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Merge pull request #2419 from mkelley/jplspec-doc-cleanup-2022.05
Test all jplspec code blocks except plots.
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‎docs/jplspec/jplspec.rst

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@@ -71,7 +71,7 @@ The units of the columns of the query can be displayed by calling
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... max_lines = 7)
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>>> print(response.info)
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<Table length=7>
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name dtype unit
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name dtype unit
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----- ------- -------
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FREQ float64 MHz
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ERR float64 MHz
@@ -213,108 +213,99 @@ to query these directly.
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>>> from astroquery.jplspec import JPLSpec
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>>> import astropy.units as u
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>>> response = JPLSpec.query_lines_async(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule="H2O",
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... parse_name_locally=True)
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>>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule="H2O",
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... parse_name_locally=True)
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>>> print(result)
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FREQ ERR LGINT DR ELO GUP TAG QNFMT QN' QN"
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MHz MHz MHz nm2 1 / cm
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----------- -------- -------- --- --------- --- ------ ----- -------- --------
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115542.5692 0.6588 -13.2595 3 4606.1683 35 18003 1404 17 810 0 18 513 0
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139614.293 0.15 -9.3636 3 3080.1788 87 -18003 1404 14 6 9 0 15 312 0
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177317.068 0.15 -10.3413 3 3437.2774 31 -18003 1404 15 610 0 16 313 0
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183310.087 0.001 -3.6463 3 136.1639 7 -18003 1404 3 1 3 0 2 2 0 0
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...
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Length = 2000 rows
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Searches like these can lead to very broad queries, and may be limited in
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response length:
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Searches like these can lead to very broad queries. Since the table yields
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extensive results, we will only show a dictionary of the tags that
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went into the payload to create a response:
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.. doctest-remote-data::
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>>> print(result.meta['comments'])
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['', '', '', '', '', 'form is currently limited to 2000 lines. Please limit your search.']
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.. We don't get these dictionaries as reponses, fix these examples and
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remove skip. #2408
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Inspecting the returned molecules shows that the 'H2O' string was processed as a
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regular expression, and the search matched any molecule that contained the
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combination of characters 'H2O':
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.. doctest-skip::
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.. doctest-remote-data::
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>>> {'CH2OO': 46014,
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... 'H2O': 18003,
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... 'H2O v2,2v2,v': 18005,
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... 'H2O-17': 19003,
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... 'H2O-18': 20003,
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... 'H2O2': 34004,
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... 'HCCCH2OD': 57003,
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... 'HCCCH2OH': 56010,
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... 'HCOCH2OH': 60006,
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... 'NH2CH2CH2OH': 61004}
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As you can see, the 'H2O' string was processed as a regular expression,
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and the search matched any molecule that contained the combination of
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characters 'H20'.
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>>> tags = set(abs(result['TAG'])) # discard negative signs
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>>> species = {species: tag
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... for (species, tag) in JPLSpec.lookup_ids.items()
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... if tag in tags}
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>>> print(species)
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{'H2O': 18003, 'H2O v2,2v2,v': 18005, 'H2O-17': 19003, 'H2O-18': 20003, 'H2O2': 34004}
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A few examples that show the power of the regex option are the following:
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.. doctest-remote-data::
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>>> response = JPLSpec.query_lines_async(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule="H2O$",
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... parse_name_locally=True)
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The response:
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.. doctest-skip::
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>>> {'H2O': 18003}
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>>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule="H2O$",
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... parse_name_locally=True)
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>>> tags = set(abs(result['TAG'])) # discard negative signs
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>>> species = {species: tag
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... for (species, tag) in JPLSpec.lookup_ids.items()
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... if tag in tags}
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>>> print(species)
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{'H2O': 18003}
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As seen above, the regular expression "H2O$" yields only an exact match because
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the special character $ matches the end of the line. This functionality allows
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you to be as specific or vague as you want to allow the results to be:
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.. doctest-remote-data::
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>>> from astroquery.jplspec import JPLSpec
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>>> import astropy.units as u
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>>> response = JPLSpec.query_lines_async(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule="^H.O$",
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... parse_name_locally=True)
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>>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule="^H.O$",
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... parse_name_locally=True)
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>>> tags = set(abs(result['TAG'])) # discard negative signs
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>>> species = {species: tag
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... for (species, tag) in JPLSpec.lookup_ids.items()
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... if tag in tags}
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>>> print(species)
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{'H2O': 18003, 'HDO': 19002, 'HCO': 29004, 'HNO': 31005}
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This pattern matches any word that starts with an H, ends with an O, and
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contains any character in between, it results in the following molecules
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being queried:
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.. doctest-skip::
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>>> {'H2O': 18003,
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... 'HDO': 19002
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... 'HCO': 29004
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... 'HNO': 31005 }
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contains any character in between.
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Another example of the functionality of this option is the option to obtain
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results from a molecule and its isotopes, in this case H2O and HDO:
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.. doctest-remote-data::
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>>> from astroquery.jplspec import JPLSpec
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>>> import astropy.units as u
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>>> response = JPLSpec.query_lines_async(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule=r"^H[2D]O(-\d\d|)$",
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... parse_name_locally=True)
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This pattern matches any H2O and HDO isotopes and it results in the following
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molecules being part of the payload:
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.. doctest-skip::
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>>> {'H2O': 18003,
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... 'H2O-17': 19003,
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... 'H2O-18': 20003,
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... 'HDO': 19002,
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... 'HDO-18': 21001}
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Remember to print your response to see the table of your results.
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>>> result = JPLSpec.query_lines(min_frequency=100 * u.GHz,
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... max_frequency=1000 * u.GHz,
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... min_strength=-500,
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... molecule=r"^H[2D]O(-\d\d|)$",
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... parse_name_locally=True)
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>>> tags = set(abs(result['TAG'])) # discard negative signs
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>>> species = {species: tag
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... for (species, tag) in JPLSpec.lookup_ids.items()
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... if tag in tags}
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>>> print(species)
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{'H2O': 18003, 'HDO': 19002, 'H2O-17': 19003, 'H2O-18': 20003, 'HDO-18': 21001}
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This pattern matches any H2O and HDO isotopes.
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Reference/API

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