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
α 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
-------- --------------------------- --------- -------- ------------- ------------- ... ------------------- ----------- ------- ----------- ------- --------
Hα Hydrogen Recombination Line 85.68839 0 -- -- ... -- 0.0 0.0 0.0 0.0 Recomb
Hα Hydrogen Recombination Line 92.03443 0 -- -- ... -- 0.0 0.0 0.0 0.0 Recomb
Hα Hydrogen Recombination Line 99.02295 0 -- -- ... -- 0.0 0.0 0.0 0.0 Recomb
Hα 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
--------- --------------------------- -------- -------- ------------- ------------- ... ------------------- ----------- ------- ----------- ------- --------
Hγ Hydrogen Recombination Line 84.91439 0 -- -- ... -- 0.0 0.0 0.0 0.0 Recomb
Heγ Helium Recombination Line 84.949 0 -- -- ... -- 0.0 0.0 0.0 0.0 Recomb
Cγ 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¶
|
Initialize a Splatalogue query class with default arguments set. |
|
Configuration parameters for |