class BaseTestRawIO:
'''
This class make common tests for all IOs.
Basically download files from G-node portal.
And test the IO is working.
'''
# ~ __test__ = False
# all IO test need to modify this:
rawioclass = None # the IOclass to be tested
files_to_test = [] # list of files to test compliances
files_to_download = [] # when files are at G-Node
# allow environment to tell avoid using network
use_network = can_use_network()
local_test_dir = None
def setUp(self):
'''
Set up the test fixture. This is run for every test
'''
self.shortname = self.rawioclass.__name__.lower().replace('rawio', '')
self.create_local_dir_if_not_exists()
self.download_test_files_if_not_present()
def create_local_dir_if_not_exists(self):
'''
Create a local directory to store testing files and return it.
The directory path is also written to self.local_test_dir
'''
self.local_test_dir = create_local_temp_dir(self.shortname)
return self.local_test_dir
def download_test_files_if_not_present(self):
'''
Download %s file at G-node for testing
url_for_tests is global at beginning of this file.
''' % self.rawioclass.__name__
if not self.use_network:
raise unittest.SkipTest("Requires download of data from the web")
url = url_for_tests + self.shortname
try:
make_all_directories(self.files_to_download, self.local_test_dir)
download_test_file(self.files_to_download, self.local_test_dir,
url)
except OSError as exc:
raise unittest.SkipTest(exc)
download_test_files_if_not_present.__test__ = False
def cleanup_file(self, path):
'''
Remove test files or directories safely.
'''
cleanup_test_file(self.rawioclass, path, directory=self.local_test_dir)
def get_filename_path(self, filename):
'''
Get the path to a filename in the current temporary file directory
'''
return os.path.join(self.local_test_dir, filename)
def test_read_all(self):
# Read all file in self.entities_to_test
for entity_name in self.entities_to_test:
entity_name = self.get_filename_path(entity_name)
if self.rawioclass.rawmode.endswith('-file'):
reader = self.rawioclass(filename=entity_name)
elif self.rawioclass.rawmode.endswith('-dir'):
reader = self.rawioclass(dirname=entity_name)
txt = reader.__repr__()
assert 'nb_block' not in txt, 'Before parser_header() nb_block should be NOT known'
reader.parse_header()
txt = reader.__repr__()
assert 'nb_block' in txt, 'After parser_header() nb_block should be known'
# ~ print(txt)
#
txt = reader._repr_annotations()
# ~ reader.print_annotations()
# ~ sigs = reader.get_analogsignal_chunk(block_index=0, seg_index=0,
# ~ i_start=None, i_stop=None, channel_indexes=[1])
# ~ import matplotlib.pyplot as plt
# ~ fig, ax = plt.subplots()
# ~ ax.plot(sigs[:, 0])
# ~ plt.show()
# ~ nb_unit = reader.unit_channels_count()
# ~ for unit_index in range(nb_unit):
# ~ wfs = reader.spike_raw_waveforms(block_index=0, seg_index=0,
# ~ unit_index=unit_index)
# ~ if wfs is not None:
# ~ import matplotlib.pyplot as plt
# ~ fig, ax = plt.subplots()
# ~ ax.plot(wfs[:, 0, :50].T)
# ~ plt.show()
# lanch a series of test compliance
compliance.header_is_total(reader)
compliance.count_element(reader)
compliance.read_analogsignals(reader)
compliance.read_spike_times(reader)
compliance.read_spike_waveforms(reader)
compliance.read_events(reader)
compliance.has_annotations(reader)
# basic benchmark
level = logging.getLogger().getEffectiveLevel()
logging.getLogger().setLevel(logging.INFO)
compliance.benchmark_speed_read_signals(reader)
logging.getLogger().setLevel(level)
class BaseTestIO:
'''
This class make common tests for all IOs.
Several startegies:
* for IO able to read write : test_write_then_read
* for IO able to read write with hash conservation (optional):
test_read_then_write
* for all IOs : test_assert_readed_neo_object_is_compliant
2 cases:
* files are at G-node and downloaded:
download_test_files_if_not_present
* files are generated by MyIO.write()
'''
# ~ __test__ = False
# all IO test need to modify this:
ioclass = None # the IOclass to be tested
files_to_test = [] # list of files to test compliances
files_to_download = [] # when files are at G-Node
# when reading then writing produces files with identical hashes
hash_conserved_when_write_read = False
# when writing then reading creates an identical neo object
read_and_write_is_bijective = True
# allow environment to tell avoid using network
use_network = can_use_network()
local_test_dir = None
def setUp(self):
'''
Set up the test fixture. This is run for every test
'''
self.files_to_test = copy(self.__class__.files_to_test)
self.higher = self.ioclass.supported_objects[0]
self.shortname = self.ioclass.__name__.lower().rstrip('io')
# these objects can both be written and read
self.io_readandwrite = list(
set(self.ioclass.readable_objects)
& set(self.ioclass.writeable_objects))
# these objects can be either written or read
self.io_readorwrite = list(
set(self.ioclass.readable_objects)
| set(self.ioclass.writeable_objects))
self.create_local_dir_if_not_exists()
self.download_test_files_if_not_present()
self.files_generated = []
self.generate_files_for_io_able_to_write()
self.files_to_test.extend(self.files_generated)
def create_local_dir_if_not_exists(self):
'''
Create a local directory to store testing files and return it.
The directory path is also written to self.local_test_dir
'''
self.local_test_dir = create_local_temp_dir(self.shortname,
directory=os.environ.get(
"NEO_TEST_FILE_DIR",
None))
return self.local_test_dir
def download_test_files_if_not_present(self):
'''
Download %s file at G-node for testing
url_for_tests is global at beginning of this file.
''' % self.ioclass.__name__
if not self.use_network:
raise unittest.SkipTest("Requires download of data from the web")
url = url_for_tests + self.shortname
try:
make_all_directories(self.files_to_download, self.local_test_dir)
download_test_file(self.files_to_download, self.local_test_dir,
url)
except OSError as exc:
raise unittest.TestCase.failureException(exc)
download_test_files_if_not_present.__test__ = False
def cleanup_file(self, path):
'''
Remove test files or directories safely.
'''
cleanup_test_file(self.ioclass, path, directory=self.local_test_dir)
def able_to_write_or_read(self, writeread=False, readwrite=False):
'''
Return True if generalized writing or reading is possible.
If writeread=True, return True if writing then reading is
possible and produces identical neo objects.
If readwrite=True, return True if reading then writing is possible
and produces files with identical hashes.
'''
# Find the highest object that is supported by the IO
# Test only if it is a Block or Segment, and if it can both read
# and write this object.
if self.higher not in self.io_readandwrite:
return False
if self.higher not in [Block, Segment]:
return False
# when io need external knowldge for writting or read such as
# sampling_rate (RawBinaryIO...) the test is too much complex to design
# genericaly.
if (self.higher in self.ioclass.read_params
and len(self.ioclass.read_params[self.higher]) != 0):
return False
# handle cases where the test should write then read
if writeread and not self.read_and_write_is_bijective:
return False
# handle cases where the test should read then write
if readwrite and not self.hash_conserved_when_write_read:
return False
return True
def get_filename_path(self, filename):
'''
Get the path to a filename in the current temporary file directory
'''
return os.path.join(self.local_test_dir, filename)
def generic_io_object(self, filename=None, return_path=False, clean=False):
'''
Create an io object in a generic way that can work with both
file-based and directory-based io objects.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the io object. return ioobj, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
'''
return create_generic_io_object(ioclass=self.ioclass,
filename=filename,
directory=self.local_test_dir,
return_path=return_path,
clean=clean)
def create_file_reader(self,
filename=None,
return_path=False,
clean=False,
target=None,
readall=False):
'''
Create a function that can read from the specified filename.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the reader function. return reader, 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.
If readall is True, use the read_all_ method instead of the read_
method. Default is False.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True,
clean=clean)
res = create_generic_reader(ioobj, target=target, readall=readall)
if return_path:
return res, path
return res
def create_file_writer(self,
filename=None,
return_path=False,
clean=False,
target=None):
'''
Create a function that can write from the specified filename.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the writer function. return writer, 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 'write' method.
If target is the Block or Segment class, use write_block or
write_segment, respectively.
If target is a string, use 'write_'+target.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True,
clean=clean)
res = create_generic_writer(ioobj, target=target)
if return_path:
return res, path
return res
def read_file(self,
filename=None,
return_path=False,
clean=False,
target=None,
readall=False,
lazy=False):
'''
Read from the specified filename.
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.
The lazy parameter is passed to the reader. Defaults is True.
If readall is True, use the read_all_ method instead of the read_
method. Default is False.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True,
clean=clean)
obj = read_generic(ioobj,
target=target,
lazy=lazy,
readall=readall,
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 iter_io_objects(self, return_path=False, clean=False):
'''
Return an iterable over the io objects created from files_to_test
If return_path is True, yield the full path of the file along with
the io object. yield ioobj, path Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
'''
return iter_generic_io_objects(ioclass=self.ioclass,
filenames=self.files_to_test,
directory=self.local_test_dir,
return_path=return_path,
clean=clean)
def iter_readers(self,
target=None,
readall=False,
return_path=False,
return_ioobj=False,
clean=False):
'''
Return an iterable over readers created from files_to_test.
If return_path is True, return the full path of the file along with
the reader object. return reader, path.
If return_ioobj is True, return the io object as well as the reader.
return reader, ioobj. Default is False.
If both return_path and return_ioobj is True,
return reader, path, ioobj. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If readall is True, use the read_all_ method instead of the
read_ method. Default is False.
'''
return iter_generic_readers(ioclass=self.ioclass,
filenames=self.files_to_test,
directory=self.local_test_dir,
return_path=return_path,
return_ioobj=return_ioobj,
target=target,
clean=clean,
readall=readall)
def iter_objects(self,
target=None,
return_path=False,
return_ioobj=False,
return_reader=False,
clean=False,
readall=False,
lazy=False):
'''
Iterate over objects read from the list of filenames in files_to_test.
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.
If return_path is True, yield the full path of the file along with
the object. yield obj, path.
If return_ioobj is True, yield the io object as well as the object.
yield obj, ioobj. Default is False.
If return_reader is True, yield the io reader function as well as the
object. yield obj, reader. Default is False.
If some combination of return_path, return_ioobj, and return_reader
is True, they are yielded in the order: obj, path, ioobj, reader.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
The lazy parameters is passed to the reader. Defaults is True.
If readall is True, use the read_all_ method instead of the read_
method. Default is False.
'''
return iter_read_objects(ioclass=self.ioclass,
filenames=self.files_to_test,
directory=self.local_test_dir,
target=target,
return_path=return_path,
return_ioobj=return_ioobj,
return_reader=return_reader,
clean=clean,
readall=readall,
lazy=lazy)
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
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()[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:
raise
close_object_safe(ioobj2)
def test_read_then_write(self):
'''
Test for IO that are able to read and write, here %s:
1 - Read a file
2 Write object set in another file
3 Compare the 2 files hash
NOTE: TODO: Not implemented yet
''' % self.ioclass.__name__
if not self.able_to_write_or_read(readwrite=True):
return
# assert_file_contents_equal(a, b)
def test_assert_readed_neo_object_is_compliant(self):
'''
Reading %s files in `files_to_test` produces compliant objects.
Compliance test: neo.test.tools.assert_neo_object_is_compliant for
lazy mode.
''' % self.ioclass.__name__
for obj, path in self.iter_objects(lazy=False, return_path=True):
try:
# Check compliance of the block
assert_neo_object_is_compliant(obj)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s' % os.path.basename(path), )
raise
def test_readed_with_lazy_is_compliant(self):
'''
Reading %s files in `files_to_test` with `lazy` is compliant.
Test the reader with lazy = True.
The schema must contain proxy objects.
''' % self.ioclass.__name__
# This is for files presents at G-Node or generated
if self.ioclass.support_lazy:
for obj, path in self.iter_objects(lazy=True, return_path=True):
try:
assert_sub_schema_is_lazy_loaded(obj)
# intercept exceptions and add more information
except BaseException as exc:
raise
class BaseTestRawIO:
'''
This class make common tests for all IOs.
Basically download files from G-node portal.
And test the IO is working.
'''
# ~ __test__ = False
# all IO test need to modify this:
rawioclass = None # the IOclass to be tested
entities_to_test = [] # list of files to test compliances
entities_to_download = [] # when files are at gin
# allow environment to tell avoid using network
use_network = can_use_network()
local_test_dir = get_local_testing_data_folder()
def setUp(self):
'''
Set up the test fixture. This is run for every test
'''
self.shortname = self.rawioclass.__name__.lower().replace('rawio', '')
if HAVE_DATALAD:
for remote_path in self.entities_to_download:
download_dataset(repo=repo_for_test, remote_path=remote_path)
else:
raise unittest.SkipTest(
"Requires datalad download of data from the web")
def get_local_base_folder(self):
return get_local_testing_data_folder()
def get_local_path(self, sub_path):
root_local_path = self.get_local_base_folder()
local_path = root_local_path / sub_path
# TODO later : remove the str when all IOs handle the pathlib.Path objects
local_path = str(local_path)
return local_path
def test_read_all(self):
# Read all file in self.entities_to_test
if not HAVE_DATALAD:
return
for entity_name in self.entities_to_test:
# entity_name = self.get_filename_path(entity_name)
# local path is a folder or a file
local_path = self.get_local_path(entity_name)
if self.rawioclass.rawmode.endswith('-file'):
reader = self.rawioclass(filename=local_path)
elif self.rawioclass.rawmode.endswith('-dir'):
reader = self.rawioclass(dirname=local_path)
txt = reader.__repr__()
assert 'nb_block' not in txt, 'Before parser_header() nb_block should be NOT known'
reader.parse_header()
txt = reader.__repr__()
assert 'nb_block' in txt, 'After parser_header() nb_block should be known'
# print(txt)
#
txt = reader._repr_annotations()
# reader.print_annotations()
# lanch a series of test compliance
compliance.header_is_total(reader)
compliance.count_element(reader)
compliance.read_analogsignals(reader)
compliance.read_spike_times(reader)
compliance.read_spike_waveforms(reader)
compliance.read_events(reader)
compliance.has_annotations(reader)
# basic benchmark
level = logging.getLogger().getEffectiveLevel()
logging.getLogger().setLevel(logging.INFO)
compliance.benchmark_speed_read_signals(reader)
logging.getLogger().setLevel(level)