hierclust 0.1.0

data/History.txt

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+== 0.1.0 2008-02-01
+
+* 1 major enhancement:
+  * Initial release

data/License.txt

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+Copyright (c) 2008 Brandt Kurowski <brandt@kurowski.net>
+
+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/Manifest.txt

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+History.txt
+License.txt
+Manifest.txt
+README.txt
+Rakefile
+config/hoe.rb
+config/requirements.rb
+lib/hierclust.rb
+lib/hierclust/cluster.rb
+lib/hierclust/clusterer.rb
+lib/hierclust/distances.rb
+lib/hierclust/point.rb
+lib/hierclust/version.rb
+log/debug.log
+script/destroy
+script/generate
+script/txt2html
+setup.rb
+spec/hierclust/cluster_spec.rb
+spec/hierclust/clusterer_spec.rb
+spec/hierclust/distances_spec.rb
+spec/hierclust/point_spec.rb
+spec/hierclust_spec.rb
+spec/spec.opts
+spec/spec_helper.rb
+tasks/deployment.rake
+tasks/environment.rake
+tasks/rspec.rake
+tasks/website.rake
+website/index.html
+website/index.txt
+website/javascripts/rounded_corners_lite.inc.js
+website/stylesheets/screen.css
+website/template.rhtml

data/README.txt

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+= Hierclust
+
+A simple hierarchical clustering library for spatial data.
+
+== Example
+
+  require 'hierclust'
+  points = (1..6).map { Hierclust::Point.new(rand(10), rand(10)) }
+  clusterer = Hierclust::Clusterer.new(points)
+  puts clusterer.clusters => [[[(4, 9), (4, 8)], (9, 6)], [[(1, 4), (3, 1)], (6, 3)]]
+
+== Contact
+
+Brandt Kurowski <brandt@kurowski.net>

data/Rakefile

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+require 'config/requirements'
+require 'config/hoe' # setup Hoe + all gem configuration
+
+Dir['tasks/**/*.rake'].each { |rake| load rake }

data/config/hoe.rb

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+require 'hierclust/version'
+
+AUTHOR = 'Brandt Kurowski'  # can also be an array of Authors
+EMAIL = "brandt@kurowski.net"
+DESCRIPTION = "performs hierarchical clustering on geometric points"
+GEM_NAME = 'hierclust' # what ppl will type to install your gem
+RUBYFORGE_PROJECT = 'hierclust' # The unix name for your project
+HOMEPATH = "http://#{RUBYFORGE_PROJECT}.rubyforge.org"
+DOWNLOAD_PATH = "http://rubyforge.org/projects/#{RUBYFORGE_PROJECT}"
+
+@config_file = "~/.rubyforge/user-config.yml"
+@config = nil
+RUBYFORGE_USERNAME = "kurowski"
+def rubyforge_username
+  unless @config
+    begin
+      @config = YAML.load(File.read(File.expand_path(@config_file)))
+    rescue
+      puts <<-EOS
+ERROR: No rubyforge config file found: #{@config_file}
+Run 'rubyforge setup' to prepare your env for access to Rubyforge
+ - See http://newgem.rubyforge.org/rubyforge.html for more details
+      EOS
+      exit
+    end
+  end
+  RUBYFORGE_USERNAME.replace @config["username"]
+end
+
+
+REV = nil 
+# UNCOMMENT IF REQUIRED: 
+# REV = `svn info`.each {|line| if line =~ /^Revision:/ then k,v = line.split(': '); break v.chomp; else next; end} rescue nil
+VERS = Hierclust::VERSION::STRING + (REV ? ".#{REV}" : "")
+RDOC_OPTS = ['--quiet', '--title', 'hierclust documentation',
+    "--opname", "index.html",
+    "--line-numbers", 
+    "--main", "README",
+    "--inline-source"]
+
+class Hoe
+  def extra_deps 
+    @extra_deps.reject! { |x| Array(x).first == 'hoe' } 
+    @extra_deps
+  end 
+end
+
+# Generate all the Rake tasks
+# Run 'rake -T' to see list of generated tasks (from gem root directory)
+hoe = Hoe.new(GEM_NAME, VERS) do |p|
+  p.author = AUTHOR 
+  p.description = DESCRIPTION
+  p.email = EMAIL
+  p.summary = DESCRIPTION
+  p.url = HOMEPATH
+  p.rubyforge_name = RUBYFORGE_PROJECT if RUBYFORGE_PROJECT
+  p.test_globs = ["spec/**/*_spec.rb"]
+  p.clean_globs |= ['**/.*.sw?', '*.gem', '.config', '**/.DS_Store']  #An array of file patterns to delete on clean.
+  
+  # == Optional
+  p.changes = p.paragraphs_of("History.txt", 0..1).join("\n\n")
+  #p.extra_deps = []     # An array of rubygem dependencies [name, version], e.g. [ ['active_support', '>= 1.3.1'] ]
+  
+  #p.spec_extras = {}    # A hash of extra values to set in the gemspec.
+  
+end
+
+CHANGES = hoe.paragraphs_of('History.txt', 0..1).join("\\n\\n")
+PATH    = (RUBYFORGE_PROJECT == GEM_NAME) ? RUBYFORGE_PROJECT : "#{RUBYFORGE_PROJECT}/#{GEM_NAME}"
+hoe.remote_rdoc_dir = File.join(PATH.gsub(/^#{RUBYFORGE_PROJECT}\/?/,''), 'rdoc')
+hoe.rsync_args = '-av --delete --ignore-errors'

data/config/requirements.rb

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+require 'fileutils'
+include FileUtils
+
+require 'rubygems'
+%w[rake hoe newgem rubigen].each do |req_gem|
+  begin
+    require req_gem
+  rescue LoadError
+    puts "This Rakefile requires the '#{req_gem}' RubyGem."
+    puts "Installation: gem install #{req_gem} -y"
+    exit
+  end
+end
+
+$:.unshift(File.join(File.dirname(__FILE__), %w[.. lib]))
+
+require 'hierclust'

data/lib/hierclust/cluster.rb

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+module Hierclust
+  # A Cluster represents a collection of Points. A Cluster has it's own
+  # coordinates that are the mean of the coordinates of it's points.
+  # Because a Cluster has coordinates, it can act as a Point and therefore
+  # be included in other Clusters.
+  class Cluster < Point
+    # An array of items in this cluster
+    attr_accessor :items
+    
+    # Create a Cluster for the given set of +items+.
+    def initialize(items)
+      @items = items
+    end
+    
+    # Returns the average x-coordinates of all items in this Cluster.
+    def x
+      return nil if size == 0
+      @x ||= @items.inject(0) {|sum, p| sum + p.x} / size
+    end
+
+    # Returns the average y-coordinates of all items in this Cluster.
+    def y
+      return nil if size == 0
+      @y ||= @items.inject(0) {|sum, p| sum + p.y} / size
+    end
+    
+    # Returns the number of items in this Cluster.
+    def size
+      @items.size
+    end
+    
+    # Returns +true+ if this Cluster includes the given +item+, otherwise
+    # returns +false+.
+    def include?(item)
+      @items.include? item
+    end
+    
+    # Returns a legible representation of this Cluster and it's items.
+    def to_s
+      "[#{@items.join(', ')}]"
+    end
+  end
+end

data/lib/hierclust/clusterer.rb

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+module Hierclust
+  # Clusters a set of Points using Hierarchical Clustering, stopping either
+  # when the hierarchy is complete or the clusters are separated by a given
+  # minimum distance.
+  class Clusterer
+    # The Distances for the items being clustered
+    attr_reader :distances
+
+    # Create a new Clusterer for the given data.
+    # 
+    # Specify +separation+ to stop the clustering process once all the
+    # items are at least +separation+ units apart.
+    def initialize(data, separation = nil)
+      @data = data.dup
+      @separation = separation
+      @distances = Distances.new(@data)
+    end
+
+    # Calculates and returns the set of clusters.
+    def clusters
+      return @data if @separation && @distances.separation > @separation
+      while @data.length > 1
+        @distances = Distances.new(@data)
+        return @data if @separation && @distances.separation > @separation
+        @data = find_cluster
+      end
+      @data
+    end
+
+    private
+    
+    def find_cluster
+      case @data.length
+      when 0
+        []
+      when 1
+        [Cluster.new([@data[0]])]
+      when 2
+        [Cluster.new([@data[0], @data[1]])]
+      else
+        nearest = @distances.nearest
+        outliers = @distances.outliers
+        [Cluster.new(nearest), *outliers]
+      end
+    end
+  end
+end

data/lib/hierclust/distances.rb

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+module Hierclust
+  # Represents the pair-wise distances between a set of items.
+  class Distances
+    # Create a new Distances for the given +items+
+    def initialize(items)
+      @items = items
+      @distances = {}
+    end
+
+    # Returns the distance between items +a+ and +b+.
+    def [](a, b)
+      key = (a.object_id < b.object_id) ?
+            "#{a.object_id},#{b.object_id}" :
+            "#{b.object_id},#{a.object_id}"
+      @distances[key] ||= Math.sqrt((a.x - b.x) ** 2 + (a.y - b.y) ** 2)  
+    end
+
+    # Returns the pair of items that are nearest to each other.
+    def nearest
+      @nearest ||= begin
+        key = nearest_pair[0]
+        a_id, b_id = key.split ','
+        a = @items.select {|item| item.object_id.to_s == a_id}.first
+        b = @items.select {|item| item.object_id.to_s == b_id}.first
+        [a, b]
+      end
+    end
+    
+    # Returns all items except the pair that are nearest to each other.
+    def outliers
+      @outliers ||= begin
+        @items - nearest
+      end
+    end
+    
+    # Returns the smallest distance between any pair of items.
+    def separation
+      @separation ||= @items.size < 2 ? 0 : nearest_pair[1]
+    end
+
+    private
+
+    def nearest_pair
+      prepopulate_cache
+      @distances.to_a.sort{|a, b| a[1] <=> b[1]}.first
+    end
+    
+    def prepopulate_cache
+      items = @items.dup
+      while !items.empty?
+        origin = items.shift
+        items.each {|item| self[origin, item]}
+      end
+    end
+  end
+end

data/lib/hierclust/point.rb

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+module Hierclust
+  # A Point represents a single point in 2-dimensional space.
+  class Point
+    # x-coordinate
+    attr_accessor :x
+
+    # y-coordinate
+    attr_accessor :y
+    
+    # Create a new Point with the given x- and y-coordinates.
+    def initialize(x, y)
+      @x = x
+      @y = y
+    end
+
+    # Simplifies code by letting us treat Clusters and Points interchangeably
+    def size #:nodoc:
+      1
+    end
+    
+    # Returns a legible representation of this Point.
+    def to_s
+      "(#{x}, #{y})"
+    end
+    
+    # Sorts points relative to each other on the x-axis.
+    def <=>(other)
+      return self.x <=> other.x
+    end
+  end
+end

data/lib/hierclust/version.rb

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+module Hierclust #:nodoc:
+  module VERSION #:nodoc:
+    MAJOR = 0
+    MINOR = 1
+    TINY  = 0
+
+    STRING = [MAJOR, MINOR, TINY].join('.')
+  end
+end

data/lib/hierclust.rb

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+$:.unshift File.dirname(__FILE__)
+
+require 'hierclust/point'
+require 'hierclust/cluster'
+require 'hierclust/distances'
+require 'hierclust/clusterer'
+
+module Hierclust
+end

data/script/destroy

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+#!/usr/bin/env ruby
+APP_ROOT = File.join(File.dirname(__FILE__), '..')
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/destroy'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

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+#!/usr/bin/env ruby
+APP_ROOT = File.join(File.dirname(__FILE__), '..')
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/generate'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Generate.new.run(ARGV)

data/script/txt2html

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+#!/usr/bin/env ruby
+
+require 'rubygems'
+begin
+  require 'newgem'
+rescue LoadError
+  puts "\n\nGenerating the website requires the newgem RubyGem"
+  puts "Install: gem install newgem\n\n"
+  exit(1)
+end
+require 'redcloth'
+require 'syntax/convertors/html'
+require 'erb'
+require File.dirname(__FILE__) + '/../lib/hierclust/version.rb'
+
+version  = Hierclust::VERSION::STRING
+download = 'http://rubyforge.org/projects/hierclust'
+
+class Fixnum
+  def ordinal
+    # teens
+    return 'th' if (10..19).include?(self % 100)
+    # others
+    case self % 10
+    when 1: return 'st'
+    when 2: return 'nd'
+    when 3: return 'rd'
+    else    return 'th'
+    end
+  end
+end
+
+class Time
+  def pretty
+    return "#{mday}#{mday.ordinal} #{strftime('%B')} #{year}"
+  end
+end
+
+def convert_syntax(syntax, source)
+  return Syntax::Convertors::HTML.for_syntax(syntax).convert(source).gsub(%r!^<pre>|</pre>$!,'')
+end
+
+if ARGV.length >= 1
+  src, template = ARGV
+  template ||= File.join(File.dirname(__FILE__), '/../website/template.rhtml')
+  
+else
+  puts("Usage: #{File.split($0).last} source.txt [template.rhtml] > output.html")
+  exit!
+end
+
+template = ERB.new(File.open(template).read)
+
+title = nil
+body = nil
+File.open(src) do |fsrc|
+  title_text = fsrc.readline
+  body_text = fsrc.read
+  syntax_items = []
+  body_text.gsub!(%r!<(pre|code)[^>]*?syntax=['"]([^'"]+)[^>]*>(.*?)</\1>!m){
+    ident = syntax_items.length
+    element, syntax, source = $1, $2, $3
+    syntax_items << "<#{element} class='syntax'>#{convert_syntax(syntax, source)}</#{element}>"
+    "syntax-temp-#{ident}"
+  }
+  title = RedCloth.new(title_text).to_html.gsub(%r!<.*?>!,'').strip
+  body = RedCloth.new(body_text).to_html
+  body.gsub!(%r!(?:<pre><code>)?syntax-temp-(\d+)(?:</code></pre>)?!){ syntax_items[$1.to_i] }
+end
+stat = File.stat(src)
+created = stat.ctime
+modified = stat.mtime
+
+$stdout << template.result(binding)