feldtruby 0.4.9 → 0.4.10

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    feldtruby (0.4.8)
+    feldtruby (0.4.9)
       bson_ext
       json
       mongo

data/lib/feldtruby/optimize/archive.rb

@@ -0,0 +1,189 @@
+require 'feldtruby/optimize'
+require 'feldtruby/logger'
+
+module FeldtRuby::Optimize
+
+# An archive keeps a record of all "interesting" candidate solutions found
+# during optimization. It has two purposes: to contribute to the optimization
+# itself (since seeding a search with previously "good" solutions can improve
+# convergence speed) but also to provide a current view of the best and most
+# interesting solutions found.
+#
+# Interestingness is hard to define but we posit that two elements are always
+# important:
+#  1. Being good, i.e. having good values for one or many of the sub-objectives
+#  2. Being different, i.e. behaving differently (phenotypic diversity) or 
+#       looking different (genotypic diversity), than other candidate solutions.
+#
+# Different types of optimization can require different trade-offs between 
+# these elements but all archives should support both types inherently.
+# The default choices for the main class is to use the quality calculated by the
+# objective class to judge "being good" and to use a diversity objective to
+# judge "being different".
+# 
+# We also posit that it is not enough only to be diverse (although there is
+# some research showing that novelty search in itself may be as good/important
+# as directed search) so the default behavior is to only add a solution to the
+# diversity top lists if it is within a certain percentage of the best solutions
+# on the other (being good) top list. Thus the basic design is to keep one top 
+# list per fitness goal, one overall aggregate fitness top list and then one 
+# top list per diversity goal.
+#
+# We note that diversity is just another type of objective (although a relative 
+# rather than an absolute one) and we can use the existing
+# classes to implement that. A default diversity objective looks at genotypic
+# and fitness diversity by default but more elaborate schemes can be used.
+#
+# One way to make this model easier to understand is to call the three types:
+#  generalists    (overall good, aggregated fitness best)
+#  specialists    (doing one thing very, very good, sub-objective fitness best)
+#  weirdos        (different but with clear qualitites, ok but diverse)
+class Archive
+  #include FeldtRuby::Logging
+
+  DefaultParams = {
+    :NumTopPerGoal => 5, # Number of solutions in top list per individual goal
+    :NumTopAggregate => 20, # Number of solutions in top list for aggregate quality
+
+    # Number of solutions in diversity top list. This often needs to 
+    # be larger than the other top lists since there are "more" ways to be 
+    # diverse than to be good... OTOH it costs CPU power to have large values
+    # here since the quality values needs to be recalculated whenever there is
+    # a new best. So we keep them small.
+    :NumTopDiversityAggregate => 10,
+
+    # Max percent distance (given as a ratio, i.e. 0.05 means 5%) from best 
+    # solution (top of Aggregate list) that a solution is allowed to have 
+    # to be allowed on the diversity list. If it is more than 5% from best
+    # we don't consider adding it to a diversity list.
+    :MaxPercentDistanceToBestForDiversity => 0.05
+  }
+
+  attr_reader :objective, :diversity_objective
+
+  attr_reader :specialists, :generalists, :weirdos
+
+  def initialize(fitnessObjective, diversityObjective, params = DefaultParams.clone)
+    @objective = fitnessObjective
+    self.diversity_objective = diversityObjective
+    @params = DefaultParams.clone.update(params)
+    init_top_lists
+  end
+
+  def diversity_objective=(diversityObjective)
+    @diversity_objective = diversityObjective
+    @diversity_objective.archive = self if @diversity_objective.respond_to?(:archive=)
+    @diversity_objective.quality_objective = @objective if @diversity_objective.respond_to?(:quality_objective=)
+  end
+
+  def best
+    # The top of the Generalists top list is the overall best
+    @generalists[0]
+  end
+
+  def init_top_lists
+    @specialists = Array.new
+    @objective.num_goals.times do |i|
+      @specialists << GoalTopList.new(@params[:NumTopPerGoal], @objective, i)
+    end
+
+    @generalists = GlobalTopList.new(@params[:NumTopAggregate], @objective)
+
+    @weirdos = GlobalTopList.new(@params[:NumTopDiversityAggregate], @diversity_objective)
+  end
+
+  # Add a candidate to the top lists if it is good enough to be there. Throws
+  # out worse candidates as appropriate.
+  def add(candidate)
+    @specialists.each {|tl| tl.add(candidate)}
+
+    # Detect if we get a new best one by saving the previous best.
+    prev_best = best
+    @generalists.add candidate
+
+    # If there was a new best we invalidate the diversity quality values since
+    # they are relative and must be recalculated. Note that this might incur
+    # a big penalty if there are frequent changes at the top.
+    if prev_best != best
+#      logger.log_data :new_best, {
+#        "New best" => best,
+#        "New quality" => @objective.quality_of(best),
+#        "Old best" => prev_best,
+#        "Old quality" => @objective.quality_of(prev_best)}, 
+#        "Archive: New best solution found", true
+
+      @weirdos.each {|w| @diversity_objective.invalidate_quality_of(w)}
+    elsif good_enough_quality_to_be_interesting?(candidate)
+      # When we add a new one this will lead to re-calc of the diversity quality
+      # of the previous ones if there has been a new best since last time.
+      @weirdos.add candidate
+    end
+  end
+
+  # Is quality of candidate good enough (within MaxPercentDistanceToBestForDiversity
+  # from quality of best candidate)
+  def good_enough_quality_to_be_interesting?(candidate)
+    qv_best = @objective.quality_of(best).value
+    ((qv_best - @objective.quality_of(candidate).value).abs / qv_best) <= @params[:MaxPercentDistanceToBestForDiversity]
+  end
+
+  # A top list is an array of a fixed size that saves the top candidates
+  # based on their (aggregate) quality values.
+  class GlobalTopList
+    def initialize(maxSize, objective)
+      @max_size =maxSize
+      @top_list = Array.new
+      @objective = objective
+    end
+    def length; @top_list.length; end
+
+    def each
+      @top_list.each {|e| yield(e)}
+    end
+
+    def [](index)
+      @top_list[index]
+    end
+
+    def add(candidate)
+      last = @top_list.last
+      #puts "In #{self},\nlast = #{last}, candidate = #{candidate}, top_list = #{@top_list}"
+      if @top_list.length < @max_size || last.nil? || is_better_than?(candidate, last)
+        @top_list.pop if @top_list.length >= @max_size
+        @top_list << candidate
+        @top_list = sort_top_list
+      end
+      #puts "top_list = #{@top_list}"
+    end
+
+    def is_better_than?(candidate1, candidate2)
+      @objective.is_better_than?(candidate1, candidate2)
+    end
+
+    def sort_top_list
+      @top_list.sort_by {|c| @objective.quality_of(c).value}
+    end
+
+    def inspect
+      self.class.inspect + @top_list.inspect
+    end
+  end
+
+  class GoalTopList < GlobalTopList
+    def initialize(maxSize, objective, goalIndex)
+      super(maxSize, objective)
+      @index = goalIndex
+    end
+    def is_better_than?(candidate1, candidate2)
+      @objective.is_better_than_for_goal?(@index, candidate1, candidate2)
+    end
+    def sort_top_list
+      @top_list.sort_by {|c| 
+        qv = @objective.quality_of(c)
+        qv.sub_quality(@index, true) # We want the sub quality value posed as a minimization goal regardless of whether it is a min or max goal
+      }
+    end
+  end
+end
+
+end

data/lib/feldtruby/optimize/differential_evolution.rb

@@ -70,11 +70,11 @@ class DEOptimizerBase < EvolutionaryOptimizer
 				}, "DE (step #{@num_optimization_steps}): Trial vector was better than target vector"
 			update_candidate_in_population(target_index, trial)
 			feedback_on_trial_vs_target(trial, target, true)
+			[best]
 		else
 			feedback_on_trial_vs_target(trial, target, false)
+			[]
 		end
-
-		[best]
 	end
 
 	#####################################

data/lib/feldtruby/optimize/objective.rb

@@ -163,6 +163,13 @@ class Objective
 
   end
 
+  # Invalidate the current quality object to ensure it will be recalculated
+  # the next time quality_of is called with this candidate. This is needed
+  # when there is a new best candidate set in an Archive, for example.
+  def invalidate_quality_of(candidate)
+    update_quality_value_in_object candidate, nil
+  end
+
   # Rank candidates from best to worst. Candidates that have the same quality
   # are randomly ordered.
   def rank_candidates(candidates, weights = self.weights)
@@ -510,4 +517,21 @@ class ObjectiveMaximizeBlock < Objective
   end
 end
 
+# A diversity objective often is a secondary goal and is measured relative
+# to quality goals/objectives or relative to candidates in the archive.
+# Thus it needs to have access to these other two objects.
+class DiversityObjective < Objective
+  attr_accessor :archive
+  attr_accessor :quality_objective
+end
+
+# The standard diversity objective is to just use the Euclidean distance
+# to the best candidate found so far.
+class FeldtRuby::Optimize::EuclideanDistanceToBest < FeldtRuby::Optimize::DiversityObjective
+  # Euclidean distance to best candidate. Genotype diversity.
+  def goal_max_euclidean_distance_to_best(candidate)
+    candidate.rms_from(archive.best)
+  end
+end
+
 end

data/lib/feldtruby/optimize/optimizer.rb

@@ -2,6 +2,7 @@ require 'feldtruby/optimize'
 require 'feldtruby/optimize/objective'
 require 'feldtruby/optimize/search_space'
 require 'feldtruby/optimize/max_steps_termination_criterion'
+require 'feldtruby/optimize/archive'
 require 'feldtruby/math/rand'
 require 'feldtruby/array'
 require 'feldtruby/logger'
@@ -13,14 +14,15 @@ module FeldtRuby::Optimize
 class Optimizer
 	include FeldtRuby::Logging
 
-	attr_reader :options, :objective, :search_space, :best, :best_quality_value
-	attr_reader :best_sub_quality_values, :num_optimization_steps, :termination_criterion
+	attr_reader :options, :objective, :search_space, :archive
+	attr_reader :num_optimization_steps, :termination_criterion
 
 	def initialize(objective, searchSpace = FeldtRuby::Optimize::DefaultSearchSpace, options = {})
-		@best = nil # To avoid warnings if not set
 		@objective, @search_space = objective, searchSpace
 		@options = FeldtRuby::Optimize.override_default_options_with(options)
 
+		init_archive
+
 		# Must setup logger before setting options since verbosity of logger is
 		# an option!
 		setup_logger_and_distribute_to_instance_variables(options)
@@ -28,6 +30,28 @@ class Optimizer
 		initialize_options(@options)
 	end
 
+	def init_archive
+		if @options[:archive]
+
+			@archive = @options[:archive]
+
+		else
+
+			if @options[:archiveDiversityObjective]
+				diversity_objective = @options[:archiveDiversityObjective]
+			else
+				diversity_objective = @options[:archiveDiversityObjectiveClass].new
+			end
+		
+			@archive = @options[:archiveClass].new(@objective, diversity_objective)
+
+		end
+	end
+
+	def best
+		@archive.best
+	end
+
 	def initialize_options(options)
 		self.logger.verbose = options[:verbose]
 		@termination_criterion = options[:terminationCriterion]
@@ -37,15 +61,18 @@ class Optimizer
 	def optimize()
 		logger.log "Optimization with optimizer #{self.class.inspect} started"
 		@num_optimization_steps = 0
-		# Set up a random best since other methods require it
-		update_best([search_space.gen_candidate()])
+
+		# Set up a random best for now that we can later compare to.
+		update_archive [search_space.gen_candidate()]
+
 		begin
 			while !termination_criterion.terminate?(self)
 				new_candidates = optimization_step()
 				@num_optimization_steps += 1
-				update_best(new_candidates)
+				update_archive new_candidates
 			end
 		rescue Exception => e
+			puts e.inspect
 			logger.log_data :exception, {
 				:exception_class => e.class.inspect, 
 				:backtrace => e.backtrace.join("\n")
@@ -53,16 +80,18 @@ class Optimizer
 		ensure
 			logger.log "!!! - Optimization FINISHED after #{@num_optimization_steps} steps - !!!"
 		end
+
 		@objective.note_end_of_optimization(self)
 		log_end_of_optimization
-		@best # return the best
+
+		archive.best # return the best
 	end
 
 	def log_end_of_optimization
 		logger.log("End of optimization\n" + 
 			"  Optimizer: #{self.class}\n" +
-			"  Best found: #{@best}\n" +
-			"  Quality of best: #{@objective.quality_of(@best)}\n" +
+			"  Best found: #{@archive.best}\n" +
+			"  Quality of best: #{@objective.quality_of(@archive.best)}\n" +
 			"  Time used = #{Time.human_readable_timestr(logger.elapsed_time)}, " + 
 			  "Steps performed = #{@num_optimization_steps}, " + 
 			  "#{Time.human_readable_timestr(time_per_step, true)}/step")
@@ -77,21 +106,10 @@ class Optimizer
 	def optimization_step()
 	end
 
-	# Update the best if a new best was found.
-	def update_best(candidates)
-		best_new, rest = objective.rank_candidates(candidates)
-		if @best.nil? || @objective.is_better_than?(best_new, @best)
-			qb = @best.nil? ? nil : @objective.quality_of(@best)
-			logger.log_data :new_best, {
-				"New best" => best_new,
-				"New quality" => @objective.quality_of(best_new), 
-				"Old best" => @best,
-				"Old quality" => qb}, "Optimizer (step #{@num_optimization_steps}): New best solution found", true
-			@best = best_new
-			true
-		else
-			false
-		end
+	# Update the archive with newly found candidates. Array of candidates may be empty if
+	# no new candidates found.
+	def update_archive(candidates)
+		candidates.each {|c| @archive.add(c)}
 	end
 end
 
@@ -211,7 +229,11 @@ DefaultOptimizationOptions = {
 	:verbose => true,
 	:populationSize => 100,
 	:samplerClass => FeldtRuby::Optimize::RadiusLimitedPopulationSampler,
-	:samplerRadius => 8 # Max distance between individuals selected in same tournament.
+	:samplerRadius => 8, # Max distance between individuals selected in same tournament.
+	:archive => nil, # If this is set it takes precedence over archiveClass.
+	:archiveClass => FeldtRuby::Optimize::Archive,
+	:archiveDiversityObjective => nil, # If this is set it takes precedence over the class in archiveDiversityObjectiveClass
+	:archiveDiversityObjectiveClass => FeldtRuby::Optimize::EuclideanDistanceToBest,
 }
 
 def self.override_default_options_with(options)

data/lib/feldtruby/version.rb

@@ -1,3 +1,3 @@
 module FeldtRuby
-  VERSION = "0.4.9"
+  VERSION = "0.4.10"
 end

data/test/test_optimize_archive.rb

@@ -0,0 +1,218 @@
+require 'feldtruby/optimize/archive'
+
+class TwoMinOneMax < FeldtRuby::Optimize::Objective
+  def objective_min_1(x)
+    x.sum
+  end
+
+  def objective_min_2(x)
+    x.max
+  end
+
+  def objective_max_1(x)
+    x.min
+  end
+end
+
+class DivObj2 < FeldtRuby::Optimize::EuclideanDistanceToBest
+  # Diversity goal 2: AMGA2 crowding distance to nearest neighbours in fitness 
+  # space. Phenotype diversity.
+  def goal_max_crowding_distance_to_nearest_neighbours(candidate)
+    # FIX: Below we need to handle the case where the candidate is an extremal
+    # solution and thus only has one nearest neighbour. Give it very high diversity?
+    nn1, nn2 = archive.find_nearest_neighbours_in_fitness(candidate)
+    sqv1 = archive.objective.quality_of(nn1).sub_qualitites
+    sqv2 = archive.objective.quality_of(nn2).sub_qualitites
+    sqvme = archive.objective.quality_of(candidate).sub_qualitites
+    ((sqv1 - sqvme) * (sqv2 - sqvme)).abs.sum
+  end
+end
+
+describe "Archive" do
+  before do
+    @o = TwoMinOneMax.new(FeldtRuby::Optimize::Objective::WeightedSumAggregator.new)
+    @do = FeldtRuby::Optimize::EuclideanDistanceToBest.new(FeldtRuby::Optimize::Objective::WeightedSumAggregator.new)
+    @a = FeldtRuby::Optimize::Archive.new(@o, @do, {
+    :NumTopPerGoal => 2,
+    :NumTopAggregate => 3,
+    :NumTopDiversityAggregate => 2})
+  end
+
+  it 'is adapted to objectives when created' do
+    @a.objective.must_equal @o
+    @a.diversity_objective.must_equal @do
+    @a.specialists.length.must_equal @o.num_goals
+    @a.generalists.must_be_kind_of FeldtRuby::Optimize::Archive::GlobalTopList
+    @a.weirdos.must_be_kind_of FeldtRuby::Optimize::Archive::GlobalTopList
+  end
+
+  it 'does not yet have a best value when created' do
+    @a.best.must_equal nil
+  end
+
+  it 'properly handles additions' do
+    i1 = [1,2,3]
+    @a.add i1 # [6, 3, 1] => 10
+
+    @a.best.must_equal i1
+
+    @a.generalists.length.must_equal 1
+    @a.generalists[0].must_equal i1
+
+    @a.specialists[0].length.must_equal 1
+    @a.specialists[1].length.must_equal 1
+    @a.specialists[2].length.must_equal 1
+
+    @a.weirdos.length.must_equal 0
+
+    i2 = [1,2,4]
+    @a.add i2 # [7, 4, 1] => 12
+
+    @a.best.must_equal i1
+
+    @a.generalists.length.must_equal 2
+    @a.generalists[0].must_equal i1
+    @a.generalists[1].must_equal i2
+
+    @a.specialists[0].length.must_equal 2
+    @a.specialists[1].length.must_equal 2
+    @a.specialists[2].length.must_equal 2
+    @a.specialists[0][0].must_equal i1
+    @a.specialists[0][1].must_equal i2
+    @a.specialists[1][0].must_equal i1
+    @a.specialists[1][1].must_equal i2
+
+    @a.weirdos.length.must_equal 0
+
+    i3 = [1,2,0] # [3, 2, 0] => 5
+    @a.add i3
+
+    @a.best.must_equal i3
+    @a.generalists.length.must_equal 3
+    @a.generalists[0].must_equal i3
+    @a.generalists[1].must_equal i1
+    @a.generalists[2].must_equal i2
+
+    @a.specialists[0].length.must_equal 2
+    @a.specialists[1].length.must_equal 2
+    @a.specialists[2].length.must_equal 2
+    @a.specialists[0][0].must_equal i3
+    @a.specialists[0][1].must_equal i1
+    @a.specialists[1][0].must_equal i3
+    @a.specialists[1][1].must_equal i1
+
+    @a.weirdos.length.must_equal 0
+
+    # Introduce a new baddest one
+    i4 = [5,5,10] # [20, 10, 5] => 35
+    @a.add i4
+
+    @a.best.must_equal i3
+    @a.generalists.length.must_equal 3
+    @a.generalists[0].must_equal i3
+    @a.generalists[1].must_equal i1
+    @a.generalists[2].must_equal i2
+
+    @a.specialists[0].length.must_equal 2
+    @a.specialists[1].length.must_equal 2
+    @a.specialists[2].length.must_equal 2
+    @a.specialists[0][0].must_equal i3
+    @a.specialists[0][1].must_equal i1
+    @a.specialists[1][0].must_equal i3
+    @a.specialists[1][1].must_equal i1
+
+    @a.weirdos.length.must_equal 0
+
+    # Introduce a new 2nd best
+    i5 = [3,0,1] # [4, 3, 0] => 7
+    @a.add i5
+
+    @a.best.must_equal i3
+    @a.generalists.length.must_equal 3
+    @a.generalists[0].must_equal i3
+    @a.generalists[1].must_equal i5
+    @a.generalists[2].must_equal i1
+
+    @a.specialists[0].length.must_equal 2
+    @a.specialists[1].length.must_equal 2
+    @a.specialists[2].length.must_equal 2
+    @a.specialists[0][0].must_equal i3
+    @a.specialists[0][1].must_equal i5
+    @a.specialists[1][0].must_equal i3
+    @a.specialists[1][1].must_equal i1
+
+    @a.weirdos.length.must_equal 0
+
+    # Introduce 2 new that is close to best and goes into top list but also into
+    # weirdos.
+    i6 = [1.05,2.05,0] # [3.1, 2.05, 0] => 5.15
+    @a.add i6
+
+    i7 = [1.01,2.00,0.10] # [3.11, 2.00, 0.1] => 5.01
+    @a.add i7
+
+    @a.best.must_equal i3
+    @a.generalists.length.must_equal 3
+    @a.generalists[0].must_equal i3
+    @a.generalists[1].must_equal i7
+    @a.generalists[2].must_equal i6
+
+    @a.specialists[0].length.must_equal 2
+    @a.specialists[1].length.must_equal 2
+    @a.specialists[2].length.must_equal 2
+    @a.specialists[0][0].must_equal i3
+    @a.specialists[0][1].must_equal i6
+    @a.specialists[1][0].must_equal i3
+    @a.specialists[1][1].must_equal i7
+
+    @a.weirdos.length.must_equal 2
+    @a.weirdos[0].must_equal i7
+    @a.weirdos[1].must_equal i6
+
+    # Introduce one weird which is not good enough to go into the generalists
+    # or specialists but goes on top of weirdos.
+    i8 = [1.03, 2.10, 0.1] # [3.23, 2.10, 0.1] => 5.23
+    @a.good_enough_quality_to_be_interesting?(i8).must_equal true
+    @a.add i8
+
+    @a.best.must_equal i3
+    @a.generalists.length.must_equal 3
+    @a.generalists[0].must_equal i3
+    @a.generalists[1].must_equal i7
+    @a.generalists[2].must_equal i6
+
+    @a.specialists[0].length.must_equal 2
+    @a.specialists[1].length.must_equal 2
+    @a.specialists[2].length.must_equal 2
+    @a.specialists[0][0].must_equal i3
+    @a.specialists[0][1].must_equal i6
+    @a.specialists[1][0].must_equal i3
+    @a.specialists[1][1].must_equal i7
+
+    @a.weirdos.length.must_equal 2
+    @a.weirdos[0].must_equal i8
+    @a.weirdos[1].must_equal i7
+
+    # Less weird than i8 but still goes into weirdos.
+    i9 = [1.04, 2.08, 0.05] # [3.17, 2.08, 0.05] => 5.20
+    @a.add i9
+
+    @a.best.must_equal i3
+    @a.generalists.length.must_equal 3
+    @a.generalists[0].must_equal i3
+    @a.generalists[1].must_equal i7
+    @a.generalists[2].must_equal i6
+
+    @a.specialists[0].length.must_equal 2
+    @a.specialists[1].length.must_equal 2
+    @a.specialists[2].length.must_equal 2
+    @a.specialists[0][0].must_equal i3
+    @a.specialists[0][1].must_equal i6
+    @a.specialists[1][0].must_equal i3
+    @a.specialists[1][1].must_equal i7
+
+    @a.weirdos.length.must_equal 2
+    @a.weirdos[0].must_equal i8
+    @a.weirdos[1].must_equal i9
+  end
+end

metadata

@@ -1,83 +1,94 @@
 --- !ruby/object:Gem::Specification
 name: feldtruby
 version: !ruby/object:Gem::Version
-  version: 0.4.9
+  version: 0.4.10
+  prerelease: 
 platform: ruby
 authors:
 - Robert Feldt
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-11 00:00:00.000000000 Z
+date: 2013-04-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rinruby
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: mongo
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: bson_ext
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '>='
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: Robert Feldt's Common Ruby Code lib
@@ -112,8 +123,8 @@ files:
 - lib/feldtruby/mongodb_logger.rb
 - lib/feldtruby/net/html_doc_getter.rb
 - lib/feldtruby/optimize.rb
+- lib/feldtruby/optimize/archive.rb
 - lib/feldtruby/optimize/differential_evolution.rb
-- lib/feldtruby/optimize/elite_archive.rb
 - lib/feldtruby/optimize/max_steps_termination_criterion.rb
 - lib/feldtruby/optimize/objective.rb
 - lib/feldtruby/optimize/optimizer.rb
@@ -167,8 +178,8 @@ files:
 - test/test_normalization.rb
 - test/test_object_annotations.rb
 - test/test_optimize.rb
+- test/test_optimize_archive.rb
 - test/test_optimize_differential_evolution.rb
-- test/test_optimize_elite_archive.rb
 - test/test_optimize_objective.rb
 - test/test_optimize_populationbasedoptimizer.rb
 - test/test_optimize_random_search.rb
@@ -185,26 +196,27 @@ files:
 - test/tmp_shorter.csv
 homepage: https://github.com/robertfeldt/feldtruby
 licenses: []
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - '>='
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.0
+rubygems_version: 1.8.25
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Robert Feldt's Common Ruby Code lib
 test_files:
 - test/helper.rb
@@ -226,8 +238,8 @@ test_files:
 - test/test_normalization.rb
 - test/test_object_annotations.rb
 - test/test_optimize.rb
+- test/test_optimize_archive.rb
 - test/test_optimize_differential_evolution.rb
-- test/test_optimize_elite_archive.rb
 - test/test_optimize_objective.rb
 - test/test_optimize_populationbasedoptimizer.rb
 - test/test_optimize_random_search.rb

checksums.yaml

@@ -1,7 +0,0 @@
----
-SHA1:
-  metadata.gz: 649d3dfa9702ca3b927e1f439220f1aeed6ca970
-  data.tar.gz: 3bc58c5d5c11417907254bc22d4b974b1725bed6
-SHA512:
-  metadata.gz: e02ff98f8487db6542dc5d9d86c53d7e1a8e228b872d2a1e51f075fcc6b8f4ad2025d5123d1e8f2e84a3ee7efc72b4fce411464696e8181e07a8227fbbd06f0e
-  data.tar.gz: 79e5b1e5ee1cd35181e3675c159d242a9cd1861218f361a6b545f4753b38af329427dd28d1b2d83c690aebe96d915e97c3894d24c71d1ddca8da689c0f39040e

data/lib/feldtruby/optimize/elite_archive.rb

@@ -1,91 +0,0 @@
-require 'feldtruby/optimize'
-
-module FeldtRuby::Optimize
-
-# This keeps a record of the best/elite candidate solutions found during
-# an optimization search. It keeps separate top lists per goal being optimized
-# as well as for the aggregate quality value (fitness) itself. The top lists
-# are all sorted to allow for fast checks and insertion.
-class EliteArchive
-  DefaultParams = {
-    :NumTopPerGoal => 10,
-    :NumTopAggregate => 25
-  }
-
-  attr_reader :objective, :top_per_goal, :best
-
-  def initialize(objective, options = DefaultParams.clone)
-    @objective = objective
-    @options = options
-    init_top_lists
-  end
-
-  # A top list is an array of a fixed size that saves the top candidates
-  # based on their quality values.
-  class GlobalTopList
-    def initialize(maxSize, objective)
-      @max_size =maxSize
-      @top_list = Array.new
-      @objective = objective
-    end
-    def length; @top_list.length; end
-
-    def [](index)
-      @top_list[index]
-    end
-
-    def add(candidate)
-      last = @top_list.last
-      #puts "In #{self},\nlast = #{last}, candidate = #{candidate}, top_list = #{@top_list}"
-      if @top_list.length < @max_size || last.nil? || is_better_than?(candidate, last)
-        @top_list.pop if @top_list.length >= @max_size
-        @top_list << candidate
-        @top_list = sort_top_list
-      end
-      #puts "top_list = #{@top_list}"
-    end
-
-    def is_better_than?(candidate1, candidate2)
-      @objective.is_better_than?(candidate1, candidate2)
-    end
-
-    def sort_top_list
-      @top_list.sort_by {|c| @objective.quality_of(c).value}
-    end
-
-    def inspect
-      self.class.inspect + @top_list.inspect
-    end
-  end
-
-  class GoalTopList < GlobalTopList
-    def initialize(maxSize, objective, goalIndex)
-      super(maxSize, objective)
-      @index = goalIndex
-    end
-    def is_better_than?(candidate1, candidate2)
-      @objective.is_better_than_for_goal?(@index, candidate1, candidate2)
-    end
-    def sort_top_list
-      @top_list.sort_by {|c| 
-        qv = @objective.quality_of(c)
-        qv.sub_quality(@index, true) # We want the sub quality value posed as a minimization goal regardless of whether it is a min or max goal
-      }
-    end
-  end
-
-  def init_top_lists
-    @top_per_goal = Array.new
-    @objective.num_goals.times do |i|
-      @top_per_goal << GoalTopList.new(@options[:NumTopPerGoal], @objective, i)
-    end
-    @best = GlobalTopList.new(@options[:NumTopAggregate], @objective)
-  end
-
-  def add(candidate)
-    @best.add candidate
-    @top_per_goal.each {|tl| tl.add(candidate)}
-  end
-end
-
-end

data/test/test_optimize_elite_archive.rb

@@ -1,85 +0,0 @@
-require 'feldtruby/optimize/elite_archive'
-
-class TwoMinOneMax < FeldtRuby::Optimize::Objective
-  def objective_min_1(x)
-    x.sum
-  end
-
-  def objective_min_2(x)
-    x.max
-  end
-
-  def objective_max_1(x)
-    x.min
-  end
-end
-
-describe "EliteArchive" do
-  before do
-    @o = TwoMinOneMax.new(FeldtRuby::Optimize::Objective::WeightedSumAggregator.new)
-    @a = FeldtRuby::Optimize::EliteArchive.new(@o, {
-    :NumTopPerGoal => 2,
-    :NumTopAggregate => 3})
-  end
-
-  it 'is adapted to an objective when created' do
-    @a.objective.must_equal @o
-    @a.top_per_goal.length.must_equal @o.num_goals
-  end
-
-  it 'properly handles additions' do
-    i1 = [1,2,3]
-    @a.add i1 # [6, 3, 1] => 8
-    @a.best.length.must_equal 1
-    @a.top_per_goal[0].length.must_equal 1
-    @a.top_per_goal[1].length.must_equal 1
-    @a.top_per_goal[2].length.must_equal 1
-
-    i2 = [1,2,4]
-    @a.add i2 # [7, 4, 1] => 10
-    @a.best.length.must_equal 2
-    @a.top_per_goal[0].length.must_equal 2
-    @a.top_per_goal[1].length.must_equal 2
-    @a.top_per_goal[2].length.must_equal 2
-    @a.top_per_goal[0][0].must_equal i1
-    @a.top_per_goal[0][1].must_equal i2
-    @a.top_per_goal[1][0].must_equal i1
-    @a.top_per_goal[1][1].must_equal i2
-
-    i3 = [1,2,0] # [3, 2, 0] => 5 
-    @a.add i3
-
-    @a.best.length.must_equal 3
-    @a.top_per_goal[0].length.must_equal 2
-    @a.top_per_goal[1].length.must_equal 2
-    @a.top_per_goal[2].length.must_equal 2
-
-    @a.best[0].must_equal i3
-    @a.best[1].must_equal i1
-    @a.best[2].must_equal i2
-
-    @a.top_per_goal[0][0].must_equal i3
-    @a.top_per_goal[0][1].must_equal i1
-
-    @a.top_per_goal[1][0].must_equal i3
-    @a.top_per_goal[1][1].must_equal i1
-
-    @a.top_per_goal[2][0].must_equal i1
-    @a.top_per_goal[2][1].must_equal i2
-
-    i4 = [5,5,10] # [20, 10, 5] => 25
-    @a.add i4
-
-    @a.best.length.must_equal 3
-    @a.top_per_goal[0].length.must_equal 2
-    @a.top_per_goal[1].length.must_equal 2
-    @a.top_per_goal[2].length.must_equal 2
-
-    @a.best[0].must_equal i3
-    @a.best[1].must_equal i1
-    @a.best[2].must_equal i2
-
-    @a.top_per_goal[2][0].must_equal i4
-    @a.top_per_goal[2][1].must_equal i1
-  end
-end