som 0.0.1

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC

data/LICENSE

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+Copyright (c) 2009 reddavis
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= SOM - Self Organising Map
+
+A pure Ruby implementation of the Self Organising Map machine learning Algorithm.
+
+== Install
+ 
+  gem sources -a -http://gemcutter.org
+  sudo gem install som
+  
+== How To Use
+  
+  require 'rubygems'
+  require 'som'
+  
+  a = SOM.new(:number_of_nodes => 4, :dimensions => 3)
+  a.train(data)
+
+  # Returns the index of the data you gave it
+  a.inspect
+    #=> [[1, 0...], [99, 84...], [11, 23...], [2, 6...]]
+
+== Copyright
+
+Copyright (c) 2009 Red Davis. See LICENSE for details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "som"
+    gem.summary = %Q{A Self Organising Map}
+    gem.description = %Q{A Self Organising Map}
+    gem.email = "reddavis@gmail.com"
+    gem.homepage = "http://github.com/reddavis/som"
+    gem.authors = ["reddavis"]
+    gem.add_development_dependency "rspec", ">= 1.2.9"
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
+end
+
+require 'spec/rake/spectask'
+Spec::Rake::SpecTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.spec_files = FileList['spec/**/*_spec.rb']
+end
+
+Spec::Rake::SpecTask.new(:rcov) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :spec => :check_dependencies
+
+task :default => :spec
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "som #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/examples/example.rb

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+require File.expand_path(File.dirname(__FILE__) + '/../lib/som')
+
+data = Array.new(100) {Array.new(3) {rand}}
+
+a = SOM.new(:number_of_nodes => 4, :dimensions => 3)
+
+a.train(data)
+
+# Returns the index of the data you gave it
+puts a.inspect.inspect

data/lib/som/node.rb

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+class Node
+  
+  attr_reader :bucket
+  
+  def initialize(number_of_weights)
+    create_weights(number_of_weights)
+    @bucket = []
+  end
+  
+  def weights
+    @weights ||= []
+  end
+  
+  def update_weight(learning_rate, inputs, neighborhood_function=1)
+    weights.each_with_index do |weight, index|
+      @weights[index] += learning_rate * neighborhood_function * (inputs[index] - weight)
+    end
+  end
+  
+  # A bucket is a place to put the data that is closest to it
+  def <<(data)
+    @bucket << data
+  end
+  
+  # Euclidean Distance
+  def distance_from(data_points)
+    distance = 0
+    data_points.each_with_index do |point, index|
+      distance += (point - weights[index]) ** 2
+    end
+    Math.sqrt(distance)
+  end
+  
+  private
+  
+  def create_weights(number_of_weights)
+    number_of_weights.times do
+      weights << (rand > 0.5 ? -rand : rand)
+    end
+  end
+  
+end

data/lib/som.rb

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+require File.expand_path(File.dirname(__FILE__) + '/som/node')
+
+class SOM
+  
+  def initialize(options={})
+    @number_of_nodes = options[:nodes] || 5
+    @dimensions = options[:dimensions]
+    @learning_rate = options[:learning_rate] || 0.5
+    @radius = options[:radius] || @number_of_nodes / 2
+    @iteration_count = 0
+    @max_iterations = options[:max_iterations] || 500
+    # TODO: Allow a lambda so we can use different neighborhood functions
+    @neighborhood_function = options[:neighborhood_function] || 1
+    create_nodes
+  end
+  
+  def nodes
+    @nodes ||= []
+  end
+  
+  def train(data)
+    while train_it!(data)
+    end
+    # Place the data in the nodes buckets so we can see how
+    # The data has been clustered
+    place_data_into_buckets(data)
+  end
+  
+  # Returns an array of buckets containing the index of the data given
+  def inspect
+    nodes.map {|x| x.bucket.map {|x| x[0]}}
+  end
+  
+  # Return data from node that is closest to data
+  # You are returned a bucket which contains arrays that look like:
+  # [index, [data]]
+  # The index is the original index of that that was pumped into the classifier
+  # during the training process
+  def classify(data)
+    closest_node = find_closest_node(data)
+    closest_node.bucket
+  end
+  
+  private
+  
+  def train_it!(data)
+    return false if @iteration_count >= @max_iterations
+    
+    data.each do |input|
+      # Update closest node
+      closest_node = find_closest_node(input)
+      closest_node.update_weight(@learning_rate, input)
+    
+      # Update nodes that closer than the radius
+      other_nodes = nodes - [closest_node]
+      other_nodes.each do |node|
+        next if @radius > node.distance_from(closest_node.weights)
+      
+        node.update_weight(@learning_rate, input, neighborhood_function)
+      end
+    end
+    
+    decrease_radius!
+    decrease_learning_rate!
+    increase_iteration_count!
+  end
+  
+  def place_data_into_buckets(data)
+    data.each_with_index do |input, index|
+      closest_node = find_closest_node(input)
+      closest_node << [index, input]
+    end
+  end
+  
+  def decrease_radius!
+    @radius = 0.5 * @radius * @iteration_count / @max_iterations
+  end
+  
+  def decrease_learning_rate!
+    @learning_rate = 0.5 * @learning_rate * @iteration_count / @max_iterations
+  end
+  
+  def increase_iteration_count!
+    @iteration_count += 1
+  end
+  
+  def neighborhood_function
+    0.5 * @neighborhood_function * @iteration_count / @max_iterations
+  end
+  
+  def find_closest_node(data)
+    closest_node = [nodes[0], nodes[0].distance_from(data)]
+    
+    nodes[1..-1].each do |node|
+      distance = node.distance_from(data)
+      if distance < closest_node[1]
+        closest_node = [node, distance]
+      end
+    end
+    closest_node[0]
+  end
+  
+  def create_nodes
+    @number_of_nodes.times { nodes << Node.new(@dimensions) }
+  end
+  
+end

data/som.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{som}
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["reddavis"]
+  s.date = %q{2009-11-26}
+  s.description = %q{A Self Organising Map}
+  s.email = %q{reddavis@gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+     ".gitignore",
+     "LICENSE",
+     "README.rdoc",
+     "Rakefile",
+     "VERSION",
+     "examples/example.rb",
+     "lib/som.rb",
+     "lib/som/node.rb",
+     "som.gemspec",
+     "spec/node_spec.rb",
+     "spec/som_spec.rb",
+     "spec/spec.opts",
+     "spec/spec_helper.rb"
+  ]
+  s.homepage = %q{http://github.com/reddavis/som}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.5}
+  s.summary = %q{A Self Organising Map}
+  s.test_files = [
+    "spec/node_spec.rb",
+     "spec/som_spec.rb",
+     "spec/spec_helper.rb",
+     "examples/example.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<rspec>, [">= 1.2.9"])
+    else
+      s.add_dependency(%q<rspec>, [">= 1.2.9"])
+    end
+  else
+    s.add_dependency(%q<rspec>, [">= 1.2.9"])
+  end
+end
+

data/spec/node_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Node" do
+  describe "Initialization" do
+    before do
+      @a = Node.new(5)
+    end
+    
+    it "should have 5 weights" do
+      @a.weights.size.should == 5
+    end
+  end
+  
+  describe "Distance Calculation" do
+    before do
+      @a = Node.new(2)
+      @b = Node.new(2)
+    end
+    
+    it "should return 0" do
+      @a.weights[0] = @b.weights[0]
+      @a.weights[1] = @b.weights[1]
+      @a.distance_from(@b.weights).should == 0
+    end
+    
+    it "should return 1" do
+      @b.weights[0] = 0.0
+      @b.weights[1] = 0.0
+      
+      @a.weights[0] = 1.0
+      @a.weights[1] = 0.0
+      
+      @a.distance_from(@b.weights).should == 1
+    end
+  end
+  
+  describe "Update Weight" do
+    describe "Closest" do
+      before do
+        @a = Node.new(2)
+        @data = [1,2]
+      end
+    
+      it "should change the weight" do
+        before = @a.weights.clone
+        @a.update_weight(0.5, @data)
+        @a.weights.should_not == before
+      end
+    end
+    
+    describe "Neighbor" do
+      before do
+        @a = Node.new(2)
+        @data = [1,2]
+      end
+    
+      it "should change the weight" do
+        before = @a.weights.clone
+        @a.update_weight(0.5, @data, 0.23)
+        @a.weights.should_not == before
+      end
+    end
+  end
+  
+  describe "Bucket" do
+    before do
+      @a = Node.new(2)
+    end
+    
+    it "should put data into the nodes bucket" do
+      @a << 'some_data'
+      @a.bucket.size.should == 1
+    end
+  end
+end

data/spec/som_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Som" do
+  describe "Initialization" do
+    before do
+      @a = SOM.new(:nodes => 10, :dimensions => 5)
+    end
+    
+    it "should have 10 nodes" do
+      @a.nodes.size.should == 10
+    end
+  end
+  
+  describe "Training" do
+    before do
+      @a = SOM.new(:nodes => 1, :dimensions => 2)
+      @data = [[2,3]]
+    end
+    
+    it "should change the weight of the best matching node" do
+      before = @a.nodes.map {|x| x.weights.clone}
+      @a.train(@data)
+      after = @a.nodes.map {|x| x.weights}
+      
+      before.should_not == after
+    end
+    
+    it "should will the nodes bucket with the data" do
+      @a.train(@data)
+      @a.nodes[0].bucket.should_not be_empty
+    end
+    
+    it "should preserve data indexes" do
+      data = [[0,0], [0,0.5], [2,4], [6,5]]
+      @a.train(data)
+      
+      index_returned = @a.nodes[0].bucket[0][0]
+      data_returned = @a.nodes[0].bucket[0][1]
+      
+      data[index_returned].should == data_returned
+    end
+  end
+  
+  describe "Inspect" do
+    before do
+      @a = SOM.new(:nodes => 1, :dimensions => 2)
+      @data = [[2,3]]
+    end
+    
+    it "should show the clusters of data indexes" do
+      @a.train(@data)
+      @a.inspect.should be_an(Array)
+      @a.inspect.size.should == 1
+    end
+  end
+  
+  describe "Clustering" do
+    before do
+      @a = SOM.new(:nodes => 2, :dimensions => 2)
+    end
+    
+    it "should belong to 2 seperate nodes" do
+      data = [[0,0], [999,999]]
+      @a.train(data)
+      @a.inspect[0].should_not be_empty
+      @a.inspect[1].should_not be_empty
+    end
+  end
+  
+  describe "Classify" do
+    before do
+      @a = SOM.new(:nodes => 2, :dimensions => 2)
+    end
+    
+    it "should belong to 2 seperate nodes" do
+      data = [[0,0], [999,999]]
+      @a.train(data)
+      @a.classify([1,1]).should be_an(Array)
+      @a.classify([1,1]).size.should == 1
+    end
+  end
+end

data/spec/spec.opts

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+--color

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'som'
+require 'spec'
+require 'spec/autorun'
+
+Spec::Runner.configure do |config|
+  
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: som
+version: !ruby/object:Gem::Version 
+  version: 0.0.1
+platform: ruby
+authors: 
+- reddavis
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-11-26 00:00:00 +00:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.2.9
+    version: 
+description: A Self Organising Map
+email: reddavis@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- examples/example.rb
+- lib/som.rb
+- lib/som/node.rb
+- som.gemspec
+- spec/node_spec.rb
+- spec/som_spec.rb
+- spec/spec.opts
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/reddavis/som
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: A Self Organising Map
+test_files: 
+- spec/node_spec.rb
+- spec/som_spec.rb
+- spec/spec_helper.rb
+- examples/example.rb