def test_annotate_flat(first_samp):
"""Test marking flat segments."""
# Test if ECG analysis will work on data that is not preloaded
n_ch, n_times = 11, 1000
data = np.random.RandomState(0).randn(n_ch, n_times)
assert not (np.diff(data, axis=-1) == 0).any() # nothing flat at first
info = create_info(n_ch, 1000., 'eeg')
info['meas_date'] = (1, 2)
# test first_samp != for gh-6295
raw = RawArray(data, info, first_samp=first_samp)
raw.info['bads'] = [raw.ch_names[-1]]
#
# First make a channel flat the whole time
#
raw_0 = raw.copy()
raw_0._data[0] = 0.
for kwargs, bads, want_times in [
# Anything < 1 will mark spatially
(dict(bad_percent=100.), [], 0),
(dict(bad_percent=99.9), [raw.ch_names[0]], n_times),
(dict(), [raw.ch_names[0]], n_times)
]: # default (1)
raw_time = raw_0.copy()
annot, got_bads = annotate_flat(raw_0, verbose='debug', **kwargs)
assert got_bads == bads
raw_time.set_annotations(raw_time.annotations + annot)
raw_time.info['bads'] += got_bads
n_good_times = raw_time.get_data(reject_by_annotation='omit').shape[1]
assert n_good_times == want_times
with pytest.deprecated_call(match='annotate_flat'):
raw_time_2 = mark_flat(raw_0.copy(), verbose='debug', **kwargs)
_assert_annotations_equal(raw_time_2.annotations, raw_time.annotations)
assert raw_time_2.info['bads'] == raw_time.info['bads']
#
# Now make a channel flat for 20% of the time points
#
raw_0 = raw.copy()
n_good_times = int(round(0.8 * n_times))
raw_0._data[0, n_good_times:] = 0.
threshold = 100 * (n_times - n_good_times) / n_times
for kwargs, bads, want_times in [
# Should change behavior at bad_percent=20
(dict(bad_percent=100), [], n_good_times),
(dict(bad_percent=threshold), [], n_good_times),
(dict(bad_percent=threshold - 1e-5), [raw.ch_names[0]], n_times),
(dict(), [raw.ch_names[0]], n_times)
]:
annot, got_bads = annotate_flat(raw_0, verbose='debug', **kwargs)
assert got_bads == bads
raw_time = raw_0.copy()
raw_time.set_annotations(raw_time.annotations + annot)
raw_time.info['bads'] += got_bads
n_good_times = raw_time.get_data(reject_by_annotation='omit').shape[1]
assert n_good_times == want_times
with pytest.raises(TypeError, match='must be an instance of BaseRaw'):
annotate_flat(0.)
with pytest.raises(ValueError, match='not convert string to float'):
annotate_flat(raw, 'x')
def test_movement_annotation_head_correction(meas_date):
"""Test correct detection movement artifact and dev_head_t."""
raw = read_raw_fif(raw_fname, allow_maxshield='yes').load_data()
pos = read_head_pos(pos_fname)
if meas_date is None:
raw.set_meas_date(None)
else:
assert meas_date == 'orig'
# Check 5 rotation segments are detected
annot_rot, [] = annotate_movement(raw, pos, rotation_velocity_limit=5)
assert annot_rot.orig_time == raw.info["meas_date"]
assert annot_rot.duration.size == 5
# Check 2 translation vel. segments are detected
annot_tra, [] = annotate_movement(raw, pos, translation_velocity_limit=.05)
assert annot_tra.duration.size == 2
# Check 1 movement distance segment is detected
annot_dis, _ = annotate_movement(raw, pos, mean_distance_limit=.02)
assert annot_dis.duration.size == 1
# Check correct trans mat
annot_all_2 = annotate_movement(
raw, pos, rotation_velocity_limit=5,
translation_velocity_limit=.05,
mean_distance_limit=.02)[0]
assert (annot_rot.orig_time ==
annot_tra.orig_time ==
annot_dis.orig_time ==
raw.info['meas_date'])
annot_all = annot_rot + annot_tra + annot_dis
_assert_annotations_equal(annot_all_2, annot_all)
assert annot_all.orig_time == raw.info['meas_date']
raw.set_annotations(annot_all)
dev_head_t = compute_average_dev_head_t(raw, pos)
dev_head_t_ori = np.array([
[0.9957292, -0.08688804, 0.03120615, 0.00698271],
[0.09020767, 0.9875856, -0.12859731, -0.0159098],
[-0.01964518, 0.1308631, 0.99120578, 0.07258289],
[0., 0., 0., 1.]])
assert_allclose(dev_head_t_ori, dev_head_t['trans'], rtol=1e-5, atol=0)
# Smoke test skipping time due to previous annotations.
raw.set_annotations(Annotations([raw.times[0]], 0.1, 'bad'))
annot_dis, _ = annotate_movement(raw, pos, mean_distance_limit=.02)
assert annot_dis.duration.size == 1
def test_read_annot(tmp_path):
"""Test parsing the tal channel."""
EXPECTED_ANNOTATIONS = [[180.0, 0, 'Lights off'], [180.0, 0, 'Close door'],
[180.0, 0, 'Lights off'], [180.0, 0, 'Close door'],
[3.14, 4.2, 'nothing'], [1800.2, 25.5, 'Apnea']]
EXPECTED_ONSET = [180.0, 180.0, 180.0, 180.0, 3.14, 1800.2]
EXPECTED_DURATION = [0, 0, 0, 0, 4.2, 25.5]
EXPECTED_DESC = [
'Lights off', 'Close door', 'Lights off', 'Close door', 'nothing',
'Apnea'
]
EXPECTED_ANNOTATIONS = Annotations(onset=EXPECTED_ONSET,
duration=EXPECTED_DURATION,
description=EXPECTED_DESC,
orig_time=None)
annot = (b'+180\x14Lights off\x14Close door\x14\x00\x00\x00\x00\x00'
b'+180\x14Lights off\x14\x00\x00\x00\x00\x00\x00\x00\x00'
b'+180\x14Close door\x14\x00\x00\x00\x00\x00\x00\x00\x00'
b'+3.14\x1504.20\x14nothing\x14\x00\x00\x00\x00'
b'+1800.2\x1525.5\x14Apnea\x14\x00\x00\x00\x00\x00\x00\x00'
b'+123\x14\x14\x00\x00\x00\x00\x00\x00\x00')
annot_file = tmp_path / 'annotations.txt'
with open(annot_file, "wb") as f:
f.write(annot)
onset, duration, desc = _read_annotations_edf(annotations=str(annot_file))
annotation = Annotations(onset=onset,
duration=duration,
description=desc,
orig_time=None)
_assert_annotations_equal(annotation, EXPECTED_ANNOTATIONS)
# Now test when reading from buffer of data
with open(annot_file, 'rb') as fid:
ch_data = np.fromfile(fid, dtype='<i2', count=len(annot))
onset, duration, desc = _read_annotations_edf([ch_data])
annotation = Annotations(onset=onset,
duration=duration,
description=desc,
orig_time=None)
_assert_annotations_equal(annotation, EXPECTED_ANNOTATIONS)
def test_read_ctf_annotations_smoke_test():
"""Test reading CTF marker file.
`testdata_ctf_mc.ds` has no trials or offsets therefore its a plain reading
of whatever is in the MarkerFile.mrk.
"""
EXPECTED_ONSET = [
0., 0.1425, 0.285, 0.42833333, 0.57083333, 0.71416667, 0.85666667,
0.99916667, 1.1425, 1.285, 1.4275, 1.57083333, 1.71333333, 1.85666667,
1.99916667, 2.14166667, 2.285, 2.4275, 2.57083333, 2.71333333,
2.85583333, 2.99916667, 3.14166667, 3.28416667, 3.4275, 3.57,
3.71333333, 3.85583333, 3.99833333, 4.14166667, 4.28416667, 4.42666667,
4.57, 4.7125, 4.85583333, 4.99833333
]
fname = op.join(ctf_dir, 'testdata_ctf_mc.ds')
annot = read_annotations(fname)
assert_allclose(annot.onset, EXPECTED_ONSET)
raw = read_raw_ctf(fname)
_assert_annotations_equal(raw.annotations, annot)
def test_no_data_channels():
"""Test that we can load with no data channels."""
# analog
raw = read_raw_edf(edf_path, preload=True)
picks = pick_types(raw.info, stim=True)
assert list(picks) == [len(raw.ch_names) - 1]
stim_data = raw[picks][0]
raw = read_raw_edf(edf_path, exclude=raw.ch_names[:-1])
stim_data_2 = raw[0][0]
assert_array_equal(stim_data, stim_data_2)
raw.plot() # smoke test
# annotations
raw = read_raw_edf(edf_overlap_annot_path)
picks = pick_types(raw.info, stim=True)
assert picks.size == 0
annot = raw.annotations
raw = read_raw_edf(edf_overlap_annot_path, exclude=raw.ch_names)
annot_2 = raw.annotations
_assert_annotations_equal(annot, annot_2)
# only annotations (should warn)
with pytest.warns(RuntimeWarning, match='read_annotations'):
read_raw_edf(edf_annot_only)
