Splatalogue Queries (astroquery.splatalogue)¶
Getting Started¶
This module provides an interface to the Splatalogue web service It returns tables of spectral lines with features that you can specify by the same means generally available on the Splatalogue website.
Searching for Lines¶
In the Splatalogue web interface, you select “species” of interest using the left side menu seen in the query interface. You can access the line list:
>>> from astroquery.splatalogue import Splatalogue
>>> line_ids = Splatalogue.get_species_ids()
This will return the complete Splatalogue chemical species list, including all isotopologues, etc. To search within this list for a particular species, you can use regular expressions:
>>> CO_containing_species = Splatalogue.get_species_ids(species_regex='CO')
>>> len(CO_containing_species)
105
>>> just_CO = Splatalogue.get_species_ids(species_regex=' CO ') # note the spaces
>>> len(just_CO)
4
>>> just_CO
{'02812 CO v = 0 - Carbon Monoxide': '204',
'02813 CO v = 1 - Carbon Monoxide': '990',
'02814 CO v = 2 - Carbon Monoxide': '991',
'02815 CO v = 3 - Carbon Monoxide': '1343'}
>>> carbon_monoxide = Splatalogue.get_species_ids('Carbon Monoxide')
>>> len(carbon_monoxide) # includes isotopologues
17
>>> carbon_monoxide
{'02931 13CO+ - Carbon Monoxide Ion': '21107',
'03027 C18O+ - Carbon Monoxide Ion': '21108',
'03119 13C18O+ - Carbon Monoxide Ion': '21109',
'02812 CO v = 0 - Carbon Monoxide': '204',
'02813 CO v = 1 - Carbon Monoxide': '990',
'02816 CO+ v = 0 - Carbon Monoxide Ion': '709',
'02910 13CO v = 0 - Carbon Monoxide': '4',
'02913 C17O - Carbon Monoxide': '226',
'03005 C18O - Carbon Monoxide': '245',
'03006 13C17O - Carbon Monoxide': '264',
'03101 13C18O - Carbon Monoxide': '14',
'02814 CO v = 2 - Carbon Monoxide': '991',
'02815 CO v = 3 - Carbon Monoxide': '1343',
'02817 CO+ v = 1 - Carbon Monoxide Ion': '21273',
'02911 13CO v = 1 - Carbon Monoxide': '992',
'02912 13CO v = 2 - Carbon Monoxide': '993',
'03004 14CO - Carbon Monoxide': '778'}
>>> atomic_weight_88 = Splatalogue.get_species_ids('^088')
>>> atomic_weight_88
{'08801 SiC5 - Silicon Tetracarbide': '265',
'08803 C6O - Hexacarbon monoxide': '585',
'08802 CH3C6H - Methyltriacetylene': '388'}
The returned items are dictionaries, but they are also searchable.
>>> # note leading space
>>> carbon_monoxide.find(' 13')
{'02931 13CO+ - Carbon Monoxide Ion': '21107',
'03119 13C18O+ - Carbon Monoxide Ion': '21109',
'02910 13CO v = 0 - Carbon Monoxide': '4',
'03006 13C17O - Carbon Monoxide': '264',
'03101 13C18O - Carbon Monoxide': '14',
'02911 13CO v = 1 - Carbon Monoxide': '992',
'02912 13CO v = 2 - Carbon Monoxide': '993'}
Querying Splatalogue: Getting Line Information¶
Unlike most astroquery tools, the Splatalogue tool closely resembles the online interface. In principle, we can make a higher level wrapper, but it is not obvious what other parameters one might want to query on (whereas with catalogs, you almost always need a sky-position based query tool).
Any feature you can change on the Splatalogue web form
can be modified in the
query_lines() tool.
For any Splatalogue query, you must specify a minimum/maximum frequency. However, you can do it with astropy units, so wavelengths are OK too.
(note that in the following examples, max_width=100 is set to minimize the
size of the printout and assist with doctests; it is not needed as the default
pprint behavior is to fill the terminal width)
>>> from astropy import units as u
>>> CO1to0 = Splatalogue.query_lines(115.271*u.GHz, 115.273*u.GHz)
>>> CO1to0.pprint(max_width=100)
Species Chemical Name ... E_U (K) Linelist
------------------- ------------------------------------ ... ---------- --------
GA-n-C4H9CN n-Butyl cyanide ... 332.23706 CDMS
NH2CH2CH2OHv26=1 Aminoethanol ... 390.35352 JPL
COv=0 Carbon Monoxide ... 5.53211 CDMS
COv=0 Carbon Monoxide ... 5.53211 JPL
COv=0 Carbon Monoxide ... 0.0 Lovas
COv=0 Carbon Monoxide ... 5.53211 SLAIM
FeCO Iron Monocarbonyl ... 103.95656 CDMS
CH3CHNH2COOH-I α-Alanine ... 129.92964 CDMS
s-trans-H2C=CHCOOH Propenoic acid ... 18.49667 CDMS
CH3CHOv=0,1&2 Acetaldehyde ... 223.65667 SLAIM
CH3CHOv=0,1&2 Acetaldehyde ... 223.6558 JPL
c-C5H5N Pyridine ... 230.47644 CDMS
c-C5H5N Pyridine ... 230.47644 CDMS
c-CH2CHCHO Propenal ... 1266.35462 JPL
c-CH2CHCHO Propenal ... 1266.35462 JPL
NH2CH2CH2OHv26=1 Aminoethanol ... 766.11681 JPL
NH2CH2CH2OHv26=1 Aminoethanol ... 766.11681 JPL
NH2CH2CH2OHv26=1 Aminoethanol ... 766.11681 JPL
NH2CH2CH2OHv26=1 Aminoethanol ... 766.11681 JPL
CH3O13CHO(TopModel) Methyl Formate ... 272.75041 TopModel
CH3O13CHO,vt=0,1 Methyl formate, v<sub>t</sub> = 0, 1 ... 272.75358 CDMS
H2NCH2COOH-IIv=1 Glycine ... 2355.1427 JPL
cis-CH2OHCHOv=3 Glycolaldehyde ... 887.56625 JPL
Querying just by frequency isn’t particularly effective; a nicer approach is to use both frequency and chemical name. If you can remember that CO 2-1 is approximately in the 1 mm band, but you don’t know its exact frequency (after all, why else would you be using splatalogue?), this query works:
>>> CO2to1 = Splatalogue.query_lines(1*u.mm, 2*u.mm, chemical_name=" CO ")
>>> CO2to1.pprint(max_width=100)
Species Chemical Name Freq-GHz(rest frame,redshifted) ... E_U (cm^-1) E_U (K) Linelist
------- --------------- ------------------------------- ... ----------- ---------- --------
COv=3 Carbon Monoxide 224.2417699 ... 6361.659 9152.9556 CDMS
COv=2 Carbon Monoxide -- ... 4271.3871 6145.5379 CDMS
COv=2 Carbon Monoxide 226.340357 ... 4271.3869 6145.53761 SLAIM
COv=1 Carbon Monoxide -- ... 2154.70101 3100.11628 CDMS
COv=1 Carbon Monoxide 228.43911 ... 2154.70191 3100.11758 SLAIM
COv=0 Carbon Monoxide -- ... 11.53492 16.59608 CDMS
COv=0 Carbon Monoxide -- ... 11.53492 16.59608 JPL
COv=0 Carbon Monoxide 230.538 ... 0.0 0.0 Lovas
COv=0 Carbon Monoxide 230.538 ... 11.53492 16.59608 SLAIM
Of course, there’s some noise in there: both the vibrationally excited line and a whole lot of different line lists. Start by thinning out the line lists used:
>>> CO2to1 = Splatalogue.query_lines(1*u.mm, 2*u.mm, chemical_name=" CO ",only_NRAO_recommended=True)
>>> CO2to1.pprint(max_width=100)
Species Chemical Name Freq-GHz(rest frame,redshifted) ... E_U (cm^-1) E_U (K) Linelist
------- --------------- ------------------------------- ... ----------- ---------- --------
COv=1 Carbon Monoxide -- ... 2154.70101 3100.11628 CDMS
COv=0 Carbon Monoxide -- ... 11.53492 16.59608 CDMS
Then get rid of the vibrationally excited line by setting an energy upper limit in Kelvin:
>>> CO2to1 = Splatalogue.query_lines(1*u.mm, 2*u.mm, chemical_name=" CO ",
... only_NRAO_recommended=True,
... energy_max=50, energy_type='eu_k')
>>> CO2to1.pprint(max_width=100)
Species Chemical Name Freq-GHz(rest frame,redshifted) ... E_U (cm^-1) E_U (K) Linelist
------- --------------- ------------------------------- ... ----------- -------- --------
COv=0 Carbon Monoxide -- ... 11.53492 16.59608 CDMS
A note on recombination lines¶
Radio recombination lines are included in the splatalogue catalog under the
names “Hydrogen Recombination Line”, “Helium Recombination Line”, and “Carbon
Recombination Line”. If you want to search specifically for the alpha, beta,
delta, gamma, epsilon, or zeta lines, you need to use the unicode character for
these symbols (Hα, Hβ, Hγ, Hδ, Hε, Hζ), even though they will show up as
α in the ASCII table. For example:
>>> ha_result = Splatalogue.query_lines(84*u.GHz, 115*u.GHz, chemical_name='Hα')
>>> ha_result.pprint(max_width=100)
Species Chemical Name Freq-GHz(rest frame,redshifted) ... E_U (K) Linelist
-------- --------------------------- ------------------------------- ... ------- --------
Hα Hydrogen Recombination Line 85.68839 ... 0.0 Recomb
Hα Hydrogen Recombination Line 92.034434 ... 0.0 Recomb
Hα Hydrogen Recombination Line 99.022952 ... 0.0 Recomb
Hα Hydrogen Recombination Line 106.737357 ... 0.0 Recomb
You could also search by specifying the line list
>>> recomb_result = Splatalogue.query_lines(84*u.GHz, 85*u.GHz, line_lists=['Recomb'])
>>> recomb_result.pprint(max_width=100)
Species Chemical Name Freq-GHz(rest frame,redshifted) ... E_U (K) Linelist
--------- --------------------------- ------------------------------- ... ------- --------
Hγ Hydrogen Recombination Line 84.914394 ... 0.0 Recomb
Heγ Helium Recombination Line 84.948997 ... 0.0 Recomb
Cγ Carbon Recombination Line 84.956762 ... 0.0 Recomb
Cleaning Up the Returned Data¶
Depending on what sub-field you work in, you may be interested in fine-tuning splatalogue queries to return only a subset of the columns and lines on a regular basis. For example, if you want data returned preferentially in units of K rather than inverse cm, you’re interested in low-energy lines, and you want your data sorted by energy, you can use an approach like this:
(note that as of March 2023, there is an upstream error in which the noHFS keyword
is not respected; we include it here as a demonstration in the hope that that error will
be fixed)
>>> S = Splatalogue(energy_max=500,
... energy_type='eu_k',energy_levels=['el4'],
... line_strengths=['ls4'],
... only_NRAO_recommended=True,
... noHFS=True,
... displayHFS=False)
>>> def trimmed_query(*args,**kwargs):
... 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 = S.query_lines(*args, **kwargs)[columns]
... table.rename_column('Log<sub>10</sub> (A<sub>ij</sub>)','log10(Aij)')
... table.rename_column('E_U (K)','EU_K')
... table.rename_column('Resolved QNs','QNs')
... table.rename_column('Freq-GHz(rest frame,redshifted)', 'Freq-GHz'),
... table.rename_column('Meas Freq-GHz(rest frame,redshifted)', 'Meas Freq-GHz'),
... table.sort('EU_K')
... return table
>>> trimmed_query(1*u.GHz,30*u.GHz,
... chemical_name='(H2.*Formaldehyde)|( HDCO )',
... energy_max=50)[:10].pprint(max_width=100)
Species Chemical Name QNs Freq-GHz Meas Freq-GHz log10(Aij) EU_K
------- ------------- ------------------- --------- ------------- ---------- --------
HDCO Formaldehyde 1(1,0)-1(1,1) -- 5.3461416 -8.31616 11.18301
H2C18O Formaldehyde 1(1,0)-1(1,1),F=1-0 4.3887783 -- -9.0498 15.30206
H2C18O Formaldehyde 1(1,0)-1(1,1),F=0-1 4.3887957 -- -8.57268 15.30206
H2C18O Formaldehyde 1(1,0)-1(1,1),F=2-2 4.3887965 -- -8.69765 15.30206
H2C18O Formaldehyde 1(1,0)-1(1,1) 4.388797 -- -8.57272 15.30206
H2C18O Formaldehyde 1(1,0)-1(1,1),F=2-1 4.3888012 -- -9.17475 15.30206
H2C18O Formaldehyde 1(1,0)-1(1,1),F=1-2 4.3888036 -- -8.9529 15.30206
H2C18O Formaldehyde 1(1,0)-1(1,1),F=1-1 4.3888083 -- -9.1748 15.30206
H213CO Formaldehyde 1(1,0)-1(1,1) -- 4.5930885 -8.51332 15.34693
H2CO Formaldehyde 1(1,0)-1(1,1),F=1-2 4.8296665 -- -8.82819 15.39497
Reference/API¶
astroquery.splatalogue Package¶
Splatalogue Catalog Query Tool¶
- Author:
Adam Ginsburg (adam.g.ginsburg@gmail.com)
- Originally contributed by:
Magnus Vilhelm Persson (magnusp@vilhelm.nu)
Classes¶
|
Initialize a Splatalogue query class with default arguments set. |
|
Configuration parameters for |