# Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-
"""
Module to search Splatalogue.net via splat, modeled loosely on
ftp://ftp.cv.nrao.edu/NRAO-staff/bkent/slap/idl/
:author: Adam Ginsburg <adam.g.ginsburg@gmail.com>
"""
import warnings
from astropy.io import ascii
from astropy import units as u
from astroquery import log
from ..query import BaseQuery
from ..utils import async_to_sync, prepend_docstr_nosections
from . import conf
from . import load_species_table
from .utils import clean_column_headings
__all__ = ['Splatalogue', 'SplatalogueClass']
# example query of SPLATALOGUE directly:
# https://www.cv.nrao.edu/php/splat/c.php?sid%5B%5D=64&sid%5B%5D=108&calcIn=&data_version=v3.0&from=&to=&frequency_units=MHz&energy_range_from=&energy_range_to=&lill=on&tran=&submit=Search&no_atmospheric=no_atmospheric&no_potential=no_potential&no_probable=no_probable&include_only_nrao=include_only_nrao&displayLovas=displayLovas&displaySLAIM=displaySLAIM&displayJPL=displayJPL&displayCDMS=displayCDMS&displayToyaMA=displayToyaMA&displayOSU=displayOSU&displayRecomb=displayRecomb&displayLisa=displayLisa&displayRFI=displayRFI&ls1=ls1&ls5=ls5&el1=el1
[docs]@async_to_sync
class SplatalogueClass(BaseQuery):
SLAP_URL = conf.slap_url
QUERY_URL = conf.query_url
TIMEOUT = conf.timeout
LINES_LIMIT = conf.lines_limit
versions = ('v1.0', 'v2.0', 'v3.0', 'vall')
# global constant, not user-configurable
ALL_LINE_LISTS = ('Lovas', 'SLAIM', 'JPL', 'CDMS', 'ToyoMA', 'OSU',
'Recomb', 'Lisa', 'RFI')
TOP20_LIST = ('comet', 'planet', 'top20', 'ism_hotcore', 'ism_darkcloud',
'ism_diffusecloud')
FREQUENCY_BANDS = {"any": "Any",
"alma3": "ALMA Band 3 (84-116 GHz)",
"alma4": " ALMA Band 4 (125-163 GHz)",
"alma5": " ALMA Band 5 (163-211 GHz)",
"alma6": "ALMA Band 6 (211-275 GHz)",
"alma7": "ALMA Band 7 (275-373 GHz)",
"alma8": "ALMA Band 8 (385-500 GHz)",
"alma9": "ALMA Band 9 (602-720 GHz)",
"alma10": "ALMA Band 10 (787-950 GHz)",
"pf1": "GBT PF1 (0.29-0.92 GHz)",
"pf2": "GBT PF2 (0.91-1.23 GHz)",
"l": "GBT/VLA L (1-2 GHz)",
"s": "GBT/VLA S (1.7-4 GHz)",
"c": "GBT/VLA C (3.9-8 GHz)",
"x": "GBT/VLA X (8-12 GHz)",
"ku": " GBT/VLA Ku (12-18 GHz)",
"kfpa": "GBT KFPA (18-27.5 GHz)",
"k": "VLA K (18-26.5 GHz)",
"ka": " GBT/VLA Ka (26-40 GHz)",
"q": "GBT/VLA Q (38-50 GHz)",
"w": "GBT W (67-93.3 GHz)",
"mustang": "GBT Mustang (80-100 GHz)", }
def __init__(self, **kwargs):
"""
Initialize a Splatalogue query class with default arguments set.
Frequency specification is required for *every* query, but any
default keyword arguments (see `query_lines`) can be overridden
here.
"""
super(SplatalogueClass, self).__init__()
self.data = self._default_kwargs()
self.set_default_options(**kwargs)
[docs] def set_default_options(self, **kwargs):
"""
Modify the default options.
See `query_lines`
"""
self.data.update(self._parse_kwargs(**kwargs))
[docs] def get_species_ids(self, restr=None, reflags=0, recache=False):
"""
Get a dictionary of "species" IDs, where species refers to the molecule
name, mass, and chemical composition.
Parameters
----------
restr : str
String to compile into an re, if specified. Searches table for
species whose names match
reflags : int
Flags to pass to `re`.
recache : bool
Flag whether to refresh the local cache of species IDs
Examples
--------
>>> import re
>>> import pprint # unfortunate hack required for documentation testing
>>> rslt = Splatalogue.get_species_ids('Formaldehyde')
>>> pprint.pprint(rslt)
{'03023 H2CO - Formaldehyde': '194',
'03106 H213CO - Formaldehyde': '324',
'03107 HDCO - Formaldehyde': '109',
'03108 H2C17O - Formaldehyde': '982',
'03202 H2C18O - Formaldehyde': '155',
'03203 D2CO - Formaldehyde': '94',
'03204 HD13CO - Formaldehyde': '1219',
'03301 D213CO - Formaldehyde': '1220',
'03315 HDC18O - Formaldehyde': '21141',
'0348 D2C18O - Formaldehyde': '21140'}
>>> rslt = Splatalogue.get_species_ids('H2CO')
>>> pprint.pprint(rslt)
{'03023 H2CO - Formaldehyde': '194',
'03109 H2COH+ - Hydroxymethylium ion': '224',
'04406 c-H2COCH2 - Ethylene Oxide': '21',
'06029 NH2CONH2 - Urea': '21166',
'07510 H2NCH2COOH - I v=0 - Glycine': '389',
'07511 H2NCH2COOH - I v=1 - Glycine': '1312',
'07512 H2NCH2COOH - I v=2 - Glycine': '1313',
'07513 H2NCH2COOH - II v=0 - Glycine': '262',
'07514 H2NCH2COOH - II v=1 - Glycine': '1314',
'07515 H2NCH2COOH - II v=2 - Glycine': '1315',
'07517 NH2CO2CH3 v=0 - Methyl Carbamate': '1334',
'07518 NH2CO2CH3 v=1 - Methyl Carbamate': '1335',
'08902 CH3CHNH2COOH - I - α-Alanine': '1321',
'08903 CH3CHNH2COOH - II - α-Alanine': '1322'}
>>> # note the whitespace, preventing H2CO within other
>>> # more complex molecules
>>> Splatalogue.get_species_ids(' H2CO ')
{'03023 H2CO - Formaldehyde': '194'}
>>> Splatalogue.get_species_ids(' h2co ', re.IGNORECASE)
{'03023 H2CO - Formaldehyde': '194'}
"""
# loading can be an expensive operation and should not change at
# runtime: do it lazily
if not hasattr(self, '_species_ids'):
self._species_ids = load_species_table.species_lookuptable(recache=recache)
if restr is not None:
return self._species_ids.find(restr, reflags)
else:
return self._species_ids
def _default_kwargs(self):
kwargs = dict(min_frequency=0 * u.GHz,
max_frequency=100 * u.THz,
chemical_name='',
line_lists=self.ALL_LINE_LISTS,
line_strengths=('ls1', 'ls2', 'ls3', 'ls4', 'ls5'),
energy_levels=('el1', 'el2', 'el3', 'el4'),
exclude=('potential', 'atmospheric', 'probable'),
version='v3.0',
only_NRAO_recommended=None,
export=True,
export_limit=self.LINES_LIMIT,
noHFS=False, displayHFS=False, show_unres_qn=False,
show_upper_degeneracy=False, show_molecule_tag=False,
show_qn_code=False, show_lovas_labref=False,
show_lovas_obsref=False, show_orderedfreq_only=False,
show_nrao_recommended=False,)
return self._parse_kwargs(**kwargs)
def _parse_kwargs(self, min_frequency=None, max_frequency=None,
band='any', top20=None, chemical_name=None,
chem_re_flags=0, energy_min=None, energy_max=None,
energy_type=None, intensity_lower_limit=None,
intensity_type=None, transition=None, version=None,
exclude=None,
only_astronomically_observed=None,
only_NRAO_recommended=None,
line_lists=None, line_strengths=None, energy_levels=None,
export=None, export_limit=None, noHFS=None,
displayHFS=None, show_unres_qn=None,
show_upper_degeneracy=None, show_molecule_tag=None,
show_qn_code=None, show_lovas_labref=None,
show_lovas_obsref=None, show_orderedfreq_only=None,
show_nrao_recommended=None,
parse_chemistry_locally=True):
"""
The Splatalogue service returns lines with rest frequencies in the
range [min_frequency, max_frequency].
Parameters
----------
min_frequency : `astropy.units`
Minimum frequency (or any spectral() equivalent)
max_frequency : `astropy.units`
Maximum frequency (or any spectral() equivalent)
band : str
The observing band. If it is not 'any', it overrides
minfreq/maxfreq.
top20: str
One of ``'comet'``, ``'planet'``, ``'top20'``, ``'ism_hotcore'``,
``'ism_darkcloud'``, ``'ism_diffusecloud'``.
Overrides chemical_name
chemical_name : str
Name of the chemical to search for. Treated as a regular
expression. An empty set ('', (), [], {}) will match *any*
species. Examples:
``'H2CO'`` - 13 species have H2CO somewhere in their formula.
``'Formaldehyde'`` - There are 8 isotopologues of Formaldehyde
(e.g., H213CO).
``'formaldehyde'`` - Thioformaldehyde,Cyanoformaldehyde.
``'formaldehyde',chem_re_flags=re.I`` - Formaldehyde,thioformaldehyde,
and Cyanoformaldehyde.
``' H2CO '`` - Just 1 species, H2CO. The spaces prevent including
others.
parse_chemistry_locally : bool
Attempt to determine the species ID #'s locally before sending the
query? This will prevent queries that have no matching species.
It also performs a more flexible regular expression match to the
species IDs. See the examples in `get_species_ids`
chem_re_flags : int
See the `re` module
energy_min : `None` or float
Energy range to include. See energy_type
energy_max : `None` or float
Energy range to include. See energy_type
energy_type : ``'el_cm1'``, ``'eu_cm1'``, ``'eu_k'``, ``'el_k'``
Type of energy to restrict. L/U for lower/upper state energy,
cm/K for *inverse* cm, i.e. wavenumber, or K for Kelvin
intensity_lower_limit : `None` or float
Lower limit on the intensity. See intensity_type
intensity_type : `None` or ``'sij'``, ``'cdms_jpl'``, ``'aij'``
The type of intensity on which to place a lower limit
transition : str
e.g. 1-0
version : ``'v1.0'``, ``'v2.0'``, ``'v3.0'`` or ``'vall'``
Data version
exclude : list
Types of lines to exclude. Default is:
(``'potential'``, ``'atmospheric'``, ``'probable'``)
Can also exclude ``'known'``.
To exclude nothing, use 'none', not the python object None, since
the latter is meant to indicate 'leave as default'
only_astronomically_observed : bool
Show only astronomically observed species?
only_NRAO_recommended : bool
Show only NRAO recommended species?
line_lists : list
Options:
Lovas, SLAIM, JPL, CDMS, ToyoMA, OSU, Recomb, Lisa, RFI
line_strengths : list
* CDMS/JPL Intensity : ls1
* Sij : ls3
* Aij : ls4
* Lovas/AST : ls5
energy_levels : list
* E_lower (cm^-1) : el1
* E_lower (K) : el2
* E_upper (cm^-1) : el3
* E_upper (K) : el4
export : bool
Set up arguments for the export server (as opposed to the HTML
server)?
export_limit : int
Maximum number of lines in output file
noHFS : bool
No HFS Display
displayHFS : bool
Display HFS Intensity
show_unres_qn : bool
Display Unresolved Quantum Numbers
show_upper_degeneracy : bool
Display Upper State Degeneracy
show_molecule_tag : bool
Display Molecule Tag
show_qn_code : bool
Display Quantum Number Code
show_lovas_labref : bool
Display Lab Ref
show_lovas_obsref : bool
Display Obs Ref
show_orderedfreq_only : bool
Display Ordered Frequency ONLY
show_nrao_recommended : bool
Display NRAO Recommended Frequencies
Returns
-------
payload : dict
Dictionary of the parameters to send to the SPLAT page
"""
payload = {'submit': 'Search',
'frequency_units': 'GHz',
}
if band != 'any':
if band not in self.FREQUENCY_BANDS:
raise ValueError("Invalid frequency band.")
if min_frequency is not None or max_frequency is not None:
warnings.warn("Band was specified, so the frequency "
"specification is overridden")
payload['band'] = band
elif min_frequency is not None and max_frequency is not None:
# allow setting payload without having *ANY* valid frequencies set
min_frequency = min_frequency.to(u.GHz, u.spectral())
max_frequency = max_frequency.to(u.GHz, u.spectral())
if min_frequency > max_frequency:
min_frequency, max_frequency = max_frequency, min_frequency
payload['from'] = min_frequency.value
payload['to'] = max_frequency.value
if top20 is not None:
if top20 in self.TOP20_LIST:
payload['top20'] = top20
else:
raise ValueError("Top20 is not one of the allowed values")
elif chemical_name in ('', {}, (), [], set()):
# include all
payload['sid[]'] = []
elif chemical_name is not None:
if parse_chemistry_locally:
species_ids = self.get_species_ids(chemical_name, chem_re_flags)
if len(species_ids) == 0:
raise ValueError("No matching chemical species found.")
payload['sid[]'] = list(species_ids.values())
else:
payload['chemical_name'] = chemical_name
if energy_min is not None:
payload['energy_range_from'] = float(energy_min)
if energy_max is not None:
payload['energy_range_to'] = float(energy_max)
if energy_type is not None:
validate_energy_type(energy_type)
payload['energy_range_type'] = energy_type
if intensity_type is not None:
payload['lill'] = 'lill_' + intensity_type
if intensity_lower_limit is not None:
payload[payload['lill']] = intensity_lower_limit
if transition is not None:
payload['tran'] = transition
if version in self.versions:
payload['data_version'] = version
elif version is not None:
raise ValueError("Invalid version specified. Allowed versions "
"are {vers}".format(vers=str(self.versions)))
if exclude == 'none':
for e in ('potential', 'atmospheric', 'probable', 'known'):
# Setting a keyword value to 'None' removes it (see query_lines_async)
log.debug("Setting no_{0} to None".format(e))
payload['no_' + e] = None
elif exclude is not None:
for e in exclude:
payload['no_' + e] = 'no_' + e
if only_astronomically_observed:
payload['include_only_observed'] = 'include_only_observed'
if only_NRAO_recommended:
payload['include_only_nrao'] = 'include_only_nrao'
if line_lists is not None:
if type(line_lists) not in (tuple, list):
raise TypeError("Line lists should be a list of linelist "
"names. See Splatalogue.ALL_LINE_LISTS")
for L in self.ALL_LINE_LISTS:
kwd = 'display' + L
if L in line_lists:
payload[kwd] = kwd
else:
payload[kwd] = ''
if line_strengths is not None:
for LS in line_strengths:
payload[LS] = LS
if energy_levels is not None:
for EL in energy_levels:
payload[EL] = EL
for b in ("noHFS", "displayHFS", "show_unres_qn",
"show_upper_degeneracy", "show_molecule_tag",
"show_qn_code", "show_lovas_labref",
"show_orderedfreq_only", "show_lovas_obsref",
"show_nrao_recommended"):
if locals()[b]:
payload[b] = b
# default arg, unmodifiable...
payload['jsMath'] = 'font:symbol,warn:0'
payload['__utma'] = ''
payload['__utmc'] = ''
if export:
payload['submit'] = 'Export'
payload['export_delimiter'] = 'colon' # or tab or comma
payload['export_type'] = 'current'
payload['offset'] = 0
payload['range'] = 'on'
if export_limit is not None:
payload['limit'] = export_limit
else:
payload['limit'] = self.LINES_LIMIT
return payload
def _validate_kwargs(self, min_frequency=None, max_frequency=None,
band='any', **kwargs):
"""
Check that either min_frequency + max_frequency or band are specified
"""
if band == 'any':
if min_frequency is None or max_frequency is None:
raise ValueError("Must specify either min/max frequency or "
"a valid Band.")
[docs] @prepend_docstr_nosections("\n" + _parse_kwargs.__doc__)
def query_lines_async(self, min_frequency=None, max_frequency=None,
cache=True, **kwargs):
"""
Returns
-------
response : `requests.Response`
The response of the HTTP request.
"""
# have to chomp this kwd here...
get_query_payload = kwargs.pop('get_query_payload', False)
self._validate_kwargs(min_frequency=min_frequency,
max_frequency=max_frequency, **kwargs)
if hasattr(self, 'data'):
data_payload = self.data.copy()
data_payload.update(self._parse_kwargs(min_frequency=min_frequency,
max_frequency=max_frequency,
**kwargs))
else:
data_payload = self._default_kwargs()
data_payload.update(self._parse_kwargs(min_frequency=min_frequency,
max_frequency=max_frequency,
**kwargs))
# Add an extra step: sometimes, need to REMOVE keywords
data_payload = {k: v for k, v in data_payload.items() if v is not None}
if get_query_payload:
return data_payload
response = self._request(method='POST',
url=self.QUERY_URL,
data=data_payload,
timeout=self.TIMEOUT,
cache=cache)
self.response = response
return response
def _parse_result(self, response, verbose=False):
"""
Parse a response into an `~astropy.table.Table`
Parameters
----------
clean_headers : bool
Attempt to simplify / clean up the column headers returned by
splatalogue to make them more terminal-friendly
"""
result = ascii.read(response.text.split('\n'), delimiter=':',
format='basic', fast_reader=False)
return result
[docs] def get_fixed_table(self, columns=None):
"""
Convenience function to get the table with html column names made human
readable. It returns only the columns identified with the ``columns``
keyword. See the source for the defaults.
"""
if columns is None:
columns = ('Species', 'Chemical Name', 'Resolved QNs',
'Freq-GHz(rest frame,redshifted)',
'Meas Freq-GHz(rest frame,redshifted)',
'Log<sub>10</sub> (A<sub>ij</sub>)',
'E_U (K)')
table = clean_column_headings(self.table[columns])
return table
def validate_energy_type(etype):
valid_energy_types = ('el_cm1', 'eu_cm1', 'eu_k', 'el_k')
if etype not in valid_energy_types:
raise ValueError("Energy type must be one of {0}"
.format(valid_energy_types))
Splatalogue = SplatalogueClass()