evosynth 0.1.0

data/examples/tsp.rb

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+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	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.
+
+
+require 'evosynth'
+require 'set'
+
+
+module Examples
+	module TSP
+
+		def TSP.create_individual(problem)
+			individual = EvoSynth::MinimizingIndividual.new
+			shuffeld = (0..problem.size - 1).to_a.sort_by { EvoSynth.rand(2) }
+			individual.genome = EvoSynth::ArrayGenome.new(shuffeld)
+			individual
+		end
+
+		def TSP.optimal_tour(problem)
+			optimal = TSP.create_individual(problem)
+			opt_tour = [1,28,6,12,9,5,26,29,3,2,20,10,4,15,18,17,14,22,11,19,25,7,23,27,8,24,16,13,21].map! { |num| num -= 1 }
+			optimal.genome = EvoSynth::ArrayGenome.new(opt_tour)
+			optimal
+		end
+
+		tsp = nil
+		begin
+			tsp = EvoSynth::Problems::TSP.new('testdata/bays29.tsp')
+		rescue
+			puts "Could not load test data. Please see testdata/README for instructions..."
+			exit(0)
+		end
+
+		optimal_tour = TSP.optimal_tour(tsp)
+
+		profile = EvoSynth::Profile.new(
+			:individual			=> TSP.create_individual(tsp),
+			:mutation			=> EvoSynth::MetaOperators::ProportionalCombinedOperator.new(EvoSynth::Mutations::InversionMutation.new,
+																							 EvoSynth::Mutations::ShiftingMutation.new,
+																							 EvoSynth::Mutations::MixingMutation.new),
+			:parent_selection	=> EvoSynth::Selections::TournamentSelection.new(3),
+			:recombination		=> EvoSynth::Recombinations::EdgeRecombination.new,
+			:population			=> EvoSynth::Population.new(100) { TSP.create_individual(tsp) },
+			:evaluator			=> tsp
+		)
+		profile.evaluator.calculate_and_set_fitness(optimal_tour)
+
+		puts "read testdata/bays29.tsp - problem contains #{tsp.size} cities...\n"
+		puts "Optimal Individual for this problem: #{optimal_tour}"
+
+		evolver = EvoSynth::Evolvers::GeneticAlgorithm.new(profile)
+		EvoSynth::Evolvers.add_weak_elistism(evolver)
+		evolver.add_observer(EvoSynth::Output.create_console_logger(25,
+			"generations"	=> ->{ evolver.generations_computed },
+			"bestfitness"   => ->{ evolver.best_solution.fitness },
+			"worstfitness"  => ->{ evolver.worst_solution.fitness }
+		))
+
+		puts "\nRunning #{evolver}...\n"
+		result = evolver.run_until_generations_reached(200)
+		puts "\nBest Individual after evolution:  #{result.best}"
+	end
+end

data/lib/evosynth.rb

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+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	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.
+
+
+require 'evosynth/core'
+require 'evosynth/decoder'
+require 'evosynth/problems'
+require 'evosynth/operators'
+require 'evosynth/evolvers'
+require 'evosynth/output'
+
+# anthing that is needed to setup EvoSynth should be here!

data/lib/evosynth/core.rb

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+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	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.
+
+
+require 'evosynth/core/randomizer'
+require 'evosynth/core/binary_genome'
+require 'evosynth/core/array_genome'
+require 'evosynth/core/individual'
+require 'evosynth/core/minimizing_individual'
+require 'evosynth/core/maximizing_individual'
+require 'evosynth/core/evaluator'
+require 'evosynth/core/population'
+require 'evosynth/core/profile'

data/lib/evosynth/core/array_genome.rb

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+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	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.
+
+
+module EvoSynth
+
+	# Array based genome which keeps track of changes (changed attribute)
+	# to reduce the need to recalculate the fitness function (see Evaluator)
+	#
+	# This genome can contain any type of genes.
+	#
+	# TODO: complete documentation
+
+	class ArrayGenome < Array
+
+		# Set the changed flag (boolean) of the genome
+
+		def changed=(value)
+			@changed = value
+		end
+
+		# True if the genome has changed, false otherwise. Has to be set to false manually.
+
+		def changed?
+			@changed
+		end
+
+		# Return a printable version of this genome.
+
+		def to_s
+			self * ", "
+		end
+
+		# Returns a clone of this genome
+
+		def clone
+			my_clone = super
+			my_clone.changed = false
+			my_clone
+		end
+
+		# see http://ruby-doc.org/doxygen/1.8.4/group__ruby__ary.html#ga9
+		# see rb_ary_store and rb_ary_modify
+
+		METHODS_THAT_CHANGE_ARRAY = ['initialize', '[]=', 'delete', 'delete_at', 'collect!', 'map!', '<<', 'reject!', 'uniq!', 'unshift',
+									 'shift', 'sort!', 'pop', 'push', 'flatten!', 'reverse!', 'slice!', 'clear']
+
+		METHODS_THAT_CHANGE_ARRAY.each do |method_name|
+			ArrayGenome.class_eval("def #{method_name}(*args)
+									  @changed = true
+									  super
+									end")
+		end
+
+	end
+
+end

data/lib/evosynth/core/binary_genome.rb

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+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	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.
+
+
+module EvoSynth
+
+	# Binary genome which keeps track of changes (changed attribute)
+	# to reduce the need to recalculate the fitness function (see Evaluator)
+	#
+	# This genome is a simple bitstring and each gene is a boolean.
+	#
+	# FIXME: implment in C for better performance - right now its pretty useless
+	# TODO: complete documentation
+
+	class BinaryGenome < Array
+
+		# Creates a BinaryGenome with a given initial (Integer) value. Default constructs a new
+		# BinaryGenome with the initial value of 0.
+
+		def initialize(intial_value = 0)
+			@data = intial_value
+			@changed = true
+		end
+
+		# Set the changed flag (boolean) of the genome
+
+		def changed=(value)
+			@changed = value
+		end
+
+		# True if the genome has changed, false otherwise. Has to be set to false manually.
+
+		def changed?
+			@changed
+		end
+
+		# Returns a clone of this genome
+
+		def clone
+			my_clone = BinaryGenome.new(@data)
+			my_clone.changed = false
+			my_clone
+		end
+
+		# Array like index accessor
+		#
+		# [index]
+		# [index, length]
+		# [range]
+
+		def [](*args)
+			if args.size == 1
+
+				case args[0]
+					when Numeric
+						@data[args[0]]
+					when Range
+						get_sub_range args[0]
+					else
+						raise ArgumentError, "argument should be either index or range"
+					end
+
+			elsif args.size == 2
+				get_sub_range Range.new(args[0], args[0] + args[1] - 1)
+			else
+				raise ArgumentError, "wrong number of arguments"
+			end
+		end
+
+		# Array like index accessor
+
+		def []=(*args)
+			if args.size == 2
+
+				case args[0]
+					when Numeric
+						set_gene(args[0], args[1])
+					when Range
+						case args[1]
+							when Numeric
+								args[0].each { |index| set_gene(index, args[1]) }
+							when Array
+								offset = args[0].begin
+								args[0].each { |index| set_gene(index, args[1][index - offset]) }
+							else
+								raise ArgumentError, "argument (1) should be either index or range"
+						end
+
+					else
+						raise ArgumentError, "argument (0) should be either index or range"
+					end
+
+			elsif args.size == 3
+				args[1].times { |offset| set_gene(args[0] + offset, args[2]) }
+			else
+				raise ArgumentError, "wrong number of arguments"
+			end
+		end
+
+		# Flips (inverts) the gene at the given index
+
+		def flip!(index)
+			@data = @data ^ (1 << index)
+		end
+
+		# Returns the size (in bits) of this genome.
+
+		def size
+			@size = @data.to_s(2).size unless defined? @size
+			@size
+		end
+
+		# Return a printable version of the genome
+
+		def to_s
+			@data.to_s(2)
+		end
+
+		private
+
+		def get_sub_range(range)
+			subarray = []
+			range.each { |index| subarray << @data[index] }
+			subarray
+		end
+
+		def set_gene(index, gene)
+			if gene == 0
+				@data = @data ^ (1 << index) unless @data[index] == 0
+			else
+				@data = @data | (1 << index)
+			end
+		end
+	end
+
+end

data/lib/evosynth/core/evaluator.rb

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+#	Copyright (c) 2009, 2010 Yves Adler <yves.adler@googlemail.com>
+#
+#	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.
+
+
+require 'observer'
+
+
+module EvoSynth
+
+	# Baseclass for all fitness evaluators. It also counts how often it was used to calculate
+	# the fitness of a given individual and how often it actually calculated the fitness.
+	#
+	# For simple problems you just need to overwrite calculate_fitness(individual)
+	#
+	# Obervers get notified each time calculate_and_set_fitness(individual) gets called, not on actual calculations
+
+	class Evaluator
+		include Observable
+
+		# How often did the Evaluator return a fitness value
+
+		attr_reader :called
+
+		# How often did the Evaluator actually calculate a fitness value
+
+		attr_reader :calculated
+
+		# Returns a new Evaluator object
+
+		def initialize
+			reset_counters
+		end
+
+		# Calculates and sets the fitness of the given individual if the individual has changed,
+		# otherwise it just returns the cached fitness of the individual
+
+		def calculate_and_set_fitness(individual)
+			@called += 1
+
+			if individual.changed?
+				@calculated += 1
+				individual.fitness = calculate_fitness(individual)
+			end
+
+			changed
+			notify_observers self, @called
+			individual.fitness
+		end
+
+		# Calculates and sets the initial fitness of the given individual.
+
+		def calculate_and_set_initial_fitness(individual)
+			@called += 1
+			@calculated += 1
+
+			individual.fitness = calculate_initial_fitness(individual)
+
+			changed
+			notify_observers self, @called
+			individual.fitness
+		end
+
+		# This function is actually used to calculate the fitness of a individual. It's the "fitness function".
+
+		def calculate_fitness(individual)
+			raise NotImplementedError, "please implement calculate_fitness!"
+		end
+
+		# This function is used to calculate an intitial fitness value for a individual. Calls calculate_fitness by default.
+
+		def calculate_initial_fitness(individual)
+			calculate_fitness(individual)
+		end
+
+		# Reset the called/calculated counters of the Evaluator
+
+		def reset_counters
+			@called = 0
+			@calculated = 0
+		end
+
+		# Returns a human readable reprasentation of the Evaluator
+
+		def to_s
+			"Evaluator <called: #{@called}, calculated: #{@calculated}>"
+		end
+	end
+
+end