def test_basics():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is not None # XXX to be fixed in #5416
assert len(raw.annotations.onset) == 0 # XXX to be fixed in #5416
pytest.raises(IOError, read_annotations, fif_fname)
onset = np.array(range(10))
duration = np.ones(10)
description = np.repeat('test', 10)
dt = datetime.utcnow()
meas_date = raw.info['meas_date']
# Test time shifts.
for orig_time in [None, dt, meas_date[0], meas_date]:
annot = Annotations(onset, duration, description, orig_time)
pytest.raises(ValueError, Annotations, onset, duration, description[:9])
pytest.raises(ValueError, Annotations, [onset, 1], duration, description)
pytest.raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
delta = raw.times[-1] + 1. / raw.info['sfreq']
orig_time = (meas_date[0] + meas_date[1] * 1e-6 + raw2._first_time)
offset = orig_time - _handle_meas_date(raw2.info['meas_date'])
annot = Annotations(onset, duration, description, orig_time)
assert ' segments' in repr(annot)
raw2.set_annotations(annot)
assert_array_equal(raw2.annotations.onset, onset + offset)
assert id(raw2.annotations) != id(annot)
concatenate_raws([raw, raw2])
assert_and_remove_boundary_annot(raw)
assert_allclose(onset + offset + delta, raw.annotations.onset, rtol=1e-5)
assert_array_equal(annot.duration, raw.annotations.duration)
assert_array_equal(raw.annotations.description, np.repeat('test', 10))
def test_crop_more():
"""Test more cropping."""
raw = mne.io.read_raw_fif(fif_fname).crop(0, 11).load_data()
raw._data[:] = np.random.RandomState(0).randn(*raw._data.shape)
onset = np.array([0.47058824, 2.49773765, 6.67873287, 9.15837097])
duration = np.array([0.89592767, 1.13574672, 1.09954739, 0.48868752])
annotations = mne.Annotations(onset, duration, 'BAD')
raw.set_annotations(annotations)
assert len(raw.annotations) == 4
delta = 1. / raw.info['sfreq']
offset = raw.first_samp * delta
raw_concat = mne.concatenate_raws(
[raw.copy().crop(0, 4 - delta),
raw.copy().crop(4, 8 - delta),
raw.copy().crop(8, None)])
assert_allclose(raw_concat.times, raw.times)
assert_allclose(raw_concat[:][0], raw[:][0])
assert raw_concat.first_samp == raw.first_samp
assert_and_remove_boundary_annot(raw_concat, 2)
assert len(raw_concat.annotations) == 4
assert_array_equal(raw_concat.annotations.description,
raw.annotations.description)
assert_allclose(raw.annotations.duration, duration)
assert_allclose(raw_concat.annotations.duration, duration)
assert_allclose(raw.annotations.onset, onset + offset)
assert_allclose(raw_concat.annotations.onset, onset + offset,
atol=1. / raw.info['sfreq'])
def test_basics():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is not None # XXX to be fixed in #5416
assert len(raw.annotations.onset) == 0 # XXX to be fixed in #5416
pytest.raises(IOError, read_annotations, fif_fname)
onset = np.array(range(10))
duration = np.ones(10)
description = np.repeat('test', 10)
dt = datetime.utcnow()
meas_date = raw.info['meas_date']
# Test time shifts.
for orig_time in [None, dt, meas_date[0], meas_date]:
annot = Annotations(onset, duration, description, orig_time)
pytest.raises(ValueError, Annotations, onset, duration, description[:9])
pytest.raises(ValueError, Annotations, [onset, 1], duration, description)
pytest.raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
delta = raw.times[-1] + 1. / raw.info['sfreq']
orig_time = (meas_date[0] + meas_date[1] * 1e-6 + raw2._first_time)
offset = orig_time - _handle_meas_date(raw2.info['meas_date'])
annot = Annotations(onset, duration, description, orig_time)
assert ' segments' in repr(annot)
raw2.set_annotations(annot)
assert_array_equal(raw2.annotations.onset, onset + offset)
assert id(raw2.annotations) != id(annot)
concatenate_raws([raw, raw2])
assert_and_remove_boundary_annot(raw)
assert_allclose(onset + offset + delta, raw.annotations.onset, rtol=1e-5)
assert_array_equal(annot.duration, raw.annotations.duration)
assert_array_equal(raw.annotations.description, np.repeat('test', 10))
def test_raw_array_orig_times():
"""Test combining with RawArray and orig_times."""
data = np.random.randn(2, 1000) * 10e-12
sfreq = 100.
info = create_info(ch_names=['MEG1', 'MEG2'], ch_types=['grad'] * 2,
sfreq=sfreq)
meas_date = _handle_meas_date(np.pi)
info['meas_date'] = meas_date
raws = []
for first_samp in [12300, 100, 12]:
raw = RawArray(data.copy(), info, first_samp=first_samp)
ants = Annotations([1., 2.], [.5, .5], 'x', np.pi + first_samp / sfreq)
raw.set_annotations(ants)
raws.append(raw)
assert_allclose(raws[0].annotations.onset, [124, 125])
raw = RawArray(data.copy(), info)
assert not len(raw.annotations)
raw.set_annotations(Annotations([1.], [.5], 'x', None))
assert_allclose(raw.annotations.onset, [1.])
raws.append(raw)
raw = concatenate_raws(raws, verbose='debug')
assert raw.info['meas_date'] == raw.annotations.orig_time == meas_date
assert_and_remove_boundary_annot(raw, 3)
assert_array_equal(raw.annotations.onset, [124., 125., 134., 135.,
144., 145., 154.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [124., 125., 135., 144.,
145., 154.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset,
[5., 124., 125., 135., 144., 145., 154.])
assert_array_equal(raw.annotations.duration,
[1.5, .5, .5, .5, .5, .5, .5])
assert_array_equal(raw.annotations.description,
['y', 'x', 'x', 'x', 'x', 'x', 'x'])
# These three things should be equivalent
stamp = _dt_to_stamp(raw.info['meas_date'])
orig_time = _handle_meas_date(stamp)
for empty_annot in (
Annotations([], [], [], stamp),
Annotations([], [], [], orig_time),
Annotations([], [], [], None),
None):
raw.set_annotations(empty_annot)
assert isinstance(raw.annotations, Annotations)
assert len(raw.annotations) == 0
assert raw.annotations.orig_time == orig_time
def test_basics():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is not None # XXX to be fixed in #5416
assert len(raw.annotations.onset) == 0 # XXX to be fixed in #5416
pytest.raises(IOError, read_annotations, fif_fname)
onset = np.array(range(10))
duration = np.ones(10)
description = np.repeat('test', 10)
dt = raw.info['meas_date']
assert isinstance(dt, datetime)
stamp = _dt_to_stamp(dt)
# Test time shifts.
for orig_time in [None, dt, stamp[0], stamp]:
annot = Annotations(onset, duration, description, orig_time)
if orig_time is None:
assert annot.orig_time is None
else:
assert isinstance(annot.orig_time, datetime)
assert annot.orig_time.tzinfo is timezone.utc
pytest.raises(ValueError, Annotations, onset, duration, description[:9])
pytest.raises(ValueError, Annotations, [onset, 1], duration, description)
pytest.raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
delta = raw.times[-1] + 1. / raw.info['sfreq']
orig_time = (stamp[0] + stamp[1] * 1e-6 + raw2._first_time)
offset = _dt_to_stamp(_handle_meas_date(raw2.info['meas_date']))
offset = offset[0] + offset[1] * 1e-6
offset = orig_time - offset
assert_allclose(offset, raw._first_time)
annot = Annotations(onset, duration, description, orig_time)
assert annot.orig_time is not None
assert ' segments' in repr(annot)
raw2.set_annotations(annot)
assert_allclose(raw2.annotations.onset, onset + offset)
assert raw2.annotations is not annot
assert raw2.annotations.orig_time is not None
concatenate_raws([raw, raw2])
assert_and_remove_boundary_annot(raw)
assert_allclose(onset + offset + delta, raw.annotations.onset, rtol=1e-5)
assert_array_equal(annot.duration, raw.annotations.duration)
assert_array_equal(raw.annotations.description, np.repeat('test', 10))
def test_raw_array_orig_times():
"""Test combining with RawArray and orig_times."""
data = np.random.randn(2, 1000) * 10e-12
sfreq = 100.
info = create_info(ch_names=['MEG1', 'MEG2'], ch_types=['grad'] * 2,
sfreq=sfreq)
info['meas_date'] = (np.pi, 0)
raws = []
for first_samp in [12300, 100, 12]:
raw = RawArray(data.copy(), info, first_samp=first_samp)
ants = Annotations([1., 2.], [.5, .5], 'x', np.pi + first_samp / sfreq)
raw.set_annotations(ants)
raws.append(raw)
raw = RawArray(data.copy(), info)
raw.set_annotations(Annotations([1.], [.5], 'x', None))
raws.append(raw)
raw = concatenate_raws(raws, verbose='debug')
assert_and_remove_boundary_annot(raw, 3)
assert_array_equal(raw.annotations.onset, [124., 125., 134., 135.,
144., 145., 154.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [124., 125., 135., 144.,
145., 154.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset,
[5., 124., 125., 135., 144., 145., 154.])
assert_array_equal(raw.annotations.duration,
[1.5, .5, .5, .5, .5, .5, .5])
assert_array_equal(raw.annotations.description,
['y', 'x', 'x', 'x', 'x', 'x', 'x'])
# These three things should be equivalent
expected_orig_time = (raw.info['meas_date'][0] +
raw.info['meas_date'][1] / 1000000)
for empty_annot in (
Annotations([], [], [], expected_orig_time),
Annotations([], [], [], None),
None):
raw.set_annotations(empty_annot)
assert isinstance(raw.annotations, Annotations)
assert len(raw.annotations) == 0
assert raw.annotations.orig_time == expected_orig_time
def test_basics():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is not None # XXX to be fixed in #5416
assert len(raw.annotations.onset) == 0 # XXX to be fixed in #5416
pytest.raises(IOError, read_annotations, fif_fname)
onset = np.array(range(10))
duration = np.ones(10)
description = np.repeat('test', 10)
dt = datetime.utcnow()
meas_date = raw.info['meas_date']
# Test time shifts.
for orig_time in [None, dt, meas_date[0], meas_date]:
annot = Annotations(onset, duration, description, orig_time)
pytest.raises(ValueError, Annotations, onset, duration, description[:9])
pytest.raises(ValueError, Annotations, [onset, 1], duration, description)
pytest.raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
delta = raw.times[-1] + 1. / raw.info['sfreq']
orig_time = (meas_date[0] + meas_date[1] * 1e-6 + raw2._first_time)
offset = orig_time - _handle_meas_date(raw2.info['meas_date'])
annot = Annotations(onset, duration, description, orig_time)
assert ' segments' in repr(annot)
raw2.set_annotations(annot)
assert_array_equal(raw2.annotations.onset, onset + offset)
assert id(raw2.annotations) != id(annot)
concatenate_raws([raw, raw2])
assert_and_remove_boundary_annot(raw)
assert_allclose(onset + offset + delta, raw.annotations.onset, rtol=1e-5)
assert_array_equal(annot.duration, raw.annotations.duration)
assert_array_equal(raw.annotations.description, np.repeat('test', 10))
# Test combining with RawArray and orig_times
data = np.random.randn(2, 1000) * 10e-12
sfreq = 100.
info = create_info(ch_names=['MEG1', 'MEG2'], ch_types=['grad'] * 2,
sfreq=sfreq)
info['meas_date'] = (np.pi, 0)
raws = []
for first_samp in [12300, 100, 12]:
raw = RawArray(data.copy(), info, first_samp=first_samp)
ants = Annotations([1., 2.], [.5, .5], 'x', np.pi + first_samp / sfreq)
raw.set_annotations(ants)
raws.append(raw)
raw = RawArray(data.copy(), info)
raw.set_annotations(Annotations([1.], [.5], 'x', None))
raws.append(raw)
raw = concatenate_raws(raws, verbose='debug')
assert_and_remove_boundary_annot(raw, 3)
assert_array_equal(raw.annotations.onset, [124., 125., 134., 135.,
144., 145., 154.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [124., 125., 135., 144.,
145., 154.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset,
[5., 124., 125., 135., 144., 145., 154.])
assert_array_equal(raw.annotations.duration,
[1.5, .5, .5, .5, .5, .5, .5])
assert_array_equal(raw.annotations.description,
['y', 'x', 'x', 'x', 'x', 'x', 'x'])
# These three things should be equivalent
expected_orig_time = (raw.info['meas_date'][0] +
raw.info['meas_date'][1] / 1000000)
for empty_annot in (
Annotations([], [], [], expected_orig_time),
Annotations([], [], [], None),
None):
raw.set_annotations(empty_annot)
assert isinstance(raw.annotations, Annotations)
assert len(raw.annotations) == 0
assert raw.annotations.orig_time == expected_orig_time
def test_crop():
"""Test cropping with annotations."""
raw = read_raw_fif(fif_fname)
events = mne.find_events(raw)
onset = events[events[:, 2] == 1, 0] / raw.info['sfreq']
duration = np.full_like(onset, 0.5)
description = ['bad %d' % k for k in range(len(onset))]
annot = mne.Annotations(onset, duration, description,
orig_time=raw.info['meas_date'])
raw.set_annotations(annot)
split_time = raw.times[-1] / 2. + 2.
split_idx = len(onset) // 2 + 1
raw_cropped_left = raw.copy().crop(0., split_time - 1. / raw.info['sfreq'])
assert_array_equal(raw_cropped_left.annotations.description,
raw.annotations.description[:split_idx])
assert_allclose(raw_cropped_left.annotations.duration,
raw.annotations.duration[:split_idx])
assert_allclose(raw_cropped_left.annotations.onset,
raw.annotations.onset[:split_idx])
raw_cropped_right = raw.copy().crop(split_time, None)
assert_array_equal(raw_cropped_right.annotations.description,
raw.annotations.description[split_idx:])
assert_allclose(raw_cropped_right.annotations.duration,
raw.annotations.duration[split_idx:])
assert_allclose(raw_cropped_right.annotations.onset,
raw.annotations.onset[split_idx:])
raw_concat = mne.concatenate_raws([raw_cropped_left, raw_cropped_right],
verbose='debug')
assert_allclose(raw_concat.times, raw.times)
assert_allclose(raw_concat[:][0], raw[:][0], atol=1e-20)
assert_and_remove_boundary_annot(raw_concat)
# Ensure we annotations survive round-trip crop->concat
assert_array_equal(raw_concat.annotations.description,
raw.annotations.description)
for attr in ('onset', 'duration'):
assert_allclose(getattr(raw_concat.annotations, attr),
getattr(raw.annotations, attr),
err_msg='Failed for %s:' % (attr,))
raw.set_annotations(None) # undo
# Test concatenating annotations with and without orig_time.
raw2 = raw.copy()
raw.set_annotations(Annotations([45.], [3], 'test', raw.info['meas_date']))
raw2.set_annotations(Annotations([2.], [3], 'BAD', None))
expected_onset = [45., 2. + raw._last_time]
raw = concatenate_raws([raw, raw2])
assert_and_remove_boundary_annot(raw)
assert_array_almost_equal(raw.annotations.onset, expected_onset, decimal=2)
# Test IO
tempdir = _TempDir()
fname = op.join(tempdir, 'test-annot.fif')
raw.annotations.save(fname)
annot_read = read_annotations(fname)
for attr in ('onset', 'duration', 'orig_time'):
assert_allclose(getattr(annot_read, attr),
getattr(raw.annotations, attr))
assert_array_equal(annot_read.description, raw.annotations.description)
annot = Annotations((), (), ())
annot.save(fname)
pytest.raises(IOError, read_annotations, fif_fname) # none in old raw
annot = read_annotations(fname)
assert isinstance(annot, Annotations)
assert len(annot) == 0
# Test that empty annotations can be saved with an object
fname = op.join(tempdir, 'test_raw.fif')
raw.set_annotations(annot)
raw.save(fname)
raw_read = read_raw_fif(fname)
assert isinstance(raw_read.annotations, Annotations)
assert len(raw_read.annotations) == 0
raw.set_annotations(None)
raw.save(fname, overwrite=True)
raw_read = read_raw_fif(fname)
assert raw_read.annotations is not None # XXX to be fixed in #5416
assert len(raw_read.annotations.onset) == 0 # XXX to be fixed in #5416
