Class: AgeHierarchyTree

Inherits:
AlgorithmBase show all
Defined in:
../algorithm/age_hierarchy_tree.rb

Instance Attribute Summary (collapse)

Attributes inherited from AlgorithmBase

#init, #population_size, #probabilities, #termination

Instance Method Summary (collapse)

Methods inherited from AlgorithmBase

#finished?, #teardown

Instance Attribute Details

- (Object) age_gap

Returns the value of attribute age_gap 



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# File '../algorithm/age_hierarchy_tree.rb', line 91

def age_gap
  @age_gap
end

- (Object) aging_scheme

Returns the value of attribute aging_scheme 



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# File '../algorithm/age_hierarchy_tree.rb', line 91

def aging_scheme
  @aging_scheme
end

- (Object) deme_size

Returns the value of attribute deme_size 



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# File '../algorithm/age_hierarchy_tree.rb', line 91

def deme_size
  @deme_size
end

- (Object) dominance (readonly)

Returns the value of attribute dominance 



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# File '../algorithm/age_hierarchy_tree.rb', line 92

def dominance
  @dominance
end

- (Object) elite_size

Returns the value of attribute elite_size 



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# File '../algorithm/age_hierarchy_tree.rb', line 91

def elite_size
  @elite_size
end

- (Object) layer_diagnostic

Returns the value of attribute layer_diagnostic 



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# File '../algorithm/age_hierarchy_tree.rb', line 91

def layer_diagnostic
  @layer_diagnostic
end

- (Object) max_layers

Returns the value of attribute max_layers 



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# File '../algorithm/age_hierarchy_tree.rb', line 91

def max_layers
  @max_layers
end

- (Object) report

Returns the value of attribute report 



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# File '../algorithm/age_hierarchy_tree.rb', line 91

def report
  @report
end

Instance Method Details

- (Object) breeding(parents) 



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# File '../algorithm/age_hierarchy_tree.rb', line 174

def breeding( parents ) 

 layer = sort_spea2( parents )

  # xover, mutations
  children = []   
  while children.size + @elite_size  < @deme_size
   
    parent1 = tournament(layer)  # assuming the layer is sorted 

    if rand < @probabilities['crossover']

      parent2 = tournament(layer)

      child1, child2 = @crossover.crossover( 
                            parent1.genotype, parent2.genotype, 
                            parent1.track_support, parent2.track_support ) 

      individual = @cfg.factory( 'individual', @mapper, child1 ) 
      individual.parents( parent1, parent2 )
      @invalid_individuals += 1 unless individual.valid?       
      children << individual if individual.valid? 
     

      individual = @cfg.factory( 'individual', @mapper, child2 ) 
      individual.parents( parent1, parent2 )  
      @invalid_individuals += 1 unless individual.valid?       
      children << individual if individual.valid?

    end

    if rand < @probabilities['mutation']

      child = @mutation.mutation( parent1.genotype, parent1.track_support )

      individual = @cfg.factory( 'individual', @mapper, child ) 
      individual.parents( parent1 )       
      @invalid_individuals += 1 unless individual.valid?       
      children << individual if individual.valid?
      
    end

  end

  @evaluator.run children if defined? @evaluator
  children
end

- (Object) init_deme 



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# File '../algorithm/age_hierarchy_tree.rb', line 170

def init_deme
  init_population( [], @deme_size ) 
end

- (Object) setup(config) 



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# File '../algorithm/age_hierarchy_tree.rb', line 94

def setup config
  super
   
  AlpsIndividual.age_gap @age_gap
  AlpsIndividual.aging_scheme @aging_scheme
  AlpsIndividual.layers @max_layers
  @report['age_limits'] << AlpsIndividual.age_limits.inspect

  SubPopulation.set_algo self

  @dominance = Dominance.new
  @population = []
  @parents_stats = []

  @layers = [[ SubPopulation.new ]]

  @report.next    
  return @report    
end

- (Object) sort_spea2(unsorted) 



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# File '../algorithm/age_hierarchy_tree.rb', line 222

def sort_spea2 unsorted
  # sort a layer by pareto strength        
  layer = @dominance.rank_count( unsorted ).sort {|a,b| a.spea <=> b.spea }
    
  # extract individuals from dominance's shell     
  layer.map! { |fields| fields.original } 

  layer
end

- (Object) step 



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# File '../algorithm/age_hierarchy_tree.rb', line 114

def step
  @report << "--------- step #{@steps}"
  
  if AlpsIndividual.age_limits.include? @steps

      @report << "--------- opening a new layer"       

      @layers.flatten.each { |deme| deme.level += 1 }
      new_layer = []
      @layers.first.each do |parent|
         new_layer << SubPopulation.new(parent)
         new_layer << SubPopulation.new(parent)
      end
      @layers.unshift new_layer

  elsif @steps>0
     
      reminder = @steps.divmod(@age_gap).last
      @layers.first.each_with_index do |deme,index|
         next unless reminder == index.divmod(@age_gap).last
         @report << "--------- restarting a deme #{deme.name}, index=#{index}"
         deme.restart
      end

  end

  # reporting
  @population = []
  @layers.flatten.each { |deme| @population.concat deme.current }
  @report.report @population
 
  # breeding
  @layers.flatten.each { |deme| deme.breed }

  # pde, copying...
  @layers.flatten.each { |deme| deme.environmental }   

  # layer diagnostic
  @report['deme_sizes'] << (@layers.flatten.map { |layer| layer.current.size }).inspect
  @layers.flatten.each_with_index do |deme,index| 
    current = deme.current     
    current.first.objective_symbols.each do |objective|     
      values = current.map { |individual| individual.send(objective) }   
      min, max, avg, n = Util.statistics values  
      @report["deme_#{deme.name}_#{objective}"] << "min: #{min} max: #{max} avg: #{avg} n: #{n}"
    end
  end if @layer_diagnostic

  @report['numof_evaluations'] << @evaluator.jobs_processed if defined? @evaluator   
  @report['individuals_generated'] << @mapper.mapped_count
  
  @steps += 1   
  @report.next 
  return @report    
end