import numpy as np
import pandas as pd
from tardis.io.model.readers.cmfgen_deprecated import (
read_cmfgen_composition,
read_cmfgen_density,
)
from tardis.io.model.readers.generic_readers import (
ConfigurationError,
read_csv_composition,
read_simple_ascii_density,
read_simple_ascii_mass_fractions,
)
[docs]
def read_mass_fractions_file(
mass_fractions_filename,
mass_fractions_filetype,
inner_boundary_idx=None,
outer_boundary_idx=None,
density_filename=None,
):
"""
read different density file formats
Parameters
----------
mass_fractions_filename : str
filename or path of the density file
mass_fractions_filetype : str
type of the density file
inner_boundary_idx : int
index of the inner shell, default None
outer_boundary_idx : int
index of the outer shell, default None
density_filename : str or pathlib.Path
Matching density file. Required for ARTIS isotope mass fractions,
which are stored in the ARTIS density file.
"""
file_parsers = {
"simple_ascii": read_simple_ascii_mass_fractions,
"cmfgen_model": read_cmfgen_composition,
"custom_composition": read_csv_composition,
}
isotope_mass_fractions = pd.DataFrame()
if mass_fractions_filetype in ["cmfgen_model", "custom_composition"]:
index, mass_fractions, isotope_mass_fractions = file_parsers[
mass_fractions_filetype
](mass_fractions_filename)
elif mass_fractions_filetype == "artis":
from tardis.io.model.artis.readers import (
read_artis_composition,
read_artis_mass_fractions,
)
if density_filename is None:
mass_fractions = read_artis_mass_fractions(mass_fractions_filename)
index = mass_fractions.T.index
else:
index, mass_fractions, isotope_mass_fractions = (
read_artis_composition(
density_filename, mass_fractions_filename
)
)
index = mass_fractions.T.index
else:
index, mass_fractions = file_parsers[mass_fractions_filetype](
mass_fractions_filename
)
if outer_boundary_idx is not None:
outer_boundary_idx_m1 = outer_boundary_idx - 1
else:
outer_boundary_idx_m1 = None
index = index[inner_boundary_idx:outer_boundary_idx]
mass_fractions = mass_fractions.loc[
:, slice(inner_boundary_idx, outer_boundary_idx_m1)
]
mass_fractions.columns = np.arange(len(mass_fractions.columns))
if not isotope_mass_fractions.empty:
isotope_mass_fractions = isotope_mass_fractions.loc[
:, slice(inner_boundary_idx, outer_boundary_idx_m1)
]
isotope_mass_fractions.columns = np.arange(
len(isotope_mass_fractions.columns)
)
return index, mass_fractions, isotope_mass_fractions
[docs]
def read_density_file(filename, filetype):
"""
read different density file formats
Parameters
----------
filename : str
filename or path of the density file
filetype : str
type of the density file
Returns
-------
time_of_model : astropy.units.Quantity
time at which the model is valid
velocity : np.ndarray
the array containing the velocities
unscaled_mean_densities : np.ndarray
the array containing the densities
electron_densities : np.ndarray
The array containing electron densities
temperature : np.ndarray
The array containing temperatures
"""
# Lazy import to avoid circular dependency
from tardis.io.model.artis.readers import (
read_artis_density,
)
file_parsers = {
"artis": read_artis_density,
"simple_ascii": read_simple_ascii_density,
"cmfgen_model": read_cmfgen_density,
}
electron_densities = None
temperature = None
if filetype == "cmfgen_model":
(
time_of_model,
velocity,
unscaled_mean_densities,
electron_densities,
temperature,
) = read_cmfgen_density(filename)
else:
(time_of_model, velocity, unscaled_mean_densities) = file_parsers[
filetype
](filename)
v_inner = velocity[:-1]
v_outer = velocity[1:]
invalid_volume_mask = (v_outer - v_inner) <= 0
if invalid_volume_mask.sum() > 0:
message = "\n".join(
[
f"cell {i:d}: v_inner {v_inner_i:s}, v_outer {v_outer_i:s}"
for i, v_inner_i, v_outer_i in zip(
np.arange(len(v_outer))[invalid_volume_mask],
v_inner[invalid_volume_mask],
v_outer[invalid_volume_mask],
)
]
)
raise ConfigurationError(
f"Invalid volume of following cell(s):\n{message:s}"
)
return (
time_of_model,
velocity,
unscaled_mean_densities,
electron_densities,
temperature,
)