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add linelist exposure to atom data and reader #2427

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add linelist exposure to atom data and reader #2427

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35 changes: 14 additions & 21 deletions tardis/io/atom_data/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,7 @@ class AtomData(object):
"photoionization_data",
"yg_data",
"two_photon_data",
"linelist",
]

# List of tuples of the related dataframes.
Expand Down Expand Up @@ -165,10 +166,9 @@ def from_hdf(cls, fname=None):
fname = resolve_atom_data_fname(fname)

with pd.HDFStore(fname, "r") as store:

for name in cls.hdf_names:
try:
dataframes[name] = store.select(name)
dataframes[name] = store[name]
except KeyError:
logger.debug(f"Dataframe does not contain {name} column")
nonavailable.append(name)
Expand All @@ -182,7 +182,6 @@ def from_hdf(cls, fname=None):
# Checks for various collisional data from Carsus files
if "collisions_data" in store:
try:

dataframes["collision_data_temperatures"] = store[
"collisions_metadata"
].temperatures
Expand Down Expand Up @@ -211,6 +210,8 @@ def from_hdf(cls, fname=None):
raise ValueError(
f"Current carsus version, {carsus_version}, is not supported."
)
if "linelist" in store:
dataframes["linelist"] = store["linelist"]

atom_data = cls(**dataframes)

Expand Down Expand Up @@ -273,8 +274,8 @@ def __init__(
photoionization_data=None,
yg_data=None,
two_photon_data=None,
linelist=None,
):

self.prepared = False

# CONVERT VALUES TO CGS UNITS
Expand All @@ -287,33 +288,25 @@ def __init__(
if u.u.cgs == const.u.cgs:
atom_data.loc[:, "mass"] = Quantity(
atom_data["mass"].values, "u"
).cgs.value
).cgs
else:
atom_data.loc[:, "mass"] = (
atom_data["mass"].values * const.u.cgs.value
)
atom_data.loc[:, "mass"] = atom_data["mass"].values * const.u.cgs

# Convert ionization energies to CGS
ionization_data = ionization_data.squeeze()
ionization_data[:] = Quantity(ionization_data[:], "eV").cgs.value
ionization_data[:] = Quantity(ionization_data[:], "eV").cgs

# Convert energy to CGS
levels.loc[:, "energy"] = Quantity(
levels["energy"].values, "eV"
).cgs.value
levels.loc[:, "energy"] = Quantity(levels["energy"].values, "eV").cgs

# Create a new columns with wavelengths in the CGS units
lines["wavelength_cm"] = Quantity(
lines["wavelength"], "angstrom"
).cgs.value
lines["wavelength_cm"] = Quantity(lines["wavelength"], "angstrom").cgs

# SET ATTRIBUTES

self.atom_data = atom_data
self.ionization_data = ionization_data
self.levels = levels
# Not sure why this is need - WEK 17 Sep 2023
self.levels.energy = self.levels.energy.astype(np.float64)
self.lines = lines

# Rename these (drop "_all") when `prepare_atom_data` is removed!
Expand All @@ -333,6 +326,9 @@ def __init__(

self.two_photon_data = two_photon_data

if linelist is not None:
self.linelist = linelist

self._check_related()

self.symbol2atomic_number = OrderedDict(
Expand Down Expand Up @@ -426,7 +422,6 @@ def prepare_atom_data(
self.macro_atom_data_all is not None
and not line_interaction_type == "scatter"
):

self.macro_atom_data = self.macro_atom_data_all.loc[
self.macro_atom_data_all["atomic_number"].isin(
self.selected_atomic_numbers
Expand Down Expand Up @@ -530,9 +525,7 @@ def prepare_atom_data(
self.macro_atom_data.loc[:, "destination_level_idx"] = -1

if self.yg_data is not None:
self.yg_data = self.yg_data.reindex(
self.selected_atomic_numbers, level=0
)
self.yg_data = self.yg_data.loc[self.selected_atomic_numbers]

self.nlte_data = NLTEData(self, nlte_species)

Expand Down