class Neuron(object):
""" A simple sigmoidal neuron """
# TODO: Get rid of these global indexers.
indexer = Indexer(0)
def __init__(self, neuron_type, ID, bias, response, activation_type):
assert neuron_type in ('INPUT', 'OUTPUT', 'HIDDEN')
self.type = neuron_type
self.ID = self.indexer.next(ID)
self.bias = bias
self.response = response
self.activation = activation_functions.get(activation_type)
self._synapses = []
self.output = 0.0 # for recurrent networks all neurons must have an "initial state"
def activate(self):
"""Activates the neuron"""
assert self.type is not 'INPUT'
z = self.bias + self.response * self._update_activation()
return self.activation(z)
def _update_activation(self):
soma = 0.0
for s in self._synapses:
soma += s.incoming()
return soma
def create_synapse(self, s):
self._synapses.append(s)
def __repr__(self):
return '{0:d} {1!s}'.format(self.ID, self.type)
def __init__(self, config):
"""
:param config: Either a config.Config object or path to a configuration file.
"""
# If config is not a Config object, assume it is a path to the config file.
if not isinstance(config, Config):
config = Config(config)
# Configure statistics and reporting as requested by the user.
self.reporters = ReporterSet()
if config.collect_statistics:
self.statistics = StatisticsReporter()
self.add_reporter(self.statistics)
else:
self.statistics = None
if config.report:
self.add_reporter(StdOutReporter())
self.config = config
print(self.config.genotype.__name__)
## Check if we have a society directory defined and may be this a continuation on an existing run.
if self.config.society_directory != None:
## Check if latest society file is available
if os.path.isdir(self.config.society_directory):
print("Society Directory")
self.species_indexer = Indexer(1)
self.genome_indexer = Indexer(1)
self.innovation_indexer = InnovationIndexer(0)
self.reproduction = config.reproduction_type(self.config,
self.reporters,
self.genome_indexer,
self.innovation_indexer)
self.species = []
self.generation = -1
self.total_evaluations = 0
# Create a population if one is not given, then partition into species.
self.population = self._create_population()
self._speciate(self.population)
def __init__(self, config):
"""
:param config: Either a config.Config object or path to a configuration file.
"""
# If config is not a Config object, assume it is a path to the config file.
if not isinstance(config, Config):
config = Config(config)
# Configure statistics and reporting as requested by the user.
self.reporters = ReporterSet()
if config.collect_statistics:
self.statistics = StatisticsReporter()
self.add_reporter(self.statistics)
else:
self.statistics = None
if config.report:
self.add_reporter(StdOutReporter())
self.config = config
## Check if we have a society directory defined and may be this a continuation on an existing run.
if self.config.society_directory != None:
## Check if latest society file is available
if os.path.isdir(self.config.society_directory):
print("Society Directory")
self.species_indexer = Indexer(1)
self.genome_indexer = Indexer(1)
self.innovation_indexer = InnovationIndexer(0)
self.reproduction = config.reproduction_type(self.config, self.reporters,
self.genome_indexer, self.innovation_indexer)
self.species = []
self.generation = -1
self.total_evaluations = 0
# Create a population if one is not given, then partition into species.
self.population = self._create_population()
self._speciate(initial_population)
class Population(object):
"""
This class implements the core NEAT algorithm. It maintains a list of Species instances,
each of which contains a collection of Genome instances.
"""
def __init__(self, config):
"""
:param config: Either a config.Config object or path to a configuration file.
"""
# If config is not a Config object, assume it is a path to the config file.
if not isinstance(config, Config):
config = Config(config)
# Configure statistics and reporting as requested by the user.
self.reporters = ReporterSet()
if config.collect_statistics:
self.statistics = StatisticsReporter()
self.add_reporter(self.statistics)
else:
self.statistics = None
if config.report:
self.add_reporter(StdOutReporter())
self.config = config
## Check if we have a society directory defined and may be this a continuation on an existing run.
if self.config.society_directory != None:
## Check if latest society file is available
if os.path.isdir(self.config.society_directory):
print("Society Directory")
self.species_indexer = Indexer(1)
self.genome_indexer = Indexer(1)
self.innovation_indexer = InnovationIndexer(0)
self.reproduction = config.reproduction_type(self.config,
self.reporters,
self.genome_indexer,
self.innovation_indexer)
self.species = []
self.generation = -1
self.total_evaluations = 0
# Create a population if one is not given, then partition into species.
self.population = self._create_population()
self._speciate(initial_population)
def add_reporter(self, reporter):
self.reporters.add(reporter)
def remove_reporter(self, reporter):
self.reporters.remove(reporter)
def load_checkpoint(self, filename):
'''Resumes the simulation from a previous saved point.'''
self.reporters.loading_checkpoint(filename)
with gzip.open(filename) as f:
(self.species, self.generation, random_state) = pickle.load(f)
random.setstate(random_state)
def save_checkpoint(self, filename=None, checkpoint_type="user"):
""" Save the current simulation state. """
if filename is None:
filename = os.path.join(
self.config.checkpoint_time_interval.models_directory,
'neatsociety-checkpoint-{0}'.format(self.generation))
self.reporters.saving_checkpoint(checkpoint_type, filename)
with gzip.open(filename, 'w', compresslevel=5) as f:
data = (self.species, self.generation, random.getstate())
pickle.dump(data, f, protocol=pickle.HIGHEST_PROTOCOL)
def _create_population(self):
# Create a collection of unconnected genomes with no hidden nodes.
new_population = []
# TODO: The genotype class should know how to do everything below, based
# solely on what's in the config object. This allows users to completely
# replace the initial population creation scheme if they choose.
for i in range(self.config.init_pop_size):
g_id = self.genome_indexer.next()
g = self.config.genotype.create_unconnected(g_id, self.config)
new_population.append(g)
# Add hidden nodes if requested.
if self.config.hidden_nodes > 0:
for g in new_population:
g.add_hidden_nodes(self.config.hidden_nodes)
# Add connections based on initial connectivity type.
if self.config.initial_connection == 'fully_connected':
for g in new_population:
g.connect_full(self.innovation_indexer)
elif self.config.initial_connection == 'partial':
for g in new_population:
g.connect_partial(self.innovation_indexer,
self.config.connection_fraction)
elif self.config.initial_connection == 'fs_neat':
for g in new_population:
g.connect_fs_neat(self.innovation_indexer)
else:
raise Exception("Invalid initial connection type: {!r}".format(
self.config.initial_connection))
return new_population
def _speciate(self, 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.
"""
for individual in population:
# Find the species with the most similar representative.
min_distance = None
closest_species = None
for s in self.species:
distance = individual.distance(s.representative)
if distance < self.config.compatibility_threshold:
if min_distance is None or distance < min_distance:
closest_species = s
min_distance = distance
if closest_species:
closest_species.add(individual)
else:
# No species is similar enough, create a new species for this individual.
self.species.append(
Species(individual, self.species_indexer.next()))
# Only keep non-empty species.
self.species = [s for s in self.species if s.members]
# Select a random current member as the new representative.
for s in self.species:
s.representative = random.choice(s.members)
def run(self, fitness_function, n):
"""
Runs NEAT's genetic algorithm for n generations.
The user-provided fitness_function should take one argument, 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. The only requirement is that each individual'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, or the genomes themselves, apart
from updating the fitness member.
"""
# Remember start time for saving timed checkpoints.
last_checkpoint = time.time()
for g in range(n):
self.generation += 1
self.reporters.start_generation(self.generation)
# Collect a list of all members from all species.
population = []
for s in self.species:
population.extend(s.members)
# 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.
unevaluated_population = [
p for p in population if p.fitness == None
]
fitness_function(unevaluated_population)
self.total_evaluations += len(unevaluated_population)
# Gather and report statistics.
best = max(population)
self.reporters.post_evaluate(population, self.species, best)
# Save 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 if the fitness threshold is reached.
if best.fitness >= self.config.max_fitness_threshold:
self.reporters.found_solution(self.generation, best)
break
# Create the next generation from the current generation.
self.species, new_population = self.reproduction.reproduce(
self.species, self.config.pop_size)
# Check for complete extinction
#if not self.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:
# new_population = self._create_population()
# else:
# raise CompleteExtinctionException()
# Update species age.
for s in self.species:
s.age += 1
# Divide the new population into species.
self._speciate(new_population)
# Save checkpoints if necessary.
if self.config.checkpoint_time_interval is not None:
timed_checkpoint_due = last_checkpoint + 60 * self.config.checkpoint_time_interval
if time.time() >= timed_checkpoint_due:
self.save_checkpoint(checkpoint_type="timed")
last_checkpoint = time.time()
if self.config.checkpoint_gen_interval is not None \
and self.generation % self.config.checkpoint_gen_interval == 0:
self.save_checkpoint(checkpoint_type="generation")
self.reporters.end_generation()
class Population(object):
"""
This class implements the core NEAT algorithm. It maintains a list of Species instances,
each of which contains a collection of Genome instances.
"""
def __init__(self, config):
"""
:param config: Either a config.Config object or path to a configuration file.
"""
# If config is not a Config object, assume it is a path to the config file.
if not isinstance(config, Config):
config = Config(config)
# Configure statistics and reporting as requested by the user.
self.reporters = ReporterSet()
if config.collect_statistics:
self.statistics = StatisticsReporter()
self.add_reporter(self.statistics)
else:
self.statistics = None
if config.report:
self.add_reporter(StdOutReporter())
self.config = config
## Check if we have a society directory defined and may be this a continuation on an existing run.
if self.config.society_directory != None:
## Check if latest society file is available
if os.path.isdir(self.config.society_directory):
print("Society Directory")
self.species_indexer = Indexer(1)
self.genome_indexer = Indexer(1)
self.innovation_indexer = InnovationIndexer(0)
self.reproduction = config.reproduction_type(self.config, self.reporters,
self.genome_indexer, self.innovation_indexer)
self.species = []
self.generation = -1
self.total_evaluations = 0
# Create a population if one is not given, then partition into species.
self.population = self._create_population()
self._speciate(initial_population)
def add_reporter(self, reporter):
self.reporters.add(reporter)
def remove_reporter(self, reporter):
self.reporters.remove(reporter)
def load_checkpoint(self, filename):
'''Resumes the simulation from a previous saved point.'''
self.reporters.loading_checkpoint(filename)
with gzip.open(filename) as f:
(self.species,
self.generation,
random_state) = pickle.load(f)
random.setstate(random_state)
def save_checkpoint(self, filename=None, checkpoint_type="user"):
""" Save the current simulation state. """
if filename is None:
filename = os.path.join(self.config.checkpoint_time_interval.models_directory,'neatsociety-checkpoint-{0}'.format(self.generation))
self.reporters.saving_checkpoint(checkpoint_type, filename)
with gzip.open(filename, 'w', compresslevel=5) as f:
data = (self.species,
self.generation,
random.getstate())
pickle.dump(data, f, protocol=pickle.HIGHEST_PROTOCOL)
def _create_population(self):
# Create a collection of unconnected genomes with no hidden nodes.
new_population = []
# TODO: The genotype class should know how to do everything below, based
# solely on what's in the config object. This allows users to completely
# replace the initial population creation scheme if they choose.
for i in range(self.config.init_pop_size):
g_id = self.genome_indexer.next()
g = self.config.genotype.create_unconnected(g_id, self.config)
new_population.append(g)
# Add hidden nodes if requested.
if self.config.hidden_nodes > 0:
for g in new_population:
g.add_hidden_nodes(self.config.hidden_nodes)
# Add connections based on initial connectivity type.
if self.config.initial_connection == 'fully_connected':
for g in new_population:
g.connect_full(self.innovation_indexer)
elif self.config.initial_connection == 'partial':
for g in new_population:
g.connect_partial(self.innovation_indexer, self.config.connection_fraction)
elif self.config.initial_connection == 'fs_neat':
for g in new_population:
g.connect_fs_neat(self.innovation_indexer)
else:
raise Exception("Invalid initial connection type: {!r}".format(self.config.initial_connection))
return new_population
def _speciate(self, 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.
"""
for individual in population:
# Find the species with the most similar representative.
min_distance = None
closest_species = None
for s in self.species:
distance = individual.distance(s.representative)
if distance < self.config.compatibility_threshold:
if min_distance is None or distance < min_distance:
closest_species = s
min_distance = distance
if closest_species:
closest_species.add(individual)
else:
# No species is similar enough, create a new species for this individual.
self.species.append(Species(individual, self.species_indexer.next()))
# Only keep non-empty species.
self.species = [s for s in self.species if s.members]
# Select a random current member as the new representative.
for s in self.species:
s.representative = random.choice(s.members)
def run(self, fitness_function, n):
"""
Runs NEAT's genetic algorithm for n generations.
The user-provided fitness_function should take one argument, 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. The only requirement is that each individual'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, or the genomes themselves, apart
from updating the fitness member.
"""
# Remember start time for saving timed checkpoints.
last_checkpoint = time.time()
for g in range(n):
self.generation += 1
self.reporters.start_generation(self.generation)
# Collect a list of all members from all species.
population = []
for s in self.species:
population.extend(s.members)
# 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.
unevaluated_population = [p for p in population if p.fitness == None]
fitness_function(unevaluated_population)
self.total_evaluations += len(unevaluated_population)
# Gather and report statistics.
best = max(population)
self.reporters.post_evaluate(population, self.species, best)
# Save 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 if the fitness threshold is reached.
if best.fitness >= self.config.max_fitness_threshold:
self.reporters.found_solution(self.generation, best)
break
# Create the next generation from the current generation.
self.species, new_population = self.reproduction.reproduce(self.species, self.config.pop_size)
# Check for complete extinction
#if not self.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:
# new_population = self._create_population()
# else:
# raise CompleteExtinctionException()
# Update species age.
for s in self.species:
s.age += 1
# Divide the new population into species.
self._speciate(new_population)
# Save checkpoints if necessary.
if self.config.checkpoint_time_interval is not None:
timed_checkpoint_due = last_checkpoint + 60 * self.config.checkpoint_time_interval
if time.time() >= timed_checkpoint_due:
self.save_checkpoint(checkpoint_type="timed")
last_checkpoint = time.time()
if self.config.checkpoint_gen_interval is not None \
and self.generation % self.config.checkpoint_gen_interval == 0:
self.save_checkpoint(checkpoint_type="generation")
self.reporters.end_generation()
