agglomerative_clustering 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +36 -0
- data/.rspec +3 -0
- data/Gemfile +3 -0
- data/Gemfile.lock +46 -0
- data/LICENSE +22 -0
- data/LICENSE.txt +22 -0
- data/README.md +33 -0
- data/Rakefile +2 -0
- data/agglomerative_clustering.gemspec +23 -0
- data/cluster.rb +58 -0
- data/lib/agglomerative_clustering.rb +10 -0
- data/lib/agglomerative_clustering/cluster.rb +19 -0
- data/lib/agglomerative_clustering/euclidean_distance.rb +8 -0
- data/lib/agglomerative_clustering/linkage/average.rb +20 -0
- data/lib/agglomerative_clustering/linkage/base.rb +22 -0
- data/lib/agglomerative_clustering/linkage/center.rb +20 -0
- data/lib/agglomerative_clustering/linkage/complete.rb +22 -0
- data/lib/agglomerative_clustering/linkage/single.rb +21 -0
- data/lib/agglomerative_clustering/point.rb +3 -0
- data/lib/agglomerative_clustering/set.rb +75 -0
- data/lib/agglomerative_clustering/version.rb +3 -0
- data/spec/factories/lib/agglomerative_clustering/cluster.rb +5 -0
- data/spec/factories/lib/agglomerative_clustering/point.rb +7 -0
- data/spec/factories/lib/agglomerative_clustering/set.rb +5 -0
- data/spec/lib/agglomerative_clustering/cluster_spec.rb +11 -0
- data/spec/lib/agglomerative_clustering/euclidean_distance_spec.rb +15 -0
- data/spec/lib/agglomerative_clustering/linkage/average_spec.rb +25 -0
- data/spec/lib/agglomerative_clustering/linkage/base_spec.rb +13 -0
- data/spec/lib/agglomerative_clustering/linkage/center_spec.rb +23 -0
- data/spec/lib/agglomerative_clustering/linkage/complete_spec.rb +19 -0
- data/spec/lib/agglomerative_clustering/linkage/single_spec.rb +19 -0
- data/spec/lib/agglomerative_clustering/set_spec.rb +75 -0
- data/spec/spec_helper.rb +7 -0
- metadata +133 -0
checksums.yaml
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SHA1:
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metadata.gz: d52ff4f84aef0fbd56aa453833ea2e5b9c9772e2
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data.tar.gz: 4abb19bb148f77989f43be805769e0676a7182f7
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SHA512:
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metadata.gz: b31e61ad6c08ecdce2326bdab94c412aaee32227775f662ad62361896d69124acbad3ed4c6f8a40f2298de30ac77d65c0fcabd0bfe58c16b6d11bd89e75a7dd5
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data.tar.gz: 8a2a08bda0f2975166536d1ec85cd0f2254044689d8b6f422b6f2170bd64301ae914c05f1264d14a81d7b4b2fb4deb9c4da0fa82abb9b94f57a462ba1689c11d
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data/.gitignore
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*.gem
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*.rbc
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/InstalledFiles
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/test/version_tmp/
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/tmp/
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## Specific to RubyMotion:
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.dat*
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build/
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## Documentation cache and generated files:
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/.yardoc/
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/doc/
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/rdoc/
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## Environment normalisation:
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/.bundle/
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/lib/bundler/man/
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# for a library or gem, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# Gemfile.lock
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# .ruby-version
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# .ruby-gemset
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# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
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.rvmrc
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outliers.csv
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points.csv
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data/.rspec
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data/Gemfile
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data/Gemfile.lock
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PATH
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remote: .
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specs:
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agglomerative_clustering (0.0.1)
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GEM
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remote: https://rubygems.org/
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specs:
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activesupport (4.1.6)
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i18n (~> 0.6, >= 0.6.9)
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json (~> 1.7, >= 1.7.7)
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minitest (~> 5.1)
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thread_safe (~> 0.1)
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tzinfo (~> 1.1)
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diff-lcs (1.2.5)
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factory_girl (4.4.0)
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activesupport (>= 3.0.0)
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i18n (0.6.11)
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json (1.8.1)
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minitest (5.4.2)
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rake (10.3.2)
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rspec (3.1.0)
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rspec-core (~> 3.1.0)
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rspec-expectations (~> 3.1.0)
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rspec-mocks (~> 3.1.0)
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rspec-core (3.1.6)
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rspec-support (~> 3.1.0)
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rspec-expectations (3.1.2)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.1.0)
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rspec-mocks (3.1.3)
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rspec-support (~> 3.1.0)
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rspec-support (3.1.2)
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thread_safe (0.3.4)
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tzinfo (1.2.2)
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thread_safe (~> 0.1)
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PLATFORMS
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ruby
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DEPENDENCIES
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agglomerative_clustering!
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bundler (~> 1.7)
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factory_girl
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rake (~> 10.0)
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rspec
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data/LICENSE
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The MIT License (MIT)
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Copyright (c) 2014 Bryan Mulvihill
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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data/LICENSE.txt
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Copyright (c) 2014 Bryan Mulvihill
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# AgglomerativeClustering
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Hierarchical Agglomerative Clustering Algorithm
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Input Set of 3 dimensional points, group into nearest k clusters
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## Installation
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Add this line to your application's Gemfile:
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```ruby
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gem 'agglomerative_clustering'
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```
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install agglomerative_clustering
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## Usage
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TODO: Write usage instructions here
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## Contributing
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1. Fork it ( https://github.com/[my-github-username]/agglomerative_clustering/fork )
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create a new Pull Request
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data/Rakefile
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# coding: utf-8
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'agglomerative_clustering/version'
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Gem::Specification.new do |spec|
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spec.name = "agglomerative_clustering"
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spec.version = AgglomerativeClustering::VERSION
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spec.authors = ["Bryan Mulvihill"]
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spec.email = ["bmulvihill@pinsonault.com"]
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spec.summary = %q{Ruby Agglomerative Clustering Algorithm}
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spec.homepage = ""
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spec.license = "MIT"
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spec.files = `git ls-files -z`.split("\x0")
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spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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spec.require_paths = ["lib"]
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spec.add_development_dependency "bundler", "~> 1.7"
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spec.add_development_dependency "rake", "~> 10.0"
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spec.add_development_dependency 'rspec'
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end
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data/cluster.rb
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#!/usr/bin/env ruby
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require 'agglomerative_clustering'
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set = AgglomerativeClustering::Set.new(AgglomerativeClustering::Linkage::Single.new)
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for i in 0..99
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x = Random.rand(0..100)
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y = Random.rand(0..100)
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z = Random.rand(0..100)
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p = Point.new(x,y,z)
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set.push(p)
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end
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for i in 100..199
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x = Random.rand(200..299)
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y = Random.rand(200..299)
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z = Random.rand(200..299)
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p = Point.new(x,y,z)
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set.push(p)
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end
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for i in 200..299
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x = Random.rand(400..499)
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y = Random.rand(400..499)
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z = Random.rand(400..499)
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p = Point.new(x,y,z)
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set.push(p)
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end
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percentage = 80
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distance = 150
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open('points.csv', 'w') do |f|
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set.points.each do |point|
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f << "#{point.x},#{point.y},#{point.z}\n"
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end
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end
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open('outliers.csv', 'w') do |f|
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set.find_outliers(percentage, distance).each do |point|
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f << "#{point.x},#{point.y},#{point.z}\n"
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end
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end
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if set.outliers.any?
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puts 'Outliers Removed from Set:'
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set.outliers.each do |outlier|
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puts outlier
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end
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else
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puts "There are no outliers where #{percentage}% of the points lie at a distance greater than #{distance}"
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end
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clusters = set.cluster(3)
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clusters.each_with_index do |cluster, index|
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open("cluster#{index}.csv", 'w') do |f|
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cluster.points.each do |point|
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f << "#{point.x},#{point.y},#{point.z}\n"
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end
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end
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end
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require "agglomerative_clustering/version"
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require "agglomerative_clustering/euclidean_distance"
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require "agglomerative_clustering/linkage/base"
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require "agglomerative_clustering/linkage/single"
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require "agglomerative_clustering/linkage/complete"
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require "agglomerative_clustering/linkage/average"
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require "agglomerative_clustering/linkage/center"
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require "agglomerative_clustering/point"
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require "agglomerative_clustering/cluster"
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require "agglomerative_clustering/set"
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module AgglomerativeClustering
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class Cluster
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attr_reader :points
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def initialize(point)
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points << point
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end
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def points
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@points ||= []
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end
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def merge(cluster)
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cluster.points.each { |point| points << point }
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self
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end
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end
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end
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module AgglomerativeClustering
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module Linkage
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class Average < Base
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def calculate_distance(cluster1, cluster2)
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distances = []
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cluster1.points.each do |point1|
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cluster2.points.each do |point2|
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distances << euclidean_distance(point1, point2)
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end
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end
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distances.inject(:+)/distances.size
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end
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def clusters_to_merge
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@clusters_to_merge ||= []
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end
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end
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end
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end
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module AgglomerativeClustering
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module Linkage
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class Base
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include EuclideanDistance
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def cluster(clusters)
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min_cluster_dist = 1.0/0
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clusters.each_with_index do |cluster1, index|
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clusters[index + 1..clusters.size].each do |cluster2|
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distance = calculate_distance(cluster1, cluster2)
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if distance < min_cluster_dist
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min_cluster_dist = distance
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@clusters_to_merge = [cluster1, cluster2]
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end
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end
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end
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clusters_to_merge
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end
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end
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end
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end
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module AgglomerativeClustering
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module Linkage
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class Center < Base
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def calculate_distance(cluster1, cluster2)
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point1, point2 = center_point(cluster1), center_point(cluster2)
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euclidean_distance(point1, point2)
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end
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9
|
+
|
10
|
+
def center_point cluster
|
11
|
+
cluster.points.first.zip(*cluster.points[1..cluster.points.size-1]).map { |a,b| (a + b)/cluster.points.size.to_f }
|
12
|
+
end
|
13
|
+
|
14
|
+
def clusters_to_merge
|
15
|
+
@clusters_to_merge ||= []
|
16
|
+
end
|
17
|
+
|
18
|
+
end
|
19
|
+
end
|
20
|
+
end
|
@@ -0,0 +1,22 @@
|
|
1
|
+
module AgglomerativeClustering
|
2
|
+
module Linkage
|
3
|
+
class Complete < Base
|
4
|
+
|
5
|
+
def calculate_distance(cluster1, cluster2)
|
6
|
+
max_point_distance = 0
|
7
|
+
cluster1.points.each do |point1|
|
8
|
+
cluster2.points.each do |point2|
|
9
|
+
distance = euclidean_distance(point1, point2)
|
10
|
+
max_point_distance = distance if distance > max_point_distance
|
11
|
+
end
|
12
|
+
end
|
13
|
+
max_point_distance
|
14
|
+
end
|
15
|
+
|
16
|
+
def clusters_to_merge
|
17
|
+
@clusters_to_merge ||= []
|
18
|
+
end
|
19
|
+
|
20
|
+
end
|
21
|
+
end
|
22
|
+
end
|
@@ -0,0 +1,21 @@
|
|
1
|
+
module AgglomerativeClustering
|
2
|
+
module Linkage
|
3
|
+
class Single < Base
|
4
|
+
|
5
|
+
def calculate_distance(cluster1, cluster2)
|
6
|
+
min_point_distance = 1.0/0
|
7
|
+
cluster1.points.each do |point1|
|
8
|
+
cluster2.points.each do |point2|
|
9
|
+
distance = euclidean_distance(point1, point2)
|
10
|
+
min_point_distance = distance if distance < min_point_distance
|
11
|
+
end
|
12
|
+
end
|
13
|
+
min_point_distance
|
14
|
+
end
|
15
|
+
|
16
|
+
def clusters_to_merge
|
17
|
+
@clusters_to_merge ||= []
|
18
|
+
end
|
19
|
+
end
|
20
|
+
end
|
21
|
+
end
|
@@ -0,0 +1,75 @@
|
|
1
|
+
require 'matrix'
|
2
|
+
module AgglomerativeClustering
|
3
|
+
class Set
|
4
|
+
include EuclideanDistance
|
5
|
+
attr_reader :points
|
6
|
+
|
7
|
+
def initialize(linkage)
|
8
|
+
@linkage = linkage
|
9
|
+
@points = []
|
10
|
+
end
|
11
|
+
|
12
|
+
def push point
|
13
|
+
point.index = points.size
|
14
|
+
points << point
|
15
|
+
end
|
16
|
+
|
17
|
+
def clusters
|
18
|
+
@clusters ||= points.map{ |point| AgglomerativeClustering::Cluster.new(point) }
|
19
|
+
end
|
20
|
+
|
21
|
+
def distance_matrix
|
22
|
+
@distance_matrix ||= build_distance_matrix
|
23
|
+
end
|
24
|
+
|
25
|
+
def print_distance_matrix
|
26
|
+
puts distance_matrix.to_a.map(&:inspect)
|
27
|
+
end
|
28
|
+
|
29
|
+
def cluster total_clusters
|
30
|
+
clusters_to_merge =[]
|
31
|
+
while clusters.size > total_clusters
|
32
|
+
clusters_to_merge = @linkage.cluster(clusters)
|
33
|
+
merge_clusters(clusters_to_merge)
|
34
|
+
end
|
35
|
+
clusters
|
36
|
+
end
|
37
|
+
|
38
|
+
def merge_clusters(min_clusters)
|
39
|
+
min_clusters[0].merge(min_clusters[1])
|
40
|
+
clusters.reject! { |cluster| cluster == min_clusters[1] }
|
41
|
+
min_clusters[0]
|
42
|
+
end
|
43
|
+
|
44
|
+
def outliers
|
45
|
+
set_outliers.uniq
|
46
|
+
end
|
47
|
+
|
48
|
+
def find_outliers percentage_of_clusters, distance
|
49
|
+
distance_matrix.each_with_index do |index, row, column|
|
50
|
+
count_hash[row] ||= 0
|
51
|
+
count_hash[row] += 1 if distance_matrix[row, column] > distance
|
52
|
+
set_outliers << points[row] if count_hash[row]/(distance_matrix.row_count - 1) > percentage_of_clusters/100
|
53
|
+
end
|
54
|
+
points.reject! { |point| outliers.include?(point) }
|
55
|
+
outliers
|
56
|
+
end
|
57
|
+
|
58
|
+
private
|
59
|
+
|
60
|
+
def set_outliers
|
61
|
+
@set_outliers ||= []
|
62
|
+
end
|
63
|
+
|
64
|
+
def count_hash
|
65
|
+
@count_hash ||= {}
|
66
|
+
end
|
67
|
+
|
68
|
+
def build_distance_matrix
|
69
|
+
Matrix.build(points.size, points.size) do |row, column|
|
70
|
+
euclidean_distance(points[row], points[column]).round(2)
|
71
|
+
end
|
72
|
+
end
|
73
|
+
|
74
|
+
end
|
75
|
+
end
|
@@ -0,0 +1,11 @@
|
|
1
|
+
describe AgglomerativeClustering::Cluster do
|
2
|
+
|
3
|
+
context '#merge' do
|
4
|
+
it 'will merge two clusters' do
|
5
|
+
cluster1 = FactoryGirl.build(:cluster)
|
6
|
+
cluster2 = FactoryGirl.build(:cluster)
|
7
|
+
points = cluster1.points + cluster2.points
|
8
|
+
expect(cluster1.merge(cluster2).points).to eql(points)
|
9
|
+
end
|
10
|
+
end
|
11
|
+
end
|
@@ -0,0 +1,15 @@
|
|
1
|
+
describe AgglomerativeClustering::EuclideanDistance do
|
2
|
+
before do
|
3
|
+
class Dummy
|
4
|
+
include AgglomerativeClustering::EuclideanDistance
|
5
|
+
end
|
6
|
+
end
|
7
|
+
|
8
|
+
context '#distance' do
|
9
|
+
it 'will return the distance between two points' do
|
10
|
+
p1 = FactoryGirl.build(:point, x: -1, y: 2, z: 3)
|
11
|
+
p2 = FactoryGirl.build(:point, x: 4 ,y: 0, z: -3)
|
12
|
+
expect(Dummy.new.euclidean_distance(p1,p2).round(3)).to eql(8.062)
|
13
|
+
end
|
14
|
+
end
|
15
|
+
end
|
@@ -0,0 +1,25 @@
|
|
1
|
+
describe AgglomerativeClustering::Linkage::Average do
|
2
|
+
|
3
|
+
context '#calculate_distance' do
|
4
|
+
it 'will calculate distance between clusters based on the average distnace between points' do
|
5
|
+
average_linkage = AgglomerativeClustering::Linkage::Average.new
|
6
|
+
point1 = FactoryGirl.build(:point, x: 1, y: 1, z: 1)
|
7
|
+
point2 = FactoryGirl.build(:point, x: 7, y: 7, z: 7)
|
8
|
+
point3 = FactoryGirl.build(:point, x: 2, y: 2, z: 2)
|
9
|
+
point4 = FactoryGirl.build(:point, x: 5, y: 5, z: 5)
|
10
|
+
cluster1 = AgglomerativeClustering::Cluster.new(point1)
|
11
|
+
cluster2 = AgglomerativeClustering::Cluster.new(point2)
|
12
|
+
cluster3 = AgglomerativeClustering::Cluster.new(point3)
|
13
|
+
cluster4 = AgglomerativeClustering::Cluster.new(point4)
|
14
|
+
cluster1 = cluster1.merge(cluster2)
|
15
|
+
cluster3 = cluster3.merge(cluster4)
|
16
|
+
distance1 = average_linkage.euclidean_distance(point1, point3)
|
17
|
+
distance2 = average_linkage.euclidean_distance(point1, point4)
|
18
|
+
distance3 = average_linkage.euclidean_distance(point2, point3)
|
19
|
+
distance4 = average_linkage.euclidean_distance(point2, point4)
|
20
|
+
average_distance = (distance1 + distance2 + distance3 + distance4)/4
|
21
|
+
expect(average_linkage.calculate_distance(cluster1, cluster3)).to eql(average_distance)
|
22
|
+
end
|
23
|
+
end
|
24
|
+
|
25
|
+
end
|
@@ -0,0 +1,13 @@
|
|
1
|
+
describe AgglomerativeClustering::Linkage::Base do
|
2
|
+
|
3
|
+
context '#cluster' do
|
4
|
+
it 'will return the clusters where min distance is closest' do
|
5
|
+
single_linkage = AgglomerativeClustering::Linkage::Single.new
|
6
|
+
set = FactoryGirl.build(:set)
|
7
|
+
set.push(FactoryGirl.build(:point))
|
8
|
+
set.push(FactoryGirl.build(:point))
|
9
|
+
expect(single_linkage.cluster(set.clusters)).to eql([set.clusters[0], set.clusters[1]])
|
10
|
+
end
|
11
|
+
end
|
12
|
+
|
13
|
+
end
|
@@ -0,0 +1,23 @@
|
|
1
|
+
describe AgglomerativeClustering::Linkage::Center do
|
2
|
+
|
3
|
+
context '#calculate_distance' do
|
4
|
+
it 'will calculate distance between clusters based on the center distance between points' do
|
5
|
+
center_linkage = AgglomerativeClustering::Linkage::Center.new
|
6
|
+
point1 = FactoryGirl.build(:point, x: 1, y: 1, z: 1)
|
7
|
+
point2 = FactoryGirl.build(:point, x: 2, y: 2, z: 2)
|
8
|
+
point3 = FactoryGirl.build(:point, x: 7, y: 7, z: 7)
|
9
|
+
point4 = FactoryGirl.build(:point, x: 5, y: 5, z: 5)
|
10
|
+
cluster1 = AgglomerativeClustering::Cluster.new(point1)
|
11
|
+
cluster2 = AgglomerativeClustering::Cluster.new(point2)
|
12
|
+
cluster3 = AgglomerativeClustering::Cluster.new(point3)
|
13
|
+
cluster4 = AgglomerativeClustering::Cluster.new(point4)
|
14
|
+
cluster1 = cluster1.merge(cluster2)
|
15
|
+
cluster3 = cluster3.merge(cluster4)
|
16
|
+
center_point1 = Point.new(1.5, 1.5, 1.5)
|
17
|
+
center_point2 = Point.new(6, 6, 6)
|
18
|
+
center_distance = center_linkage.euclidean_distance(center_point1, center_point2)
|
19
|
+
expect(center_linkage.calculate_distance(cluster1, cluster3)).to eql(center_distance)
|
20
|
+
end
|
21
|
+
end
|
22
|
+
|
23
|
+
end
|
@@ -0,0 +1,19 @@
|
|
1
|
+
describe AgglomerativeClustering::Linkage::Complete do
|
2
|
+
|
3
|
+
context '#calculate_distance' do
|
4
|
+
it 'will calculate distance between clusters based on the max distnace between points' do
|
5
|
+
complete_linkage = AgglomerativeClustering::Linkage::Complete.new
|
6
|
+
min_point = FactoryGirl.build(:point, x: 1, y: 1, z: 1)
|
7
|
+
max_point = FactoryGirl.build(:point, x: 7, y: 7, z: 7)
|
8
|
+
cluster1 = AgglomerativeClustering::Cluster.new(min_point)
|
9
|
+
cluster2 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 2, y: 2, z: 2))
|
10
|
+
cluster3 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 5, y: 5, z: 5))
|
11
|
+
cluster4 = AgglomerativeClustering::Cluster.new(max_point)
|
12
|
+
cluster1 = cluster1.merge(cluster2)
|
13
|
+
cluster3 = cluster3.merge(cluster4)
|
14
|
+
max_distance = complete_linkage.euclidean_distance(min_point, max_point)
|
15
|
+
expect(complete_linkage.calculate_distance(cluster1, cluster3)).to eql(max_distance)
|
16
|
+
end
|
17
|
+
end
|
18
|
+
|
19
|
+
end
|
@@ -0,0 +1,19 @@
|
|
1
|
+
describe AgglomerativeClustering::Linkage::Single do
|
2
|
+
|
3
|
+
context '#calculate_distance' do
|
4
|
+
it 'will calculate distance between clusters based on the min distnace between points' do
|
5
|
+
single_linkage = AgglomerativeClustering::Linkage::Single.new
|
6
|
+
min_point = FactoryGirl.build(:point, x: 2, y: 2, z: 2)
|
7
|
+
max_point = FactoryGirl.build(:point, x: 5, y: 5, z: 5)
|
8
|
+
cluster1 = AgglomerativeClustering::Cluster.new(min_point)
|
9
|
+
cluster2 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 1, y: 1, z: 1))
|
10
|
+
cluster3 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 7, y: 7, z: 7))
|
11
|
+
cluster4 = AgglomerativeClustering::Cluster.new(max_point)
|
12
|
+
cluster1 = cluster1.merge(cluster2)
|
13
|
+
cluster3 = cluster3.merge(cluster4)
|
14
|
+
min_distance = single_linkage.euclidean_distance(min_point, max_point)
|
15
|
+
expect(single_linkage.calculate_distance(cluster1, cluster3)).to eql(min_distance)
|
16
|
+
end
|
17
|
+
end
|
18
|
+
|
19
|
+
end
|
@@ -0,0 +1,75 @@
|
|
1
|
+
describe AgglomerativeClustering::Set do
|
2
|
+
|
3
|
+
before do
|
4
|
+
@set = FactoryGirl.build(:set)
|
5
|
+
@point1 = FactoryGirl.build(:point, x:2, y:2, z:3)
|
6
|
+
@point2 = FactoryGirl.build(:point, x:1, y:4, z:1)
|
7
|
+
@point3 = FactoryGirl.build(:point, x:5, y:2, z:2)
|
8
|
+
@point4 = FactoryGirl.build(:point, x:5, y:2, z:3)
|
9
|
+
@set.push(@point1)
|
10
|
+
@set.push(@point2)
|
11
|
+
@set.push(@point3)
|
12
|
+
@set.push(@point4)
|
13
|
+
end
|
14
|
+
|
15
|
+
context '#cluster' do
|
16
|
+
it 'will return clusters of points based on requested number of clusters' do
|
17
|
+
expect(@set.cluster(3).size).to eql(3)
|
18
|
+
end
|
19
|
+
|
20
|
+
it 'will cluster points that are closest to each other' do
|
21
|
+
@point5 = FactoryGirl.build(:point, x:5, y:2, z:4)
|
22
|
+
@point6 = FactoryGirl.build(:point, x:5, y:3, z:4)
|
23
|
+
@point7 = FactoryGirl.build(:point, x:15, y:20, z:21)
|
24
|
+
@point8 = FactoryGirl.build(:point, x:18, y:21, z:21)
|
25
|
+
@point9 = FactoryGirl.build(:point, x:16, y:22, z:21)
|
26
|
+
@set.push(@point5)
|
27
|
+
@set.push(@point6)
|
28
|
+
@set.push(@point7)
|
29
|
+
@set.push(@point8)
|
30
|
+
@set.push(@point9)
|
31
|
+
clusters = @set.cluster(3)
|
32
|
+
clusters[0].points.each do |point|
|
33
|
+
expect([@point1, @point2].include?(point)).to be true
|
34
|
+
end
|
35
|
+
clusters[1].points.each do |point|
|
36
|
+
expect([@point3, @point4, @point5, @point6].include?(point)).to be true
|
37
|
+
end
|
38
|
+
clusters[2].points.each do |point|
|
39
|
+
expect([@point7, @point8, @point9].include?(point)).to be true
|
40
|
+
end
|
41
|
+
end
|
42
|
+
end
|
43
|
+
|
44
|
+
context '#merge_clusters' do
|
45
|
+
it 'will merge two clusters into one and update the distance matrix' do
|
46
|
+
expect(@set.merge_clusters([@set.clusters[0],@set.clusters[1]]).points).to eql([@point1, @point2])
|
47
|
+
end
|
48
|
+
end
|
49
|
+
|
50
|
+
context '#find_outliers' do
|
51
|
+
it 'will return a list of outliers' do
|
52
|
+
outlier1 = FactoryGirl.build(:point, x:100, y:200, z:300)
|
53
|
+
outlier2 = FactoryGirl.build(:point, x:-100, y:-200, z:-300)
|
54
|
+
@set.push(outlier1)
|
55
|
+
@set.push(outlier2)
|
56
|
+
|
57
|
+
percentage_of_points = 90
|
58
|
+
distance = 10
|
59
|
+
expect(@set.find_outliers(percentage_of_points, distance)).to eql([outlier1, outlier2])
|
60
|
+
end
|
61
|
+
end
|
62
|
+
|
63
|
+
context '#outliers' do
|
64
|
+
it 'will return the set of points without outliers' do
|
65
|
+
outlier1 = FactoryGirl.build(:point, x:100, y:200, z:300)
|
66
|
+
outlier2 = FactoryGirl.build(:point, x:-100, y:-200, z:-300)
|
67
|
+
@set.push(outlier1)
|
68
|
+
@set.push(outlier2)
|
69
|
+
percentage_of_points = 90
|
70
|
+
distance = 10
|
71
|
+
@set.find_outliers(percentage_of_points, distance)
|
72
|
+
expect(@set.outliers).to eql([outlier1,outlier2])
|
73
|
+
end
|
74
|
+
end
|
75
|
+
end
|
data/spec/spec_helper.rb
ADDED
metadata
ADDED
@@ -0,0 +1,133 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: agglomerative_clustering
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Bryan Mulvihill
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2014-10-30 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bundler
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.7'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.7'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rake
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - "~>"
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '10.0'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - "~>"
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '10.0'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: rspec
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - ">="
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '0'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - ">="
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
description:
|
56
|
+
email:
|
57
|
+
- bmulvihill@pinsonault.com
|
58
|
+
executables: []
|
59
|
+
extensions: []
|
60
|
+
extra_rdoc_files: []
|
61
|
+
files:
|
62
|
+
- ".gitignore"
|
63
|
+
- ".rspec"
|
64
|
+
- Gemfile
|
65
|
+
- Gemfile.lock
|
66
|
+
- LICENSE
|
67
|
+
- LICENSE.txt
|
68
|
+
- README.md
|
69
|
+
- Rakefile
|
70
|
+
- agglomerative_clustering.gemspec
|
71
|
+
- cluster.rb
|
72
|
+
- lib/agglomerative_clustering.rb
|
73
|
+
- lib/agglomerative_clustering/cluster.rb
|
74
|
+
- lib/agglomerative_clustering/euclidean_distance.rb
|
75
|
+
- lib/agglomerative_clustering/linkage/average.rb
|
76
|
+
- lib/agglomerative_clustering/linkage/base.rb
|
77
|
+
- lib/agglomerative_clustering/linkage/center.rb
|
78
|
+
- lib/agglomerative_clustering/linkage/complete.rb
|
79
|
+
- lib/agglomerative_clustering/linkage/single.rb
|
80
|
+
- lib/agglomerative_clustering/point.rb
|
81
|
+
- lib/agglomerative_clustering/set.rb
|
82
|
+
- lib/agglomerative_clustering/version.rb
|
83
|
+
- outliers.csv
|
84
|
+
- points.csv
|
85
|
+
- spec/factories/lib/agglomerative_clustering/cluster.rb
|
86
|
+
- spec/factories/lib/agglomerative_clustering/point.rb
|
87
|
+
- spec/factories/lib/agglomerative_clustering/set.rb
|
88
|
+
- spec/lib/agglomerative_clustering/cluster_spec.rb
|
89
|
+
- spec/lib/agglomerative_clustering/euclidean_distance_spec.rb
|
90
|
+
- spec/lib/agglomerative_clustering/linkage/average_spec.rb
|
91
|
+
- spec/lib/agglomerative_clustering/linkage/base_spec.rb
|
92
|
+
- spec/lib/agglomerative_clustering/linkage/center_spec.rb
|
93
|
+
- spec/lib/agglomerative_clustering/linkage/complete_spec.rb
|
94
|
+
- spec/lib/agglomerative_clustering/linkage/single_spec.rb
|
95
|
+
- spec/lib/agglomerative_clustering/set_spec.rb
|
96
|
+
- spec/spec_helper.rb
|
97
|
+
homepage: ''
|
98
|
+
licenses:
|
99
|
+
- MIT
|
100
|
+
metadata: {}
|
101
|
+
post_install_message:
|
102
|
+
rdoc_options: []
|
103
|
+
require_paths:
|
104
|
+
- lib
|
105
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
106
|
+
requirements:
|
107
|
+
- - ">="
|
108
|
+
- !ruby/object:Gem::Version
|
109
|
+
version: '0'
|
110
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
111
|
+
requirements:
|
112
|
+
- - ">="
|
113
|
+
- !ruby/object:Gem::Version
|
114
|
+
version: '0'
|
115
|
+
requirements: []
|
116
|
+
rubyforge_project:
|
117
|
+
rubygems_version: 2.2.2
|
118
|
+
signing_key:
|
119
|
+
specification_version: 4
|
120
|
+
summary: Ruby Agglomerative Clustering Algorithm
|
121
|
+
test_files:
|
122
|
+
- spec/factories/lib/agglomerative_clustering/cluster.rb
|
123
|
+
- spec/factories/lib/agglomerative_clustering/point.rb
|
124
|
+
- spec/factories/lib/agglomerative_clustering/set.rb
|
125
|
+
- spec/lib/agglomerative_clustering/cluster_spec.rb
|
126
|
+
- spec/lib/agglomerative_clustering/euclidean_distance_spec.rb
|
127
|
+
- spec/lib/agglomerative_clustering/linkage/average_spec.rb
|
128
|
+
- spec/lib/agglomerative_clustering/linkage/base_spec.rb
|
129
|
+
- spec/lib/agglomerative_clustering/linkage/center_spec.rb
|
130
|
+
- spec/lib/agglomerative_clustering/linkage/complete_spec.rb
|
131
|
+
- spec/lib/agglomerative_clustering/linkage/single_spec.rb
|
132
|
+
- spec/lib/agglomerative_clustering/set_spec.rb
|
133
|
+
- spec/spec_helper.rb
|