Created method to retrieve the wavelength lines from NIST.

.rtd-environment.yml

@@ -1,4 +1,4 @@
-name: packagename
+name: specreduce
 
 channels:
     - astropy
@@ -8,5 +8,7 @@ dependencies:
     - Cython
     - matplotlib
     - numpy
+    - pandas
+    - beautifulsoup4
 #   - pip:
 #       - dependency_from_pip

.travis.yml

@@ -38,7 +38,7 @@ env:
         # For this package-template, we include examples of Cython modules,
         # so Cython is required for testing. If your package does not include
         # Cython code, you can set CONDA_DEPENDENCIES=''
-        - CONDA_DEPENDENCIES='Cython'
+        - CONDA_DEPENDENCIES='Cython beautifulsoup4 lxml pandas requests'
 
         # Conda packages for affiliated packages are hosted in channel
         # "astropy" while builds for astropy LTS with recent numpy versions

setup.cfg

@@ -46,7 +46,7 @@ license = BSD
 url = http://astropy.org/
 edit_on_github = False
 github_project = astropy/specreduce
-install_requires = astropy, numpy
+install_requires = astropy, beautifulsoup4, lxml, numpy, pandas, requests
 # version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
 version = 0.0.dev
 

specreduce/tests/test_nist.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python 
+# -*- coding: utf8 -*-
+
+from __future__ import division, print_function
+
+import unittest
+import numpy
+
+from specreduce.utils import nist
+
+__author__ = 'Bruno Quint'
+
+
+class NistTest(unittest.TestCase):
+
+    def test_get_data(self):
+
+        df = nist.get_nist_data('Ne', 6570., 6630.)
+
+        test_ne_wav = numpy.array([6598.9528, 6602.9007])
+        test_ne_int = numpy.array([10000., 1000.])
+
+        self.assertTrue('spectrum' in df.columns)
+        self.assertTrue('wavelength' in df.columns)
+        self.assertTrue('rel_int' in df.columns)
+        self.assertTrue('reference' in df.columns)
+
+        numpy.testing.assert_almost_equal(df.wavelength, test_ne_wav)
+        numpy.testing.assert_almost_equal(df.rel_int, test_ne_int)
+
+
+if __name__ == '__main__':
+    unittest.main()

specreduce/utils/__init__.py

@@ -0,0 +1,2 @@
+
+from . import nist

specreduce/utils/nist.py

@@ -0,0 +1,120 @@
+#!/usr/bin/env python 
+# -*- coding: utf8 -*-
+"""
+    File which contains a method that can be used to retrieve data from
+    the National Institute of Standards and Technology (NIST) Atomic Spectra
+    Database.
+"""
+
+from __future__ import print_function, absolute_import, division
+
+import pandas as pd
+import requests
+
+from bs4 import BeautifulSoup
+
+
+__author__ = 'Bruno Quint'
+
+
+NIST_URL = 'https://physics.nist.gov/cgi-bin/ASD/lines1.pl'
+NIST_PAYLOAD = {
+        'spectra': None,
+        'limits_type': 0,
+        'low_w': None,
+        'upp_w': None,
+        'unit': 0,
+        'submit': 'Retrieve Data',
+        'de': 0,
+        'format': 0,
+        'line_out': 0,
+        'en_unit': 0,
+        'output': 0,
+        'bibrefs': 1,
+        'page_size': 15,
+        'show_obs_wl': 1,
+        'show_calc_wl': 1,
+        'unc_out': 1,
+        'order_out': 0,
+        'max_low_enrg': '',
+        'show_av': 2,
+        'max_upp_enrg': '',
+        'tsb_value': 0,
+        'min_str': '',
+        'A_out': 0,
+        'intens_out': 'on',
+        'max_str': '',
+        'allowed_out': 1,
+        'forbid_out': 1,
+        'min_accur': '',
+        'min_intens': '',
+        'conf_out': 'on',
+        'term_out': 'on',
+        'enrg_out': 'on',
+        'J_out': 'on',
+    }
+
+
+def get_nist_data(element, blue_limit, red_limit):
+    """
+    Retrieve data from NIST using a GET request and parsing the results into
+    two NumPy arrays: one for the wavelengths and other for the intensities.
+
+    Parameters
+    ----------
+        element : str
+            A string that matches a element (e.g.: "Th", "Cu", "Na").
+
+        blue_limit : float
+            Blue wavelength in Angstrom.
+
+        red_limit : float
+            Red wavelength in Angstrom.
+
+    Returns
+    -------
+        df : DataFrame
+            A Pandas DataFrame containing four columns
+            [spectrum, wavelength, rel_int, reference].
+
+    References
+    ----------
+
+        - Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2018).
+          NIST Atomic Spectra Database (ver. 5.5.6), [Online].
+          Available: https://physics.nist.gov/asd [2018, June 22].
+          National Institute of Standards and Technology, Gaithersburg, MD.
+
+    """
+    NIST_PAYLOAD['spectra'] = element
+    NIST_PAYLOAD['low_w'] = blue_limit
+    NIST_PAYLOAD['upp_w'] = red_limit
+
+    r = requests.get(NIST_URL, params=NIST_PAYLOAD)
+    soup = BeautifulSoup(r.content, 'lxml')
+
+    _ = [s.extract() for s in soup.find_all('table',
+                                            attrs={'width': ['75%', '100%']})]
+
+    _ = [s.extract() for s in soup(['script', 'span'])]
+
+    table = soup.find('table', attrs={'rules': 'groups'})
+    header, body = table.find_all('tbody')
+    header.name = 'theader'
+
+    _ = [s.extract() for s in table('theader')]
+
+    _df = pd.read_html(str(table))[0]
+    _df = _df[[0, 1, 5, 13]]
+
+    _df.columns = ['spectrum', 'wavelength', 'rel_int', 'reference']
+
+    _df['wavelength'] = _df['wavelength'].str.replace(" ", "")
+    _df['wavelength'] = _df['wavelength'].astype(float)
+
+    _df = _df[_df['rel_int'].apply(lambda x: str(x).isnumeric())]
+    _df['rel_int'] = _df['rel_int'].astype(float)
+
+    _df = _df.dropna()
+
+    return _df