def test_nwb_extractor(self):
path1 = self.test_dir + '/test.nwb'
se.NwbRecordingExtractor.write_recording(self.RX, path1)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
del RX_nwb
se.NwbRecordingExtractor.write_recording(recording=self.RX, save_path=path1, overwrite=True)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
# append sorting to existing file
se.NwbSortingExtractor.write_sorting(sorting=self.SX, save_path=path1, overwrite=False)
path2 = self.test_dir + "/firings_true.nwb"
se.NwbRecordingExtractor.write_recording(recording=self.RX, save_path=path2)
se.NwbSortingExtractor.write_sorting(sorting=self.SX, save_path=path2)
SX_nwb = se.NwbSortingExtractor(path2)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling unit property descriptions argument
property_descriptions = dict(stability="This is a description of stability.")
se.NwbRecordingExtractor.write_recording(recording=self.RX, save_path=path1, overwrite=True)
se.NwbSortingExtractor.write_sorting(
sorting=self.SX,
save_path=path1,
property_descriptions=property_descriptions
)
SX_nwb = se.NwbSortingExtractor(path1)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling skip_properties argument
se.NwbRecordingExtractor.write_recording(recording=self.RX, save_path=path1, overwrite=True)
se.NwbSortingExtractor.write_sorting(
sorting=self.SX,
save_path=path1,
skip_properties=['stability']
)
SX_nwb = se.NwbSortingExtractor(path1)
assert 'stability' not in SX_nwb.get_shared_unit_property_names()
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling skip_features argument
se.NwbRecordingExtractor.write_recording(recording=self.RX, save_path=path1, overwrite=True)
se.NwbSortingExtractor.write_sorting(
sorting=self.SX2,
save_path=path1,
skip_features=['widths']
)
SX_nwb = se.NwbSortingExtractor(path1)
assert 'widths' not in SX_nwb.get_shared_unit_spike_feature_names()
check_sortings_equal(self.SX2, SX_nwb)
check_dumping(SX_nwb)
def test_write_sorting(self):
path = self.test_dir + '/test.nwb'
sf = self.RX.get_sampling_frequency()
# Append sorting to existing file
write_recording(recording=self.RX, save_path=path, overwrite=True)
write_sorting(sorting=self.SX, save_path=path, overwrite=False)
SX_nwb = se.NwbSortingExtractor(path)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling unit property descriptions argument
property_descriptions = dict(stability="This is a description of stability.")
write_sorting(
sorting=self.SX,
save_path=path,
property_descriptions=property_descriptions,
overwrite=True
)
SX_nwb = se.NwbSortingExtractor(path, sampling_frequency=sf)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling skip_properties argument
write_sorting(
sorting=self.SX,
save_path=path,
skip_properties=['stability'],
overwrite=True
)
SX_nwb = se.NwbSortingExtractor(path, sampling_frequency=sf)
assert 'stability' not in SX_nwb.get_shared_unit_property_names()
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling skip_features argument
# SX2 has timestamps, so loading it back from Nwb will not recover the same spike frames. Set use_times=False
write_sorting(
sorting=self.SX2,
save_path=path,
skip_features=['widths'],
use_times=False,
overwrite=True
)
SX_nwb = se.NwbSortingExtractor(path, sampling_frequency=sf)
assert 'widths' not in SX_nwb.get_shared_unit_spike_feature_names()
check_sortings_equal(self.SX2, SX_nwb)
check_dumping(SX_nwb)
def test_nwb_extractor(self):
path1 = self.test_dir + '/test.nwb'
se.NwbRecordingExtractor.write_recording(self.RX, path1)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
del RX_nwb
# overwrite
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path1,
overwrite=True)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
# add sorting to existing
se.NwbSortingExtractor.write_sorting(sorting=self.SX, save_path=path1)
# create new
path2 = self.test_dir + '/firings_true.nwb'
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path2)
se.NwbSortingExtractor.write_sorting(sorting=self.SX, save_path=path2)
SX_nwb = se.NwbSortingExtractor(path2)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling unit property descriptions argument
property_descriptions = {
'stability': 'this is a description of stability'
}
se.NwbSortingExtractor.write_sorting(
sorting=self.SX,
save_path=path1,
property_descriptions=property_descriptions)
# create new
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path2,
overwrite=True)
se.NwbSortingExtractor.write_sorting(
sorting=self.SX,
save_path=path2,
property_descriptions=property_descriptions)
SX_nwb = se.NwbSortingExtractor(path2)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
def test_nwb_extractor(self):
path1 = self.test_dir + '/test.nwb'
se.NwbRecordingExtractor.write_recording(self.RX, path1)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
del RX_nwb
# overwrite
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path1)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
# add sorting to existing
se.NwbSortingExtractor.write_sorting(sorting=self.SX, save_path=path1)
# create new
path2 = self.test_dir + '/firings_true.nwb'
se.NwbSortingExtractor.write_sorting(sorting=self.SX, save_path=path2)
SX_nwb = se.NwbSortingExtractor(path1)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
def test_convert_sorting_extractor_to_nwb(self, se_class, dataset_path, se_kwargs):
print(f"\n\n\n TESTING {se_class.extractor_name}...")
dataset_stem = Path(dataset_path).stem
self.dataset.get(dataset_path)
sorting = se_class(**se_kwargs)
sf = sorting.get_sampling_frequency()
if sf is None: # need to set dummy sampling frequency since no associated acquisition in file
sf = 30000
sorting.set_sampling_frequency(sf)
if test_nwb:
nwb_save_path = self.savedir / f"{se_class.__name__}_test_{dataset_stem}.nwb"
se.NwbSortingExtractor.write_sorting(sorting, nwb_save_path)
nwb_sorting = se.NwbSortingExtractor(nwb_save_path, sampling_frequency=sf)
check_sortings_equal(sorting, nwb_sorting)
if test_caching:
sort_cache = se.CacheSortingExtractor(sorting)
check_sortings_equal(sorting, sort_cache)
def test_nwb_extractor(self):
path1 = self.test_dir + '/test.nwb'
se.NwbRecordingExtractor.write_recording(self.RX, path1)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
del RX_nwb
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path1,
overwrite=True)
RX_nwb = se.NwbRecordingExtractor(path1)
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
# append sorting to existing file
se.NwbSortingExtractor.write_sorting(sorting=self.SX,
save_path=path1,
overwrite=False)
path2 = self.test_dir + "/firings_true.nwb"
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path2)
se.NwbSortingExtractor.write_sorting(sorting=self.SX, save_path=path2)
SX_nwb = se.NwbSortingExtractor(path2)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling unit property descriptions argument
property_descriptions = dict(
stability="This is a description of stability.")
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path1,
overwrite=True)
se.NwbSortingExtractor.write_sorting(
sorting=self.SX,
save_path=path1,
property_descriptions=property_descriptions)
SX_nwb = se.NwbSortingExtractor(path1)
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling skip_properties argument
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path1,
overwrite=True)
se.NwbSortingExtractor.write_sorting(sorting=self.SX,
save_path=path1,
skip_properties=['stability'])
SX_nwb = se.NwbSortingExtractor(path1)
assert 'stability' not in SX_nwb.get_shared_unit_property_names()
check_sortings_equal(self.SX, SX_nwb)
check_dumping(SX_nwb)
# Test for handling skip_features argument
se.NwbRecordingExtractor.write_recording(recording=self.RX,
save_path=path1,
overwrite=True)
# SX2 has timestamps, so loading it back from Nwb will not recover the same spike frames. USe use_times=False
se.NwbSortingExtractor.write_sorting(sorting=self.SX2,
save_path=path1,
skip_features=['widths'],
use_times=False)
SX_nwb = se.NwbSortingExtractor(path1)
assert 'widths' not in SX_nwb.get_shared_unit_spike_feature_names()
check_sortings_equal(self.SX2, SX_nwb)
check_dumping(SX_nwb)
# Test writting multiple recordings using metadata
metadata = get_default_nwbfile_metadata()
path_nwb = self.test_dir + '/test_multiple.nwb'
se.NwbRecordingExtractor.write_recording(
recording=self.RX,
save_path=path_nwb,
metadata=metadata,
write_as='raw',
es_key='ElectricalSeries_raw',
)
se.NwbRecordingExtractor.write_recording(
recording=self.RX2,
save_path=path_nwb,
metadata=metadata,
write_as='processed',
es_key='ElectricalSeries_processed',
)
se.NwbRecordingExtractor.write_recording(
recording=self.RX3,
save_path=path_nwb,
metadata=metadata,
write_as='lfp',
es_key='ElectricalSeries_lfp',
)
RX_nwb = se.NwbRecordingExtractor(file_path=path_nwb,
electrical_series_name='raw_traces')
check_recording_return_types(RX_nwb)
check_recordings_equal(self.RX, RX_nwb)
check_dumping(RX_nwb)
del RX_nwb
