tsne 0.1.0

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data/CHANGELOG.md

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+## 0.1.0 (2020-02-11)
+
+- First release

data/LICENSE.txt

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+BSD 3-Clause License
+
+Copyright (c) 2020, Andrew Kane
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/README.md

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+# t-SNE
+
+High performance t-SNE for Ruby, powered by [Multicore t-SNE](https://github.com/DmitryUlyanov/tsne)
+
+## Installation
+
+Add this line to your application’s Gemfile:
+
+```ruby
+gem 'tsne'
+```
+
+## Getting Started
+
+Prep your data
+
+```ruby
+x = Numo::DFloat.cast([[0, 0, 0], [0, 1, 1], [1, 0, 1], [1, 1, 1]])
+```
+
+Run
+
+```ruby
+tsne = TSNE.new
+tsne.fit_transform(x)
+```
+
+Get Kullback-Leibler divergence
+
+```ruby
+tsne.kl_divergence
+```
+
+## Parameters
+
+```ruby
+TSNE.new(
+  n_components: 2,
+  perplexity: 30.0,
+  early_exaggeration: 12,
+  learning_rate: 200,
+  n_iter: 1000,
+  n_iter_early_exag: 250,
+  verbose: 0,
+  random_state: -1,
+  angle: 0.5,
+  n_jobs: 1,
+  cheat_metric: true
+)
+```
+
+## History
+
+View the [changelog](https://github.com/ankane/tsne/blob/master/CHANGELOG.md)
+
+## Contributing
+
+Everyone is encouraged to help improve this project. Here are a few ways you can help:
+
+- [Report bugs](https://github.com/ankane/tsne/issues)
+- Fix bugs and [submit pull requests](https://github.com/ankane/tsne/pulls)
+- Write, clarify, or fix documentation
+- Suggest or add new features
+
+To get started with development:
+
+```sh
+git clone https://github.com/ankane/tsne.git
+cd tsne
+bundle install
+bundle exec rake vendor:all
+bundle exec rake test
+```

data/lib/tsne/ffi.rb

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+module TSNE
+  module FFI
+    extend Fiddle::Importer
+
+    libs = Array(TSNE.ffi_lib).dup
+    begin
+      dlload Fiddle.dlopen(libs.shift)
+    rescue Fiddle::DLError => e
+      retry if libs.any?
+      raise e if ENV["TSNE_DEBUG"]
+      raise LoadError, "Could not find t-SNE"
+    end
+
+    typealias "bool", "char"
+
+    extern "void tsne_run_double(
+      double* X, int N, int D, double* Y,
+      int no_dims, double perplexity, double theta,
+      int num_threads, int max_iter, int n_iter_early_exag,
+      int random_state, bool init_from_Y, int verbose,
+      double early_exaggeration, double learning_rate,
+      double *final_error, int distance
+    )"
+  end
+end

data/lib/tsne/model.rb

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+module TSNE
+  class Model
+    attr_reader :kl_divergence, :n_iter
+
+    def initialize(n_components: 2, perplexity: 30.0,
+      early_exaggeration: 12, learning_rate: 200,
+      n_iter: 1000, n_iter_early_exag: 250, verbose: 0,
+      random_state: -1, angle: 0.5, n_jobs: 1, cheat_metric: true)
+
+      @n_components = n_components
+      @perplexity = perplexity
+      @early_exaggeration = early_exaggeration
+      @learning_rate = learning_rate
+      @n_iter = n_iter
+      @n_iter_early_exag = n_iter_early_exag
+      @verbose = verbose
+      @random_state = random_state
+      @angle = angle
+      @n_jobs = n_jobs
+      @cheat_metric = cheat_metric
+    end
+
+    def fit(x)
+      fit_transform(x)
+      self
+    end
+
+    def fit_transform(x)
+      x = Numo::DFloat.cast(x) unless x.is_a?(Numo::NArray)
+      x = x.cast_to(Numo::DFloat) unless x.is_a?(Numo::DFloat)
+      n, d = x.shape
+
+      x = Fiddle::Pointer[x.to_binary]
+      y = Fiddle::Pointer.malloc(n * @n_components * Fiddle::SIZEOF_DOUBLE)
+      final_error = Fiddle::Pointer.malloc(Fiddle::SIZEOF_DOUBLE)
+
+      FFI.tsne_run_double(
+        x, n, d, y, @n_components, @perplexity, @angle, @n_jobs,
+        @n_iter, @n_iter_early_exag, @random_state, 0, @verbose, @early_exaggeration,
+        @learning_rate, final_error, @cheat_metric ? 1 : 0
+      )
+
+      @kl_divergence = final_error[0, final_error.size].unpack1("d")
+
+      Numo::DFloat.from_binary(y[0, y.size]).reshape(n, @n_components)
+    end
+  end
+end

data/lib/tsne/version.rb

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+module TSNE
+  VERSION = "0.1.0"
+end

data/lib/tsne.rb

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+# dependencies
+require "numo/narray"
+
+# stdlib
+require "fiddle/import"
+
+# modules
+require "tsne/model"
+require "tsne/version"
+
+module TSNE
+  class Error < StandardError; end
+
+  class << self
+    attr_accessor :ffi_lib
+  end
+  lib_name =
+    if Gem.win_platform?
+      "tsne_multicore.dll"
+    elsif RbConfig::CONFIG["host_os"] =~ /darwin/i
+      "libtsne_multicore.dylib"
+    else
+      "libtsne_multicore.so"
+    end
+  vendor_lib = File.expand_path("../vendor/#{lib_name}", __dir__)
+  self.ffi_lib = [vendor_lib]
+
+  # friendlier error message
+  autoload :FFI, "tsne/ffi"
+
+  def self.new(*args, **options)
+    Model.new(*args, **options)
+  end
+end

data/vendor/LICENSE.txt

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+BSD 3-Clause License
+
+Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology)
+Copyright (c) 2016, Dmitry Ulyanov
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

metadata

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+--- !ruby/object:Gem::Specification
+name: tsne
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Andrew Kane
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2020-02-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: numo-narray
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '5'
+description: 
+email: andrew@chartkick.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- CHANGELOG.md
+- LICENSE.txt
+- README.md
+- lib/tsne.rb
+- lib/tsne/ffi.rb
+- lib/tsne/model.rb
+- lib/tsne/version.rb
+- vendor/LICENSE.txt
+- vendor/libtsne_multicore.dylib
+- vendor/libtsne_multicore.so
+- vendor/tsne_multicore.dll
+homepage: https://github.com/ankane/tsne
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '2.4'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.2
+signing_key: 
+specification_version: 4
+summary: High performance t-SNE for Ruby
+test_files: []