Skip to content

Update HITRAN module to use class-based query API #1028

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 4 commits into from
May 30, 2018
Merged

Update HITRAN module to use class-based query API #1028

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
cf7dbf1
Update HITRAN module to use class-based query API
migueldvb Jan 19, 2018
41b8966
Adding HITRAN remote test
migueldvb Jan 25, 2018
0071d03
link astroquery.hitran in docs
migueldvb Feb 13, 2018
966ea40
Moving changelog to 0.3.9
migueldvb Apr 30, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion CHANGES
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
0.3.9 (unreleased)
------------------

- none yet
- HITRAN: use class-based API [#824]

0.3.8 (2018-04-27)
------------------
Expand Down
23 changes: 22 additions & 1 deletion astroquery/hitran/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,25 @@

:Author: Adam Ginsburg (adam.g.ginsburg@gmail.com)
"""
from .reader import download_hitran, read_hitran_file, cache_location
import os
from astropy import config as _config


class Conf(_config.ConfigNamespace):
"""
Configuration parameters for `astroquery.hitran`.
"""
query_url = _config.ConfigItem('http://hitran.org/lbl/api',
'HITRAN web interface URL.')
timeout = _config.ConfigItem(60,
'Time limit for connecting to HITRAN server.')
data_dir = os.path.join(os.path.dirname(__file__), 'data')
formatfile = _config.ConfigItem(os.path.join(data_dir, 'readme.txt'),
'Format file.')


conf = Conf()

from .core import Hitran, HitranClass

__all__ = ['Hitran', 'HitranClass', 'conf']
252 changes: 252 additions & 0 deletions astroquery/hitran/core.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,252 @@
from astropy.table import Table
from astropy import units as u

from ..query import BaseQuery
from ..utils import async_to_sync, prepend_docstr_nosections
from . import conf
from .utils import parse_readme

__all__ = ['Hitran', 'HitranClass']


@async_to_sync
class HitranClass(BaseQuery):

QUERY_URL = conf.query_url
TIMEOUT = conf.timeout
FORMATFILE = conf.formatfile
ISO_INDEX = {'id': 0, 'iso_name': 1, 'abundance': 2, 'mass': 3,
'mol_name': 4}

# Copied from the hapi.py code (Academic Free License)
# http://hitran.org/static/hapi/hapi.py
# M I id iso_name abundance mass mol_name
ISO = {
(1, 1): [1, 'H2(16O)', 0.997317, 18.010565, 'H2O'],
(1, 2): [2, 'H2(18O)', 0.00199983, 20.014811, 'H2O'],
(1, 3): [3, 'H2(17O)', 0.000372, 19.01478, 'H2O'],
(1, 4): [4, 'HD(16O)', 0.00031069, 19.01674, 'H2O'],
(1, 5): [5, 'HD(18O)', 0.000000623, 21.020985, 'H2O'],
(1, 6): [6, 'HD(17O)', 0.000000116, 20.020956, 'H2O'],
(2, 1): [7, '(12C)(16O)2', 0.9842, 43.98983, 'CO2'],
(2, 2): [8, '(13C)(16O)2', 0.01106, 44.993185, 'CO2'],
(2, 3): [9, '(16O)(12C)(18O)', 0.0039471, 45.994076, 'CO2'],
(2, 4): [10, '(16O)(12C)(17O)', 0.000734, 44.994045, 'CO2'],
(2, 5): [11, '(16O)(13C)(18O)', 0.00004434, 46.997431, 'CO2'],
(2, 6): [12, '(16O)(13C)(17O)', 0.00000825, 45.9974, 'CO2'],
(2, 7): [13, '(12C)(18O)2', 0.0000039573, 47.998322, 'CO2'],
(2, 8): [14, '(17O)(12C)(18O)', 0.00000147, 46.998291, 'CO2'],
(2, 0): [15, '(13C)(18O)2', 0.000000044967, 49.001675, 'CO2'],
(2, 11): [120, '(18O)(13C)(17O)', 0.00000001654, 48.00165, 'CO2'],
(2, 9): [121, '(12C)(17O)2', 0.0000001368, 45.998262, 'CO2'],
(3, 1): [16, '(16O)3', 0.992901, 47.984745, 'O3'],
(3, 2): [17, '(16O)(16O)(18O)', 0.00398194, 49.988991, 'O3'],
(3, 3): [18, '(16O)(18O)(16O)', 0.00199097, 49.988991, 'O3'],
(3, 4): [19, '(16O)(16O)(17O)', 0.00074, 48.98896, 'O3'],
(3, 5): [20, '(16O)(17O)(16O)', 0.00037, 48.98896, 'O3'],
(4, 1): [21, '(14N)2(16O)', 0.990333, 44.001062, 'N2O'],
(4, 2): [22, '(14N)(15N)(16O)', 0.0036409, 44.998096, 'N2O'],
(4, 3): [23, '(15N)(14N)(16O)', 0.0036409, 44.998096, 'N2O'],
(4, 4): [24, '(14N)2(18O)', 0.00198582, 46.005308, 'N2O'],
(4, 5): [25, '(14N)2(17O)', 0.000369, 45.005278, 'N2O'],
(5, 1): [26, '(12C)(16O)', 0.98654, 27.994915, 'CO'],
(5, 2): [27, '(13C)(16O)', 0.01108, 28.99827, 'CO'],
(5, 3): [28, '(12C)(18O)', 0.0019782, 29.999161, 'CO'],
(5, 4): [29, '(12C)(17O)', 0.000368, 28.99913, 'CO'],
(5, 5): [30, '(13C)(18O)', 0.00002222, 31.002516, 'CO'],
(5, 6): [31, '(13C)(17O)', 0.00000413, 30.002485, 'CO'],
(6, 1): [32, '(12C)H4', 0.98827, 16.0313, 'CH4'],
(6, 2): [33, '(13C)H4', 0.0111, 17.034655, 'CH4'],
(6, 3): [34, '(12C)H3D', 0.00061575, 17.037475, 'CH4'],
(6, 4): [35, '(13C)H3D', 0.0000049203, 18.04083, 'CH4'],
(7, 1): [36, '(16O)2', 0.995262, 31.98983, 'O2'],
(7, 2): [37, '(16O)(18O)', 0.00399141, 33.994076, 'O2'],
(7, 3): [38, '(16O)(17O)', 0.000742, 32.994045, 'O2'],
(8, 1): [39, '(14N)(16O)', 0.993974, 29.997989, 'NO'],
(8, 2): [40, '(15N)(16O)', 0.0036543, 30.995023, 'NO'],
(8, 3): [41, '(14N)(18O)', 0.00199312, 32.002234, 'NO'],
(9, 1): [42, '(32S)(16O)2', 0.94568, 63.961901, 'SO2'],
(9, 2): [43, '(34S)(16O)2', 0.04195, 65.957695, 'SO2'],
(10, 1): [44, '(14N)(16O)2', 0.991616, 45.992904, 'NO2'],
(11, 1): [45, '(14N)H3', 0.9958715, 17.026549, 'NH3'],
(11, 2): [46, '(15N)H3', 0.0036613, 18.023583, 'NH3'],
(12, 1): [47, 'H(14N)(16O)3', 0.98911, 62.995644, 'HNO3'],
(12, 2): [117, 'H(15N)(16O)3', 0.003636, 63.99268, 'HNO3'],
(13, 1): [48, '(16O)H', 0.997473, 17.00274, 'OH'],
(13, 2): [49, '(18O)H', 0.00200014, 19.006986, 'OH'],
(13, 3): [50, '(16O)D', 0.00015537, 18.008915, 'OH'],
(14, 1): [51, 'H(19F)', 0.99984425, 20.006229, 'HF'],
(14, 2): [110, 'D(19F)', 0.000115, 21.0125049978, 'HF'],
(15, 1): [52, 'H(35Cl)', 0.757587, 35.976678, 'HCl'],
(15, 2): [53, 'H(37Cl)', 0.242257, 37.973729, 'HCl'],
(15, 3): [107, 'D(35Cl)', 0.000118005, 36.9829544578, 'HCl'],
(15, 4): [108, 'D(37Cl)', 0.000037735, 38.9800043678, 'HCl'],
(16, 1): [54, 'H(79Br)', 0.50678, 79.92616, 'HBr'],
(16, 2): [55, 'H(81Br)', 0.49306, 81.924115, 'HBr'],
(16, 3): [111, 'D(79Br)', 0.0000582935, 80.9324388778, 'HBr'],
(16, 4): [112, 'D(81Br)', 0.0000567065, 82.9303923778, 'HBr'],
(17, 1): [56, 'H(127I)', 0.99984425, 127.912297, 'HI'],
(17, 2): [113, 'D(127I)', 0.000115, 128.918574778, 'HI'],
(18, 1): [57, '(35Cl)(16O)', 0.75591, 50.963768, 'ClO'],
(18, 2): [58, '(37Cl)(16O)', 0.24172, 52.960819, 'ClO'],
(19, 1): [59, '(16O)(12C)(32S)', 0.93739, 59.966986, 'OCS'],
(19, 2): [60, '(16O)(12C)(34S)', 0.04158, 61.96278, 'OCS'],
(19, 3): [61, '(16O)(13C)(32S)', 0.01053, 60.970341, 'OCS'],
(19, 4): [62, '(16O)(12C)(33S)', 0.01053, 60.966371, 'OCS'],
(19, 5): [63, '(18O)(12C)(32S)', 0.00188, 61.971231, 'OCS'],
(20, 1): [64, 'H2(12C)(16O)', 0.98624, 30.010565, 'H2CO'],
(20, 2): [65, 'H2(13C)(16O)', 0.01108, 31.01392, 'H2CO'],
(20, 3): [66, 'H2(12C)(18O)', 0.0019776, 32.014811, 'H2CO'],
(21, 1): [67, 'H(16O)(35Cl)', 0.75579, 51.971593, 'HOCl'],
(21, 2): [68, 'H(16O)(37Cl)', 0.24168, 53.968644, 'HOCl'],
(22, 1): [69, '(14N)2', 0.9926874, 28.006147, 'N2'],
(22, 2): [118, '(14N)(15N)', 0.0072535, 29.997989, 'N2'],
(23, 1): [70, 'H(12C)(14N)', 0.98511, 27.010899, 'HCN'],
(23, 2): [71, 'H(13C)(14N)', 0.01107, 28.014254, 'HCN'],
(23, 3): [72, 'H(12C)(15N)', 0.0036217, 28.007933, 'HCN'],
(24, 1): [73, '(12C)H3(35Cl)', 0.74894, 49.992328, 'CH3Cl'],
(24, 2): [74, '(12C)H3(37Cl)', 0.23949, 51.989379, 'CH3Cl'],
(25, 1): [75, 'H2(16O)2', 0.994952, 34.00548, 'H2O2'],
(26, 1): [76, '(12C)2H2', 0.9776, 26.01565, 'C2H2'],
(26, 2): [77, '(12C)(13C)H2', 0.02197, 27.019005, 'C2H2'],
(26, 3): [105, '(12C)2HD', 0.00030455, 27.021825, 'C2H2'],
(27, 1): [78, '(12C)2H6', 0.97699, 30.04695, 'C2H6'],
(27, 2): [106, '(12C)H3(13C)H3', 0.021952611, 31.050305, 'C2H6'],
(28, 1): [79, '(31P)H3', 0.99953283, 33.997238, 'PH3'],
(29, 1): [80, '(12C)(16O)(19F)2', 0.98654, 65.991722, 'COF2'],
(29, 2): [119, '(13C)(16O)(19F)2', 0.0110834, 66.995083, 'COF2'],
(31, 1): [81, 'H2(32S)', 0.94988, 33.987721, 'H2S'],
(31, 2): [82, 'H2(34S)', 0.04214, 35.983515, 'H2S'],
(31, 3): [83, 'H2(33S)', 0.007498, 34.987105, 'H2S'],
(32, 1): [84, 'H(12C)(16O)(16O)H', 0.983898, 46.00548, 'HCOOH'],
(33, 1): [85, 'H(16O)2', 0.995107, 32.997655, 'HO2'],
(34, 1): [86, '(16O)', 0.997628, 15.994915, 'O'],
(36, 1): [87, '(14N)(16O)+', 0.993974, 29.997989, 'NOp'],
(37, 1): [88, 'H(16O)(79Br)', 0.5056, 95.921076, 'HOBr'],
(37, 2): [89, 'H(16O)(81Br)', 0.4919, 97.919027, 'HOBr'],
(38, 1): [90, '(12C)2H4', 0.9773, 28.0313, 'C2H4'],
(38, 2): [91, '(12C)H2(13C)H2', 0.02196, 29.034655, 'C2H4'],
(39, 1): [92, '(12C)H3(16O)H', 0.98593, 32.026215, 'CH3OH'],
(40, 1): [93, '(12C)H3(79Br)', 0.5013, 93.941811, 'CH3Br'],
(40, 2): [94, '(12C)H3(81Br)', 0.48766, 95.939764, 'CH3Br'],
(41, 1): [95, '(12C)H3(12C)(14N)', 0.97482, 41.026549, 'CH3CN'],
(42, 1): [96, '(12C)(19F)4', 0.9893, 87.993616, 'CF4'],
(43, 1): [116, '(12C)4H2', 0.955998, 50.01565, 'C4H2'],
(44, 1): [109, 'H(12C)3(14N)', 0.9646069, 51.01089903687, 'HC3N'],
(45, 1): [103, 'H2', 0.999688, 2.01565, 'H2'],
(45, 2): [115, 'HD', 0.00022997, 3.021825, 'H2'],
(46, 1): [97, '(12C)(32S)', 0.939624, 43.971036, 'CS'],
(46, 2): [98, '(12C)(34S)', 0.0416817, 45.966787, 'CS'],
(46, 3): [99, '(13C)(32S)', 0.0105565, 44.974368, 'CS'],
(46, 4): [100, '(12C)(33S)', 0.00741668, 44.970399, 'CS'],
(47, 1): [114, '(32S)(16O)3', 0.9423964, 79.95682, 'SO3'],
(1001, 1): [101, 'H', None, None, 'H'],
(1002, 1): [102, 'He', None, None, 'He'],
(1018, 1): [104, 'Ar', None, None, 'Ar'],
}

def __init__(self, **kwargs):
"""
Initialize a Hitran query class.
"""
super(HitranClass, self).__init__()

def _args_to_payload(self, molecule_number=1, isotopologue_number=1,
min_frequency=None, max_frequency=None):
"""
Code to parse input and construct the payload dictionary.

Parameters
----------
molecule_number : int
HITRAN molecule number
isotopologue_number : int
HITRAN isotopologue number
min_frequency : `astropy.units`
Minimum frequency (or any spectral() equivalent)
max_frequency : `astropy.units`
Maximum frequency (or any spectral() equivalent)

Returns
-------
payload : dict
Dictionary of the parameters to send to the SPLAT page

"""

payload = dict()

iso_id = str(self.ISO[(molecule_number,
isotopologue_number)][self.ISO_INDEX['id']])
# mol_name = self.ISO[(molecule_number,
# isotopologue_number)][self.ISO_INDEX['mol_name']]

payload['iso_ids_list'] = iso_id

if min_frequency is not None:
min_frequency = min_frequency.to(u.cm**-1, u.spectral())

if max_frequency is not None:
max_frequency = max_frequency.to(u.cm**-1, u.spectral())

if min_frequency is not None and max_frequency is not None:
if min_frequency > max_frequency:
min_frequency, max_frequency = max_frequency, min_frequency

payload['numin'] = min_frequency.value
payload['numax'] = max_frequency.value

return payload

@prepend_docstr_nosections("\n" + _args_to_payload.__doc__)
def query_lines_async(self, get_query_payload=False, cache=True, **kwargs):
"""
Queries Hitran class for a particular molecule with default arguments
set. Based on fetch function from hapi.py.

Returns
-------
response : `requests.Response`
The response of the HTTP request.
"""

params = self._args_to_payload(**kwargs)

if get_query_payload:
return params

response = self._request(method='GET',
url=self.QUERY_URL,
params=params,
timeout=self.TIMEOUT,
cache=cache)

return response

def _parse_result(self, response, verbose=False):
"""
Parse a response into an `~astropy.table.Table`
"""
formats = parse_readme(self.FORMATFILE)

dtypes = [entry['dtype'] for entry in formats.values()]

rows = []
for line in response.text.split('\n'):
if line.strip():
row = []
start = 0
for key, entry in formats.items():
formatter = entry['formatter']
length = entry['length']
value = formatter(line[start:start+length])
row.append(value)
start = start + length
rows.append(row)

result = Table(rows=rows, names=formats.keys(), dtype=dtypes)

return result


Hitran = HitranClass()
Loading