def test_common_reference():
rec, sort = se.example_datasets.toy_example(duration=10, num_channels=4)
# no groups
rec_cmr = common_reference(rec, reference='median')
rec_car = common_reference(rec, reference='average')
rec_sin = common_reference(rec, reference='single', ref_channels=0)
rec_cmr_int16 = common_reference(rec, dtype='int16')
traces = rec.get_traces()
assert np.allclose(
traces,
rec_cmr.get_traces() + np.median(traces, axis=0, keepdims=True))
assert np.allclose(
traces,
rec_car.get_traces() + np.mean(traces, axis=0, keepdims=True))
assert not np.all(rec_sin.get_traces()[0])
assert np.allclose(rec_sin.get_traces()[1], traces[1] - traces[0])
assert 'int16' in str(rec_cmr_int16.get_dtype())
# test groups
groups = [[0, 1], [2, 3]]
rec_cmr_g = common_reference(rec, reference='median', groups=groups)
rec_car_g = common_reference(rec, reference='average', groups=groups)
rec_sin_g = common_reference(rec,
reference='single',
ref_channels=[0, 2],
groups=groups)
rec_cmr_int16_g = common_reference(rec, groups=groups, dtype='int16')
traces = rec.get_traces()
assert np.allclose(
traces[:2],
rec_cmr_g.get_traces()[:2] +
np.median(traces[:2], axis=0, keepdims=True))
assert np.allclose(
traces[2:],
rec_cmr_g.get_traces()[2:] +
np.median(traces[2:], axis=0, keepdims=True))
assert np.allclose(
traces[:2],
rec_car_g.get_traces()[:2] +
np.mean(traces[:2], axis=0, keepdims=True))
assert np.allclose(
traces[2:],
rec_car_g.get_traces()[2:] +
np.mean(traces[2:], axis=0, keepdims=True))
assert not np.all(rec_sin_g.get_traces()[0])
assert np.allclose(rec_sin_g.get_traces()[1], traces[1] - traces[0])
assert not np.all(rec_sin_g.get_traces()[2])
assert np.allclose(rec_sin_g.get_traces()[3], traces[3] - traces[2])
assert 'int16' in str(rec_cmr_int16_g.get_dtype())
def test_common_reference():
rec, sort = se.example_datasets.create_dumpable_extractors(duration=10,
num_channels=4,
folder='test')
# no groups
rec_cmr = common_reference(rec, reference='median')
rec_car = common_reference(rec, reference='average')
rec_sin = common_reference(rec, reference='single', ref_channels=0)
rec_cmr_int16 = common_reference(rec, dtype='int16')
traces = rec.get_traces()
assert np.allclose(traces,
rec_cmr.get_traces() +
np.median(traces, axis=0, keepdims=True),
atol=0.01)
assert np.allclose(traces,
rec_car.get_traces() +
np.mean(traces, axis=0, keepdims=True),
atol=0.01)
assert not np.all(rec_sin.get_traces()[0])
assert np.allclose(rec_sin.get_traces()[1], traces[1] - traces[0])
assert 'int16' in str(rec_cmr_int16.get_dtype())
# test groups
groups = [[0, 1], [2, 3]]
rec_cmr_g = common_reference(rec, reference='median', groups=groups)
rec_car_g = common_reference(rec, reference='average', groups=groups)
rec_sin_g = common_reference(rec,
reference='single',
ref_channels=[0, 2],
groups=groups)
rec_cmr_int16_g = common_reference(rec, groups=groups, dtype='int16')
traces = rec.get_traces()
assert np.allclose(traces[:2],
rec_cmr_g.get_traces()[:2] +
np.median(traces[:2], axis=0, keepdims=True),
atol=0.01)
assert np.allclose(traces[2:],
rec_cmr_g.get_traces()[2:] +
np.median(traces[2:], axis=0, keepdims=True),
atol=0.01)
assert np.allclose(traces[:2],
rec_car_g.get_traces()[:2] +
np.mean(traces[:2], axis=0, keepdims=True),
atol=0.01)
assert np.allclose(traces[2:],
rec_car_g.get_traces()[2:] +
np.mean(traces[2:], axis=0, keepdims=True),
atol=0.01)
assert not np.all(rec_sin_g.get_traces()[0])
assert np.allclose(rec_sin_g.get_traces()[1], traces[1] - traces[0])
assert not np.all(rec_sin_g.get_traces()[2])
assert np.allclose(rec_sin_g.get_traces()[3], traces[3] - traces[2])
assert 'int16' in str(rec_cmr_int16_g.get_dtype())
check_dumping(rec_cmr)
check_dumping(rec_car)
check_dumping(rec_sin)
check_dumping(rec_cmr_int16)
shutil.rmtree('test')
def test_common_reference():
rec, sort = se.example_datasets.toy_example(dump_folder='test', dumpable=True, duration=2, num_channels=4, seed=0)
# no groups
rec_cmr = common_reference(rec, reference='median')
rec_car = common_reference(rec, reference='average')
rec_sin = common_reference(rec, reference='single', ref_channels=0)
rec_local_car = common_reference(rec, reference='local', local_radius=(1, 3))
rec_cmr_int16 = common_reference(rec, dtype='int16')
traces = rec.get_traces()
assert np.allclose(traces, rec_cmr.get_traces() + np.median(traces, axis=0, keepdims=True), atol=0.01)
assert np.allclose(traces, rec_car.get_traces() + np.mean(traces, axis=0, keepdims=True), atol=0.01)
assert not np.all(rec_sin.get_traces()[0])
assert np.allclose(rec_sin.get_traces()[1], traces[1] - traces[0])
assert np.allclose(traces[0], rec_local_car.get_traces()[0] + np.mean(traces[[2, 3]], axis=0, keepdims=True),
atol=0.01)
assert np.allclose(traces[1], rec_local_car.get_traces()[1] + np.mean(traces[[3]], axis=0, keepdims=True),
atol=0.01)
assert 'int16' in str(rec_cmr_int16.get_dtype())
# test groups
groups = [[0, 1], [2, 3]]
rec_cmr_g = common_reference(rec, reference='median', groups=groups)
rec_car_g = common_reference(rec, reference='average', groups=groups)
rec_sin_g = common_reference(rec, reference='single', ref_channels=[0, 2], groups=groups)
rec_cmr_int16_g = common_reference(rec, groups=groups, dtype='int16')
traces = rec.get_traces()
assert np.allclose(traces[:2], rec_cmr_g.get_traces()[:2] + np.median(traces[:2], axis=0, keepdims=True), atol=0.01)
assert np.allclose(traces[2:], rec_cmr_g.get_traces()[2:] + np.median(traces[2:], axis=0, keepdims=True), atol=0.01)
assert np.allclose(traces[:2], rec_car_g.get_traces()[:2] + np.mean(traces[:2], axis=0, keepdims=True), atol=0.01)
assert np.allclose(traces[2:], rec_car_g.get_traces()[2:] + np.mean(traces[2:], axis=0, keepdims=True), atol=0.01)
assert not np.all(rec_sin_g.get_traces()[0])
assert np.allclose(rec_sin_g.get_traces()[1], traces[1] - traces[0])
assert not np.all(rec_sin_g.get_traces()[2])
assert np.allclose(rec_sin_g.get_traces()[3], traces[3] - traces[2])
assert 'int16' in str(rec_cmr_int16_g.get_dtype())
check_dumping(rec_cmr)
check_dumping(rec_car)
check_dumping(rec_sin)
check_dumping(rec_cmr_int16)
check_dumping(rec_local_car)
# test with channels_ids
channels_ids = np.arange(0, 2)
assert np.allclose(traces[channels_ids],
rec_car.get_traces(channel_ids=channels_ids) + np.mean(traces, axis=0, keepdims=True), atol=0.01)
assert np.allclose(traces[channels_ids],
rec_cmr_g.get_traces(channel_ids=channels_ids) + np.median(traces[[0, 1]], axis=0,
keepdims=True), atol=0.01)
# Add test on a higher probes
rec2, sort = se.example_datasets.toy_example(dump_folder='test', dumpable=True, duration=2, num_channels=8, seed=0)
rec_local_car2 = common_reference(rec2, reference='local', local_radius=(2, 4))
traces = rec2.get_traces()
assert np.allclose(traces[3], rec_local_car2.get_traces()[3] + np.mean(traces[[0, 6, 7]], axis=0, keepdims=True),
atol=0.01)
shutil.rmtree('test')