def _list_tables(filename, pedantic=False):
votable = parse(filename, pedantic=pedantic)
tables = {}
for i, table in enumerate(votable.iter_tables()):
tables[i] = table.name
return tables
def read(self, filename, pedantic=False, tid=-1, verbose=True):
'''
Read a table from a VOT file
Required Arguments:
*filename*: [ string ]
The VOT file to read the table from
Optional Keyword Arguments:
*tid*: [ integer ]
The ID of the table to read from the VO file (this is
only required if there are more than one table in the VO file)
*pedantic*: [ True | False ]
When *pedantic* is True, raise an error when the file violates
the VO Table specification, otherwise issue a warning.
'''
_check_vo_installed()
self.reset()
# If no table is requested, check that there is only one table
if tid==-1:
tables = _list_tables(filename, pedantic=pedantic)
if len(tables) == 1:
tid = 0
elif len(tables) == 0:
raise Exception("There are no tables present in this file")
else:
raise TableException(tables, 'tid')
votable = parse(filename, pedantic=pedantic)
for id, table in enumerate(votable.iter_tables()):
if id==tid:
break
if table.ID:
self.table_name = str(table.ID)
elif table.name:
self.table_name = str(table.name)
for field in table.fields:
if type(field.name) == str:
colname = field.name
else:
if type(field._ID) == str:
colname = field._ID
else:
raise Exception("Error reading in the VO table: no name or ID for field")
data = table.array[colname]
if len(data) > 0 and data.ndim == 1 and not np.all([np.isscalar(x) for x in data]):
warnings.warn("VO Variable length vector column detected (%s) - converting to string" % colname)
data = np.array([str(x) for x in data])
if self._masked:
self.add_column(colname, data, \
unit=field.unit, mask=table.mask[colname])
else:
self.add_column(colname, data, \
unit=field.unit)
def read(self, filename, pedantic=False, tid=-1, verbose=True):
"""
Read a table from a VOT file
Required Arguments:
*filename*: [ string ]
The VOT file to read the table from
Optional Keyword Arguments:
*tid*: [ integer ]
The ID of the table to read from the VO file (this is
only required if there are more than one table in the VO file)
*pedantic*: [ True | False ]
When *pedantic* is True, raise an error when the file violates
the VO Table specification, otherwise issue a warning.
"""
_check_vo_installed()
self.reset()
# If no table is requested, check that there is only one table
if tid == -1:
tables = _list_tables(filename, pedantic=pedantic)
if len(tables) == 1:
tid = 0
elif len(tables) == 0:
raise Exception("There are no tables present in this file")
else:
raise TableException(tables, "tid")
votable = parse(filename, pedantic=pedantic)
for id, table in enumerate(votable.iter_tables()):
if id == tid:
break
if table.ID:
self.table_name = str(table.ID)
elif table.name:
self.table_name = str(table.name)
for field in table.fields:
if type(field.name) == str:
colname = field.name
else:
if type(field._ID) == str:
colname = field._ID
else:
raise Exception("Error reading in the VO table: no name or ID for field")
# ensure that colname is a valid python variable name (i.e. contains no non-allowed chars)
# the following will replace any invalid chars with underscores, and/or prepend an initial
# underscore to names that begin with a digit.
clean = lambda varStr: re.sub("\W|^(?=\d)", "_", varStr)
colname = clean(colname)
data = table.array[colname]
if len(data) > 0 and data.ndim == 1 and not np.all([np.isscalar(x) for x in data]):
warnings.warn("VO Variable length vector column detected (%s) - converting to string" % colname)
data = np.array([str(x) for x in data])
if self._masked:
self.add_column(colname, data, unit=field.unit, mask=table.mask[colname], description=field.description)
else:
self.add_column(colname, data, unit=field.unit, description=field.description)