help = "Seed the random number generator such that the same labeled nodes will be chosen on runs with the same number of nodes.")
parser.add_argument("--deterministic_labeled", "-ds", action = "store_true",
help = "Seed the random number generator to ensure labeled node subset is deterministic.")
args = parser.parse_args()
if args.data_logfile:
change_logfile_name(args.data_logfile)
start_logging()
else:
stop_logging()
write_log("args", args)
print("Loading population.", flush = True)
with open(args.population, "rb") as pickle_file:
population = PopulationUnpickler(pickle_file).load()
print("Loading classifier", flush = True)
with open(args.classifier, "rb") as pickle_file:
classifier = load(pickle_file)
nodes = set(member for member in population.members
if member.genome is not None)
# nodes = set(member for member in population.generations[-1].members
# if member.genome is not None)
if args.subset_labeled:
# we want the labeled nodes to be chosen randomly, but the same
# random nodes chosen every time if the same number of labeled
# nodes is chosen.
sorted_labeled = list(classifier._labeled_nodes)
with open(args.expansion_rounds_data, "rb") as expansion_file:
expansion_data = load(expansion_file)
else:
expansion_data = None
if args.data_logfile:
change_logfile_name(args.data_logfile)
start_logging()
else:
stop_logging()
write_log("args", args)
print("Loading population.", flush=True)
with open(args.population, "rb") as pickle_file:
population = PopulationUnpickler(pickle_file).load()
fix_twin_parents(population)
if args.recombination_dir:
print("Generating new genomes for population.")
print("Loading recombination rates")
recombinators = recombinators_from_directory(args.recombination_dir)
chrom_sizes = recombinators[Sex.Male]._num_bases
genome_generator = RecombGenomeGenerator(chrom_sizes)
population.clean_genomes()
print("Generating genomes")
generate_genomes(population, genome_generator, recombinators, 3)
print("Loading classifier", flush=True)
with open(args.classifier, "rb") as pickle_file:
classifier = load(pickle_file)