[1113] | 1 | import argparse |
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| 2 | import os |
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| 3 | import sys |
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| 4 | from enum import Enum |
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| 5 | |
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| 6 | import numpy as np |
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| 7 | |
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| 8 | from FramsticksLib import FramsticksLib |
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| 9 | from evolalg.base.lambda_step import LambdaStep |
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| 10 | from evolalg.dissimilarity.frams_dissimilarity import FramsDissimilarity |
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| 11 | from evolalg.dissimilarity.levenshtein import LevenshteinDissimilarity |
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| 12 | from evolalg.experiment import Experiment |
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| 13 | from evolalg.fitness.fitness_step import FitnessStep |
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| 14 | from evolalg.mutation_cross.frams_cross_and_mutate import FramsCrossAndMutate |
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| 15 | from evolalg.population.frams_population import FramsPopulation |
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| 16 | from evolalg.repair.remove.field import FieldRemove |
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| 17 | from evolalg.repair.remove.remove import Remove |
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| 18 | from evolalg.selection.tournament import TournamentSelection |
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| 19 | from evolalg.statistics.halloffame_stats import HallOfFameStatistics |
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| 20 | from evolalg.statistics.statistics_deap import StatisticsDeap |
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| 21 | from evolalg.base.union_step import UnionStep |
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| 22 | from evolalg.utils.population_save import PopulationSave |
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| 23 | |
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| 24 | |
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| 25 | def ensureDir(string): |
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| 26 | if os.path.isdir(string): |
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| 27 | return string |
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| 28 | else: |
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| 29 | raise NotADirectoryError(string) |
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| 30 | |
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| 31 | |
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| 32 | class Dissim(Enum): |
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| 33 | levenshtein = "levenshtein" |
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| 34 | frams = "frams" |
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| 35 | |
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| 36 | def __str__(self): |
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| 37 | return self.name |
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| 38 | |
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| 39 | |
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| 40 | class Fitness(Enum): |
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| 41 | raw = "raw" |
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| 42 | niching = "niching" |
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| 43 | novelty = "novelty" |
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| 44 | |
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| 45 | def __str__(self): |
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| 46 | return self.name |
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| 47 | |
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| 48 | |
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| 49 | def parseArguments(): |
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| 50 | parser = argparse.ArgumentParser( |
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| 51 | description='Run this program with "python -u %s" if you want to disable buffering of its output.' % sys.argv[ |
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| 52 | 0]) |
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| 53 | parser.add_argument('-path', type=ensureDir, required=True, help='Path to Framsticks without trailing slash.') |
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| 54 | parser.add_argument('-opt', required=True, |
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| 55 | help='optimization criteria : vertpos, velocity, distance, vertvel, lifespan, numjoints, numparts, numneurons, numconnections. Single or multiple criteria.') |
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| 56 | parser.add_argument('-lib', required=False, help="Filename of .so or .dll with framsticks library") |
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| 57 | parser.add_argument('-genformat', required=False, default="1", |
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| 58 | help='Genetic format for the demo run, for example 4, 9, or B. If not given, f1 is assumed.') |
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| 59 | parser.add_argument('-sim', required=False, default="eval-allcriteria.sim", help="Name of .sim file") |
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| 60 | parser.add_argument('-dissim', required=False, type=Dissim, default=Dissim.frams, |
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| 61 | help=' Dissimilarity measure DEFAULT = frams', choices=list(Dissim)) |
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| 62 | parser.add_argument('-fit', required=False, default=Fitness.raw, type=Fitness, |
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| 63 | help=' Fitness criteria DEFAULT = raw', choices=list(Fitness)) |
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| 64 | parser.add_argument('-popsize', type=int, default=50, help="Size of population, default 50.") |
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| 65 | parser.add_argument('-num_parts', type=int, default=None, help="Maximum number of parts. Default None") |
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| 66 | parser.add_argument('-checkpoint_path', required=False, default=None, help="Path to checkpoint path") |
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| 67 | parser.add_argument('-checkpoint_interval', required=False, type=int, default=100, help="Checkpoint interval") |
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| 68 | return parser.parse_args() |
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| 69 | |
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| 70 | |
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| 71 | def extract_fitness(ind): |
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| 72 | return ind.fitness_raw |
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| 73 | |
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| 74 | |
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| 75 | def print_population_count(pop): |
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| 76 | print("Current:", len(pop)) |
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| 77 | return pop # Each step must return a population |
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| 78 | |
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| 79 | |
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| 80 | class NumPartsGreater(Remove): |
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| 81 | def __init__(self, numparts): |
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| 82 | super(NumPartsGreater, self).__init__() |
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| 83 | self.numparts = numparts |
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| 84 | |
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| 85 | def remove(self, individual): |
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| 86 | return individual.numparts > self.numparts |
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| 87 | |
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| 88 | |
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| 89 | def func_niching(ind): setattr(ind, "fitness", ind.fitness_raw * (1 + ind.dissim)) |
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| 90 | |
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| 91 | |
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| 92 | def func_raw(ind): setattr(ind, "fitness", ind.fitness_raw) |
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| 93 | |
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| 94 | |
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| 95 | def func_novelty(ind): setattr(ind, "fitness", ind.dissim) |
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| 96 | |
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| 97 | |
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| 98 | def main(): |
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| 99 | print("Running experiment with", sys.argv) |
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| 100 | parsed_args = parseArguments() |
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| 101 | frams = FramsticksLib(parsed_args.path, parsed_args.lib, |
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| 102 | parsed_args.sim) |
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| 103 | # Steps for generating first population |
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| 104 | init_stages = [FramsPopulation(frams, parsed_args.genformat, parsed_args.popsize)] |
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| 105 | |
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| 106 | # Selection procedure |
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| 107 | selection = TournamentSelection(5, copy=True) # 'fitness' by default, the targeted attribute can be changed, e.g. fit_attr="fitness_raw" |
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| 108 | |
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| 109 | # Procedure for generating new population. This steps will be run as long there is less than |
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| 110 | # popsize individuals in the new population |
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| 111 | new_generation_stages = [FramsCrossAndMutate(frams, cross_prob=0.2, mutate_prob=0.9)] |
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| 112 | |
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| 113 | # Steps after new population is created. Executed exacly once per generation. |
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| 114 | generation_modifications = [] |
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| 115 | |
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| 116 | # ------------------------------------------------- |
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| 117 | # Fitness |
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| 118 | |
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| 119 | fitness_raw = FitnessStep(frams, fields={parsed_args.opt: "fitness_raw", "numparts": "numparts"}, |
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| 120 | fields_defaults={parsed_args.opt: None, "numparts": float("inf")}, |
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| 121 | evaluation_count=1) |
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| 122 | |
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| 123 | fitness_end = FitnessStep(frams, fields={parsed_args.opt: "fitness_raw"}, |
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| 124 | fields_defaults={parsed_args.opt: None}, |
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| 125 | evaluation_count=100) # evaluate the contents of the last population 100 times (TODO replace this approach and evaluate HOF instead of the last population) |
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| 126 | # Remove |
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| 127 | remove = [] |
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| 128 | remove.append(FieldRemove("fitness_raw", None)) # Remove individuals if they have default value for fitness |
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| 129 | if parsed_args.num_parts is not None: |
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| 130 | # This could be also implemented by "LambdaRemove(lambda x: x.numparts > parsed_args.num_parts) |
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| 131 | # But this will not serialize in checkpoint. |
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| 132 | remove.append(NumPartsGreater(parsed_args.num_parts)) |
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| 133 | remove_step = UnionStep(remove) |
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| 134 | |
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| 135 | fitness_remove = UnionStep([fitness_raw, remove_step]) |
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| 136 | |
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| 137 | init_stages.append(fitness_remove) |
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| 138 | new_generation_stages.append(fitness_remove) |
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| 139 | |
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| 140 | # ------------------------------------------------- |
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| 141 | # Novelty or niching |
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| 142 | dissim = None |
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| 143 | if parsed_args.dissim == Dissim.levenshtein: |
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| 144 | dissim = LevenshteinDissimilarity(reduction="mean", output_field="dissim") |
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| 145 | elif parsed_args.dissim == Dissim.frams: |
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| 146 | dissim = FramsDissimilarity(frams, reduction="mean", output_field="dissim") |
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| 147 | |
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| 148 | if parsed_args.fit == Fitness.raw: |
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| 149 | # Fitness is equal to finess raw |
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| 150 | raw = LambdaStep(func_raw) |
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| 151 | init_stages.append(raw) |
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| 152 | new_generation_stages.append(raw) |
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| 153 | generation_modifications.append(raw) |
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| 154 | |
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| 155 | if parsed_args.fit == Fitness.niching: |
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| 156 | niching = UnionStep([ |
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| 157 | dissim, |
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| 158 | LambdaStep(func_niching) |
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| 159 | ]) |
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| 160 | init_stages.append(niching) |
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| 161 | new_generation_stages.append(niching) |
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| 162 | generation_modifications.append(niching) |
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| 163 | |
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| 164 | if parsed_args.fit == Fitness.novelty: |
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| 165 | novelty = UnionStep([ |
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| 166 | dissim, |
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| 167 | LambdaStep(func_novelty) |
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| 168 | ]) |
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| 169 | init_stages.append(novelty) |
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| 170 | new_generation_stages.append(novelty) |
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| 171 | generation_modifications.append(novelty) |
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| 172 | |
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| 173 | # ------------------------------------------------- |
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| 174 | # Statistics |
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| 175 | hall_of_fame = HallOfFameStatistics(100, "fitness_raw") # Wrapper for halloffamae |
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| 176 | statistics_deap = StatisticsDeap([ |
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| 177 | ("avg", np.mean), |
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| 178 | ("stddev", np.std), |
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| 179 | ("min", np.min), |
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| 180 | ("max", np.max) |
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| 181 | ], extract_fitness) # Wrapper for deap statistics |
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| 182 | |
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| 183 | statistics_union = UnionStep([ |
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| 184 | hall_of_fame, |
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| 185 | statistics_deap |
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| 186 | ]) # Union of two statistics steps. |
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| 187 | |
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| 188 | init_stages.append(statistics_union) |
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| 189 | generation_modifications.append(statistics_union) |
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| 190 | |
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| 191 | # ------------------------------------------------- |
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| 192 | # End stages: this will execute exacly once after all generations. |
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| 193 | end_stages = [ |
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| 194 | fitness_end, |
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| 195 | PopulationSave("halloffame.gen", provider=hall_of_fame.haloffame, fields={"genotype": "genotype", |
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| 196 | "fitness": "fitness_raw"})] |
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| 197 | # ...but custom fields can be added, e.g. "custom": "recording" |
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| 198 | |
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| 199 | # ------------------------------------------------- |
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| 200 | # Experiment creation |
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| 201 | |
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| 202 | experiment = Experiment(init_population=init_stages, |
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| 203 | selection=selection, |
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| 204 | new_generation_steps=new_generation_stages, |
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| 205 | generation_modification=generation_modifications, |
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| 206 | end_steps=end_stages, |
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| 207 | population_size=parsed_args.popsize, |
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| 208 | checkpoint_path=parsed_args.checkpoint_path, |
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| 209 | checkpoint_interval=parsed_args.checkpoint_interval |
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| 210 | ) |
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| 211 | experiment.init() # init is mandatory |
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| 212 | experiment.run(10) |
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| 213 | # Next call for experiment.run(10) will do nothing. Parameter 10 specifies how many generations should be |
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| 214 | # in one experiment. Previous call generated 10 generations. |
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| 215 | # Example 1: |
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| 216 | # experiment.init() |
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| 217 | # experiment.run(10) |
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| 218 | # experiment.run(12) |
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| 219 | # #This will run for total of 12 generations |
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| 220 | # |
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| 221 | # Example 2 |
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| 222 | # experiment.init() |
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| 223 | # experiment.run(10) |
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| 224 | # experiment.init() |
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| 225 | # experiment.run(10) |
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| 226 | # # All work produced by first run will be "destroyed" by second init(). |
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| 227 | |
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| 228 | for ind in hall_of_fame.haloffame: |
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| 229 | print("%g\t%s" % (ind.fitness, ind.genotype)) |
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| 230 | |
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| 231 | |
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| 232 | if __name__ == '__main__': |
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| 233 | main() |
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