evosynth 0.1.0

data/lib/evosynth/problems/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 'matrix'
+
+
+module EvoSynth
+	module Problems
+
+		class TSP < EvoSynth::Evaluator
+			attr_reader :matrix
+
+			# TODO: refactor and generalize this class, externalize parsing of problem
+			# definition file
+			# 
+			# needs a .tsp file
+
+			def initialize(filename)
+				super()
+				@matrix = read_matrix_from_file(filename)
+			end
+
+			def calculate_fitness(individual)
+				fitness = 0.0
+
+				individual.genome.each_with_index do |node, index|
+					index_two = (index + 1) % individual.genome.size
+					fitness += distance(node, individual.genome[index_two])
+				end
+
+				fitness
+			end
+
+			def distance(from, to)
+				@matrix[from, to]
+			end
+
+			def size
+				@matrix.column_size
+			end
+
+			def to_s
+				@matrix.to_s
+			end
+
+			private
+
+			def read_matrix_from_file(filename)
+				nodes = []
+
+				File.open(filename) do |file|
+					file.each_line do |line|
+						break if line =~ /DISPLAY_DATA_SECTION/
+						next if line !~ /^\s*\d+/
+						line =~ /(\d+)\s*(\d+.\d+)\s*(\d+.\d+)/
+
+						nodes << line.split.map { |node| node.to_f }
+					end
+				end
+
+				Matrix.rows(nodes)
+			end
+
+		end
+
+	end
+end

data/test/benchmark/decoder_benchmark.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 'benchmark'
+#require 'profile'
+
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+module DecoderBenchmark
+
+	GENOME_SIZE = 1000
+	BENCHMARK_TIMES = 10000
+
+	individual = TestArrayBinaryIndividual.new(GENOME_SIZE)
+	GENOME_SIZE.times { |index| individual.genome[index] = (index % 2 == 1) ? true : false }
+
+	puts "Running decoder benchmark (on ArrayGenome filled with BOOLEANS!) with #{BENCHMARK_TIMES} decodings (genome=#{GENOME_SIZE}):"
+	timing = Benchmark.measure do
+		BENCHMARK_TIMES.times { EvoSynth::Decoder.binary_to_gray(individual.genome) }
+	end
+	puts "\t#{timing.format("%r")} - EvoSynth::Decoder.binary_to_gray"
+
+	timing = Benchmark.measure do
+		BENCHMARK_TIMES.times { EvoSynth::Decoder.gray_to_binary(individual.genome) }
+	end
+	puts "\t#{timing.format("%r")} - EvoSynth::Decoder.gray_to_binary"
+
+	timing = Benchmark.measure do
+		BENCHMARK_TIMES.times { EvoSynth::Decoder.binary_to_real(individual.genome) }
+	end
+	puts "\t#{timing.format("%r")} - EvoSynth::Decoder.binary_to_real"
+
+	individual = TestArrayBinaryIndividual.new(GENOME_SIZE)
+	GENOME_SIZE.times { |index| individual.genome[index] = (index % 2 == 1) ? 1 : 0 }
+
+	puts "Running decoder benchmark (on ArrayGenome filled with INTEGERS!) with #{BENCHMARK_TIMES} decodings (genome=#{GENOME_SIZE}):"
+	timing = Benchmark.measure do
+		BENCHMARK_TIMES.times { EvoSynth::Decoder.binary_to_gray(individual.genome) }
+	end
+	puts "\t#{timing.format("%r")} - EvoSynth::Decoder.binary_to_gray"
+
+	timing = Benchmark.measure do
+		BENCHMARK_TIMES.times { EvoSynth::Decoder.gray_to_binary(individual.genome) }
+	end
+	puts "\t#{timing.format("%r")} - EvoSynth::Decoder.gray_to_binary"
+
+	timing = Benchmark.measure do
+		BENCHMARK_TIMES.times { EvoSynth::Decoder.binary_to_real(individual.genome) }
+	end
+	puts "\t#{timing.format("%r")} - EvoSynth::Decoder.binary_to_real"
+
+end

data/test/benchmark/mutation_benchmark.rb

@@ -0,0 +1,88 @@
+#	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 'benchmark'
+#require 'profile'
+
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+module MutationBenchmark
+
+	GENOME_SIZE = 1000
+	MUTATE_TIMES = 1000
+
+	def MutationBenchmark.benchmark_mutation(mutation, individual)
+		timing = Benchmark.measure do
+			MUTATE_TIMES.times { mutation.mutate(individual) }
+		end
+		puts "\t#{timing.format("%r")} - #{mutation.class}"
+	end
+
+	def MutationBenchmark.run_benchmark(individual, flip_function)
+		EvoSynth::Mutations.constants.each do |mutation|
+			mutation_class = EvoSynth::Mutations.const_get(mutation)
+			next if mutation_class == EvoSynth::Mutations::GaussMutation
+			next if mutation_class == EvoSynth::Mutations::SelfAdaptiveGaussMutation
+			next if mutation_class == EvoSynth::Mutations::UniformRealMutation
+
+			begin
+				mutation = mutation_class.new
+			rescue
+				mutation = mutation_class.new(flip_function) rescue next
+			end
+
+			MutationBenchmark.benchmark_mutation(mutation, individual)
+		end
+	end
+
+	individual = TestArrayBinaryIndividual.new(GENOME_SIZE)
+	GENOME_SIZE.times { |index| individual.genome[index] = (index % 2 == 1) ? true : false }
+
+	puts "Running mutation benchmark (on ArrayGenome) with #{MUTATE_TIMES} mutations (genome=#{GENOME_SIZE}):"
+	MutationBenchmark.run_benchmark(individual, EvoSynth::Mutations::Functions::FLIP_BOOLEAN)
+
+	number = 2 ** (GENOME_SIZE - 1)
+	add = number
+	while add > 2
+		add = add / 4
+		number += add
+	end
+
+	individual = TestBinaryGenomeIndividual.new(number)
+	puts "Running mutation benchmark (on BinaryGenome) with #{MUTATE_TIMES} mutations (genome=#{GENOME_SIZE}):"
+	MutationBenchmark.run_benchmark(individual, EvoSynth::Mutations::Functions::FLIP_BINARY)
+
+	individual = TestArrayGenomeIndividual.new([EvoSynth.rand]*GENOME_SIZE)
+	puts "Running mutation benchmark (on ArrayGenome filled with Float's) with #{MUTATE_TIMES} mutations (genome=#{GENOME_SIZE}):"
+	mutation = EvoSynth::Mutations::GaussMutation.new
+	MutationBenchmark.benchmark_mutation(mutation, individual)
+
+	mutation = EvoSynth::Mutations::SelfAdaptiveGaussMutation.new
+	MutationBenchmark.benchmark_mutation(mutation, individual)
+
+	mutation = EvoSynth::Mutations::UniformRealMutation.new
+	MutationBenchmark.benchmark_mutation(mutation, individual)
+end

data/test/benchmark/recombination_benchmark.rb

@@ -0,0 +1,58 @@
+#	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 'benchmark'
+#require 'profile'
+
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+module RecombinationBenchmark
+
+	GENOME_SIZE = 1000
+	RECOMBINATION_TIMES = 1000
+
+	def RecombinationBenchmark.benchmark_recombination(recombination, individual_one, individual_two)
+		timing = Benchmark.measure do
+			RECOMBINATION_TIMES.times { recombination.recombine(individual_one, individual_two) }
+		end
+		puts "\t#{timing.format("%r")} - #{recombination.class}"
+	end
+
+	individual_one = TestArrayBinaryIndividual.new(GENOME_SIZE)
+	individual_two = TestArrayBinaryIndividual.new(GENOME_SIZE)
+	GENOME_SIZE.times { |index| individual_one.genome[index] = index }
+	GENOME_SIZE.times { |index| individual_two.genome[index] = index }
+
+	puts "Running recombination benchmark with #{RECOMBINATION_TIMES} recombinations (genome=#{GENOME_SIZE}):"
+	EvoSynth::Recombinations.constants.each do |recombination|
+		recombination = EvoSynth::Recombinations.const_get(recombination).new rescue next
+		RecombinationBenchmark.benchmark_recombination(recombination, individual_one, individual_two)
+	end
+
+	interpolation = lambda { |gene_one, gene_two, factor| EvoSynth.rand < factor ? gene_one : gene_two }
+	recombination = EvoSynth::Recombinations::ArithmeticCrossover.new(interpolation)
+	RecombinationBenchmark.benchmark_recombination(recombination, individual_one, individual_two)
+end

data/test/benchmark/selection_benchmark.rb

@@ -0,0 +1,52 @@
+#	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 'benchmark'
+#require 'profile'
+
+
+require 'evosynth'
+require 'test/test_util/test_helper'
+
+module SelectionBenchmark
+
+	POPULATION_SIZE = 1000
+	SELECTION_TIMES = 1000
+	SELECT_COUNT = 10
+
+	population = EvoSynth::Population.new
+	POPULATION_SIZE.times { |i| population.add(TestMaximizingIndividual.new(i)) }
+
+	puts "Running selection benchmark with #{SELECTION_TIMES} selections (population size=#{POPULATION_SIZE}, select count=#{SELECT_COUNT}):"
+	EvoSynth::Selections.constants.each do |selection|
+		selection = EvoSynth::Selections.const_get(selection).new
+	#	selection = EvoSynth::Selections::NStageTournamentSelection.new
+
+		timing = Benchmark.measure do
+			SELECTION_TIMES.times { selection.select(population, SELECT_COUNT) }
+		end
+		puts "\t#{timing.format("%r")} - #{selection.class}"
+	end
+
+end

data/test/core/tc_array_genome.rb

@@ -0,0 +1,154 @@
+#	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 'shoulda'
+
+require 'evosynth'
+
+
+class ArrayGenomeTest < Test::Unit::TestCase
+
+	GENOME_SIZE = 20
+
+	context "when created with size=#{GENOME_SIZE}" do
+		setup do
+			@genome = EvoSynth::ArrayGenome.new(GENOME_SIZE)
+		end
+
+		should "#changed be true" do
+			assert @genome.changed?
+		end
+
+	end
+
+	context "after #changed is set to false" do
+		setup do
+			@genome = EvoSynth::ArrayGenome.new(GENOME_SIZE)
+			@genome.map! { 1 }
+			@genome.changed = false
+		end
+
+		should "#changed be false" do
+			assert !@genome.changed?
+		end
+
+		should "sort do nothing" do
+			@genome.sort
+			assert !@genome.changed?
+			@genome.changed = false
+		end
+
+		should "reject! set changed to true" do
+			@genome.reject! { |foo| foo != nil }
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "reverse! set changed to true" do
+			@genome.reverse!
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "slice! set changed to true" do
+			@genome.slice!(0)
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "flatten! set changed to true" do
+			@genome.flatten!
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "push set changed to true" do
+			@genome.push(2)
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "pop set changed to true" do
+			@genome.pop
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "sort! set changed to true" do
+			@genome.sort!
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "shift set changed to true" do
+			@genome.shift
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "unshift set changed to true" do
+			@genome.unshift("bar")
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "[]= set changed to true" do
+			@genome[0] = "foo"
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "collect! set changed to true" do
+			@genome.collect! { |foo| "foo" }
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "map! set changed to true" do
+			@genome.map! { |foo| "foo" }
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "<< set changed to true" do
+			@genome << "baz"
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "uniq! set changed to true" do
+			@genome.uniq!
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+		should "clear set changed to true" do
+			@genome.clear
+			assert @genome.changed?
+			@genome.changed = false
+		end
+
+	end
+
+end