.. _astroquery.linelists.jplspec: ******************************************************* JPL Spectroscopy Queries (astroquery.linelists.jplspec) ******************************************************* Getting Started =============== The JPLSpec module provides a query interface for `JPL Molecular Spectroscopy Catalog `_. The module outputs the results that would arise from the `browser form `_, using similar search criteria as the ones found in the form, and presents the output as a `~astropy.table.Table`. .. warning:: Starting in mid-2025, the JPL web interface query tool went down for a prolonged period. As of November 2025, it is still not up, but JPL staff are aware of and seeking solutions to the problem. Until that web interface is restored, the astroquery.jplspec module relies on workarounds that involve downloading the full catalog files, which results in slightly larger data transfers and un-filtered full-table results. Some metadata may also be different. The examples and documents have been updated to show what to expect in the current, partially-functional state. Examples ======== Querying the catalog -------------------- The default option to return the query payload is set to false, in the following examples we have explicitly set it to False and True to show the what each setting yields: .. doctest-remote-data:: >>> from astroquery.linelists.jplspec import JPLSpec >>> import astropy.units as u >>> response = JPLSpec.query_lines(min_frequency=100 * u.GHz, ... max_frequency=1000 * u.GHz, ... min_strength=-500, ... molecule="28001 CO", ... get_query_payload=False) >>> response.pprint(max_lines=10) FREQ ERR LGINT DR ELO GUP TAG QNFMT QN' QN" Lab MHz MHz nm2 MHz 1 / cm ------------ ------ -------- --- ---------- --- ----- ----- --- --- ----- 115271.2018 0.0005 -5.0105 2 0.0 3 28001 101 1 0 True 230538.0 0.0005 -4.1197 2 3.845 5 28001 101 2 1 True ... ... ... ... ... ... ... ... ... ... ... 9747448.9491 3.0112 -31.6588 2 14684.516 179 28001 101 89 88 False 9845408.2504 3.1938 -32.4351 2 15009.6559 181 28001 101 90 89 False 9942985.9145 3.3849 -33.2361 2 15338.0634 183 28001 101 91 90 False Length = 91 rows >>> response.meta {'TAG': 28001, 'NAME': 'CO', 'NLINE': 91, 'QLOG1': 2.0369, 'QLOG2': 1.9123, 'QLOG3': 1.737, 'QLOG4': 1.4386, 'QLOG5': 1.1429, 'QLOG6': 0.8526, 'QLOG7': 0.5733, 'VER': '4*', 'molecule_id': '28001 CO', 'molecule_name': {}} The following example, with ``get_query_payload = True``, returns the payload: .. doctest-remote-data:: >>> response = JPLSpec.query_lines(min_frequency=100 * u.GHz, ... max_frequency=1000 * u.GHz, ... min_strength=-500, ... molecule="28001 CO", ... get_query_payload=True) >>> print(response) [('MinNu', 100.0), ('MaxNu', 1000.0), ('MaxLines', 2000), ('UnitNu', 'GHz'), ('StrLim', -500), ('Mol', '28001 CO')] The units of the columns of the query can be displayed by calling ``response.info``: .. doctest-remote-data:: >>> response = JPLSpec.query_lines(min_frequency=100 * u.GHz, ... max_frequency=1000 * u.GHz, ... min_strength=-500, ... molecule="28001 CO") >>> print(response.info) name dtype unit ----- ------- ------- FREQ float64 MHz ERR float64 MHz LGINT float64 nm2 MHz DR int64 ELO float64 1 / cm GUP int64 TAG int64 QNFMT int64 QN' int64 QN" int64 Lab bool These come in handy for converting to other units easily, an example using a simplified version of the data above is shown below: .. doctest-remote-data:: >>> response['FREQ', 'ERR', 'ELO'].pprint(max_lines=10) FREQ ERR ELO MHz MHz 1 / cm ------------ ------ ---------- 115271.2018 0.0005 0.0 230538.0 0.0005 3.845 ... ... ... 9747448.9491 3.0112 14684.516 9845408.2504 3.1938 15009.6559 9942985.9145 3.3849 15338.0634 Length = 91 rows >>> response['FREQ'][:10].quantity >>> response['FREQ'][:10].to('GHz') The parameters and response keys are described in detail under the Reference/API section. Looking Up More Information from the catdir.cat file ---------------------------------------------------- If you have found a molecule you are interested in, the TAG field in the results provides enough information to access specific molecule information such as the partition functions at different temperatures. A negative TAG value signifies that the line frequency has been measured in the laboratory. .. doctest-remote-data:: >>> import matplotlib.pyplot as plt >>> from astroquery.linelists.jplspec import JPLSpec >>> result = JPLSpec.get_species_table() >>> mol = result[result['TAG'] == 28001] #do not include signs of TAG for this >>> print(mol) TAG NAME NLINE QLOG1 QLOG2 QLOG3 QLOG4 QLOG5 QLOG6 QLOG7 VER ----- ---- ----- ------ ------ ----- ------ ------ ------ ------ --- 28001 CO 91 2.0369 1.9123 1.737 1.4386 1.1429 0.8526 0.5733 4* You can also access the temperature of the partition function through metadata: .. doctest-remote-data:: >>> result['QLOG2'].meta {'Temperature (K)': 225} >>> result.meta {'Temperature (K)': [300, 225, 150, 75, 37.5, 18.5, 9.375]} JPLSpec catalogs the partition function at several temperatures for each molecule. This example accesses and plots the partition function against the temperatures found in the metadata: .. doctest-skip:: >>> temp = result.meta['Temperature (K)'] >>> part = list(mol['QLOG1','QLOG2','QLOG3', 'QLOG4', 'QLOG5','QLOG6', ... 'QLOG7'][0]) >>> plt.scatter(temp,part) >>> plt.xlabel('Temperature (K)') >>> plt.ylabel('Partition Function Value') >>> plt.title('Partition Fn vs Temp') >>> plt.show() .. figure:: images/docplot_jplspec.png :scale: 50% :alt: Plot of Partition Function vs Temperature The resulting plot from the example above For non-linear molecules like H2O, curve fitting methods can be used to calculate production rates at different temperatures with the proportionality: ``a*T**(3./2.)``. Calling the process above for the H2O molecule (instead of for the CO molecule) we can continue to determine the partition function at other temperatures using curve fitting models: .. doctest-skip:: >>> from scipy.optimize import curve_fit >>> def f(T,a): return np.log10(a*T**(1.5)) >>> param, cov = curve_fit(f,temp,part) >>> print(param) # array([0.03676998]) >>> x = np.linspace(5,305) >>> y = f(x,0.03676998) >>> plt.scatter(temp,part,c='r') >>> plt.plot(x,y,'k') >>> plt.title('Partition Function vs Temperature') >>> plt.xlabel('Temperature') >>> plt.ylabel('Log10 of Partition Function') >>> plt.show() .. figure:: images/docplot_curvefit.png :scale: 50% :alt: Plot of Partition Function vs Temperature and resulting Curve Fit The resulting plot from the example above Retrieving Complete Molecule Catalogs ------------------------------------- If you need all spectral lines for a specific molecule without filtering by frequency range or strength, you can use the ``get_molecule`` method. This method retrieves the complete catalog file for a given molecule. Starting in 2025, during a prolonged outage of the JPL web query tool, this is the only way to retrieve data from JPLSpec via astroquery. .. doctest-remote-data:: >>> from astroquery.linelists.jplspec import JPLSpec >>> # Retrieve all lines for CO (molecule tag 28001) >>> table = JPLSpec.get_molecule(28001) >>> print(f"Retrieved {len(table)} lines for CO") Retrieved 91 lines for CO >>> table[:5].pprint() FREQ ERR LGINT DR ELO GUP TAG QNFMT QN' QN" Lab MHz MHz nm2 MHz 1 / cm ----------- ------ ------- --- ------- --- ----- ----- --- --- ---- 115271.2018 0.0005 -5.0105 2 0.0 3 28001 101 1 0 True 230538.0 0.0005 -4.1197 2 3.845 5 28001 101 2 1 True 345795.9899 0.0005 -3.6118 2 11.535 7 28001 101 3 2 True 461040.7682 0.0005 -3.2657 2 23.0695 9 28001 101 4 3 True 576267.9305 0.0005 -3.0118 2 38.4481 11 28001 101 5 4 True The ``get_molecule`` method accepts either an integer or a zero-padded 6-character string as the molecule identifier: .. doctest-remote-data:: >>> # These are equivalent >>> table1 = JPLSpec.get_molecule(18003) # H2O as integer >>> table2 = JPLSpec.get_molecule('018003') # H2O as string >>> len(table1) == len(table2) True .. _regex_querying_linelists: Querying the Catalog with Regexes and Relative names ---------------------------------------------------- Although you could print the species table and see what molecules you're interested in, maybe you just want a general search of any H2O molecule, or maybe you want a specific range of H2O molecules in your result. This module allows you to enter a regular expression or string as a parameter by adding the parameter ``parse_name_locally = True`` and returns the results that the regex matched with by parsing through the local catalog file. It is recommended that if you are using just the corresponding molecule number found in the JPL query catalog or a string with the exact name found in the catalog, that you do not set the local parse parameter since the module will be able to query these directly. .. doctest-remote-data:: >>> from astroquery.linelists.jplspec import JPLSpec >>> import astropy.units as u >>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz, ... max_frequency=1000 * u.GHz, ... min_strength=-500, ... molecule="H2O", ... parse_name_locally=True) >>> result.pprint(max_lines=10) FREQ ERR LGINT DR ELO GUP TAG QNFMT QN'1 QN"1 QN'2 QN"2 QN'3 QN"3 QN'4 QN"4 Lab MHz MHz nm2 MHz 1 / cm ------------ ------ -------- --- --------- --- ----- ----- ---- ---- ---- ---- ---- ---- ---- ---- ----- 8006.5805 2.851 -18.6204 3 6219.6192 45 18003 1404 22 21 4 7 18 15 0 0 False 12478.2535 0.2051 -13.1006 3 3623.7652 31 18003 1404 15 16 7 4 9 12 0 0 False ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 9981215.769 6.1776 -12.0101 3 5271.3682 45 18003 1404 22 23 2 1 20 23 0 0 False 9981323.7676 6.1773 -11.5329 3 5271.3682 135 18003 1404 22 23 3 0 20 23 0 0 False 9992065.9213 0.0482 -5.528 3 882.8904 15 18003 1404 7 8 6 1 2 7 0 0 False Length = 1376 rows Searches like these can lead to very broad queries, and may be limited in response length: .. doctest-remote-data:: >>> # the 'comments' metadata field is only populated if the query tool is run >>> # the get-whole-table workaround (November 2025) will not populate it >>> print(result.meta['comments']) # doctest: +SKIP ['', '', '', '', '', 'form is currently limilted to 2000 lines. Please limit your search.'] Inspecting the returned molecules shows that the 'H2O' string was processed as a regular expression, and the search matched any molecule that contained the combination of characters 'H2O': .. doctest-remote-data:: >>> tags = set(abs(result['TAG'])) # discard negative signs >>> species = {species: tag ... for (species, tag) in JPLSpec.lookup_ids.items() ... if tag in tags} >>> print(species) {'H2O': 18003} A few examples that show the power of the regex option are the following: .. doctest-remote-data:: >>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz, ... max_frequency=1000 * u.GHz, ... min_strength=-500, ... molecule="H2O$", ... parse_name_locally=True) >>> tags = set(abs(result['TAG'])) # discard negative signs >>> species = {species: tag ... for (species, tag) in JPLSpec.lookup_ids.items() ... if tag in tags} >>> print(species) {'H2O': 18003} As seen above, the regular expression "H2O$" yields only an exact match because the special character $ matches the end of the line. This functionality allows you to be as specific or vague as you want to allow the results to be: .. doctest-remote-data:: >>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz, ... max_frequency=1000 * u.GHz, ... min_strength=-500, ... molecule="^H.O$", ... parse_name_locally=True) >>> tags = set(abs(result['TAG'])) # discard negative signs >>> species = {species: tag ... for (species, tag) in JPLSpec.lookup_ids.items() ... if tag in tags} >>> print(species) {'H2O': 18003, 'HDO': 19002, 'HCO': 29004, 'HNO': 31005} This pattern matches any word that starts with an H, ends with an O, and contains any character in between. Another example of the functionality of this option is the option to obtain results from a molecule and its isotopes, in this case H2O and HDO: .. doctest-remote-data:: >>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz, ... max_frequency=1000 * u.GHz, ... min_strength=-500, ... molecule=r"^H[2D]O(-\d\d|)$", ... parse_name_locally=True) >>> tags = set(abs(result['TAG'])) # discard negative signs >>> species = {species: tag ... for (species, tag) in JPLSpec.lookup_ids.items() ... if tag in tags} >>> print(species) {'H2O': 18003, 'HDO': 19002, 'H2O-17': 19003, 'H2O-18': 20003, 'HDO-18': 21001} This pattern matches any H2O and HDO isotopes. Troubleshooting =============== If you are repeatedly getting failed queries, or bad/out-of-date results, try clearing your cache: .. code-block:: python >>> from astroquery.linelists.jplspec import JPLSpec >>> JPLSpec.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 ============= .. automodapi:: astroquery.linelists.jplspec :no-inheritance-diagram: