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=200)
species_id name chemical_name ... searchErrorMessage sqlquery requestnumber
---------- -------------------------------------------------------------------------------------- ------------------------------------ ... ------------------ -------- -------------
21228 <i>GA</i>-<i>n</i>-C<sub>4</sub>H<sub>9</sub>CN n-Butyl cyanide ... None 0
1288 NH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>OH <font color="red">v<sub>26</sub>=1</font> Aminoethanol ... None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide ... None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide ... None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide ... None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide ... None 0
8 FeCO Iron Monocarbonyl ... None 0
1321 CH<sub>3</sub>CHNH<sub>2</sub>COOH - I α-Alanine ... None 0
21092 s-trans-H2C=CHCOOH Propenoic acid ... None 0
529 CH<sub>3</sub>CHO <font color="red">v = 0, 1 & 2 </font> Acetaldehyde ... None 0
529 CH<sub>3</sub>CHO <font color="red">v = 0, 1 & 2 </font> Acetaldehyde ... None 0
21067 <i>c</i>-C<sub>5</sub>H<sub>5</sub>N Pyridine ... None 0
21067 <i>c</i>-C<sub>5</sub>H<sub>5</sub>N Pyridine ... None 0
1275 <i>c</i>-CH<sub>2</sub>CHCHO Propenal ... None 0
1275 <i>c</i>-CH<sub>2</sub>CHCHO Propenal ... None 0
1288 NH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>OH <font color="red">v<sub>26</sub>=1</font> Aminoethanol ... None 0
1288 NH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>OH <font color="red">v<sub>26</sub>=1</font> Aminoethanol ... None 0
1288 NH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>OH <font color="red">v<sub>26</sub>=1</font> Aminoethanol ... None 0
1288 NH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>OH <font color="red">v<sub>26</sub>=1</font> Aminoethanol ... None 0
1370 CH<sub>3</sub>O<sup>13</sup>CHO (TopModel) Methyl Formate ... None 0
21026 CH3O13CHO, vt = 0, 1 Methyl formate, v<sub>t</sub> = 0, 1 ... None 0
1314 H<sub>2</sub>NCH<sub>2</sub>COOH - II <font color="red">v=1</font> Glycine ... None 0
1284 cis-CH<sub>2</sub>OHCHO <font color="red">v=3</font> Glycolaldehyde ... None 0
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=200)
species_id name chemical_name resolved_QNs linelist LovasASTIntensity ... telescope_Lovas_NIST transitionBandColor searchErrorMessage sqlquery requestnumber
---------- --------------------------------- --------------- ------------ -------- ----------------- ... -------------------- -------------------- ------------------ -------- -------------
1343 CO <font color="red">v = 3 Carbon Monoxide 2- 1 CDMS ... datatablelightpurple None 0
991 CO <font color="red">v = 2</font> Carbon Monoxide 2- 1 CDMS ... datatablelightpurple None 0
991 CO <font color="red">v = 2</font> Carbon Monoxide 2- 1 SLAIM ... datatablelightpurple None 0
990 CO <font color="red">v = 1</font> Carbon Monoxide 2- 1 CDMS ... datatablelightpurple None 0
990 CO <font color="red">v = 1</font> Carbon Monoxide 2- 1 SLAIM 0.62 Jy ... datatablelightpurple None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide 2-1 CDMS 70. ... NRAO 11m datatablelightpurple None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide 2-1 JPL ... datatablelightpurple None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide 2-1 Lovas 70. ... NRAO 11m datatablelightpurple None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide 2- 1 SLAIM 70. ... datatablelightpurple None 0
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=200)
species_id name chemical_name resolved_QNs linelist LovasASTIntensity ... telescope_Lovas_NIST transitionBandColor searchErrorMessage sqlquery requestnumber
---------- --------------------------------- --------------- ------------ -------- ----------------- ... -------------------- -------------------- ------------------ -------- -------------
990 CO <font color="red">v = 1</font> Carbon Monoxide 2- 1 CDMS ... datatablelightpurple None 0
204 CO <font color="red">v = 0</font> Carbon Monoxide 2-1 CDMS 70. ... NRAO 11m datatablelightpurple None 0
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=200)
species_id name chemical_name resolved_QNs linelist LovasASTIntensity ... telescope_Lovas_NIST transitionBandColor searchErrorMessage sqlquery requestnumber
---------- --------------------------------- --------------- ------------ -------- ----------------- ... -------------------- -------------------- ------------------ -------- -------------
204 CO <font color="red">v = 0</font> Carbon Monoxide 2-1 CDMS 70. ... NRAO 11m datatablelightpurple None 0
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=200)
species_id name chemical_name resolved_QNs linelist LovasASTIntensity ... source_Lovas_NIST telescope_Lovas_NIST transitionBandColor searchErrorMessage sqlquery requestnumber
---------- -------- --------------------------- ------------------ -------- ----------------- ... ----------------- -------------------- ------------------- ------------------ -------- -------------
1154 Hα Hydrogen Recombination Line H ( 42 ) α Recomb ... datatableskyblue None 0
1154 Hα Hydrogen Recombination Line H ( 41 ) α Recomb ... datatableskyblue None 0
1154 Hα Hydrogen Recombination Line H ( 40 ) α Recomb ... datatableskyblue None 0
1154 Hα Hydrogen Recombination Line H ( 39 ) α Recomb ... datatableskyblue None 0
You could also search by specifying the line list
>>> recomb_result = Splatalogue.query_lines(84*u.GHz, 85*u.GHz, line_lists=['Recombination'])
>>> recomb_result.pprint(max_width=200)
species_id name chemical_name resolved_QNs linelist LovasASTIntensity ... source_Lovas_NIST telescope_Lovas_NIST transitionBandColor searchErrorMessage sqlquery requestnumber
---------- --------- --------------------------- ------------------- -------- ----------------- ... ----------------- -------------------- ------------------- ------------------ -------- -------------
1156 Hγ Hydrogen Recombination Line H ( 60 ) γ Recomb ... datatableskyblue None 0
1162 Heγ Helium Recombination Line He ( 60 ) γ Recomb ... datatableskyblue None 0
1166 Cγ Carbon Recombination Line C ( 60 ) γ Recomb ... datatableskyblue None 0
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:
>>> S = Splatalogue(energy_max=500,
... energy_type='eu_k', energy_levels=['Four'],
... line_strengths=['CDMSJPL'])
>>> def trimmed_query(*args,**kwargs):
... columns = ('species_id', 'chemical_name', 'name', 'resolved_QNs',
... 'orderedfreq',
... 'aij',
... 'upper_state_energy_K')
... table = S.query_lines(*args, **kwargs)[columns]
... table.sort('upper_state_energy_K')
... return table
>>> trimmed_query(1*u.GHz,30*u.GHz,
... chemical_name='(H2.*Formaldehyde)|( HDCO )',
... energy_max=50)[:10].pprint(max_width=150)
species_id chemical_name name resolved_QNs orderedfreq aij upper_state_energy_K
---------- ------------- ---------------------------- ---------------------------- ----------- -------- --------------------
109 Formaldehyde HDCO 1( 1, 0)- 1( 1, 1) 5346.142 -8.44112 11.18258
109 Formaldehyde HDCO 1( 1, 0)- 1( 1, 1) 5346.1616 -8.31295 11.18287
109 Formaldehyde HDCO 1(1,0) - 1(1,1) 5346.1416 -8.31616 11.18301
155 Formaldehyde H<sub>2</sub>C<sup>18</sup>O 1( 1, 0)- 1( 1, 1) 4388.797 -8.22052 15.30187
155 Formaldehyde H<sub>2</sub>C<sup>18</sup>O 1( 1, 0)- 1( 1, 1), F= 1- 0 4388.7783 -9.0498 15.30206
155 Formaldehyde H<sub>2</sub>C<sup>18</sup>O 1( 1, 0)- 1( 1, 1), F= 0- 1 4388.7957 -8.57268 15.30206
155 Formaldehyde H<sub>2</sub>C<sup>18</sup>O 1( 1, 0)- 1( 1, 1), F= 2- 2 4388.7965 -8.69765 15.30206
155 Formaldehyde H<sub>2</sub>C<sup>18</sup>O 1(1,0) - 1(1,1) 4388.797 -8.57272 15.30206
155 Formaldehyde H<sub>2</sub>C<sup>18</sup>O 1( 1, 0)- 1( 1, 1), F= 2- 1 4388.8012 -9.17475 15.30206
155 Formaldehyde H<sub>2</sub>C<sup>18</sup>O 1( 1, 0)- 1( 1, 1), F= 1- 2 4388.8036 -8.9529 15.30206
There are utility functions in astroquery.splatalogue.utils that automate
some of the above cleanup.
Troubleshooting¶
If you are repeatedly getting failed queries, or bad/out-of-date results, try clearing your cache:
>>> from astroquery.splatalogue import Splatalogue
>>> Splatalogue.clear_cache()
If this function is unavailable, upgrade your version of astroquery.
The clear_cache function was introduced in version 0.4.7.dev8479.
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 |