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.

Examples

An example ipynb from an interactive tutorial session at NRAO in April 2014

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('CO')
>>> len(CO_containing_species)
91
>>> just_CO = Splatalogue.get_species_ids(' CO ') # note the spaces
>>> len(just_CO)
4
>>> just_CO  # includes different vibrationally excited states
{u'02812 CO v = 0 - Carbon Monoxide': u'204',
 u'02813 CO v = 1 - Carbon Monoxide': u'990',
 u'02814 CO v = 2 - Carbon Monoxide': u'991',
 u'02815 CO v = 3 - Carbon Monoxide': u'1343'}
>>> carbon_monoxide = Splatalogue.get_species_ids('Carbon Monoxide')
>>> len(carbon_monoxide) # includes isotopologues
13
>>> carbon_monoxide
>>>
{u'02812 CO v = 0 - Carbon Monoxide': u'204',
 u'02813 CO v = 1 - Carbon Monoxide': u'990',
 u'02814 CO v = 2 - Carbon Monoxide': u'991',
 u'02815 CO v = 3 - Carbon Monoxide': u'1343',
 u'02816 CO+ - Carbon Monoxide Ion': u'709',
 u'02910 13CO v = 0 - Carbon Monoxide': u'4',
 u'02911 13CO v = 1 - Carbon Monoxide': u'992',
 u'02912 13CO v = 2 - Carbon Monoxide': u'993',
 u'02913 C17O - Carbon Monoxide': u'226',
 u'03004 14CO - Carbon Monoxide': u'778',
 u'03005 C18O - Carbon Monoxide': u'245',
 u'03006 13C17O - Carbon Monoxide': u'264',
 u'03101 13C18O - Carbon Monoxide': u'14'}
>>> atomic_weight_88 = Splatalogue.get_species_ids('^088')
>>> atomic_weight_88
{u'08801 SiC5 - ': u'265',
 u'08802 CH3C6H - Methyltriacetylene': u'388',
 u'08803 C6O - Hexacarbon monoxide': u'585'}

The returned items are dictionaries, but they are also searchable.

>>> carbon_monoxide.find(' 13')  # note leading space
{u'02910 13CO v = 0 - Carbon Monoxide': u'4',
 u'02911 13CO v = 1 - Carbon Monoxide': u'992',
 u'02912 13CO v = 2 - Carbon Monoxide': u'993',
 u'03006 13C17O - Carbon Monoxide': u'264',
 u'03101 13C18O - Carbon Monoxide': u'14'}

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.

>>> from astropy import units as u
>>> CO1to0 = Splatalogue.query_lines(115.271*u.GHz,115.273*u.GHz)
>>> CO1to0.pprint()
      Species        Chemical Name   Freq-GHz ... E<sub>U</sub> (K) Linelist
------------------- --------------- --------- ... ----------------- --------
              COv=0 Carbon Monoxide        -- ...           5.53211     CDMS
              COv=0 Carbon Monoxide        -- ...           5.53211      JPL
              COv=0 Carbon Monoxide  115.2712 ...               0.0    Lovas
              COv=0 Carbon Monoxide  115.2712 ...           5.53211    SLAIM
         CH3CHOvt=1    Acetaldehyde 115.27182 ...         223.65667    SLAIM
         CH3CHOvt=1    Acetaldehyde        -- ...         223.65581      JPL
CH3O13CHO(TopModel)  Methyl Formate  115.2728 ...         272.75041 TopModel

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()
Species  Chemical Name   Freq-GHz ... E<sub>U</sub> (K) Linelist
------- --------------- --------- ... ----------------- --------
  COv=1 Carbon Monoxide        -- ...        3100.11628     CDMS
  COv=1 Carbon Monoxide 228.43911 ...        3100.11758    SLAIM
  COv=0 Carbon Monoxide        -- ...          16.59608     CDMS
  COv=0 Carbon Monoxide        -- ...          16.59608      JPL
  COv=0 Carbon Monoxide   230.538 ...               0.0    Lovas
  COv=0 Carbon Monoxide   230.538 ...          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()
Species  Chemical Name   Freq-GHz ... E<sub>U</sub> (K) Linelist
------- --------------- --------- ... ----------------- --------
  COv=1 Carbon Monoxide 228.43911 ...        3100.11758    SLAIM
  COv=0 Carbon Monoxide   230.538 ...          16.59608    SLAIM

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()
Species  Chemical Name  Freq-GHz ... E<sub>U</sub> (K) Linelist
------- --------------- -------- ... ----------------- --------
  COv=0 Carbon Monoxide  230.538 ...          16.59608    SLAIM

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 &alpha; in the ASCII table. For example:

>>> Splatalogue.query_lines(84*u.GHz, 115*u.GHz, chemical_name='Hα')
<Table masked=True length=4>
Species         Chemical Name         Freq-GHz Freq Err Meas Freq-GHz Meas Freq Err ... Lovas/AST Intensity E_L (cm^-1) E_L (K) E_U (cm^-1) E_U (K) Linelist
  str8              str27             float64   int64       int64         int64     ...        int64          float64   float64   float64   float64   str6
-------- --------------------------- --------- -------- ------------- ------------- ... ------------------- ----------- ------- ----------- ------- --------
H&alpha; Hydrogen Recombination Line  85.68839        0            --            -- ...                  --         0.0     0.0         0.0     0.0   Recomb
H&alpha; Hydrogen Recombination Line  92.03443        0            --            -- ...                  --         0.0     0.0         0.0     0.0   Recomb
H&alpha; Hydrogen Recombination Line  99.02295        0            --            -- ...                  --         0.0     0.0         0.0     0.0   Recomb
H&alpha; Hydrogen Recombination Line 106.73736        0            --            -- ...                  --         0.0     0.0         0.0     0.0   Recomb

You could also search by specifying the line list

>>> Splatalogue.query_lines(84*u.GHz, 85*u.GHz, line_lists=['Recomb'])
<Table masked=True length=3>
 Species         Chemical Name        Freq-GHz Freq Err Meas Freq-GHz Meas Freq Err ... Lovas/AST Intensity E_L (cm^-1) E_L (K) E_U (cm^-1) E_U (K) Linelist
   str9              str27            float64   int64       int64         int64     ...        int64          float64   float64   float64   float64   str6
--------- --------------------------- -------- -------- ------------- ------------- ... ------------------- ----------- ------- ----------- ------- --------
 H&gamma; Hydrogen Recombination Line 84.91439        0            --            -- ...                  --         0.0     0.0         0.0     0.0   Recomb
He&gamma;   Helium Recombination Line   84.949        0            --            -- ...                  --         0.0     0.0         0.0     0.0   Recomb
 C&gamma;   Carbon Recombination Line 84.95676        0            --            -- ...                  --         0.0     0.0         0.0     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:

>>> S = Splatalogue(energy_max=500,
...    energy_type='eu_k',energy_levels=['el4'],
...    line_strengths=['ls4'],
...    only_NRAO_recommended=True,noHFS=True)
>>> def trimmed_query(*args,**kwargs):
...     columns = ('Species','Chemical Name','Resolved QNs','Freq-GHz',
...                'Meas Freq-GHz','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.sort('EU_K')
...     return table
>>> trimmed_query(1*u.GHz,30*u.GHz,
...     chemical_name='(H2.*Formaldehyde)|( HDCO )',
...     energy_max=50).pprint()
Species Chemical Name      QNs      Freq-GHz Meas Freq-GHz log10(Aij)   EU_K
------- ------------- ------------- -------- ------------- ---------- --------
   HDCO  Formaldehyde 1(1,0)-1(1,1)       --       5.34614   -8.31616 11.18287
 H2C18O  Formaldehyde 1(1,0)-1(1,1)   4.3888        4.3888   -8.22052 15.30187
 H213CO  Formaldehyde 1(1,0)-1(1,1)       --       4.59309   -8.51332 15.34693
   H2CO  Formaldehyde 1(1,0)-1(1,1)  4.82966            --   -8.44801 15.39497
   HDCO  Formaldehyde 2(1,1)-2(1,2)       --      16.03787   -7.36194 17.62746
 H2C18O  Formaldehyde 2(1,1)-2(1,2) 13.16596      13.16596   -6.86839 22.17455
 H213CO  Formaldehyde 2(1,1)-2(1,2)       --       13.7788   -7.55919 22.38424
   H2CO  Formaldehyde 2(1,1)-2(1,2) 14.48848            --   -7.49383 22.61771
 H2C18O  Formaldehyde 3(1,2)-3(1,3) 26.33012      26.33014   -6.03008 32.48204
 H213CO  Formaldehyde 3(1,2)-3(1,3)       --      27.55567   -6.95712  32.9381
   H2CO  Formaldehyde 3(1,2)-3(1,3)       --       28.9748   -6.89179 33.44949

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

SplatalogueClass(**kwargs) Initialize a Splatalogue query class with default arguments set.
Conf Configuration parameters for astroquery.splatalogue.