Splatalogue — Module for performing splatalogue queries.

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> :updated for CASA: Brian Kent <bkent@nrao.edu> :updated for ADMIT: Douglas Friedel <friedel@illinois.edu>

Dependencies for python requests and astropy modules have been removed.

class admit.util.Splatalogue.SpeciesLookuptable

Simple class that extends the dictionary class so that keys can be searched

Methods

clear(() -> None.  Remove all items from D.)
copy(() -> a shallow copy of D)
find(s[, flags, return_dict])	Search dictionary keys for a regex match to string s
fromkeys(...)	v defaults to None.
get((k[,d]) -> D[k] if k in D, ...)
has_key((k) -> True if D has a key k, else False)
items(() -> list of D’s (key, value) pairs, ...)
iteritems(() -> an iterator over the (key, ...)
iterkeys(() -> an iterator over the keys of D)
itervalues(...)
keys(() -> list of D’s keys)
pop((k[,d]) -> v, ...)	If key is not found, d is returned if given, otherwise KeyError is raised
popitem(() -> (k, v), ...)	2-tuple; but raise KeyError if D is empty.
setdefault((k[,d]) -> D.get(k,d), ...)
update(([E, ...)	If E present and has a .keys() method, does: for k in E: D[k] = E[k]
values(() -> list of D’s values)
viewitems(...)
viewkeys(...)
viewvalues(...)

find(s, flags=0, return_dict=True)

Search dictionary keys for a regex match to string s

Parameters:

s : str

String to compile as a regular expression

return_dict : bool

Return a dictionary if true or just the matching values if false. Default: True

flags : int

re (regular expression) flags. Default: 0

Returns:

Subset of parent dictionary if return_dict, else list of values

corresponding to matches

class admit.util.Splatalogue.Splatalogue(**kwargs)

Class for searching for lines in the online Splatalogue database. The resulting Splatalogue tables can be returned as a list of dictionaries.

Parameters:

kwargs : dict

The keyword value pairs of the arguments, possible keywords are:

min_frequency

: float

Lower limit of frequency search range in GHz. Default: 0.0

max_frequency

: float

Upper limit of frequency search range in GHz. Defualt: 100000.0

band

: str

The frequency band to search in. ‘min/max_frequency’ and ‘band’ are mutually exclusive. If both are given then ‘band’ is preferred. Possibles are

“any”: All bands

“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)

Default: ‘any’

top20

: list

Limit results to the given top20 list(s). Possibles are:

‘comet’: molecules most likely found in comets

‘planet’: molecules most likely planetary atmospheres

‘top20’: most common molecules

‘ism_hotcore’: molecules most likely found in hot cores

‘ism_darkcloud’: molecules most likely found in dark clouds

‘ism_diffusecloud’: molecules most likely found in diffuse clouds

Default: None

chemical_name

: str

Limit results to the specified chemical, by name. Default: ‘’

line_lists

: list

Which line list(s) to use for the search. Possibles are:

‘Lovas’: Search the Lovas/NIST list of molecules

‘SLAIM’: Search the SLAIM list of molecules

‘JPL’: Search the Jet Propulsion Lab list of molecules

‘CDMS’: Search the Cologne database of molecules

‘ToyoMA’: Search the ToyoMA list of moleules

‘OSU’: Search the Ohio State list of molecules

‘Recomb’: Search for recombination lines

‘Lisa’: Search the TopModel list

‘RFI’: Search for radio frequency interference lines

Default: [‘Lovas’, ‘SLAIM’, ‘JPL’, ‘CDMS’, ‘ToyoMA’, ‘OSU’, ‘Recomb’, ‘Lisa’, ‘RFI’]

line_strengths

: list

Which line strength units should be reported, several can be given. Possibles are:

‘ls1’: JPL/CDMS

‘ls2’: Sijmu^2

‘ls3’: Sij

‘ls4’: Aij

‘ls5’: Lovas/SLAIM

Default: (‘ls1’, ‘ls2’, ‘ls3’, ‘ls4’, ‘ls5’)

energy_levels

: list

Which energies should be reported. Possibles are:

‘el1’: Lower state in cm^-1

‘el2’: Lower state in K

‘el3’: Upper state in cm^-1

‘el4’: Upper state in K

Default: [‘el1’, ‘el2’, ‘el3’, ‘el4’]

exclude

: list

Which types of molecules to exclude from the search. Possibles are:

‘potential’: Species that may be found in the ISM

‘atmospheric’: Species know to be in the Earth’s atmosphere

‘probable’: Species that might be found in the ISM

Default: [‘potential’, ‘atmospheric’, ‘probable’]

version

: str

Which Splatalogue interface is being used. Default: ‘v2.0’

only_NRAO_recommended

: bool

Only return lines that are recommended by NROA. Can eliminate duplicate lines from multiple databases. Default: False

export

: bool

Wherther splatalogue should return an export formatted list rather than HTML. Default: True

export_limit

: int

The maximum number of lines to return. Default: 10000

noHFS

: bool

Whether or not to suppress hyperfine components in the results. Default: False

displayHFS

: bool

Whether or not to return the hyperfine line strength. Default: False

show_unres_qn

: bool

Whether or not to return the unresolved quantum numbers. Typically in a machine readable format. Default: False

show_upper_degeneracy

: bool

Whether or not th return the upper state degeneracy of each transition. Default: False

show_molecule_tag

: bool

Whether or not to return the molecule tag. Default: False

show_qn_code

: bool

Whether or not to return the quantum number encoding (the encoding of ‘show_unres_qn’). Default: False

show_lovas_labref

: bool

Whether or not to return the lab reference frequency from the Lovas/NIST list. Default: False

show_lovas_obsref

: bool

Whether or not to return the observational reference from the Loval/NIST list. Default: False

show_orderedfreq_only

: bool

Default: False

show_nrao_recommended

: bool

Whether or not to return the NRAO recommended rest frequency. Default: False

chem_re_flags

: int

Default: 0

energy_min

: float

Minimum lower/upper state energy to search for. Units are specified in ‘energy_type’. Default None

energy_max

: float

Maximum lower/upper state energy to search for. Units are specified in ‘energy_type’. Default None

energy_type

: str

The energy units for the ‘energy_min’ and ‘energy_max’ columns. Possibles are:

‘el_cm1’: Lower state in cm^-1

‘el_k’: Lower state in K

‘eu_cm1’: Upper state in cm^-1

‘eu_k’: Upper state in K

Default: None

intensity_lower_limit

: float

Lower limit for the transition strength, units are specified in ‘intensity_type’. Default: None

intensity_type

: str

The units for the ‘intensity_lower_limit’ parameter. Possibles are:

‘cdms_jpl’: Cologne database/JPL intensity units

‘aij’: Einstein A units

‘sijmu2’: Smu^2, line strength times the square of the relevant dipole

moment

Default: None

transition

: str

Seach for a specific transition (i.e. ‘(1-0)’‘). Default: None

fel

: bool

Whether or not to remove results that have an uncertainty of over 50 MHz. Default: False

Examples

>>> from splatalogue import Splatalogue
>>> sp = Splatalogue  #Create an object of type Splatalogue

>>> # Query by frequency range in units of GHz
>>> sp.query_lines(min_frequency=114.0, max_frequency=116.0)

>>> # Query by frequency range and chemical name
>>> sp.query_lines(min_frequency=114.0, max_frequency=116.0, chemical_name=" CO ")

>>> # Query by frequency range (no keywords needed and chemical name)
>>> sp.query_lines(0.1,1000.0, chemical_name='Ethylene Glycol')

>>> # Query by line list and energy
>>> sp.query_lines(218.40, 218.50, energy_max=300, energy_type='eu_k', line_lists='JPL')

>>> # Parse response into a list of dictionaries and store in result
>>> result = sp.parse_response()

Attributes

None

Methods

get_species_ids([restr, reflags])	Get a dictionary of “species” IDs, where species refers to the molecule name, mass, and chemical composition.
parse_response()	Parse a response (of type urllib2.urlopen) into a list of dictionaries.
query_lines([min_frequency, max_frequency])	Query Splatalogue for transitions between min_frequency and max_frequency with the given kwargs.
set_default_options(\*\*kwargs)	Method to modify the default options.

ALL_LINE_LISTS = ('Lovas', 'SLAIM', 'JPL', 'CDMS', 'ToyoMA', 'OSU', 'Recomb', 'Lisa', 'RFI')

FREQUENCY_BANDS = {'pf1': 'GBT PF1 (0.29-0.92 GHz)', 'pf2': 'GBT PF2 (0.91-1.23 GHz)', 'mustang': 'GBT Mustang (80-100 GHz)', 'any': 'Any', 'kfpa': 'GBT KFPA (18-27.5 GHz)', 'alma10': 'ALMA Band 10 (787-950 GHz)', 'ku': ' GBT/VLA Ku (12-18 GHz)', 'ka': ' GBT/VLA Ka (26-40 GHz)', 'alma6': 'ALMA Band 6 (211-275 GHz)', 'alma7': 'ALMA Band 7 (275-373 GHz)', 'alma4': ' ALMA Band 4 (125-163 GHz)', 'alma5': ' ALMA Band 5 (163-211 GHz)', 'alma3': 'ALMA Band 3 (84-116 GHz)', 'alma8': 'ALMA Band 8 (385-500 GHz)', 'alma9': 'ALMA Band 9 (602-720 GHz)', 'c': 'GBT/VLA C (3.9-8 GHz)', 'k': 'VLA K (18-26.5 GHz)', 'l': 'GBT/VLA L (1-2 GHz)', 'q': 'GBT/VLA Q (38-50 GHz)', 's': 'GBT/VLA S (1.7-4 GHz)', 'w': 'GBT W (67-93.3 GHz)', 'x': 'GBT/VLA X (8-12 GHz)'}

LINES_LIMIT = 10000

QUERY_URL = 'http://www.cv.nrao.edu/php/splat/c_export.php'

TIMEOUT = 60

TOP20_LIST = ('comet', 'planet', 'top20', 'ism_hotcore', 'ism_darkcloud', 'ism_diffusecloud')

get_species_ids(restr=None, reflags=0)

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. Default: None

reflags : int

Flags to pass to re. Default: 0

Returns:

The id of the species

parse_response()

Parse a response (of type urllib2.urlopen) into a list of dictionaries.

Parameters:None Returns:A dictonary of the response

query_lines(min_frequency=None, max_frequency=None, **kwargs)

Query Splatalogue for transitions between min_frequency and max_frequency with the given kwargs.

Parameters:

min_frequency : float

The starting frequency for the search in GHz. Default: None

max_frequency : float

The ending frequency for the search in GHz. Default: None

kwargs : dict

Any additional arguments for the search.

Returns:

response : requests.Response

The response of the HTTP request.

set_default_options(**kwargs)

Method to modify the default options.

Parameters:

kwargs : dict

See the class description for the key words and their meaning

Returns:

None

versions = ('v1.0', 'v2.0')

admit.util.Splatalogue.clean_column_headings(header, renaming_dict={'Resolved QNs': 'QNs', 'Log₁₀ (A_ij)': 'log10(Aij)', 'E_U (K)': 'EU_K', 'S_ij': 'Sij'})

Rename column headings to shorter version that are easier for display on-screen / at the terminal

Parameters:

header : dict

A dictionary of the header keywords

renaming_dict : dict

A dictionary containing the old names (as the key) and the new names (as the value)

Returns:

The new header.

admit.util.Splatalogue.species_lookuptable(filename='species.json')

Method to read in a file and turn it into a searchable dictionary

Parameters:

filename : str

The name of the file to read. Default: ‘species.json’

Returns:

A lookup table with the contents of the input file