Spectral line search classes and functions

Spectral line search classes and functions#

Classes and functions associated with searching spectral line databases

class dysh.line.SpectralLineSearchClass[source]#

Bases: object

Attributes:

colnames: Returns ——- colname : list The list of column names present in the default returned table.

Methods

`clear_cache`()	Clear the local caches.
`get_species_ids`(species_regex[, reflags, ...])	Convenience call-through to `get_species_id()`.
`localquery`(min_frequency, max_frequency[, ...])	Query a local file for lines and return a table object.
`query_lines`(min_frequency, max_frequency[, ...])	Query locally or remotely for lines and return a table object.
`recomb`(min_frequency, max_frequency, line[, ...])	Search for recombination lines of H, He, and C.
`recomball`(min_frequency, max_frequency[, ...])	Fetch all recombination lines of H, He, C in the given frequency range from the catalog.

clear_cache()[source]#

Clear the local caches. This will clear the Splatalogue cache and any local tables that have been cached.

See https://astroquery.readthedocs.io/en/stable/splatalogue/splatalogue.html#troubleshooting

Returns:

None.

property colnames#

Returns:

colnamelist: The list of column names present in the default returned table. You can choose a subset of these when performing a search.

get_species_ids(species_regex, reflags=0, recache=False)[source]#

Convenience call-through to get_species_id().

Get a dictionary of “species” IDs, where species refers to the molecule name, mass, and chemical composition.

Parameters:

species_regexstr: String to search for among the species names, if specified. The string will be compiled into a regular expression using the python re module.
reflagsint: Flags to pass to re.
recachebool: Flag whether to refresh the local cache of species IDs

Examples

>>> import re
>>> import pprint # unfortunate hack required for documentation testing
>>> rslt = Splatalogue.get_species_ids(species_regex='Formaldehyde')
>>> pprint.pprint(rslt)
{'03023 H2CO - Formaldehyde': '194',
 '03106 H213CO - Formaldehyde': '324',
 '03107 HDCO - Formaldehyde': '109',
 '03108 H2C17O - Formaldehyde': '982',
 '03202 H2C18O - Formaldehyde': '155',
 '03203 D2CO - Formaldehyde': '94',
 '03204 HD13CO - Formaldehyde': '1219',
 '03301 D213CO - Formaldehyde': '1220',
 '03315 HDC18O - Formaldehyde': '21141',
 '03410 D2C18O - Formaldehyde': '21140'}
>>> rslt = Splatalogue.get_species_ids(species_regex='H2CO')
>>> pprint.pprint(rslt)
{'03023 H2CO - Formaldehyde': '194',
 '03109 H2COH+ - Hydroxymethylium ion': '224',
 '04406 c-H2COCH2 - Ethylene Oxide': '21',
 '06029 NH2CONH2 - Urea': '21166',
 '07510 H2NCH2COOH - I v=0 - Glycine': '389',
 '07511 H2NCH2COOH - I v=1 - Glycine': '1312',
 '07512 H2NCH2COOH - I v=2 - Glycine': '1313',
 '07513 H2NCH2COOH - II v=0 - Glycine': '262',
 '07514 H2NCH2COOH - II v=1 - Glycine': '1314',
 '07515 H2NCH2COOH - II v=2 - Glycine': '1315',
 '07517 NH2CO2CH3 v=0 - Methyl Carbamate': '1334',
 '07518 NH2CO2CH3 v=1 - Methyl Carbamate': '1335',
 '08902 CH3CHNH2COOH - I - α-Alanine': '1321',
 '08903 CH3CHNH2COOH - II - α-Alanine': '1322'}
>>> # note the whitespace, preventing H2CO within other
>>> # more complex molecules
>>> Splatalogue.get_species_ids(species_regex=' H2CO ')
{'03023 H2CO - Formaldehyde': '194'}
>>> Splatalogue.get_species_ids(species_regex=' h2co ', reflags=re.IGNORECASE)
{'03023 H2CO - Formaldehyde': '194'}

localquery(min_frequency: ~astropy.units.quantity.Quantity, max_frequency: ~astropy.units.quantity.Quantity, cat: ~typing.Literal[<generator object SpectralLineSearchClass.<genexpr> at 0x77aedad67760>] | ~pathlib.Path = 'gbtlines', columns: str | list = ['species_id', 'name', 'chemical_name', 'resolved_QNs', 'linelist', 'LovasASTIntensity', 'lower_state_energy', 'upper_state_energy', 'sijmu2', 'sij', 'aij', 'intintensity', 'Lovas_NRAO', 'orderedfreq', 'lower_state_energy_K', 'upper_state_energy_K', 'upperStateDegen', 'moleculeTag', 'qnCode', 'labref_Lovas_NIST', 'rel_int_HFS_Lovas', 'unres_quantum_numbers', 'lineid', 'transition_in_space', 'transition_in_G358', 'obsref_Lovas_NIST', 'source_Lovas_NIST', 'telescope_Lovas_NIST', 'searchErrorMessage'], chemical_name: str | None = None, chem_re_flags: int = 0, energy_min: float | None = None, energy_max: float | None = None, energy_type: ~typing.Literal[<generator object SpectralLineSearchClass.<genexpr> at 0x77aedad677d0>] | None = None, intensity_lower_limit=None, intensity_type: ~typing.Literal[<generator object SpectralLineSearchClass.<genexpr> at 0x77aedad67840>] | None = None, line_lists: ~typing.Literal[<generator object SpectralLineSearchClass.<genexpr> at 0x77aedad678b0>] | None = None, cache: bool = False, format: str = 'ascii.ecsv', **kwargs) → Table[source]#

Query a local file for lines and return a table object. The query returns lines with rest frequencies in the range [min_frequency,`max_frequency`].

Note:

If the search parameters result no matches, a zero-length Table will be returned.
Many of the keywords are only supported if cat='splatalogue' because local tables do not have all the columns that the Splatalogue database has.

Parameters:

min_frequencyQuantity

The minimum frequency to search (or any u.spectral() equivalent). No default.

max_frequencyQuantity

The maximum frequency to search (or any u.spectral() equivalent). No default.

catstr

The catalog to use. One of: [‘splatalogue’, ‘gbtlines’, ‘gbtrecomb’] (minimum string match) or a valid local astropy-compatible table. The local table must have all the columns listed in the columns parameter. The default is a GBT-specific line catalog, ‘gbtlines’.

columns: str or list

The query result columns to include in the returned table. Any of [‘species_id’, ‘name’, ‘chemical_name’, ‘resolved_QNs’, ‘linelist’, ‘LovasASTIntensity’, ‘lower_state_energy’, ‘upper_state_energy’, ‘sijmu2’, ‘sij’, ‘aij’, ‘intintensity’, ‘Lovas_NRAO’, ‘orderedfreq’, ‘lower_state_energy_K’, ‘upper_state_energy_K’, ‘upperStateDegen’, ‘moleculeTag’, ‘qnCode’, ‘labref_Lovas_NIST’, ‘rel_int_HFS_Lovas’, ‘unres_quantum_numbers’, ‘lineid’, ‘transition_in_space’, ‘transition_in_G358’, ‘obsref_Lovas_NIST’, ‘source_Lovas_NIST’, ‘telescope_Lovas_NIST’, ‘searchErrorMessage’]. The default is all columns.

chemical_namestr

Name of the chemical to search for. Treated as a regular expression. An empty set will match any species. Examples:

'H2CO' - 13 species have H2CO somewhere in their formula.

'Formaldehyde' - There are 8 isotopologues of Formaldehyde: (e.g., H213CO).

'formaldehyde' - Thioformaldehyde,Cyanoformaldehyde.

'formaldehyde',chem_re_flags=re.I - Formaldehyde,thioformaldehyde,: and Cyanoformaldehyde.
' H2CO ' - Just 1 species, H2CO. The spaces prevent including: others.

chem_re_flagsint

See the re module

energy_minNone or float

Energy range to include. See energy_type

energy_maxNone or float

Energy range to include. See energy_type

energy_type'el_cm1', 'eu_cm1', 'eu_k', 'el_k'

Type of energy to restrict. L/U for lower/upper state energy, cm/K for inverse cm, i.e. wavenumber, or K for Kelvin

intensity_lower_limitNone or float

Lower limit on the intensity. See intensity_type

intensity_typeNone, 'CDMS/JPL (log)', 'Sij-mu2', 'Aij (log)'

The type of intensity on which to place a lower limit

line_listslist

Options: Lovas, SLAIM, JPL, CDMS, ToyaMA, OSU, Recombination, RFI

cache: bool

Make an in-memory copy of the input table to be used in subsequent queries to this catalog.

format: str

The astropy IO format string for the input table. Default is ECSV format.

Returns:

Table: An astropy table containing the results of the search

query_lines(min_frequency: ~astropy.units.quantity.Quantity, max_frequency: ~astropy.units.quantity.Quantity, cat: ~typing.Literal[<generator object SpectralLineSearchClass.<genexpr> at 0x77aedb10b300>] | ~pathlib.Path = 'splatalogue', columns: str | list = ['species_id', 'name', 'chemical_name', 'resolved_QNs', 'linelist', 'LovasASTIntensity', 'lower_state_energy', 'upper_state_energy', 'sijmu2', 'sij', 'aij', 'intintensity', 'Lovas_NRAO', 'orderedfreq', 'lower_state_energy_K', 'upper_state_energy_K', 'upperStateDegen', 'moleculeTag', 'qnCode', 'labref_Lovas_NIST', 'rel_int_HFS_Lovas', 'unres_quantum_numbers', 'lineid', 'transition_in_space', 'transition_in_G358', 'obsref_Lovas_NIST', 'source_Lovas_NIST', 'telescope_Lovas_NIST', 'searchErrorMessage'], asynchronous: bool = False, cache: bool = True, format: str = 'ascii.ecsv', only_NRAO_recommended=True, **kwargs) → Table[source]#

Query locally or remotely for lines and return a table object. The query returns lines with rest frequencies in the range [min_frequency,`max_frequency`].

Note: If the search parameters result in no matches, a zero-length Table will be returned.

Parameters:

min_frequencyQuantity

The minimum frequency to search (or any u.spectral() equivalent)

max_frequencyQuantity

The maximum frequency to search (or any u.spectral() equivalent)

catstr or Path

The catalog to use. One of: [‘splatalogue’, ‘gbtlines’, ‘gbtrecomb’] (minimum string match) or a valid Path to a local astropy-compatible table. The local table must have all the columns listed in the columns parameter.

'gbtlines' is a local catalog of spectral lines between 300 MHz and 120 GHz with CDMS/JP log(intensity) > -9.

'gbtrecomb' is a local catalog of H, He, and C recombination lnes between 300 MHz and 120 GHz.

columns: str or list The query result columns to include in the returned table. Any of [‘species_id’, ‘name’, ‘chemical_name’, ‘resolved_QNs’, ‘linelist’, ‘LovasASTIntensity’, ‘lower_state_energy’, ‘upper_state_energy’, ‘sijmu2’, ‘sij’, ‘aij’, ‘intintensity’, ‘Lovas_NRAO’, ‘orderedfreq’, ‘lower_state_energy_K’, ‘upper_state_energy_K’, ‘upperStateDegen’, ‘moleculeTag’, ‘qnCode’, ‘labref_Lovas_NIST’, ‘rel_int_HFS_Lovas’, ‘unres_quantum_numbers’, ‘lineid’, ‘transition_in_space’, ‘transition_in_G358’, ‘obsref_Lovas_NIST’, ‘source_Lovas_NIST’, ‘telescope_Lovas_NIST’, ‘searchErrorMessage’]. The default is all columns.

cache: bool

For a local file query, make an in-memory copy of the input catalog to be used in subsequent queries to this catalog.

asynchronous: bool

Use asynchronous query

format: str

Stringe describing the format of a local input table. Must be a valid astropy.io.ascii format string. Default is ‘ascii.ecsv’

chemical_namestr

Name of the chemical to search for. Treated as a regular expression. An empty set (‘’, (), [], {}) will match any species. Examples:

'H2CO' - 13 species have H2CO somewhere in their formula.

'Formaldehyde' - There are 8 isotopologues of Formaldehyde: (e.g., H213CO).

'formaldehyde' - Thioformaldehyde,Cyanoformaldehyde.

'formaldehyde',chem_re_flags=re.I - Formaldehyde,thioformaldehyde,: and Cyanoformaldehyde.
' H2CO ' - Just 1 species, H2CO. The spaces prevent including: others.

parse_chemistry_locallybool

Attempt to determine the species ID #’s locally before sending the query? This will prevent queries that have no matching species. It also performs a more flexible regular expression match to the species IDs. See the examples in get_species_ids

chem_re_flagsint

See the re module

energy_minNone or float

Energy range to include. See energy_type

energy_maxNone or float

Energy range to include. See energy_type

energy_type'el_cm1', 'eu_cm1', 'eu_k', 'el_k'

Type of energy to restrict. L/U for lower/upper state energy, cm/K for inverse cm, i.e. wavenumber, or K for Kelvin

intensity_lower_limitNone or float

Lower limit on the intensity. See intensity_type

intensity_typeNone or 'sij', 'cdms_jpl', 'aij'

The type of intensity on which to place a lower limit

transitionstr

e.g. 1-0

version'v1.0', 'v2.0', 'v3.0' or 'vall'

Data version

excludelist

Types of lines to exclude. Default is: ('potential', 'atmospheric', 'probable') Can also exclude 'known'. To exclude nothing, use ‘none’, not the python object None, since the latter is meant to indicate ‘leave as default’

only_astronomically_observedbool

Show only astronomically observed species?

only_NRAO_recommendedbool

Show only NRAO recommended species?

line_listslist

Options: Lovas, SLAIM, JPL, CDMS, ToyaMA, OSU, Recombination, RFI

line_strengthslist

CDMS/JPL Intensity : ls1
Sij : ls3
Aij : ls4
Lovas/AST : ls5

energy_levelslist

E_lower (cm^-1) : “One”
E_lower (K) : “Two”
E_upper (cm^-1) : “Three”
E_upper (K) : “Four”

exportbool

Set up arguments for the export server (as opposed to the HTML server)?

export_limitint

Maximum number of lines in output file

noHFSbool

No HFS Display

displayHFSbool

Display HFS Intensity

show_unres_qnbool

Display Unresolved Quantum Numbers

show_upper_degeneracybool

Display Upper State Degeneracy

show_molecule_tagbool

Display Molecule Tag

show_qn_codebool

Display Quantum Number Code

show_lovas_labrefbool

Display Lab Ref

show_lovas_obsrefbool

Display Obs Ref

show_orderedfreq_onlybool

Display Ordered Frequency ONLY

show_nrao_recommendedbool

Display NRAO Recommended Frequencies

Returns:

Table: An astropy.table.Table containing the results of the search.

recomb(min_frequency: ~astropy.units.quantity.Quantity, max_frequency: ~astropy.units.quantity.Quantity, line: str, cat: ~typing.Literal[<generator object SpectralLineSearchClass.<genexpr> at 0x77aedb10b290>] | ~pathlib.Path = 'splatalogue', columns: str | list = ['species_id', 'name', 'chemical_name', 'resolved_QNs', 'linelist', 'LovasASTIntensity', 'lower_state_energy', 'upper_state_energy', 'sijmu2', 'sij', 'aij', 'intintensity', 'Lovas_NRAO', 'orderedfreq', 'lower_state_energy_K', 'upper_state_energy_K', 'upperStateDegen', 'moleculeTag', 'qnCode', 'labref_Lovas_NIST', 'rel_int_HFS_Lovas', 'unres_quantum_numbers', 'lineid', 'transition_in_space', 'transition_in_G358', 'obsref_Lovas_NIST', 'source_Lovas_NIST', 'telescope_Lovas_NIST', 'searchErrorMessage'], convert_to_unicode: bool = True, only_NRAO_recommended: bool = True, **kwargs) → Table[source]#

Search for recombination lines of H, He, and C.

Parameters:

min_frequencyQuantity: The minimum frequency to search (or any u.spectral() equivalent). No default.
max_frequencyQuantity: The maximum frequency to search (or any u.spectral() equivalent). No default.
linestr: A string describing the line or series to search for, e.g. “Hydrogen”, “Halpha”, “Hebeta”, “C”, “carbon”. No default.
catstr or Path: The catalog to use. One of: {0} (minimum string match) or a valid Path to a local astropy-compatible table. The local table must have all the columns listed in the columns parameter. Default is ‘splatalogue’.
columns: str or list: The query result columns to include in the returned table. Any of {1}. The default is all columns.
convert_to_unicodebool, optional: Splatalogue stores line names using the unicode characters for Greek symbols, e.g. α for ‘alpha’. dysh will convert for you, if you put in e.g., ‘Halpha’. You should only change this if a) you are inputing unicode or b) you are searching a local file that you know doesn’t use unicode. The default is True.
**kwargsdict: Other keyword arguments supported by query_lines() if cat is ‘splatalogue’.

Returns:

Table: An astropy table containing the results of the search

recomball(min_frequency: ~astropy.units.quantity.Quantity, max_frequency: ~astropy.units.quantity.Quantity, cat: ~typing.Literal[<generator object SpectralLineSearchClass.<genexpr> at 0x77aedad67920>] | ~pathlib.Path = 'splatalogue', columns: str | list = ['species_id', 'name', 'chemical_name', 'resolved_QNs', 'linelist', 'LovasASTIntensity', 'lower_state_energy', 'upper_state_energy', 'sijmu2', 'sij', 'aij', 'intintensity', 'Lovas_NRAO', 'orderedfreq', 'lower_state_energy_K', 'upper_state_energy_K', 'upperStateDegen', 'moleculeTag', 'qnCode', 'labref_Lovas_NIST', 'rel_int_HFS_Lovas', 'unres_quantum_numbers', 'lineid', 'transition_in_space', 'transition_in_G358', 'obsref_Lovas_NIST', 'source_Lovas_NIST', 'telescope_Lovas_NIST', 'searchErrorMessage'], cache: bool = False, only_NRAO_recommended: bool = True, **kwargs) → Table[source]#

Fetch all recombination lines of H, He, C in the given frequency range from the catalog.

Parameters:

min_frequencyQuantity: The minimum frequency to search (or any u.spectral() equivalent). No default.
max_frequencyQuantity: The maximum frequency to search (or any u.spectral() equivalent). No default.
catstr or Path: The catalog to use. One of: {0} (minimum string match) or a valid Path to a local astropy-compatible table. The local table must have all the columns listed in the columns parameter. Default is ‘splatalogue’.
columns: str or list: The query result columns to include in the returned table. Any of {1}. The default is all columns.
cache: bool: For a local file query, make an in-memory copy of the input table to be used in subsequent queries to this catalog.
**kwargsdict: Other keyword arguments supported by query_lines() if cat is ‘splatalogue’.

Returns:

Table: An astropy table containing the results of the search.

Spectral line search classes and functions

Contents

Spectral line search classes and functions#