def test_parser_with_default_prior_file(self):
known_args_list = ["4s", "--n-injection", "3"]
parser = bilby_pipe.create_injections.create_parser()
args, unknown_args = parse_args(known_args_list, parser)
self.assertEqual(args.prior_file, "4s")
self.assertEqual(args.n_injection, 3)
def write_ini_file(args):
"""
Takes the parser args and writes the complete ini file in the job output directory
:param args: Args as generated by the bilby_pipe parser
:return: The updated Args, and the MainInput object representing the complete bilby_pipe input object
"""
# Create an argument parser
parser = create_parser()
# Because we don't know the correct ini file name yet, we need to save the ini data to a temporary file
# and then read the data back in to create a MainInput object, which we can then use to get the name of the ini
# file
with NamedTemporaryFile() as f:
# Write the temporary ini file
parser.write_to_file(f.name, args, overwrite=True)
# Make sure the data is flushed
f.flush()
# Read the data from the ini file
args, unknown_args = parse_args([f.name], parser)
# Generate the Input object so that we can determine the correct ini file
inputs = MainInput(args, unknown_args)
# Write the real ini file
parser.write_to_file(inputs.complete_ini_file, args, overwrite=True)
return args, inputs
def bilby_ini_string_to_args(ini):
"""
Parses an ini string in to an argument Namespace
:params ini: The ini string to parse
:return: An ArgParser Namespace of the parsed arguments from the ini
"""
# Create an bilby argument parser
parser = create_parser()
# Bilby pipe requires a real file in order to parse the ini file
with NamedTemporaryFile() as f:
# Write the temporary ini file
f.write(ini)
# Make sure the data is written to the temporary file
f.flush()
# Read the data from the ini file
args, unknown_args = parse_args([f.name], parser)
# ini and verbose are not kept in the ini file, so remove them
delattr(args, 'ini')
delattr(args, 'verbose')
return args
def test_parser_with_json(self):
example_prior_file = "tests/example_prior.prior"
known_args_list = [example_prior_file, "--n-injection", "3", "-e", "json"]
parser = bilby_pipe.create_injections.create_parser()
args, unknown_args = parse_args(known_args_list, parser)
self.assertEqual(args.extension, "json")
def test_parser_with_prior_file(self):
example_prior_file = "tests/example_prior.prior"
known_args_list = [example_prior_file, "--n-injection", "3", "-s", "1234"]
parser = bilby_pipe.create_injections.create_parser()
args, unknown_args = parse_args(known_args_list, parser)
self.assertEqual(args.prior_file, example_prior_file)
self.assertEqual(args.n_injection, 3)
self.assertEqual(args.generation_seed, 1234)
def test_parser_defaults(self):
example_prior_file = "tests/example_prior.prior"
known_args_list = [example_prior_file, "-n", "1"]
parser = bilby_pipe.create_injections.create_parser()
args, unknown_args = parse_args(known_args_list, parser)
self.assertEqual(args.prior_file, example_prior_file)
self.assertEqual(args.n_injection, 1)
self.assertEqual(args.extension, "dat")
def main():
args, unknown_args = parse_args(sys.argv[1:], create_parser(__prog__))
logger = logging.getLogger(__prog__)
result = read_in_result(args.result)
label = result.label
# Test if the result was generated by parallel_bilby
result_from_pbilby = False
try:
if result.meta_data["command_line_args"][
"sampler"] == "parallel_bilby":
result_from_pbilby = True
except:
pass
if args.generate_samples_for_marginalized_parameters:
single_trigger_likelihoods = []
if result_from_pbilby:
for i in range(args.n_triggers):
l, _, _ = load_run_from_pbilby(args.data_dump_files[i])
single_trigger_likelihoods.append(l)
else:
for i in range(args.n_triggers):
l, _, _ = load_run_from_bilby(args.data_dump_files[i],
args.trigger_ini_files[i])
single_trigger_likelihoods.append(l)
generate_joint_posterior_samples_from_marginalized_likelihood(
result, single_trigger_likelihoods, ncores=args.ncores)
label += "_marginalized_parameter_reconstructed"
if args.flat_in_component_masses:
result = reweight_flat_in_component_masses(result)
label += "_reweighted"
if args.uniform_in_comoving_volume:
result = reweight_uniform_in_comoving_volume(result)
label += "_reweighted"
# Save to file
logger.info("Done. Saving to file")
result.label = label
result.save_to_file(outdir=".")
def bilby_ini_to_args(ini):
"""
Parses an ini string in to an argument Namespace
:params ini: The ini string to parse
:return: An ArgParser Namespace of the parsed arguments from the ini
"""
# Create a bilby argument parser
parser = create_parser()
# Bilby pipe requires a real file in order to parse the ini file
with NamedTemporaryFile() as f:
# Write the temporary ini file
f.write(ini.encode('utf-8'))
# Make sure the data is written to the temporary file
f.flush()
# Read the data from the ini file
args, unknown_args = parse_args([f.name], parser)
return args
def main():
args, unknown_args = parse_args(sys.argv[1:], create_parser(__prog__))
logger = logging.getLogger(__prog__)
result = read_in_result(args.result)
label = result.label
# Test if the result was generated by parallel_bilby
result_from_pbilby = False
try:
if result.meta_data["command_line_args"][
"sampler"] == "parallel_bilby":
result_from_pbilby = True
except:
pass
if args.generate_samples_for_marginalized_parameters:
single_trigger_likelihoods = reconstruct_likelihoods(
n_triggers=args.n_triggers,
trigger_ini_files=args.trigger_ini_files,
data_dump_files=args.data_dump_files,
result_from_pbilby=result_from_pbilby,
)
if not args.not_from_hanabi:
result = generate_joint_posterior_samples_from_marginalized_likelihood(
result, single_trigger_likelihoods, ncores=args.ncores)
else:
if args.n_triggers != 1:
raise ValueError("Does not understand input")
result = generate_posterior_samples_from_marginalized_likelihood(
result, single_trigger_likelihoods[0], ncores=args.ncores)
label += "_marginalized_parameter_reconstructed"
if args.generate_component_mass_parameters:
# Edit file **in-place**
result = generate_component_mass_parameters(result)
if args.generate_snrs:
single_trigger_likelihoods = reconstruct_likelihoods(
n_triggers=args.n_triggers,
trigger_ini_files=args.trigger_ini_files,
data_dump_files=args.data_dump_files,
result_from_pbilby=result_from_pbilby,
)
# Edit file **in-place**
if not args.not_from_hanabi:
result = generate_joint_snrs(result,
single_trigger_likelihoods,
ncores=args.ncores)
else:
if args.n_triggers != 1:
raise ValueError("Does not understand input")
result = generate_snrs(result,
single_trigger_likelihoods[0],
ncores=args.ncores)
if args.reweight_to_prior is not None:
result = reweight_to_prior(
result,
bilby.core.prior.PriorDict(filename=args.reweight_to_prior))
label += "_reweighted"
if args.flat_in_component_masses:
result = reweight_flat_in_component_masses(result)
label += "_reweighted"
if args.uniform_in_comoving_volume:
result = reweight_uniform_in_comoving_volume(result)
label += "_reweighted"
# Save to file
logger.info("Done. Saving to file")
result.label = label
result.save_to_file(outdir=".", filename=args.output_filename)