following levels:
* **PROTOTYPE**. On this level there are no compatibility guarantees. All methods and classes form those modules could * **PROTOTYPE**. On this level there are no compatibility guarantees. All methods and classes form those modules could
break any moment. You can still use it, but be sure to fix the specific version. break any moment. You can still use it, but be sure to fix the specific version.
* **EXPERIMENTAL**. The general API is decided, but some changes could be made. Volatile API is marked * **EXPERIMENTAL**. The general API is decided, but some changes could be made. Volatile API is marked
with `@UnstableKMathAPI` or other stability warning annotations. with `@UnstableKmathAPI` or other stability warning annotations.
* **DEVELOPMENT**. API breaking generally follows semantic versioning ideology. There could be changes in minor * **DEVELOPMENT**. API breaking generally follows semantic versioning ideology. There could be changes in minor
versions, but not in patch versions. API is protected versions, but not in patch versions. API is protected
with [binary-compatibility-validator](https://github.com/Kotlin/binary-compatibility-validator) tool. with [binary-compatibility-validator](https://github.com/Kotlin/binary-compatibility-validator) tool.
@ -63,24 +59,23 @@ ${modules}
KMath is developed as a multi-platform library, which means that most of the interfaces are declared in the KMath is developed as a multi-platform library, which means that most of the interfaces are declared in the
[common source sets](/kmath-core/src/commonMain) and implemented there wherever it is possible. In some cases, features [common source sets](/kmath-core/src/commonMain) and implemented there wherever it is possible. In some cases, features
are delegated to platform-specific implementations even if they could be provided in the common module for performance are delegated to platform-specific implementations even if they could be provided in the common module for performance
reasons. Currently, Kotlin/JVM is the primary platform, however, Kotlin/Native and Kotlin/JS contributions and reasons. Currently, the Kotlin/JVM is the primary platform, however Kotlin/Native and Kotlin/JS contributions and
feedback are also welcome. feedback are also welcome.
## Performance ## Performance
Calculation of performance is one of the major goals of KMath in the future, but in some cases it is impossible to Calculation performance is one of major goals of KMath in the future, but in some cases it is impossible to achieve both
achieve both
performance and flexibility. performance and flexibility.
We expect to focus on creating a convenient universal API first and then work on increasing performance for specific We expect to focus on creating convenient universal API first and then work on increasing performance for specific
cases. We expect the worst KMath benchmarks will perform better than native Python, but worse than optimized cases. We expect the worst KMath benchmarks will perform better than native Python, but worse than optimized
native/SciPy (mostly due to boxing operations on primitive numbers). The best performance of optimized parts could be native/SciPy (mostly due to boxing operations on primitive numbers). The best performance of optimized parts could be
better than SciPy. better than SciPy.
## Requirements ## Requirements
KMath currently relies on JDK 11 for compilation and execution of Kotlin-JVM part. We recommend using GraalVM-CE or KMath currently relies on JDK 11 for compilation and execution of Kotlin-JVM part. We recommend to use GraalVM-CE 11 for
Oracle GraalVM for execution to get better performance. execution to get better performance.
### Repositories ### Repositories
@ -100,10 +95,11 @@ dependencies {
} }
``` ```
Gradle `6.0+` is required for multiplatform artifacts.
## Contributing ## Contributing
The project requires a lot of additional work. The most important thing we need is feedback about what features are The project requires a lot of additional work. The most important thing we need is a feedback about what features are
required the most. Feel free to create feature requests. We are also welcome to code contributions, especially in issues required the most. Feel free to create feature requests. We are also welcome to code contributions, especially in issues
marked marked with
with [good first issue](hhttps://github.com/SciProgCentre/kmath/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22) [waiting for a hero](https://github.com/mipt-npm/kmath/labels/waiting%20for%20a%20hero) label.
label.

View File

@ -1,5 +1,3 @@
import org.jetbrains.kotlin.gradle.tasks.KotlinJvmCompile
plugins { plugins {
kotlin("jvm") kotlin("jvm")
} }
@ -17,7 +15,6 @@ dependencies {
implementation(project(":kmath-coroutines")) implementation(project(":kmath-coroutines"))
implementation(project(":kmath-commons")) implementation(project(":kmath-commons"))
implementation(project(":kmath-complex")) implementation(project(":kmath-complex"))
implementation(project(":kmath-functions"))
implementation(project(":kmath-optimization")) implementation(project(":kmath-optimization"))
implementation(project(":kmath-stat")) implementation(project(":kmath-stat"))
implementation(project(":kmath-viktor")) implementation(project(":kmath-viktor"))
@ -31,10 +28,7 @@ dependencies {
implementation(project(":kmath-jafama")) implementation(project(":kmath-jafama"))
//multik //multik
implementation(project(":kmath-multik")) implementation(project(":kmath-multik"))
implementation(libs.multik.default)
//datetime
implementation("org.jetbrains.kotlinx:kotlinx-datetime:0.4.0")
implementation("org.nd4j:nd4j-native:1.0.0-beta7") implementation("org.nd4j:nd4j-native:1.0.0-beta7")
@ -48,28 +42,29 @@ dependencies {
// } else // } else
implementation("org.nd4j:nd4j-native-platform:1.0.0-beta7") implementation("org.nd4j:nd4j-native-platform:1.0.0-beta7")
// multik implementation
implementation("org.jetbrains.kotlinx:multik-default:0.1.0")
implementation("org.slf4j:slf4j-simple:1.7.32") implementation("org.slf4j:slf4j-simple:1.7.32")
// plotting // plotting
implementation("space.kscience:plotlykt-server:0.7.0") implementation("space.kscience:plotlykt-server:0.5.0")
} }
kotlin { kotlin.sourceSets.all {
jvmToolchain(11) with(languageSettings) {
sourceSets.all { optIn("kotlin.contracts.ExperimentalContracts")
languageSettings { optIn("kotlin.ExperimentalUnsignedTypes")
optIn("kotlin.contracts.ExperimentalContracts") optIn("space.kscience.kmath.misc.UnstableKMathAPI")
optIn("kotlin.ExperimentalUnsignedTypes")
optIn("space.kscience.kmath.UnstableKMathAPI")
}
} }
} }
tasks.withType<KotlinJvmCompile> { tasks.withType<org.jetbrains.kotlin.gradle.dsl.KotlinJvmCompile> {
compilerOptions { kotlinOptions {
freeCompilerArgs.addAll("-Xjvm-default=all", "-Xopt-in=kotlin.RequiresOptIn", "-Xlambdas=indy") jvmTarget = "11"
freeCompilerArgs = freeCompilerArgs + "-Xjvm-default=all" + "-Xopt-in=kotlin.RequiresOptIn" + "-Xlambdas=indy"
} }
} }
readme { readme {
maturity = space.kscience.gradle.Maturity.EXPERIMENTAL maturity = ru.mipt.npm.gradle.Maturity.EXPERIMENTAL
} }

View File

@ -1,418 +0,0 @@
{
"cells": [
{
"cell_type": "code",
"source": [
"%use kmath(0.3.1-dev-5)\n",
"%use plotly(0.5.0)\n",
"@file:DependsOn(\"space.kscience:kmath-commons:0.3.1-dev-5\")"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "lQbSB87rNAn9lV6poArVWW",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "code",
"source": [
"//Uncomment to work in Jupyter classic or DataLore\n",
"//Plotly.jupyter.notebook()"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "0UP158hfccGgjQtHz0wAi6",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "markdown",
"source": [
"# The model\n",
"\n",
"Defining the input data format, the statistic abstraction and the statistic implementation based on a weighted sum of elements."
],
"metadata": {
"collapsed": false
}
},
{
"cell_type": "code",
"source": [
"class XYValues(val xValues: DoubleArray, val yValues: DoubleArray) {\n",
" init {\n",
" require(xValues.size == yValues.size)\n",
" }\n",
"}\n",
"\n",
"fun interface XYStatistic {\n",
" operator fun invoke(values: XYValues): Double\n",
"}\n",
"\n",
"class ConvolutionalXYStatistic(val weights: DoubleArray) : XYStatistic {\n",
" override fun invoke(values: XYValues): Double {\n",
" require(weights.size == values.yValues.size)\n",
" val norm = values.yValues.sum()\n",
" return values.yValues.zip(weights) { value, weight -> value * weight }.sum()/norm\n",
" }\n",
"}"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "Zhgz1Ui91PWz0meJiQpHol",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "markdown",
"source": [
"# Generator\n",
"Generate sample data for parabolas and hyperbolas"
],
"metadata": {
"collapsed": false
}
},
{
"cell_type": "code",
"execution_count": null,
"outputs": [],
"source": [
"fun generateParabolas(xValues: DoubleArray, a: Double, b: Double, c: Double): XYValues {\n",
" val yValues = xValues.map { x -> a * x * x + b * x + c }.toDoubleArray()\n",
" return XYValues(xValues, yValues)\n",
"}\n",
"\n",
"fun generateHyperbols(xValues: DoubleArray, gamma: Double, x0: Double, y0: Double): XYValues {\n",
" val yValues = xValues.map { x -> y0 + gamma / (x - x0) }.toDoubleArray()\n",
" return XYValues(xValues, yValues)\n",
"}"
],
"metadata": {
"collapsed": false
}
},
{
"cell_type": "code",
"source": [
"val xValues = (1.0..10.0).step(1.0).toDoubleArray()\n",
"\n",
"val xy = generateHyperbols(xValues, 1.0, 0.0, 0.0)\n",
"\n",
"Plotly.plot {\n",
" scatter {\n",
" this.x.doubles = xValues\n",
" this.y.doubles = xy.yValues\n",
" }\n",
"}"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "ZE2atNvFzQsCvpAF8KK4ch",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "markdown",
"source": [
"Create a default statistic with uniform weights"
],
"metadata": {
"collapsed": false
}
},
{
"cell_type": "code",
"source": [
"val statistic = ConvolutionalXYStatistic(DoubleArray(xValues.size){1.0})\n",
"statistic(xy)"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "EA5HaydTddRKYrtAUwd29h",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "code",
"source": [
"import kotlin.random.Random\n",
"\n",
"val random = Random(1288)\n",
"\n",
"val parabolas = buildList{\n",
" repeat(500){\n",
" add(\n",
" generateParabolas(\n",
" xValues, \n",
" random.nextDouble(), \n",
" random.nextDouble(), \n",
" random.nextDouble()\n",
" )\n",
" )\n",
" }\n",
"}\n",
"\n",
"val hyperbolas: List<XYValues> = buildList{\n",
" repeat(500){\n",
" add(\n",
" generateHyperbols(\n",
" xValues, \n",
" random.nextDouble()*10, \n",
" random.nextDouble(), \n",
" random.nextDouble()\n",
" )\n",
" )\n",
" }\n",
"}"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "t5t6IYmD7Q1ykeo9uijFfQ",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "code",
"source": [
"Plotly.plot { \n",
" scatter { \n",
" x.doubles = xValues\n",
" y.doubles = parabolas[257].yValues\n",
" }\n",
" scatter { \n",
" x.doubles = xValues\n",
" y.doubles = hyperbolas[252].yValues\n",
" }\n",
" }"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "oXB8lmju7YVYjMRXITKnhO",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "code",
"source": [
"Plotly.plot { \n",
" histogram { \n",
" name = \"parabolae\"\n",
" x.numbers = parabolas.map { statistic(it) }\n",
" }\n",
" histogram { \n",
" name = \"hyperbolae\"\n",
" x.numbers = hyperbolas.map { statistic(it) }\n",
" }\n",
"}"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "8EIIecUZrt2NNrOkhxG5P0",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "code",
"source": [
"val lossFunction: (XYStatistic) -> Double = { statistic ->\n",
" - abs(parabolas.sumOf { statistic(it) } - hyperbolas.sumOf { statistic(it) })\n",
"}"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "h7UmglJW5zXkAfKHK40oIL",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "markdown",
"source": [
"Using commons-math optimizer to optimize weights"
],
"metadata": {
"collapsed": false
}
},
{
"cell_type": "code",
"source": [
"import org.apache.commons.math3.optim.*\n",
"import org.apache.commons.math3.optim.nonlinear.scalar.*\n",
"import org.apache.commons.math3.optim.nonlinear.scalar.noderiv.*\n",
"\n",
"val optimizer = SimplexOptimizer(1e-1, Double.MAX_VALUE)\n",
"\n",
"val result = optimizer.optimize(\n",
" ObjectiveFunction { point ->\n",
" lossFunction(ConvolutionalXYStatistic(point))\n",
" },\n",
" NelderMeadSimplex(xValues.size),\n",
" InitialGuess(DoubleArray(xValues.size){ 1.0 }),\n",
" GoalType.MINIMIZE,\n",
" MaxEval(100000)\n",
")"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "0EG3K4aCUciMlgGQKPvJ57",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "markdown",
"source": [
"Print resulting weights of optimization"
],
"metadata": {
"collapsed": false
}
},
{
"cell_type": "code",
"source": [
"result.point"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "LelUlY0ZSlJEO9yC6SLk5B",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "code",
"source": [
"Plotly.plot { \n",
" scatter { \n",
" y.doubles = result.point\n",
" }\n",
"}"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "AuFOq5t9KpOIkGrOLsVXNf",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "markdown",
"source": [
"# The resulting statistic distribution"
],
"metadata": {
"collapsed": false
}
},
{
"cell_type": "code",
"source": [
"val resultStatistic = ConvolutionalXYStatistic(result.point)\n",
"Plotly.plot { \n",
" histogram { \n",
" name = \"parabolae\"\n",
" x.numbers = parabolas.map { resultStatistic(it) }\n",
" }\n",
" histogram { \n",
" name = \"hyperbolae\"\n",
" x.numbers = hyperbolas.map { resultStatistic(it) }\n",
" }\n",
"}"
],
"execution_count": null,
"outputs": [],
"metadata": {
"datalore": {
"node_id": "zvmq42DRdM5mZ3SpzviHwI",
"type": "CODE",
"hide_input_from_viewers": false,
"hide_output_from_viewers": false
}
}
},
{
"cell_type": "code",
"execution_count": null,
"outputs": [],
"source": [],
"metadata": {
"collapsed": false
}
}
],
"metadata": {
"kernelspec": {
"display_name": "Kotlin",
"language": "kotlin",
"name": "kotlin"
},
"datalore": {
"version": 1,
"computation_mode": "JUPYTER",
"package_manager": "pip",
"base_environment": "default",
"packages": []
}
},
"nbformat": 4,
"nbformat_minor": 4
}

View File

@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */

View File

@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -8,13 +8,13 @@ package space.kscience.kmath.ast
import space.kscience.kmath.asm.compileToExpression import space.kscience.kmath.asm.compileToExpression
import space.kscience.kmath.expressions.MstExtendedField import space.kscience.kmath.expressions.MstExtendedField
import space.kscience.kmath.expressions.Symbol.Companion.x import space.kscience.kmath.expressions.Symbol.Companion.x
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
fun main() { fun main() {
val expr = MstExtendedField { val expr = MstExtendedField {
x * 2.0 + number(2.0) / x - number(16.0) + asinh(x) / sin(x) x * 2.0 + number(2.0) / x - number(16.0) + asinh(x) / sin(x)
}.compileToExpression(Float64Field) }.compileToExpression(DoubleField)
val m = DoubleArray(expr.indexer.symbols.size) val m = DoubleArray(expr.indexer.symbols.size)
val xIdx = expr.indexer.indexOf(x) val xIdx = expr.indexer.indexOf(x)

View File

@ -1,16 +1,16 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.ast package space.kscience.kmath.ast
import space.kscience.kmath.expressions.Symbol.Companion.x
import space.kscience.kmath.expressions.derivative import space.kscience.kmath.expressions.derivative
import space.kscience.kmath.expressions.invoke import space.kscience.kmath.expressions.invoke
import space.kscience.kmath.expressions.Symbol.Companion.x
import space.kscience.kmath.expressions.toExpression import space.kscience.kmath.expressions.toExpression
import space.kscience.kmath.kotlingrad.toKotlingradExpression import space.kscience.kmath.kotlingrad.toKotlingradExpression
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
/** /**
* In this example, *x<sup>2</sup> &minus; 4 x &minus; 44* function is differentiated with Kotlin, and the * In this example, *x<sup>2</sup> &minus; 4 x &minus; 44* function is differentiated with Kotlin, and the
@ -19,9 +19,9 @@ import space.kscience.kmath.operations.Float64Field
fun main() { fun main() {
val actualDerivative = "x^2-4*x-44" val actualDerivative = "x^2-4*x-44"
.parseMath() .parseMath()
.toKotlingradExpression(Float64Field) .toKotlingradExpression(DoubleField)
.derivative(x) .derivative(x)
val expectedDerivative = "2*x-4".parseMath().toExpression(Float64Field) val expectedDerivative = "2*x-4".parseMath().toExpression(DoubleField)
check(actualDerivative(x to 123.0) == expectedDerivative(x to 123.0)) check(actualDerivative(x to 123.0) == expectedDerivative(x to 123.0))
} }

View File

@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -9,7 +9,7 @@ import space.kscience.kmath.expressions.Symbol.Companion.x
import space.kscience.kmath.expressions.derivative import space.kscience.kmath.expressions.derivative
import space.kscience.kmath.expressions.invoke import space.kscience.kmath.expressions.invoke
import space.kscience.kmath.expressions.toExpression import space.kscience.kmath.expressions.toExpression
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.symja.toSymjaExpression import space.kscience.kmath.symja.toSymjaExpression
/** /**
@ -19,9 +19,9 @@ import space.kscience.kmath.symja.toSymjaExpression
fun main() { fun main() {
val actualDerivative = "x^2-4*x-44" val actualDerivative = "x^2-4*x-44"
.parseMath() .parseMath()
.toSymjaExpression(Float64Field) .toSymjaExpression(DoubleField)
.derivative(x) .derivative(x)
val expectedDerivative = "2*x-4".parseMath().toExpression(Float64Field) val expectedDerivative = "2*x-4".parseMath().toExpression(DoubleField)
check(actualDerivative(x to 123.0) == expectedDerivative(x to 123.0)) check(actualDerivative(x to 123.0) == expectedDerivative(x to 123.0))
} }

View File

@ -1,92 +0,0 @@
/*
* Copyright 2018-2024 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.expressions
import space.kscience.kmath.UnstableKMathAPI
// Only kmath-core is needed.
// Let's declare some variables
val x by symbol
val y by symbol
val z by symbol
@OptIn(UnstableKMathAPI::class)
fun main() {
// Let's define some random expression.
val someExpression = Double.autodiff.differentiate {
// We bind variables `x` and `y` to the builder scope,
val x = bindSymbol(x)
val y = bindSymbol(y)
// Then we use the bindings to define expression `xy + x + y - 1`
x * y + x + y - 1
}
// Then we can evaluate it at any point ((-1, -1) in the case):
println(someExpression(x to -1.0, y to -1.0))
// >>> -2.0
// We can also construct its partial derivatives:
val dxExpression = someExpression.derivative(x) // ∂/∂x. Must be `y+1`
val dyExpression = someExpression.derivative(y) // ∂/∂y. Must be `x+1`
val dxdxExpression = someExpression.derivative(x, x) // ∂^2/∂x^2. Must be `0`
// We can evaluate them as well
println(dxExpression(x to 57.0, y to 6.0))
// >>> 7.0
println(dyExpression(x to -1.0, y to 179.0))
// >>> 0.0
println(dxdxExpression(x to 239.0, y to 30.0))
// >>> 0.0
// You can also provide extra arguments that obviously won't affect the result:
println(dxExpression(x to 57.0, y to 6.0, z to 42.0))
// >>> 7.0
println(dyExpression(x to -1.0, y to 179.0, z to 0.0))
// >>> 0.0
println(dxdxExpression(x to 239.0, y to 30.0, z to 100_000.0))
// >>> 0.0
// But in case you forgot to specify bound symbol's value, exception is thrown:
println(runCatching { someExpression(z to 4.0) })
// >>> Failure(java.lang.IllegalStateException: Symbol 'x' is not supported in ...)
// The reason is that the expression is evaluated lazily,
// and each `bindSymbol` operation actually substitutes the provided symbol with the corresponding value.
// For example, let there be an expression
val simpleExpression = Double.autodiff.differentiate {
val x = bindSymbol(x)
x pow 2
}
// When you evaluate it via
simpleExpression(x to 1.0, y to 57.0, z to 179.0)
// lambda above has the context of map `{x: 1.0, y: 57.0, z: 179.0}`.
// When x is bound, you can think of it as substitution `x -> 1.0`.
// Other values are unused which does not make any problem to us.
// But in the case the corresponding value is not provided,
// we cannot bind the variable. Thus, exception is thrown.
// There is also a function `bindSymbolOrNull` that fixes the problem:
val fixedExpression = Double.autodiff.differentiate {
val x = bindSymbolOrNull(x) ?: const(8.0)
x pow -2
}
println(fixedExpression())
// >>> 0.015625
// It works!
// The expression provides a bunch of operations:
// 1. Constant bindings (via `const` and `number`).
// 2. Variable bindings (via `bindVariable`, `bindVariableOrNull`).
// 3. Arithmetic operations (via `+`, `-`, `*`, and `-`).
// 4. Exponentiation (via `pow` or `power`).
// 5. `exp` and `ln`.
// 6. Trigonometrical functions (`sin`, `cos`, `tan`, `cot`).
// 7. Inverse trigonometrical functions (`asin`, `acos`, `atan`, `acot`).
// 8. Hyperbolic functions and inverse hyperbolic functions.
}

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -7,18 +7,21 @@ package space.kscience.kmath.fit
import kotlinx.html.br import kotlinx.html.br
import kotlinx.html.h3 import kotlinx.html.h3
import space.kscience.kmath.commons.expressions.DSProcessor
import space.kscience.kmath.commons.optimization.CMOptimizer import space.kscience.kmath.commons.optimization.CMOptimizer
import space.kscience.kmath.distributions.NormalDistribution import space.kscience.kmath.distributions.NormalDistribution
import space.kscience.kmath.expressions.autodiff import space.kscience.kmath.expressions.chiSquaredExpression
import space.kscience.kmath.expressions.symbol import space.kscience.kmath.expressions.symbol
import space.kscience.kmath.operations.asIterable import space.kscience.kmath.operations.asIterable
import space.kscience.kmath.operations.toList import space.kscience.kmath.operations.toList
import space.kscience.kmath.optimization.* import space.kscience.kmath.optimization.FunctionOptimizationTarget
import space.kscience.kmath.random.RandomGenerator import space.kscience.kmath.optimization.optimizeWith
import space.kscience.kmath.optimization.resultPoint
import space.kscience.kmath.optimization.resultValue
import space.kscience.kmath.real.DoubleVector import space.kscience.kmath.real.DoubleVector
import space.kscience.kmath.real.map import space.kscience.kmath.real.map
import space.kscience.kmath.real.step import space.kscience.kmath.real.step
import space.kscience.kmath.stat.chiSquaredExpression import space.kscience.kmath.stat.RandomGenerator
import space.kscience.plotly.* import space.kscience.plotly.*
import space.kscience.plotly.models.ScatterMode import space.kscience.plotly.models.ScatterMode
import space.kscience.plotly.models.TraceValues import space.kscience.plotly.models.TraceValues
@ -64,7 +67,7 @@ suspend fun main() {
val yErr = y.map { sqrt(it) }//RealVector.same(x.size, sigma) val yErr = y.map { sqrt(it) }//RealVector.same(x.size, sigma)
// compute differentiable chi^2 sum for given model ax^2 + bx + c // compute differentiable chi^2 sum for given model ax^2 + bx + c
val chi2 = Double.autodiff.chiSquaredExpression(x, y, yErr) { arg -> val chi2 = DSProcessor.chiSquaredExpression(x, y, yErr) { arg ->
//bind variables to autodiff context //bind variables to autodiff context
val a = bindSymbol(a) val a = bindSymbol(a)
val b = bindSymbol(b) val b = bindSymbol(b)
@ -77,9 +80,8 @@ suspend fun main() {
val result = chi2.optimizeWith( val result = chi2.optimizeWith(
CMOptimizer, CMOptimizer,
mapOf(a to 1.5, b to 0.9, c to 1.0), mapOf(a to 1.5, b to 0.9, c to 1.0),
) { FunctionOptimizationTarget.MINIMIZE
FunctionOptimizationTarget(OptimizationDirection.MINIMIZE) )
}
//display a page with plot and numerical results //display a page with plot and numerical results
val page = Plotly.page { val page = Plotly.page {
@ -96,7 +98,7 @@ suspend fun main() {
scatter { scatter {
mode = ScatterMode.lines mode = ScatterMode.lines
x(x) x(x)
y(x.map { result.result[a]!! * it.pow(2) + result.result[b]!! * it + 1 }) y(x.map { result.resultPoint[a]!! * it.pow(2) + result.resultPoint[b]!! * it + 1 })
name = "fit" name = "fit"
} }
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -7,19 +7,21 @@ package space.kscience.kmath.fit
import kotlinx.html.br import kotlinx.html.br
import kotlinx.html.h3 import kotlinx.html.h3
import space.kscience.attributes.Attributes import space.kscience.kmath.commons.expressions.DSProcessor
import space.kscience.kmath.data.XYErrorColumnarData import space.kscience.kmath.data.XYErrorColumnarData
import space.kscience.kmath.distributions.NormalDistribution import space.kscience.kmath.distributions.NormalDistribution
import space.kscience.kmath.expressions.Symbol import space.kscience.kmath.expressions.Symbol
import space.kscience.kmath.expressions.autodiff
import space.kscience.kmath.expressions.binding import space.kscience.kmath.expressions.binding
import space.kscience.kmath.expressions.symbol import space.kscience.kmath.expressions.symbol
import space.kscience.kmath.operations.asIterable import space.kscience.kmath.operations.asIterable
import space.kscience.kmath.operations.toList import space.kscience.kmath.operations.toList
import space.kscience.kmath.optimization.* import space.kscience.kmath.optimization.QowOptimizer
import space.kscience.kmath.random.RandomGenerator import space.kscience.kmath.optimization.chiSquaredOrNull
import space.kscience.kmath.optimization.fitWith
import space.kscience.kmath.optimization.resultPoint
import space.kscience.kmath.real.map import space.kscience.kmath.real.map
import space.kscience.kmath.real.step import space.kscience.kmath.real.step
import space.kscience.kmath.stat.RandomGenerator
import space.kscience.plotly.* import space.kscience.plotly.*
import space.kscience.plotly.models.ScatterMode import space.kscience.plotly.models.ScatterMode
import kotlin.math.abs import kotlin.math.abs
@ -30,8 +32,6 @@ import kotlin.math.sqrt
private val a by symbol private val a by symbol
private val b by symbol private val b by symbol
private val c by symbol private val c by symbol
private val d by symbol
private val e by symbol
/** /**
@ -63,23 +63,17 @@ suspend fun main() {
val result = XYErrorColumnarData.of(x, y, yErr).fitWith( val result = XYErrorColumnarData.of(x, y, yErr).fitWith(
QowOptimizer, QowOptimizer,
Double.autodiff, DSProcessor,
mapOf(a to 0.9, b to 1.2, c to 2.0, e to 1.0, d to 1.0, e to 0.0), mapOf(a to 0.9, b to 1.2, c to 2.0)
attributes = Attributes(OptimizationParameters, listOf(a, b, c, d))
) { arg -> ) { arg ->
//bind variables to autodiff context //bind variables to autodiff context
val a by binding val a by binding
val b by binding val b by binding
//Include default value for c if it is not provided as a parameter //Include default value for c if it is not provided as a parameter
val c = bindSymbolOrNull(c) ?: one val c = bindSymbolOrNull(c) ?: one
val d by binding a * arg.pow(2) + b * arg + c
val e by binding
a * arg.pow(2) + b * arg + c + d * arg.pow(3) + e / arg
} }
println("Resulting chi2/dof: ${result.chiSquaredOrNull}/${result.dof}")
//display a page with plot and numerical results //display a page with plot and numerical results
val page = Plotly.page { val page = Plotly.page {
plot { plot {
@ -95,16 +89,16 @@ suspend fun main() {
scatter { scatter {
mode = ScatterMode.lines mode = ScatterMode.lines
x(x) x(x)
y(x.map { result.model(result.startPoint + result.result + (Symbol.x to it)) }) y(x.map { result.model(result.resultPoint + (Symbol.x to it)) })
name = "fit" name = "fit"
} }
} }
br() br()
h3 { h3 {
+"Fit result: ${result.result}" +"Fit result: ${result.resultPoint}"
} }
h3 { h3 {
+"Chi2/dof = ${result.chiSquaredOrNull!! / result.dof}" +"Chi2/dof = ${result.chiSquaredOrNull!! / (x.size - 3)}"
} }
} }

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@ -1,37 +1,23 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.functions package space.kscience.kmath.functions
import space.kscience.kmath.complex.Complex
import space.kscience.kmath.complex.ComplexField
import space.kscience.kmath.complex.ComplexField.div
import space.kscience.kmath.complex.ComplexField.minus
import space.kscience.kmath.complex.algebra
import space.kscience.kmath.integration.gaussIntegrator import space.kscience.kmath.integration.gaussIntegrator
import space.kscience.kmath.integration.integrate import space.kscience.kmath.integration.integrate
import space.kscience.kmath.integration.value import space.kscience.kmath.integration.value
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.structures.Float64
import kotlin.math.pow import kotlin.math.pow
fun main() { fun main() {
//Define a function //Define a function
val function: Function1D<Float64> = { x -> 3 * x.pow(2) + 2 * x + 1 } val function: UnivariateFunction<Double> = { x -> 3 * x.pow(2) + 2 * x + 1 }
//get the result of the integration //get the result of the integration
val result = Float64Field.gaussIntegrator.integrate(0.0..10.0, function = function) val result = DoubleField.gaussIntegrator.integrate(0.0..10.0, function = function)
//the value is nullable because in some cases the integration could not succeed //the value is nullable because in some cases the integration could not succeed
println(result.value) println(result.value)
repeat(100000) {
Complex.algebra.gaussIntegrator.integrate(0.0..1.0, intervals = 1000) { x: Double ->
// sin(1 / x) + i * cos(1 / x)
1 / x - ComplexField.i / x
}.value
}
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -7,8 +7,8 @@ package space.kscience.kmath.functions
import space.kscience.kmath.interpolation.SplineInterpolator import space.kscience.kmath.interpolation.SplineInterpolator
import space.kscience.kmath.interpolation.interpolatePolynomials import space.kscience.kmath.interpolation.interpolatePolynomials
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.structures.Float64 import space.kscience.kmath.structures.DoubleBuffer
import space.kscience.plotly.Plotly import space.kscience.plotly.Plotly
import space.kscience.plotly.UnstablePlotlyAPI import space.kscience.plotly.UnstablePlotlyAPI
import space.kscience.plotly.makeFile import space.kscience.plotly.makeFile
@ -24,9 +24,11 @@ fun main() {
x to sin(x) x to sin(x)
} }
val polynomial: PiecewisePolynomial<Float64> = SplineInterpolator(Float64Field).interpolatePolynomials(data) val polynomial: PiecewisePolynomial<Double> = SplineInterpolator(
DoubleField, ::DoubleBuffer
).interpolatePolynomials(data)
val function = polynomial.asFunction(Float64Field, 0.0) val function = polynomial.asFunction(DoubleField, 0.0)
val cmInterpolate = org.apache.commons.math3.analysis.interpolation.SplineInterpolator().interpolate( val cmInterpolate = org.apache.commons.math3.analysis.interpolation.SplineInterpolator().interpolate(
data.map { it.first }.toDoubleArray(), data.map { it.first }.toDoubleArray(),

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -7,10 +7,9 @@ package space.kscience.kmath.functions
import space.kscience.kmath.interpolation.interpolatePolynomials import space.kscience.kmath.interpolation.interpolatePolynomials
import space.kscience.kmath.interpolation.splineInterpolator import space.kscience.kmath.interpolation.splineInterpolator
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.real.map import space.kscience.kmath.real.map
import space.kscience.kmath.real.step import space.kscience.kmath.real.step
import space.kscience.kmath.structures.Float64
import space.kscience.plotly.Plotly import space.kscience.plotly.Plotly
import space.kscience.plotly.UnstablePlotlyAPI import space.kscience.plotly.UnstablePlotlyAPI
import space.kscience.plotly.makeFile import space.kscience.plotly.makeFile
@ -19,7 +18,7 @@ import space.kscience.plotly.scatter
@OptIn(UnstablePlotlyAPI::class) @OptIn(UnstablePlotlyAPI::class)
fun main() { fun main() {
val function: Function1D<Float64> = { x -> val function: UnivariateFunction<Double> = { x ->
if (x in 30.0..50.0) { if (x in 30.0..50.0) {
1.0 1.0
} else { } else {
@ -29,9 +28,9 @@ fun main() {
val xs = 0.0..100.0 step 0.5 val xs = 0.0..100.0 step 0.5
val ys = xs.map(function) val ys = xs.map(function)
val polynomial: PiecewisePolynomial<Float64> = Float64Field.splineInterpolator.interpolatePolynomials(xs, ys) val polynomial: PiecewisePolynomial<Double> = DoubleField.splineInterpolator.interpolatePolynomials(xs, ys)
val polyFunction = polynomial.asFunction(Float64Field, 0.0) val polyFunction = polynomial.asFunction(DoubleField, 0.0)
Plotly.plot { Plotly.plot {
scatter { scatter {

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -12,22 +12,23 @@ import space.kscience.kmath.nd.StructureND
import space.kscience.kmath.nd.structureND import space.kscience.kmath.nd.structureND
import space.kscience.kmath.nd.withNdAlgebra import space.kscience.kmath.nd.withNdAlgebra
import space.kscience.kmath.operations.algebra import space.kscience.kmath.operations.algebra
import space.kscience.kmath.structures.Float64 import space.kscience.kmath.operations.invoke
import kotlin.math.pow
fun main(): Unit = Double.algebra.withNdAlgebra(2, 2) { fun main(): Unit = Double.algebra {
withNdAlgebra(2, 2) {
//Produce a diagonal StructureND //Produce a diagonal StructureND
fun diagonal(v: Double) = structureND { (i, j) -> fun diagonal(v: Double) = structureND { (i, j) ->
if (i == j) v else 0.0 if (i == j) v else 0.0
}
//Define a function in a nd space
val function: (Double) -> StructureND<Double> = { x: Double -> 3 * x.pow(2) + 2 * diagonal(x) + 1 }
//get the result of the integration
val result = gaussIntegrator.integrate(0.0..10.0, function = function)
//the value is nullable because in some cases the integration could not succeed
println(result.value)
} }
//Define a function in a nd space
val function: (Double) -> StructureND<Float64> = { x: Double -> 3 * x.pow(2) + 2 * diagonal(x) + 1 }
//get the result of the integration
val result = gaussIntegrator.integrate(0.0..10.0, function = function)
//the value is nullable because in some cases the integration could not succeed
println(result.value)
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */

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@ -1,28 +1,31 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.linear package space.kscience.kmath.linear
import space.kscience.kmath.operations.algebra
import kotlin.random.Random import kotlin.random.Random
import kotlin.time.measureTime import kotlin.system.measureTimeMillis
fun main() = with(Float64ParallelLinearSpace) { fun main() {
val random = Random(12224) val random = Random(12224)
val dim = 1000 val dim = 1000
//creating invertible matrix //creating invertible matrix
val matrix1 = buildMatrix(dim, dim) { i, j -> val matrix1 = Double.algebra.linearSpace.buildMatrix(dim, dim) { i, j ->
if (i <= j) random.nextDouble() else 0.0 if (i <= j) random.nextDouble() else 0.0
} }
val matrix2 = buildMatrix(dim, dim) { i, j -> val matrix2 = Double.algebra.linearSpace.buildMatrix(dim, dim) { i, j ->
if (i <= j) random.nextDouble() else 0.0 if (i <= j) random.nextDouble() else 0.0
} }
val time = measureTime { val time = measureTimeMillis {
repeat(30) { with(Double.algebra.linearSpace) {
matrix1 dot matrix2 repeat(10) {
matrix1 dot matrix2
}
} }
} }

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@ -1,40 +0,0 @@
/*
* Copyright 2018-2024 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.linear
import space.kscience.kmath.commons.linear.CMLinearSpace
import space.kscience.kmath.ejml.EjmlLinearSpaceDDRM
import space.kscience.kmath.nd.StructureND
import space.kscience.kmath.operations.algebra
import space.kscience.kmath.structures.Float64
import kotlin.random.Random
fun main() {
val dim = 46
val random = Random(123)
val u = Float64.algebra.linearSpace.buildMatrix(dim, dim) { i, j -> if (i <= j) random.nextDouble() else 0.0 }
listOf(CMLinearSpace, EjmlLinearSpaceDDRM).forEach { algebra ->
with(algebra) {
//create a simmetric matrix
val matrix = buildMatrix(dim, dim) { row, col ->
if (row >= col) u[row, col] else u[col, row]
}
val eigen = matrix.getOrComputeAttribute(EIG) ?: error("Failed to compute eigenvalue decomposition")
check(
StructureND.contentEquals(
matrix,
eigen.v dot eigen.d dot eigen.v.transposed(),
1e-4
)
) { "$algebra decomposition failed" }
println("$algebra eigenvalue decomposition complete and checked" )
}
}
}

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@ -1,28 +1,27 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.linear package space.kscience.kmath.linear
import space.kscience.kmath.real.* import space.kscience.kmath.real.*
import space.kscience.kmath.structures.Float64 import space.kscience.kmath.structures.DoubleBuffer
import space.kscience.kmath.structures.Float64Buffer
fun main() { fun main() {
val x0 = DoubleVector(0.0, 0.0, 0.0) val x0 = DoubleVector(0.0, 0.0, 0.0)
val sigma = DoubleVector(1.0, 1.0, 1.0) val sigma = DoubleVector(1.0, 1.0, 1.0)
val gaussian: (Point<Float64>) -> Double = { x -> val gaussian: (Point<Double>) -> Double = { x ->
require(x.size == x0.size) require(x.size == x0.size)
kotlin.math.exp(-((x - x0) / sigma).square().sum()) kotlin.math.exp(-((x - x0) / sigma).square().sum())
} }
fun ((Point<Float64>) -> Double).grad(x: Point<Float64>): Point<Float64> { fun ((Point<Double>) -> Double).grad(x: Point<Double>): Point<Double> {
require(x.size == x0.size) require(x.size == x0.size)
return Float64Buffer(x.size) { i -> return DoubleBuffer(x.size) { i ->
val h = sigma[i] / 5 val h = sigma[i] / 5
val dVector = Float64Buffer(x.size) { if (it == i) h else 0.0 } val dVector = DoubleBuffer(x.size) { if (it == i) h else 0.0 }
val f1 = this(x + dVector / 2) val f1 = this(x + dVector / 2)
val f0 = this(x - dVector / 2) val f0 = this(x - dVector / 2)
(f1 - f0) / h (f1 - f0) / h

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@ -1,27 +0,0 @@
/*
* Copyright 2018-2024 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.linear
import kotlin.random.Random
import kotlin.time.measureTime
fun main(): Unit = with(Float64LinearSpace) {
val random = Random(1224)
val dim = 500
//creating invertible matrix
val u = buildMatrix(dim, dim) { i, j -> if (i <= j) random.nextDouble() else 0.0 }
val l = buildMatrix(dim, dim) { i, j -> if (i >= j) random.nextDouble() else 0.0 }
val matrix = l dot u
val time = measureTime {
repeat(20) {
lupSolver().inverse(matrix)
}
}
println(time)
}

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -7,6 +7,7 @@ package space.kscience.kmath.operations
import space.kscience.kmath.complex.Complex import space.kscience.kmath.complex.Complex
import space.kscience.kmath.complex.algebra import space.kscience.kmath.complex.algebra
import space.kscience.kmath.complex.bufferAlgebra
import space.kscience.kmath.complex.ndAlgebra import space.kscience.kmath.complex.ndAlgebra
import space.kscience.kmath.nd.BufferND import space.kscience.kmath.nd.BufferND
import space.kscience.kmath.nd.StructureND import space.kscience.kmath.nd.StructureND
@ -17,7 +18,7 @@ fun main() = Complex.algebra {
println(complex * 8 - 5 * i) println(complex * 8 - 5 * i)
//flat buffer //flat buffer
val buffer = with(bufferAlgebra) { val buffer = with(bufferAlgebra){
buffer(8) { Complex(it, -it) }.map { Complex(it.im, it.re) } buffer(8) { Complex(it, -it) }.map { Complex(it.im, it.re) }
} }
println(buffer) println(buffer)
@ -29,7 +30,7 @@ fun main() = Complex.algebra {
println(element) println(element)
// 1d element operation // 1d element operation
val result: StructureND<Complex> = ndAlgebra { val result: StructureND<Complex> = ndAlgebra{
val a = structureND(8) { (it) -> i * it - it.toDouble() } val a = structureND(8) { (it) -> i * it - it.toDouble() }
val b = 3 val b = 3
val c = Complex(1.0, 1.0) val c = Complex(1.0, 1.0)

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -7,23 +7,21 @@ package space.kscience.kmath.operations
import space.kscience.kmath.commons.linear.CMLinearSpace import space.kscience.kmath.commons.linear.CMLinearSpace
import space.kscience.kmath.linear.matrix import space.kscience.kmath.linear.matrix
import space.kscience.kmath.nd.Float64BufferND import space.kscience.kmath.nd.DoubleBufferND
import space.kscience.kmath.nd.Shape
import space.kscience.kmath.nd.Structure2D import space.kscience.kmath.nd.Structure2D
import space.kscience.kmath.nd.mutableStructureND
import space.kscience.kmath.nd.ndAlgebra import space.kscience.kmath.nd.ndAlgebra
import space.kscience.kmath.structures.Float64 import space.kscience.kmath.viktor.ViktorStructureND
import space.kscience.kmath.viktor.viktorAlgebra import space.kscience.kmath.viktor.viktorAlgebra
import kotlin.collections.component1
import kotlin.collections.component2
fun main() { fun main() {
val viktorStructure = Float64Field.viktorAlgebra.mutableStructureND(2, 2) { (i, j) -> val viktorStructure: ViktorStructureND = DoubleField.viktorAlgebra.structureND(Shape(2, 2)) { (i, j) ->
if (i == j) 2.0 else 0.0 if (i == j) 2.0 else 0.0
} }
val cmMatrix: Structure2D<Float64> = CMLinearSpace.matrix(2, 2)(0.0, 1.0, 0.0, 3.0) val cmMatrix: Structure2D<Double> = CMLinearSpace.matrix(2, 2)(0.0, 1.0, 0.0, 3.0)
val res: Float64BufferND = Float64Field.ndAlgebra { val res: DoubleBufferND = DoubleField.ndAlgebra {
exp(viktorStructure) + 2.0 * cmMatrix exp(viktorStructure) + 2.0 * cmMatrix
} }

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@ -1,17 +0,0 @@
/*
* Copyright 2018-2024 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.series
import kotlinx.datetime.Instant
import space.kscience.kmath.operations.algebra
import space.kscience.kmath.operations.bufferAlgebra
import kotlin.time.Duration
fun SeriesAlgebra.Companion.time(zero: Instant, step: Duration) = MonotonicSeriesAlgebra(
bufferAlgebra = Double.algebra.bufferAlgebra,
offsetToLabel = { zero + step * it },
labelToOffset = { (it - zero) / step }
)

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@ -1,65 +0,0 @@
/*
* Copyright 2018-2024 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.series
import kotlinx.html.h1
import kotlinx.html.p
import space.kscience.kmath.operations.algebra
import space.kscience.kmath.operations.bufferAlgebra
import space.kscience.kmath.operations.toList
import space.kscience.kmath.stat.KMComparisonResult
import space.kscience.kmath.stat.ksComparisonStatistic
import space.kscience.kmath.structures.Buffer
import space.kscience.kmath.structures.Float64
import space.kscience.kmath.structures.slice
import space.kscience.plotly.*
import kotlin.math.PI
fun Double.Companion.seriesAlgebra() = Double.algebra.bufferAlgebra.seriesAlgebra()
fun main() = with(Double.seriesAlgebra()) {
fun Plot.plotSeries(name: String, buffer: Buffer<Float64>) {
scatter {
this.name = name
x.numbers = buffer.labels
y.numbers = buffer.toList()
}
}
val s1 = series(100) { sin(2 * PI * it / 100) + 1.0 }
val s2 = s1.slice(20..50).moveTo(40)
val s3: Buffer<Float64> = s1.zip(s2) { l, r -> l + r } //s1 + s2
val s4 = s3.map { ln(it) }
val kmTest: KMComparisonResult<Float64> = ksComparisonStatistic(s1, s2)
Plotly.page {
h1 { +"This is my plot" }
p {
+"Kolmogorov-smirnov test for s1 and s2: ${kmTest.value}"
}
plot {
plotSeries("s1", s1)
plotSeries("s2", s2)
plotSeries("s3", s3)
plotSeries("s4", s4)
layout {
xaxis {
range(0.0..100.0)
}
}
}
}.makeFile()
}

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@ -1,47 +0,0 @@
/*
* 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.kmath.series
import space.kscience.kmath.structures.*
import space.kscience.plotly.*
import space.kscience.plotly.models.Scatter
import space.kscience.plotly.models.ScatterMode
import kotlin.random.Random
fun main(): Unit = with(Double.seriesAlgebra()) {
val random = Random(1234)
val arrayOfRandoms = DoubleArray(20) { random.nextDouble() }
val series1: Float64Buffer = arrayOfRandoms.asBuffer()
val series2: Series<Float64> = series1.moveBy(3)
val res = series2 - series1
println(res.size)
println(res)
fun Plot.series(name: String, buffer: Buffer<Float64>, block: Scatter.() -> Unit = {}) {
scatter {
this.name = name
x.numbers = buffer.offsetIndices
y.doubles = buffer.toDoubleArray()
block()
}
}
Plotly.plot {
series("series1", series1)
series("series2", series2)
series("dif", res) {
mode = ScatterMode.lines
line.color("magenta")
}
}.makeFile(resourceLocation = ResourceLocation.REMOTE)
}

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -10,7 +10,6 @@ import kotlinx.coroutines.async
import kotlinx.coroutines.runBlocking import kotlinx.coroutines.runBlocking
import org.apache.commons.rng.sampling.distribution.BoxMullerNormalizedGaussianSampler import org.apache.commons.rng.sampling.distribution.BoxMullerNormalizedGaussianSampler
import org.apache.commons.rng.simple.RandomSource import org.apache.commons.rng.simple.RandomSource
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.samplers.GaussianSampler import space.kscience.kmath.samplers.GaussianSampler
import java.time.Duration import java.time.Duration
import java.time.Instant import java.time.Instant
@ -36,28 +35,8 @@ private suspend fun runKMathChained(): Duration {
return Duration.between(startTime, Instant.now()) return Duration.between(startTime, Instant.now())
} }
private fun runKMathBlocking(): Duration { private fun runApacheDirect(): Duration {
val generator = RandomGenerator.fromSource(RandomSource.MT, 123L) val rng = RandomSource.create(RandomSource.MT, 123L)
val normal = GaussianSampler(7.0, 2.0)
val chain = normal.sample(generator)
val startTime = Instant.now()
var sum = 0.0
repeat(10000001) { counter ->
sum += chain.nextBlocking()
if (counter % 100000 == 0) {
val duration = Duration.between(startTime, Instant.now())
val meanValue = sum / counter
println("Chain sampler completed $counter elements in $duration: $meanValue")
}
}
return Duration.between(startTime, Instant.now())
}
private fun runCMDirect(): Duration {
val rng = RandomSource.MT.create(123L)
val sampler = CMGaussianSampler.of( val sampler = CMGaussianSampler.of(
BoxMullerNormalizedGaussianSampler.of(rng), BoxMullerNormalizedGaussianSampler.of(rng),
@ -85,10 +64,8 @@ private fun runCMDirect(): Duration {
* Comparing chain sampling performance with direct sampling performance * Comparing chain sampling performance with direct sampling performance
*/ */
fun main(): Unit = runBlocking(Dispatchers.Default) { fun main(): Unit = runBlocking(Dispatchers.Default) {
val directJob = async { runCMDirect() } val directJob = async { runApacheDirect() }
val chainJob = async { runKMathChained() } val chainJob = async { runKMathChained() }
val blockingJob = async { runKMathBlocking() }
println("KMath Chained: ${chainJob.await()}") println("KMath Chained: ${chainJob.await()}")
println("KMath Blocking: ${blockingJob.await()}")
println("Apache Direct: ${directJob.await()}") println("Apache Direct: ${directJob.await()}")
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -9,15 +9,13 @@ import kotlinx.coroutines.runBlocking
import space.kscience.kmath.chains.Chain import space.kscience.kmath.chains.Chain
import space.kscience.kmath.chains.combineWithState import space.kscience.kmath.chains.combineWithState
import space.kscience.kmath.distributions.NormalDistribution import space.kscience.kmath.distributions.NormalDistribution
import space.kscience.kmath.random.RandomGenerator
import space.kscience.kmath.structures.Float64
private data class AveragingChainState(var num: Int = 0, var value: Double = 0.0) private data class AveragingChainState(var num: Int = 0, var value: Double = 0.0)
/** /**
* Averaging. * Averaging.
*/ */
private fun Chain<Float64>.mean(): Chain<Float64> = combineWithState(AveragingChainState(), { it.copy() }) { chain -> private fun Chain<Double>.mean(): Chain<Double> = combineWithState(AveragingChainState(), { it.copy() }) { chain ->
val next = chain.next() val next = chain.next()
num++ num++
value += next value += next

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -8,12 +8,12 @@
package space.kscience.kmath.structures package space.kscience.kmath.structures
import space.kscience.kmath.complex.* import space.kscience.kmath.complex.*
import space.kscience.kmath.linear.transposed import space.kscience.kmath.linear.transpose
import space.kscience.kmath.nd.StructureND import space.kscience.kmath.nd.StructureND
import space.kscience.kmath.nd.as2D import space.kscience.kmath.nd.as2D
import space.kscience.kmath.nd.ndAlgebra import space.kscience.kmath.nd.ndAlgebra
import space.kscience.kmath.nd.structureND import space.kscience.kmath.nd.structureND
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
import kotlin.system.measureTimeMillis import kotlin.system.measureTimeMillis
@ -21,12 +21,12 @@ fun main() {
val dim = 1000 val dim = 1000
val n = 1000 val n = 1000
val realField = Float64Field.ndAlgebra(dim, dim) val realField = DoubleField.ndAlgebra(dim, dim)
val complexField: ComplexFieldND = ComplexField.ndAlgebra(dim, dim) val complexField: ComplexFieldND = ComplexField.ndAlgebra(dim, dim)
val realTime = measureTimeMillis { val realTime = measureTimeMillis {
realField { realField {
var res: StructureND<Float64> = one var res: StructureND<Double> = one
repeat(n) { repeat(n) {
res += 1.0 res += 1.0
} }
@ -60,7 +60,7 @@ fun complexExample() {
val sum = matrix + x + 1.0 val sum = matrix + x + 1.0
//Represent the sum as 2d-structure and transpose //Represent the sum as 2d-structure and transpose
sum.as2D().transposed() sum.as2D().transpose()
} }
} }
} }

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -10,7 +10,7 @@ import kotlinx.coroutines.GlobalScope
import org.nd4j.linalg.factory.Nd4j import org.nd4j.linalg.factory.Nd4j
import space.kscience.kmath.nd.* import space.kscience.kmath.nd.*
import space.kscience.kmath.nd4j.nd4j import space.kscience.kmath.nd4j.nd4j
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
import space.kscience.kmath.viktor.ViktorFieldND import space.kscience.kmath.viktor.ViktorFieldND
import kotlin.contracts.InvocationKind import kotlin.contracts.InvocationKind
@ -29,57 +29,66 @@ fun main() {
Nd4j.zeros(0) Nd4j.zeros(0)
val dim = 1000 val dim = 1000
val n = 1000 val n = 1000
val shape = ShapeND(dim, dim) val shape = Shape(dim, dim)
// automatically build context most suited for given type.
val autoField = BufferedFieldOpsND(DoubleField, Buffer.Companion::auto)
// specialized nd-field for Double. It works as generic Double field as well. // specialized nd-field for Double. It works as generic Double field as well.
val doubleField = Float64Field.ndAlgebra val realField = DoubleField.ndAlgebra
//A generic field. It should be used for objects, not primitives. //A generic boxing field. It should be used for objects, not primitives.
val genericField = BufferedFieldOpsND(Float64Field) val boxingField = BufferedFieldOpsND(DoubleField, Buffer.Companion::boxing)
// Nd4j specialized field. // Nd4j specialized field.
val nd4jField = Float64Field.nd4j val nd4jField = DoubleField.nd4j
//viktor field //viktor field
val viktorField = ViktorFieldND(dim, dim) val viktorField = ViktorFieldND(dim, dim)
//parallel processing based on Java Streams //parallel processing based on Java Streams
val parallelField = Float64Field.ndStreaming(dim, dim) val parallelField = DoubleField.ndStreaming(dim, dim)
measureAndPrint("Boxing addition") { measureAndPrint("Boxing addition") {
genericField { boxingField {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
} }
} }
measureAndPrint("Specialized addition") { measureAndPrint("Specialized addition") {
doubleField { realField {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
} }
} }
measureAndPrint("Nd4j specialized addition") { measureAndPrint("Nd4j specialized addition") {
nd4jField { nd4jField {
var res: StructureND<Float64> = one(shape) var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
} }
} }
measureAndPrint("Viktor addition") { measureAndPrint("Viktor addition") {
viktorField { viktorField {
var res: StructureND<Float64> = one var res: StructureND<Double> = one
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
} }
} }
measureAndPrint("Parallel stream addition") { measureAndPrint("Parallel stream addition") {
parallelField { parallelField {
var res: StructureND<Float64> = one var res: StructureND<Double> = one
repeat(n) { res += 1.0 }
}
}
measureAndPrint("Automatic field addition") {
autoField {
var res: StructureND<Double> = one(shape)
repeat(n) { res += 1.0 } repeat(n) { res += 1.0 }
} }
} }
measureAndPrint("Lazy addition") { measureAndPrint("Lazy addition") {
val res = doubleField.one(shape).mapAsync(GlobalScope) { val res = realField.one(shape).mapAsync(GlobalScope) {
var c = 0.0 var c = 0.0
repeat(n) { repeat(n) {
c += 1.0 c += 1.0

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@ -1,15 +1,13 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.structures package space.kscience.kmath.structures
import space.kscience.kmath.PerformancePitfall
import space.kscience.kmath.nd.* import space.kscience.kmath.nd.*
import space.kscience.kmath.operations.DoubleField import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.ExtendedField import space.kscience.kmath.operations.ExtendedField
import space.kscience.kmath.operations.Float64Field
import space.kscience.kmath.operations.NumbersAddOps import space.kscience.kmath.operations.NumbersAddOps
import java.util.* import java.util.*
import java.util.stream.IntStream import java.util.stream.IntStream
@ -18,67 +16,51 @@ import java.util.stream.IntStream
* A demonstration implementation of NDField over Real using Java [java.util.stream.DoubleStream] for parallel * A demonstration implementation of NDField over Real using Java [java.util.stream.DoubleStream] for parallel
* execution. * execution.
*/ */
class StreamDoubleFieldND(override val shape: ShapeND) : FieldND<Double, Float64Field>, class StreamDoubleFieldND(override val shape: IntArray) : FieldND<Double, DoubleField>,
NumbersAddOps<StructureND<Float64>>, NumbersAddOps<StructureND<Double>>,
ExtendedField<StructureND<Float64>> { ExtendedField<StructureND<Double>> {
private val strides = ColumnStrides(shape) private val strides = DefaultStrides(shape)
override val elementAlgebra: Float64Field get() = Float64Field override val elementAlgebra: DoubleField get() = DoubleField
override val zero: BufferND<Float64> by lazy { structureND(shape) { zero } } override val zero: BufferND<Double> by lazy { structureND(shape) { zero } }
override val one: BufferND<Float64> by lazy { structureND(shape) { one } } override val one: BufferND<Double> by lazy { structureND(shape) { one } }
override fun number(value: Number): BufferND<Float64> { override fun number(value: Number): BufferND<Double> {
val d = value.toDouble() // minimize conversions val d = value.toDouble() // minimize conversions
return structureND(shape) { d } return structureND(shape) { d }
} }
@OptIn(PerformancePitfall::class) private val StructureND<Double>.buffer: DoubleBuffer
private val StructureND<Float64>.buffer: Float64Buffer
get() = when { get() = when {
shape != this@StreamDoubleFieldND.shape -> throw ShapeMismatchException( !shape.contentEquals(this@StreamDoubleFieldND.shape) -> throw ShapeMismatchException(
this@StreamDoubleFieldND.shape, this@StreamDoubleFieldND.shape,
shape shape
) )
this is BufferND && this.indices == this@StreamDoubleFieldND.strides -> this.buffer as DoubleBuffer
this is BufferND && indices == this@StreamDoubleFieldND.strides -> this.buffer as Float64Buffer else -> DoubleBuffer(strides.linearSize) { offset -> get(strides.index(offset)) }
else -> Float64Buffer(strides.linearSize) { offset -> get(strides.index(offset)) }
} }
override fun structureND(shape: ShapeND, initializer: Float64Field.(IntArray) -> Double): BufferND<Float64> { override fun structureND(shape: Shape, initializer: DoubleField.(IntArray) -> Double): BufferND<Double> {
val array = IntStream.range(0, strides.linearSize).parallel().mapToDouble { offset ->
val index = strides.index(offset)
Float64Field.initializer(index)
}.toArray()
return BufferND(strides, array.asBuffer())
}
override fun mutableStructureND(
shape: ShapeND,
initializer: DoubleField.(IntArray) -> Double,
): MutableBufferND<Float64> {
val array = IntStream.range(0, strides.linearSize).parallel().mapToDouble { offset -> val array = IntStream.range(0, strides.linearSize).parallel().mapToDouble { offset ->
val index = strides.index(offset) val index = strides.index(offset)
DoubleField.initializer(index) DoubleField.initializer(index)
}.toArray() }.toArray()
return MutableBufferND(strides, array.asBuffer())
}
@OptIn(PerformancePitfall::class)
override fun StructureND<Float64>.map(
transform: Float64Field.(Double) -> Double,
): BufferND<Float64> {
val array = Arrays.stream(buffer.array).parallel().map { Float64Field.transform(it) }.toArray()
return BufferND(strides, array.asBuffer()) return BufferND(strides, array.asBuffer())
} }
@OptIn(PerformancePitfall::class) override fun StructureND<Double>.map(
override fun StructureND<Float64>.mapIndexed( transform: DoubleField.(Double) -> Double,
transform: Float64Field.(index: IntArray, Double) -> Double, ): BufferND<Double> {
): BufferND<Float64> { val array = Arrays.stream(buffer.array).parallel().map { DoubleField.transform(it) }.toArray()
return BufferND(strides, array.asBuffer())
}
override fun StructureND<Double>.mapIndexed(
transform: DoubleField.(index: IntArray, Double) -> Double,
): BufferND<Double> {
val array = IntStream.range(0, strides.linearSize).parallel().mapToDouble { offset -> val array = IntStream.range(0, strides.linearSize).parallel().mapToDouble { offset ->
Float64Field.transform( DoubleField.transform(
strides.index(offset), strides.index(offset),
buffer.array[offset] buffer.array[offset]
) )
@ -87,41 +69,40 @@ class StreamDoubleFieldND(override val shape: ShapeND) : FieldND<Double, Float64
return BufferND(strides, array.asBuffer()) return BufferND(strides, array.asBuffer())
} }
@OptIn(PerformancePitfall::class)
override fun zip( override fun zip(
left: StructureND<Float64>, left: StructureND<Double>,
right: StructureND<Float64>, right: StructureND<Double>,
transform: Float64Field.(Double, Double) -> Double, transform: DoubleField.(Double, Double) -> Double,
): BufferND<Float64> { ): BufferND<Double> {
val array = IntStream.range(0, strides.linearSize).parallel().mapToDouble { offset -> val array = IntStream.range(0, strides.linearSize).parallel().mapToDouble { offset ->
Float64Field.transform(left.buffer.array[offset], right.buffer.array[offset]) DoubleField.transform(left.buffer.array[offset], right.buffer.array[offset])
}.toArray() }.toArray()
return BufferND(strides, array.asBuffer()) return BufferND(strides, array.asBuffer())
} }
override fun StructureND<Float64>.unaryMinus(): StructureND<Float64> = map { -it } override fun StructureND<Double>.unaryMinus(): StructureND<Double> = map { -it }
override fun scale(a: StructureND<Float64>, value: Double): StructureND<Float64> = a.map { it * value } override fun scale(a: StructureND<Double>, value: Double): StructureND<Double> = a.map { it * value }
override fun power(arg: StructureND<Float64>, pow: Number): BufferND<Float64> = arg.map { power(it, pow) } override fun power(arg: StructureND<Double>, pow: Number): BufferND<Double> = arg.map { power(it, pow) }
override fun exp(arg: StructureND<Float64>): BufferND<Float64> = arg.map { exp(it) } override fun exp(arg: StructureND<Double>): BufferND<Double> = arg.map { exp(it) }
override fun ln(arg: StructureND<Float64>): BufferND<Float64> = arg.map { ln(it) } override fun ln(arg: StructureND<Double>): BufferND<Double> = arg.map { ln(it) }
override fun sin(arg: StructureND<Float64>): BufferND<Float64> = arg.map { sin(it) } override fun sin(arg: StructureND<Double>): BufferND<Double> = arg.map { sin(it) }
override fun cos(arg: StructureND<Float64>): BufferND<Float64> = arg.map { cos(it) } override fun cos(arg: StructureND<Double>): BufferND<Double> = arg.map { cos(it) }
override fun tan(arg: StructureND<Float64>): BufferND<Float64> = arg.map { tan(it) } override fun tan(arg: StructureND<Double>): BufferND<Double> = arg.map { tan(it) }
override fun asin(arg: StructureND<Float64>): BufferND<Float64> = arg.map { asin(it) } override fun asin(arg: StructureND<Double>): BufferND<Double> = arg.map { asin(it) }
override fun acos(arg: StructureND<Float64>): BufferND<Float64> = arg.map { acos(it) } override fun acos(arg: StructureND<Double>): BufferND<Double> = arg.map { acos(it) }
override fun atan(arg: StructureND<Float64>): BufferND<Float64> = arg.map { atan(it) } override fun atan(arg: StructureND<Double>): BufferND<Double> = arg.map { atan(it) }
override fun sinh(arg: StructureND<Float64>): BufferND<Float64> = arg.map { sinh(it) } override fun sinh(arg: StructureND<Double>): BufferND<Double> = arg.map { sinh(it) }
override fun cosh(arg: StructureND<Float64>): BufferND<Float64> = arg.map { cosh(it) } override fun cosh(arg: StructureND<Double>): BufferND<Double> = arg.map { cosh(it) }
override fun tanh(arg: StructureND<Float64>): BufferND<Float64> = arg.map { tanh(it) } override fun tanh(arg: StructureND<Double>): BufferND<Double> = arg.map { tanh(it) }
override fun asinh(arg: StructureND<Float64>): BufferND<Float64> = arg.map { asinh(it) } override fun asinh(arg: StructureND<Double>): BufferND<Double> = arg.map { asinh(it) }
override fun acosh(arg: StructureND<Float64>): BufferND<Float64> = arg.map { acosh(it) } override fun acosh(arg: StructureND<Double>): BufferND<Double> = arg.map { acosh(it) }
override fun atanh(arg: StructureND<Float64>): BufferND<Float64> = arg.map { atanh(it) } override fun atanh(arg: StructureND<Double>): BufferND<Double> = arg.map { atanh(it) }
} }
fun Float64Field.ndStreaming(vararg shape: Int): StreamDoubleFieldND = StreamDoubleFieldND(ShapeND(shape)) fun DoubleField.ndStreaming(vararg shape: Int): StreamDoubleFieldND = StreamDoubleFieldND(shape)

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@ -1,23 +1,20 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.structures package space.kscience.kmath.structures
import space.kscience.kmath.PerformancePitfall
import space.kscience.kmath.nd.BufferND import space.kscience.kmath.nd.BufferND
import space.kscience.kmath.nd.ColumnStrides import space.kscience.kmath.nd.DefaultStrides
import space.kscience.kmath.nd.ShapeND
import kotlin.system.measureTimeMillis import kotlin.system.measureTimeMillis
@Suppress("ASSIGNED_BUT_NEVER_ACCESSED_VARIABLE") @Suppress("ASSIGNED_BUT_NEVER_ACCESSED_VARIABLE")
@OptIn(PerformancePitfall::class)
fun main() { fun main() {
val n = 6000 val n = 6000
val array = DoubleArray(n * n) { 1.0 } val array = DoubleArray(n * n) { 1.0 }
val buffer = Float64Buffer(array) val buffer = DoubleBuffer(array)
val strides = ColumnStrides(ShapeND(n, n)) val strides = DefaultStrides(intArrayOf(n, n))
val structure = BufferND(strides, buffer) val structure = BufferND(strides, buffer)
measureTimeMillis { measureTimeMillis {

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@ -1,25 +1,20 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.structures package space.kscience.kmath.structures
import space.kscience.kmath.nd.BufferND import space.kscience.kmath.nd.StructureND
import space.kscience.kmath.operations.mapToBuffer import space.kscience.kmath.nd.mapToBuffer
import kotlin.system.measureTimeMillis import kotlin.system.measureTimeMillis
private inline fun <T, reified R : Any> BufferND<T>.mapToBufferND(
bufferFactory: BufferFactory<R> = BufferFactory(),
crossinline block: (T) -> R,
): BufferND<R> = BufferND(indices, buffer.mapToBuffer(bufferFactory, block))
@Suppress("UNUSED_VARIABLE") @Suppress("UNUSED_VARIABLE")
fun main() { fun main() {
val n = 6000 val n = 6000
val structure = BufferND(n, n) { 1.0 } val structure = StructureND.buffered(intArrayOf(n, n), Buffer.Companion::auto) { 1.0 }
structure.mapToBufferND { it + 1 } // warm-up structure.mapToBuffer { it + 1 } // warm-up
val time1 = measureTimeMillis { val res = structure.mapToBufferND { it + 1 } } val time1 = measureTimeMillis { val res = structure.mapToBuffer { it + 1 } }
println("Structure mapping finished in $time1 millis") println("Structure mapping finished in $time1 millis")
val array = DoubleArray(n * n) { 1.0 } val array = DoubleArray(n * n) { 1.0 }
@ -30,10 +25,10 @@ fun main() {
println("Array mapping finished in $time2 millis") println("Array mapping finished in $time2 millis")
val buffer = Float64Buffer(DoubleArray(n * n) { 1.0 }) val buffer = DoubleBuffer(DoubleArray(n * n) { 1.0 })
val time3 = measureTimeMillis { val time3 = measureTimeMillis {
val target = Float64Buffer(DoubleArray(n * n)) val target = DoubleBuffer(DoubleArray(n * n))
val res = array.forEachIndexed { index, value -> val res = array.forEachIndexed { index, value ->
target[index] = value + 1 target[index] = value + 1
} }

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@ -1,23 +1,23 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.structures package space.kscience.kmath.structures
import space.kscience.kmath.operations.Float64Field import space.kscience.kmath.operations.DoubleField
import space.kscience.kmath.operations.buffer import space.kscience.kmath.operations.buffer
import space.kscience.kmath.operations.bufferAlgebra import space.kscience.kmath.operations.bufferAlgebra
import space.kscience.kmath.operations.withSize import space.kscience.kmath.operations.withSize
inline fun <reified R : Any> MutableBuffer.Companion.same( inline fun <reified R : Any> MutableBuffer.Companion.same(
n: Int, n: Int,
value: R, value: R
): MutableBuffer<R> = MutableBuffer(n) { value } ): MutableBuffer<R> = auto(n) { value }
fun main() { fun main() {
with(Float64Field.bufferAlgebra.withSize(5)) { with(DoubleField.bufferAlgebra.withSize(5)) {
println(number(2.0) + buffer(1, 2, 3, 4, 5)) println(number(2.0) + buffer(1, 2, 3, 4, 5))
} }
} }

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@ -1,26 +0,0 @@
/*
* 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.kmath.structures
import space.kscience.kmath.PerformancePitfall
import space.kscience.kmath.nd.*
import space.kscience.kmath.operations.algebra
@OptIn(PerformancePitfall::class)
fun main(): Unit = with(Double.algebra.ndAlgebra) {
val structure: MutableStructure2D<Float64> = mutableStructureND(ShapeND(2, 2)) { (i, j) ->
i.toDouble() + j.toDouble()
}.as2D()
structure[0, 1] = -2.0
val structure2 = mutableStructureND(2, 2) { (i, j) -> i.toDouble() + j.toDouble() }.as2D()
structure2[0, 1] = 2.0
println(structure + structure2)
}

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@ -1,5 +1,5 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * Use of this source code is governed by the Apache 2.0 license that can be found in the license/LICENSE.txt file.
*/ */
@ -15,7 +15,7 @@ private fun DMatrixContext<Double, *>.simple() {
val m2 = produce<D3, D2> { i, j -> (i + j).toDouble() } val m2 = produce<D3, D2> { i, j -> (i + j).toDouble() }
//Dimension-safe addition //Dimension-safe addition
m1.transposed() + m2 m1.transpose() + m2
} }
private object D5 : Dimension { private object D5 : Dimension {

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@ -1,92 +0,0 @@
/*
* Copyright 2018-2024 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.tensors.LevenbergMarquardt.StaticLm
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.nd.as2D
import space.kscience.kmath.nd.component1
import space.kscience.kmath.tensors.LevenbergMarquardt.funcDifficultForLm
import space.kscience.kmath.tensors.core.BroadcastDoubleTensorAlgebra
import space.kscience.kmath.tensors.core.BroadcastDoubleTensorAlgebra.div
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra
import space.kscience.kmath.tensors.core.LMInput
import space.kscience.kmath.tensors.core.levenbergMarquardt
import kotlin.math.roundToInt
fun main() {
val NData = 200
var t_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(NData, 1))).as2D()
for (i in 0 until NData) {
t_example[i, 0] = t_example[i, 0] * (i + 1) - 104
}
val Nparams = 15
var p_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_example[i, 0] = p_example[i, 0] + i - 25
}
val exampleNumber = 1
var y_hat = funcDifficultForLm(t_example, p_example, exampleNumber)
var p_init = DoubleTensorAlgebra.zeros(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_init[i, 0] = (p_example[i, 0] + 0.9)
}
var t = t_example
val y_dat = y_hat
val weight = 1.0 / Nparams * 1.0 - 0.085
val dp = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), DoubleArray(1) { -0.01 }
).as2D()
var p_min = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0)
val opts = doubleArrayOf(3.0, 10000.0, 1e-6, 1e-6, 1e-6, 1e-6, 1e-2, 11.0, 9.0, 1.0)
// val opts = doubleArrayOf(3.0, 10000.0, 1e-6, 1e-6, 1e-6, 1e-6, 1e-3, 11.0, 9.0, 1.0)
val inputData = LMInput(
::funcDifficultForLm,
p_init.as2D(),
t,
y_dat,
weight,
dp,
p_min.as2D(),
p_max.as2D(),
opts[1].toInt(),
doubleArrayOf(opts[2], opts[3], opts[4], opts[5]),
doubleArrayOf(opts[6], opts[7], opts[8]),
opts[9].toInt(),
10,
1
)
val result = DoubleTensorAlgebra.levenbergMarquardt(inputData)
println("Parameters:")
for (i in 0 until result.resultParameters.shape.component1()) {
val x = (result.resultParameters[i, 0] * 10000).roundToInt() / 10000.0
print("$x ")
}
println()
println("Y true and y received:")
var y_hat_after = funcDifficultForLm(t_example, result.resultParameters, exampleNumber)
for (i in 0 until y_hat.shape.component1()) {
val x = (y_hat[i, 0] * 10000).roundToInt() / 10000.0
val y = (y_hat_after[i, 0] * 10000).roundToInt() / 10000.0
println("$x $y")
}
println("Сhi_sq:")
println(result.resultChiSq)
println("Number of iterations:")
println(result.iterations)
}

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@ -1,59 +0,0 @@
/*
* Copyright 2018-2024 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.tensors.LevenbergMarquardt.StaticLm
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.nd.as2D
import space.kscience.kmath.nd.component1
import space.kscience.kmath.tensors.LevenbergMarquardt.funcDifficultForLm
import space.kscience.kmath.tensors.LevenbergMarquardt.funcEasyForLm
import space.kscience.kmath.tensors.LevenbergMarquardt.getStartDataForFuncEasy
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra
import space.kscience.kmath.tensors.core.LMInput
import space.kscience.kmath.tensors.core.levenbergMarquardt
import kotlin.math.roundToInt
fun main() {
val startedData = getStartDataForFuncEasy()
val inputData = LMInput(
::funcEasyForLm,
DoubleTensorAlgebra.ones(ShapeND(intArrayOf(4, 1))).as2D(),
startedData.t,
startedData.y_dat,
startedData.weight,
startedData.dp,
startedData.p_min,
startedData.p_max,
startedData.opts[1].toInt(),
doubleArrayOf(startedData.opts[2], startedData.opts[3], startedData.opts[4], startedData.opts[5]),
doubleArrayOf(startedData.opts[6], startedData.opts[7], startedData.opts[8]),
startedData.opts[9].toInt(),
10,
startedData.example_number
)
val result = DoubleTensorAlgebra.levenbergMarquardt(inputData)
println("Parameters:")
for (i in 0 until result.resultParameters.shape.component1()) {
val x = (result.resultParameters[i, 0] * 10000).roundToInt() / 10000.0
print("$x ")
}
println()
println("Y true and y received:")
var y_hat_after = funcDifficultForLm(startedData.t, result.resultParameters, startedData.example_number)
for (i in 0 until startedData.y_dat.shape.component1()) {
val x = (startedData.y_dat[i, 0] * 10000).roundToInt() / 10000.0
val y = (y_hat_after[i, 0] * 10000).roundToInt() / 10000.0
println("$x $y")
}
println("Сhi_sq:")
println(result.resultChiSq)
println("Number of iterations:")
println(result.iterations)
}

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@ -1,91 +0,0 @@
/*
* Copyright 2018-2024 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.tensors.LevenbergMarquardt.StaticLm
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.nd.as2D
import space.kscience.kmath.nd.component1
import space.kscience.kmath.tensors.LevenbergMarquardt.funcMiddleForLm
import space.kscience.kmath.tensors.core.BroadcastDoubleTensorAlgebra
import space.kscience.kmath.tensors.core.BroadcastDoubleTensorAlgebra.div
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra
import space.kscience.kmath.tensors.core.LMInput
import space.kscience.kmath.tensors.core.levenbergMarquardt
import kotlin.math.roundToInt
fun main() {
val NData = 100
var t_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(NData, 1))).as2D()
for (i in 0 until NData) {
t_example[i, 0] = t_example[i, 0] * (i + 1)
}
val Nparams = 20
var p_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_example[i, 0] = p_example[i, 0] + i - 25
}
val exampleNumber = 1
var y_hat = funcMiddleForLm(t_example, p_example, exampleNumber)
var p_init = DoubleTensorAlgebra.zeros(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_init[i, 0] = (p_example[i, 0] + 0.9)
}
var t = t_example
val y_dat = y_hat
val weight = 1.0
val dp = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), DoubleArray(1) { -0.01 }
).as2D()
var p_min = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0)
val opts = doubleArrayOf(3.0, 7000.0, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 11.0, 9.0, 1.0)
val inputData = LMInput(
::funcMiddleForLm,
p_init.as2D(),
t,
y_dat,
weight,
dp,
p_min.as2D(),
p_max.as2D(),
opts[1].toInt(),
doubleArrayOf(opts[2], opts[3], opts[4], opts[5]),
doubleArrayOf(opts[6], opts[7], opts[8]),
opts[9].toInt(),
10,
1
)
val result = DoubleTensorAlgebra.levenbergMarquardt(inputData)
println("Parameters:")
for (i in 0 until result.resultParameters.shape.component1()) {
val x = (result.resultParameters[i, 0] * 10000).roundToInt() / 10000.0
print("$x ")
}
println()
var y_hat_after = funcMiddleForLm(t_example, result.resultParameters, exampleNumber)
for (i in 0 until y_hat.shape.component1()) {
val x = (y_hat[i, 0] * 10000).roundToInt() / 10000.0
val y = (y_hat_after[i, 0] * 10000).roundToInt() / 10000.0
println("$x $y")
}
println("Сhi_sq:")
println(result.resultChiSq)
println("Number of iterations:")
println(result.iterations)
}

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@ -1,76 +0,0 @@
/*
* Copyright 2018-2024 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.tensors.LevenbergMarquardt.StreamingLm
import kotlinx.coroutines.delay
import kotlinx.coroutines.flow.Flow
import kotlinx.coroutines.flow.flow
import space.kscience.kmath.nd.MutableStructure2D
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.nd.as2D
import space.kscience.kmath.nd.component1
import space.kscience.kmath.structures.Float64
import space.kscience.kmath.tensors.LevenbergMarquardt.StartDataLm
import space.kscience.kmath.tensors.core.BroadcastDoubleTensorAlgebra.zeros
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra
import space.kscience.kmath.tensors.core.LMInput
import space.kscience.kmath.tensors.core.levenbergMarquardt
import kotlin.random.Random
fun streamLm(
lm_func: (MutableStructure2D<Float64>, MutableStructure2D<Float64>, Int) -> (MutableStructure2D<Float64>),
startData: StartDataLm, launchFrequencyInMs: Long, numberOfLaunches: Int,
): Flow<MutableStructure2D<Float64>> = flow {
var example_number = startData.example_number
var p_init = startData.p_init
var t = startData.t
var y_dat = startData.y_dat
val weight = startData.weight
val dp = startData.dp
val p_min = startData.p_min
val p_max = startData.p_max
val opts = startData.opts
var steps = numberOfLaunches
val isEndless = (steps <= 0)
val inputData = LMInput(
lm_func,
p_init,
t,
y_dat,
weight,
dp,
p_min,
p_max,
opts[1].toInt(),
doubleArrayOf(opts[2], opts[3], opts[4], opts[5]),
doubleArrayOf(opts[6], opts[7], opts[8]),
opts[9].toInt(),
10,
example_number
)
while (isEndless || steps > 0) {
val result = DoubleTensorAlgebra.levenbergMarquardt(inputData)
emit(result.resultParameters)
delay(launchFrequencyInMs)
inputData.realValues = generateNewYDat(y_dat, 0.1)
inputData.startParameters = result.resultParameters
if (!isEndless) steps -= 1
}
}
fun generateNewYDat(y_dat: MutableStructure2D<Float64>, delta: Double): MutableStructure2D<Float64> {
val n = y_dat.shape.component1()
val y_dat_new = zeros(ShapeND(intArrayOf(n, 1))).as2D()
for (i in 0 until n) {
val randomEps = Random.nextDouble(delta + delta) - delta
y_dat_new[i, 0] = y_dat[i, 0] + randomEps
}
return y_dat_new
}

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@ -1,33 +0,0 @@
/*
* Copyright 2018-2024 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.tensors.LevenbergMarquardt.StreamingLm
import space.kscience.kmath.nd.component1
import space.kscience.kmath.tensors.LevenbergMarquardt.funcDifficultForLm
import space.kscience.kmath.tensors.LevenbergMarquardt.getStartDataForFuncDifficult
import kotlin.math.roundToInt
suspend fun main() {
val startData = getStartDataForFuncDifficult()
// Создание потока:
val lmFlow = streamLm(::funcDifficultForLm, startData, 0, 100)
var initialTime = System.currentTimeMillis()
var lastTime: Long
val launches = mutableListOf<Long>()
// Запуск потока
lmFlow.collect { parameters ->
lastTime = System.currentTimeMillis()
launches.add(lastTime - initialTime)
initialTime = lastTime
for (i in 0 until parameters.shape.component1()) {
val x = (parameters[i, 0] * 10000).roundToInt() / 10000.0
print("$x ")
if (i == parameters.shape.component1() - 1) println()
}
}
println("Average without first is: ${launches.subList(1, launches.size - 1).average()}")
}

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@ -1,233 +0,0 @@
/*
* Copyright 2018-2024 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.tensors.LevenbergMarquardt
import space.kscience.kmath.nd.MutableStructure2D
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.nd.as2D
import space.kscience.kmath.nd.component1
import space.kscience.kmath.structures.Float64
import space.kscience.kmath.tensors.core.BroadcastDoubleTensorAlgebra
import space.kscience.kmath.tensors.core.BroadcastDoubleTensorAlgebra.div
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra.Companion.max
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra.Companion.plus
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra.Companion.pow
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra.Companion.times
import space.kscience.kmath.tensors.core.asDoubleTensor
public data class StartDataLm(
var lm_matx_y_dat: MutableStructure2D<Float64>,
var example_number: Int,
var p_init: MutableStructure2D<Float64>,
var t: MutableStructure2D<Float64>,
var y_dat: MutableStructure2D<Float64>,
var weight: Double,
var dp: MutableStructure2D<Float64>,
var p_min: MutableStructure2D<Float64>,
var p_max: MutableStructure2D<Float64>,
var consts: MutableStructure2D<Float64>,
var opts: DoubleArray,
)
fun funcEasyForLm(
t: MutableStructure2D<Float64>,
p: MutableStructure2D<Float64>,
exampleNumber: Int,
): MutableStructure2D<Float64> {
val m = t.shape.component1()
var y_hat = DoubleTensorAlgebra.zeros(ShapeND(intArrayOf(m, 1)))
if (exampleNumber == 1) {
y_hat = DoubleTensorAlgebra.exp((t.times(-1.0 / p[1, 0]))).times(p[0, 0]) + t.times(p[2, 0]).times(
DoubleTensorAlgebra.exp((t.times(-1.0 / p[3, 0])))
)
} else if (exampleNumber == 2) {
val mt = t.max()
y_hat = (t.times(1.0 / mt)).times(p[0, 0]) +
(t.times(1.0 / mt)).pow(2).times(p[1, 0]) +
(t.times(1.0 / mt)).pow(3).times(p[2, 0]) +
(t.times(1.0 / mt)).pow(4).times(p[3, 0])
} else if (exampleNumber == 3) {
y_hat = DoubleTensorAlgebra.exp((t.times(-1.0 / p[1, 0])))
.times(p[0, 0]) + DoubleTensorAlgebra.sin((t.times(1.0 / p[3, 0]))).times(p[2, 0])
}
return y_hat.as2D()
}
fun funcMiddleForLm(
t: MutableStructure2D<Float64>,
p: MutableStructure2D<Float64>,
exampleNumber: Int,
): MutableStructure2D<Float64> {
val m = t.shape.component1()
var y_hat = DoubleTensorAlgebra.zeros(ShapeND(intArrayOf(m, 1)))
val mt = t.max()
for (i in 0 until p.shape.component1()) {
y_hat += (t.times(1.0 / mt)).times(p[i, 0])
}
for (i in 0 until 5) {
y_hat = funcEasyForLm(y_hat.as2D(), p, exampleNumber).asDoubleTensor()
}
return y_hat.as2D()
}
fun funcDifficultForLm(
t: MutableStructure2D<Float64>,
p: MutableStructure2D<Float64>,
exampleNumber: Int,
): MutableStructure2D<Float64> {
val m = t.shape.component1()
var y_hat = DoubleTensorAlgebra.zeros(ShapeND(intArrayOf(m, 1)))
val mt = t.max()
for (i in 0 until p.shape.component1()) {
y_hat = y_hat.plus((t.times(1.0 / mt)).times(p[i, 0]))
}
for (i in 0 until 4) {
y_hat = funcEasyForLm((y_hat.as2D() + t).as2D(), p, exampleNumber).asDoubleTensor()
}
return y_hat.as2D()
}
fun getStartDataForFuncDifficult(): StartDataLm {
val NData = 200
var t_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(NData, 1))).as2D()
for (i in 0 until NData) {
t_example[i, 0] = t_example[i, 0] * (i + 1) - 104
}
val Nparams = 15
var p_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_example[i, 0] = p_example[i, 0] + i - 25
}
val exampleNumber = 1
var y_hat = funcDifficultForLm(t_example, p_example, exampleNumber)
var p_init = DoubleTensorAlgebra.zeros(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_init[i, 0] = (p_example[i, 0] + 0.9)
}
var t = t_example
val y_dat = y_hat
val weight = 1.0 / Nparams * 1.0 - 0.085
val dp = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), DoubleArray(1) { -0.01 }
).as2D()
var p_min = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0)
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 10000.0, 1e-2, 1e-3, 1e-2, 1e-2, 1e-2, 11.0, 9.0, 1.0)
return StartDataLm(y_dat, 1, p_init, t, y_dat, weight, dp, p_min.as2D(), p_max.as2D(), consts, opts)
}
fun getStartDataForFuncMiddle(): StartDataLm {
val NData = 100
var t_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(NData, 1))).as2D()
for (i in 0 until NData) {
t_example[i, 0] = t_example[i, 0] * (i + 1)
}
val Nparams = 20
var p_example = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_example[i, 0] = p_example[i, 0] + i - 25
}
val exampleNumber = 1
var y_hat = funcMiddleForLm(t_example, p_example, exampleNumber)
var p_init = DoubleTensorAlgebra.zeros(ShapeND(intArrayOf(Nparams, 1))).as2D()
for (i in 0 until Nparams) {
p_init[i, 0] = (p_example[i, 0] + 10.0)
}
var t = t_example
val y_dat = y_hat
val weight = 1.0
val dp = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), DoubleArray(1) { -0.01 }
).as2D()
var p_min = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / -50.0)
val p_max = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(Nparams, 1)))
p_min = p_min.div(1.0 / 50.0)
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 10000.0, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 11.0, 9.0, 1.0)
var example_number = 1
return StartDataLm(y_dat, example_number, p_init, t, y_dat, weight, dp, p_min.as2D(), p_max.as2D(), consts, opts)
}
fun getStartDataForFuncEasy(): StartDataLm {
val lm_matx_y_dat = doubleArrayOf(
19.6594, 18.6096, 17.6792, 17.2747, 16.3065, 17.1458, 16.0467, 16.7023, 15.7809, 15.9807,
14.7620, 15.1128, 16.0973, 15.1934, 15.8636, 15.4763, 15.6860, 15.1895, 15.3495, 16.6054,
16.2247, 15.9854, 16.1421, 17.0960, 16.7769, 17.1997, 17.2767, 17.5882, 17.5378, 16.7894,
17.7648, 18.2512, 18.1581, 16.7037, 17.8475, 17.9081, 18.3067, 17.9632, 18.2817, 19.1427,
18.8130, 18.5658, 18.0056, 18.4607, 18.5918, 18.2544, 18.3731, 18.7511, 19.3181, 17.3066,
17.9632, 19.0513, 18.7528, 18.2928, 18.5967, 17.8567, 17.7859, 18.4016, 18.9423, 18.4959,
17.8000, 18.4251, 17.7829, 17.4645, 17.5221, 17.3517, 17.4637, 17.7563, 16.8471, 17.4558,
17.7447, 17.1487, 17.3183, 16.8312, 17.7551, 17.0942, 15.6093, 16.4163, 15.3755, 16.6725,
16.2332, 16.2316, 16.2236, 16.5361, 15.3721, 15.3347, 15.5815, 15.6319, 14.4538, 14.6044,
14.7665, 13.3718, 15.0587, 13.8320, 14.7873, 13.6824, 14.2579, 14.2154, 13.5818, 13.8157
)
var example_number = 1
val p_init = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(4, 1)), doubleArrayOf(5.0, 2.0, 0.2, 10.0)
).as2D()
var t = DoubleTensorAlgebra.ones(ShapeND(intArrayOf(100, 1))).as2D()
for (i in 0 until 100) {
t[i, 0] = t[i, 0] * (i + 1)
}
val y_dat = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(100, 1)), lm_matx_y_dat
).as2D()
val weight = 4.0
val dp = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), DoubleArray(1) { -0.01 }
).as2D()
val p_min = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(4, 1)), doubleArrayOf(-50.0, -20.0, -2.0, -100.0)
).as2D()
val p_max = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(4, 1)), doubleArrayOf(50.0, 20.0, 2.0, 100.0)
).as2D()
val consts = BroadcastDoubleTensorAlgebra.fromArray(
ShapeND(intArrayOf(1, 1)), doubleArrayOf(0.0)
).as2D()
val opts = doubleArrayOf(3.0, 100.0, 1e-3, 1e-3, 1e-1, 1e-1, 1e-2, 11.0, 9.0, 1.0)
return StartDataLm(y_dat, example_number, p_init, t, y_dat, weight, dp, p_min, p_max, consts, opts)
}

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@ -1,16 +1,14 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.tensors package space.kscience.kmath.tensors
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.operations.invoke import space.kscience.kmath.operations.invoke
import space.kscience.kmath.tensors.core.DoubleTensor import space.kscience.kmath.tensors.core.DoubleTensor
import space.kscience.kmath.tensors.core.DoubleTensorAlgebra import space.kscience.kmath.tensors.core.DoubleTensorAlgebra
import space.kscience.kmath.tensors.core.randomNormal
import space.kscience.kmath.tensors.core.randomNormalLike
import kotlin.math.abs import kotlin.math.abs
// OLS estimator using SVD // OLS estimator using SVD
@ -23,10 +21,10 @@ fun main() {
DoubleTensorAlgebra { DoubleTensorAlgebra {
// take coefficient vector from normal distribution // take coefficient vector from normal distribution
val alpha = randomNormal( val alpha = randomNormal(
ShapeND(5), intArrayOf(5),
randSeed randSeed
) + fromArray( ) + fromArray(
ShapeND(5), intArrayOf(5),
doubleArrayOf(1.0, 2.5, 3.4, 5.0, 10.1) doubleArrayOf(1.0, 2.5, 3.4, 5.0, 10.1)
) )
@ -34,37 +32,35 @@ fun main() {
// also take sample of size 20 from normal distribution for x // also take sample of size 20 from normal distribution for x
val x = randomNormal( val x = randomNormal(
ShapeND(20, 5), intArrayOf(20, 5),
randSeed randSeed
) )
// calculate y and add gaussian noise (N(0, 0.05)) // calculate y and add gaussian noise (N(0, 0.05))
val y = x dot alpha val y = x dot alpha
y += randomNormalLike(y, randSeed) * 0.05 y += y.randomNormalLike(randSeed) * 0.05
// now restore the coefficient vector with OSL estimator with SVD // now restore the coefficient vector with OSL estimator with SVD
val (u, singValues, v) = svd(x) val (u, singValues, v) = x.svd()
// we have to make sure the singular values of the matrix are not close to zero // we have to make sure the singular values of the matrix are not close to zero
println("Singular values:\n$singValues") println("Singular values:\n$singValues")
// inverse Sigma matrix can be restored from singular values with diagonalEmbedding function // inverse Sigma matrix can be restored from singular values with diagonalEmbedding function
val sigma = diagonalEmbedding(singValues.map { if (abs(it) < 1e-3) 0.0 else 1.0 / it }) val sigma = diagonalEmbedding(singValues.map{ if (abs(it) < 1e-3) 0.0 else 1.0/it })
val alphaOLS = v dot sigma dot u.transposed() dot y val alphaOLS = v dot sigma dot u.transpose() dot y
println( println("Estimated alpha:\n" +
"Estimated alpha:\n" + "$alphaOLS")
"$alphaOLS"
)
// figure out MSE of approximation // figure out MSE of approximation
fun mse(yTrue: DoubleTensor, yPred: DoubleTensor): Double { fun mse(yTrue: DoubleTensor, yPred: DoubleTensor): Double {
require(yTrue.shape.size == 1) require(yTrue.shape.size == 1)
require(yTrue.shape == yPred.shape) require(yTrue.shape contentEquals yPred.shape)
val diff = yTrue - yPred val diff = yTrue - yPred
return sqrt(diff.dot(diff)).value() return diff.dot(diff).sqrt().value()
} }
println("MSE: ${mse(alpha, alphaOLS)}") println("MSE: ${mse(alpha, alphaOLS)}")

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@ -1,12 +1,12 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.tensors package space.kscience.kmath.tensors
import space.kscience.kmath.nd.ShapeND import space.kscience.kmath.tensors.core.tensorAlgebra
import space.kscience.kmath.tensors.core.* import space.kscience.kmath.tensors.core.withBroadcast
// simple PCA // simple PCA
@ -16,49 +16,49 @@ fun main(): Unit = Double.tensorAlgebra.withBroadcast { // work in context with
// assume x is range from 0 until 10 // assume x is range from 0 until 10
val x = fromArray( val x = fromArray(
ShapeND(10), intArrayOf(10),
DoubleArray(10) { it.toDouble() } DoubleArray(10) { it.toDouble() }
) )
// take y dependent on x with noise // take y dependent on x with noise
val y = 2.0 * x + (3.0 + randomNormalLike(x, seed) * 1.5) val y = 2.0 * x + (3.0 + x.randomNormalLike(seed) * 1.5)
println("x:\n$x") println("x:\n$x")
println("y:\n$y") println("y:\n$y")
// stack them into single dataset // stack them into single dataset
val dataset = stack(listOf(x, y)).transposed() val dataset = stack(listOf(x, y)).transpose()
// normalize both x and y // normalize both x and y
val xMean = mean(x) val xMean = x.mean()
val yMean = mean(y) val yMean = y.mean()
val xStd = std(x) val xStd = x.std()
val yStd = std(y) val yStd = y.std()
val xScaled: DoubleTensor = (x - xMean) / xStd val xScaled = (x - xMean) / xStd
val yScaled: DoubleTensor = (y - yMean) / yStd val yScaled = (y - yMean) / yStd
// save means ans standard deviations for further recovery // save means ans standard deviations for further recovery
val mean = fromArray( val mean = fromArray(
ShapeND(2), intArrayOf(2),
doubleArrayOf(xMean, yMean) doubleArrayOf(xMean, yMean)
) )
println("Means:\n$mean") println("Means:\n$mean")
val std = fromArray( val std = fromArray(
ShapeND(2), intArrayOf(2),
doubleArrayOf(xStd, yStd) doubleArrayOf(xStd, yStd)
) )
println("Standard deviations:\n$std") println("Standard deviations:\n$std")
// calculate the covariance matrix of scaled x and y // calculate the covariance matrix of scaled x and y
val covMatrix = covariance(listOf(xScaled.asDoubleTensor1D(), yScaled.asDoubleTensor1D())) val covMatrix = cov(listOf(xScaled, yScaled))
println("Covariance matrix:\n$covMatrix") println("Covariance matrix:\n$covMatrix")
// and find out eigenvector of it // and find out eigenvector of it
val (_, evecs) = symEig(covMatrix) val (_, evecs) = covMatrix.symEig()
val v = evecs.getTensor(0) val v = evecs[0]
println("Eigenvector:\n$v") println("Eigenvector:\n$v")
// reduce dimension of dataset // reduce dimension of dataset
@ -68,7 +68,7 @@ fun main(): Unit = Double.tensorAlgebra.withBroadcast { // work in context with
// we can restore original data from reduced data; // we can restore original data from reduced data;
// for example, find 7th element of dataset. // for example, find 7th element of dataset.
val n = 7 val n = 7
val restored = (datasetReduced.getTensor(n) dot v.view(ShapeND(1, 2))) * std + mean val restored = (datasetReduced[n] dot v.view(intArrayOf(1, 2))) * std + mean
println("Original value:\n${dataset.getTensor(n)}") println("Original value:\n${dataset[n]}")
println("Restored value:\n$restored") println("Restored value:\n$restored")
} }

View File

@ -1,12 +1,10 @@
/* /*
* Copyright 2018-2024 KMath contributors. * Copyright 2018-2021 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. * 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.tensors package space.kscience.kmath.tensors
import space.kscience.kmath.nd.ShapeND
import space.kscience.kmath.tensors.core.randomNormal
import space.kscience.kmath.tensors.core.tensorAlgebra import space.kscience.kmath.tensors.core.tensorAlgebra
import space.kscience.kmath.tensors.core.withBroadcast import space.kscience.kmath.tensors.core.withBroadcast
@ -15,17 +13,17 @@ import space.kscience.kmath.tensors.core.withBroadcast
fun main() = Double.tensorAlgebra.withBroadcast { // work in context with broadcast methods fun main() = Double.tensorAlgebra.withBroadcast { // work in context with broadcast methods
// take dataset of 5-element vectors from normal distribution // take dataset of 5-element vectors from normal distribution
val dataset = randomNormal(ShapeND(100, 5)) * 1.5 // all elements from N(0, 1.5) val dataset = randomNormal(intArrayOf(100, 5)) * 1.5 // all elements from N(0, 1.5)
dataset += fromArray( dataset += fromArray(
ShapeND(5), intArrayOf(5),
doubleArrayOf(0.0, 1.0, 1.5, 3.0, 5.0) // row means doubleArrayOf(0.0, 1.0, 1.5, 3.0, 5.0) // row means
) )
// find out mean and standard deviation of each column // find out mean and standard deviation of each column
val mean = mean(dataset, 0, false) val mean = dataset.mean(0, false)
val std = std(dataset, 0, false) val std = dataset.std(0, false)
println("Mean:\n$mean") println("Mean:\n$mean")
println("Standard deviation:\n$std") println("Standard deviation:\n$std")
@ -37,8 +35,8 @@ fun main() = Double.tensorAlgebra.withBroadcast { // work in context with broad
// now we can scale dataset with mean normalization // now we can scale dataset with mean normalization
val datasetScaled = (dataset - mean) / std val datasetScaled = (dataset - mean) / std
// find out mean and standardDiviation of scaled dataset // find out mean and std of scaled dataset
println("Mean of scaled:\n${mean(datasetScaled, 0, false)}") println("Mean of scaled:\n${datasetScaled.mean(0, false)}")
println("Mean of scaled:\n${std(datasetScaled, 0, false)}") println("Mean of scaled:\n${datasetScaled.std(0, false)}")
} }

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