charlie 0.8.0 → 0.8.1

data/examples/tsp.rb

@@ -40,7 +40,7 @@ GABenchmark.benchmark(TSP,'output/tsp.html') {
   selection TruncationSelection(1), Elitism(ScaledRouletteSelection), TournamentSelection(4)
   crossover EdgeRecombinationCrossover, PermutationCrossover,
             PCross(0.5,EdgeRecombinationCrossover,PermutationCrossover),
-            PCross(0.01,EdgeRecombinationCrossover), NullCrossover 
+            PCross(0.01,EdgeRecombinationCrossover), NullCrossover, PartiallyMappedCrossover 
 
   mutator   TranspositionMutator, InversionMutator, InsertionMutator,
             PMutateN(InversionMutator=>0.4,InsertionMutator=>0.4),

data/lib/charlie.rb

@@ -4,7 +4,7 @@ $:.unshift File.dirname(__FILE__)
 
 # This is just a dummy module to avoid making the VERSION constant a global.
 module Charlie
-  VERSION = '0.8.0'
+  VERSION = '0.8.1'
 end
 
 require 'charlie/etc/monkey'

data/lib/charlie/1.9fixes.rb

@@ -1,6 +1,6 @@
 #1.9 versions of some functions, to avoid bug #16493. 
 #TODO: remove on bugfix/1.9.1
-
+#Bug fixed by now, really should update
 
 
 def Elitism(sel_module,elite_n=1) # :nodoc:
@@ -43,4 +43,4 @@ module Enumerable
   def zip_with(a2) # avoid Enumerable#zip in 1.9
     r=[]; each_with_index{|e,i| r << yield(e,a2[i]) }; r
   end
-end
+end

data/lib/charlie/etc/monkey.rb

@@ -45,11 +45,11 @@ class Array
   end
 
   def rand_index
-    rand(size)
+    Kernel.rand(size)
   end
 
   def at_rand
-    self[rand(size)]
+    self[Kernel.rand(size)]
   end
 
   def stats # TODO 1.9, use minmax
@@ -71,6 +71,13 @@ class Array
    each_with_index{|e,i| r << yield(e,i) }
    r
   end
+
+  # Finds value and swaps it with the element at index.
+  def swap_element_at_index!(index, value)
+    old_element_index = self.index(value)
+    self[index], self[old_element_index] = value, self[index]
+  end
+
 end
 
 

data/lib/charlie/list/list_crossover.rb

@@ -30,7 +30,7 @@ def NPointCrossover(n=2)
  }
 end
 TwoPointCrossover   = NPointCrossover(2)
-ThreePointCrossover = NPointCrossover(2)
+ThreePointCrossover = NPointCrossover(3)
 
 # Uniform crossover, returns two children.
 module UniformCrossover

data/lib/charlie/permutation/permutation.rb

@@ -124,3 +124,40 @@ module EdgeRecombinationCrossover
   end
 end
 
+# Two point Partial Preservation Crossover for PermutationGenotype, also known as Partially Mapped Crossover (PMX).
+#
+# The PMX proceeds by choosing two cut points at random:
+#   Parent 1: hkcefd bla igj
+#   Parent 2: abcdef ghi jkl
+#
+# The cut-out section defines a series of swapping operations to be performed on the second parent.
+# In the example case, we swap b with g, l with h and a with i and end up with the following offspring:
+#   Offspring: igcdef bla jkh
+# Performing similar swapping on the first parent gives the other offspring:
+#   Offspring: lkcefd ghi abj
+#
+# Algortithm and description taken from:
+#
+#   "A New Genetic Algorithm For VPRTW", Kenny Qili Zhu, National University of Singapure,
+#   April 13, 2000.
+#
+# (maybe should be revised with some original documentation)
+module PartiallyMappedCrossover
+  def cross(parent1,parent2)
+    p1, p2 = parent1.genes, parent2.genes
+    raise "Chromosomes too small, should be >= 4" if p1.size < 4
+    
+    # Cut-off points must be after first element and before last.
+    cp1 = rand(p1.size-2) + 1
+    cp2 = rand(p1.size-2) + 1 while cp2 == cp1 or cp2.nil?
+    
+    of1, of2 = Array.new(p2), Array.new(p1)
+    (cp1..cp2).each do |index|
+      of1.swap_element_at_index!(index, p1[index])
+      of2.swap_element_at_index!(index, p2[index])
+    end
+    
+    [of1, of2].map{|of| from_genes(of) }
+  end
+end
+

data/lib/charlie/population.rb

@@ -12,7 +12,7 @@ class Population < Array
     replace Array.new(population_size){ genotype_class.new } 
   end
 
-  # yields population and generation number to block each generation, for a maximum of max_generations.
+  # Yields the population and the generation number to block for each generation at a maximum of max_generations times.
   def evolve_block(max_generations=DEFAULT_MAX_GENS)
     yield self, 0
     (max_generations || DEFAULT_MAX_GENS).times {|generation|
@@ -91,6 +91,8 @@ class Population < Array
 
   # Effectively runs Population#evolve_until_best  multiple times.
   # * See Population.evolve_multiple_until_population for arguments
+  #
+  # Aliased also as Population.evolve_multiple_until.
   def self.evolve_multiple_until_best(*args,&b)
     evolve_multiple_until_population(*args) {|pop| b.call(pop.max) }
   end

data/lib/charlie/selection.rb

@@ -91,8 +91,9 @@ def ScaledRouletteSelection(&block)
  
    if @@index_size != population.size # build index, cache for constant population size
      @@index_size = population.size
-     @@index = []
-     (0...population.size).map(&@@block).each_with_index{|e,i| @@index += Array.new(e.round,i)  }
+     index = []
+     (0...population.size).map(&@@block).each_with_index{|e,i| index += Array.new(e.round,i)  }
+     @@index = index # ruby 1.9 fix, @@index can't be used in block(?) -- TODO:  figure out why
    end
    population = population.sort_by(&:fitness)
 
@@ -137,17 +138,19 @@ end
 
 
 
-# Tournament selection.
-# Default: select the 2 individuals with the highest fitness out of a random population with size group_size
+# Tournament selection
+#
+# Default: selects the 2 individuals with the highest fitness out of a random population with size group_size
 # and replaces the others with offspring of these 2.
-# Does this n_times. n_times==nil takes population size / (group_size-2)  , i.e. about the same number of new individuals as roulette selection etc.
+#
+# Runs the selection for n_times. If n_times == nil (default), it sets it equal to population size / (group_size-2), 
+# i.e. about the same number of new individuals as roulette selection etc.
 def TournamentSelection(group_size=4,n_times=nil)
   Module::new{
     @@group_size = group_size
     @@n_times    = n_times
     def next_generation(population)
-      psz = population.size
-      n_times = @@n_times || (psz / (@@group_size-2))
+      n_times = @@n_times || (population.size / (@@group_size-2))
       n_times.times{
         population.shuffle!
         ix = (0...@@group_size).sort_by{|i| population[i].fitness }
@@ -191,8 +194,7 @@ def CoTournamentSelection(group_size=4,full_tournament=false,n_times=nil)
     @@full_tournament = full_tournament
     @@n_times    = n_times
     def next_generation(population)
-      psz = population.size
-      n_times = @@n_times || (psz / @@group_size)     #(psz / (@@group_size-2))
+      n_times = @@n_times || (population.size / @@group_size)     #(population.size / (@@group_size-2))
       n_times.times{
         population.shuffle!
         points = Array.new(@@group_size,0.0)

data/test/test_permutation.rb

@@ -24,6 +24,10 @@ class PermutationTestInsert < PermutationTest
   use InsertionMutator, NullCrossover
 end
 
+class PermutationTestPMX < PermutationTest
+  use InsertionMutator, PartiallyMappedCrossover, RandomSelection
+end
+
 
 
 class PermTests < Test::Unit::TestCase
@@ -47,12 +51,20 @@ class PermTests < Test::Unit::TestCase
   def test_edge_recombination_rand # test if permutation doesn't just stay preserved because of fitness
     p=nil
     assert_nothing_raised{
-      klass = Class.new(PermutationTestERO){ use RandomSelection } 
+      klass = Class.new(PermutationTestPMX){ use  } 
       p=Population.new(klass,20).evolve_silent(20)
     }
     p.each{|s| assert_equal s.genes.sort, (0...N).to_a }
   end
 
+  def test_pmx
+    p=nil
+    assert_nothing_raised{
+      p=Population.new(PermutationTestERO,20).evolve_silent(20)
+    }
+    p.each{|s| assert_equal s.genes.sort, (0...N).to_a }
+  end
+
   def test_inversion_mutator # test if inversion mutator works
     p=nil
     assert_nothing_raised{

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: charlie
 version: !ruby/object:Gem::Version 
-  version: 0.8.0
+  version: 0.8.1
 platform: ruby
 authors: 
 - Sander Land
@@ -9,17 +9,18 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2008-02-12 00:00:00 +01:00
+date: 2009-02-12 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: hoe
+  type: :development
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.4.0
+        version: 1.8.3
     version: 
 description: "== DESCRIPTION: Charlie is a library for genetic algorithms (GA) and genetic programming (GP).  == FEATURES: - Quickly develop GAs by combining several parts (genotype, selection, crossover, mutation) provided by the library. - Sensible defaults are provided with any genotype, so often you only need to define a fitness function. - Easily replace any of the parts by your own code. - Test different strategies in GA, and generate reports comparing them.  Example report: http://charlie.rubyforge.org/example_report.html  == INSTALL: * sudo gem install charlie  == EXAMPLES: This example solves a TSP problem (also quiz #142): N=5 CITIES = (0...N).map{|i| (0...N).map{|j| [i,j] } }.inject{|a,b|a+b} class TSP < PermutationGenotype(CITIES.size) def fitness d=0 (genes + [genes[0]]).each_cons(2){|a,b|  a,b=CITIES[a],CITIES[b] d += Math.sqrt( (a[0]-b[0])**2 + (a[1]-b[1])**2 )  } -d # lower distance -> higher fitness. end use EdgeRecombinationCrossover, InversionMutator end Population.new(TSP,20).evolve_on_console(50)  This example finds a polynomial which approximates cos(x) class Cos < TreeGenotype([proc{3*rand-1.5},:x], [:-@], [:+,:*,:-]) def fitness -[0,0.33,0.66,1].map{|x| (eval_genes(:x=>x) - Math.cos(x)).abs }.max end use TournamentSelection(4) end Population.new(Cos).evolve_on_console(500)"
 email: sander.land+ruby@gmail.com
@@ -56,6 +57,7 @@ files:
 - examples/function_optimization.rb
 - examples/matrix.rb
 - examples/neural.rb
+- examples/output/bitstring_royalroad.html
 - examples/output/function_optimization_sombrero.html
 - examples/output/function_optimization_twopeak.csv
 - examples/output/function_optimization_twopeak.html
@@ -117,7 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: charlie
-rubygems_version: 1.0.1
+rubygems_version: 1.3.1
 signing_key: 
 specification_version: 2
 summary: A genetic algorithms library for Ruby.