def test_annot_sanitizing(tmpdir):
"""Test description sanitizing."""
annot = Annotations([0], [1], ['a;:b'])
fname = str(tmpdir.join('custom-annot.fif'))
annot.save(fname)
annot_read = read_annotations(fname)
_assert_annotations_equal(annot, annot_read)
# make sure pytest raises error on char-sequence that is not allowed
with pytest.raises(ValueError, match='in descriptions not supported'):
Annotations([0], [1], ['a{COLON}b'])
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
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)
# Get rid of the boundary events
raw_concat.annotations.delete(-1)
raw_concat.annotations.delete(-1)
# 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])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
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