def cdsd2df(
fname, version="hitemp", count=-1, cache=False, verbose=True, drop_non_numeric=True
):
""" Convert a CDSD-HITEMP [1]_ or CDSD-4000 [2]_ file to a Pandas dataframe
Parameters
----------
fname: str
CDSD file name
version: str ('4000', 'hitemp')
CDSD version
count: int
number of items to read (-1 means all file)
cache: boolean, or 'regen'
if ``True``, a pandas-readable HDF5 file is generated on first access,
and later used. This saves on the datatype cast and conversion and
improves performances a lot (but changes in the database are not
taken into account). If ``False``, no database is used. If 'regen', temp
file are reconstructed. Default ``False``.
Other Parameters
----------------
drop_non_numeric: boolean
if ``True``, non numeric columns are dropped. This improves performances,
but make sure all the columns you need are converted to numeric formats
before hand. Default ``True``. Note that if a cache file is loaded it
will be left untouched.
Returns
-------
df: pandas Dataframe
dataframe containing all lines and parameters
Notes
-----
CDSD-4000 Database can be downloaded from [3]_
Performances: I had huge performance trouble with this function, because the files are
huge (500k lines) and the format is to special (no space between numbers...)
to apply optimized methods such as pandas's. A line by line reading isn't
so bad, using struct to parse each line. However, we waste typing determining
what every line is. I ended up using the fromfiles functions from numpy,
not considering *\\n* (line return) as a special character anymore, and a second call
to numpy to cast the correct format. That ended up being twice as fast.
- initial: 20s / loop
- with mmap: worse
- w/o readline().rstrip('\\n'): still 20s
- numpy fromfiles: 17s
- no more readline, 2x fromfile 9s
Think about using cache mode too:
- no cache mode 9s
- cache mode, first time 22s
- cache mode, then 2s
Moving to HDF5:
On cdsd_02069_02070 (56 Mb)
Reading::
cdsd2df(): 9.29 s
cdsd2df(cache=True [old .txt version]): 2.3s
cdsd2df(cache=True [new h5 version, table]): 910ms
cdsd2df(cache=True [new h5 version, fixed]): 125ms
Storage::
%timeit df.to_hdf("cdsd_02069_02070.h5", "df", format="fixed") 337ms
%timeit df.to_hdf("cdsd_02069_02070.h5", "df", format="table") 1.03s
References
----------
Note that CDSD-HITEMP is used as the line database for CO2 in HITEMP 2010
.. [1] `HITEMP 2010, Rothman et al., 2010 <https://www.sciencedirect.com/science/article/pii/S002240731000169X>`_
.. [2] `CDSD-4000 article, Tashkun et al., 2011 <https://www.sciencedirect.com/science/article/pii/S0022407311001154>`_
.. [3] `CDSD-4000 database <ftp://ftp.iao.ru/pub/CDSD-4000/>`_
See Also
--------
:func:`~radis.io.hitran.hit2df`
"""
if verbose >= 2:
print(
"Opening file {0} (format=CDSD {1}, cache={2})".format(
fname, version, cache
)
)
if version == "hitemp":
columns = columns_hitemp
elif version == "4000":
columns = columns_4000
else:
raise ValueError("Unknown CDSD version: {0}".format(version))
# Use cache file if possible
fcache = splitext(fname)[0] + ".h5"
check_cache_file(fcache=fcache, use_cached=cache, verbose=verbose)
if cache and exists(fcache):
return get_cache_file(fcache, verbose=verbose)
# %% Start reading the full file
df = parse_binary_file(fname, columns, count)
# Remove non numerical attributes
if drop_non_numeric:
replace_PQR_with_m101(df)
df = drop_object_format_columns(df, verbose=verbose)
# 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={},
version=radis.__version__,
key="df",
overwrite=True,
verbose=verbose,
)
except:
if verbose:
print("An error occured in cache file generation. Lookup access rights")
pass
return df
def __init__(
self,
energy_levels,
isotope,
levelsfmt, # ='cdsd-pc',
use_cached=True,
use_json=None,
verbose=True,
):
# %% Init
# Initialize PartitionFunctionCalculator for this electronic state
ElecState = ElectronicState("CO2", isotope, "X", "1Σu+")
super(PartFuncCO2_CDSDcalc, self).__init__(ElecState)
# Check inputs ('return' is not mentionned in signature. it will just return
# after cache name is given)
assert use_cached in [True, False, "regen", "force", "return"]
if isotope not in [1, 2]:
raise ValueError(
"CDSD Energies not defined for isotope: {0}".format(isotope)
)
if use_json is not None:
warn(
DeprecationWarning(
"use_json replaced with faster HDF5-based use_cached"
)
)
# Get vibrational level definitions that match Energy Database (in particular
# how Evib and Erot are calculated)
# This is needed to be able to match the levels in the Line Database and
# the levels in the Energy database
if levelsfmt == "cdsd-p":
viblvl_label = "p"
elif levelsfmt == "cdsd-pc":
viblvl_label = "pc"
elif levelsfmt == "cdsd-pcN":
viblvl_label = "pcN"
elif levelsfmt == "cdsd-hamil":
viblvl_label = "pcJN"
elif levelsfmt is None:
# dont label the levels. Wont be able to use the EnergyDatabase to fetch
# vibrational energies for lines, however it can still be used to
# calculate Partition functions independently from a Spectrum calculation
viblvl_label = None
else:
raise ValueError(
"Unknown Energy database format: levelsfmt = `{0}`".format(levelsfmt)
+ ". Use one of: `cdsd-p`, `cdsd-pc`, `cdsd-pcN`,`cdsd-hamil`"
)
# Store defaults
self.verbose = verbose
self.use_cached = use_cached
self.levelsfmt = levelsfmt
self.viblvl_label = viblvl_label
# Get variables to store in metadata (after default values have been set)
molecule = "CO2" # will be stored in cache file metadata
_discard = [
"self",
"energy_levels",
"verbose",
"ElecState",
"electronic_state",
"use_json",
"use_cached",
]
# (dev) locals() automatically stores all variables: levelsfmt, viblvl_label, etc.
metadata = filter_metadata(locals(), discard_variables=_discard)
# %% Get levels
# Function of use_cached value:
# ... if True, use (and generate if doesnt exist) cache file.
# ... if 'regen', regenerate cache file. If 'force', raise an error
# ... if file doesnt exist.
# If file is deprecated, regenerate it unless 'force' was used
# Load cache file if exists
cachefile = energy_levels + ".h5"
self.cachefile = cachefile
# If return, return after cachefile generated (used for tests)
if use_cached == "return":
return
df = load_h5_cache_file(
cachefile,
use_cached,
metadata=metadata,
current_version=radis.__version__,
last_compatible_version=OLDEST_COMPATIBLE_VERSION,
verbose=verbose,
)
if df is None: # Read normal file
df = pd.read_csv(energy_levels, comment="#", delim_whitespace=True)
df = self._add_degeneracies(df)
df = self._add_levels(df)
self.df = df # Store
if use_cached and not exists(cachefile):
save_to_hdf(
self.df,
cachefile,
metadata=metadata,
version=radis.__version__,
key="df",
overwrite=True,
verbose=verbose,
)
def hit2df(fname, count=-1, cache=False, verbose=True, drop_non_numeric=True):
""" Convert a HITRAN/HITEMP [1]_ file to a Pandas dataframe
Parameters
----------
fname: str
HITRAN-HITEMP file name
count: int
number of items to read (-1 means all file)
cache: boolean, or ``'regen'`` or ``'force'``
if ``True``, a pandas-readable HDF5 file is generated on first access,
and later used. This saves on the datatype cast and conversion and
improves performances a lot (but changes in the database are not
taken into account). If False, no database is used. If ``'regen'``, temp
file are reconstructed. Default ``False``.
Other Parameters
----------------
drop_non_numeric: boolean
if ``True``, non numeric columns are dropped. This improves performances,
but make sure all the columns you need are converted to numeric formats
before hand. Default ``True``. Note that if a cache file is loaded it
will be left untouched.
Returns
-------
df: pandas Dataframe
dataframe containing all lines and parameters
References
----------
.. [1] `HITRAN 1996, Rothman et al., 1998 <https://www.sciencedirect.com/science/article/pii/S0022407398000788>`__
Notes
-----
Performances: see CDSD-HITEMP parser
See Also
--------
:func:`~radis.io.cdsd.cdsd2df`
"""
if verbose >= 2:
print("Opening file {0} (cache={1})".format(fname, cache))
columns = columns_2004
# Use cache file if possible
fcache = splitext(fname)[0] + ".h5"
check_cache_file(fcache=fcache, use_cached=cache, verbose=verbose)
if cache and exists(fcache):
return get_cache_file(fcache, verbose=verbose)
# Detect the molecule by reading the start of the file
try:
with open(fname) as f:
mol = get_molecule(int(f.read(2)))
except UnicodeDecodeError as err:
raise ValueError(
"You're trying to read a binary file {0} ".format(fname) +
"instead of an HITRAN file") from err
# %% Start reading the full file
df = parse_hitran_file(fname, columns, count)
# %% Post processing
# assert one molecule per database only. Else the groupbase data reading
# above doesnt make sense
nmol = len(set(df["id"]))
if nmol == 0:
raise ValueError("Databank looks empty")
elif nmol != 1:
# Crash, give explicity error messages
try:
secondline = df.iloc[1]
except IndexError:
secondline = ""
raise ValueError(
"Multiple molecules in database ({0}). Current ".format(nmol) +
"spectral code only computes 1 species at the time. Use MergeSlabs. "
+
"Verify the parsing was correct by looking at the first row below: "
+ "\n{0}".format(df.iloc[0]) +
"\n----------------\nand the second row " +
"below: \n{0}".format(secondline))
# dd local quanta attributes, based on the HITRAN group
df = parse_local_quanta(df, mol)
# Add global quanta attributes, based on the HITRAN class
df = parse_global_quanta(df, mol)
# Remove non numerical attributes
if drop_non_numeric:
if "branch" in df:
replace_PQR_with_m101(df)
df = drop_object_format_columns(df, verbose=verbose)
# 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={},
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,
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
