def fetch_astroquery(molecule, isotope, wmin, wmax, verbose=True):
''' Wrapper to Astroquery [1]_ fetch function to download a line database
Notes
-----
Astroquery [1]_ is itself based on [HAPI]_
Parameters
----------
molecule: str, or int
molecule name or identifier
isotope: int
isotope number
wmin, wmax: float (cm-1)
wavenumber min and max
Other Parameters
----------------
verbose: boolean
Default ``True``
References
----------
.. [1] `Astroquery <https://astroquery.readthedocs.io>`_
See Also
--------
:func:`astroquery.hitran.reader.download_hitran`, :func:`astroquery.hitran.reader.read_hitran_file`
'''
# Check input
if not is_float(molecule):
mol_id = get_molecule_identifier(molecule)
else:
mol_id = molecule
molecule = get_molecule(mol_id)
assert is_float(isotope)
empty_range = False
# tbl = Hitran.query_lines_async(molecule_number=mol_id,
# isotopologue_number=isotope,
# min_frequency=wmin / u.cm,
# max_frequency=wmax / u.cm)
# # Download using the astroquery library
response = Hitran.query_lines_async(molecule_number=mol_id,
isotopologue_number=isotope,
min_frequency=wmin / u.cm,
max_frequency=wmax / u.cm)
if response.status_code == 404:
# Maybe there are just no lines for this species in this range
# In that case we usually end up with errors like:
# (<class 'Exception'>, Exception('Query failed: 404 Client Error:
# Not Found for url: http://hitran.org/lbl/api?numax=25000&numin=19000&iso_ids_list=69\n',),
# <traceback object at 0x7f0967c91708>)
if response.reason == 'Not Found':
# Let's bet it's just that there are no lines in this range
empty_range = True
if verbose:
print((
'No lines for {0} (id={1}), iso={2} in range {3:.2f}-{4:.2f}cm-1. '
.format(molecule, mol_id, isotope, wmin, wmax)))
else:
raise ValueError(
'An error occured during the download of HITRAN files ' +
'for {0} (id={1}), iso={2} between {3:.2f}-{4:.2f}cm-1. '.
format(molecule, mol_id, isotope, wmin, wmax) +
'Are you online?\n' +
'See details of the error below:\n\n {0}'.format(
response.reason))
# Rename columns from Astroquery to RADIS format
rename_columns = {
'molec_id': 'id',
'local_iso_id': 'iso',
'nu': 'wav',
'sw': 'int',
'a': 'A',
'gamma_air': 'airbrd',
'gamma_self': 'selbrd',
'elower': 'El',
'n_air': 'Tdpair',
'delta_air': 'Pshft',
'global_upper_quanta': 'globu',
'global_lower_quanta': 'globl',
'local_upper_quanta': 'locu',
'local_lower_quanta': 'locl',
'line_mixing_flag': 'lmix',
'gp': 'gp',
'gpp': 'gpp',
}
if not empty_range:
# _fix_astroquery_file_format(filename)
# Note: as of 0.9.16 we're not fixing astroquery_file_format anymore.
# maybe we should.
tbl = Hitran._parse_result(response)
df = tbl.to_pandas()
df = df.rename(columns=rename_columns)
else:
df = pd.DataFrame(columns=list(rename_columns.values()))
# Cast type to float64
cast_type = {
'wav': np.float64,
'int': np.float64,
'A': np.float64,
'airbrd': np.float64,
'selbrd': np.float64,
'El': np.float64,
'Tdpair': np.float64,
'Pshft': np.float64,
}
for c, typ in cast_type.items():
df[c] = df[c].astype(typ)
return df
def fetch_astroquery(molecule,
isotope,
wmin,
wmax,
verbose=True,
cache=True,
metadata={}):
''' Wrapper to Astroquery [1]_ fetch function to download a line database
Notes
-----
Astroquery [1]_ is itself based on [HAPI]_
Parameters
----------
molecule: str, or int
molecule name or identifier
isotope: int
isotope number
wmin, wmax: float (cm-1)
wavenumber min and max
Other Parameters
----------------
verbose: boolean
Default ``True``
cache: boolean
if ``True``, tries to find a ``.h5`` cache file in the Astroquery
:py:attr:`~astroquery.query.BaseQuery.cache_location`, that would match
the requirements. If not found, downloads it and saves the line dataframe
as a ``.h5`` file in the Astroquery.
metadata: dict
if ``cache=True``, check that the metadata in the cache file correspond
to these attributes. Arguments ``molecule``, ``isotope``, ``wmin``, ``wmax``
are already added by default.
References
----------
.. [1] `Astroquery <https://astroquery.readthedocs.io>`_
See Also
--------
:py:func:`astroquery.hitran.reader.download_hitran`,
:py:func:`astroquery.hitran.reader.read_hitran_file`,
:py:attr:`~astroquery.query.BaseQuery.cache_location`
'''
# Check input
if not is_float(molecule):
mol_id = get_molecule_identifier(molecule)
else:
mol_id = molecule
molecule = get_molecule(mol_id)
assert is_float(isotope)
empty_range = False
# If cache, tries to find from Astroquery:
if cache:
# Update metadata with physical properties from the database.
metadata.update({
'molecule': molecule,
'isotope': isotope,
'wmin': wmin,
'wmax': wmax
})
fcache = join(
Hitran.cache_location,
CACHE_FILE_NAME.format(
**{
'molecule': molecule,
'isotope': isotope,
'wmin': wmin,
'wmax': wmax
}))
check_cache_file(fcache=fcache,
use_cached=cache,
metadata=metadata,
verbose=verbose)
if exists(fcache):
try:
return get_cache_file(fcache, verbose=verbose)
except Exception as err:
if verbose:
printr(
'Problem reading cache file {0}:\n{1}\nDeleting it!'.
format(fcache, str(err)))
os.remove(fcache)
# tbl = Hitran.query_lines_async(molecule_number=mol_id,
# isotopologue_number=isotope,
# min_frequency=wmin / u.cm,
# max_frequency=wmax / u.cm)
# # Download using the astroquery library
try:
response = Hitran.query_lines_async(molecule_number=mol_id,
isotopologue_number=isotope,
min_frequency=wmin / u.cm,
max_frequency=wmax / u.cm)
except KeyError as err:
raise KeyError(str(err)+' <<w this error occured in Astroquery. Maybe these molecule '+\
'({0}) and isotope ({1}) are not supported'.format(molecule, isotope)) from err
# Deal with usual errors
if response.status_code == 404:
# Maybe there are just no lines for this species in this range
# In that case we usually end up with errors like:
# (<class 'Exception'>, Exception('Query failed: 404 Client Error:
# Not Found for url: http://hitran.org/lbl/api?numax=25000&numin=19000&iso_ids_list=69\n',),
# <traceback object at 0x7f0967c91708>)
if response.reason == 'Not Found':
# Let's bet it's just that there are no lines in this range
empty_range = True
if verbose:
print((
'No lines for {0} (id={1}), iso={2} in range {3:.2f}-{4:.2f}cm-1. '
.format(molecule, mol_id, isotope, wmin, wmax)))
else:
raise ValueError(
'An error occured during the download of HITRAN files ' +
'for {0} (id={1}), iso={2} between {3:.2f}-{4:.2f}cm-1. '.
format(molecule, mol_id, isotope, wmin, wmax) +
'Are you online?\n' +
'See details of the error below:\n\n {0}'.format(
response.reason))
elif response.status_code == 500:
raise ValueError('{0} while querying the HITRAN server: '.format(response.status_code)+\
'\n\n{0}'.format(response.text))
# Process response
# Rename columns from Astroquery to RADIS format
rename_columns = {
'molec_id': 'id',
'local_iso_id': 'iso',
'nu': 'wav',
'sw': 'int',
'a': 'A',
'gamma_air': 'airbrd',
'gamma_self': 'selbrd',
'elower': 'El',
'n_air': 'Tdpair',
'delta_air': 'Pshft',
'global_upper_quanta': 'globu',
'global_lower_quanta': 'globl',
'local_upper_quanta': 'locu',
'local_lower_quanta': 'locl',
'line_mixing_flag': 'lmix',
'gp': 'gp',
'gpp': 'gpp',
}
if not empty_range:
# _fix_astroquery_file_format(filename)
# Note: as of 0.9.16 we're not fixing astroquery_file_format anymore.
# maybe we should.
tbl = Hitran._parse_result(response)
df = tbl.to_pandas()
df = df.rename(columns=rename_columns)
else:
df = pd.DataFrame(columns=list(rename_columns.values()))
# Cast type to float64
cast_type = {
'wav': np.float64,
'int': np.float64,
'A': np.float64,
'airbrd': np.float64,
'selbrd': np.float64,
'El': np.float64,
'Tdpair': np.float64,
'Pshft': np.float64,
}
for c, typ in cast_type.items():
df[c] = df[c].astype(typ)
# cached file mode but cached file doesn't exist yet (else we had returned)
if cache:
if verbose:
print('Generating cached file: {0}'.format(fcache))
try:
save_to_hdf(df,
fcache,
metadata=metadata,
version=radis.__version__,
key='df',
overwrite=True,
verbose=verbose)
except:
if verbose:
print(sys.exc_info())
print(
'An error occured in cache file generation. Lookup access rights'
)
pass
return df
def fetch_astroquery(molecule, isotope, wmin, wmax, verbose=True):
''' Wrapper to Astroquery [1]_ fetch function to download a line database
Notes
-----
Astroquery [1]_ is itself based on HAPI [2]_
Parameters
----------
molecule: str, or int
molecule name or identifier
isotope: int
isotope number
wmin, wmax: float (cm-1)
wavenumber min and max
Other Parameters
----------------
verbose: boolean
Default True
References
----------
.. [1] `Astroquery <https://astroquery.readthedocs.io>`_
.. [2] `HAPI: The HITRAN Application Programming Interface <http://hitran.org/hapi>`_
'''
# Check input
if not is_float(molecule):
mol_id = get_molecule_identifier(molecule)
else:
mol_id = molecule
molecule = get_molecule(mol_id)
assert is_float(isotope)
empty_range = False
# Download using the astroquery library
try:
download_hitran(mol_id, isotope, wmin, wmax)
except:
# Maybe there are just no lines for this species in this range
# In that case we usually end up with errors like:
# (<class 'Exception'>, Exception('Query failed: 404 Client Error:
# Not Found for url: http://hitran.org/lbl/api?numax=25000&numin=19000&iso_ids_list=69\n',),
# <traceback object at 0x7f0967c91708>)
import sys
_err_class, _err_details, _err_obj = sys.exc_info()
if 'Not Found for url:' in str(_err_details):
# Let's bet it's just that there are no lines in this range
empty_range = True
if verbose:
print((
'Not lines for {0} (id={1}), iso={2} between {3:.2f}-{4:.2f}cm-1. '
.format(molecule, mol_id, isotope, wmin, wmax)))
else:
raise ValueError('An error occured during the download of HITRAN files '+\
'for {0} (id={1}), iso={2} between {3:.2f}-{4:.2f}cm-1. '.format(
molecule, mol_id, isotope, wmin, wmax)+\
'See details of the error below: {0}'.format(_err_details))
# Rename columns from Astroquery to RADIS format
rename_columns = {
'molec_id': 'id',
'local_iso_id': 'iso',
'nu': 'wav',
'sw': 'int',
'a': 'A',
'gamma_air': 'airbrd',
'gamma_self': 'selbrd',
'elower': 'El',
'n_air': 'Tdpair',
'delta_air': 'Pshft',
'global_upper_quanta': 'globu',
'global_lower_quanta': 'globl',
'local_upper_quanta': 'locu',
'local_lower_quanta': 'locl',
'line_mixing_flag': 'lmix',
'gp': 'gp',
'gpp': 'gpp',
}
if not empty_range:
tbl = read_hitran_file(join(cache_location, molecule + '.data'))
df = tbl.to_pandas()
df = df.rename(columns=rename_columns)
else:
df = pd.DataFrame(columns=list(rename_columns.values()))
# Cast type to float64
cast_type = {
'wav': np.float64,
'int': np.float64,
'A': np.float64,
'airbrd': np.float64,
'selbrd': np.float64,
'El': np.float64,
'Tdpair': np.float64,
'Pshft': np.float64,
}
for c, typ in cast_type.items():
df[c] = df[c].astype(typ)
return df
def fetch_astroquery(
molecule, isotope, wmin, wmax, verbose=True, cache=True, expected_metadata={}
):
"""Download a HITRAN line database to a Pandas DataFrame.
Wrapper to Astroquery [1]_ fetch function
Parameters
----------
molecule: str, or int
molecule name or identifier
isotope: int
isotope number
wmin, wmax: float (cm-1)
wavenumber min and max
Other Parameters
----------------
verbose: boolean
Default ``True``
cache: boolean or ``'regen'``
if ``True``, tries to find a ``.h5`` cache file in the Astroquery
:py:attr:`~astroquery.query.BaseQuery.cache_location`, that would match
the requirements. If not found, downloads it and saves the line dataframe
as a ``.h5`` file in the Astroquery.
If ``'regen'``, delete existing cache file to regerenate it.
expected_metadata: dict
if ``cache=True``, check that the metadata in the cache file correspond
to these attributes. Arguments ``molecule``, ``isotope``, ``wmin``, ``wmax``
are already added by default.
Notes
-----
The HITRAN module in Astroquery [1]_ is itself based on [HAPI]_
References
----------
.. [1] `Astroquery <https://astroquery.readthedocs.io>`_
See Also
--------
:py:func:`astroquery.hitran.reader.download_hitran`,
:py:func:`astroquery.hitran.reader.read_hitran_file`,
:py:attr:`~astroquery.query.BaseQuery.cache_location`
"""
# Check input
if not is_float(molecule):
mol_id = get_molecule_identifier(molecule)
else:
mol_id = molecule
molecule = get_molecule(mol_id)
assert is_float(isotope)
empty_range = False
if cache:
# Cache file location in Astroquery cache
# TODO: move full HITRAN databases in ~/radisdb cache like io/hitemp/fetch_hitemp ?
fcache = join(
Hitran.cache_location,
CACHE_FILE_NAME.format(
**{"molecule": molecule, "isotope": isotope, "wmin": wmin, "wmax": wmax}
),
)
# ... Update metadata with physical properties from the database.
expected_metadata.update(
{"molecule": molecule, "isotope": isotope, "wmin": wmin, "wmax": wmax}
)
if cache == "regen":
if exists(fcache):
if verbose:
print(f"Cache file {fcache} deleted to be regenerated")
os.remove(fcache)
else:
# Load cache file if valid
check_cache_file(
fcache=fcache,
use_cached=cache,
expected_metadata=expected_metadata,
verbose=verbose,
)
if exists(fcache):
try:
return get_cache_file(fcache, verbose=verbose)
except Exception as err:
if verbose:
printr(
"Problem reading cache file {0}:\n{1}\nDeleting it!".format(
fcache, str(err)
)
)
os.remove(fcache)
# Download using the astroquery library
try:
response = Hitran.query_lines_async(
molecule_number=mol_id,
isotopologue_number=isotope,
min_frequency=wmin / u.cm,
max_frequency=wmax / u.cm,
)
except KeyError as err:
raise KeyError(
str(err)
+ " <<w this error occured in Astroquery. Maybe these molecule "
+ "({0}) and isotope ({1}) are not supported".format(molecule, isotope)
) from err
# Deal with usual errors
if response.status_code == 404:
# Maybe there are just no lines for this species in this range
# In that case we usually end up with errors like:
# (<class 'Exception'>, Exception('Query failed: 404 Client Error:
# Not Found for url: http://hitran.org/lbl/api?numax=25000&numin=19000&iso_ids_list=69\n',),
# <traceback object at 0x7f0967c91708>)
if response.reason == "Not Found":
# Let's bet it's just that there are no lines in this range
empty_range = True
if verbose:
print(
(
"No lines for {0} (id={1}), iso={2} in range {3:.2f}-{4:.2f}cm-1. ".format(
molecule, mol_id, isotope, wmin, wmax
)
)
)
else:
raise ValueError(
"An error occured during the download of HITRAN files "
+ "for {0} (id={1}), iso={2} between {3:.2f}-{4:.2f}cm-1. ".format(
molecule, mol_id, isotope, wmin, wmax
)
+ "Are you online?\n"
+ "See details of the error below:\n\n {0}".format(response.reason)
)
elif response.status_code == 500:
raise ValueError(
"{0} while querying the HITRAN server: ".format(response.status_code)
+ "\n\n{0}".format(response.text)
)
# Process response
# Rename columns from Astroquery to RADIS format
rename_columns = {
"molec_id": "id",
"local_iso_id": "iso",
"nu": "wav",
"sw": "int",
"a": "A",
"gamma_air": "airbrd",
"gamma_self": "selbrd",
"elower": "El",
"n_air": "Tdpair",
"delta_air": "Pshft",
"global_upper_quanta": "globu",
"global_lower_quanta": "globl",
"local_upper_quanta": "locu",
"local_lower_quanta": "locl",
"line_mixing_flag": "lmix",
"gp": "gp",
"gpp": "gpp",
}
if not empty_range:
tbl = Hitran._parse_result(response)
df = tbl.to_pandas()
df = df.rename(columns=rename_columns)
else:
df = pd.DataFrame(columns=list(rename_columns.values()))
# Cast type to float64
cast_type = {
"wav": np.float64,
"int": np.float64,
"A": np.float64,
"airbrd": np.float64,
"selbrd": np.float64,
"El": np.float64,
"Tdpair": np.float64,
"Pshft": np.float64,
}
for c, typ in cast_type.items():
df[c] = df[c].astype(typ)
# cached file mode but cached file doesn't exist yet (else we had returned)
if cache:
new_metadata = {
"molecule": molecule,
"isotope": isotope,
"wmin": wmin,
"wmax": wmax,
}
if verbose:
print(
"Generating cache file {0} with metadata :\n{1}".format(
fcache, new_metadata
)
)
try:
save_to_hdf(
df,
fcache,
metadata=new_metadata,
version=radis.__version__,
key="df",
overwrite=True,
verbose=verbose,
)
except PermissionError:
if verbose:
print(sys.exc_info())
print("An error occured in cache file generation. Lookup access rights")
pass
return df