def write(self, dbtype, *args, **kwargs):
#self._raise_vector_columns()
# Check if table overwrite is requested
if 'overwrite' in kwargs:
overwrite = kwargs.pop('overwrite')
else:
overwrite = False
# Open the connection
connection, cursor = sql.connect_database(dbtype, *args, **kwargs)
# Check that table name is set
if not self.table_name:
raise Exception("Table name is not set")
else:
table_name = str(self.table_name)
# Check that table name is ok
# todo
# lowercase because pgsql automatically converts
# table names to lower case
# Check if table already exists
existing_tables = sql.list_tables(cursor, dbtype).values()
if table_name in existing_tables or \
table_name.lower() in existing_tables:
if overwrite:
sql.drop_table(cursor, table_name)
else:
raise ExistingTableException()
# Create table
columns = [(name, smart_dtype(self.columns[name].dtype)) \
for name in self.names]
shapes = [self.data[name].shape for name in self.names]
sql.create_table(cursor, dbtype, table_name, columns, shapes, primary_key=self._primary_key)
mapper = sql.get_sql_row_mapper(shapes)
# Insert row
float_column = [self.columns[name].dtype.type in [np.float32, np.float64] for name in self.names]
for i in range(self.__len__()):
row = self.row(i, python_types=True)
sql.insert_row(cursor, dbtype, table_name, mapper(row), fixnan=not self._masked)
# Close connection
connection.commit()
cursor.close()
def _to_table(self, VOTable):
'''
Return the current table as a VOT object
'''
table = Table(VOTable)
# Define some fields
n_rows = len(self)
fields = []
for i, name in enumerate(self.names):
data = self.data[name]
unit = self.columns[name].unit
dtype = self.columns[name].dtype
column_type = smart_dtype(dtype)
if data.ndim > 1:
arraysize = str(data.shape[1])
else:
arraysize = None
if column_type == np.string_:
arraysize = "1024"
if column_type in type_dict:
datatype = type_dict[column_type]
elif column_type == np.int8:
warnings.warn("int8 unsupported - converting to int16")
datatype = type_dict[np.int16]
elif column_type == np.uint16:
warnings.warn("uint16 unsupported - converting to int32")
datatype = type_dict[np.int32]
elif column_type == np.uint32:
warnings.warn("uint32 unsupported - converting to int64")
datatype = type_dict[np.int64]
elif column_type == np.uint64:
raise Exception("uint64 unsupported")
else:
raise Exception("cannot use numpy type " + str(column_type))
if column_type == np.float32:
precision = 'F9'
elif column_type == np.float64:
precision = 'F17'
else:
precision = None
fields.append(Field(VOTable, ID="col" + str(i), name=name, \
datatype=datatype, unit=unit, arraysize=arraysize, \
precision=precision))
table.fields.extend(fields)
table.create_arrays(n_rows)
# Character columns are stored as object columns in the VOTable
# instance. Leaving the type as string should work, but causes
# a segmentation fault on MacOS X with Python 2.6 64-bit so
# we force the conversion to object type columns.
for name in self.names:
dtype = self.columns[name].dtype
column_type = smart_dtype(dtype)
# Add data to the table
# At the moment, null values in VO table are dealt with via a
# 'mask' record array
if column_type == np.string_:
table.array[name] = self.data[name]
if self._masked:
table.mask[name] = self.data[name].mask.astype(np.object_)
else:
table.mask[name] = (self.data[name] == \
self.columns[name].null).astype(np.object_)
else:
table.array[name] = self.data[name]
if self._masked:
table.mask[name] = self.data[name].mask
else:
table.mask[name] = self.data[name] == \
self.columns[name].null
table.name = self.table_name
return table
def _to_hdu(self):
'''
Return the current table as a pyfits HDU object
'''
columns = []
for name in self.names:
if self._masked:
data = self.data[name].filled()
null = self.data[name].fill_value
if data.ndim > 1:
null = null[0]
if type(null) in [np.bool_, np.bool]:
null = bool(null)
else:
data = self.data[name]
null = self.columns[name].null
unit = self.columns[name].unit
dtype = self.columns[name].dtype
elemwidth = None
if unit == None:
unit = ''
if data.ndim > 1:
elemwidth = str(data.shape[1])
column_type = smart_dtype(dtype)
if column_type == np.string_:
elemwidth = dtype.itemsize
if column_type in type_dict:
if elemwidth:
format = str(elemwidth) + type_dict[column_type]
else:
format = type_dict[column_type]
else:
raise Exception("cannot use numpy type " + str(column_type))
if column_type == np.uint16:
bzero = - np.iinfo(np.int16).min
elif column_type == np.uint32:
bzero = - np.iinfo(np.int32).min
elif column_type == np.uint64:
raise Exception("uint64 unsupported")
elif column_type == np.int8:
bzero = -128
else:
bzero = None
columns.append(pyfits.Column(name=name, format=format, unit=unit, \
null=null, array=data, bzero=bzero))
hdu = pyfits.new_table(pyfits.ColDefs(columns))
hdu.name = self.table_name
for key in self.keywords:
if len(key) > 8:
keyname = "hierarch " + key
else:
keyname = key
hdu.header.update(keyname, self.keywords[key])
for comment in self.comments:
hdu.header.add_comment(comment)
return hdu