Create an utility function to read table files

pcigale/analysis_modules/psum.py

@@ -30,6 +30,7 @@ from copy import deepcopy
 from scipy import stats
 from progressbar import ProgressBar
 from matplotlib import pyplot as plt
+from ..utils import read_table
 from . import AnalysisModule
 from ..creation_modules import get_module
 from ..warehouse import SedWarehouse
@@ -183,10 +184,7 @@ class Psum(AnalysisModule):
 
         # Read the observation table and complete it by adding error where
         # none is provided and by adding the systematic deviation.
-        if data_file.endswith(('fits', 'vot', 'xml')):
-            obs_table = Table.read(data_file)
-        else:
-            obs_table = Table.read(data_file, format='ascii')
+        obs_table = read_table(data_file)
         for name in filter_list:
             name_err = name + '_err'
             if name_err not in column_list:

pcigale/creation_modules/loadfile.py

@@ -13,6 +13,7 @@ This module reads a SED spectrum from a file.
 
 from astropy.table import Table
 from collections import OrderedDict
+from ..utils import read_table
 from . import CreationModule
 
 
@@ -49,7 +50,7 @@ class LoadSpecFile(CreationModule):
 
         """
         filename = self.parameters['filename']
-        table = Table(filename, verbose=False)
+        table = read_table(filename)
 
         sed.add_module(self.name, self.parameters)
 

pcigale/creation_modules/sfhfromfile.py

@@ -14,6 +14,7 @@ This module reads the star formation history in a file.
 from astropy.table import Table
 import numpy as np
 from collections import OrderedDict
+from ..utils import read_table
 from . import CreationModule
 
 
@@ -64,10 +65,7 @@ class SfhFromFile(CreationModule):
 
         """
         filename = self.parameters['filename']
-        if filename.endswith(('fits', 'vot', 'xml')):
-            table = Table.read(filename)
-        else:
-            table = Table.read(filename, format='ascii')
+        table = read_table(filename)
 
         time_column_name = table.columns.keys[0]
         time_grid = table[time_column_name]

pcigale/session/configuration.py

@@ -14,6 +14,7 @@ from glob import glob # To allow the use of glob() in "eval..."
 from textwrap import wrap
 from .tools import param_dict_combine
 from ..data import Database
+from ..utils import read_table
 from .. import creation_modules
 from .. import analysis_modules
 
@@ -149,10 +150,7 @@ class Configuration(object):
             filter_list = base.get_filter_list()[0]
 
         # Finding the known filters in the data table
-        if self.config['data_file'].endswith(('fits', 'vot', 'xml')):
-            obs_table = Table.read(self.config['data_file'])
-        else:
-            obs_table = Table.read(self.config['data_file'], format='ascii')
+        obs_table = read_table(self.config['data_file'])
         column_list = []
         for column in obs_table.columns:
             filter_name = column[:-4] if column.endswith('_err') else column

pcigale/utils.py

+# -*- coding: utf-8 -*-
+# Copyright (C) 2014 Yannick Roehlly
+# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
+# Author: Yannick Roehlly
+
+"""
+Various utility function for pcigale
+"""
+
+from astropy.table import Table
+from astropy.io.ascii.core import InconsistentTableError
+
+
+def read_table(file_):
+    """Read a data table using astropy
+
+    This function first tries to automatically read the table with astropy,
+    if that fails, it tries with the ascii format.
+
+    Parameters
+    ----------
+    file_ : string
+        Name of the file to read.
+
+    Return
+    ------
+    an astropy.table.Table object
+
+    Raise
+    -----
+    An error is raised when the table can not be parsed.
+
+    """
+    try:
+        table = Table.read(file_)
+    except Exception:  # astropy should raise a specific exception
+        try:
+            table = Table.read(file_, format="ascii")
+        except InconsistentTableError:
+            raise StandardError("The file <{}> can not be parsed as a data "
+                                "table.".format(file_))
+
+    return table