def test_remove_bad_channels():
rec, sort = se.example_datasets.toy_example(dump_folder='test', dumpable=True, duration=2, num_channels=4, seed=0)
rec_rm = remove_bad_channels(rec, bad_channel_ids=[0])
assert 0 not in rec_rm.get_channel_ids()
rec_rm = remove_bad_channels(rec, bad_channel_ids=[1, 2])
assert 1 not in rec_rm.get_channel_ids() and 2 not in rec_rm.get_channel_ids()
check_dumping(rec_rm)
shutil.rmtree('test')
timeseries = np.random.randn(4, 60000)
timeseries[1] = 10 * timeseries[1]
rec_np = se.NumpyRecordingExtractor(timeseries=timeseries, sampling_frequency=30000)
rec_np.set_channel_locations(np.ones((rec_np.get_num_channels(), 2)))
se.MdaRecordingExtractor.write_recording(rec_np, 'test')
rec = se.MdaRecordingExtractor('test')
rec_rm = remove_bad_channels(rec, bad_channel_ids=None, bad_threshold=2)
assert 1 not in rec_rm.get_channel_ids()
check_dumping(rec_rm)
rec_rm = remove_bad_channels(rec, bad_channel_ids=None, bad_threshold=2, seconds=0.1)
assert 1 not in rec_rm.get_channel_ids()
check_dumping(rec_rm)
rec_rm = remove_bad_channels(rec, bad_channel_ids=None, bad_threshold=2, seconds=10)
assert 1 not in rec_rm.get_channel_ids()
check_dumping(rec_rm)
shutil.rmtree('test')
def test_remove_bad_channels():
rec, sort = se.example_datasets.toy_example(duration=10, num_channels=4)
rec_rm = remove_bad_channels(rec, bad_channel_ids=[0])
assert 0 not in rec_rm.get_channel_ids()
rec_rm = remove_bad_channels(rec, bad_channel_ids=[1, 2])
assert 1 not in rec_rm.get_channel_ids(
) and 2 not in rec_rm.get_channel_ids()
timeseries = np.random.randn(4, 60000)
timeseries[1] = 3 * timeseries[1]
rec_np = se.NumpyRecordingExtractor(timeseries=timeseries,
sampling_frequency=30000)
rec_rm = remove_bad_channels(rec_np, bad_channel_ids=None, bad_threshold=2)
assert 1 not in rec_rm.get_channel_ids()
rec_rm = remove_bad_channels(rec_np,
bad_channel_ids=None,
bad_threshold=2,
seconds=0.1)
assert 1 not in rec_rm.get_channel_ids()
rec_rm = remove_bad_channels(rec_np,
bad_channel_ids=None,
bad_threshold=2,
seconds=10)
assert 1 not in rec_rm.get_channel_ids()
def test_export_to_phy():
folder = 'test'
if os.path.isdir(folder):
shutil.rmtree(folder)
rec, sort = se.example_datasets.toy_example(dump_folder=folder,
dumpable=True,
duration=10,
num_channels=8)
export_to_phy(rec, sort, output_folder='phy')
rec.set_channel_groups([0, 0, 0, 0, 1, 1, 1, 1])
export_to_phy(rec,
sort,
output_folder='phy_group',
grouping_property='group',
recompute_info=True)
export_to_phy(rec,
sort,
output_folder='phy_max_channels',
max_channels_per_template=4,
recompute_info=True)
export_to_phy(rec,
sort,
output_folder='phy_no_feat',
grouping_property='group',
compute_pc_features=False,
recompute_info=True)
export_to_phy(rec,
sort,
output_folder='phy_no_amp',
compute_amplitudes=False)
export_to_phy(rec,
sort,
output_folder='phy_no_amp_feat',
compute_amplitudes=False,
compute_pc_features=False)
export_to_phy(rec, sort, output_folder='phy_par', n_jobs=2)
rec_phy = se.PhyRecordingExtractor('phy')
rec_phyg = se.PhyRecordingExtractor('phy_group')
assert np.allclose(rec.get_traces(), rec_phy.get_traces())
assert np.allclose(rec.get_traces(), rec_phyg.get_traces())
assert not (Path('phy_no_feat') / 'pc_features.npy').is_file()
assert not (Path('phy_no_feat') / 'pc_feature_ind.npy').is_file()
assert not (Path('phy_no_amp') / 'amplitudes.npy').is_file()
assert not (Path('phy_no_amp_feat') / 'amplitudes.npy').is_file()
assert not (Path('phy_no_amp_feat') / 'pc_features.npy').is_file()
assert not (Path('phy_no_amp_feat') / 'pc_feature_ind.npy').is_file()
sort_phy = se.PhySortingExtractor('phy', load_waveforms=True)
sort_phyg = se.PhySortingExtractor('phy_group', load_waveforms=True)
assert np.allclose(sort_phy.get_unit_spike_train(0),
sort.get_unit_spike_train(sort.get_unit_ids()[0]))
assert np.allclose(sort_phyg.get_unit_spike_train(2),
sort.get_unit_spike_train(sort.get_unit_ids()[2]))
assert sort_phy.get_unit_spike_features(1, 'waveforms').shape[1] == 8
assert sort_phyg.get_unit_spike_features(3, 'waveforms').shape[1] == 4
rec.set_channel_groups([0, 0, 0, 0, 1, 1, 1, 1])
recrm = remove_bad_channels(rec, [1, 2, 5])
export_to_phy(recrm,
sort,
output_folder='phy_rm',
grouping_property='group',
recompute_info=True,
verbose=True)
templates_ind = np.load('phy_rm/template_ind.npy')
assert len(np.where(templates_ind == -1)[0]) > 0 # removed channels are -1
try:
shutil.rmtree('test')
shutil.rmtree('phy')
shutil.rmtree('phy_group')
shutil.rmtree('phy_max_channels')
shutil.rmtree('phy_no_feat')
shutil.rmtree('phy_no_amp')
shutil.rmtree('phy_no_amp_feat')
shutil.rmtree('phy_rm')
shutil.rmtree('phy_par')
except:
print("Could not delete some test folders")