def write_file(self,
obj=None,
filename=None,
return_path=False,
clean=False,
target=None):
'''
Write the target object to a file using the given neo io object ioobj.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the object. return obj, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If target is None, use the first supported_objects from ioobj
If target is False, use the 'read' method.
If target is the Block or Segment class, use read_block or
read_segment, respectively.
If target is a string, use 'read_'+target.
obj is the object to write. If obj is None, an object is created
automatically for the io class.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True,
clean=clean)
obj = write_generic(ioobj, target=target, return_reader=False)
if return_path:
return obj, path
return obj
def write_file(self, obj=None, filename=None, return_path=False,
clean=False, target=None):
'''
Write the target object to a file using the given neo io object ioobj.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the object. return obj, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If target is None, use the first supported_objects from ioobj
If target is False, use the 'read' method.
If target is the Block or Segment class, use read_block or
read_segment, respectively.
If target is a string, use 'read_'+target.
obj is the object to write. If obj is None, an object is created
automatically for the io class.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True, clean=clean)
obj = write_generic(ioobj, target=target, return_reader=False)
if return_path:
return obj, path
return obj
def generate_files_for_io_able_to_write(self):
'''
Write files for use in testing.
'''
self.files_generated = []
if not self.able_to_write_or_read():
return
generate_from_supported_objects(self.ioclass.supported_objects)
ioobj, path = self.generic_io_object(return_path=True, clean=True)
if ioobj is None:
return
self.files_generated.append(path)
write_generic(ioobj, target=self.higher)
close_object_safe(ioobj)
def generate_files_for_io_able_to_write(self):
'''
Write files for use in testing.
'''
self.files_generated = []
if not self.able_to_write_or_read():
return
generate_from_supported_objects(self.ioclass.supported_objects)
ioobj, path = self.generic_io_object(return_path=True, clean=True)
if ioobj is None:
return
self.files_generated.append(path)
write_generic(ioobj, target=self.higher)
close_object_safe(ioobj)
def test_write_then_read(self):
'''
Test for IO that are able to write and read - here %s:
1 - Generate a full schema with supported objects.
2 - Write to a file
3 - Read from the file
4 - Check the hierachy
5 - Check data
Work only for IO for Block and Segment for the highest object
(main cases).
''' % self.ioclass.__name__
if not self.able_to_write_or_read(writeread=True):
return
for cascade in self.cascade_modes:
ioobj1 = self.generic_io_object(clean=True)
if ioobj1 is None:
return
ob1 = write_generic(ioobj1, target=self.higher)
close_object_safe(ioobj1)
ioobj2 = self.generic_io_object()
# Read the highest supported object from the file
obj_reader = create_generic_reader(ioobj2, target=False)
ob2 = obj_reader(cascade=cascade)[0]
if self.higher == Segment:
ob2 = ob2.segments[0]
# some formats (e.g. elphy) do not support double floating
# point spiketrains
try:
assert_same_sub_schema(ob1, ob2, True, 1e-8)
assert_neo_object_is_compliant(ob1)
assert_neo_object_is_compliant(ob2)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('with cascade=%s ' % cascade, )
raise
close_object_safe(ioobj2)
def test_write_then_read(self):
'''
Test for IO that are able to write and read - here %s:
1 - Generate a full schema with supported objects.
2 - Write to a file
3 - Read from the file
4 - Check the hierachy
5 - Check data
Work only for IO for Block and Segment for the highest object
(main cases).
''' % self.ioclass.__name__
if not self.able_to_write_or_read(writeread=True):
return
for cascade in self.cascade_modes:
ioobj1 = self.generic_io_object(clean=True)
if ioobj1 is None:
return
ob1 = write_generic(ioobj1, target=self.higher)
close_object_safe(ioobj1)
ioobj2 = self.generic_io_object()
# Read the highest supported object from the file
obj_reader = create_generic_reader(ioobj2, target=False)
ob2 = obj_reader(cascade=cascade)[0]
if self.higher == Segment:
ob2 = ob2.segments[0]
# some formats (e.g. elphy) do not support double floating
# point spiketrains
try:
assert_same_sub_schema(ob1, ob2, True, 1e-8)
assert_neo_object_is_compliant(ob1)
assert_neo_object_is_compliant(ob2)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('with cascade=%s ' % cascade,)
raise
close_object_safe(ioobj2)