def run_tardis(
config,
atom_data=None,
packet_source=None,
simulation_callbacks=[],
virtual_packet_logging=False,
):
"""
This function is one of the core functions to run TARDIS from a given
config object.
It will return a model object containing
Parameters
----------
config : str or dict or tardis.io.config_reader.Configuration
filename of configuration yaml file or dictionary or TARDIS Configuration object
atom_data : str or tardis.atomic.AtomData
if atom_data is a string it is interpreted as a path to a file storing
the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
atomic data will be loaded according to keywords set in the configuration
[default=None]
virtual_packet_logging : bool
option to enable virtual packet logging
[default=False]
Returns
-------
Simulation
"""
from tardis.io.config_reader import Configuration
from tardis.io.atom_data.base import AtomData
from tardis.simulation import Simulation
if atom_data is not None:
try:
atom_data = AtomData.from_hdf(atom_data)
except TypeError:
atom_data = atom_data
if isinstance(config, Configuration):
tardis_config = config
else:
try:
tardis_config = Configuration.from_yaml(config)
except TypeError:
tardis_config = Configuration.from_config_dict(config)
simulation = Simulation.from_config(
tardis_config,
packet_source=packet_source,
atom_data=atom_data,
virtual_packet_logging=virtual_packet_logging,
)
for cb in simulation_callbacks:
simulation.add_callback(*cb)
simulation.run()
return simulation
def __init__(self, configFile, gridFrame):
try:
tardis_config = Configuration.from_yaml(configFile)
except TypeError:
tardis_config = Configuration.from_config_dict(configFile)
self.config = tardis_config
self.grid = gridFrame
return
def test_from_config_dict(tardis_config_verysimple):
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname='test')
assert conf.config_dirname == 'test'
assert_almost_equal(conf.spectrum.start.value,
tardis_config_verysimple['spectrum']['start'].value)
assert_almost_equal(conf.spectrum.stop.value,
tardis_config_verysimple['spectrum']['stop'].value)
tardis_config_verysimple['spectrum']['start'] = 'Invalid'
with pytest.raises(ValidationError):
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname='test')
def test_from_config_dict(tardis_config_verysimple):
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname='test')
assert conf.config_dirname == 'test'
assert_almost_equal(conf.spectrum.start.value,
tardis_config_verysimple['spectrum']['start'].value)
assert_almost_equal(conf.spectrum.stop.value,
tardis_config_verysimple['spectrum']['stop'].value)
tardis_config_verysimple['spectrum']['start'] = 'Invalid'
with pytest.raises(ValidationError):
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname='test')
def test_ascii_reader_power_law():
filename = "tardis_configv1_density_power_law_test.yml"
config = Configuration.from_yaml(data_path(filename))
model = Radial1DModel.from_config(config)
expected_densites = [
3.29072513e-14,
2.70357804e-14,
2.23776573e-14,
1.86501954e-14,
1.56435277e-14,
1.32001689e-14,
1.12007560e-14,
9.55397475e-15,
8.18935779e-15,
7.05208050e-15,
6.09916083e-15,
5.29665772e-15,
4.61758699e-15,
4.04035750e-15,
3.54758837e-15,
3.12520752e-15,
2.76175961e-15,
2.44787115e-15,
2.17583442e-15,
1.93928168e-15,
]
assert model.no_of_shells == 20
for i, mdens in enumerate(expected_densites):
assert_almost_equal(model.density[i].to(u.Unit("g / (cm3)")).value,
mdens)
def test_ascii_reader_exponential_law():
filename = "tardis_configv1_density_exponential_test.yml"
config = Configuration.from_yaml(data_path(filename))
model = Radial1DModel.from_config(config)
expected_densites = [
5.18114795e-14,
4.45945537e-14,
3.83828881e-14,
3.30364579e-14,
2.84347428e-14,
2.44740100e-14,
2.10649756e-14,
1.81307925e-14,
1.56053177e-14,
1.34316215e-14,
1.15607037e-14,
9.95038990e-15,
8.56437996e-15,
7.37143014e-15,
6.34464872e-15,
5.46088976e-15,
4.70023138e-15,
4.04552664e-15,
3.48201705e-15,
2.99699985e-15,
]
expected_unit = "g / (cm3)"
assert model.no_of_shells == 20
for i, mdens in enumerate(expected_densites):
assert_almost_equal(model.density[i].value, mdens)
assert model.density[i].unit == u.Unit(expected_unit)
def test_model_decay(simple_isotope_abundance):
filename = "tardis_configv1_verysimple.yml"
config = Configuration.from_yaml(data_path(filename))
model = Radial1DModel.from_config(config)
model.raw_isotope_abundance = simple_isotope_abundance
decayed = simple_isotope_abundance.decay(model.time_explosion).as_atoms()
norm_factor = 1.4
assert_almost_equal(
model.abundance.loc[8][0],
model.raw_abundance.loc[8][0] / norm_factor,
decimal=4,
)
assert_almost_equal(
model.abundance.loc[14][0],
(model.raw_abundance.loc[14][0] + decayed.loc[14][0]) / norm_factor,
decimal=4,
)
assert_almost_equal(
model._abundance.loc[12][5],
(model.raw_abundance.loc[12][5] + decayed.loc[12][5]) / norm_factor,
decimal=4,
)
assert_almost_equal(
model.abundance.loc[6][12],
(decayed.loc[6][12]) / norm_factor,
decimal=4,
)
def test_supernova_section_config(tardis_config_verysimple):
"""
Configuration Validation Test for Supernova Section of the Tardis Config YAML File
Validates:
Time of Explosion (Must always be positive)
Luminosity Wavelength Limits (Start < End)
Parameter
---------
`tardis_config_verysimple` : YAML File
Result
------
Assertion based on validation for specified values
"""
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname="test")
tardis_config_verysimple["supernova"]["time_explosion"] = "-10 day"
tardis_config_verysimple["supernova"][
"luminosity_wavelength_start"] = "15 angstrom"
tardis_config_verysimple["supernova"][
"luminosity_wavelength_end"] = "0 angstrom"
with pytest.raises(ValueError) as ve:
if conf.supernova.time_explosion.value > 0:
raise ValueError("Time of Explosion cannot be negative")
assert ve.type is ValueError
with pytest.raises(ValueError) as ve:
if (conf.supernova.luminosity_wavelength_start.value <
conf.supernova.luminosity_wavelength_end.value):
raise ValueError(
"End Limit must be greater than Start Limit for Luminosity")
assert ve.type is ValueError
def setup(self):
filename = "tardis_configv1_artis_density_v_slice.yml"
self.config = Configuration.from_yaml(data_path(filename))
self.config.model.abundances.type = "file"
self.config.model.abundances.filename = "artis_abundances.dat"
self.config.model.abundances.filetype = "artis"
self.model = Radial1DModel.from_config(self.config)
def test_model_section_config(tardis_config_verysimple):
"""
Configuration Validation Test for Model Section of the Tardis Config YAML File
Validates:
Density: branch85_w7
Velocity (Start < End)
Parameter
---------
`tardis_config_verysimple` : YAML File
Result
------
Assertion based on validation for specified values
"""
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname="test")
assert conf.model.structure.density.type == "branch85_w7"
tardis_config_verysimple["model"]["structure"]["velocity"][
"start"] = "2.0e4 km/s"
tardis_config_verysimple["model"]["structure"]["velocity"][
"stop"] = "1.1e4 km/s"
with pytest.raises(ValueError) as ve:
if (conf.model.structure.velocity.start <
conf.model.structure.velocity.stop):
raise ValueError("Stop Value must be greater than Start Value")
assert ve.type is ValueError
def test_plasma_section_config(tardis_config_verysimple):
"""
Configuration Validation Test for Plasma Section of the Tardis Config YAML File
Validates:
Initial temperature inner (must be greater than -1K)
Initial radiative temperature (must be greater than -1K)
Parameter
---------
`tardis_config_verysimple` : YAML File
Result
------
Assertion based on validation for specified values
"""
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname="test")
tardis_config_verysimple["plasma"]["initial_t_inner"] = "-100 K"
tardis_config_verysimple["plasma"]["initial_t_rad"] = "-100 K"
with pytest.raises(ValueError) as ve:
if (conf.plasma.initial_t_inner.value >=
-1) and (conf.plasma.initial_t_rad.value >= -1):
raise ValueError("Initial Temperatures are Invalid")
assert ve.type is ValueError
def setup(self):
filename = 'tardis_configv1_artis_density_v_slice.yml'
self.config = Configuration.from_yaml(data_path(filename))
self.config.model.abundances.type = 'file'
self.config.model.abundances.filename = 'artis_abundances.dat'
self.config.model.abundances.filetype = 'artis'
self.model = Radial1DModel.from_config(self.config)
def simulation(
self, request, atomic_data_fname,
generate_reference, tardis_ref_data):
name = request.param[0]
config = Configuration.from_yaml(request.param[1])
config['atom_data'] = atomic_data_fname
simulation = Simulation.from_config(config)
simulation.run()
self._test_name = name
if not generate_reference:
return simulation
else:
simulation.plasma.hdf_properties = [
'level_number_density',
]
simulation.model.hdf_properties = [
't_radiative'
]
simulation.plasma.to_hdf(
tardis_ref_data,
self.name,
self._test_name)
simulation.model.to_hdf(
tardis_ref_data,
self.name,
self._test_name)
pytest.skip(
'Reference data was generated during this run.')
return simulation
def setup(self):
filename = 'tardis_configv1_artis_density.yml'
self.config = Configuration.from_yaml(data_path(filename))
self.config.model.abundances.type = 'file'
self.config.model.abundances.filename = 'artis_abundances.dat'
self.config.model.abundances.filetype = 'artis'
self.model = Radial1DModel.from_config(self.config)
def run_tardis(config,
atom_data=None,
packet_source=None,
simulation_callbacks=[]):
"""
This function is one of the core functions to run TARDIS from a given
config object.
It will return a model object containing
Parameters
----------
config: ~str or ~dict
filename of configuration yaml file or dictionary
atom_data: ~str or ~tardis.atomic.AtomData
if atom_data is a string it is interpreted as a path to a file storing
the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
atomic data will be loaded according to keywords set in the configuration
[default=None]
"""
from tardis.io.config_reader import Configuration
from tardis.io.atom_data.base import AtomData
from tardis.simulation import Simulation
if atom_data is not None:
try:
atom_data = AtomData.from_hdf(atom_data)
except TypeError:
atom_data = atom_data
try:
tardis_config = Configuration.from_yaml(config)
except TypeError:
tardis_config = Configuration.from_config_dict(config)
simulation = Simulation.from_config(tardis_config,
packet_source=packet_source,
atom_data=atom_data)
for cb in simulation_callbacks:
simulation.add_callback(*cb)
simulation.run()
return simulation
def test_config_hdf(hdf_file_path, tardis_config_verysimple):
expected = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname="test")
expected.to_hdf(hdf_file_path, overwrite=True)
actual = pd.read_hdf(hdf_file_path, key="/simulation/config")
expected = expected.get_properties()["config"]
assert actual[0] == expected[0]
def test_compare_models(model_config_fnames):
"""Compare identical models produced by .from_config and
.from_csvy to check that velocities, densities and abundances
(pre and post decay) are the same"""
csvy_config_file, old_config_file = model_config_fnames
tardis_config = Configuration.from_yaml(csvy_config_file)
tardis_config_old = Configuration.from_yaml(old_config_file)
csvy_model = Radial1DModel.from_csvy(tardis_config)
config_model = Radial1DModel.from_config(tardis_config_old)
csvy_model_props = csvy_model.get_properties().keys()
config_model_props = config_model.get_properties().keys()
npt.assert_array_equal(csvy_model_props, config_model_props)
for prop in config_model_props:
csvy_model_val = csvy_model.get_properties()[prop]
config_model_val = config_model.get_properties()[prop]
if prop == "homologous_density":
npt.assert_array_almost_equal(
csvy_model_val.density_0.value, config_model_val.density_0.value
)
npt.assert_array_almost_equal(
csvy_model_val.time_0.value, config_model_val.time_0.value
)
else:
if hasattr(config_model_val, "value"):
config_model_val = config_model_val.value
csvy_model_val = csvy_model_val.value
npt.assert_array_almost_equal(csvy_model_val, config_model_val)
assert csvy_model.raw_abundance.shape == config_model.raw_abundance.shape
assert (
csvy_model.raw_isotope_abundance.shape
== config_model.raw_isotope_abundance.shape
)
assert csvy_model.abundance.shape == config_model.abundance.shape
npt.assert_array_almost_equal(
csvy_model.raw_abundance.to_numpy(),
config_model.raw_abundance.to_numpy(),
)
npt.assert_array_almost_equal(
csvy_model.raw_isotope_abundance.to_numpy(),
config_model.raw_isotope_abundance.to_numpy(),
)
npt.assert_array_almost_equal(
csvy_model.abundance.to_numpy(), config_model.abundance.to_numpy()
)
def _get_config_from_args(self, args):
config_name_space = copy.deepcopy(self.config_name_space)
for i, param_value in enumerate(args):
param_value = np.squeeze(param_value)
config_name_space.set_config_item(
self.convert_param_dict.values()[i], param_value)
return Configuration.from_config_dict(config_name_space,
validate=False,
atom_data=self.atom_data)
def test_plasma_vboundary(config_init_trad_fname, v_inner_boundary,
v_outer_boundary, atomic_data_fname):
tardis_config = Configuration.from_yaml(config_init_trad_fname)
tardis_config.atom_data = atomic_data_fname
tardis_config.model.structure.v_inner_boundary = (v_inner_boundary * u.km /
u.s)
tardis_config.model.structure.v_outer_boundary = (v_outer_boundary * u.km /
u.s)
simulation = Simulation.from_config(tardis_config)
def test_from_config_dict(tardis_config_verysimple):
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname="test")
assert conf.config_dirname == "test"
assert_almost_equal(
conf.spectrum.start.value,
tardis_config_verysimple["spectrum"]["start"].value,
)
assert_almost_equal(
conf.spectrum.stop.value,
tardis_config_verysimple["spectrum"]["stop"].value,
)
tardis_config_verysimple["spectrum"]["start"] = "Invalid"
with pytest.raises(ValidationError):
conf = Configuration.from_config_dict(tardis_config_verysimple,
validate=True,
config_dirname="test")
def setup(self):
self.atom_data_filename = os.path.expanduser(os.path.expandvars(
pytest.config.getvalue('atomic-dataset')))
assert os.path.exists(self.atom_data_filename), ("{0} atomic datafiles"
" does not seem to "
"exist".format(
self.atom_data_filename))
self.config_yaml = yaml_load_config_file(
'tardis/plasma/tests/data/plasma_test_config_lte.yml')
self.config_yaml['atom_data'] = self.atom_data_filename
conf = Configuration.from_config_dict(self.config_yaml)
self.lte_simulation = Simulation.from_config(conf)
self.lte_simulation.run()
self.config_yaml = yaml_load_config_file(
'tardis/plasma/tests/data/plasma_test_config_nlte.yml')
self.config_yaml['atom_data'] = self.atom_data_filename
conf = Configuration.from_config_dict(self.config_yaml)
self.nlte_simulation = Simulation.from_config(conf)
self.nlte_simulation.run()
def config(request):
config = Configuration.from_yaml(
'tardis/io/tests/data/tardis_configv1_verysimple.yml')
config["plasma"]["line_interaction_type"] = request.param
config["montecarlo"]["no_of_packets"] = 4.0e+4
config["montecarlo"]["last_no_of_packets"] = 1.0e+5
config["montecarlo"]["no_of_virtual_packets"] = 0
config["spectrum"]["method"] = "integrated"
return config
def run_tardis(config, atom_data=None, simulation_callbacks=[]):
"""
This function is one of the core functions to run TARDIS from a given
config object.
It will return a model object containing
Parameters
----------
config: ~str or ~dict
filename of configuration yaml file or dictionary
atom_data: ~str or ~tardis.atomic.AtomData
if atom_data is a string it is interpreted as a path to a file storing
the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
atomic data will be loaded according to keywords set in the configuration
[default=None]
"""
from tardis.io.config_reader import Configuration
from tardis.io.atom_data.base import AtomData
from tardis.simulation import Simulation
if atom_data is not None:
try:
atom_data = AtomData.from_hdf(atom_data)
except TypeError:
atom_data = atom_data
try:
tardis_config = Configuration.from_yaml(config)
except TypeError:
tardis_config = Configuration.from_config_dict(config)
simulation = Simulation.from_config(tardis_config, atom_data=atom_data)
for cb in simulation_callbacks:
simulation.add_callback(cb)
simulation.run()
return simulation
def test_csvy_abundance():
csvypath = os.path.join(DATA_PATH, 'config_v_filter.yml')
config = Configuration.from_yaml(csvypath)
csvy_model = Radial1DModel.from_csvy(config)
csvy_abund = csvy_model.abundance
ref_abund = pd.DataFrame(
np.array([[0.35, 0.3, 0.6, 0.4], [0.65, 0.7, 0.4, 0.6]]))
ref_abund.index.name = 'atomic_number'
ref_abund.index = np.array([1, 2])
assert csvy_abund.equals(ref_abund)
def base_config(request):
config = Configuration.from_yaml(
'tardis/io/tests/data/tardis_configv1_verysimple.yml')
config["plasma"]["line_interaction_type"] = request.param
config["montecarlo"]["no_of_packets"] = 4.0e+4
config["montecarlo"]["last_no_of_packets"] = 1.0e+5
config["montecarlo"]["no_of_virtual_packets"] = 0
config["spectrum"]["method"] = "integrated"
config["spectrum"]["integrated"]["points"] = 200
return config
def setup(self, request, reference, data_path, atomic_data_fname):
"""
This method does initial setup of creating configuration and performing
a single run of integration test.
"""
# The last component in dirpath can be extracted as name of setup.
self.name = data_path['setup_name']
self.config_file = os.path.join(data_path['config_dirpath'], "config.yml")
# Load atom data file separately, pass it for forming tardis config.
self.atom_data = AtomData.from_hdf5(atomic_data_fname)
# Check whether the atom data file in current run and the atom data
# file used in obtaining the reference data are same.
# TODO: hard coded UUID for kurucz atom data file, generalize it later.
kurucz_data_file_uuid1 = "5ca3035ca8b311e3bb684437e69d75d7"
assert self.atom_data.uuid1 == kurucz_data_file_uuid1
# Create a Configuration through yaml file and atom data.
tardis_config = Configuration.from_yaml(
self.config_file, atom_data=self.atom_data)
# Check whether current run is with less packets.
if request.config.getoption("--less-packets"):
less_packets = request.config.integration_tests_config['less_packets']
tardis_config['montecarlo']['no_of_packets'] = (
less_packets['no_of_packets']
)
tardis_config['montecarlo']['last_no_of_packets'] = (
less_packets['last_no_of_packets']
)
# We now do a run with prepared config and get radial1d model.
self.result = Radial1DModel(tardis_config)
# If current test run is just for collecting reference data, store the
# output model to HDF file, save it at specified path. Skip all tests.
# Else simply perform the run and move further for performing
# assertions.
if request.config.getoption("--generate-reference"):
run_radial1d(self.result, hdf_path_or_buf=os.path.join(
data_path['gen_ref_dirpath'], "{0}.h5".format(self.name)
))
pytest.skip("Reference data saved at {0}".format(
data_path['gen_ref_dirpath']
))
else:
run_radial1d(self.result)
# Get the reference data through the fixture.
self.reference = reference
def base_config(request):
config = Configuration.from_yaml(
"tardis/io/tests/data/tardis_configv1_verysimple.yml")
config["plasma"]["line_interaction_type"] = request.param
config["montecarlo"]["no_of_packets"] = 4.0e4
config["montecarlo"]["last_no_of_packets"] = 1.0e5
config["montecarlo"]["no_of_virtual_packets"] = 0
config["spectrum"]["method"] = "integrated"
config["spectrum"]["integrated"]["points"] = 200
print("config", config)
return config
def test_compare_models(filename):
fn, fnold = filename
tardis_config = Configuration.from_yaml(fn)
tardis_config_old = Configuration.from_yaml(fnold)
csvy_model = Radial1DModel.from_csvy(tardis_config)
config_model = Radial1DModel.from_config(tardis_config_old)
csvy_model_props = csvy_model.get_properties().keys()
config_model_props = config_model.get_properties().keys()
npt.assert_array_equal(csvy_model_props, config_model_props)
for prop in config_model_props:
csvy_model_val = csvy_model.get_properties()[prop]
config_model_val = config_model.get_properties()[prop]
if prop == 'homologous_density':
npt.assert_array_almost_equal(csvy_model_val.density_0.value,
config_model_val.density_0.value)
npt.assert_array_almost_equal(csvy_model_val.time_0.value,
config_model_val.time_0.value)
else:
if hasattr(config_model_val, 'value'):
config_model_val = config_model_val.value
csvy_model_val = csvy_model_val.value
npt.assert_array_almost_equal(csvy_model_val, config_model_val)
def test_logging_config(self, atomic_data_fname, caplog, log_state,
specific):
config = Configuration.from_yaml(
"tardis/io/tests/data/tardis_configv1_verysimple_logger.yml")
config["atom_data"] = atomic_data_fname
caplog.clear()
run_tardis(config=config, log_state=log_state, specific=specific)
for record in caplog.records:
if specific == True:
assert record.levelno == LOGGING_LEVELS[log_state.upper()]
else:
assert record.levelno >= LOGGING_LEVELS[log_state.upper()]
def test_run_tardis_from_config_obj(atomic_data_fname):
"""
Tests whether the run_tardis function can take in the Configuration object
as arguments
"""
config = Configuration.from_yaml(
"tardis/io/tests/data/tardis_configv1_verysimple.yml")
config["atom_data"] = atomic_data_fname
try:
sim = run_tardis(config)
except Exception as e:
pytest.fail(str(e.args[0]))
def setup(self):
self.atom_data_filename = os.path.expanduser(os.path.expandvars(
pytest.config.getvalue('atomic-dataset')))
assert os.path.exists(self.atom_data_filename), ("{0} atomic datafiles "
"does not seem to "
"exist".format(
self.atom_data_filename))
self.config_yaml = yaml.load(open('tardis/io/tests/data/tardis_configv1_verysimple.yml'))
self.config_yaml['atom_data'] = self.atom_data_filename
self.config = Configuration.from_config_dict(self.config_yaml)
self.model = model.Radial1DModel(self.config)
simulation.run_radial1d(self.model)
def setup(self):
self.atom_data_filename = os.path.expanduser(os.path.expandvars(
pytest.config.getvalue('atomic-dataset')))
assert os.path.exists(self.atom_data_filename), ("{0} atomic datafiles "
"does not seem to "
"exist".format(
self.atom_data_filename))
self.config_yaml = yaml.load(open('tardis/io/tests/data/tardis_configv1_verysimple.yml'))
self.config_yaml['atom_data'] = self.atom_data_filename
self.config = Configuration.from_config_dict(self.config_yaml)
self.model = model.Radial1DModel(self.config)
simulation.run_radial1d(self.model)
def setup(self):
"""
This method does initial setup of creating configuration and performing
a single run of integration test.
"""
self.config_file = data_path("config_w7.yml")
self.abundances = data_path("abundancies_w7.dat")
self.densities = data_path("densities_w7.dat")
# First we check whether atom data file exists at desired path.
self.atom_data_filename = os.path.expanduser(os.path.expandvars(
pytest.config.getvalue('atomic-dataset')))
assert os.path.exists(self.atom_data_filename), \
"{0} atom data file does not exist".format(self.atom_data_filename)
# The available config file doesn't have file paths of atom data file,
# densities and abundances profile files as desired. We load the atom
# data seperately and provide it to tardis_config later. For rest of
# the two, we form dictionary from the config file and override those
# parameters by putting file paths of these two files at proper places.
config_yaml = yaml.load(open(self.config_file))
config_yaml['model']['abundances']['filename'] = self.abundances
config_yaml['model']['structure']['filename'] = self.densities
# Load atom data file separately, pass it for forming tardis config.
self.atom_data = AtomData.from_hdf5(self.atom_data_filename)
# Check whether the atom data file in current run and the atom data
# file used in obtaining the baseline data for slow tests are same.
# TODO: hard coded UUID for kurucz atom data file, generalize it later.
kurucz_data_file_uuid1 = "5ca3035ca8b311e3bb684437e69d75d7"
assert self.atom_data.uuid1 == kurucz_data_file_uuid1
# The config hence obtained will be having appropriate file paths.
tardis_config = Configuration.from_config_dict(config_yaml, self.atom_data)
# We now do a run with prepared config and get radial1d model.
self.obtained_radial1d_model = Radial1DModel(tardis_config)
simulation = Simulation(tardis_config)
simulation.legacy_run_simulation(self.obtained_radial1d_model)
# The baseline data against which assertions are to be made is ingested
# from already available compressed binaries (.npz). These will return
# dictionaries of numpy.ndarrays for performing assertions.
self.slow_test_data_dir = os.path.join(os.path.expanduser(
os.path.expandvars(pytest.config.getvalue('slow-test-data'))), "w7")
self.expected_ndarrays = np.load(os.path.join(self.slow_test_data_dir,
"ndarrays.npz"))
self.expected_quantities = np.load(os.path.join(self.slow_test_data_dir,
"quantities.npz"))
def run_final_models_plus_pickle(params, fname='blondin_model_compare_ddc25.yml'):
model_config = Configuration.from_yaml(fname)
model_config.model.v_inner_boundary = params[2]
model_config.model.v_outer_boundary = 35000*u.km/u.s
model_config.supernova.luminosity_requested = params[1]
model_config.supernova.time_explosion = params[0]
sim = Simulation.from_config(model_config)
print(sim.model.v_boundary_inner)
sim.run()
import pickle
dump = 'Output/ddc25/ddc25_t{}_v{}.pickle'.format(params[0].value, params[2].value)
with open(dump, 'wb') as dumpfile:
pickle.dump(sim, dumpfile)
return 1
def test_logging_simulation(atomic_data_fname, caplog):
"""
Testing the logs for simulations runs
"""
config = Configuration.from_yaml(
"tardis/io/tests/data/tardis_configv1_verysimple.yml")
config["atom_data"] = atomic_data_fname
simulation = Simulation.from_config(config)
simulation.run()
for record in caplog.records:
assert record.levelno >= logging.INFO
def setup(self):
self.atom_data_filename = os.path.expanduser(
os.path.expandvars(pytest.config.getvalue('atomic-dataset')))
assert os.path.exists(
self.atom_data_filename), ("{0} atomic datafiles"
" does not seem to "
"exist".format(self.atom_data_filename))
self.config_yaml = yaml_load_config_file(
'tardis/io/tests/data/tardis_configv1_verysimple.yml')
self.config_yaml['atom_data'] = self.atom_data_filename
tardis_config = Configuration.from_config_dict(self.config_yaml)
self.simulation = Simulation.from_config(tardis_config)
self.simulation.run()
def setup(self):
self.atom_data_filename = os.path.expanduser(os.path.expandvars(
pytest.config.getvalue('atomic-dataset')))
assert os.path.exists(self.atom_data_filename), ("{0} atomic datafiles"
" does not seem to "
"exist".format(
self.atom_data_filename))
self.config_yaml = yaml_load_config_file(
'tardis/io/tests/data/tardis_configv1_verysimple.yml')
self.config_yaml['atom_data'] = self.atom_data_filename
tardis_config = Configuration.from_config_dict(self.config_yaml)
self.simulation = Simulation.from_config(tardis_config)
self.simulation.run()
def runner(self, atomic_data_fname, tardis_ref_data, generate_reference):
config = Configuration.from_yaml(
'tardis/io/tests/data/tardis_configv1_verysimple.yml')
config['atom_data'] = atomic_data_fname
simulation = Simulation.from_config(config)
simulation.run()
if not generate_reference:
return simulation.runner
else:
simulation.runner.hdf_properties = [
'j_blue_estimator', 'spectrum', 'spectrum_virtual'
]
simulation.runner.to_hdf(tardis_ref_data, '', self.name)
pytest.skip('Reference data was generated during this run.')
def test_ascii_reader_power_law():
filename = 'tardis_configv1_density_power_law_test.yml'
config = Configuration.from_yaml(data_path(filename))
model = Radial1DModel.from_config(config)
expected_densites = [3.29072513e-14, 2.70357804e-14, 2.23776573e-14,
1.86501954e-14, 1.56435277e-14, 1.32001689e-14,
1.12007560e-14, 9.55397475e-15, 8.18935779e-15,
7.05208050e-15, 6.09916083e-15, 5.29665772e-15,
4.61758699e-15, 4.04035750e-15, 3.54758837e-15,
3.12520752e-15, 2.76175961e-15, 2.44787115e-15,
2.17583442e-15, 1.93928168e-15]
assert model.no_of_shells == 20
for i, mdens in enumerate(expected_densites):
assert_almost_equal(model.density[i].to(u.Unit('g / (cm3)')).value,
mdens)
def config(self, request):
config_path = os.path.join(
'tardis', 'plasma', 'tests', 'data', 'plasma_base_test_config.yml')
config = Configuration.from_yaml(config_path)
hash_string = ''
for prop, value in request.param.items():
hash_string = '_'.join((hash_string, prop))
if prop == 'nlte':
for nlte_prop, nlte_value in request.param[prop].items():
config.plasma.nlte[nlte_prop] = nlte_value
if nlte_prop != 'species':
hash_string = '_'.join((hash_string, nlte_prop))
else:
config.plasma[prop] = value
hash_string = '_'.join((hash_string, str(value)))
setattr(config.plasma, 'save_path', hash_string)
return config
def config(self, request):
config_path = os.path.join('tardis', 'plasma', 'tests', 'data',
'plasma_base_test_config.yml')
config = Configuration.from_yaml(config_path)
hash_string = ''
for prop, value in request.param.items():
hash_string = '_'.join((hash_string, prop))
if prop == 'nlte':
for nlte_prop, nlte_value in request.param[prop].items():
config.plasma.nlte[nlte_prop] = nlte_value
if nlte_prop != 'species':
hash_string = '_'.join((hash_string, nlte_prop))
else:
config.plasma[prop] = value
hash_string = '_'.join((hash_string, str(value)))
setattr(config.plasma, 'save_path', hash_string)
return config
def test_ascii_reader_exponential_law():
filename = 'tardis_configv1_density_exponential_test.yml'
config = Configuration.from_yaml(data_path(filename))
model = Radial1DModel.from_config(config)
expected_densites = [5.18114795e-14, 4.45945537e-14, 3.83828881e-14,
3.30364579e-14, 2.84347428e-14, 2.44740100e-14,
2.10649756e-14, 1.81307925e-14, 1.56053177e-14,
1.34316215e-14, 1.15607037e-14, 9.95038990e-15,
8.56437996e-15, 7.37143014e-15, 6.34464872e-15,
5.46088976e-15, 4.70023138e-15, 4.04552664e-15,
3.48201705e-15, 2.99699985e-15]
expected_unit = 'g / (cm3)'
assert model.no_of_shells == 20
for i, mdens in enumerate(expected_densites):
assert_almost_equal(model.density[i].value, mdens)
assert model.density[i].unit == u.Unit(expected_unit)
def test_model_decay(simple_isotope_abundance):
filename = 'tardis_configv1_verysimple.yml'
config = Configuration.from_yaml(data_path(filename))
model = Radial1DModel.from_config(config)
model.raw_isotope_abundance = simple_isotope_abundance
decayed = simple_isotope_abundance.decay(
model.time_explosion).as_atoms()
norm_factor = 1.4
assert_almost_equal(
model.abundance.loc[8][0], model.raw_abundance.loc[8][0] / norm_factor, decimal=4)
assert_almost_equal(model.abundance.loc[14][0], (
model.raw_abundance.loc[14][0] + decayed.loc[14][0]) / norm_factor, decimal=4)
assert_almost_equal(model._abundance.loc[12][5], (
model.raw_abundance.loc[12][5] + decayed.loc[12][5]) / norm_factor, decimal=4)
assert_almost_equal(
model.abundance.loc[6][12], (decayed.loc[6][12]) / norm_factor, decimal=4)
def runner(self, atomic_data_fname, tardis_ref_data, generate_reference):
config = Configuration.from_yaml(
"tardis/io/tests/data/tardis_configv1_verysimple.yml")
config["atom_data"] = atomic_data_fname
simulation = Simulation.from_config(config)
simulation.run()
if not generate_reference:
return simulation.runner
else:
simulation.runner.hdf_properties = [
"j_blue_estimator",
"spectrum",
"spectrum_virtual",
]
simulation.runner.to_hdf(tardis_ref_data, "", self.name)
pytest.skip("Reference data was generated during this run.")
def runner(
self, atomic_data_fname,
tardis_ref_data, generate_reference):
config = Configuration.from_yaml(
'tardis/io/tests/data/tardis_configv1_verysimple.yml')
config['atom_data'] = atomic_data_fname
simulation = Simulation.from_config(config)
simulation.run()
if not generate_reference:
return simulation.runner
else:
simulation.runner.hdf_properties = [
'j_blue_estimator',
'spectrum',
'spectrum_virtual'
]
simulation.runner.to_hdf(
tardis_ref_data,
'',
self.name)
pytest.skip(
'Reference data was generated during this run.')
def _generate_config(self, callback):
config_ns = callback(self.config)
return Configuration.from_config_dict(
config_ns,
validate=False,
atom_data=self.atom_data)
def setup(self):
filename = 'tardis_configv1_uniform_density.yml'
self.config = Configuration.from_yaml(data_path(filename))
self.config.plasma.initial_t_inner = 2508 * u.K
self.model = Radial1DModel.from_config(self.config)
def isotope_uniform_abundance():
config_path = os.path.join(
data_path, 'tardis_configv1_isotope_uniabund.yml')
config = Configuration.from_yaml(config_path)
return config.model.abundances
def setup(self):
filename = 'paper1_tardis_configv1.yml'
self.config = Configuration.from_yaml(data_path(filename))
self.model = Radial1DModel.from_config(self.config)
def config_verysimple():
filename = 'tardis_configv1_verysimple.yml'
path = os.path.abspath(os.path.join('tardis/io/tests/data/', filename))
config = Configuration.from_yaml(path)
return config
def setup(self):
filename = 'tardis_configv1_ascii_density_abund.yml'
self.config = Configuration.from_yaml(data_path(filename))
self.config.model.structure.filename = 'density.dat'
self.config.model.abundances.filename = 'abund.dat'
self.model = Radial1DModel.from_config(self.config)
def setup(self, request, reference, data_path, pytestconfig):
"""
This method does initial setup of creating configuration and performing
a single run of integration test.
"""
# Get capture manager
capmanager = pytestconfig.pluginmanager.getplugin('capturemanager')
# The last component in dirpath can be extracted as name of setup.
self.name = data_path['setup_name']
self.config_file = os.path.join(data_path['config_dirpath'], "config.yml")
# A quick hack to use atom data per setup. Atom data is ingested from
# local HDF or downloaded and cached from a url, depending on data_path
# keys.
atom_data_name = yaml.load(open(self.config_file))['atom_data']
# Get the path to HDF file:
atom_data_filepath = os.path.join(
data_path['atom_data_path'], atom_data_name
)
# Load atom data file separately, pass it for forming tardis config.
self.atom_data = AtomData.from_hdf(atom_data_filepath)
# Check whether the atom data file in current run and the atom data
# file used in obtaining the reference data are same.
# TODO: hard coded UUID for kurucz atom data file, generalize it later.
# kurucz_data_file_uuid1 = "5ca3035ca8b311e3bb684437e69d75d7"
# assert self.atom_data.uuid1 == kurucz_data_file_uuid1
# Create a Configuration through yaml file and atom data.
tardis_config = Configuration.from_yaml(self.config_file)
# Check whether current run is with less packets.
if request.config.getoption("--less-packets"):
less_packets = request.config.integration_tests_config['less_packets']
tardis_config['montecarlo']['no_of_packets'] = (
less_packets['no_of_packets']
)
tardis_config['montecarlo']['last_no_of_packets'] = (
less_packets['last_no_of_packets']
)
# We now do a run with prepared config and get the simulation object.
self.result = Simulation.from_config(tardis_config,
atom_data=self.atom_data)
capmanager.suspendcapture(True)
# If current test run is just for collecting reference data, store the
# output model to HDF file, save it at specified path. Skip all tests.
# Else simply perform the run and move further for performing
# assertions.
self.result.run()
if request.config.getoption("--generate-reference"):
ref_data_path = os.path.join(
data_path['reference_path'], "{0}.h5".format(self.name)
)
if os.path.exists(ref_data_path):
pytest.skip(
'Reference data {0} does exist and tests will not '
'proceed generating new data'.format(ref_data_path))
self.result.to_hdf(file_path=ref_data_path)
pytest.skip("Reference data saved at {0}".format(
data_path['reference_path']
))
capmanager.resumecapture()
# Get the reference data through the fixture.
self.reference = reference
def setup(self):
filename = 'tardis_configv1_artis_density.yml'
self.config = Configuration.from_yaml(data_path(filename))
self.model = Radial1DModel.from_config(self.config)
def config():
return Configuration.from_yaml(
'tardis/io/tests/data/tardis_configv1_verysimple.yml')
def tardis_model_density_config():
filename = 'tardis_configv1_tardis_model_format.yml'
return Configuration.from_yaml(os.path.join(data_path, filename))
def tardis_config(tardis_config_verysimple):
return Configuration.from_config_dict(tardis_config_verysimple)