[WIP] Adding support for linetools line lists as default

tests/test_line_database.py

@@ -62,6 +62,14 @@ def test_line_database_from_input():
     assert ld.lines_all[0].identifier == HI.identifier
     print(ld)
 
+def test_line_database_add_line_linetools():
+    ld = LineDatabase()
+    HI = Line('H', 'I', 1216, 626500000.0, 2.3, identifier='Ly a')
+    ld.add_line('H', 'I', 1216, use_linetools=True, identifier='Ly a')
+    np.testing.assert_allclose( ld.lines_all[0].gamma, HI.gamma )
+    assert ld.lines_all[0].identifier == HI.identifier
+    print(ld)
+
 def test_select_lines_from_line_database():
     ld = LineDatabase('lines.txt')
     assert len(ld.select_lines('Ne')) == 8 # 8 listed Ne lines

trident/constants.py

@@ -0,0 +1,49 @@
+"""
+Constants and Tables
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2016, Trident Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+#-----------------------------------------------------------------------------
+
+# Taken from Cloudy documentation.
+solar_abundance = {
+    'H' : 1.00e+00, 'He': 1.00e-01, 'Li': 2.04e-09,
+    'Be': 2.63e-11, 'B' : 6.17e-10, 'C' : 2.45e-04,
+    'N' : 8.51e-05, 'O' : 4.90e-04, 'F' : 3.02e-08,
+    'Ne': 1.00e-04, 'Na': 2.14e-06, 'Mg': 3.47e-05,
+    'Al': 2.95e-06, 'Si': 3.47e-05, 'P' : 3.20e-07,
+    'S' : 1.84e-05, 'Cl': 1.91e-07, 'Ar': 2.51e-06,
+    'K' : 1.32e-07, 'Ca': 2.29e-06, 'Sc': 1.48e-09,
+    'Ti': 1.05e-07, 'V' : 1.00e-08, 'Cr': 4.68e-07,
+    'Mn': 2.88e-07, 'Fe': 2.82e-05, 'Co': 8.32e-08,
+    'Ni': 1.78e-06, 'Cu': 1.62e-08, 'Zn': 3.98e-08}
+
+atomic_mass = {
+    'H' : 1.00794,   'He': 4.002602,  'Li': 6.941,
+    'Be': 9.012182,  'B' : 10.811,    'C' : 12.0107,
+    'N' : 14.0067,   'O' : 15.9994,   'F' : 18.9984032,
+    'Ne': 20.1797,   'Na': 22.989770, 'Mg': 24.3050,
+    'Al': 26.981538, 'Si': 28.0855,   'P' : 30.973761,
+    'S' : 32.065,    'Cl': 35.453,    'Ar': 39.948,
+    'K' : 39.0983,   'Ca': 40.078,    'Sc': 44.955910,
+    'Ti': 47.867,    'V' : 50.9415,   'Cr': 51.9961,
+    'Mn': 54.938049, 'Fe': 55.845,    'Co': 58.933200,
+    'Ni': 58.6934,   'Cu': 63.546,    'Zn': 65.409}
+
+atomic_number = {
+    'H' : 1,  'He': 2,  'Li': 3,
+    'Be': 4,  'B' : 5,  'C' : 6,
+    'N' : 7,  'O' : 8,  'F' : 9,
+    'Ne': 10, 'Na': 11, 'Mg': 12,
+    'Al': 13, 'Si': 14, 'P' : 15,
+    'S' : 16, 'Cl': 17, 'Ar': 18,
+    'K' : 19, 'Ca': 20, 'Sc': 21,
+    'Ti': 22, 'V' : 23, 'Cr': 24,
+    'Mn': 25, 'Fe': 26, 'Co': 27,
+    'Ni': 28, 'Cu': 29, 'Zn': 30}

trident/ion_balance.py

@@ -29,6 +29,8 @@
     uniquify
 from trident.roman import \
     from_roman
+from trident.constants import \
+    solar_abundance, atomic_mass, atomic_number
 
 H_mass_fraction = 0.76
 to_nH = H_mass_fraction / mh
@@ -245,7 +247,8 @@ def add_ion_fields(ds, ions, ftype='gas',
     # If line_database is set, then use the underlying file as the line list
     # to select ions from.
     if line_database is not None:
-        line_database = LineDatabase(line_database)
+        if not isinstance( line_database, LineDatabase ):
+            line_database = LineDatabase(line_database)
         ion_list = line_database.parse_subset_to_ions(ions)
 
     # Otherwise, any ion can be selected (not just ones in the line list).
@@ -861,41 +864,3 @@ def _alias_field(ds, alias_name, name):
         ds.field_info.alias(alias_name, name)
         ds.derived_field_list.append(alias_name)
     return
-
-
-# Taken from Cloudy documentation.
-solar_abundance = {
-    'H' : 1.00e+00, 'He': 1.00e-01, 'Li': 2.04e-09,
-    'Be': 2.63e-11, 'B' : 6.17e-10, 'C' : 2.45e-04,
-    'N' : 8.51e-05, 'O' : 4.90e-04, 'F' : 3.02e-08,
-    'Ne': 1.00e-04, 'Na': 2.14e-06, 'Mg': 3.47e-05,
-    'Al': 2.95e-06, 'Si': 3.47e-05, 'P' : 3.20e-07,
-    'S' : 1.84e-05, 'Cl': 1.91e-07, 'Ar': 2.51e-06,
-    'K' : 1.32e-07, 'Ca': 2.29e-06, 'Sc': 1.48e-09,
-    'Ti': 1.05e-07, 'V' : 1.00e-08, 'Cr': 4.68e-07,
-    'Mn': 2.88e-07, 'Fe': 2.82e-05, 'Co': 8.32e-08,
-    'Ni': 1.78e-06, 'Cu': 1.62e-08, 'Zn': 3.98e-08}
-
-atomic_mass = {
-    'H' : 1.00794,   'He': 4.002602,  'Li': 6.941,
-    'Be': 9.012182,  'B' : 10.811,    'C' : 12.0107,
-    'N' : 14.0067,   'O' : 15.9994,   'F' : 18.9984032,
-    'Ne': 20.1797,   'Na': 22.989770, 'Mg': 24.3050,
-    'Al': 26.981538, 'Si': 28.0855,   'P' : 30.973761,
-    'S' : 32.065,    'Cl': 35.453,    'Ar': 39.948,
-    'K' : 39.0983,   'Ca': 40.078,    'Sc': 44.955910,
-    'Ti': 47.867,    'V' : 50.9415,   'Cr': 51.9961,
-    'Mn': 54.938049, 'Fe': 55.845,    'Co': 58.933200,
-    'Ni': 58.6934,   'Cu': 63.546,    'Zn': 65.409}
-
-atomic_number = {
-    'H' : 1,  'He': 2,  'Li': 3,
-    'Be': 4,  'B' : 5,  'C' : 6,
-    'N' : 7,  'O' : 8,  'F' : 9,
-    'Ne': 10, 'Na': 11, 'Mg': 12,
-    'Al': 13, 'Si': 14, 'P' : 15,
-    'S' : 16, 'Cl': 17, 'Ar': 18,
-    'K' : 19, 'Ca': 20, 'Sc': 21,
-    'Ti': 22, 'V' : 23, 'Cr': 24,
-    'Mn': 25, 'Fe': 26, 'Co': 27,
-    'Ni': 28, 'Cu': 29, 'Zn': 30}

trident/line_database.py

@@ -12,12 +12,16 @@
 #-----------------------------------------------------------------------------
 
 import os
+import warnings
 from yt.funcs import \
     mylog
 from trident.config import \
     trident_path
 from trident.roman import \
-    from_roman
+    from_roman, to_roman
+from trident.constants import \
+    atomic_number
+import astropy.units as u
 
 
 def uniquify(list):
@@ -145,10 +149,10 @@ def __init__(self, input_file=None):
         if input_file is not None:
             self.load_line_list_from_file(input_file)
         else:
-            self.input_file = 'Manually Entered'
+            self.load_line_list_from_linetools()
 
-    def add_line(self, element, ion_state, wavelength, gamma,
-                 f_value, field=None, identifier=None):
+    def add_line(self, element, ion_state, wavelength, gamma=None,
+                 f_value=None, field=None, identifier=None, use_linetools=False):
         """
         Manually add a line to the :class:`~trident.LineDatabase`.
 
@@ -188,6 +192,10 @@ def add_line(self, element, ion_state, wavelength, gamma,
             An optional identifier for the transition
             Example: 'Ly a' for Lyman alpha
 
+        :use_linetools: bool
+
+            If True retrieve the values for wavelength, gamma, and f_value
+            from the linetools python package (linetools.readthedocs.io).
 
         **Example**
 
@@ -199,9 +207,67 @@ def add_line(self, element, ion_state, wavelength, gamma,
         >>> ldb.add_line('H', 'I', 1215.67, 469860000, 0.41641, 'Ly a')
         >>> print(ldb.lines_all)
         """
+
+        if use_linetools:
+            # Retrieve
+            def linetools_id( wrest ):
+                return '%s%s %d' % (element, ion_state, round(float(wrest), 0))
+            line = self.linetools_linelist[ linetools_id(wavelength) ]
+
+            # Check for rounding differences
+            if line is None:
+                warnings.warn( 'Line ' + linetools_id(wavelength) + \
+                    ' not found in linetools database. Checking adjacent wavelengths.')
+                line = self.linetools_linelist[ linetools_id(wavelength-1) ]
+                if line is None:
+                    line = self.linetools_linelist[ linetools_id(wavelength+1) ]
+                    if line is None:
+                        raise KeyError( 'No line found in linetools database.' )
+
+            # Format
+            wavelength = line['wrest'].value
+            gamma = line['gamma'].value
+            f_value = line['f']
+
+        else:
+            assert gamma is not None
+            assert f_value is not None
+
         self.lines_all.append(Line(element, ion_state, wavelength, gamma,
                                    f_value, field, identifier))
 
+    def add_line_from_linetools(self, name):
+        """
+        name is the linetools name for a feature: "ion wrest"
+        e.g., HI 1215
+        """
+        line = self.linetools_linelist[name]
+        reversed_atomic_number = {value : key for (key, value) in atomic_number.items()}
+        if line['Z'] not in reversed_atomic_number.keys():
+            # Not a line < Zn so not a line we care about.
+            return
+        element = reversed_atomic_number[line['Z']]
+        ion_state = to_roman(line['ion'])
+        wavelength = line['wrest'].value
+        gamma = line['gamma'].value
+        f_value = line['f']
+        identifier = line['name']
+        self.add_line(element, ion_state, wavelength, gamma, f_value,
+                      identifier=identifier)
+
+    def load_line_list_from_linetools(self):
+        """
+        Create a line list that incorporates all of the "ISM" lines between 100 and
+        1 micron angstroms from the external linetools code.
+        """
+        bounds = [100, 10000] * u.AA
+        name_list = self.linetools_linelist.available_transitions(bounds)['name']
+        for name in name_list:
+            # Don't include fine structure lines or deuterium lines
+            if "*" not in name and \
+               "DI" not in name:
+                self.add_line_from_linetools(name)
+
     def load_line_list_from_file(self, filename):
         """
         Load a line list from a file into the LineDatabase.
@@ -451,6 +517,21 @@ def parse_subset_to_ions(self, subsets=None):
         ions = uniquify(ions)
         return ions
 
+    @property
+    def linetools_linelist(self):
+        '''Handler for a linetools LineList class.
+        '''
+
+        if not hasattr( self, '_linetools_linelist' ):
+
+            # Only doing the import here so rest of the class doesn't
+            # break if the feature isn't enabled.
+            from linetools.lists.linelist import LineList
+
+            self._linetools_linelist = LineList('ISM')
+
+        return self._linetools_linelist
+
     def __repr__(self):
         disp = ""
         for line in self.lines_all:

trident/ray_generator.py

@@ -24,7 +24,7 @@
     from_roman
 from yt.data_objects.static_output import \
     Dataset
-from trident.ion_balance import \
+from trident.constants import \
     atomic_number
 
 def make_simple_ray(dataset_file, start_position, end_position,

trident/spectrum_generator.py

@@ -35,7 +35,8 @@
 from trident.instrument import \
     Instrument
 from trident.ion_balance import \
-    add_ion_number_density_field, \
+    add_ion_number_density_field
+from trident.constants import \
     atomic_mass
 from trident.line_database import \
     LineDatabase