def from_hdf(cls, fname=None):
"""
Function to read the atom data from a TARDIS atom HDF Store
Parameters
----------
fname : str, optional
Path to the HDFStore file or name of known atom data file
(default: None)
"""
dataframes = dict()
nonavailable = list()
fname = resolve_atom_data_fname(fname)
with pd.HDFStore(fname, "r") as store:
for name in cls.hdf_names:
try:
dataframes[name] = store[name]
except KeyError:
logger.debug("Dataframe does not contain NAME column")
nonavailable.append(name)
atom_data = cls(**dataframes)
try:
atom_data.uuid1 = store.root._v_attrs["uuid1"].decode("ascii")
except KeyError:
logger.debug(
"UUID not available for Atom Data. Setting value to None")
atom_data.uuid1 = None
try:
atom_data.md5 = store.root._v_attrs["md5"].decode("ascii")
except KeyError:
logger.debug(
"MD5 not available for Atom Data. Setting value to None")
atom_data.md5 = None
try:
atom_data.version = store.root._v_attrs["database_version"]
except KeyError:
logger.debug(
"VERSION not available for Atom Data. Setting value to None"
)
atom_data.version = None
# ToDo: strore data sources as attributes in carsus
logger.info(
f"Reading Atom Data with: UUID = {atom_data.uuid1} MD5 = {atom_data.md5} "
)
if nonavailable:
logger.info("Non provided Atomic Data: {0}".format(
", ".join(nonavailable)))
return atom_data
def from_hdf(cls, fname=None):
"""
Function to read the atom data from a TARDIS atom HDF Store
Parameters
----------
fname : str, optional
Path to the HDFStore file or name of known atom data file
(default: None)
"""
dataframes = dict()
nonavailable = list()
fname = resolve_atom_data_fname(fname)
with pd.HDFStore(fname, "r") as store:
for name in cls.hdf_names:
try:
dataframes[name] = store[name]
except KeyError:
nonavailable.append(name)
atom_data = cls(**dataframes)
try:
atom_data.uuid1 = store.root._v_attrs["uuid1"].decode("ascii")
except KeyError:
atom_data.uuid1 = None
try:
atom_data.md5 = store.root._v_attrs["md5"].decode("ascii")
except KeyError:
atom_data.md5 = None
try:
atom_data.version = store.root._v_attrs["database_version"]
except KeyError:
atom_data.version = None
# ToDo: strore data sources as attributes in carsus
logger.info(
"Read Atom Data with UUID={0} and MD5={1}.".format(
atom_data.uuid1, atom_data.md5
)
)
if nonavailable:
logger.info(
"Non provided atomic data: {0}".format(
", ".join(nonavailable)
)
)
return atom_data
def from_hdf(cls, fname=None):
"""
Function to read the atom data from a TARDIS atom HDF Store
Parameters
----------
fname: str, optional
Path to the HDFStore file or name of known atom data file
(default: None)
"""
dataframes = dict()
nonavailable = list()
fname = resolve_atom_data_fname(fname)
with pd.HDFStore(fname, 'r') as store:
for name in cls.hdf_names:
try:
dataframes[name] = store[name]
except KeyError:
nonavailable.append(name)
atom_data = cls(**dataframes)
try:
atom_data.uuid1 = store.root._v_attrs['uuid1'].decode('ascii')
except KeyError:
atom_data.uuid1 = None
try:
atom_data.md5 = store.root._v_attrs['md5'].decode('ascii')
except KeyError:
atom_data.md5 = None
try:
atom_data.version = store.root._v_attrs['database_version']
except KeyError:
atom_data.version = None
# ToDo: strore data sources as attributes in carsus
logger.info(
"Read Atom Data with UUID={0} and MD5={1}.".format(
atom_data.uuid1, atom_data.md5))
if nonavailable:
logger.info("Non provided atomic data: {0}".format(
", ".join(nonavailable)))
return atom_data
def from_hdf(cls, fname=None):
"""
Function to read the atom data from a TARDIS atom HDF Store
Parameters
----------
fname : str, optional
Path to the HDFStore file or name of known atom data file
(default: None)
"""
dataframes = dict()
nonavailable = list()
fname = resolve_atom_data_fname(fname)
with pd.HDFStore(fname, "r") as store:
for name in cls.hdf_names:
try:
dataframes[name] = store[name]
except KeyError:
logger.debug(f"Dataframe does not contain {name} column")
nonavailable.append(name)
if "metadata" in store:
carsus_version_str = (store["metadata"].loc[("format",
"version")].value)
carsus_version = tuple(map(int, carsus_version_str.split(".")))
if carsus_version == (1, 0):
# Checks for various collisional data from Carsus files
if "collisions_data" in store:
try:
dataframes["collision_data_temperatures"] = store[
"collisions_metadata"].temperatures
if "cmfgen" in store[
"collisions_metadata"].dataset:
dataframes["yg_data"] = store[
"collisions_data"]
dataframes["collision_data"] = "dummy value"
elif ("chianti"
in store["collisions_metadata"].dataset):
dataframes["collision_data"] = store[
"collisions_data"]
else:
raise KeyError(
"Atomic Data Collisions Not a Valid Chanti or CMFGEN Carsus Data File"
)
except KeyError as e:
logger.warn(
"Atomic Data is not a Valid Carsus Atomic Data File"
)
raise
dataframes["levels"] = store["levels_data"]
dataframes["lines"] = store["lines_data"]
else:
raise ValueError(
f"Current carsus version, {carsus_version}, is not supported."
)
atom_data = cls(**dataframes)
try:
atom_data.uuid1 = store.root._v_attrs["uuid1"]
if hasattr(atom_data.uuid1, "decode"):
atom_data.uuid1 = store.root._v_attrs["uuid1"].decode(
"ascii")
except KeyError:
logger.debug(
"UUID not available for Atom Data. Setting value to None")
atom_data.uuid1 = None
try:
atom_data.md5 = store.root._v_attrs["md5"]
if hasattr(atom_data.md5, "decode"):
atom_data.md5 = store.root._v_attrs["md5"].decode("ascii")
except KeyError:
logger.debug(
"MD5 not available for Atom Data. Setting value to None")
atom_data.md5 = None
try:
atom_data.version = store.root._v_attrs["database_version"]
except KeyError:
logger.debug(
"VERSION not available for Atom Data. Setting value to None"
)
atom_data.version = None
# ToDo: strore data sources as attributes in carsus
logger.info(
f"Reading Atom Data with: UUID = {atom_data.uuid1} MD5 = {atom_data.md5} "
)
if nonavailable:
logger.info("Non provided Atomic Data: {0}".format(
", ".join(nonavailable)))
return atom_data