gene 0.0.1 → 0.1.0

data/Manifest

@@ -0,0 +1,46 @@
+Manifest
+Rakefile
+TODO
+initializers/functional_extensions.rb
+initializers/module_extensions.rb
+initializers/object_extensions.rb
+initializers/range_extensions.rb
+initializers/runner.rb
+initializers/symbol_extensions.rb
+initializers/unbound_method_extensions.rb
+lib/aligner.rb
+lib/calculator.rb
+lib/cell.rb
+lib/color.rb
+lib/dsl.rb
+lib/gene.rb
+lib/generator.rb
+lib/geometry.rb
+lib/hungarian.rb
+lib/imagine.rb
+lib/petri.rb
+lib/point.rb
+lib/trait.rb
+tasks/test.rake
+test/assets/Nova.jpg
+test/assets/Rex.jpg
+test/assets/Squares.jpg
+test/test_helper.rb
+test/unit/aligner_test.rb
+test/unit/calculator_test.rb
+test/unit/cell_test.rb
+test/unit/color_test.rb
+test/unit/dsl_test.rb
+test/unit/functionals_extensions_test.rb
+test/unit/gene_test.rb
+test/unit/generator_test.rb
+test/unit/geometry_test.rb
+test/unit/hungarian_test.rb
+test/unit/imagine_test.rb
+test/unit/module_extensions_test.rb
+test/unit/object_extensions_test.rb
+test/unit/petri_test.rb
+test/unit/range_extensions_test.rb
+test/unit/symbol_extensions_test.rb
+test/unit/trait_test.rb
+test/unit/unbound_method_extensions_test.rb

data/Rakefile

@@ -1,12 +1,15 @@
-# -*- ruby -*-
+require "rubygems"
+require "rake"
+require "echoe"
 
-require 'rubygems'
-require 'hoe'
-require './lib/gene.rb'
-
-Hoe.new('gene', Gene::VERSION) do |p|
-  # p.rubyforge_name = 'genex' # if different than lowercase project name
-  p.developer('Evan Senter', 'evansenter@gmail.com')
+Echoe.new("gene", "0.1.0") do |config|
+  config.description              = "Sample genetic program in Ruby"
+  config.url                      = "http://github.com/evansenter/gene"
+  config.author                   = "Evan Senter"
+  config.email                    = "evansenter@gmail.com"
+  config.ignore_pattern           = ["tmp/*", "script/*"]
+  config.dependencies             = ["rmagick"]
+  config.development_dependencies = []
 end
 
-# vim: syntax=Ruby
+Dir["#{File.dirname(__FILE__)}/tasks/*.rake"].sort.each { |task| load task }

data/TODO

@@ -0,0 +1,7 @@
+* Things aren't working because the image is coming out white! (Cell#draw_image)
+* Reflesh test coverage in Generator
+* Think about using the garbage collector...
+
+require "initializers/runner.rb"
+petri = Petri.new("./test/assets/Squares.jpg")
+petri.evolve while petri.dish.first.fitness < 0.7

data/gene.gemspec

@@ -0,0 +1,34 @@
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{gene}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 1.2") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Evan Senter"]
+  s.date = %q{2010-07-20}
+  s.description = %q{Sample genetic program in Ruby}
+  s.email = %q{evansenter@gmail.com}
+  s.extra_rdoc_files = ["TODO", "lib/aligner.rb", "lib/calculator.rb", "lib/cell.rb", "lib/color.rb", "lib/dsl.rb", "lib/gene.rb", "lib/generator.rb", "lib/geometry.rb", "lib/hungarian.rb", "lib/imagine.rb", "lib/petri.rb", "lib/point.rb", "lib/trait.rb", "tasks/test.rake"]
+  s.files = ["Manifest", "Rakefile", "TODO", "initializers/functional_extensions.rb", "initializers/module_extensions.rb", "initializers/object_extensions.rb", "initializers/range_extensions.rb", "initializers/runner.rb", "initializers/symbol_extensions.rb", "initializers/unbound_method_extensions.rb", "lib/aligner.rb", "lib/calculator.rb", "lib/cell.rb", "lib/color.rb", "lib/dsl.rb", "lib/gene.rb", "lib/generator.rb", "lib/geometry.rb", "lib/hungarian.rb", "lib/imagine.rb", "lib/petri.rb", "lib/point.rb", "lib/trait.rb", "tasks/test.rake", "test/assets/Nova.jpg", "test/assets/Rex.jpg", "test/assets/Squares.jpg", "test/test_helper.rb", "test/unit/aligner_test.rb", "test/unit/calculator_test.rb", "test/unit/cell_test.rb", "test/unit/color_test.rb", "test/unit/dsl_test.rb", "test/unit/functionals_extensions_test.rb", "test/unit/gene_test.rb", "test/unit/generator_test.rb", "test/unit/geometry_test.rb", "test/unit/hungarian_test.rb", "test/unit/imagine_test.rb", "test/unit/module_extensions_test.rb", "test/unit/object_extensions_test.rb", "test/unit/petri_test.rb", "test/unit/range_extensions_test.rb", "test/unit/symbol_extensions_test.rb", "test/unit/trait_test.rb", "test/unit/unbound_method_extensions_test.rb", "gene.gemspec"]
+  s.homepage = %q{http://github.com/evansenter/gene}
+  s.rdoc_options = ["--line-numbers", "--inline-source", "--title", "Gene"]
+  s.require_paths = ["lib"]
+  s.rubyforge_project = %q{gene}
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{Sample genetic program in Ruby}
+  s.test_files = ["test/test_helper.rb", "test/unit/aligner_test.rb", "test/unit/calculator_test.rb", "test/unit/cell_test.rb", "test/unit/color_test.rb", "test/unit/dsl_test.rb", "test/unit/functionals_extensions_test.rb", "test/unit/gene_test.rb", "test/unit/generator_test.rb", "test/unit/geometry_test.rb", "test/unit/hungarian_test.rb", "test/unit/imagine_test.rb", "test/unit/module_extensions_test.rb", "test/unit/object_extensions_test.rb", "test/unit/petri_test.rb", "test/unit/range_extensions_test.rb", "test/unit/symbol_extensions_test.rb", "test/unit/trait_test.rb", "test/unit/unbound_method_extensions_test.rb"]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<rmagick>, [">= 0"])
+    else
+      s.add_dependency(%q<rmagick>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<rmagick>, [">= 0"])
+  end
+end

data/initializers/functional_extensions.rb

@@ -0,0 +1,44 @@
+module FunctionalExtensions
+  def apply(enum)
+    enum.map &self
+  end
+  alias | apply
+  
+  def reduce(enum)
+    enum.inject &self
+  end
+  alias <= reduce
+  
+  def compose(function)
+    if self.respond_to?(:arity) && self.arity == 1
+      lambda { |*args| self[function[*args]] }
+    else
+      lambda { |*args| self[*function[*args]] }
+    end
+  end
+  alias * compose
+  
+  def apply_head(*first)
+    lambda { |*rest| self[*first.concat(rest)] }
+  end
+  alias >> apply_head
+  
+  def apply_tail(*last)
+    lambda { |*rest| self[*rest.concat(last)] }
+  end
+  alias << apply_tail
+  
+  def memoize
+    cache = {}
+    lambda do |*args|
+      unless cache.has_key?(args)
+        cache[args] = self[*args]
+      end
+      cache[args]
+    end
+  end
+  alias +@ memoize
+end
+
+class Method; include FunctionalExtensions; end
+class Proc; include FunctionalExtensions; end

data/initializers/module_extensions.rb

@@ -0,0 +1,14 @@
+class Module
+  alias [] instance_method
+
+  def []=(symbol, function)
+    self.instance_eval { define_method(symbol, function) }
+  end
+
+  def alias_method_chain(target, feature)
+    method_name, extension = target.to_s.match(/(\w+)(\W?)/).to_a[1..-1]
+    
+    alias_method "#{method_name}_without_#{feature}#{extension}", target
+    alias_method target, "#{method_name}_with_#{feature}#{extension}"
+  end
+end

data/initializers/object_extensions.rb

@@ -0,0 +1,25 @@
+class Object
+  def returning(value)
+    yield value
+    value
+  end
+  
+  def send_if(condition, method, *arguments)
+    block = arguments.pop if arguments.last.is_a?(Proc) && arguments.length == 1
+    if condition
+      block ? eval("self.#{method} &block") : self.send(method, *arguments)
+    else
+      self
+    end
+  end
+
+  def assert_at_least(number_required, number_present, message = nil)
+    unless number_present >= number_required
+      raise(ArgumentError, message || "You must provide at least #{number_required} objects (#{number_present} #{number_present == 1 ? 'was' : 'were'} provided)")
+    end
+  end
+  
+  def class_metaclass
+    class << self.class; self; end
+  end
+end

data/initializers/range_extensions.rb

@@ -0,0 +1,9 @@
+class Range
+  def min
+    self.begin.is_a?(Float) ? self.begin : super
+  end
+
+  def max
+    self.end.is_a?(Float) ? self.end : super
+  end
+end

data/initializers/runner.rb

@@ -0,0 +1,15 @@
+# Pull in necessary libraries.
+require "RMagick"
+
+# Get all source files except this one, pulling initializers before the lib_files.
+initializers = Dir.glob(File.join(File.dirname(__FILE__), "**", "*.rb")) - [__FILE__]
+lib_files    = Dir.glob(File.join(File.dirname(__FILE__), "..", "lib", "**", "*.rb"))
+
+# Set dynamic autoload on all of them based on their filename.
+constants = (initializers + lib_files).inject([]) do |constants, file_path|  
+  constant = File.basename(file_path, ".rb").split(/_/).map(&:capitalize).join.to_sym
+  autoload(constant, file_path)
+end
+
+# Pull in the initializer files!
+initializers.map(&method(:require))

data/initializers/symbol_extensions.rb

@@ -0,0 +1,11 @@
+class Symbol
+  def [](object)
+    object.method(self)
+  end
+
+  def []=(object, function)
+    symbol = self
+    eigenclass = (class << object; self; end)
+    eigenclass.instance_eval { define_method(symbol, function) }
+  end
+end

data/initializers/unbound_method_extensions.rb

@@ -0,0 +1,3 @@
+class UnboundMethod
+  alias [] bind
+end

data/lib/aligner.rb

@@ -0,0 +1,34 @@
+module Aligner
+  def align_crossover
+    optimal_alignment = Hungarian.new(crossover_map).solve
+
+    returning({ :cell_1 => [], :cell_2 => [] }) do |alignment_hash|
+      optimal_alignment.each do |tuple|
+        alignment_hash[:cell_1] << tuple.first
+        alignment_hash[:cell_2] << tuple.last
+      end
+    end
+  end
+  
+  private
+  
+  def crossover_map
+    @cells.first.genes.map do |gene_1|
+      @cells.last.genes.map do |gene_2|
+        distance_between(middle_point_of(gene_1), middle_point_of(gene_2))
+      end
+    end
+  end
+
+  def distance_between(point_1, point_2)
+    square = lambda { |value| value ** 2 }
+    Math.sqrt(square[point_2.x - point_1.x] + square[point_2.y - point_1.y])
+  end
+
+  def middle_point_of(gene)
+    sum     = lambda { |a, b| a + b }
+    average = lambda { |axis| (sum <= gene.polygon.points.map(&axis).map(&:value)) / gene.polygon.num_points.to_f }
+
+    Point.new(average[:x], average[:y])
+  end
+end

data/lib/calculator.rb

@@ -0,0 +1,42 @@
+module Calculator
+  def self.included(base)
+    base.extend ClassMethods
+  end
+  
+  module ClassMethods
+    def generate_value(max)
+      case max
+      when 0:      raise(ArgumentError, "Trying to call Calculator.generate_value(0), which is not supported at this time due to ambiguity of intention")
+      when Float:  rand(0)
+      when Fixnum: rand(max)
+      else         raise(ArgumentError, "Can't generate values of type #{max.class} in Calculator.generate_value(max)")
+      end
+    end
+    
+    def get_normal_random_variable
+      x = y = sum = 0
+      loop do
+        x = get_uniform_random_variable
+        y = get_uniform_random_variable
+        break if (sum = (x ** 2) + (y ** 2)) < 1
+      end
+      rand(2).zero? ? convert(x, sum) : convert(y, sum)
+    end
+    
+    def get_uniform_random_variable
+      rand(0) * random_sign_change
+    end
+    
+    private
+  
+    def random_sign_change
+      rand(2).zero? ? 1 : -1
+    end
+  
+    def convert(variable, sum)
+      # http://en.wikipedia.org/wiki/Marsaglia_polar_method
+      return 0 if sum.zero?
+      variable * Math.sqrt(-2 * Math.log(sum) / sum)
+    end
+  end
+end

data/lib/cell.rb

@@ -0,0 +1,41 @@
+class Cell < Dsl  
+  attr_accessor :fitness
+  attr_reader   :genes, :image
+  
+  def genes_by_alpha
+    genes.sort { |gene_1, gene_2| gene_2.color.a.value <=> gene_1.color.a.value }
+  end
+  
+  def genes_from_alignment_map(alignment)
+    alignment.map { |index| genes[index] }
+  end
+  
+  private
+  
+  def finish_init
+    fill_out_genes
+    draw_image
+  end
+  
+  def fill_out_genes
+    @genes = num_genes.times.map { |index| (@genes ||= [])[index] || Gene.new }
+  end
+  
+  def draw_image
+    @image = Magick::Image.new(image_dimensions.x, image_dimensions.y)
+    pen    = Magick::Draw.new
+  
+    genes_by_alpha.each do |gene|
+      pen.fill(gene.color.rgba_format)
+      pen.polygon(*gene.hulled_sequence)
+      pen.draw(@image)
+    end
+  end
+  
+  def method_missing(name, *args, &block)
+    case name.to_s
+    when /^gene_(\d+)$/: (@genes ||= [])[$1.to_i] = Gene.new(&block)
+    else super
+    end
+  end
+end

data/lib/color.rb

@@ -0,0 +1,9 @@
+Color = Struct.new(:r, :g, :b, :a) do
+  def rgb
+    [r, g, b]
+  end
+  
+  def rgba_format
+    "rgba(" + (rgb.map(&:percentify) << a.value).join(", ") + ")"
+  end
+end

data/lib/dsl.rb

@@ -0,0 +1,16 @@
+class Dsl
+  def initialize(*args, &block)
+    if block_given?
+      @_original_self = block.binding.eval("self")
+      instance_eval(&block)
+      remove_instance_variable :@_original_self
+    end
+    finish_init if defined? :finish_init
+  end
+  
+  def method_missing(name, *args, &block)
+    return Petri.send(name) if Petri.respond_to?(name)
+    
+    @_original_self ? @_original_self.send(name, *args, &block) : super
+  end
+end

data/lib/gene.rb

@@ -1,3 +1,67 @@
-class Gene
-  VERSION = "0.0.1"
-end
+class Gene < Dsl
+  include Geometry
+  
+  attr_reader :polygon, :color
+  
+  private
+  
+  def finish_init
+    fill_out_polygon
+    fill_out_color
+    initialize_singleton_methods_for_polygon_and_color
+  end
+  
+  def fill_out_polygon
+    @polygon ||= []
+    @polygon   = num_points.times.map do |index|
+      if polygon[index]
+        returning(polygon[index]) do |point|
+          point.x ||= Trait.new(0...image_dimensions.x)
+          point.y ||= Trait.new(0...image_dimensions.y)
+        end
+      else
+        Point.new(
+          Trait.new(0...image_dimensions.x),
+          Trait.new(0...image_dimensions.y)
+        )
+      end
+    end
+  end
+  
+  def fill_out_color
+    @color ||= Color.new
+    color.each_pair { |channel, trait| color.send(:"#{channel}=", Trait.new(0.0..1.0)) unless trait }
+  end
+  
+  def initialize_singleton_methods_for_polygon_and_color
+    :points[polygon]     = lambda { self }
+    :num_points[polygon] = lambda { size }
+  end
+  
+  def point_at(index, x, y)
+    point = (@polygon ||= [])[index] ||= Point.new
+    
+    point.x = Trait.new(0...image_dimensions.x) { set_value x }
+    point.y = Trait.new(0...image_dimensions.y) { set_value y }
+  end
+  
+  def point_from(index, name, &block)
+    point = (@polygon ||= [])[index] ||= Point.new
+    
+    point.send(:"#{name}=", Trait.new(0...image_dimensions.send(:"#{name}"), &block))
+  end
+  
+  def color_from(channel, &block)
+    @color ||= Color.new
+    color.send(:"#{channel}=", Trait.new(0.0..1.0, &block))
+  end
+  
+  def method_missing(name, *args, &block)
+    case name.to_s
+    when /^point_(\d+)$/:      point_at($1.to_i, *args)
+    when /^point_(\d+)_(\w)$/: point_from($1.to_i, $2, &block)
+    when /^trait_(\w)$/:       color_from($1, &block)
+    else super
+    end
+  end
+end