def test_spykingcircus_extractor(self): path1 = self.test_dir + '/sc' se.SpykingCircusSortingExtractor.write_sorting(self.SX, path1) SX_spy = se.SpykingCircusSortingExtractor(path1) check_sorting_return_types(SX_spy) check_sortings_equal(self.SX, SX_spy) check_dumping(SX_spy)
def test_cache_extractor(self): cache_rec = se.CacheRecordingExtractor(self.RX) check_recording_return_types(cache_rec) check_recordings_equal(self.RX, cache_rec) cache_rec.move_to('cache_rec') assert cache_rec.filename == 'cache_rec.dat' check_dumping(cache_rec, test_relative=True) cache_rec = se.CacheRecordingExtractor(self.RX, save_path='cache_rec2') check_recording_return_types(cache_rec) check_recordings_equal(self.RX, cache_rec) assert cache_rec.filename == 'cache_rec2.dat' check_dumping(cache_rec, test_relative=True) # test saving to file del cache_rec assert Path('cache_rec2.dat').is_file() # test tmp cache_rec = se.CacheRecordingExtractor(self.RX) tmp_file = cache_rec.filename del cache_rec assert not Path(tmp_file).is_file() cache_sort = se.CacheSortingExtractor(self.SX) check_sorting_return_types(cache_sort) check_sortings_equal(self.SX, cache_sort) cache_sort.move_to('cache_sort') assert cache_sort.filename == 'cache_sort.npz' check_dumping(cache_sort, test_relative=True) # test saving to file del cache_sort assert Path('cache_sort.npz').is_file() cache_sort = se.CacheSortingExtractor(self.SX, save_path='cache_sort2') check_sorting_return_types(cache_sort) check_sortings_equal(self.SX, cache_sort) assert cache_sort.filename == 'cache_sort2.npz' check_dumping(cache_sort, test_relative=True) # test saving to file del cache_sort assert Path('cache_sort2.npz').is_file() # test tmp cache_sort = se.CacheSortingExtractor(self.SX) tmp_file = cache_sort.filename del cache_sort assert not Path(tmp_file).is_file() # cleanup os.remove('cache_rec.dat') os.remove('cache_rec2.dat') os.remove('cache_sort.npz') os.remove('cache_sort2.npz')
def test_hs2_extractor(self): path1 = self.test_dir + '/firings_true.hdf5' se.HS2SortingExtractor.write_sorting(self.SX, path1) SX_hs2 = se.HS2SortingExtractor(path1) check_sorting_return_types(SX_hs2) check_sortings_equal(self.SX, SX_hs2) self.assertEqual(SX_hs2.get_sampling_frequency(), self.SX.get_sampling_frequency()) check_dumping(SX_hs2)
def test_cell_explorer_extractor(self): sorter_id = "cell_explorer_sorter" cell_explorer_dir = Path(self.test_dir) / sorter_id spikes_matfile_path = cell_explorer_dir / f"{sorter_id}.spikes.cellinfo.mat" se.CellExplorerSortingExtractor.write_sorting( sorting=self.SX, save_path=spikes_matfile_path) SX_cell_explorer = se.CellExplorerSortingExtractor( spikes_matfile_path=spikes_matfile_path) check_sorting_return_types(SX_cell_explorer) check_sortings_equal(self.SX, SX_cell_explorer) check_dumping(SX_cell_explorer)
def test_hdsort_extractor(self): path = self.test_dir + '/results_test_hdsort_extractor.mat' locations = np.ones((10, 2)) se.HDSortSortingExtractor.write_sorting(self.SX, path, locations=locations, noise_std_by_channel=None) SX_hd = se.HDSortSortingExtractor(path) check_sorting_return_types(SX_hd) check_sortings_equal(self.SX, SX_hd) check_dumping(SX_hd)
def test_npz_extractor(self): path = self.test_dir + '/sorting.npz' se.NpzSortingExtractor.write_sorting(self.SX, path) SX_npz = se.NpzSortingExtractor(path) # empty write sorting_empty = se.NumpySortingExtractor() path_empty = self.test_dir + '/sorting_empty.npz' se.NpzSortingExtractor.write_sorting(sorting_empty, path_empty) check_sorting_return_types(SX_npz) check_sortings_equal(self.SX, SX_npz) check_dumping(SX_npz)
def test_mda_extractor(self): path1 = self.test_dir + '/mda' path2 = path1 + '/firings_true.mda' se.MdaRecordingExtractor.write_recording(self.RX, path1) se.MdaSortingExtractor.write_sorting(self.SX, path2) RX_mda = se.MdaRecordingExtractor(path1) SX_mda = se.MdaSortingExtractor(path2) check_recording_return_types(RX_mda) check_recordings_equal(self.RX, RX_mda) check_sorting_return_types(SX_mda) check_sortings_equal(self.SX, SX_mda) check_dumping(RX_mda) check_dumping(SX_mda)
def test_exdir_extractors(self): path1 = self.test_dir + '/raw.exdir' se.ExdirRecordingExtractor.write_recording(self.RX, path1) RX_exdir = se.ExdirRecordingExtractor(path1) check_recording_return_types(RX_exdir) check_recordings_equal(self.RX, RX_exdir) check_dumping(RX_exdir) path2 = self.test_dir + '/firings.exdir' se.ExdirSortingExtractor.write_sorting(self.SX, path2, self.RX) SX_exdir = se.ExdirSortingExtractor(path2) check_sorting_return_types(SX_exdir) check_sortings_equal(self.SX, SX_exdir) check_dumping(SX_exdir)
def test_mearec_extractors(self): path1 = self.test_dir + '/raw.h5' se.MEArecRecordingExtractor.write_recording(self.RX, path1) RX_mearec = se.MEArecRecordingExtractor(path1) tr = RX_mearec.get_traces(channel_ids=[0, 1], end_frame=1000) check_recording_return_types(RX_mearec) check_recordings_equal(self.RX, RX_mearec) check_dumping(RX_mearec) path2 = self.test_dir + '/firings_true.h5' se.MEArecSortingExtractor.write_sorting( self.SX, path2, self.RX.get_sampling_frequency()) SX_mearec = se.MEArecSortingExtractor(path2) check_sorting_return_types(SX_mearec) check_sortings_equal(self.SX, SX_mearec) check_dumping(SX_mearec)
def test_shybrid_extractors(self): # test sorting extractor se.SHYBRIDSortingExtractor.write_sorting(self.SX, self.test_dir) initial_sorting_file = os.path.join(self.test_dir, 'initial_sorting.csv') SX_shybrid = se.SHYBRIDSortingExtractor(initial_sorting_file) check_sorting_return_types(SX_shybrid) check_sortings_equal(self.SX, SX_shybrid) check_dumping(SX_shybrid) # test recording extractor se.SHYBRIDRecordingExtractor.write_recording(self.RX, self.test_dir, initial_sorting_file) RX_shybrid = se.SHYBRIDRecordingExtractor( os.path.join(self.test_dir, 'recording.bin')) check_recording_return_types(RX_shybrid) check_recordings_equal(self.RX, RX_shybrid) check_dumping(RX_shybrid)
def test_nixio_extractor(self): path1 = os.path.join(self.test_dir, 'raw.nix') se.NIXIORecordingExtractor.write_recording(self.RX, path1) RX_nixio = se.NIXIORecordingExtractor(path1) check_recording_return_types(RX_nixio) check_recordings_equal(self.RX, RX_nixio) check_dumping(RX_nixio) del RX_nixio # test force overwrite se.NIXIORecordingExtractor.write_recording(self.RX, path1, overwrite=True) path2 = self.test_dir + '/firings_true.nix' se.NIXIOSortingExtractor.write_sorting(self.SX, path2) SX_nixio = se.NIXIOSortingExtractor(path2) check_sorting_return_types(SX_nixio) check_sortings_equal(self.SX, SX_nixio) check_dumping(SX_nixio)
def test_neuroscope_extractors(self): # NeuroscopeRecordingExtractor tests nscope_dir = Path(self.test_dir) / 'neuroscope_rec0' dat_file = nscope_dir / 'neuroscope_rec0.dat' se.NeuroscopeRecordingExtractor.write_recording(self.RX, nscope_dir) RX_ns = se.NeuroscopeRecordingExtractor(dat_file) check_recording_return_types(RX_ns) check_recordings_equal(self.RX, RX_ns, force_dtype='int32') check_dumping(RX_ns) check_recording_return_types(RX_ns) check_recordings_equal(self.RX, RX_ns, force_dtype='int32') check_dumping(RX_ns) del RX_ns # overwrite nscope_dir = Path(self.test_dir) / 'neuroscope_rec1' dat_file = nscope_dir / 'neuroscope_rec1.dat' se.NeuroscopeRecordingExtractor.write_recording(recording=self.RX, save_path=nscope_dir) RX_ns = se.NeuroscopeRecordingExtractor(dat_file) check_recording_return_types(RX_ns) check_recordings_equal(self.RX, RX_ns) check_dumping(RX_ns) # NeuroscopeMultiRecordingTimeExtractor tests nscope_dir = Path(self.test_dir) / "neuroscope_rec2" dat_file = nscope_dir / "neuroscope_rec2.dat" RX_multirecording = se.MultiRecordingTimeExtractor( recordings=[self.RX, self.RX]) se.NeuroscopeMultiRecordingTimeExtractor.write_recording( recording=RX_multirecording, save_path=nscope_dir) RX_mre = se.NeuroscopeMultiRecordingTimeExtractor( folder_path=nscope_dir) check_recording_return_types(RX_mre) check_recordings_equal(RX_multirecording, RX_mre) check_dumping(RX_mre) # NeuroscopeSortingExtractor tests nscope_dir = Path(self.test_dir) / 'neuroscope_sort0' sort_name = 'neuroscope_sort0' initial_sorting_resfile = Path( self.test_dir) / sort_name / f'{sort_name}.res' initial_sorting_clufile = Path( self.test_dir) / sort_name / f'{sort_name}.clu' se.NeuroscopeSortingExtractor.write_sorting(self.SX, nscope_dir) SX_neuroscope = se.NeuroscopeSortingExtractor( resfile_path=initial_sorting_resfile, clufile_path=initial_sorting_clufile) check_sorting_return_types(SX_neuroscope) check_sortings_equal(self.SX, SX_neuroscope) check_dumping(SX_neuroscope) SX_neuroscope_no_mua = se.NeuroscopeSortingExtractor( resfile_path=initial_sorting_resfile, clufile_path=initial_sorting_clufile, keep_mua_units=False) check_sorting_return_types(SX_neuroscope_no_mua) check_dumping(SX_neuroscope_no_mua) # Test for extra argument 'keep_mua_units' resulted in the right output SX_neuroscope_no_mua = se.NeuroscopeSortingExtractor( resfile_path=initial_sorting_resfile, clufile_path=initial_sorting_clufile, keep_mua_units=False) check_sorting_return_types(SX_neuroscope_no_mua) check_dumping(SX_neuroscope_no_mua) num_original_units = len(SX_neuroscope.get_unit_ids()) self.assertEqual(list(SX_neuroscope.get_unit_ids()), list(range(1, num_original_units + 1))) self.assertEqual(list(SX_neuroscope_no_mua.get_unit_ids()), list(range(1, num_original_units))) # Tests for the auto-detection of format for NeuroscopeSortingExtractor SX_neuroscope_from_fp = se.NeuroscopeSortingExtractor( folder_path=nscope_dir) check_sorting_return_types(SX_neuroscope_from_fp) check_sortings_equal(self.SX, SX_neuroscope_from_fp) check_dumping(SX_neuroscope_from_fp) # Tests for the NeuroscopeMultiSortingExtractor nscope_dir = Path(self.test_dir) / 'neuroscope_sort1' SX_multisorting = se.MultiSortingExtractor(sortings=[self.SX, self.SX]) se.NeuroscopeMultiSortingExtractor.write_sorting( SX_multisorting, nscope_dir) SX_neuroscope_mse = se.NeuroscopeMultiSortingExtractor(nscope_dir) check_sorting_return_types(SX_neuroscope_mse) check_sortings_equal(SX_multisorting, SX_neuroscope_mse) check_dumping(SX_neuroscope_mse)