pythonradex 1.0.9__py3-none-any.whl → 2.0.1__py3-none-any.whl

pythonradex/LAMDA_file.py

@@ -8,16 +8,19 @@ from pythonradex import atomic_transition
 from scipy import constants
 import numpy as np
 
+
 def is_comment(line):
-    if line.replace(' ','')[0] == '!':
+    if line.replace(" ", "")[0] == "!":
         return True
     else:
         return False
 
-def read(datafilepath,read_frequencies,read_quantum_numbers=False):
-    '''
-    Read a LAMDA data file. LAMDA files can be downloaded from the LAMDA database
-    at http://home.strw.leidenuniv.nl/~moldata
+
+def read(datafilepath, read_frequencies, read_quantum_numbers=False):
+    """
+    Read a data file that follows the LAMDA format (https://home.strw.leidenuniv.nl/~moldata/molformat.html).
+    Such files can for example be downloaded from the EMAA (https://emaa.osug.fr/)
+    or the LAMDA (http://home.strw.leidenuniv.nl/~moldata) databases.
 
     Args:
         datafilepath (:obj:`str`): The filepath to the LAMDA file.
@@ -30,100 +33,132 @@ def read(datafilepath,read_frequencies,read_quantum_numbers=False):
         read_quantum_numbers (:obj:`bool`): Whether to read the quantum numbers
             from the file. Defaults to False. The LAMDA format does not force a
             file to list quantum numbers, so they might not be present.
-    
+
     Returns:
         dict: A dictionary containing the data read from the file.
             The following keys give acces to lists containing the data.
             The elements of these lists are in the order they appear in the file.
             'levels' (a list of pythonradex.atomic_transition.Level objects);
-            'radiative transitions' (a list of 
+            'radiative transitions' (a list of
             pythonradex.atomic_transitions.RadiativeTransition objects);
             'collisional transitions' (a list of
             pythonradex.atomic_transition.CollisionalTransition objects);
             'quantum numbers' (list of str, empty if read_quantum_numbers
             was set to False)
-    '''
-    #identifiers used in the LAMDA database files:
-    LAMDA_coll_ID = {'1':'H2','2':'para-H2','3':'ortho-H2','4':'e',
-                     '5':'H','6':'He','7':'H+'}
-    datafile = open(datafilepath,'r')
+    """
+    # identifiers used in the LAMDA database files:
+    LAMDA_coll_ID = {
+        "1": "H2",
+        "2": "para-H2",
+        "3": "ortho-H2",
+        "4": "e",
+        "5": "H",
+        "6": "He",
+        "7": "H+",
+    }
+    datafile = open(datafilepath, "r")
     levels = []
     rad_transitions = []
     coll_transitions = {}
     quantum_numbers = []
     comment_offset = 0
-    for i,line in enumerate(datafile):
-        if is_comment(line) or line=='' or line=='\n':
+    for i, line in enumerate(datafile):
+        if is_comment(line) or line == "" or line == "\n":
             comment_offset += 1
             continue
-        if i == 0+comment_offset:
+        if i == 0 + comment_offset:
             continue
-        if i == 1+comment_offset:
+        if i == 1 + comment_offset:
             continue
-        if i == 2+comment_offset:
+        if i == 2 + comment_offset:
             n_levels = int(line)
             continue
-        if 3+comment_offset <= i < 3+comment_offset+n_levels:
+        if 3 + comment_offset <= i < 3 + comment_offset + n_levels:
             line_entries = line.split()
             leveldata = [float(string) for string in line_entries[:3]]
-            assert int(leveldata[0]) == i-2-comment_offset,\
-                                     'level numeration not consistent'
-            #transforming energy from cm-1 to J; level numbers starting from 0:
+            assert (
+                int(leveldata[0]) == i - 2 - comment_offset
+            ), "level numeration not consistent"
+            # transforming energy from cm-1 to J; level indices starting from 0:
             lev = atomic_transition.Level(
-                        g=leveldata[2],
-                        E=constants.c*constants.h*leveldata[1]/constants.centi,
-                        number=int(leveldata[0])-1)
+                g=leveldata[2],
+                E=constants.c * constants.h * leveldata[1] / constants.centi,
+                index=int(leveldata[0]) - 1,
+            )
             levels.append(lev)
             if read_quantum_numbers:
                 quantum_numbers.append(line_entries[3])
             continue
-        if i == 3+comment_offset+n_levels:
+        if i == 3 + comment_offset + n_levels:
             n_rad_transitions = int(line)
             continue
-        if 4+comment_offset+n_levels <= i < 4+comment_offset+n_levels+n_rad_transitions:
+        if (
+            4 + comment_offset + n_levels
+            <= i
+            < 4 + comment_offset + n_levels + n_rad_transitions
+        ):
             radtransdata = [float(string) for string in line.split()]
-            up = next(level for level in levels if level.number==radtransdata[1]-1)
-            low = next(level for level in levels if level.number==radtransdata[2]-1)
-            rad_trans_kwargs = {'up':up,'low':low,'A21':radtransdata[3]}
+            up = next(level for level in levels if level.index == radtransdata[1] - 1)
+            low = next(level for level in levels if level.index == radtransdata[2] - 1)
+            rad_trans_kwargs = {"up": up, "low": low, "A21": radtransdata[3]}
             if read_frequencies:
-                nu0 = radtransdata[4]*constants.giga
-                Delta_E = up.E-low.E
-                assert np.isclose(nu0,Delta_E/constants.h,atol=0,rtol=1e-3),\
-                     'read frequency is inconsistent with level energies'
-                rad_trans_kwargs['nu0'] = nu0
-            rad_trans = atomic_transition.RadiativeTransition(**rad_trans_kwargs) 
+                nu0 = radtransdata[4] * constants.giga
+                Delta_E = up.E - low.E
+                assert np.isclose(
+                    nu0, Delta_E / constants.h, atol=0, rtol=1e-3
+                ), "read frequency is inconsistent with level energies"
+                rad_trans_kwargs["nu0"] = nu0
+            rad_trans = atomic_transition.RadiativeTransition(**rad_trans_kwargs)
             rad_transitions.append(rad_trans)
             continue
-        if i == 4+comment_offset+n_levels+n_rad_transitions:
+        if i == 4 + comment_offset + n_levels + n_rad_transitions:
             coll_partner_offset = 0
             continue
-        if i == 5+comment_offset+n_levels+n_rad_transitions + coll_partner_offset:
+        if i == 5 + comment_offset + n_levels + n_rad_transitions + coll_partner_offset:
             coll_ID = LAMDA_coll_ID[line[0]]
             coll_transitions[coll_ID] = []
             continue
-        if i == 6+comment_offset+n_levels+n_rad_transitions + coll_partner_offset:
+        if i == 6 + comment_offset + n_levels + n_rad_transitions + coll_partner_offset:
             n_coll_transitions = int(line)
             continue
-        if i == 7+comment_offset+n_levels+n_rad_transitions + coll_partner_offset:
-            continue #this lines contains the number of temperature elements
-        if i == 8+comment_offset+n_levels+n_rad_transitions + coll_partner_offset:
+        if i == 7 + comment_offset + n_levels + n_rad_transitions + coll_partner_offset:
+            continue  # this lines contains the number of temperature elements
+        if i == 8 + comment_offset + n_levels + n_rad_transitions + coll_partner_offset:
             coll_temperatures = np.array([float(string) for string in line.split()])
             continue
-        last_coll_trans_i = 9+comment_offset+n_levels+n_rad_transitions\
-                               +coll_partner_offset+n_coll_transitions-1
-        if 9+comment_offset+n_levels+n_rad_transitions+coll_partner_offset <= i <=\
-                 last_coll_trans_i:
+        last_coll_trans_i = (
+            9
+            + comment_offset
+            + n_levels
+            + n_rad_transitions
+            + coll_partner_offset
+            + n_coll_transitions
+            - 1
+        )
+        if (
+            9 + comment_offset + n_levels + n_rad_transitions + coll_partner_offset
+            <= i
+            <= last_coll_trans_i
+        ):
             coll_trans_data = [float(string) for string in line.split()]
-            up = next(level for level in levels if level.number==coll_trans_data[1]-1)
-            low = next(level for level in levels if level.number==coll_trans_data[2]-1)
-            K21_data = np.array(coll_trans_data[3:])*constants.centi**3
+            up = next(
+                level for level in levels if level.index == coll_trans_data[1] - 1
+            )
+            low = next(
+                level for level in levels if level.index == coll_trans_data[2] - 1
+            )
+            K21_data = np.array(coll_trans_data[3:]) * constants.centi**3
             coll_trans = atomic_transition.CollisionalTransition(
-                                  up=up,low=low,K21_data=K21_data,
-                                  Tkin_data=coll_temperatures)
+                up=up, low=low, K21_data=K21_data, Tkin_data=coll_temperatures
+            )
             coll_transitions[coll_ID].append(coll_trans)
             if i == last_coll_trans_i:
-                coll_partner_offset += 4+n_coll_transitions
+                coll_partner_offset += 4 + n_coll_transitions
                 continue
     datafile.close()
-    return {'levels':levels,'radiative transitions':rad_transitions,
-            'collisional transitions':coll_transitions,'quantum numbers':quantum_numbers}
+    return {
+        "levels": levels,
+        "radiative transitions": rad_transitions,
+        "collisional transitions": coll_transitions,
+        "quantum numbers": quantum_numbers,
+    }

pythonradex/__init__.py

@@ -1,4 +1,9 @@
 # -*- coding: utf-8 -*-
 """
 Python implementation of the RADEX radiative transfer code
-"""
+"""
+
+from . import helpers, LAMDA_file, radiative_transfer
+from importlib.metadata import version
+
+__version__ = version("pythonradex")