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Carsus format support #14

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merged 2 commits into from
May 16, 2022
Merged

Carsus format support #14

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d91a3f4
Added support for carsus version 1.0
sonachitchyan May 16, 2022
2121719
small bug fixes
sonachitchyan May 16, 2022
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55 changes: 34 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 @@ -2,6 +2,8 @@


import logging
from multiprocessing.sharedctypes import Value
from matplotlib import collections
import numpy as np
import pandas as pd

Expand Down Expand Up @@ -165,44 +167,55 @@ def from_hdf(cls, fname=None):
fname = resolve_atom_data_fname(fname)

with pd.HDFStore(fname, "r") as store:
if "metadata" in store:
carsus_version = store["metadata"].loc[('format', 'version')].value
if carsus_version == "1.0":
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.")


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)
# Checks for various collisional data from Carsus files
if "collisions" in store:
try:
dataframes["collision_data_temperatures"] = store[
"collisions_metadata"
].temperatures
if store["collisions_metadata"].dataset == "cmfgen":
dataframes["yg_data"] = store["collisions"]
dataframes["collision_data"] = "dummy value"
elif store["collisions_metadata"].dataset == "chianti":
dataframes["collision_data"] = store["collisions"]
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

atom_data = cls(**dataframes)

try:
atom_data.uuid1 = store.root._v_attrs["uuid1"].decode("ascii")
atom_data.uuid1 = store.root._v_attrs["uuid1"]
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")
atom_data.md5 = store.root._v_attrs["md5"]
except KeyError:
logger.debug(
"MD5 not available for Atom Data. Setting value to None"
Expand Down