def evaluate_and_evolve(
self,
pop: Population,
n: int = 1,
parallel=True,
save_interval: int = 1,
):
"""
Evaluate the population on the same set of games.
:param pop: Population object
:param n: Number of generations
:param parallel: Parallel the code (disable parallelization for debugging purposes)
:param save_interval: Indicates how often a population gets saved
"""
multi_env = get_multi_env(pop=pop, game_config=self.game_config)
msg = f"Repetitive evaluating on games: {self.games} for {n} iterations"
pop.log(msg, print_result=False)
# Iterate and evaluate over the games
saved = True
for iteration in range(n):
# Set and randomize the games
multi_env.set_games(self.games, noise=True)
# Prepare the generation's reporters for the generation
pop.reporters.start_generation(gen=pop.generation, logger=pop.log)
# Fetch the dictionary of genomes
genomes = list(iteritems(pop.population))
if parallel:
# Initialize the evaluation-pool
pool = mp.Pool(mp.cpu_count() - self.unused_cpu)
manager = mp.Manager()
return_dict = manager.dict()
for genome in genomes:
pool.apply_async(func=multi_env.eval_genome,
args=(genome, return_dict))
pool.close() # Close the pool
pool.join(
) # Postpone continuation until everything is finished
else:
return_dict = dict()
for genome in tqdm(genomes, desc="sequential training"):
multi_env.eval_genome(genome, return_dict)
# Calculate the fitness from the given return_dict
fitness = calc_pop_fitness(
fitness_cfg=pop.config.evaluation,
game_cfg=self.game_config.game,
game_obs=return_dict,
gen=pop.generation,
)
for i, genome in genomes:
genome.fitness = fitness[i]
# Gather and report statistics
best = None
for g in itervalues(pop.population):
if best is None or g.fitness > best.fitness: best = g
pop.reporters.post_evaluate(population=pop.population,
species=pop.species,
best_genome=best,
logger=pop.log)
# Update the population's best_genome
genomes = sorted(pop.population.items(),
key=lambda x: x[1].fitness,
reverse=True)
pop.best_fitness[pop.generation] = genomes[0][1].fitness
pop.best_genome_hist[pop.generation] = genomes[0]
pop.best_genome = best
# Let population evolve
pop.evolve()
# End generation
pop.reporters.end_generation(population=pop.population,
name=str(pop),
species_set=pop.species,
logger=pop.log)
# Save the population
if (iteration + 1) % save_interval == 0:
pop.save()
saved = True
else:
saved = False
# Make sure that last iterations saves
if not saved: pop.save()
def reproduce(self, config, species, pop_size, generation):
"""
Handles creation of genomes, either from scratch or by sexual or
asexual reproduction from parents.
"""
# TODO: I don't like this modification of the species and stagnation objects,
# because it requires internal knowledge of the objects.
# Filter out stagnated species, collect the set of non-stagnated
# species members, and compute their average adjusted fitness.
# The average adjusted fitness scheme (normalized to the interval
# [0, 1]) allows the use of negative fitness values without
# interfering with the shared fitness scheme.
all_fitnesses = []
remaining_species = []
for stag_sid, stag_s, stagnant in self.stagnation.update(
species, generation):
if stagnant:
self.reporters.species_stagnant(stag_sid, stag_s)
else:
all_fitnesses.extend(m.fitness
for m in itervalues(stag_s.members))
remaining_species.append(stag_s)
# The above comment was not quite what was happening - now getting fitnesses
# only from members of non-stagnated species.
# No species left.
if not remaining_species:
species.species = {}
return {} # was []
# Find minimum/maximum fitness across the entire population, for use in
# species adjusted fitness computation.
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.
# TODO: The ``1.0`` below is rather arbitrary, and should be configurable.
fitness_range = max(1.0, max_fitness - min_fitness)
for afs in remaining_species:
# Compute adjusted fitness.
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) # type: float
self.reporters.info(
"Average adjusted fitness: {:.3f}".format(avg_adjusted_fitness))
# Compute the number of new members for each species in the new generation.
previous_sizes = [len(s.members) for s in remaining_species]
min_species_size = self.reproduction_config.min_species_size
# Isn't the effective min_species_size going to be max(min_species_size,
# self.reproduction_config.elitism)? That would probably produce more accurate tracking
# of population sizes and relative fitnesses... doing. TODO: document.
min_species_size = max(min_species_size,
self.reproduction_config.elitism)
spawn_amounts = self.compute_spawn(adjusted_fitnesses, previous_sizes,
pop_size, min_species_size)
new_population = {}
species.species = {}
for spawn, s in zip(spawn_amounts, remaining_species):
# If elitism is enabled, each species always at least gets to retain its elites.
spawn = max(spawn, self.reproduction_config.elitism)
assert spawn > 0
# The species has at least one member for the next generation, so retain it.
old_members = list(iteritems(s.members))
s.members = {}
species.species[s.key] = s
# Sort members in order of descending fitness.
old_members.sort(reverse=True, key=lambda x: x[1].fitness)
# Transfer elites to new generation.
if self.reproduction_config.elitism > 0:
for i, m in old_members[:self.reproduction_config.elitism]:
new_population[i] = m
spawn -= 1
if spawn <= 0:
continue
# Only use the survival threshold fraction to use as parents for the next generation.
repro_cutoff = int(
math.ceil(self.reproduction_config.survival_threshold *
len(old_members)))
# Use at least two parents no matter what the threshold fraction result is.
repro_cutoff = max(repro_cutoff, 2)
old_members = old_members[:repro_cutoff]
# Randomly choose parents and produce the number of offspring allotted to the species.
while spawn > 0:
spawn -= 1
parent1_id, parent1 = random.choice(old_members)
parent2_id, parent2 = random.choice(old_members)
# Note that if the parents are not distinct, crossover will produce a
# genetically identical clone of the parent (but with a different ID).
# gid = next(self.genome_indexer)
# child = config.genome_type(gid)
# child.configure_crossover(parent1, parent2, config.genome_config)
# child.mutate(config.genome_config)
# new_population[gid] = child
# self.ancestors[gid] = (parent1_id, parent2_id)
if parent1.fitness > parent2.fitness:
parent1.mutate(config.genome_config)
new_population[parent1_id] = parent1
self.ancestors[parent1_id] = (parent1_id, parent1_id)
else:
parent2.mutate(config.genome_config)
new_population[parent2_id] = parent2
self.ancestors[parent2_id] = (parent2_id, parent2_id)
'''
Check cppnon sets of both parents
If they're the same, perfrom crossover of non-cppnon-nodes and connections
Else,
Find parent with highest fitness
Transfer those nodes to child
perfrom crossover of non-cppnon-nodes and connections
'''
return new_population
def run(self, fitness_function, n=None):
"""
Runs NEAT's genetic algorithm for at most n generations. If n
is None, run until solution is found or extinction occurs.
The user-provided fitness_function must take only two arguments:
1. The population as a list of (genome id, genome) tuples.
2. The current configuration object.
The return value of the fitness function is ignored, but it must assign
a Python float to the `fitness` member of each genome.
The fitness function is free to maintain external state, perform
evaluations in parallel, etc.
It is assumed that fitness_function does not modify the list of genomes,
the genomes themselves (apart from updating the fitness member),
or the configuration object.
"""
if self.config.no_fitness_termination and (n is None):
raise RuntimeError("Cannot have no generational limit with no fitness termination")
k = 0
while n is None or k < n:
if not (self.state):
print("Training: break")
self.reached_limit = False
break
k += 1
self.reporters.start_generation(self.generation)
# Evaluate all genomes using the user-provided function.
fitness_function(list(iteritems(self.population)), self.config)
# Gather and report statistics.
best = None
for g in itervalues(self.population):
if best is None or g.fitness > best.fitness:
best = g
self.reporters.post_evaluate(self.config, self.population, self.species, best)
# Track the best genome ever seen.
if self.best_genome is None or best.fitness > self.best_genome.fitness:
self.best_genome = best
if not self.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = self.fitness_criterion(g.fitness for g in itervalues(self.population))
if fv >= self.config.fitness_threshold:
self.reporters.found_solution(self.config, self.generation, best)
self.reached_limit = False
break
# Create the next generation from the current generation.
self.population = self.reproduction.reproduce(self.config, self.species,
self.config.pop_size, self.generation)
# Check for complete extinction.
if not self.species.species:
self.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
self.population = self.reproduction.create_new(self.config.genome_type,
self.config.genome_config,
self.config.pop_size)
else:
raise CompleteExtinctionException()
# Divide the new population into species.
self.species.speciate(self.config, self.population, self.generation)
self.reporters.end_generation(self.config, self.population, self.species)
self.generation += 1
if self.config.no_fitness_termination:
self.reporters.found_solution(self.config, self.generation, self.best_genome)
return self.best_genome
def run():
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config_path = os.path.join(local_dir, my_config)
config = neat.Config(LanderGenome, neat.DefaultReproduction,
neat.DefaultSpeciesSet, neat.DefaultStagnation,
config_path)
pop = neat.Population(config)
stats = neat.StatisticsReporter()
pop.add_reporter(stats)
pop2 = neat.Population(config)
stats2 = neat.StatisticsReporter()
pop.add_reporter(stats)
pop2.add_reporter(stats2)
pop.add_reporter(neat.StdOutReporter(True))
# Checkpoint every 25 generations or 900 seconds.
rep = neat.Checkpointer(25, 900)
pop.add_reporter(rep)
# Training set index
avg_score_v = -10000000.0
avg_score_v_ant = avg_score_v
avg_score = avg_score_v
# asigna un gen_best para poder cargar los demás desde syn
for g in itervalues(pop.population):
gen_best = g
g.fitness = -10000000.0
# Run until the winner from a generation is able to solve the environment
# or the user interrupts the process.
ec = PooledErrorCompute()
temp = 0
best_fitness = -2000.0
pop_size = len(pop.population)
# sets the nuber of continuous iterations
num_iterations = round(200 / len(pop.population)) + 1
while 1:
try:
if temp > 0:
# Calcula training y validation fitness
best_genomes = stats.best_unique_genomes(3)
solved = True
best_scores = []
observation = env_t.reset()
score = 0.0
step = 0
gen_best_nn = neat.nn.FeedForwardNetwork.create(
gen_best, config)
while 1:
step += 1
output = gen_best_nn.activate(nn_format(observation))
action = (np.argmax(output[0:2]), output[3], output[4],
output[5]) # buy,sell or
observation, reward, done, info = env_t.step(action)
score += reward
env_t.render()
if done:
break
ec.episode_score.append(score)
ec.episode_length.append(step)
best_scores.append(score)
avg_score = sum(best_scores) / len(best_scores)
print("Training Set Score =", score, " avg_score=", avg_score)
# Calculate the real-validation set score
best_genomes = stats.best_unique_genomes(3)
solved = True
best_scores = []
observation = env_v.reset()
score = 0.0
step = 0
gen_best_nn = neat.nn.FeedForwardNetwork.create(
gen_best, config)
while 1:
step += 1
output = gen_best_nn.activate(nn_format(observation))
action = (np.argmax(output[0:2]), output[3], output[4],
output[5]) # buy,sell or
observation, reward, done, info = env_v.step(action)
score += reward
#env_v.render()
if done:
break
best_scores.append(score)
avg_score_v = sum(best_scores) / len(best_scores)
print("Validation Set Score = ", avg_score_v)
print(
"*********************************************************"
)
# Calcula el best_fitness (PARA SYNC)como el promedio del score de training y el promedio del fitness de los reps.
reps_local = []
reps = [gen_best]
accum = 0.0
countr = 0
for sid, s in iteritems(pop.species.species):
if pop.population[
s.representative.key].fitness is not None:
accum = accum + pop.population[
s.representative.key].fitness
countr = countr + 1
if countr > 0:
best_fitness = (3 * avg_score + (accum / countr)) / 4
else:
best_fitness = (avg_score)
#FIN de calculo de real validation
if temp >= 0:
# TODO: FUNCION DE SINCRONIZACION CON SINGULARITY
# Lee en pop2 el último checkpoint desde syn
# Hace request de getLastParam(process_hash,use_current) a syn TODO: HACER PROCESS CONFIGURABLE Y POR HASH no por id
res = requests.get(
my_url +
"/processes/1?username=harveybc&pass_hash=$2a$04$ntNHmofQoMoajG89mTEM2uSR66jKXBgRQJnCgqfNN38aq9UkN4Y6q&process_hash=ph"
)
cont = res.json()
print('\ncurrent_block_performance =',
cont['result'][0]['current_block_performance'])
print('\nlast_optimum_id =',
cont['result'][0]['last_optimum_id'])
last_optimum_id = cont['result'][0]['last_optimum_id']
# Si el perf reportado pop2_champion_fitness > pop1_champion_fitness de validation training
print("\nPerformance = ", best_fitness)
print(
"*********************************************************"
)
if cont['result'][0][
'current_block_performance'] > best_fitness:
# hace request GetParameter(id)
res_p = requests.get(
my_url + "/parameters/" + str(last_optimum_id) +
"?username=harveybc&pass_hash=$2a$04$ntNHmofQoMoajG89mTEM2uSR66jKXBgRQJnCgqfNN38aq9UkN4Y6q&process_hash=ph"
)
cont_param = res_p.json()
# descarga el checkpoint del link de la respuesta si cont.parameter_link
print('Parameter Downloaded')
print('\nmigrations =')
if cont_param['result'][0]['parameter_link'] is not None:
genom_data = requests.get(
cont_param['result'][0]['parameter_link']).content
with open('remote_reps', 'wb') as handler:
handler.write(genom_data)
handler.close()
# carga genom descargado en nueva población pop2
with open('remote_reps', 'rb') as f:
remote_reps = pickle.load(f)
# OP.MIGRATION: Reemplaza el peor de la especie pop1 más cercana por el nuevo chmpion de pop2 como http://neo.lcc.uma.es/Articles/WRH98.pdf
# para cada elemento de remote_reps, busca el closer, si remote fitness > local, lo reemplaza
for i in range(len(remote_reps)):
closer = None
min_dist = None
# initialize for less fit search
less_fit = None
less_fitness = 10000
for g in itervalues(pop.population):
if g not in remote_reps:
dist = g.distance(remote_reps[i],
config.genome_config)
if dist is None:
dist = 100000000
else:
dist = 100000000
# do not count already migrated remote_reps
if closer is None or min_dist is None:
closer = deepcopy(g)
min_dist = dist
if dist < min_dist:
closer = deepcopy(g)
min_dist = dist
if g.fitness is None:
g.fitness = -10
if g.fitness < less_fitness:
less_fitness = g.fitness
less_fit = deepcopy(g)
# For the best genom in position 0
if i == 0:
tmp_genom = deepcopy(remote_reps[i])
# Hack: overwrites original genome key with the replacing one
tmp_genom.key = closer.key
pop.population[closer.key] = deepcopy(
tmp_genom)
print(" gen_best=", closer.key)
pop.best_genome = deepcopy(tmp_genom)
gen_best = deepcopy(tmp_genom)
else:
# si el remote fitness>local, reemplazar el remote de pop2 en pop1
if closer is None:
# busca el pop con el menor fitness
closer = less_fit
if closer is not None:
if closer not in remote_reps:
if closer.fitness is None:
closer.fitness = less_fitness
if closer.fitness is not None and remote_reps[
i].fitness is not None:
if remote_reps[
i].fitness > closer.fitness:
tmp_genom = deepcopy(
remote_reps[i])
# Hack: overwrites original genome key with the replacing one
tmp_genom.key = closer.key
pop.population[
closer.key] = deepcopy(
tmp_genom)
print("Replaced=", closer.key)
# actualiza gen_best y best_genome al remoto
pop.best_genome = deepcopy(
tmp_genom)
gen_best = deepcopy(tmp_genom)
if closer.fitness is None:
tmp_genom = deepcopy(
remote_reps[i])
# Hack: overwrites original genome key with the replacing one
tmp_genom.key = len(
pop.population) + 1
pop.population[
tmp_genom.key] = tmp_genom
print(
"Created Por closer.fitness=NONE : ",
tmp_genom.key)
# actualiza gen_best y best_genome al remoto
pop.best_genome = deepcopy(
tmp_genom)
gen_best = deepcopy(tmp_genom)
else:
#si closer está en remote_reps es porque no hay ningun otro cercano así que lo adiciona
tmp_genom = deepcopy(remote_reps[i])
# Hack: overwrites original genome key with the replacing one
tmp_genom.key = len(pop.population) + 1
pop.population[
tmp_genom.key] = tmp_genom
print(
"Created por Closer in rempte_reps=",
tmp_genom.key)
# actualiza gen_best y best_genome al remoto
pop.best_genome = deepcopy(tmp_genom)
gen_best = deepcopy(tmp_genom)
#ejecuta speciate
pop.species.speciate(config, pop.population,
pop.generation)
print("\nSpeciation after migration done")
# Si el perf reportado es menor pero no igual al de pop1
if cont['result'][0][
'current_block_performance'] < best_fitness:
# Obtiene remote_reps
# hace request GetParameter(id)
remote_reps = None
res_p = requests.get(
my_url + "/parameters/" + str(last_optimum_id) +
"?username=harveybc&pass_hash=$2a$04$ntNHmofQoMoajG89mTEM2uSR66jKXBgRQJnCgqfNN38aq9UkN4Y6q&process_hash=ph"
)
cont_param = res_p.json()
# descarga el checkpoint del link de la respuesta si cont.parameter_link
print('\nNEW OPTIMUM - cont_param =', cont_param)
#print('\nmigrations =')
if cont_param['result'][0]['parameter_link'] is not None:
genom_data = requests.get(
cont_param['result'][0]['parameter_link']).content
with open('remote_reps', 'wb') as handler:
handler.write(genom_data)
handler.close()
# carga genom descargado en nueva población pop2
with open('remote_reps', 'rb') as f:
remote_reps = pickle.load(f)
#Guarda los mejores reps
reps_local = []
reps = [gen_best]
# Para cada especie, adiciona su representative a reps
for sid, s in iteritems(pop.species.species):
#print("\ns=",s)
if s.representative not in reps_local:
reps_local.append(
pop.population[s.representative.key])
reps_local[len(reps_local) - 1] = deepcopy(
pop.population[s.representative.key])
# TODO: Conservar los mejores reps, solo reemplazarlos por los mas cercanos
if remote_reps is None:
for l in reps_local:
reps.append(l)
reps[len(reps) - 1] = deepcopy(l)
else:
# para cada reps_local l
for l in reps_local:
# busca el closer a l en reps_remote
for i in range(len(remote_reps)):
closer = None
min_dist = None
for g in reps_local:
if g not in remote_reps:
dist = g.distance(
remote_reps[i],
config.genome_config)
else:
dist = 100000000
# do not count already migrated remote_reps
if closer is None or min_dist is None:
closer = deepcopy(g)
min_dist = dist
if dist < min_dist:
closer = deepcopy(g)
min_dist = dist
# si closer is in reps
if closer in reps:
# adiciona l a reps si ya no estaba en reps
if l not in reps:
reps.append(l)
reps[len(reps) - 1] = deepcopy(l)
# sino
else:
# si l tiene más fitness que closer,
if closer.fitness is not None and l.fitness is not None:
if l.fitness > pop.population[
closer.key].fitness:
# adiciona l a reps si ya no estaba en reps
if l not in reps:
reps.append(l)
reps[len(reps) - 1] = deepcopy(l)
# sino
else:
# adiciona closer a reps si ya no estaba en reps
if l not in reps:
reps.append(
pop.population[closer.key])
reps[len(reps) - 1] = deepcopy(
pop.population[closer.key])
# Guarda checkpoint de los representatives de cada especie y lo copia a ubicación para servir vía syn.
# rep.save_checkpoint(config,pop,neat.DefaultSpeciesSet,rep.current_generation)
print("\nreps=", reps)
filename = '{0}{1}'.format("reps-", rep.current_generation)
with open(filename, 'wb') as f:
pickle.dump(reps, f)
#
# Hace request de CreateParam a syn
form_data = {
"process_hash":
"ph",
"app_hash":
"ah",
"parameter_link":
my_url + "/genoms/" + filename,
"parameter_text":
pop.best_genome.key,
"parameter_blob":
"",
"validation_hash":
"",
"hash":
"h",
"performance":
best_fitness,
"redir":
"1",
"username":
"******",
"pass_hash":
"$2a$04$ntNHmofQoMoajG89mTEM2uSR66jKXBgRQJnCgqfNN38aq9UkN4Y6q"
}
# TODO: COLOCAR DIRECCION CONFIGURABLE
res = requests.post(
my_url +
"/parameters?username=harveybc&pass_hash=$2a$04$ntNHmofQoMoajG89mTEM2uSR66jKXBgRQJnCgqfNN38aq9UkN4Y6q&process_hash=ph",
data=form_data)
res_json = res.json()
# TODO FIN: FUNCION DE SINCRONIZACION CON SINGULARITY
temp = temp + 1
# EVALUATE THE GENOMES WITH THE SUBSET TRAINING DATASET
gen_best = pop.run(ec.evaluate_genomes, num_iterations)
# TODO:
# VERIFY IF THERE ARE PENDING EVALUATIONS
# EVALUATE NUM_EVALUATIONS PENDING EVALUATIONS
#print(gen_best)
#visualize.plot_stats(stats, ylog=False, view=False, filename="fitness.svg")
#plt.plot(ec.episode_score, 'g-', label='score')
#plt.plot(ec.episode_length, 'b-', label='length')
#plt.grid()
#plt.legend(loc='best')
#plt.savefig("scores.svg")
#plt.close()
#mfs = sum(stats.get_fitness_mean()[-5:]) / 5.0
#print("Average mean fitness over last 5 generations: {0}".format(mfs))
#mfs = sum(stats.get_fitness_stat(min)[-5:]) / 5.0
#print("Average min fitness over last 3 generations: {0}".format(mfs))
if avg_score < 2000000000:
solved = False
if solved:
print("Solved.")
# Save the winners.
for n, g in enumerate(best_genomes):
name = 'winner-{0}'.format(n)
with open(name + '.pickle', 'wb') as f:
pickle.dump(g, f)
visualize.draw_net(config,
g,
view=False,
filename=name + "-net.gv")
visualize.draw_net(config,
g,
view=False,
filename=name + "-net-enabled.gv",
show_disabled=False)
visualize.draw_net(config,
g,
view=False,
filename=name +
"-net-enabled-pruned.gv",
show_disabled=False,
prune_unused=True)
break
except KeyboardInterrupt:
print("User break.")
break
env.close()
def __init__(self, name, **default_dict):
self.name = name
for n, default in iteritems(default_dict):
self._config_items[n] = [self._config_items[n][0], default]
for n in iterkeys(self._config_items):
setattr(self, n + "_name", self.config_item_name(n))
def process():
global program_state, p
global config
global obj_topo, road_topo
global CAR_ROW_START, CAR_COL_START, CAR_SHAPE_COL, sand_stall
global frame, new_distance, distance_stall, old_distance, base_distance
global old_time, new_time, base_time
global fitness_val, genome_fitness, generation_fitness, generation_fitness_index, generation_average_fitness
global genome_rank, generation_rank, generation_rank_index
global generation_count, genome_count, genome_list, genome, current_net, best_genome
global key_press
global winner
print(program_state)
# Stop the data processing if the agent is currently training
if program_state == STATE_BUFFERING:
time.sleep(0.1)
pass
elif program_state == STATE_BEGIN:
program_state = STATE_BUFFERING
# Report the current generation
p.reporters.start_generation(p.generation)
genome_list = list(iteritems(p.population))
program_state = STATE_PRESSING_F1
time.sleep(0.1)
pass
elif program_state == STATE_PRESSING_F1:
time.sleep(0.1)
pass
elif program_state == STATE_RESETTED:
program_state = STATE_BUFFERING
# Grab the genome if there is still genome to check
if genome_count < NUM_GENOMES:
_, genome = genome_list[genome_count]
current_net = neat.nn.FeedForwardNetwork.create(genome, config)
program_state = STATE_EVALUATING
else:
genome_count = 0
program_state = STATE_POST_PROCESSING
pass
# Sleep for the stability of the algorithm
time.sleep(0.1)
elif program_state == STATE_EVALUATING:
old_distance = new_distance
old_time = new_time
# Get the data from the request
start = time.time()
data = request.body.read().decode('utf8')
data = json.loads(data)
#
pixels = data["Pixels"]
speed = data["Speed"]
new_time = data["Time"]
if new_time > BASE_TIME: new_time = 0
new_distance = data["Distance"]
if new_distance == BASE_DISTANCE: new_distance = 0
rank = data["Rank"]
nitro = data["Nitro"]
# Determine a set of background color, we will try to remove this color from the game.
road_topo = topo_from_original_array(pixels)[: TOPO_SHAPE[0] // 2, :]
end = time.time()
# Calculate decision from current net
input_arr = road_topo.flatten()
key_press = generate_key_presses(current_net, input_arr) + "0" # Don't press F1 to reset
# Update frame counter and distance_stall and time
if new_distance < old_distance: base_distance += BASE_DISTANCE
if new_distance == old_distance:
distance_stall += 1
else:
distance_stall = 0
frame += 1
if new_time < old_time: base_time += BASE_TIME
if not road_topo[CAR_ROW_START + SHAPE_ROW, CAR_COL_START: CAR_COL_START + SHAPE_COL].any():
sand_stall += 1
else:
sand_stall = 0
fitness_val = (base_distance + new_distance) * DIST_C \
- (base_time + new_time) * TIME_C \
- rank * RANK_C \
+ BASE_FITNESS
# Print necessary information
os.system('cls')
print("Current generation: " + str(generation_count) + "/" + str(NUM_GENERATIONS))
print("----")
print_topo(road_topo)
print(end - start)
print_key_presses(key_press, BUTTONS)
print("Speed: " + str(speed))
print("Time: " + str(base_time + new_time))
print("Distance: " + str(base_distance + new_distance))
print("Rank: " + str(rank))
print("Nitro: " + str(nitro))
print("Current genome: " + str(genome_count + 1) + "/" + str(NUM_GENOMES))
print("Fitness value: " + str(fitness_val))
print('--------------')
print('| Gen | Best Agent | Score | Rank | Avg Score |')
print('|----------------------------------------------------|')
for i in range(len(generation_fitness)):
print("| {:3d} | {:10d} | {:10d} | {:4d} | {:11.3f} |".format( \
i, generation_fitness_index[i], generation_fitness[i], generation_rank[i], generation_average_fitness[i]))
# Stop the running if stall limit is reached
if distance_stall > STALL_LIMIT:
genome.fitness = fitness_val
print("- Evaluated Genome " + str(genome_count) + ": " + str(fitness_val))
# Add a bunch of statistical variables
genome_fitness.append(fitness_val)
genome_rank.append(rank)
# Reset
reset_variables()
genome_count += 1
program_state = STATE_PRESSING_F1
# Return something cuz a post go with a get
pass
elif program_state == STATE_POST_PROCESSING:
program_state = STATE_BUFFERING
# Gather and report statistics.
best = None
for g in itervalues(p.population):
if best is None or g.fitness > best.fitness:
best = g
p.reporters.post_evaluate(p.config, p.population, p.species, best)
# Track the best gen ome ever seen.
if p.best_genome is None or best.fitness > p.best_genome.fitness:
p.best_genome = best
# End if the fitness threshold is reached.
fv = p.fitness_criterion(g.fitness for g in itervalues(p.population))
if fv >= p.config.fitness_threshold:
p.reporters.found_solution(p.config, p.generation, best)
program_state = STATE_RETURN_BEST
# Create the next generation from the current generation.
p.population = p.reproduction.reproduce(p.config, p.species,
p.config.pop_size, p.generation)
# Check for complete extinction.
if not p.species.species:
p.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if p.config.reset_on_extinction:
p.population = p.reproduction.create_new(p.config.genome_type,
p.config.genome_config,
p.config.pop_size)
else:
raise neat.CompleteExtinctionException()
# Divide the new population into species.
p.species.speciate(p.config, p.population, p.generation)
p.reporters.end_generation(p.config, p.population, p.species)
p.generation += 1
# Add the best genome value into the statistics
generation_fitness.append(max(genome_fitness))
generation_average_fitness.append(np.average(genome_fitness))
generation_fitness_index.append(np.argmax(genome_fitness))
genome_fitness = []
generation_rank.append(min(genome_rank))
generation_rank_index.append(np.argmin(genome_rank))
genome_rank = []
# Increment generation count and switch state
np.savetxt("best_genome_by_generation.npy",generation_fitness_index)
generation_count += 1
if generation_count == NUM_GENERATIONS: program_state = STATE_RETURN_BEST
else: program_state = STATE_BEGIN
pass
elif program_state == STATE_RETURN_BEST:
best_genome = p.best_genome
program_state = STATE_TEST_BEST
pass
elif program_state == STATE_TEST_BEST:
print("Should start testing stuff now")
pass
return("Finished")
def reproduce(self, config, species, pop_size, generation):
"""
Handles creation of genomes, either from scratch or by sexual or
asexual reproduction from parents.
"""
# TODO: I don't like this modification of the species and stagnation objects,
# because it requires internal knowledge of the objects.
# Filter out stagnated species, collect the set of non-stagnated
# species members, and compute their average adjusted fitness.
# The average adjusted fitness scheme (normalized to the interval
# [0, 1]) allows the use of negative fitness values without
# interfering with the shared fitness scheme.
all_fitnesses = []
remaining_species = []
old_population = []
for stag_sid, stag_s, stagnant in self.stagnation.update(
species, generation):
old_population.append(itervalues(stag_s.members))
if stagnant:
self.reporters.species_stagnant(stag_sid, stag_s)
else:
all_fitnesses.extend(m.fitness
for m in itervalues(stag_s.members))
remaining_species.append(stag_s)
# The above comment was not quite what was happening - now getting fitnesses
# only from members of non-stagnated species.
# No species left.
if not remaining_species:
species.species = {}
return {} # was []
# Find minimum/maximum fitness across the entire population, for use in
# species adjusted fitness computation.
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.
# TODO: The ``1.0`` below is rather arbitrary, and should be configurable.
fitness_range = max(1.0, max_fitness - min_fitness)
for afs in remaining_species:
# Compute adjusted fitness.
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) # type: float
self.reporters.info(
"Average adjusted fitness: {:.3f}".format(avg_adjusted_fitness))
# Compute the number of new members for each species in the new generation.
previous_sizes = [len(s.members) for s in remaining_species]
min_species_size = self.reproduction_config.min_species_size
# Isn't the effective min_species_size going to be max(min_species_size,
# self.reproduction_config.elitism)? That would probably produce more accurate tracking
# of population sizes and relative fitnesses... doing. TODO: document.
min_species_size = max(min_species_size,
self.reproduction_config.elitism)
spawn_amounts = self.compute_spawn(adjusted_fitnesses, previous_sizes,
pop_size, min_species_size)
# Bandit Update
# TODO Reconsider reward scheme to be invariant of actual fitness value
# Percentage improvement to fitness?
# Fitness improvement as a fraction of best improvement? - seems good, then one mutation is always 1, rest are < 1
# How to reward or perceive "failure"? Same as fraction but for decreases?
# 1 if best arm in generation else 0?
if generation > 0:
mutation_delta = []
for mutant, old_fitness, mutations in self.records[-1]:
fit_delta = mutant.fitness - old_fitness
for m in mutations:
mutation_delta.append((m, fit_delta))
# print(mutation_delta)
self.bandit.update_all(mutation_delta)
# if m not in mutations_deltas:
# mutations_deltas[m] = [fit_delta]
# else:
# mutations_deltas[m].append(fit_delta)
# for mutations, deltas in mutations_deltas.items():
# self.bandit.update(mutations, deltas) # len deltas can be removed, the number of rewards is the number of plays
# print([(g.key, g.fitness-f, m) for g,f,m in self.records[-1]])
self.reporters.post_reproduction(config, self.bandit, None)
self.records.append([])
new_population = {}
species.species = {}
for spawn, s in zip(spawn_amounts, remaining_species):
# If elitism is enabled, each species always at least gets to retain its elites.
spawn = max(spawn, self.reproduction_config.elitism)
assert spawn > 0
# The species has at least one member for the next generation, so retain it.
old_members = list(iteritems(s.members))
s.members = {}
species.species[s.key] = s
# Sort members in order of descending fitness.
old_members.sort(reverse=True, key=lambda x: x[1].fitness)
# Transfer elites to new generation.
if self.reproduction_config.elitism > 0:
for i, m in old_members[:self.reproduction_config.elitism]:
new_population[i] = m
spawn -= 1
if spawn <= 0:
continue
# Only use the survival threshold fraction to use as parents for the next generation.
repro_cutoff = int(
math.ceil(self.reproduction_config.survival_threshold *
len(old_members)))
# Use at least two parents no matter what the threshold fraction result is.
repro_cutoff = max(repro_cutoff, 2)
old_members = old_members[:repro_cutoff]
# Randomly choose parents and produce the number of offspring allotted to the species.
while spawn > 0:
spawn -= 1
parent1_id, parent1 = choice(old_members)
parent2_id, parent2 = (parent1_id, parent1)
gid = next(self.genome_indexer)
child = config.genome_type(gid)
child.configure_crossover(parent1, parent2,
config.genome_config)
mutation_directives = self.bandit.play(generation)
child.mutate(config.genome_config, mutation_directives)
new_population[gid] = child
self.ancestors[gid] = (parent1_id, parent2_id)
self.records[-1].append(
(child, parent1.fitness, mutation_directives))
return new_population
def get_population(self):
return list(iteritems(self.population))
def speciate(self, config: Config, population, generation, logger=None):
"""
Place genomes into species by genetic similarity.
:note: This method assumes the current representatives of the species are from the old generation, and that
after speciation has been performed, the old representatives should be dropped and replaced with
representatives from the new generation.
"""
assert isinstance(population, dict)
unspeciated = set(
iterkeys(population)) # Initially the full population
distances = GenomeDistanceCache(
config.genome) # Cache memorizing distances between genomes
# distances.warm_up(population) # No warm-up since only comparison with representatives! (expensive!)
new_representatives = dict(
) # Updated representatives for each specie (least difference with previous)
members = dict(
) # Dictionary containing for each specie its corresponding members
# Update the representatives for each specie as the genome closest to the previous representative
for sid, s in iteritems(self.species):
candidates = []
for gid in unspeciated:
genome = population[gid]
d = distances(s.representative, genome)
candidates.append((d, genome))
# Sort the genomes based on their distance towards the specie and take the closest genome
sorted_repr = sorted(candidates, key=lambda x: x[0])
new_repr = sorted_repr[0][1]
new_representatives[sid] = new_repr.key
members[sid] = [new_repr.key]
unspeciated.remove(new_repr.key)
# Partition the population into species based on their genetic similarity
while unspeciated:
# Pull unspeciated genome
gid = unspeciated.pop()
genome = population[gid]
# Find the species with the most similar representative
specie_distance = []
candidates = []
for sid, rid in iteritems(new_representatives):
rep = population[rid]
d = distances(rep, genome)
specie_distance.append((d, sid))
if d < config.population.get_compatibility_threshold(
n_species=len(new_representatives)):
candidates.append((d, sid))
# There are species close enough; add genome to most similar specie
if candidates:
_, sid = min(candidates, key=lambda x: x[0])
members[sid].append(gid)
else: # No specie is similar enough, create new specie with this genome as its representative
sid = next(self.indexer)
new_representatives[sid] = gid
members[sid] = [gid]
# Update the species collection based on the newly defined speciation
self.genome_to_species = dict()
for sid, rid in iteritems(new_representatives):
s = self.species.get(sid)
# One of the newly defined species
if s is None:
s = Species(sid, generation)
self.species[sid] = s
# Append the newly added members to the genome_to_species mapping
specie_members = members[sid]
for gid in specie_members:
self.genome_to_species[gid] = sid
# Update the specie's current representative and members
member_dict = dict((genome_id, population[genome_id])
for genome_id in specie_members)
s.update(representative=population[rid], members=member_dict)
# Report over the current species (distances)
self.reporters.info(
f'Genetic distance:'
f'\n\t- Maximum: {max(itervalues(distances.distances)):.5f}'
f'\n\t- Mean: {mean(itervalues(distances.distances)):.5f}'
f'\n\t- Minimum: {min(itervalues(distances.distances)):.5f}'
f'\n\t- Standard deviation: {stdev(itervalues(distances.distances)):.5f}',
logger=logger,
print_result=False,
)
print(
f'Maximum genetic distance: {round(max(itervalues(distances.distances)), 3)}'
) # Print reduced version
# Report over the most complex genome
most_complex = sorted([(g.size(), gid)
for gid, g in population.items()],
key=lambda x: x[0],
reverse=True)[0]
gid = most_complex[1]
size = most_complex[0]
specie_id = self.genome_to_species[gid]
distance = distances(population[gid],
self.species[specie_id].representative)
self.reporters.info(
f"Most complex genome '{gid}' "
f"of size {size} "
f"belongs to specie '{specie_id}' "
f"with distance to representative of {round(distance, 3)}",
logger=logger,
)
def run(self, fitness_function, self2, n=None):
if self.config.no_fitness_termination and (n is None):
raise RuntimeError(
"Cannot have no generational limit with no fitness termination"
)
if self2.config.no_fitness_termination and (n is None):
raise RuntimeError(
"Cannot have no generational limit with no fitness termination"
)
k = 0
while n is None or k < n:
k += 1
self.reporters.start_generation(self.generation)
self2.reporters.start_generation(self2.generation)
# Evaluate all genomes using the user-provided function.
fitness_function(list(iteritems(self.population)),
list(iteritems(self2.population)), self.config)
# Gather and report statistics.
best1 = None
for g in itervalues(self.population):
if best1 is None or g.fitness > best1.fitness:
best1 = g
self.reporters.post_evaluate(self.config, self.population,
self.species, best1)
best2 = None
for g in itervalues(self2.population):
if best2 is None or g.fitness > best2.fitness:
best2 = g
self2.reporters.post_evaluate(self2.config, self2.population,
self2.species, best2)
# Track the best genome ever seen.
if self.best_genome is None or best1.fitness > self.best_genome.fitness:
self.best_genome = best1
if not self.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = self.fitness_criterion(
g.fitness for g in itervalues(self.population))
if fv >= self.config.fitness_threshold:
self.reporters.found_solution(self.config, self.generation,
best1)
break
#Do the same with self2 <--- balances out config version
if self2.best_genome is None or best2.fitness > self2.best_genome.fitness:
self2.best_genome = best2
if not self2.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = self2.fitness_criterion(
g.fitness for g in itervalues(self2.population))
if fv >= self2.config.fitness_threshold:
self2.reporters.found_solution(self2.config,
self2.generation, best2)
break
# Create the next generation from the current generation.
self.population = self.reproduction.reproduce(
self.config, self.species, self.config.pop_size,
self.generation)
self2.population = self2.reproduction.reproduce(
self2.config, self2.species, self2.config.pop_size,
self2.generation)
# Check for complete extinction.
if not self.species.species:
self.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
self.population = self.reproduction.create_new(
self.config.genome_type, self.config.genome_config,
self.config.pop_size)
else:
raise CompleteExtinctionException()
if not self2.species.species:
self2.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self2.config.reset_on_extinction:
self2.population = self2.reproduction.create_new(
self2.config.genome_type, self2.config.genome_config,
self2.config.pop_size)
else:
raise CompleteExtinctionException()
# Divide the new population into species.
self.species.speciate(self.config, self.population,
self.generation)
self2.species.speciate(self2.config, self2.population,
self2.generation)
self.reporters.end_generation(self.config, self.population,
self.species)
self2.reporters.end_generation(self2.config, self2.population,
self2.species)
self.generation += 1
self2.generation += 1
if self.config.no_fitness_termination:
self.reporters.found_solution(self.config, self.generation,
self.best_genome)
if self2.config.no_fitness_termination:
self2.reporters.found_solution(self2.config, self2.generation,
self2.best_genome)
return (self.best_genome, self2.best_genome)
output = net.activate(input_arr)
s = ""
for val in output:
if val < THRESHOLD: s += "0"
else: s += "1"
return s
# ---------------
# PREPARE NETWORK
# ---------------
# best_agents = np.load("./data/from_tung/best_genome_by_generation.npy")
p = neat.Checkpointer.restore_checkpoint('./data/from_tung/neat-checkpoint-' +
str(CHOSEN_GEN))
genome_list = list(iteritems(p.population))
_, genome = genome_list[CHOSEN_GENOME]
current_net = neat.nn.FeedForwardNetwork.create(genome, p.config)
visualize.draw_net(p.config,
genome,
filename="Generation_" + str(CHOSEN_GEN) + "_Genome_" +
str(CHOSEN_GENOME),
fmt="pdf")
# --------------
# NEURAL NETWORK
# --------------
while (True):
r = requests.get("http://127.0.0.1:37979/get_input")
data = r.json()
def speciate(self, config, population):
"""
Place genomes into species by genetic similarity.
Note that this method assumes the current representatives of the species are from the old
generation, and that after speciation has been performed, the old representatives should be
dropped and replaced with representatives from the new generation. If you violate this
assumption, you should make sure other necessary parts of the code are updated to reflect
the new behavior.
"""
assert type(population) is dict
compatibility_threshold = config.species_set_config[
'compatibility_threshold']
# Reset all species member lists.
for s in itervalues(self.species):
s.members.clear()
self.to_species.clear()
# Partition population into species based on genetic similarity.
distances = []
for key, individual in iteritems(population):
# Find the species with the most similar representative.
min_distance = sys.float_info.max
closest_species = None
closest_species_id = None
for sid, s in iteritems(self.species):
rep = s.representative
distance = individual.distance(rep, config.genome_config)
distances.append(distance)
compatible = distance < compatibility_threshold
if compatible and distance < min_distance:
closest_species = s
closest_species_id = sid
min_distance = distance
if closest_species is not None:
closest_species.add(key, individual)
self.to_species[key] = closest_species_id
else:
# No species is similar enough, create a new species for this individual.
sid = self.indexer.get_next()
self.species[sid] = Species(sid, key, individual)
self.to_species[key] = sid
self.reporters.info('Mean genetic distance {0}, std dev {1}'.format(
mean(distances), stdev(distances)))
# Only keep non-empty species.
empty_species_ids = []
for sid, s in iteritems(self.species):
if not s.members:
empty_species_ids.append(sid)
for sid in empty_species_ids:
del self.species[sid]
# Select a random current member as the new representative.
for s in itervalues(self.species):
s.representative = random.choice(list(s.members.values()))
selection_type = sys.argv[1]
base_dir = sys.argv[2]
read_state_sequences = dict()
with open(base_dir + 'state_usages.csv', 'r') as csv_file:
csv_reader = csv.reader(csv_file)
for row in csv_reader:
if selection_type == 'scenario':
key = int(int(filter(str.isdigit, row[0])))
index = int(row[1])
elif selection_type == 'controller':
key = int(row[1])
index = int(int(filter(str.isdigit, row[0])))
else:
print('Unknown selection type')
exit(1)
if key not in read_state_sequences:
read_state_sequences[key] = []
read_state_sequences[key].append((index, int(row[2]), [int(x) for x in row[3:]]))
for key, state_sequences in iteritems(read_state_sequences):
visualizer = StateUsageVisualizer(base_dir, selection_type, key)
visualizer.state_sequences = state_sequences # Cheat to not have to append them all.
visualizer.finalize()
def distance(self, other, config)
"""
Returns the genetic distance between this genome and the other. This distance value
is used to compute genome compatibility for speciation.
"""
# Compute node gene distance component.
node_distance = 0.0
if self.nodes or other.nodes:
disjoint_nodes = 0
for k2 in iterkeys(other.nodes):
if k2 not in self.nodes:
disjoint_nodes += 1
for k1, n1 in iteritems(self.nodes):
n2 = other.nodes.get(k1)
if n2 is None:
disjoint_nodes += 1
else:
# Homologous genes compute their own distance value.
node_distance += n1.distance(n2, config)
max_nodes = max(len(self.nodes), len(other.nodes))
node_distance = (node_distance +
(config.compatibility_disjoint_coefficient *
disjoint_nodes)) / max_nodes
# Compute connection gene differences.
connection_distance = 0.0
if self.connections.keys() != [None] or other.connections.keys() != [None]:
def reproduce(self,
config: Config,
species: DefaultSpecies,
generation: int,
logger=None):
"""Handles creation of genomes, either from scratch or by sexual or asexual reproduction from parents."""
# Check is one of the species has become stagnant (i.e. must be removed)
remaining_fitness = []
remaining_species = []
for stag_sid, stag_s, stagnant in self.stagnation.update(
config=config, species_set=species, gen=generation):
# If specie is stagnant, then remove
if stagnant:
self.reporters.species_stagnant(stag_sid,
stag_s,
logger=logger)
# Add the specie to remaining_species and save each of its members' fitness
else:
remaining_fitness.extend(m.fitness
for m in itervalues(stag_s.members))
remaining_species.append(stag_s)
# If no species is left then force hard-reset
if not remaining_species:
species.species = dict()
return dict()
# Calculate the adjusted fitness, normalized by the minimum fitness across the entire population
for specie in remaining_species:
# Adjust a specie's fitness in a fitness sharing manner. A specie's fitness gets normalized by the number of
# members it has, this to ensure that a better performing specie does not takes over the population
# A specie's fitness is determined by its most fit genome
specie_fitness = max([m.fitness for m in specie.members.values()])
specie_size = len(specie.members)
specie.adjusted_fitness = specie_fitness / max(
specie_size, config.population.min_specie_size)
# Minimum specie-size is defined by the number of elites and the minimal number of genomes in a population
spawn_amounts = self.compute_spawn(
adjusted_fitness=[s.adjusted_fitness for s in remaining_species],
previous_sizes=[len(s.members) for s in remaining_species],
pop_size=config.population.pop_size,
min_species_size=max(config.population.min_specie_size,
config.population.genome_elitism))
# Setup the next generation by filling in the new species with their elites and offspring
new_population = dict()
species.species = dict()
for spawn_amount, specie in zip(spawn_amounts, remaining_species):
# If elitism is enabled, each species will always at least gets to retain its elites
spawn_amount = max(spawn_amount, config.population.genome_elitism)
assert spawn_amount > 0
# Get all the specie's old (evaluated) members
old_members = list(iteritems(
specie.members)) # Temporarily save members of last generation
specie.members = dict() # Reset members
species.species[specie.key] = specie
# Sort members in order of descending fitness (i.e. most fit members in front)
old_members.sort(reverse=True, key=lambda x: x[1].fitness)
# Make sure that all the specie's elites are added to the new generation
if config.population.genome_elitism > 0:
# Add the specie's elites to the global population
for i, m in old_members[:config.population.genome_elitism]:
new_population[i] = m
spawn_amount -= 1
# Add the specie's past elites as well if requested
for i in range(
min(len(specie.elite_list),
config.population.genome_elite_stagnation - 1)):
gid, g = specie.elite_list[-(i + 1)]
if gid not in new_population: # Only add genomes not yet present in the population
new_population[gid] = g
spawn_amount -= 1
# Update the specie's elite_list
specie.elite_list.append(old_members[0])
# Check if the specie has the right to add more genomes to the population
if spawn_amount <= 0: continue
# Only use the survival threshold fraction to use as parents for the next generation, use at least all the
# elite of a population as parents
reproduction_cutoff = max(
round(config.population.parent_selection * len(old_members)),
config.population.genome_elitism)
# Since asexual reproduction, at least one parent must be chosen
reproduction_cutoff = max(reproduction_cutoff, 1)
parents = old_members[:reproduction_cutoff]
# Add the elites again to the parent-set such that these have a greater likelihood of being chosen
parents += old_members[:config.population.genome_elitism]
# Fill the specie with offspring based, which is a mutation of the chosen parent
while spawn_amount > 0:
spawn_amount -= 1
# Init genome dummy (values are overwritten later)
gid = next(self.genome_indexer)
child: Genome = Genome(gid,
num_outputs=config.genome.num_outputs,
bot_config=config.bot)
# Choose the parents, note that if the parents are not distinct, crossover will produce a genetically
# identical clone of the parent (but with a different ID)
p1_id, p1 = choice(parents)
child.connections = copy.deepcopy(p1.connections)
child.nodes = copy.deepcopy(p1.nodes)
# Mutate the child
child.mutate(config.genome)
# Ensure that the child is connected
while len(child.get_used_connections()) == 0:
child.mutate_add_connection(config.genome)
# Add the child to the global population
new_population[gid] = child
return new_population
def create(genome, config):
""" Receives a genome and returns its phenotype (a GRUNetwork). """
genome_config = config.genome_config
required = required_for_output(genome_config.input_keys,
genome_config.output_keys,
genome.connections, genome.nodes)
connections = [
cg.key for cg in itervalues(genome.connections) if cg.enabled
]
node_evals = []
node_inputs = {}
for cg in itervalues(genome.connections):
if not cg.enabled:
continue
i, o = cg.key
if o not in required and i not in required:
continue
if o not in node_inputs:
node_inputs[o] = [(i, cg.weight)]
else:
node_inputs[o].append((i, cg.weight))
node_evals = []
gate_list = set()
# Add the gates first for proper computation order
for node_key, inputs in iteritems(node_inputs):
ng = genome.nodes[node_key]
if type(ng) is GRUNodeGene:
for gate_key in [ng.read_gate, ng.forget_gate]:
if type(gate_key) is int and gate_key not in gate_list:
gate_list = gate_list.union(gate_key)
gate_g = genome.nodes[gate_key]
activation_function = genome_config.activation_defs.get(
gate_g.activation)
aggregation_function = genome_config.aggregation_function_defs.get(
gate_g.aggregation)
node_evals.append(
(gate_key, activation_function,
aggregation_function, gate_g.bias,
gate_g.response, inputs,
[gate_g.read_gate, gate_g.forget_gate]
if type(gate_g) is GRUNodeGene else None))
for node_key, inputs in iteritems(node_inputs):
if node_key not in gate_list:
ng = genome.nodes[node_key]
activation_function = genome_config.activation_defs.get(
ng.activation)
aggregation_function = genome_config.aggregation_function_defs.get(
ng.aggregation)
node_evals.append((node_key, activation_function,
aggregation_function, ng.bias, ng.response,
inputs, [ng.read_gate, ng.forget_gate]
if type(ng) is GRUNodeGene else None))
nw = GRUNetwork(genome_config.input_keys, genome_config.output_keys,
node_evals, gate_list)
nw.genome = genome
return nw
def reproduce(self, config, species, pop_size, generation):
# TODO: I don't like this modification of the species and stagnation objects,
# because it requires internal knowledge of the objects.
# Find minimum/maximum fitness across the entire population, for use in
# species adjusted fitness computation.
all_fitnesses = []
for sid, s in iteritems(species.species):
all_fitnesses.extend(m.fitness for m in itervalues(s.members))
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(1.0, max_fitness - min_fitness)
# Filter out stagnated species, collect the set of non-stagnated
# species members, and compute their average adjusted fitness.
# The average adjusted fitness scheme (normalized to the interval
# [0, 1]) allows the use of negative fitness values without
# interfering with the shared fitness scheme.
num_remaining = 0
species_fitness = []
avg_adjusted_fitness = 0.0
for sid, s, stagnant in self.stagnation.update(species, generation):
if stagnant:
self.reporters.species_stagnant(sid, s)
else:
num_remaining += 1
# Compute adjusted fitness.
msf = mean([m.fitness for m in itervalues(s.members)])
s.adjusted_fitness = (msf - min_fitness) / fitness_range
species_fitness.append((sid, s, s.fitness))
avg_adjusted_fitness += s.adjusted_fitness
# No species left.
if 0 == num_remaining:
species.species = {}
return []
avg_adjusted_fitness /= len(species_fitness)
self.reporters.info(
"Average adjusted fitness: {:.3f}".format(avg_adjusted_fitness))
# Compute the number of new individuals to create for the new generation.
spawn_amounts = []
for sid, s, sfitness in species_fitness:
spawn = len(s.members)
if sfitness > avg_adjusted_fitness:
spawn = max(spawn + 2, spawn * 1.1)
else:
spawn = max(spawn * 0.9, 2)
spawn_amounts.append(spawn)
# Normalize the spawn amounts so that the next generation is roughly
# the population size requested by the user.
total_spawn = sum(spawn_amounts)
norm = pop_size / total_spawn
spawn_amounts = [int(round(n * norm)) for n in spawn_amounts]
new_population = {}
species.species = {}
for spawn, (sid, s, sfitness) in zip(spawn_amounts, species_fitness):
# If elitism is enabled, each species always at least gets to retain its elites.
spawn = max(spawn, self.elitism)
if spawn <= 0:
continue
# The species has at least one member for the next generation, so retain it.
old_members = list(iteritems(s.members))
s.members = {}
species.species[sid] = s
# Sort members in order of descending fitness.
old_members.sort(reverse=True, key=lambda x: x[1].fitness)
# Transfer elites to new generation.
if self.elitism > 0:
for i, m in old_members[:self.elitism]:
new_population[i] = m
spawn -= 1
if spawn <= 0:
continue
# Only use the survival threshold fraction to use as parents for the next generation.
repro_cutoff = int(
math.ceil(self.survival_threshold * len(old_members)))
# Use at least two parents no matter what the threshold fraction result is.
repro_cutoff = max(repro_cutoff, 2)
old_members = old_members[:repro_cutoff]
# Randomly choose parents and produce the number of offspring allotted to the species.
while spawn > 0:
spawn -= 1
parent1_id, parent1 = random.choice(old_members)
parent2_id, parent2 = random.choice(old_members)
# Note that if the parents are not distinct, crossover will produce a
# genetically identical clone of the parent (but with a different ID).
gid = self.genome_indexer.get_next()
child = config.genome_type(gid)
child.configure_crossover(parent1, parent2,
config.genome_config)
child.mutate(config.genome_config)
new_population[gid] = child
self.ancestors[gid] = (parent1_id, parent2_id)
return new_population
def build_population_nn(self):
nn = {}
for index, pop in list(iteritems(self.population.population)):
nn[index] = self.create_net(pop)
self.rt_population_nn = nn
def run(self, fitness_function, n=None):
# Variables needed to save archive on each update
winner_name_prefix = "archive_checkpoint_" + self.winner_name
if self.config.no_fitness_termination and (n is None):
raise RuntimeError("Cannot have no generational limit with no fitness termination")
k = 0
while n is None or k < n:
k += 1
self.reporters.start_generation(self.generation)
not_evaluated = {}
evaluated = []
# len(population) = 2*pop_size
for gid, g in self.population.items():
if g.fitness is None:
not_evaluated[gid] = g
else:
evaluated.append((gid, g))
# Evaluate all genomes using the user-provided function.
fitness_function(list(iteritems(not_evaluated)), self.config)
self.KNNdistances(self.population, self.novelty_archive, self.n_neighbors)
if len(evaluated) != 0:
self.species.speciate(self.config, self.population, self.generation)
dim = 0
max_spec_dim = 0
max_sid = -1
for sid, s in iteritems(self.species.species):
s.members = self.get_best_n_members(s.members, math.ceil(len(s.members) / 2))
d = len(s.members)
if d > max_spec_dim:
max_spec_dim = d
max_sid = sid
dim += d
diff = dim - self.config.pop_size
if diff > 0 and diff > max_spec_dim:
s = self.species.species[max_sid]
s.members = self.get_best_n_members(s.members, len(s.members) - diff)
new_population = {}
for sid, s in iteritems(self.species.species):
for gid, g in s.members.items():
new_population[gid] = g
self.population = new_population
self.species.speciate(self.config, self.population, self.generation)
# Check for complete extinction.
if not self.species.species:
self.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
self.population = self.reproduction.create_new(self.config.genome_type,
self.config.genome_config,
self.config.pop_size)
else:
raise CompleteExtinctionException()
# Gather and report statistics.
best = None
for g in itervalues(self.population):
if best is None or g.dist > best.dist:
best = g
if g.dist > self.novelty_threshold:
if g not in self.novelty_archive:
self.novelty_archive.append(g)
print("Distanza di aggiunta: ", g.dist)
self.n_add_archive += 1
self.last_archive_modified = self.generation
with open(winner_name_prefix, "wb") as f:
pickle.dump(self.novelty_archive, f)
self.reporters.post_evaluate(self.config, self.population, self.species, best)
if not self.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = self.fitness_criterion(g.dist for g in itervalues(self.population))
if fv >= self.config.fitness_threshold:
self.reporters.found_solution(self.config, self.generation, best)
break
# Create the next generation from the current generation.
self.population = self.reproduction.reproduce(self.config, self.species,
self.config.pop_size, self.generation)
# Check for complete extinction.
if not self.species.species:
self.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
self.population = self.reproduction.create_new(self.config.genome_type,
self.config.genome_config,
self.config.pop_size)
else:
raise CompleteExtinctionException()
# Divide the new population into species.
self.species.speciate(self.config, self.population, self.generation)
self.reporters.end_generation(self.config, self.population, self.species)
time_diff = self.generation - self.last_archive_modified
if time_diff > 60:
self.novelty_threshold -= self.novelty_threshold * 0.05
if self.n_add_archive > 4 and time_diff <= 30:
self.novelty_threshold += self.novelty_threshold * 0.05
self.n_add_archive = 0
if time_diff > 30:
self.n_add_archive = 0
self.reporters.info("Novelty's archive size: {}\n".format(len(self.novelty_archive)))
if len(self.novelty_archive) > 0:
self.reporters.info("Archive's best: {}".format(
max(self.novelty_archive, key=lambda x: x.fitness[0]).fitness[0]))
else:
self.reporters.info("Archive's best: 0")
self.generation += 1
if self.config.no_fitness_termination:
self.reporters.found_solution(self.config, self.generation, self.best_genome)
return self.novelty_archive
def rt_iterate(self):
self.population.reporters.start_generation(self.population.generation)
# Gather and report statistics.
best = None
worst = None
for g in itervalues(self.population.population):
if not hasattr(g, 'birth'):
g.birth = self.population.generation
if g.fitness is None:
continue
if best is None or g.fitness > best.fitness:
best = g
if (worst is None or g.fitness < worst.fitness) and \
self.population.generation - g.birth > self.population.config.stagnation_config.max_stagnation:
worst = g
population_with_fitness = dict([
p for p in iteritems(self.population.population)
if p[1].fitness is not None
])
if population_with_fitness:
self.population.reporters.post_evaluate(self.config,
population_with_fitness,
self.population.species,
best)
# Track the best genome ever seen.
if self.population.best_genome is None or best.fitness > self.population.best_genome.fitness:
self.population.best_genome = best
if not self.population.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = self.population.fitness_criterion(
g.fitness for g in itervalues(population_with_fitness))
if fv >= self.population.config.fitness_threshold:
self.population.reporters.found_solution(
self.population.config, self.population.generation, best)
return
# remove worst genome and replace with new one
if worst is not None:
new_genomes = self.population.reproduction.reproduce(
self.population.config, self.population.species, 1,
self.population.generation)
new_key = np.max(
[g.key for g in itervalues(self.population.population)]) + 1
for g in itervalues(new_genomes):
del self.population.population[worst.key]
g.key = new_key
self.population.population[new_key] = g
print(new_key)
break
# Divide the new population into species.
if population_with_fitness:
self.population.species.speciate(self.population.config,
population_with_fitness,
self.population.generation)
# self.population.reporters.end_generation(self.population.config, self.population.population,
# self.population.species)
self.population.generation += 1
from MyCheckpoint import MyCheckpointer
from GenomeVisualizer import GenomeVisualizer
root_path = '../logs/meandist_collision100/1525807840'
generation = 1029
top_x = 5
config_path = '{}/neat_config'.format(root_path)
pop_path = '{}/pop-gen-{}'.format(root_path, generation)
neat_conf = neat.Config(neat.DefaultGenome, neat.DefaultReproduction,
neat.DefaultSpeciesSet, neat.DefaultStagnation,
config_path)
pop = MyCheckpointer.restore_checkpoint(pop_path)
genomes = list(iteritems(pop.population))
def cond(item):
return item[1].fitness
sorted_genoms = sorted(genomes, reverse=True, key=cond)
genomes = sorted_genoms[0:top_x]
for i in range(0, len(genomes)):
genome_viz_file = '{}/genome-gen-{}-top-{}-viz'.format(
root_path, generation, i)
GenomeVisualizer.draw_net(neat_conf,
genomes[i][1],
False,
def neat_manual_looping(pop, generation_limit=None):
if pop.config.no_fitness_termination and (generation_limit is None):
raise RuntimeError(
"Cannot have no generational limit with no fitness termination")
yield
k = 0
while generation_limit is None or k < generation_limit:
k += 1
pop.reporters.start_generation(pop.generation)
genomes = list(iteritems(pop.population))
finesses = yield genomes
for (genome_id, genome), fitness in zip(genomes, finesses):
genome.fitness = fitness
# Gather and report statistics.
best = None
for g in itervalues(pop.population):
if best is None or g.fitness > best.fitness:
best = g
pop.reporters.post_evaluate(pop.config, pop.population, pop.species,
best)
# Track the best genome ever seen.
if pop.best_genome is None or best.fitness > pop.best_genome.fitness:
pop.best_genome = best
if not pop.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = pop.fitness_criterion(g.fitness
for g in itervalues(pop.population))
if fv >= pop.config.fitness_threshold:
pop.reporters.found_solution(pop.config, pop.generation, best)
break
# Create the next generation from the current generation.
pop.population = pop.reproduction.reproduce(pop.config, pop.species,
pop.config.pop_size,
pop.generation)
# Check for complete extinction.
if not pop.species.species:
pop.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if pop.config.reset_on_extinction:
pop.population = pop.reproduction.create_new(
pop.config.genome_type, pop.config.genome_config,
pop.config.pop_size)
else:
raise CompleteExtinctionException()
# Divide the new population into species.
pop.species.speciate(pop.config, pop.population, pop.generation)
pop.reporters.end_generation(pop.config, pop.population, pop.species)
pop.generation += 1
if pop.config.no_fitness_termination:
pop.reporters.found_solution(pop.config, pop.generation,
pop.best_genome)
def train(
population: Population,
game_config: Config,
games: list,
iterations: int,
unused_cpu: int = 0,
save_interval: int = 10,
):
"""Train the population on the requested number of iterations. Manual adaptation of main's train()."""
population.log("\n===> TRAINING <===\n")
multi_env = get_multi_env(pop=population, game_config=game_config)
msg = f"Repetitive evaluating on games: {games} for {iterations} iterations"
population.log(msg, print_result=False)
# Iterate and evaluate over the games
saved = True
for iteration in range(iterations):
# Set and randomize the games
multi_env.set_games(games, noise=True)
# Prepare the generation's reporters for the generation
population.reporters.start_generation(gen=population.generation,
logger=population.log)
# Fetch the dictionary of genomes
genomes = list(iteritems(population.population))
# Initialize the evaluation-pool
pool = mp.Pool(mp.cpu_count() - unused_cpu)
manager = mp.Manager()
return_dict = manager.dict()
for genome in genomes:
pool.apply_async(func=multi_env.eval_genome,
args=(genome, return_dict))
pool.close() # Close the pool
pool.join() # Postpone continuation until everything is finished
# Calculate the fitness from the given return_dict
fitness = calc_pop_fitness(
fitness_cfg=population.config.evaluation,
game_cfg=game_config.game,
game_obs=return_dict,
gen=population.generation,
)
for i, genome in genomes:
genome.fitness = fitness[i]
# Gather and report statistics
best = None
for g in itervalues(population.population):
if best is None or g.fitness > best.fitness: best = g
population.reporters.post_evaluate(population=population.population,
species=population.species,
best_genome=best,
logger=population.log)
# Update the population's best_genome
genomes = sorted(population.population.items(),
key=lambda x: x[1].fitness,
reverse=True)
population.best_fitness[population.generation] = genomes[0][1].fitness
population.best_genome_hist[population.generation] = genomes[0]
population.best_genome = best
# Let population evolve
population.evolve()
# Update the genomes such all have one hidden node
for g in population.population.values():
n_hidden, _ = g.size()
while n_hidden < 1:
g.mutate_add_connection(population.config.genome)
n_hidden, _ = g.size()
# End generation
population.reporters.end_generation(population=population.population,
name=str(population),
species_set=population.species,
logger=population.log)
# Save the population
if (iteration + 1) % save_interval == 0:
population.save()
saved = True
else:
saved = False
# Make sure that last iterations saves
if not saved: population.save()
def reproduce(self, config, species, pop_size, generation, exp, syllabus):
all_fitnesses = []
for sid, s in iteritems(species.species):
all_fitnesses.extend(m.fitness for m in itervalues(s.members))
min_fitness = min(all_fitnesses)
max_fitness = max(all_fitnesses)
fitness_range = max(1.0, max_fitness - min_fitness)
num_remaining = 0
species_fitness = []
avg_adjusted_fitness = 0.0
for sid, s, stagnant in self.stagnation.update(species, generation):
if stagnant:
self.reporters.species_stagnant(sid, s)
else:
num_remaining += 1
msf = mean([m.fitness for m in itervalues(s.members)])
s.adjusted_fitness = (msf - min_fitness) / fitness_range
species_fitness.append((sid, s, s.fitness))
avg_adjusted_fitness += s.adjusted_fitness
if 0 == num_remaining:
species.species = {}
return []
avg_adjusted_fitness /= len(species_fitness)
self.reporters.info(
"Average adjusted fitness: {:.3f}".format(avg_adjusted_fitness))
spawn_amounts = []
for sid, s, sfitness in species_fitness:
spawn = len(s.members)
if sfitness > avg_adjusted_fitness:
spawn = max(spawn + 2, spawn * 1.1)
else:
spawn = max(spawn * 0.9, 2)
spawn_amounts.append(spawn)
total_spawn = sum(spawn_amounts)
norm = pop_size / total_spawn
spawn_amounts = [int(round(n * norm)) for n in spawn_amounts]
new_population = {}
species.species = {}
learning_function = None
if exp.learning_function == 'BP':
learning_function = backpropagation
elif exp.learning_function == 'BT':
learning_function = batch
has_learning = not learning_function is None
if has_learning:
(writer, lessons) = syllabus
if exp.syllabus_source == 'EXP':
lessons_to_learn = random.sample(
lessons, min(exp.syllabus_size, len(lessons)))
elif exp.syllabus_source == 'RND':
lessons_to_learn = lessons
for spawn, (sid, s, sfitness) in zip(spawn_amounts, species_fitness):
spawn = max(spawn, self.elitism)
if spawn <= 0:
continue
old_members = list(iteritems(s.members))
s.members = {}
species.species[sid] = s
old_members.sort(reverse=True, key=lambda x: x[1].fitness)
if self.elitism > 0:
for i, m in old_members[:self.elitism]:
new_population[i] = m
spawn -= 1
if spawn <= 0:
continue
repro_cutoff = int(
math.ceil(self.survival_threshold * len(old_members)))
repro_cutoff = max(repro_cutoff, 2)
old_members = old_members[:repro_cutoff]
if has_learning and (exp.learning_target == 'Ambos'
or exp.learning_target == 'Pais'):
for (_, g) in old_members:
if g != writer:
learning_function(g, lessons_to_learn,
exp.learning_rate)
while spawn > 0:
spawn -= 1
parent1_id, parent1 = random.choice(old_members)
parent2_id, parent2 = random.choice(old_members)
gid = self.genome_indexer.next()
child = config.genome_type(gid)
child.configure_crossover(parent1, parent2,
config.genome_config)
child.mutate(config.genome_config)
child.net = FeedForwardNetwork.create(child, self.config)
if has_learning and (exp.learning_target == 'Ambos'
or exp.learning_target == 'Filhos'):
if exp.children_inclusion == 'Inicial' or (
exp.children_inclusion == 'Tardia'
and generation >= exp.generations / 2):
learning_function(child, lessons_to_learn,
exp.learning_rate)
new_population[gid] = child
self.ancestors[gid] = (parent1_id, parent2_id)
return new_population
def speciate(self, config, population, generation):
"""
Place genomes into species by genetic similarity.
Note that this method assumes the current representatives of the species are from the old
generation, and that after speciation has been performed, the old representatives should be
dropped and replaced with representatives from the new generation. If you violate this
assumption, you should make sure other necessary parts of the code are updated to reflect
the new behavior.
"""
assert isinstance(population, dict)
compatibility_threshold = self.species_set_config.compatibility_threshold
# Find the best representatives for each existing species.
unspeciated = set(iterkeys(population))
distances = GenomeDistanceCache(config.genome_config)
new_representatives = {}
new_members = {}
for sid, s in iteritems(self.species):
candidates = []
for gid in unspeciated:
g = population[gid]
d = distances(s.representative, g)
candidates.append((d, g))
# The new representative is the genome closest to the current representative.
ignored_rdist, new_rep = min(candidates, key=lambda x: x[0])
new_rid = new_rep.key
new_representatives[sid] = new_rid
new_members[sid] = [new_rid]
unspeciated.remove(new_rid)
# Partition population into species based on genetic similarity.
while unspeciated:
gid = unspeciated.pop()
g = population[gid]
# Find the species with the most similar representative.
candidates = []
for sid, rid in iteritems(new_representatives):
rep = population[rid]
d = distances(rep, g)
if d < compatibility_threshold:
candidates.append((d, sid))
if candidates:
ignored_sdist, sid = min(candidates, key=lambda x: x[0])
new_members[sid].append(gid)
else:
# No species is similar enough, create a new species, using
# this genome as its representative.
sid = next(self.indexer)
new_representatives[sid] = gid
new_members[sid] = [gid]
# Update species collection based on new speciation.
self.genome_to_species = {}
for sid, rid in iteritems(new_representatives):
s = self.species.get(sid)
if s is None:
s = Species(sid, generation)
self.species[sid] = s
members = new_members[sid]
for gid in members:
self.genome_to_species[gid] = sid
member_dict = dict((gid, population[gid]) for gid in members)
s.update(population[rid], member_dict)
gdmean = mean(itervalues(distances.distances))
gdstdev = stdev(itervalues(distances.distances))
self.reporters.info(
'Mean genetic distance {0:.3f}, standard deviation {1:.3f}'.format(
gdmean, gdstdev))
def single_evaluation(multi_env, parallel: bool, pop: Population,
unused_cpu: int):
"""
Perform a single evaluation-iteration.
:param multi_env: Environment used to execute the game-simulation in
:param parallel: Boolean indicating if training happens in parallel or not
:param pop: Population used to evaluate on
:param unused_cpu: Number of CPU-cores not used during evaluation
"""
# Prepare the generation's reporters for the generation
pop.reporters.start_generation(gen=pop.generation, logger=pop.log)
# Fetch the dictionary of genomes
genomes = list(iteritems(pop.population))
if parallel:
pbar = tqdm(total=len(genomes), desc="parallel training")
# Initialize the evaluation-pool
pool = mp.Pool(mp.cpu_count() - unused_cpu)
manager = mp.Manager()
return_dict = manager.dict()
def cb(*_):
"""Update progressbar after finishing a single genome's evaluation."""
pbar.update()
for genome in genomes:
pool.apply_async(func=multi_env.eval_genome,
args=(genome, return_dict),
callback=cb)
pool.close() # Close the pool
pool.join() # Postpone continuation until everything is finished
pbar.close() # Close the progressbar
else:
return_dict = dict()
for genome in tqdm(genomes, desc="sequential training"):
multi_env.eval_genome(genome, return_dict)
# Calculate the fitness from the given return_dict
try:
fitness = calc_pop_fitness(
fitness_config=pop.config.evaluation,
game_observations=return_dict,
game_params=multi_env.get_game_params(),
generation=pop.generation,
)
for i, genome in genomes:
genome.fitness = fitness[i]
except Exception: # TODO: Fix! Sometimes KeyError in fitness (path problem)
pop.log(
f"Exception at fitness calculation: \n{traceback.format_exc()}",
print_result=False)
warnings.warn(
f"Exception at fitness calculation: \n{traceback.format_exc()}")
# Set fitness to zero for genomes that have no fitness set yet
for i, genome in genomes:
if not genome.fitness: genome.fitness = 0.0
# Gather and report statistics
best = None
for g in itervalues(pop.population):
if best is None or g.fitness > best.fitness: best = g
pop.reporters.post_evaluate(population=pop.population,
species=pop.species,
best_genome=best,
logger=pop.log)
# Update the population's best_genome
genomes = sorted(pop.population.items(),
key=lambda x: x[1].fitness,
reverse=True)
pop.best_genome_hist[
pop.generation] = genomes[:pop.config.population.genome_elitism]
if pop.best_genome is None or best.fitness > pop.best_genome.fitness:
pop.best_genome = best
# Let population evolve
pop.evolve()
# End generation
pop.reporters.end_generation(population=pop.population,
name=str(pop),
species_set=pop.species,
logger=pop.log)
def run(self, fitness_function, n=None):
# Variables needed to save archive on each update
winner_name_prefix = "archive_checkpoint_" + self.winner_name
if self.config.no_fitness_termination and (n is None):
raise RuntimeError(
"Cannot have no generational limit with no fitness termination"
)
k = 0
while n is None or k < n:
k += 1
self.reporters.start_generation(self.generation)
# Evaluate all genomes using the user-provided function.
fitness_function(list(iteritems(self.population)), self.config)
self.KNNdistances(self.population, self.novelty_archive,
self.n_neighbors)
# Gather and report statistics.
best = None
for g in itervalues(self.population):
if best is None or g.dist > best.dist:
best = g
if g.dist > self.novelty_threshold:
if g not in self.novelty_archive:
self.novelty_archive.append(g)
print("Distanza di aggiunta: ", g.dist)
self.n_add_archive += 1
self.last_archive_modified = self.generation
with open(winner_name_prefix, "wb") as f:
pickle.dump(self.novelty_archive, f)
self.reporters.post_evaluate(self.config, self.population,
self.species, best)
# if self.last_genome_added is None:
# self.last_genome_added = best
# Track the best genome ever seen.
# if self.last_genome_added.fitness != best.fitness and best.dist > self.novelty_threshold:
# print("Distanza di aggiunta: ", best.dist)
# self.last_genome_added = best
# self.last_archive_modified = self.generation
# self.n_add_archive += 1
# self.novelty_archive.append(best)
# with open(winner_name_prefix, "wb") as f:
# pickle.dump(self.novelty_archive, f)
if not self.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = self.fitness_criterion(
g.dist for g in itervalues(self.population))
if fv >= self.config.fitness_threshold:
self.reporters.found_solution(self.config, self.generation,
best)
break
# Create the next generation from the current generation.
self.population = self.reproduction.reproduce(
self.config, self.species, self.config.pop_size,
self.generation)
# Check for complete extinction.
if not self.species.species:
self.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
self.population = self.reproduction.create_new(
self.config.genome_type, self.config.genome_config,
self.config.pop_size)
else:
raise CompleteExtinctionException()
# Divide the new population into species.
self.species.speciate(self.config, self.population,
self.generation)
self.reporters.end_generation(self.config, self.population,
self.species)
time_diff = self.generation - self.last_archive_modified
if time_diff > 60:
self.novelty_threshold -= self.novelty_threshold * 0.05
if self.n_add_archive > 4 and time_diff <= 30:
self.novelty_threshold += self.novelty_threshold * 0.05
self.n_add_archive = 0
if time_diff > 30:
self.n_add_archive = 0
self.reporters.info("Novelty's archive size: {}\n".format(
len(self.novelty_archive)))
self.generation += 1
if self.config.no_fitness_termination:
self.reporters.found_solution(self.config, self.generation,
self.best_genome)
return self.novelty_archive
def run(self, fitness_function, n):
"""
Runs NEAT's genetic algorithm for at most n generations.
The user-provided fitness_function should take two arguments, a list of all genomes in the population,
and its return value is ignored. This function is free to maintain external state, perform evaluations
in parallel, and probably any other thing you want. Each individual genome's fitness member must be set
to a floating point value after this function returns.
It is assumed that fitness_function does not modify the list of genomes, the genomes themselves (apart
from updating the fitness member), or the configuration object.
"""
for g in range(n):
self.generation += 1
self.reporters.start_generation(self.generation)
# Evaluate all individuals in the population using the user-provided function.
# TODO: Add an option to only evaluate each genome once, to reduce number of
# fitness evaluations in cases where the fitness is known to be the same if the
# genome doesn't change--in these cases, evaluating unmodified elites in each
# generation is a waste of time. The user can always take care of this in their
# fitness function in the time being if they wish.
fitness_function(list(iteritems(self.population)), self.config)
# Gather and report statistics.
best = None
for g in itervalues(self.population):
if best is None or g.fitness > best.fitness:
best = g
self.reporters.post_evaluate(self.config, self.population,
self.species, best)
# Track the best genome ever seen.
if self.best_genome is None or best.fitness > self.best_genome.fitness:
self.best_genome = best
# End if the fitness threshold is reached.
if best.fitness >= self.config.max_fitness_threshold:
self.reporters.found_solution(self.config, self.generation,
best)
break
# Create the next generation from the current generation.
self.population = self.reproduction.reproduce(
self.config, self.species, self.config.pop_size)
# Check for complete extinction.
if not self.species.species:
self.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
self.population = self.reproduction.create_new(
self.config.pop_size)
else:
raise CompleteExtinctionException()
# Update species age.
# TODO: Wouldn't it be easier to remember creation time?
for s in itervalues(self.species.species):
s.age += 1
# Divide the new population into species.
self.species.speciate(self.config, self.population)
self.reporters.end_generation(self.config, self.population,
self.species)
return self.best_genome
def reproduce(self, config, species, pop_size, generation):
"""
Handles creation of genomes, either from scratch or by sexual or
asexual reproduction from parents.
"""
# TODO: I don't like this modification of the species and stagnation objects,
# because it requires internal knowledge of the objects.
# Filter out stagnated species, collect the set of non-stagnated
# species members, and compute their average adjusted fitness.
# The average adjusted fitness scheme (normalized to the interval
# [0, 1]) allows the use of negative fitness values without
# interfering with the shared fitness scheme.
all_fitnesses = []
remaining_species = []
for stag_sid, stag_s, stagnant in self.stagnation.update(
species, generation):
if stagnant:
self.reporters.species_stagnant(stag_sid, stag_s)
else:
all_fitnesses.extend(m.fitness
for m in itervalues(stag_s.members))
remaining_species.append(stag_s)
# The above comment was not quite what was happening - now getting fitnesses
# only from members of non-stagnated species.
# No species left.
if not remaining_species:
species.species = {}
return {} # was []
self.calculate_adjusted_fitnesses(remaining_species, all_fitnesses)
adjusted_fitnesses = [s.adjusted_fitness for s in remaining_species]
avg_adjusted_fitness = mean(adjusted_fitnesses) # type: float
self.reporters.info(
"Average adjusted fitness: {:.3f}".format(avg_adjusted_fitness))
# Compute the number of new members for each species in the new generation.
previous_sizes = [len(s.members) for s in remaining_species]
min_species_size = self.reproduction_config.min_species_size
# Isn't the effective min_species_size going to be max(min_species_size,
# self.reproduction_config.elitism)? That would probably produce more accurate tracking
# of population sizes and relative fitnesses... doing. TODO: document.
min_species_size = max(min_species_size,
self.reproduction_config.elitism)
spawn_amounts = self.compute_spawn(adjusted_fitnesses, previous_sizes,
pop_size, min_species_size)
new_population = {}
species.species = {}
for spawn, s in zip(spawn_amounts, remaining_species):
# If elitism is enabled, each species always at least gets to retain its elites.
spawn = max(spawn, self.reproduction_config.elitism)
assert spawn > 0
# The species has at least one member for the next generation, so retain it.
old_members = list(iteritems(s.members))
s.members = {}
species.species[s.key] = s
# Sort members in order of descending fitness.
old_members.sort(reverse=True, key=lambda x: x[1].fitness)
# Transfer elites to new generation.
if self.reproduction_config.elitism > 0:
for i, m in old_members[:self.reproduction_config.elitism]:
new_population[i] = m
spawn -= 1
if spawn <= 0:
continue
repro_cutoff = self.calculated_cutoff(len(old_members))
old_members = old_members[:repro_cutoff]
# Randomly choose parents and produce the number of offspring allotted to the species.
while spawn > 0:
spawn -= 1
gid, child = self.generate_child(old_members, config)
new_population[gid] = child
return new_population
def run(self, fitness_function, n=None):
#Variables needed to save winner
winner_interval = 10
winnername_prefix = "winner_checkpoint_"
last_winner_checkpoint = 0
if self.config.no_fitness_termination and (n is None):
raise RuntimeError(
"Cannot have no generational limit with no fitness termination"
)
k = 0
while n is None or k < n:
k += 1
start_time_gen = time.time()
self.reporters.start_generation(self.generation)
# Evaluate all genomes using the user-provided function.
fitness_function(list(iteritems(self.population)), self.config)
if self.initial_best:
self.species.speciate(self.config, self.population,
self.generation)
with open("output.txt", "a") as f:
f.write("Gen: " + str(k) + " tempo: " +
str(round(time.time() - start_time_gen, 3)) + " sec\n")
start_time_gen = time.time()
# Gather and report statistics.
best = None
for g in itervalues(self.population):
if best is None or g.fitness > best.fitness:
best = g
self.reporters.post_evaluate(self.config, self.population,
self.species, best)
# Track the best genome ever seen.
if self.best_genome is None or best.fitness > self.best_genome.fitness:
self.best_genome = best
if not self.config.no_fitness_termination:
# End if the fitness threshold is reached.
fv = self.fitness_criterion(
g.fitness for g in itervalues(self.population))
if fv >= self.config.fitness_threshold:
self.reporters.found_solution(self.config, self.generation,
best)
break
# Create the next generation from the current generation.
self.population = self.reproduction.reproduce(
self.config, self.species, self.config.pop_size,
self.generation)
# Check for complete extinction.
if not self.species.species:
self.reporters.complete_extinction()
# If requested by the user, create a completely new population,
# otherwise raise an exception.
if self.config.reset_on_extinction:
self.population = self.reproduction.create_new(
self.config.genome_type, self.config.genome_config,
self.config.pop_size)
else:
raise CompleteExtinctionException()
# Divide the new population into species.
self.species.speciate(self.config, self.population,
self.generation)
self.reporters.end_generation(self.config, self.population,
self.species)
self.generation += 1
#Code to save the best after winner_interval generations
if winner_interval is not None:
dg = self.generation - last_winner_checkpoint
if dg >= winner_interval:
filename = '{0}{1}'.format(winnername_prefix,
self.generation)
last_winner_checkpoint = self.generation
with open(filename, 'wb') as f:
pickle.dump(self.best_genome, f)
with open("output.txt", "a") as f:
f.write("Gen: " + str(k) + " tempo: " +
str(round(time.time() - start_time_gen, 3)) + " sec\n")
if self.config.no_fitness_termination:
self.reporters.found_solution(self.config, self.generation,
self.best_genome)
return self.best_genome
