evosynth 0.1.0

data/lib/evosynth/output/exporter/gruff_exporter.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
+	module Output
+
+		class GruffExporter
+
+			def initialize(logger)
+				begin
+					require 'gruff'
+				rescue
+					puts "Could not require 'gruff' gem, please install with gem install gruff"
+				end
+
+				@logger = logger
+			end
+
+			def export(title, filename)
+				x, ys = [], []
+				data_sets = 0
+				@logger.data.each_pair do |key, value|
+					data_sets = value.size if value.size > data_sets
+					x << key
+					value.each_with_index do |y, index|
+						ys[index] = [] if ys[index].nil?
+						ys[index] << y
+					end
+				end
+
+				g = Gruff::Line.new
+				g.title = title
+
+				data_sets.times { |set|	g.data(@logger.column_names[set], ys[set]) }
+
+				labels = {}
+				x.each_with_index { |gen, index| labels[index] = "#{gen}"}
+				g.labels = labels
+
+				g.write(filename)
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/output/factory.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
+	module Output
+
+		def Output.create_console_logger(log_step, things_to_log = {})
+			logger = EvoSynth::Output::Logger.new(log_step, false, things_to_log)
+			logger.add_observer(EvoSynth::Output::ConsoleWriter.new)
+			logger
+		end
+
+	end
+end

data/lib/evosynth/output/logger.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
+	module Output
+
+		# Customizable logger
+		#
+		#	logger = EvoSynth::Output::Logger.new(10, true,
+		#		"gen" => ->{ evolver.generations_computed },
+		#		"best" => ->{ profile.population.best.fitness },
+		#		"worst" => ->{ profile.population.worst.fitness }
+		#	)
+		#	evolver.add_observer(logger)
+
+		class Logger
+			include Observable
+
+			attr_accessor :show_errors, :things_to_log, :save_data
+			attr_reader :data
+
+			def initialize(log_step, save_data, things_to_log = {})
+				@data = {}
+
+				@log_step = log_step
+				@save_data = save_data
+				@things_to_log = things_to_log
+				@show_errors = false
+			end
+
+			def clear_data
+				@data = {}
+			end
+
+			def column_names
+				line = []
+				@things_to_log.each_pair { |key, value|	line << key }
+				line
+			end
+
+			def update(observable, counter)
+				return unless counter % @log_step == 0
+
+				line = []
+				@things_to_log.each_pair do |key, value|
+					begin
+						line << value.call
+					rescue
+						@show_errors ? line << "ERROR while retrieving #{value.inspect}" : line << "\t"
+					end
+				end
+
+				@data[counter] = line if save_data
+
+				changed
+				notify_observers self, counter, line
+			end
+
+		end
+
+	end
+end

data/lib/evosynth/problems.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
+
+	# This module contains some predefined problems. Most of them are widely used to benchmark or demonstrate
+	# Evolutionary Computation.
+
+	module Problems
+	end
+end
+
+require 'evosynth/problems/float_benchmark_functions'
+require 'evosynth/problems/binary_benchmark_functions'
+require 'evosynth/problems/tsp'
+require 'evosynth/problems/graph_colouring'

data/lib/evosynth/problems/binary_benchmark_functions.rb

@@ -0,0 +1,74 @@
+#	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 Problems
+
+		# This module contains some multi-dimensional Benchmarkfunctions. You simply set the number of dimensions by
+		# the length of the given (boolean) array.
+
+		module BinaryBenchmarkFuntions
+
+			# count-ones function
+			#
+			# global maximum at f(x) = x at x(i) = 1 (or true), i = 1..n
+
+			def BinaryBenchmarkFuntions.count_ones(bs)
+				bs.inject(0) { |sum, b| sum += (b == true || b == 1 ? 1 : 0) }
+			end
+
+			# Royal-Road function (Mitchell et al 1992)
+			#
+			# global minimum: f(x) = 0 at x(i) = 1, i = 1..n (bs.size % k == 0)
+
+			def BinaryBenchmarkFuntions.royal_road(k, bs)
+				m = bs.size / k
+				sum = 0
+
+				m.times do |i|
+					sum += bs[(i*k)..(i+1)*k-1].inject(1) { |res, b| res = (b != 1 ? 0 : res) }
+				end
+
+				sum
+			end
+
+			# N-Peak problem presented in "Using Problem Generators to Explore the Effects of Epistasis", De Jong et al 1997
+			#
+			# global maximum: f(x) = 1.0 when peak == xs (hamming distance is 0)
+
+			def BinaryBenchmarkFuntions.n_peaks(peaks, xs)
+				max_hamming_dist = xs.size
+
+				peaks.each do |peak|
+					new_dist = 0.0
+					xs.each_with_index { |x, index| new_dist += 1 if x != peak[index] }
+					max_hamming_dist = new_dist if new_dist < max_hamming_dist
+				end
+
+				1.0 / xs.size * (xs.size - max_hamming_dist)
+			end
+
+		end
+	end
+end

data/lib/evosynth/problems/float_benchmark_functions.rb

@@ -0,0 +1,99 @@
+#	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 Problems
+
+		# This module contains some multi-dimensional Benchmarkfunctions. You simply set the number of dimensions by
+		# the length of the given (Float) array.
+
+		module FloatBenchmarkFuntions
+
+			# Sinus Sum function (Schwefel 1995)
+			#
+			# global minimum: f(x) = 0 at x(i) = 420.9687, i = 1..n
+
+			def FloatBenchmarkFuntions.sinus_sum(xs)
+				418.98289 * xs.size + xs.inject(0.0) { |sum, x| sum += -x * Math.sin(Math.sqrt(x.abs)) }
+			end
+
+			# Double Sum function (Schwefel 1977)
+			#
+			# global minimum: f(x) = 0 at x(i) = 0, i = 1..n
+
+			def FloatBenchmarkFuntions.double_sum(xs)
+				xs.inject(0.0) do |sum, i|
+					sum += xs[0..i].inject(0.0) { |sum, x| sum += x }
+				end
+			end
+
+			# Sphere function (Rechenberg 1973 and De Jong 1975)
+			#
+			# global minimum: f(x) = 0 at x(i) = 0, i = 1..n
+
+			def FloatBenchmarkFuntions.sphere(xs)
+				xs.inject(0.0) { |sum, x| sum += x**2 }
+			end
+
+			# Rastgrin (Törn & Zilinskas 1989)
+			#
+			# global minimum: f(x) = 0 at x(i) = 0, i = 1..n
+
+			def FloatBenchmarkFuntions.rastgrin(xs)
+				10 * xs.size + xs.inject(0.0) { |sum, x| sum += x**2 - 10 * Math.cos(2 * Math::PI * x) }
+			end
+
+			# Rosenbrock (De Jong 1975)
+			#
+			# global minimum: f(x) = 0 at x(i) = 1, i = 1..n
+
+			def FloatBenchmarkFuntions.rosenbrock(xs)
+				(0..xs.size - 2).inject(0.0) do |sum, i|
+					sum += 100 * (xs[i]**2 - xs[i+1])**2 + (1 - xs[i])**2
+				end
+			end
+
+			# Ackley (Ackley 1987)
+			#
+			# global minimum: f(x) = 0 at x(i) = 0, i = 1..n
+
+			def FloatBenchmarkFuntions.ackley(xs)
+				quad_sum = xs.inject(0.0) { |sum, x| sum += x**2 }
+				cos_sum = xs.inject(0.0) { |sum, x| sum += Math.cos(2 * Math::PI * x) }
+				20 + Math::E - 20 * Math.exp(-0.2 * Math.sqrt( (1.0 / xs.size) * quad_sum )) - Math.exp( (1.0 / xs.size) * cos_sum )
+			end
+
+			# Griewank (Törn & Zilinskas 1989)
+			#
+			# global minimum: f(x) = 0 at x(i) = 0, i = 1..n
+
+			def FloatBenchmarkFuntions.griewank(xs)
+				product = 1.0
+				xs.each_with_index { |x, i| product *= Math.cos x / Math.sqrt(i+1) }
+				1 + xs.inject(0.0) { |sum, x| sum += x**2 / (400 * xs.size) } - product
+			end
+
+		end
+	end
+end

data/lib/evosynth/problems/graph_colouring.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.
+
+
+require 'matrix'
+
+
+module EvoSynth
+	module Problems
+
+		class GraphColouring < EvoSynth::Evaluator
+
+			attr_reader :node_count
+			attr_reader :matrix
+
+			def initialize(filename)
+				super()
+				read_file(filename)
+			end
+
+			def verletzungen(genome)
+				verletzungen = 0
+
+				@node_count.times do |row|
+					@node_count.times do |col|
+						verletzungen += 1 if @matrix[row, col] == 1 && genome[row] == genome[col]
+					end
+				end
+
+				verletzungen
+			end
+
+			def calculate_fitness(individual)
+				fitness = 0.0 + individual.genome.uniq.size * (verletzungen(individual.genome) + 1)
+				fitness
+			end
+
+			private
+
+			# reads the node count from grapg-file
+			def get_node_count(file_name)
+				File.open(file_name).each_line do |line|
+					next if line !~ /^p\D*(\d+)/
+					return Integer($1)
+				end
+			end
+
+			# reads a graph file
+			def read_file(file_name)
+				@node_count = get_node_count(file_name)
+				@matrix = Matrix.zero(@node_count)
+
+				columns = @matrix.column_vectors
+
+
+				File.open(file_name).each_line do |line|
+					next if line !~ /^e/
+					line =~ /(\d+)\s*(\d+)/
+					arr = columns[Integer($1)-1].to_a
+					arr[Integer($2)-1] = 1
+					columns[Integer($1)-1] = Vector.elements(arr)
+				end
+				@matrix = Matrix.columns(columns)
+			end
+
+		end
+
+	end
+end