evosynth 0.1.0

data/lib/evosynth/operators/mutations/gauss_mutation.rb

@@ -0,0 +1,65 @@
+#	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
+	module Mutations
+
+		# GAUSS-MUTATION (Weicker page 60)
+		#
+		# TODO: needs rdoc
+
+		class GaussMutation
+			attr_accessor :sigma, :lower_bound, :upper_bound
+
+			DEFAULT_SIGMA = 1.0
+			DEFAULT_LOWER_BOUND = -1 * Float::MAX
+			DEFAULT_UPPER_BOUND = Float::MAX
+
+			def initialize(sigma = DEFAULT_SIGMA, lower_bound = DEFAULT_LOWER_BOUND, upper_bound = DEFAULT_UPPER_BOUND)
+				@sigma = sigma
+				@lower_bound = lower_bound
+				@upper_bound = upper_bound
+			end
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+
+				mutated.genome.map! do |gene|
+					gene += EvoSynth.nrand(0.0, @sigma)
+					gene = @lower_bound if gene < @lower_bound
+					gene = @upper_bound if gene > @upper_bound
+					gene
+				end
+
+				mutated
+			end
+
+			def to_s
+				"gauss mutation <sigma: #{@sigma}, lower bound: #{@lower_bound}, upper_bound: #{@upper_bound}>"
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/mutations/identity.rb

@@ -0,0 +1,62 @@
+#	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
+	module Mutations
+
+		# The Identity mutation does not change the genome of the given individual, it will return a clone.
+		#
+		# This mutations does not destroy permutations.
+
+		class Identity
+
+			#	:call-seq:
+			#		mutate(Individual) -> Individual
+			#
+			# Returns a clone of a given individual.
+			#
+			#     m = Identity.new
+			#     m.mutate(a_individual)   #=> a_new_individual
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+				mutated
+			end
+
+			#	:call-seq:
+			#		to_s -> string
+			#
+			# Returns description of this mutation
+			#
+			#     m = Identity.new
+			#     m.to_s                   #=> "identity (just clones individual)"
+
+			def to_s
+				"identity (just clones individual)"
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/mutations/inversion_mutation.rb

@@ -0,0 +1,73 @@
+#	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
+	module Mutations
+
+		# The InversionMutation inverts the order of a random range of genes in the genome. It is based on
+		# INVERTIERENDE-MUTATION (Weicker 2007, page 28).
+		# 
+		# This mutations does not destroy permutations.
+
+		class InversionMutation
+
+			#	:call-seq:
+			#		mutate(Individual) -> Individual
+			#
+			# Returns a clone of a given individual and inverts the order of a
+			# random range of genes in the genome of this clone.
+			#
+			#     m = InversionMutation.new
+			#     m.mutate(a_individual)   #=> a_new_individual
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+				genome = mutated.genome
+
+				index_one = EvoSynth.rand(genome.size)
+				index_two = EvoSynth.rand(genome.size)
+				index_two = EvoSynth.rand(genome.size) while index_two == index_one
+				index_one, index_two = index_two, index_one if index_one > index_two
+
+				genome[index_one..index_two] = genome[index_one..index_two].reverse
+
+				mutated
+			end
+
+			#	:call-seq:
+			#		to_s -> string
+			#
+			# Returns description of this mutation
+			#
+			#     m = Identity.new
+			#     m.to_s                   #=> "exchange mutation"
+
+			def to_s
+				"exchange mutation"
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/mutations/mixing_mutation.rb

@@ -0,0 +1,75 @@
+#	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
+	module Mutations
+
+		# The MixingMutation shuffles the order of a random range of genes in the genome. It is based on
+		# MISCHENDE-MUTATION (Weicker 2007, page 132).
+		#
+		# This mutations does not destroy permutations.
+
+		class MixingMutation
+
+			#	:call-seq:
+			#		mutate(Individual) -> Individual
+			#
+			# Returns a clone of a given individual and shuffles the order of a
+			# random range of genes in the genome of this clone.
+			#
+			#     m = InversionMutation.new
+			#     m.mutate(a_individual)   #=> a_new_individual
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+				genome = mutated.genome
+
+				index_one = EvoSynth.rand(genome.size)
+				index_two = EvoSynth.rand(genome.size)
+				index_one, index_two = index_two, index_one if index_one > index_two
+				return mutated if index_one == index_two
+
+				subsection = genome[index_one..index_two]
+				subsection.sort! { EvoSynth.rand(2) }
+				genome[index_one..index_two] = subsection
+
+				mutated
+			end
+
+			#	:call-seq:
+			#		to_s -> string
+			#
+			# Returns description of this mutation
+			#
+			#     m = MixingMutation.new
+			#     m.to_s                   #=> "mixing muation"
+
+			def to_s
+				"mixing muation"
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/mutations/one_gene_flipping.rb

@@ -0,0 +1,89 @@
+#	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
+
+	module Mutations
+
+		# This mutations flips (inverts) one gene in the genome of a given individual using the given flip function
+		# (a lambda) and returns a mutated individual. To use this mutation the flip_function has to return the
+		# negation/inverse of a given gene. This mutations is based on EIN-BIT-BINAERE-MUTATION (Weicker 2007, page 48).
+
+		class OneGeneFlipping
+
+			# This function is used to flip each gene
+
+			attr_accessor :flip_function
+
+			#	:call-seq:
+			#		OneGeneFlipping.new(Lambda) -> OneGeneFlipping
+			#
+			# Returns a new OneGeneFlipping.
+			#
+			#     custom_flip_function = lambda { |gene| EvoSynth.rand(42 * gene) }
+			#     OneGeneFlipping.new(custom_flip_function)
+
+			def initialize(flip_function)
+				@flip_function = flip_function
+			end
+
+			#	:call-seq:
+			#		mutate(Individual) -> Individual
+			#
+			# Returns the mutation (one gene will be flipped with the given flip function) of a given individual.
+			#
+			#     m = OneGeneFlipping.new
+			#     m.mutate(a_individual)   #=> a_new_individual
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+				genome = mutated.genome
+
+				rand_index = EvoSynth.rand(genome.size)
+				if @flip_function.arity == 1
+					genome[rand_index] = @flip_function.call(genome[rand_index])
+				else
+					genome[rand_index] = @flip_function.call
+				end
+
+				mutated
+			end
+
+			#	:call-seq:
+			#		to_s -> string
+			#
+			# Returns description of this mutation
+			#
+			#     m = OneGeneFlipping.new
+			#     m.to_s                   #=> "one-gene-flipping"
+
+			def to_s
+				"one-gene-flipping"
+			end
+
+		end
+
+	end
+
+end

data/lib/evosynth/operators/mutations/self_adaptive_gauss_mutation.rb

@@ -0,0 +1,73 @@
+#	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
+	module Mutations
+
+		# SELBSTADAPTIVE-GAUSS-MUTATION (Weicker page 114)
+		#
+		# TODO: needs rdoc
+
+		class SelfAdaptiveGaussMutation
+			attr_accessor :initial_sigma, :lower_bound, :upper_bound
+
+			DEFAULT_INITIAL_SIGMA = 1.0
+			DEFAULT_LOWER_BOUND = -1 * Float::MAX
+			DEFAULT_UPPER_BOUND = Float::MAX
+
+			def initialize(initial_sigma = DEFAULT_INITIAL_SIGMA, lower_bound = DEFAULT_LOWER_BOUND, upper_bound = DEFAULT_UPPER_BOUND)
+				@initial_sigma = initial_sigma
+				@lower_bound = lower_bound
+				@upper_bound = upper_bound
+			end
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+				add_sigma(mutated) unless defined? mutated.sigma
+
+				mutated.sigma *= Math.exp( (1 / Math.sqrt(mutated.genome.size)) * EvoSynth.nrand)
+
+				mutated.genome.map! do |gene|
+					gene += EvoSynth.nrand(0.0, mutated.sigma)
+					gene = @lower_bound if gene < @lower_bound
+					gene = @upper_bound if gene > @upper_bound
+					gene
+				end
+
+				mutated
+			end
+
+			def to_s
+				"self adaptive gauss mutation <sigma: #{@sigma}, lower bound: #{@lower_bound}, upper_bound: #{@upper_bound}>"
+			end
+
+			def add_sigma(individual)
+				individual.instance_eval("def sigma; @sigma end; def sigma=(value); @sigma = value end")
+				individual.sigma = @initial_sigma
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/operators/mutations/shifting_mutation.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.
+
+
+module EvoSynth
+	module Mutations
+
+		# The ShiftingMutation shifts a random range of genes by one index in the genome. It is based on
+		# VERSCHIEBENDE-MUTATION (Weicker 2007, page 132).
+		# 
+		# This mutations does not destroy permutations.
+
+		class ShiftingMutation
+
+			#	:call-seq:
+			#		mutate(Individual) -> Individual
+			#
+			# Returns a clone of a given individual and shifts a random range of
+			# genes by one index in the genome of this clone.
+			#
+			#     m = ShiftingMutation.new
+			#     m.mutate(a_individual)   #=> a_new_individual
+
+			def mutate(individual)
+				mutated = individual.deep_clone
+				genome = mutated.genome
+
+				index_one = EvoSynth.rand(genome.size)
+				index_two = EvoSynth.rand(genome.size)
+				return mutated if index_one == index_two
+
+				shift_genome(index_one, index_two, genome)
+				mutated
+			end
+
+			#	:call-seq:
+			#		to_s -> string
+			#
+			# Returns description of this mutation
+			#
+			#     m = ShiftingMutation.new
+			#     m.to_s                   #=> "shifting muation"
+
+			def to_s
+				"shifting muation"
+			end
+
+			private
+
+			# this function does the actual shift (left and right)
+
+			def shift_genome(index_one, index_two, genome)
+				if index_one > index_two
+					## shift right
+					shifted_range = genome[index_two..index_one]
+					shifted_range = shifted_range << shifted_range.shift
+					genome[index_two..index_one] = shifted_range
+				else
+					## shift left
+					shifted_range = genome[index_one..index_two]
+					shifted_range = [shifted_range.pop] + shifted_range
+					genome[index_one..index_two] = shifted_range
+				end
+			end
+		end
+
+	end
+end