def test_raw_reject():
"""Test raw data getter with annotation reject."""
info = create_info(['a', 'b', 'c', 'd', 'e'], 100, ch_types='eeg')
raw = RawArray(np.ones((5, 15000)), info)
with warnings.catch_warnings(record=True): # one outside range
raw.annotations = Annotations([2, 100, 105, 148], [2, 8, 5, 8], 'BAD')
data = raw.get_data([0, 1, 3, 4], 100, 11200, 'omit')
assert_array_equal(data.shape, (4, 9900))
# with orig_time and complete overlap
raw = read_raw_fif(fif_fname)
raw.annotations = Annotations([44, 47, 48], [1, 3, 1], 'BAD',
raw.info['meas_date'])
data, times = raw.get_data(range(10), 0, 6000, 'omit', True)
assert_array_equal(data.shape, (10, 4799))
assert_equal(times[-1], raw.times[5999])
assert_array_equal(data[:, -100:], raw[:10, 5900:6000][0])
data, times = raw.get_data(range(10), 0, 6000, 'NaN', True)
assert_array_equal(data.shape, (10, 6000))
assert_equal(times[-1], raw.times[5999])
assert_true(np.isnan(data[:, 313:613]).all()) # 1s -2s
assert_true(not np.isnan(data[:, 614].any()))
assert_array_equal(data[:, -100:], raw[:10, 5900:6000][0])
assert_array_equal(raw.get_data(), raw[:][0])
# Test _sync_onset
times = [10, -88, 190]
onsets = _sync_onset(raw, times)
assert_array_almost_equal(onsets, times - raw.first_samp /
raw.info['sfreq'])
assert_array_almost_equal(times, _sync_onset(raw, onsets, True))
def test_raw_reject():
"""Test raw data getter with annotation reject."""
info = create_info(['a', 'b', 'c', 'd', 'e'], 100, ch_types='eeg')
raw = RawArray(np.ones((5, 15000)), info)
with warnings.catch_warnings(record=True): # one outside range
raw.annotations = Annotations([2, 100, 105, 148], [2, 8, 5, 8], 'BAD')
data = raw.get_data([0, 1, 3, 4], 100, 11200, 'omit')
assert_array_equal(data.shape, (4, 9900))
# with orig_time and complete overlap
raw = read_raw_fif(fif_fname)
raw.annotations = Annotations([44, 47, 48], [1, 3, 1], 'BAD',
raw.info['meas_date'])
data, times = raw.get_data(range(10), 0, 6000, 'omit', True)
assert_array_equal(data.shape, (10, 4799))
assert_equal(times[-1], raw.times[5999])
assert_array_equal(data[:, -100:], raw[:10, 5900:6000][0])
data, times = raw.get_data(range(10), 0, 6000, 'NaN', True)
assert_array_equal(data.shape, (10, 6000))
assert_equal(times[-1], raw.times[5999])
assert_true(np.isnan(data[:, 313:613]).all()) # 1s -2s
assert_true(not np.isnan(data[:, 614].any()))
assert_array_equal(data[:, -100:], raw[:10, 5900:6000][0])
assert_array_equal(raw.get_data(), raw[:][0])
# Test _sync_onset
times = [10, -88, 190]
onsets = _sync_onset(raw, times)
assert_array_almost_equal(onsets,
times - raw.first_samp / raw.info['sfreq'])
assert_array_almost_equal(times, _sync_onset(raw, onsets, True))
def test_raw_reject():
"""Test raw data getter with annotation reject."""
sfreq = 100.
info = create_info(['a', 'b', 'c', 'd', 'e'], sfreq, ch_types='eeg')
raw = RawArray(np.ones((5, 15000)), info)
with warnings.catch_warnings(record=True): # one outside range
raw.annotations = Annotations([2, 100, 105, 148], [2, 8, 5, 8], 'BAD')
data, times = raw.get_data(
[0, 1, 3, 4],
100,
11200, # 1-112 sec
'omit',
return_times=True)
bad_times = np.concatenate([
np.arange(200, 400),
np.arange(10000, 10800),
np.arange(10500, 11000)
])
expected_times = np.setdiff1d(np.arange(100, 11200), bad_times) / sfreq
assert_allclose(times, expected_times)
# with orig_time and complete overlap
raw = read_raw_fif(fif_fname)
t_0 = raw.first_samp / raw.info['sfreq']
raw.annotations = Annotations([t_0 + 1, t_0 + 4, t_0 + 5], [1, 3, 1],
'BAD', raw.info['meas_date'])
t_stop = 18.
assert raw.times[-1] > t_stop
n_stop = int(round(t_stop * raw.info['sfreq']))
n_drop = int(round(4 * raw.info['sfreq']))
assert len(raw.times) >= n_stop
data, times = raw.get_data(range(10), 0, n_stop, 'omit', True)
assert data.shape == (10, n_stop - n_drop)
assert times[-1] == raw.times[n_stop - 1]
assert_array_equal(data[:, -100:], raw[:10, n_stop - 100:n_stop][0])
data, times = raw.get_data(range(10), 0, n_stop, 'NaN', True)
assert_array_equal(data.shape, (10, n_stop))
assert times[-1] == raw.times[n_stop - 1]
t_1, t_2 = raw.time_as_index([1, 2], use_rounding=True)
assert np.isnan(data[:, t_1:t_2]).all() # 1s -2s
assert not np.isnan(data[:, :t_1].any())
assert not np.isnan(data[:, t_2:].any())
assert_array_equal(data[:, -100:], raw[:10, n_stop - 100:n_stop][0])
assert_array_equal(raw.get_data(), raw[:][0])
# Test _sync_onset
times = [10, -88, 190]
onsets = _sync_onset(raw, times)
assert_array_almost_equal(onsets,
times - raw.first_samp / raw.info['sfreq'])
assert_array_almost_equal(times, _sync_onset(raw, onsets, True))
def test_annotation_omit():
"""Test raw.get_data with annotations."""
data = np.concatenate([np.ones((1, 1000)), 2 * np.ones((1, 1000))], -1)
info = create_info(1, 1000., 'eeg')
raw = RawArray(data, info)
raw.annotations = Annotations([0.5], [1], ['bad'])
expected = raw[0][0]
assert_allclose(raw.get_data(reject_by_annotation=None), expected)
# nan
expected[0, 500:1500] = np.nan
assert_allclose(raw.get_data(reject_by_annotation='nan'), expected)
got = np.concatenate([
raw.get_data(start=start, stop=stop, reject_by_annotation='nan')
for start, stop in ((0, 1000), (1000, 2000))
], -1)
assert_allclose(got, expected)
# omit
expected = expected[:, np.isfinite(expected[0])]
assert_allclose(raw.get_data(reject_by_annotation='omit'), expected)
got = np.concatenate([
raw.get_data(start=start, stop=stop, reject_by_annotation='omit')
for start, stop in ((0, 1000), (1000, 2000))
], -1)
assert_allclose(got, expected)
assert_raises(ValueError, raw.get_data, reject_by_annotation='foo')
def test_annotation_property_deprecation_warning():
"""Test that assigning annotations warns and nowhere else."""
with pytest.warns(None) as w:
raw = RawArray(np.random.rand(1, 1), create_info(1, 1))
assert len(w) is 0
with pytest.warns(DeprecationWarning, match='by assignment is deprecated'):
raw.annotations = None
def test_annotation_property_deprecation_warning():
"""Test that assigning annotations warns and nowhere else."""
with pytest.warns(None) as w:
raw = RawArray(np.random.rand(1, 1), create_info(1, 1))
assert len(w) is 0
with pytest.warns(DeprecationWarning, match='by assignment is deprecated'):
raw.annotations = None
def test_raw_reject():
"""Test raw data getter with annotation reject."""
sfreq = 100.
info = create_info(['a', 'b', 'c', 'd', 'e'], sfreq, ch_types='eeg')
raw = RawArray(np.ones((5, 15000)), info)
with warnings.catch_warnings(record=True): # one outside range
raw.annotations = Annotations([2, 100, 105, 148], [2, 8, 5, 8], 'BAD')
data, times = raw.get_data([0, 1, 3, 4], 100, 11200, # 1-112 sec
'omit', return_times=True)
bad_times = np.concatenate([np.arange(200, 400),
np.arange(10000, 10800),
np.arange(10500, 11000)])
expected_times = np.setdiff1d(np.arange(100, 11200), bad_times) / sfreq
assert_allclose(times, expected_times)
# with orig_time and complete overlap
raw = read_raw_fif(fif_fname)
t_0 = raw.first_samp / raw.info['sfreq']
raw.annotations = Annotations([t_0 + 1, t_0 + 4, t_0 + 5], [1, 3, 1],
'BAD', raw.info['meas_date'])
t_stop = 18.
assert raw.times[-1] > t_stop
n_stop = int(round(t_stop * raw.info['sfreq']))
n_drop = int(round(4 * raw.info['sfreq']))
assert len(raw.times) >= n_stop
data, times = raw.get_data(range(10), 0, n_stop, 'omit', True)
assert data.shape == (10, n_stop - n_drop)
assert times[-1] == raw.times[n_stop - 1]
assert_array_equal(data[:, -100:], raw[:10, n_stop - 100:n_stop][0])
data, times = raw.get_data(range(10), 0, n_stop, 'NaN', True)
assert_array_equal(data.shape, (10, n_stop))
assert times[-1] == raw.times[n_stop - 1]
t_1, t_2 = raw.time_as_index([1, 2], use_rounding=True)
assert np.isnan(data[:, t_1:t_2]).all() # 1s -2s
assert not np.isnan(data[:, :t_1].any())
assert not np.isnan(data[:, t_2:].any())
assert_array_equal(data[:, -100:], raw[:10, n_stop - 100:n_stop][0])
assert_array_equal(raw.get_data(), raw[:][0])
# Test _sync_onset
times = [10, -88, 190]
onsets = _sync_onset(raw, times)
assert_array_almost_equal(onsets, times - raw.first_samp /
raw.info['sfreq'])
assert_array_almost_equal(times, _sync_onset(raw, onsets, True))
def test_annotations():
"""Test annotation class."""
raw = read_raw_fif(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)
assert_raises(ValueError, Annotations, onset, duration, description[:9])
assert_raises(ValueError, Annotations, [onset, 1], duration, description)
assert_raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
orig_time = (meas_date[0] + meas_date[1] * 0.000001 +
raw2.first_samp / raw2.info['sfreq'])
annot = Annotations(onset, duration, description, orig_time)
raw2.annotations = annot
assert_array_equal(raw2.annotations.onset, onset)
concatenate_raws([raw, raw2])
assert_array_almost_equal(onset + 20., raw.annotations.onset, decimal=2)
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'] = 0
raws = []
for i, fs in enumerate([1000, 100, 12]):
raw = RawArray(data.copy(), info, first_samp=fs)
ants = Annotations([1., 2.], [.5, .5], 'x', fs / sfreq)
raw.annotations = ants
raws.append(raw)
raw = concatenate_raws(raws)
assert_array_equal(raw.annotations.onset, [1., 2., 11., 12., 21., 22.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 5])
assert_array_equal(raw.annotations.duration, [.5, .5, .5, .5, .5, 1.5])
assert_array_equal(raw.annotations.description, ['x', 'x', 'x', 'x', 'x',
'y'])
def test_raw_reject():
"""Test raw data getter with annotation reject."""
info = create_info(['a', 'b', 'c', 'd', 'e'], 100, ch_types='eeg')
raw = RawArray(np.ones((5, 15000)), info)
raw.annotations = Annotations([2, 100, 105, 148], [2, 8, 5, 8], 'BAD')
data = raw.get_data([0, 1, 3, 4], 100, 11200, 'omit')
assert_array_equal(data.shape, (4, 9900))
# with orig_time and complete overlap
raw = read_raw_fif(fif_fname)
raw.annotations = Annotations([44, 47, 48], [1, 3, 1], 'BAD',
raw.info['meas_date'])
data, times = raw.get_data(range(10), 0, 6000, 'omit', True)
assert_array_equal(data.shape, (10, 4799))
assert_equal(times[-1], raw.times[5999])
assert_array_equal(data[:, -100:], raw[:10, 5900:6000][0])
data, times = raw.get_data(range(10), 0, 6000, 'NaN', True)
assert_array_equal(data.shape, (10, 6000))
assert_equal(times[-1], raw.times[5999])
assert_true(np.isnan(data[:, 313:613]).all()) # 1s -2s
assert_true(not np.isnan(data[:, 614].any()))
assert_array_equal(data[:, -100:], raw[:10, 5900:6000][0])
assert_array_equal(raw.get_data(), raw[:][0])
def test_annotation_omit():
"""Test raw.get_data with annotations."""
data = np.concatenate([np.ones((1, 1000)), 2 * np.ones((1, 1000))], -1)
info = create_info(1, 1000., 'eeg')
raw = RawArray(data, info)
raw.annotations = Annotations([0.5], [1], ['bad'])
expected = raw[0][0]
assert_allclose(raw.get_data(reject_by_annotation=None), expected)
# nan
expected[0, 500:1500] = np.nan
assert_allclose(raw.get_data(reject_by_annotation='nan'), expected)
got = np.concatenate([raw.get_data(start=start, stop=stop,
reject_by_annotation='nan')
for start, stop in ((0, 1000), (1000, 2000))], -1)
assert_allclose(got, expected)
# omit
expected = expected[:, np.isfinite(expected[0])]
assert_allclose(raw.get_data(reject_by_annotation='omit'), expected)
got = np.concatenate([raw.get_data(start=start, stop=stop,
reject_by_annotation='omit')
for start, stop in ((0, 1000), (1000, 2000))], -1)
assert_allclose(got, expected)
assert_raises(ValueError, raw.get_data, reject_by_annotation='foo')
def test_basics():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is None
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_samp / raw2.info['sfreq'])
annot = Annotations(onset, duration, description, orig_time)
assert ' segments' in repr(annot)
raw2.annotations = annot
assert_array_equal(raw2.annotations.onset, onset)
concatenate_raws([raw, raw2])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
assert_allclose(onset + 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
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.annotations = ants
raws.append(raw)
raw = RawArray(data.copy(), info)
raw.annotations = Annotations([1.], [.5], 'x', None)
raws.append(raw)
raw = concatenate_raws(raws, verbose='debug')
boundary_idx = np.where(raw.annotations.description == 'BAD boundary')[0]
assert len(boundary_idx) == 3
raw.annotations.delete(boundary_idx)
boundary_idx = np.where(raw.annotations.description == 'EDGE boundary')[0]
assert len(boundary_idx) == 3
raw.annotations.delete(boundary_idx)
assert_array_equal(raw.annotations.onset,
[1., 2., 11., 12., 21., 22., 31.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31., 5])
assert_array_equal(raw.annotations.duration, [.5, .5, .5, .5, .5, .5, 1.5])
assert_array_equal(raw.annotations.description,
['x', 'x', 'x', 'x', 'x', 'x', 'y'])
def test_basics():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is None
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_samp / raw2.info['sfreq'])
annot = Annotations(onset, duration, description, orig_time)
assert ' segments' in repr(annot)
raw2.annotations = annot
assert_array_equal(raw2.annotations.onset, onset)
concatenate_raws([raw, raw2])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
assert_allclose(onset + 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
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.annotations = ants
raws.append(raw)
raw = RawArray(data.copy(), info)
raw.annotations = Annotations([1.], [.5], 'x', None)
raws.append(raw)
raw = concatenate_raws(raws, verbose='debug')
boundary_idx = np.where(raw.annotations.description == 'BAD boundary')[0]
assert len(boundary_idx) == 3
raw.annotations.delete(boundary_idx)
boundary_idx = np.where(raw.annotations.description == 'EDGE boundary')[0]
assert len(boundary_idx) == 3
raw.annotations.delete(boundary_idx)
assert_array_equal(raw.annotations.onset, [1., 2., 11., 12., 21., 22.,
31.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31., 5])
assert_array_equal(raw.annotations.duration, [.5, .5, .5, .5, .5, .5, 1.5])
assert_array_equal(raw.annotations.description, ['x', 'x', 'x', 'x', 'x',
'x', 'y'])
def bv2fif(dataf,
corf,
ch_order=None,
eogs=('VEOG', 'HEOG'),
ecg='ECG',
emg='EMG',
preload='default',
ref_ch='Fp1',
dbs=False,
new_sfreq=1000.0):
montage = read_dig_montage(bvct=corf)
if preload == 'default':
preload = os.path.dirname(dataf) + '/workfile'
raw = read_raw_brainvision(dataf, preload=preload)
if dbs:
event_ch = get_events(raw)
# save downsampled raw for multitaper spectrogram
raw_data = np.zeros(
(raw._data.shape[0],
int(raw._data.shape[1] / raw.info['sfreq'] * new_sfreq)))
raw_info = raw.info.copy()
raw_info['sfreq'] = new_sfreq
for i in tqdm(range(len(raw._data))):
ch = raw._data[i, ::int(raw.info['sfreq'] / new_sfreq)]
raw_data[i] = ch
del ch
raw_resampled = RawArray(raw_data, raw_info)
raw_resampled.annotations = raw.annotations
if dbs:
old_event_ch = [ch for ch in raw.info['ch_names'] if 'STI' in ch]
if old_event_ch:
raw_resampled.drop_channels([old_event_ch[0]])
event_ch._data = event_ch._data[:, ::int(raw.info['sfreq'] /
new_sfreq)]
event_ch.info['sfreq'] = new_sfreq
event_ch.__len__ = len(event_ch._data[0])
event_ch.info['lowpass'] = raw_resampled.info['lowpass']
raw_resampled.add_channels([event_ch])
prepInst(raw_resampled, dataf, 'raw', montage, ref_ch, eogs, ecg, emg)
events, event_ids = events_from_annotations(raw)
if len(np.unique(events[:, 2])) > 1:
events = events[np.where(events[:,
2] == events[1,
2])[0]] #skip new segment
epochs = Epochs(raw,
events,
tmin=-2,
tmax=2,
proj=False,
preload=op.dirname(dataf) + '/workfile-epo',
baseline=(-0.5, -0.1),
verbose=False,
detrend=1)
events = events[
epochs.
selection] #in case any epochs don't have data and get thrown out (poorly placed at beginning or end)
epo_data = np.zeros(
(epochs._data.shape[0], epochs._data.shape[1],
int(np.ceil(epochs._data.shape[2] / epochs.info['sfreq'] *
new_sfreq))))
for i in tqdm(range(epochs._data.shape[0])):
for j in range(epochs._data.shape[1]):
epo_curr = epochs._data[i,
j, ::int(epochs.info['sfreq'] / new_sfreq)]
epo_data[i, j] = epo_curr
del epo_curr
events[:, 0] = np.array(events[:, 0] * new_sfreq / raw.info['sfreq'],
dtype=int)
epo_resampled = EpochsArray(epo_data, epochs.info.copy(), events, tmin=-2)
epo_resampled.info['sfreq'] = new_sfreq
epo_resampled.events[:, 2] = np.arange(len(events))
epo_resampled.event_id = {str(i): i for i in range(len(events))}
prepInst(epo_resampled, dataf, 'epo', montage, ref_ch, eogs, ecg, emg)
def test_annotations():
"""Test annotation class."""
raw = read_raw_fif(fif_fname)
assert raw.annotations is None
assert_raises(ValueError, 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)
assert_raises(ValueError, Annotations, onset, duration, description[:9])
assert_raises(ValueError, Annotations, [onset, 1], duration, description)
assert_raises(ValueError, Annotations, onset, [duration, 1], description)
# Test combining annotations with concatenate_raws
raw2 = raw.copy()
orig_time = (meas_date[0] + meas_date[1] * 0.000001 +
raw2.first_samp / raw2.info['sfreq'])
annot = Annotations(onset, duration, description, orig_time)
assert_true(' segments' in repr(annot))
raw2.annotations = annot
assert_array_equal(raw2.annotations.onset, onset)
concatenate_raws([raw, raw2])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
assert_array_almost_equal(onset + 20., raw.annotations.onset, decimal=2)
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'] = 0
raws = []
for i, fs in enumerate([12300, 100, 12]):
raw = RawArray(data.copy(), info, first_samp=fs)
ants = Annotations([1., 2.], [.5, .5], 'x', fs / sfreq)
raw.annotations = ants
raws.append(raw)
raw = RawArray(data.copy(), info)
raw.annotations = Annotations([1.], [.5], 'x', None)
raws.append(raw)
raw = concatenate_raws(raws)
boundary_idx = np.where(raw.annotations.description == 'BAD boundary')[0]
assert_equal(len(boundary_idx), 3)
raw.annotations.delete(boundary_idx)
boundary_idx = np.where(raw.annotations.description == 'EDGE boundary')[0]
assert_equal(len(boundary_idx), 3)
raw.annotations.delete(boundary_idx)
assert_array_equal(raw.annotations.onset,
[1., 2., 11., 12., 21., 22., 31.])
raw.annotations.delete(2)
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31.])
raw.annotations.append(5, 1.5, 'y')
assert_array_equal(raw.annotations.onset, [1., 2., 12., 21., 22., 31., 5])
assert_array_equal(raw.annotations.duration, [.5, .5, .5, .5, .5, .5, 1.5])
assert_array_equal(raw.annotations.description,
['x', 'x', 'x', 'x', 'x', 'x', 'y'])
# Test concatenating annotations with and without orig_time.
raw = read_raw_fif(fif_fname)
last_time = raw.last_samp / raw.info['sfreq']
raw2 = raw.copy()
raw.annotations = Annotations([45.], [3], 'test', raw.info['meas_date'])
raw2.annotations = Annotations([2.], [3], 'BAD', None)
raw = concatenate_raws([raw, raw2])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
assert_array_almost_equal(raw.annotations.onset, [45., 2. + last_time],
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)
