Misc changes in isotope abund. file parser

tardis/io/model_reader.py

@@ -86,10 +86,10 @@ def read_abundances_file(abundance_filename, abundance_filetype,
 
     file_parsers = {'simple_ascii': read_simple_ascii_abundances,
                     'artis': read_simple_ascii_abundances,
-                    'isotopes': read_simple_isotope_abundances}
+                    'tardis_model': read_simple_isotope_abundances}
 
     isotope_abundance = pd.DataFrame()
-    if abundance_filetype == 'isotopes':
+    if abundance_filetype == 'tardis_model':
         index, abundances, isotope_abundance = read_simple_isotope_abundances(
             abundance_filename)
     else:
@@ -267,7 +267,7 @@ def read_simple_ascii_abundances(fname):
 
 
 def read_simple_isotope_abundances(fname, delimiter=','):
-    df = pd.read_csv(fname, header=[0, 1], comment='#', delimiter=delimiter)
+    df = pd.read_csv(fname, comment='#', delimiter=delimiter)
     df = df.transpose()
 
     abundance = pd.DataFrame(columns=np.arange(df.shape[1]),
@@ -281,14 +281,14 @@ def read_simple_isotope_abundances(fname, delimiter=','):
                                      index=isotope_index,
                                      dtype=np.float64)
 
-    for element, type_of_element in df.index:
-        if type_of_element == 'E':
-            z = element_symbol2atomic_number(element)
-            abundance.loc[z, :] = df.loc[element, type_of_element].tolist()
-        elif type_of_element == 'I':
-            z = nucname.znum(element)
-            mass_no = nucname.anum(element)
+    for element_symbol_string in df.index:
+        if element_symbol_string in nucname.name_zz:
+            z = nucname.name_zz[element_symbol_string]
+            abundance.loc[z, :] = df.loc[element_symbol_string].tolist()
+        else:
+            z = nucname.znum(element_symbol_string)
+            mass_no = nucname.anum(element_symbol_string)
             isotope_abundance.loc[(
-                z, mass_no), :] = df.loc[element, type_of_element].tolist()
+                z, mass_no), :] = df.loc[element_symbol_string].tolist()
 
     return abundance.index, abundance, isotope_abundance

tardis/util.py

@@ -437,12 +437,7 @@ def convert_abundances_format(fname, delimiter='\s+'):
     df = pd.read_csv(fname, delimiter=delimiter, comment='#', header=None)
     #Drop shell index column
     df.drop(df.columns[0], axis=1, inplace=True)
-
-    #Creating Header rows of Element Symbol and Type of Element
-    header_df = pd.DataFrame([(nucname.name(i), 'E')
-                              for i in range(1, df.shape[1] + 1)]).transpose()
-    #Align columns index with abundance dataframe
-    header_df.columns = header_df.columns + 1
-
-    # Adding header rows to top and return resultant DataFrame
-    return pd.concat([header_df, df])
+    #Assign header row
+    df.columns = [nucname.name(i)
+                  for i in range(1, df.shape[1] + 1)]
+    return df