import argparse import os import sys import numpy as np from deap import creator, base, tools, algorithms from FramsticksLib import FramsticksLib # Note: this may be less efficient than running the evolution directly in Framsticks, so if performance is key, compare both options. # The list of criteria includes 'vertpos', 'velocity', 'distance', 'vertvel', 'lifespan', 'numjoints', 'numparts', 'numneurons', 'numconnections'. OPTIMIZATION_CRITERIA = ['vertpos'] # Single or multiple criteria. Names from the standard-eval.expdef dictionary, e.g. ['vertpos', 'velocity']. def frams_evaluate(frams_cli, individual): genotype = individual[0] # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str. data = frams_cli.evaluate([genotype]) # print("Evaluated '%s'" % genotype, 'evaluation is:', data) try: first_genotype_data = data[0] evaluation_data = first_genotype_data["evaluations"] default_evaluation_data = evaluation_data[""] fitness = [default_evaluation_data[crit] for crit in OPTIMIZATION_CRITERIA] except (KeyError, TypeError) as e: # the evaluation may have failed for an invalid genotype (such as X[@][@] with "Don't simulate genotypes with warnings" option) or for some other reason fitness = [-1] * len(OPTIMIZATION_CRITERIA) # fitness of -1 is intended to discourage further propagation of this genotype via selection ("this one is very poor") print("Error '%s': could not evaluate genotype '%s', returning fitness %s" % (str(e), genotype, fitness)) return fitness def frams_crossover(frams_cli, individual1, individual2): geno1 = individual1[0] # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str. geno2 = individual2[0] # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str. individual1[0] = frams_cli.crossOver(geno1, geno2) individual2[0] = frams_cli.crossOver(geno1, geno2) return individual1, individual2 def frams_mutate(frams_cli, individual): individual[0] = frams_cli.mutate([individual[0]])[0] # individual[0] because we can't (?) have a simple str as a deap genotype/individual, only list of str. return individual, def frams_getsimplest(frams_cli, genetic_format): return frams_cli.getSimplest(genetic_format) def prepareToolbox(frams_cli, genetic_format): creator.create("FitnessMax", base.Fitness, weights=[1.0] * len(OPTIMIZATION_CRITERIA)) creator.create("Individual", list, fitness=creator.FitnessMax) # would be nice to have "str" instead of unnecessary "list of str" toolbox = base.Toolbox() toolbox.register("attr_simplest_genotype", frams_getsimplest, frams_cli, genetic_format) # "Attribute generator" # (failed) struggle to have an individual which is a simple str, not a list of str # toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_frams) # https://stackoverflow.com/questions/51451815/python-deap-library-using-random-words-as-individuals # https://github.com/DEAP/deap/issues/339 # https://gitlab.com/santiagoandre/deap-customize-population-example/-/blob/master/AGbasic.py # https://groups.google.com/forum/#!topic/deap-users/22g1kyrpKy8 toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_simplest_genotype, 1) toolbox.register("population", tools.initRepeat, list, toolbox.individual) toolbox.register("evaluate", frams_evaluate, frams_cli) toolbox.register("mate", frams_crossover, frams_cli) toolbox.register("mutate", frams_mutate, frams_cli) if len(OPTIMIZATION_CRITERIA) <= 1: toolbox.register("select", tools.selTournament, tournsize=5) else: toolbox.register("select", tools.selNSGA2) return toolbox def parseArguments(): parser = argparse.ArgumentParser(description='Run this program with "python -u %s" if you want to disable buffering of its output.' % sys.argv[0]) parser.add_argument('-path', type=ensureDir, required=True, help='Path to Framsticks CLI without trailing slash.') parser.add_argument('-exe', required=False, help='Executable name. If not given, "frams.exe" or "frams.linux" is assumed.') parser.add_argument('-genformat', required=False, help='Genetic format for the demo run, for example 4, 9, or B. If not given, f1 is assumed.') return parser.parse_args() def ensureDir(string): if os.path.isdir(string): return string else: raise NotADirectoryError(string) if __name__ == "__main__": # A demo run: optimize OPTIMIZATION_CRITERIA # random.seed(123) # see FramsticksLib.DETERMINISTIC below, set to True if you want full determinism FramsticksLib.DETERMINISTIC = False # must be set before FramsticksLib() constructor call parsed_args = parseArguments() framsLib = FramsticksLib(parsed_args.path, parsed_args.exe) toolbox = prepareToolbox(framsLib, '1' if parsed_args.genformat is None else parsed_args.genformat) POPSIZE = 10 GENERATIONS = 100 pop = toolbox.population(n=POPSIZE) hof = tools.HallOfFame(5) stats = tools.Statistics(lambda ind: ind.fitness.values) stats.register("avg", np.mean) stats.register("stddev", np.std) stats.register("min", np.min) stats.register("max", np.max) print('Evolution with population size %d for %d generations, optimization criteria: %s' % (POPSIZE, GENERATIONS, OPTIMIZATION_CRITERIA)) pop, log = algorithms.eaSimple(pop, toolbox, cxpb=0.2, mutpb=0.9, ngen=GENERATIONS, stats=stats, halloffame=hof, verbose=True) print('Best individuals:') for best in hof: print(best.fitness, '\t-->\t', best[0])