def report():
print "\nNumber of runs: %s\n" % sys.argv[2]
print "\t Gen. \t Nodes \t Conn. \t Evals. \t Score \n"
print "average %3.2f \t %2.2f \t %2.2f \t %2.2f \t %2.2f" \
% (mean(total_gens), mean(total_nodes), mean(total_conns), mean(total_evals), mean(total_score))
print "stdev %3.2f \t %2.2f \t %2.2f \t %2.2f \t %2.2f" \
% (stdev(total_gens), stdev(total_nodes), stdev(total_conns), stdev(total_evals), stdev(total_score))
def post_evaluate(self, config, population, species, best_genome):
sparse_mean, sparse_dev = self.compute_sparseness(population)
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
distances = [c.dist for c in itervalues(population)]
dist_mean = mean(distances)
dist_std = stdev(distances)
best_species_id = species.get_species_id(best_genome.key)
with open(self.filename, "a+") as f:
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.
format(fit_mean, fit_std))
f.write(
'Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}\n'.
format(fit_mean, fit_std))
print('Population\'s diversity: {0:3.5f} stdev: {1:3.5f}'.format(
dist_mean, dist_std))
f.write(
'Population\'s diversity: {0:3.5f} stdev: {1:3.5f}\n'.format(
dist_mean, dist_std))
print('Population\'s sparseness: {0:3.5f} stdev: {1:3.5f}'.format(
sparse_mean, sparse_dev))
f.write(
'Population\'s sparseness: {0:3.5f} stdev: {1:3.5f}\n'.format(
sparse_mean, sparse_dev))
print('Best fitness: {}'.format(best_genome.fitness))
print(
'Best distance: {0:3.5f}\nSize: {1!r} - species {2} - id {3}'.
format(best_genome.dist, best_genome.size(), best_species_id,
best_genome.key))
f.write('Best fitness: {}\n'.format(best_genome.fitness))
f.write(
'Best distance: {0:3.5f}\nSize: {1!r} - species {2} - id {3}\n'
.format(best_genome.dist, best_genome.size(), best_species_id,
best_genome.key))
def report():
print "\nNumber of runs: {0!s}\n".format(sys.argv[2])
print "\t Gen. \t Nodes \t Conn. \t Evals. \t Score \n"
print "average {0:3.2f} \t {1:2.2f} \t {2:2.2f} \t {3:2.2f} \t {4:2.2f}".format(
mean(total_gens), mean(total_nodes), mean(total_conns),
mean(total_evals), mean(total_score))
print "stdev {0:3.2f} \t {1:2.2f} \t {2:2.2f} \t {3:2.2f} \t {4:2.2f}".format(
stdev(total_gens), stdev(total_nodes), stdev(total_conns),
stdev(total_evals), stdev(total_score))
def compute_adjusted_fitness(all_fitnesses, remaining_species):
min_fitness = min(all_fitnesses)
max_fitness = max(all_fitnesses)
fitness_range = max(1.0, max_fitness - min_fitness)
for afs in remaining_species:
msf = mean([m.fitness for m in itervalues(afs.members)])
af = (msf - min_fitness) / fitness_range
afs.adjusted_fitness = af
adjusted_fitnesses = [s.adjusted_fitness for s in remaining_species]
avg_adjusted_fitness = mean(adjusted_fitnesses)
return adjusted_fitnesses, avg_adjusted_fitness
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
if type(fitnesses[0]) is float:
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
elif type(fitnesses[0]) is FitnessObj:
fit_mean = mean_vector(fitnesses)
fit_std = std_vector(fitnesses)
else:
fit_mean = 0
fit_std = 0
best_species_id = species.get_species_id(best_genome.key)
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
with open(self.filename, "a+") as f:
f.write(
'Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}\n'.
format(fit_mean, fit_std))
f.write(
'Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}\n'
.format(best_genome.fitness, best_genome.size(),
best_species_id, best_genome.key))
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
best = None
with open("risultati\seed" + str(self.seed) + ".csv", 'a') as f:
for key in population:
if best is None:
best = population[key]
if population[key].fitness > best.fitness:
best = population[key]
f.write(
str(fit_mean) + "," + str(fit_std) + "," + str(best.fitness))
f.write("\n")
with gzip.open("migliori_genomi\seed" + str(self.seed),
'a',
compresslevel=5) as f:
pickle.dump(best, f, protocol=pickle.HIGHEST_PROTOCOL)
#pickle.dump("\n;\n", f, protocol=pickle.HIGHEST_PROTOCOL)
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
def post_evaluate(self, config, population, species, best_genome):
# Ordinary report if not novelty search
if config.novelty is None:
StdOutReporter.post_evaluate(
self,
config,
population,
species,
best_genome)
# Special report for novelty search
else:
novelties = [c.fitness for c in population.values()]
nov_mean = mean(novelties)
nov_std = stdev(novelties)
best_species_id = species.get_species_id(best_genome.key)
print('Population\'s average novelty: %3.5f stdev: %3.5f' %
(nov_mean, nov_std))
print('Best novelty: %3.5f - size: (%d,%d) - species %d - id %d' %
(best_genome.fitness,
best_genome.size()[0],
best_genome.size()[1],
best_species_id,
best_genome.key))
print('Best actual fitness: %f ' % best_genome.actual_fitness)
print('Evaluations this generation: %d' % config.current_evaluations)
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
'''
def get_species_fitness(self,
null_value: str = ''
) -> List[List[Union[str, float]]]:
"""
世代数だけの長さの配列を返す
ret[x][sid] = x世代目における種sidに含まれる個体全体の平均適応度
"""
# 世代全体で出現した種IDセット
all_species: Set[int] = set()
for gen_data in self.generation_statistics:
all_species: Set[int] = all_species.union(gen_data.keys())
max_species: int = max(all_species)
# 各世代における各種の適応度の平均
# species_fitness[x][sid] = x世代目における種sidに含まれる全個体の適応度の平均
species_fitness: List[List[Union[str, float]]] = []
for gen_data in self.generation_statistics:
# ある世代における 各種に含まれる各個体の適応度
member_fitness: List[Union[Dict[int, float], List]] = [
gen_data.get(sid, []) for sid in range(1, max_species + 1)
]
fitness: List[Union[str, float]] = []
for mf in member_fitness:
if mf:
fitness.append(mean(mf))
else:
fitness.append(null_value)
species_fitness.append(fitness)
return species_fitness
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
body = []
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
with open('fitplot', 'a') as f:
f.write('{},{},{}\n'.format(fit_mean, fit_std,
best_genome.fitness))
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
body.append(
'Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}\n'.format(
fit_mean, fit_std))
body.append(
'Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}\n'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
if body:
img = plot_fitness_over_gen('fitplot', 'fitplot.png')
report(body, img)
def post_evaluate(self, config, population, species, best_genome):
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.format(best_genome.fitness, best_genome.size(),
best_species_id, best_genome.key))
def get_average_fitness(population):
avg_fitness = []
for stats in population.generation_statistics:
scores = []
for fitness in stats.values():
scores.extend(fitness)
avg_fitness.append(mean(scores))
return avg_fitness
def get_average_fitness(population):
avg_fitness = []
for stats in population.generation_statistics:
scores = []
for fitness in stats.values():
scores.extend(fitness)
avg_fitness.append(mean(scores))
return avg_fitness
def post_evaluate(self, config, population, species, best_genome):
if not self.ctr % self.freq:
self.best.append(best_genome.modularity())
modularities = [g.modularity() for g in itervalues(population)]
self.means.append(mean(modularities))
self.stddevs.append(stdev(modularities))
print(
"\n\nMODULARITY (MOST FIT): {:.4f}\nMEAN MODULARITY: {:.4f}\n\n"
.format(self.best[-1], self.means[-1]))
self.ctr += 1
def get_average_cross_validation_fitness(self):
"""Get the per-generation average cross_validation fitness."""
avg_cross_validation_fitness = []
for stats in self.generation_cross_validation_statistics:
scores = []
for fitness in stats.values():
scores.extend(fitness)
avg_cross_validation_fitness.append(mean(scores))
return avg_cross_validation_fitness
def get_average_cross_validation_fitness(self):
"""Get the per-generation average cross_validation fitness."""
avg_cross_validation_fitness = []
for stats in self.generation_cross_validation_statistics:
scores = []
for fitness in stats.values():
scores.extend(fitness)
avg_cross_validation_fitness.append(mean(scores))
return avg_cross_validation_fitness
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
log.info('Population\'s average fitness: %f stdev: %f', fit_mean,
fit_std)
log.info('Best fitness: %f - size: %d - species %s - id %s',
best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key)
def post_evaluate(self, population, species, best):
fit_mean = mean([c.fitness for c in population])
fit_std = stdev([c.fitness for c in population])
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.format(best.fitness, best.size(),
best.species_id, best.ID))
print('Species length: {0:d} totaling {1:d} individuals'.format(len(species), sum(
[len(s.members) for s in species])))
print('Species ID : {0!s}'.format([s.ID for s in species]))
print('Species size : {0!s}'.format([len(s.members) for s in species]))
print('Species age : {0}'.format([s.age for s in species]))
def post_evaluate(self, population, species, best):
fit_mean = mean([c.fitness for c in population])
fit_std = stdev([c.fitness for c in population])
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.format(best.fitness, best.size(),
best.species_id, best.ID))
print('Species length: {0:d} totaling {1:d} individuals'.format(len(species), sum(
[len(s.members) for s in species])))
print('Species ID : {0!s}'.format([s.ID for s in species]))
print('Species size : {0!s}'.format([len(s.members) for s in species]))
print('Species age : {0}'.format([s.age for s in species]))
def post_evaluate(self, config, population, species, best_genome):
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
species_ids = list(iterkeys(species.species))
for i in species_ids:
s = species.species[i]
self.log(self.generation, i, s.fitness, fit_mean)
best_genome = None
for g in itervalues(s.members):
if best_genome is None or (g.fitness > best_genome.fitness):
best_genome = g
def compute_adjusted_fitness(all_fitnesses, remaining_species):
min_fitness = min(all_fitnesses)
max_fitness = max(all_fitnesses)
# Do not allow the fitness range to be zero, as we divide by it below.
fitness_range = max(FitnessObj(0.1, 1), max_fitness - min_fitness)
for afs in remaining_species:
# Compute adjusted fitness.
array = [m.fitness for m in itervalues(afs.members)]
if type(array[0]) is FitnessObj:
msf = mean_vector(array)
else:
msf = mean(array)
af = (msf - min_fitness) / fitness_range
afs.adjusted_fitness = af
adjusted_fitnesses = [s.adjusted_fitness for s in remaining_species]
if type(adjusted_fitnesses[0]) is FitnessObj:
avg_adjusted_fitness = mean_vector(adjusted_fitnesses)
else:
avg_adjusted_fitness = mean(adjusted_fitnesses)
return adjusted_fitnesses, avg_adjusted_fitness
def post_evaluate(self, config, population, species, best_genome):
print("Here")
fitnesses = [c.fitness for c in itervalues(population)]
self.mean_arr.append(mean(fitnesses))
self.best_arr.append(best_genome.fitness)
# Show the thing
length_range = arange(len(self.mean_arr))
plt.plot(length_range, self.mean_arr, 'r--', length_range,
self.best_arr, 'b')
plt.pause(0.000001)
def average_fitness(self):
""" Returns the raw average fitness for this species """
avg_fitness = mean([c.fitness for c in self.members])
# Check for increase in mean fitness and adjust "no improvement" count as necessary.
if avg_fitness > self.last_avg_fitness:
self.last_avg_fitness = avg_fitness
self.no_improvement_age = 0
else:
self.no_improvement_age += 1
return avg_fitness
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
outputString = '';
outputString += ('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(fit_mean, fit_std)) + '\n'
outputString += ('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.format(best_genome.fitness,
best_genome.size(),
best_species_id,
best_genome.key)) + '\n';
self.output(outputString);
def post_evaluate(self, config: Config, population: Dict[int,
DefaultGenome],
species_set: DefaultSpeciesSet,
best_genome: DefaultGenome) -> None:
# pylint: disable=no-self-use
fitnesses: List[float] = [c.fitness for c in population.values()]
fit_mean: float = mean(fitnesses)
fit_std: float = stdev(fitnesses)
best_species_id: int = species_set.get_species_id(best_genome.key)
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
def bench(num_runs):
results = []
while len(results) < num_runs:
try:
result = run()
except population.CompleteExtinctionException:
continue
results.append(result)
if len(results) % 10 == 0:
print("Completed run %d of %d" % (len(results), num_runs))
generations = [r[0] for r in results]
hidden = [r[1] for r in results]
connections = [r[2] for r in results]
enabled = [r[3] for r in results]
print(" mean (stdev)")
print(" Generations: %.3f (%.3f)" %
(mean(generations), stdev(generations)))
print("hidden nodes: %.3f (%.3f)" % (mean(hidden), stdev(hidden)))
print(" connections: %.3f (%.3f)" %
(mean(connections), stdev(connections)))
print(" enabled: %.3f (%.3f)" % (mean(enabled), stdev(enabled)))
def post_evaluate(self, config, population, species, best_genome):
fits = [c.actual_fitness for c in population.values()]
# Save current generation info to history file
fit_max = max(fits)
self.csvfile.write('%d,%f,%+5.3f,%+5.3f,%+5.3f' %
(config.gen, time() - self.start, mean(fits),
stdev(fits), fit_max))
if config.is_novelty():
novs = [c.fitness for c in population.values()]
self.csvfile.write(',%+5.3f,%+5.3f,%+5.3f' %
(mean(novs), stdev(novs), max(novs)))
self.csvfile.write('\n')
self.csvfile.flush()
# Track best
if self.checkpoint and fit_max > self.best_fitness:
self.best_fitness = fit_max
print('############# Saving new best %f ##############' %
self.best_fitness)
config.save_genome(best_genome)
def post_evaluate(self, config, population, species, best_genome):
if config.novelty is None:
StdOutReporter.post_evaluate(self, config, population, species,
best_genome)
return
fitnesses = [c.fitness for c in population.values()]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
print('Population\'s average novelty: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
print('Best novelty: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
print('Best actual fitness: %f ' % best_genome.actual_fitness)
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
fd = open(self.filename, 'a')
fd.write(
'Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}\n'.format(
fit_mean, fit_std))
fd.write(
'Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}\n'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
fd.close()
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
# andrew add
if (best_genome.fitness > self.bestFitness):
res = open("result.txt", "a")
res.write('\nBest genome:\n{!s}'.format(best_genome))
res.close()
def post_evaluate(self, config, population, species, best_genome,
score_max, score_mean):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in population.values()]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
score_max.append(max(fitnesses))
score_mean.append(fit_mean)
best_species_id = species.get_species_id(best_genome.key)
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
self.stream(
'Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
self.stream(
'Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
msk = "[" + ", ".join(
[f"{x:,.0f}"
for x in best_genome.metascorekeeper.score_listing()]) + "]"
self.stream(f"Metascorekeeper summary: {msk}")
def post_evaluate(self, config, population, species, best_genome):
# pylint: disable=no-self-use
fitnesses = [c.fitness for c in itervalues(population)]
fit_mean = mean(fitnesses)
fit_std = stdev(fitnesses)
best_species_id = species.get_species_id(best_genome.key)
self._logger.info(
'Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(
fit_mean, fit_std))
self._logger.info(
'Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.
format(best_genome.fitness, best_genome.size(), best_species_id,
best_genome.key))
self._mlflow.log_metric(key="best_fitness", value=best_genome.fitness)
self._mlflow.log_metric(key="best_fitness_species",
value=best_species_id)
self._mlflow.log_metric(key="best_fitness_id", value=best_genome.key)
def get_species_fitness(population, null_value=''):
all_species = set()
for gen_data in population.generation_statistics:
all_species = all_species.union(gen_data.keys())
max_species = max(all_species)
species_fitness = []
for gen_data in population.generation_statistics:
member_fitness = [gen_data.get(sid, []) for sid in range(1, max_species + 1)]
fitness = []
for mf in member_fitness:
if mf:
fitness.append(mean(mf))
else:
fitness.append(null_value)
species_fitness.append(fitness)
return species_fitness
def plot_fitness(checkpoints, name):
gens = [c.generation for c in checkpoints]
bests = [c.best_genome.fitness for c in checkpoints]
avgs = [mean([f.fitness for _, f in c.population.items()]) for c in checkpoints]
fig, ax = plt.subplots(figsize = (10,5))
ax.set_title(name+" - Fitness over Generations")
ax.plot(gens, bests, color='blue', linewidth=1, label="Best")
ax.plot(gens, avgs, color='black', linewidth=1, label="Average")
ax.legend()
ax.set_xlabel('Generation')
ax.set_ylabel('Fitness (Flight Time)')
plt.tight_layout()
fig.savefig(name+'.png', format='png', dpi=300)
plt.show()
plt.close()
def get_species_fitness(self, null_value=''):
all_species = set()
for gen_data in self.generation_statistics:
all_species = all_species.union(gen_data.keys())
max_species = max(all_species)
species_fitness = []
for gen_data in self.generation_statistics:
member_fitness = [gen_data.get(sid, []) for sid in range(1, max_species + 1)]
fitness = []
for mf in member_fitness:
if mf:
fitness.append(mean(mf))
else:
fitness.append(null_value)
species_fitness.append(fitness)
return species_fitness
def post_evaluate(self, population, species, best):
fit_mean = mean([c.fitness for c in population])
fit_std = stdev([c.fitness for c in population])
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'
.format(fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'
.format(best.fitness, best.size(), best.species_id, best.ID))
print('Species length: {0:d} totaling {1:d} individuals'
.format(len(species), sum([len(s.members) for s in species])))
print('Species ID : {0!s}'.format([s.ID for s in species]))
print('Species size : {0!s}'
.format([len(s.members) for s in species]))
print('Species age : {0}'.format([s.age for s in species]))
[cl.write_message(('\n Fitness promedio de la poblacion: {0:3.5f}'
+ ' Desviacion: {1:3.5f}')
.format(fit_mean, fit_std)) for cl in clientes]
[cl.write_message(
'\n Mejor fitness: {0:3.5f} - size: {1!r} - Especie {2} - ID {3}\n'
.format(best.fitness, best.size(),
best.species_id, best.ID)) for cl in clientes]
def get_average_fitness(self):
""" Returns the average fitness over all members in the species."""
return mean([c.fitness for c in self.members])
def species_mean_fitness(species):
return mean([m.fitness for m in species.members])
def epoch(self, fitness_function, n, report=True, save_best=False, checkpoint_interval=10,
checkpoint_generation=None):
""" Runs NEAT's genetic algorithm for n epochs.
Keyword arguments:
report -- show stats at each epoch (default True)
save_best -- save the best genome from each epoch (default False)
checkpoint_interval -- time in minutes between saving checkpoints (default 10 minutes)
checkpoint_generation -- time in generations between saving checkpoints
(default None -- option disabled)
"""
t0 = time.time() # for saving checkpoints
for g in range(n):
self.generation += 1
if report:
print('\n ****** Running generation %d ****** \n' % self.generation)
# Evaluate individuals
fitness_function(self.population)
# Speciates the population
self.__speciate(report)
# Current generation's best genome
self.most_fit_genomes.append(max(self.population))
# Current population's average fitness
self.avg_fitness_scores.append(mean([c.fitness for c in self.population]))
# Print some statistics
best = self.most_fit_genomes[-1]
# saves the best genome from the current generation
if save_best:
f = open('best_genome_' + str(self.generation), 'w')
pickle.dump(best, f)
f.close()
# Stops the simulation
if best.fitness > self.config.max_fitness_threshold:
if report:
print('\nBest individual in epoch %s meets fitness threshold - complexity: %s' % (
self.generation, best.size()))
break
# Remove stagnated species and its members (except if it has the best genome)
for s in self.__species[:]:
if s.no_improvement_age > self.config.max_stagnation:
if report:
print("\n Species %2d (with %2d individuals) is stagnated: removing it" \
% (s.ID, len(s.members)))
# removing species
self.__species.remove(s)
# removing all the species' members
# TODO: can be optimized!
for c in self.population[:]:
if c.species_id == s.ID:
self.population.remove(c)
# Compute spawn levels for each remaining species
self.diversity.compute_spawn_amount(self.__species)
# Removing species with spawn amount = 0
for s in self.__species[:]:
# This rarely happens
if s.spawn_amount == 0:
if report:
print(' Species %2d age %2s removed: produced no offspring' % (s.ID, s.age))
for c in self.population[:]:
if c.species_id == s.ID:
self.population.remove(c)
# self.remove(c)
self.__species.remove(s)
# Logging speciation stats
self.__log_species()
if report:
if self.population:
std_dev = stdev([c.fitness for c in self.population])
print('Population\'s average fitness: %3.5f stdev: %3.5f' % (self.avg_fitness_scores[-1], std_dev))
print('Best fitness: %2.12s - size: %s - species %s - id %s' \
% (best.fitness, best.size(), best.species_id, best.ID))
print('Species length: %d totaling %d individuals' \
% (len(self.__species), sum([len(s.members) for s in self.__species])))
print('Species ID : %s' % [s.ID for s in self.__species])
print('Each species size: %s' % [len(s.members) for s in self.__species])
print('Amount to spawn : %s' % [s.spawn_amount for s in self.__species])
print('Species age : %s' % [s.age for s in self.__species])
print('Species no improv: %s' % [s.no_improvement_age for s in self.__species])
else:
print('All species extinct.')
# -------------------------- Producing new offspring -------------------------- #
new_population = [] # next generation's population
# If no species are left, create a new population from scratch, otherwise top off
# population by reproducing existing species.
if self.__species:
for s in self.__species:
new_population.extend(s.reproduce(self.config))
# Controls under or overflow #
fill = self.config.pop_size - len(new_population)
if fill < 0: # overflow
if report:
print(' Removing %d excess individual(s) from the new population' % -fill)
# TODO: This is dangerous! I can't remove a species' representative!
new_population = new_population[:fill] # Removing the last added members
if fill > 0: # underflow
if report:
print(' Producing %d more individual(s) to fill up the new population' % fill)
# TODO: what about producing new individuals instead of reproducing?
# increasing diversity from time to time might help
while fill > 0:
# Selects a random genome from population
parent1 = random.choice(self.population)
# Search for a mate within the same species
found = False
for c in self.population:
# what if c is parent1 itself?
if c.species_id == parent1.species_id:
child = parent1.crossover(c)
new_population.append(child.mutate())
found = True
break
if not found:
# If no mate was found, just mutate it
new_population.append(parent1.mutate())
# new_population.append(genome.FFGenome.create_fully_connected())
fill -= 1
assert self.config.pop_size == len(new_population), 'Different population sizes!'
# Updates current population
self.population = new_population[:]
else:
self.__create_population()
if checkpoint_interval is not None and time.time() > t0 + 60 * checkpoint_interval:
self.__create_checkpoint(report)
t0 = time.time() # updates the counter
elif checkpoint_generation is not None and self.generation % checkpoint_generation == 0:
self.__create_checkpoint(report)
def epoch(self, fitness_function, n):
""" Runs NEAT's genetic algorithm for n epochs. """
t0 = time.time() # for saving checkpoints
for g in range(n):
self.generation += 1
if self.config.report:
print('\n ****** Running generation {0} ****** \n'.format(self.generation))
gen_start = time.time()
# Collect a list of all members from all species.
population = []
for s in self.species:
population.extend(s.members)
# Evaluate individuals
fitness_function(population)
self.total_evaluations += len(population)
# Gather statistics.
self._log_stats(population)
# Print some statistics
best = self.most_fit_genomes[-1]
if self.config.report:
fit_mean = mean([c.fitness for c in population])
fit_std = stdev([c.fitness for c in population])
print('Population\'s average fitness: {0:3.5f} stdev: {1:3.5f}'.format(fit_mean, fit_std))
print('Best fitness: {0:3.5f} - size: {1!r} - species {2} - id {3}'.format(best.fitness, best.size(),
best.species_id, best.ID))
print('Species length: {0:d} totaling {1:d} individuals'.format(len(self.species), sum(
[len(s.members) for s in self.species])))
print('Species ID : {0!s}'.format([s.ID for s in self.species]))
print('Species size : {0!s}'.format([len(s.members) for s in self.species]))
print('Amount to spawn : {0!s}'.format([s.spawn_amount for s in self.species]))
print('Species age : {0}'.format([s.age for s in self.species]))
print('Species fitness : {0!r}'.format([s.get_average_fitness() for s in self.species]))
print('Species no improv: {0!r}'.format([s.no_improvement_age for s in self.species]))
# Saves the best genome from the current generation if requested.
if self.config.save_best:
with open('best_genome_' + str(self.generation), 'wb') as f:
pickle.dump(best, f)
# End when the fitness threshold is reached.
if best.fitness >= self.config.max_fitness_threshold:
if self.config.report:
print('\nBest individual in epoch {0} meets fitness threshold - complexity: {1!r}'.format(
self.generation, best.size()))
break
# Remove stagnated species.
# TODO: Log species removal for visualization purposes.
# TODO: Provide some sort of optional cross-species performance criteria, which
# are then used to control stagnation and possibly the mutation rate configuration.
# This scheme should be adaptive so that species do not evolve to become "cautious"
# and only make very slow progress.
new_species = []
for s in self.species:
s.update_stagnation()
if s.no_improvement_age <= self.config.max_stagnation:
new_species.append(s)
else:
if self.config.report:
print("\n Species {0} with {1} members is stagnated: removing it".format(s.ID, len(s.members)))
self.species = new_species
# TODO: Break these out into user-configurable classes
# 1. Species survival determination (currently hard-coded to be stagnation with a fixed number of generations).
# 2. Species spawn allotment (currently provided in the diversity object).
# Check for complete extinction.
new_population = []
if not self.species:
if self.config.report:
print('All species extinct.')
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
new_population = self._create_population()
else:
raise MassExtinctionException()
else:
# Compute spawn levels for all current species and then reproduce.
self.diversity.compute_spawn_amount(self.species)
for s in self.species:
# Verify that all species received non-zero spawn counts, as the speciation mechanism
# is intended to allow initially less fit species time to improve before making them
# extinct via the stagnation mechanism.
assert s.spawn_amount > 0
# The Species.reproduce keeps one random child as its new representative, and
# returns the rest as a list, which must be sorted into species.
new_population.extend(s.reproduce(self.config, self.genome_indexer))
self._speciate(new_population)
if self.config.checkpoint_interval is not None and time.time() > t0 + 60 * self.config.checkpoint_interval:
if self.config.report:
print('Creating timed checkpoint file at generation: {0}'.format(self.generation))
self.save_checkpoint()
# Update the checkpoint time.
t0 = time.time()
elif self.config.checkpoint_generation is not None and self.generation % self.config.checkpoint_generation == 0:
if self.config.report:
print('Creating generation checkpoint file at generation: {0}'.format(self.generation))
self.save_checkpoint()
if self.config.report:
print("Generation time: {0:.3f} sec".format(time.time() - gen_start))
def report():
print "\nNumber of runs: {0!s}\n".format(sys.argv[2])
print "\t Gen. \t Nodes \t Conn. \t Evals. \t Score \n"
print "average {0:3.2f} \t {1:2.2f} \t {2:2.2f} \t {3:2.2f} \t {4:2.2f}".format(mean(total_gens), mean(total_nodes), mean(total_conns), mean(total_evals), mean(total_score))
print "stdev {0:3.2f} \t {1:2.2f} \t {2:2.2f} \t {3:2.2f} \t {4:2.2f}".format(stdev(total_gens), stdev(total_nodes), stdev(total_conns), stdev(total_evals), stdev(total_score))