added download link

tardis/io/parsers/blondin_toymodel.py

@@ -0,0 +1,117 @@
+import re
+
+import yaml
+
+import numpy as np
+import pandas as pd
+
+from astropy import units as u
+
+from tardis.util.base import parse_quantity
+
+
+
+PATTERN_REMOVE_BRACKET = re.compile('\[.+\]')
+T0_PATTERN = re.compile('tend = (.+)\n')
+
+def read_blondin_toymodel(fname):
+    """
+    Reading the Blondin toy-model format and returns a dictionary and a
+    dataframe
+
+    Parameters
+    ----------
+    fname: str
+        path or filename to blondin toymodel
+
+    Returns
+    -------
+
+    blondin_dict: dict
+        dictionary containing most of the meta data of the model
+
+    blondin_csv: pandas.DataFrame
+        DataFrame containing the csv part of the toymodel
+
+    """
+    with open(fname, 'r') as fh:
+        for line in fh:
+            if line.startswith("#idx"):
+                break
+        else:
+            raise ValueError(
+                'File {0} does not conform to Toy Model format as it does '
+                'not contain #idx')
+    columns = [PATTERN_REMOVE_BRACKET.sub('', item) for item in
+               line[1:].split()]
+
+    raw_blondin_csv = pd.read_csv(fname, delim_whitespace=True, comment='#',
+                                  header=None, names=columns)
+    raw_blondin_csv.set_index('idx', inplace=True)
+
+    blondin_csv = raw_blondin_csv.loc[:,
+                  ['vel', 'dens', 'temp', 'X_56Ni0', 'X_Ti', 'X_Ca', 'X_S',
+                   'X_Si', 'X_O', 'X_C']]
+    rename_col_dict = {'vel': 'velocity', 'dens': 'density',
+                       'temp': 't_electron'}
+    rename_col_dict.update({item: item[2:] for item in blondin_csv.columns[3:]})
+    rename_col_dict['X_56Ni0'] = 'Ni56'
+    blondin_csv.rename(columns=rename_col_dict, inplace=True)
+    blondin_csv.iloc[:, 3:] = blondin_csv.iloc[:, 3:].divide(
+        blondin_csv.iloc[:, 3:].sum(axis=1), axis=0)
+
+    # changing velocities to outer boundary
+    new_velocities = 0.5 * (blondin_csv.velocity.iloc[
+                            :-1].values + blondin_csv.velocity.iloc[1:].values)
+    new_velocities = np.hstack(
+        (new_velocities, [2 * new_velocities[-1] - new_velocities[-2]]))
+    blondin_csv['velocity'] = new_velocities
+
+    with open(fname, 'r') as fh:
+        t0_string = T0_PATTERN.findall(fh.read())[0]
+
+    t0 = parse_quantity(t0_string.replace('DAYS', 'day'))
+    blondin_dict = {}
+    blondin_dict['model_density_time_0'] = str(t0)
+    blondin_dict['description'] = 'Converted {0} to csvy format'.format(fname)
+    blondin_dict['tardis_model_config_version'] = 'v1.0'
+    blondin_dict_fields = [dict(name='velocity', unit='km/s',
+                                desc='velocities of shell outer bounderies.')]
+    blondin_dict_fields.append(
+        dict(name='density', unit='g/cm^3', desc='mean density of shell.'))
+    blondin_dict_fields.append(
+        dict(name='t_electron', unit='K', desc='electron temperature.'))
+
+    for abund in blondin_csv.columns[3:]:
+        blondin_dict_fields.append(
+            dict(name=abund, desc='Fraction {0} abundance'.format(abund)))
+    blondin_dict['datatype'] = {'fields': blondin_dict_fields}
+
+    return blondin_dict, blondin_csv
+
+
+def convert_blondin_toymodel(in_fname, out_fname, v_inner, v_outer):
+    """
+    
+    Parameters
+    ----------
+    in_fname
+    out_fname
+    v_inner
+    v_outer
+
+    Returns
+    -------
+
+    """
+    blondin_dict, blondin_csv = read_blondin_toymodel(in_fname)
+    blondin_dict['v_inner_boundary'] = str(u.Quantity(v_inner, u.km / u.s))
+    blondin_dict['v_outer_boundary'] = str(u.Quantity(v_outer, u.km / u.s))
+
+    csvy_file = '---\n{0}\n---\n{1}'.format(
+        yaml.dump(blondin_dict, default_flow_style=False),
+        blondin_csv.to_csv(index=False))
+
+    with open(out_fname, 'w') as fh:
+        fh.write(csvy_file)
+