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_annotation_concat():
"""Test if two Annotations objects can be concatenated."""
a = Annotations([1, 2, 3], [5, 5, 8], ["a", "b", "c"])
b = Annotations([11, 12, 13], [1, 2, 2], ["x", "y", "z"])
# test + operator (does not modify a or b)
c = a + b
assert_array_equal(c.onset, [1, 2, 3, 11, 12, 13])
assert_array_equal(c.duration, [5, 5, 8, 1, 2, 2])
assert_array_equal(c.description, ["a", "b", "c", "x", "y", "z"])
assert_equal(len(a), 3)
assert_equal(len(b), 3)
assert_equal(len(c), 6)
# test += operator (modifies a in place)
a += b
assert_array_equal(a.onset, [1, 2, 3, 11, 12, 13])
assert_array_equal(a.duration, [5, 5, 8, 1, 2, 2])
assert_array_equal(a.description, ["a", "b", "c", "x", "y", "z"])
assert_equal(len(a), 6)
assert_equal(len(b), 3)
# test += operator (modifies a in place)
b._orig_time = _handle_meas_date(1038942070.7201)
with pytest.raises(ValueError, match='orig_time should be the same'):
a += b
def test_chunk_duration(first_samp):
"""Test chunk_duration."""
# create dummy raw
raw = RawArray(data=np.empty([10, 10], dtype=np.float64),
info=create_info(ch_names=10, sfreq=1.),
first_samp=first_samp)
raw.info['meas_date'] = _handle_meas_date(0)
raw.set_annotations(
Annotations(description='foo',
onset=[0],
duration=[10],
orig_time=None))
assert raw.annotations.orig_time == raw.info['meas_date']
assert_allclose(raw.annotations.onset, [first_samp])
# expected_events = [[0, 0, 1], [0, 0, 1], [1, 0, 1], [1, 0, 1], ..
# [9, 0, 1], [9, 0, 1]]
expected_events = np.atleast_2d(np.repeat(range(10), repeats=2)).T
expected_events = np.insert(expected_events, 1, 0, axis=1)
expected_events = np.insert(expected_events, 2, 1, axis=1)
expected_events[:, 0] += first_samp
events, events_id = events_from_annotations(raw,
chunk_duration=.5,
use_rounding=False)
assert_array_equal(events, expected_events)
# test chunk durations that do not fit equally in annotation duration
expected_events = np.zeros((3, 3))
expected_events[:, -1] = 1
expected_events[:, 0] = np.arange(0, 9, step=3) + first_samp
events, events_id = events_from_annotations(raw, chunk_duration=3.)
assert_array_equal(events, expected_events)
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_io_annotation_csv(dummy_annotation_csv_file,
dummy_broken_annotation_csv_file,
tmpdir_factory):
"""Test CSV input/output."""
annot = read_annotations(str(dummy_annotation_csv_file))
assert annot.orig_time == _handle_meas_date(1038942071.7201)
assert_array_equal(annot.onset, np.array([0., 9.], dtype=np.float32))
assert_array_almost_equal(annot.duration, [1., 2.425])
assert_array_equal(annot.description, ['AA', 'BB'])
# Now test writing
fname = str(tmpdir_factory.mktemp('data').join('annotations.csv'))
annot.save(fname)
annot2 = read_annotations(fname)
_assert_annotations_equal(annot, annot2)
# Now without an orig_time
annot._orig_time = None
annot.save(fname)
annot2 = read_annotations(fname)
_assert_annotations_equal(annot, annot2)
# Test broken .csv that does not use timestamps
with pytest.warns(RuntimeWarning, match='save your CSV as a TXT'):
annot2 = read_annotations(str(dummy_broken_annotation_csv_file))
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_events_from_annot_onset_alingment():
"""Test events and annotations onset are the same."""
raw = _raw_annot(meas_date=1, orig_time=1.5)
# sec 0 1 2 3
# raw . |--------XXXXXXXXX
# annot . |---XX
# raw.annot . |--------XX
# latency . 0 1 2
# . 0 0
assert raw.annotations.orig_time == _handle_meas_date(1)
assert raw.annotations.onset[0] == 1
assert raw.first_samp == 10
event_latencies, event_id = events_from_annotations(raw)
assert event_latencies[0, 0] == 10
assert raw.first_samp == event_latencies[0, 0]
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_io_annotation_txt(dummy_annotation_txt_file, tmpdir_factory):
"""Test TXT input/output."""
annot = read_annotations(str(dummy_annotation_txt_file))
assert annot.orig_time is None
assert_array_equal(annot.onset, [3.14, 6.28])
assert_array_equal(annot.duration, [42., 48])
assert_array_equal(annot.description, ['AA', 'BB'])
# Now test writing
fname = str(tmpdir_factory.mktemp('data').join('annotations.txt'))
annot.save(fname)
annot2 = read_annotations(fname)
_assert_annotations_equal(annot, annot2)
# Now with an orig_time
assert annot.orig_time is None
annot._orig_time = _handle_meas_date(1038942071.7201)
assert annot.orig_time is not None
annot.save(fname)
annot2 = read_annotations(fname)
assert annot2.orig_time is not None
_assert_annotations_equal(annot, annot2)
def _test_raw_reader(reader, test_preloading=True, **kwargs):
"""Test reading, writing and slicing of raw classes.
Parameters
----------
reader : function
Function to test.
test_preloading : bool
Whether not preloading is implemented for the reader. If True, both
cases and memory mapping to file are tested.
**kwargs :
Arguments for the reader. Note: Do not use preload as kwarg.
Use ``test_preloading`` instead.
Returns
-------
raw : Instance of Raw
A preloaded Raw object.
"""
tempdir = _TempDir()
rng = np.random.RandomState(0)
if test_preloading:
raw = reader(preload=True, **kwargs)
# don't assume the first is preloaded
buffer_fname = op.join(tempdir, 'buffer')
picks = rng.permutation(np.arange(len(raw.ch_names) - 1))[:10]
picks = np.append(picks, len(raw.ch_names) - 1) # test trigger channel
bnd = min(int(round(raw.buffer_size_sec * raw.info['sfreq'])),
raw.n_times)
slices = [
slice(0, bnd),
slice(bnd - 1, bnd),
slice(3, bnd),
slice(3, 300),
slice(None),
slice(1, bnd)
]
if raw.n_times >= 2 * bnd: # at least two complete blocks
slices += [
slice(bnd, 2 * bnd),
slice(bnd, bnd + 1),
slice(0, bnd + 100)
]
other_raws = [
reader(preload=buffer_fname, **kwargs),
reader(preload=False, **kwargs)
]
for sl_time in slices:
data1, times1 = raw[picks, sl_time]
for other_raw in other_raws:
data2, times2 = other_raw[picks, sl_time]
assert_allclose(data1, data2)
assert_allclose(times1, times2)
else:
raw = reader(**kwargs)
full_data = raw._data
assert raw.__class__.__name__ in repr(raw) # to test repr
assert raw.info.__class__.__name__ in repr(raw.info)
# gh-5604
assert _handle_meas_date(raw.info['meas_date']) >= 0
# Test saving and reading
out_fname = op.join(tempdir, 'test_raw.fif')
raw = concatenate_raws([raw])
raw.save(out_fname, tmax=raw.times[-1], overwrite=True, buffer_size_sec=1)
raw3 = read_raw_fif(out_fname)
assert set(raw.info.keys()) == set(raw3.info.keys())
assert_allclose(raw3[0:20][0], full_data[0:20], rtol=1e-6,
atol=1e-20) # atol is very small but > 0
assert_array_almost_equal(raw.times, raw3.times)
assert not math.isnan(raw3.info['highpass'])
assert not math.isnan(raw3.info['lowpass'])
assert not math.isnan(raw.info['highpass'])
assert not math.isnan(raw.info['lowpass'])
assert raw3.info['kit_system_id'] == raw.info['kit_system_id']
# Make sure concatenation works
first_samp = raw.first_samp
last_samp = raw.last_samp
concat_raw = concatenate_raws([raw.copy(), raw])
assert_equal(concat_raw.n_times, 2 * raw.n_times)
assert_equal(concat_raw.first_samp, first_samp)
assert_equal(concat_raw.last_samp - last_samp + first_samp, last_samp + 1)
idx = np.where(concat_raw.annotations.description == 'BAD boundary')[0]
if concat_raw.info['meas_date'] is None:
expected_bad_boundary_onset = ((last_samp - first_samp) /
raw.info['sfreq'])
else:
expected_bad_boundary_onset = raw._last_time
assert_array_almost_equal(concat_raw.annotations.onset[idx],
expected_bad_boundary_onset,
decimal=2)
if raw.info['meas_id'] is not None:
for key in ['secs', 'usecs', 'version']:
assert_equal(raw.info['meas_id'][key], raw3.info['meas_id'][key])
assert_array_equal(raw.info['meas_id']['machid'],
raw3.info['meas_id']['machid'])
assert isinstance(raw.annotations, Annotations)
return raw
def test_handle_meas_date(meas_date, out):
"""Test meas date formats."""
assert _handle_meas_date(meas_date) == out
def _test_raw_reader(reader, test_preloading=True, test_kwargs=True, **kwargs):
"""Test reading, writing and slicing of raw classes.
Parameters
----------
reader : function
Function to test.
test_preloading : bool
Whether not preloading is implemented for the reader. If True, both
cases and memory mapping to file are tested.
**kwargs :
Arguments for the reader. Note: Do not use preload as kwarg.
Use ``test_preloading`` instead.
Returns
-------
raw : instance of Raw
A preloaded Raw object.
"""
tempdir = _TempDir()
rng = np.random.RandomState(0)
if test_preloading:
raw = reader(preload=True, **kwargs)
# don't assume the first is preloaded
buffer_fname = op.join(tempdir, 'buffer')
picks = rng.permutation(np.arange(len(raw.ch_names) - 1))[:10]
picks = np.append(picks, len(raw.ch_names) - 1) # test trigger channel
bnd = min(int(round(raw.buffer_size_sec *
raw.info['sfreq'])), raw.n_times)
slices = [slice(0, bnd), slice(bnd - 1, bnd), slice(3, bnd),
slice(3, 300), slice(None), slice(1, bnd)]
if raw.n_times >= 2 * bnd: # at least two complete blocks
slices += [slice(bnd, 2 * bnd), slice(bnd, bnd + 1),
slice(0, bnd + 100)]
other_raws = [reader(preload=buffer_fname, **kwargs),
reader(preload=False, **kwargs)]
for sl_time in slices:
data1, times1 = raw[picks, sl_time]
for other_raw in other_raws:
data2, times2 = other_raw[picks, sl_time]
assert_allclose(data1, data2)
assert_allclose(times1, times2)
else:
raw = reader(**kwargs)
full_data = raw._data
assert raw.__class__.__name__ in repr(raw) # to test repr
assert raw.info.__class__.__name__ in repr(raw.info)
# gh-5604
assert _handle_meas_date(raw.info['meas_date']) >= 0
# test resetting raw
if test_kwargs:
raw2 = reader(**raw._init_kwargs)
assert set(raw.info.keys()) == set(raw2.info.keys())
assert_array_equal(raw.times, raw2.times)
# Test saving and reading
out_fname = op.join(tempdir, 'test_raw.fif')
raw = concatenate_raws([raw])
raw.save(out_fname, tmax=raw.times[-1], overwrite=True, buffer_size_sec=1)
raw3 = read_raw_fif(out_fname)
assert set(raw.info.keys()) == set(raw3.info.keys())
assert_allclose(raw3[0:20][0], full_data[0:20], rtol=1e-6,
atol=1e-20) # atol is very small but > 0
assert_array_almost_equal(raw.times, raw3.times)
assert not math.isnan(raw3.info['highpass'])
assert not math.isnan(raw3.info['lowpass'])
assert not math.isnan(raw.info['highpass'])
assert not math.isnan(raw.info['lowpass'])
assert raw3.info['kit_system_id'] == raw.info['kit_system_id']
# Make sure concatenation works
first_samp = raw.first_samp
last_samp = raw.last_samp
concat_raw = concatenate_raws([raw.copy(), raw])
assert concat_raw.n_times == 2 * raw.n_times
assert concat_raw.first_samp == first_samp
assert concat_raw.last_samp - last_samp + first_samp == last_samp + 1
idx = np.where(concat_raw.annotations.description == 'BAD boundary')[0]
if concat_raw.info['meas_date'] is None:
expected_bad_boundary_onset = ((last_samp - first_samp) /
raw.info['sfreq'])
else:
expected_bad_boundary_onset = raw._last_time
assert_array_almost_equal(concat_raw.annotations.onset[idx],
expected_bad_boundary_onset,
decimal=2)
if raw.info['meas_id'] is not None:
for key in ['secs', 'usecs', 'version']:
assert raw.info['meas_id'][key] == raw3.info['meas_id'][key]
assert_array_equal(raw.info['meas_id']['machid'],
raw3.info['meas_id']['machid'])
assert isinstance(raw.annotations, Annotations)
# Make a "soft" test on units: They have to be valid SI units as in
# mne.io.meas_info.valid_units, but we accept any lower/upper case for now.
valid_units = _get_valid_units()
valid_units_lower = [unit.lower() for unit in valid_units]
if raw._orig_units is not None:
assert isinstance(raw._orig_units, dict)
for ch_name, unit in raw._orig_units.items():
assert unit.lower() in valid_units_lower, ch_name
return raw
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'])
def test_handle_meas_date(meas_date, out):
"""Test meas date formats."""
assert _handle_meas_date(meas_date) == out
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])
raw.annotations.delete(-1) # remove boundary annotations
raw.annotations.delete(-1)
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')
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, [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, [124., 125., 135., 144.,
145., 154., 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_raw_reader(reader,
test_preloading=True,
test_kwargs=True,
boundary_decimal=2,
**kwargs):
"""Test reading, writing and slicing of raw classes.
Parameters
----------
reader : function
Function to test.
test_preloading : bool
Whether not preloading is implemented for the reader. If True, both
cases and memory mapping to file are tested.
test_kwargs : dict
Test _init_kwargs support.
boundary_decimal : int
Number of decimals up to which the boundary should match.
**kwargs :
Arguments for the reader. Note: Do not use preload as kwarg.
Use ``test_preloading`` instead.
Returns
-------
raw : instance of Raw
A preloaded Raw object.
"""
tempdir = _TempDir()
rng = np.random.RandomState(0)
montage = None
if "montage" in kwargs:
montage = kwargs['montage']
del kwargs['montage']
if test_preloading:
raw = reader(preload=True, **kwargs)
if montage is not None:
raw.set_montage(montage)
# don't assume the first is preloaded
buffer_fname = op.join(tempdir, 'buffer')
picks = rng.permutation(np.arange(len(raw.ch_names) - 1))[:10]
picks = np.append(picks, len(raw.ch_names) - 1) # test trigger channel
bnd = min(int(round(raw.buffer_size_sec * raw.info['sfreq'])),
raw.n_times)
slices = [
slice(0, bnd),
slice(bnd - 1, bnd),
slice(3, bnd),
slice(3, 300),
slice(None),
slice(1, bnd)
]
if raw.n_times >= 2 * bnd: # at least two complete blocks
slices += [
slice(bnd, 2 * bnd),
slice(bnd, bnd + 1),
slice(0, bnd + 100)
]
other_raws = [
reader(preload=buffer_fname, **kwargs),
reader(preload=False, **kwargs)
]
for sl_time in slices:
data1, times1 = raw[picks, sl_time]
for other_raw in other_raws:
data2, times2 = other_raw[picks, sl_time]
assert_allclose(data1, data2)
assert_allclose(times1, times2)
else:
raw = reader(**kwargs)
full_data = raw._data
assert raw.__class__.__name__ in repr(raw) # to test repr
assert raw.info.__class__.__name__ in repr(raw.info)
assert isinstance(raw.info['dig'], (type(None), list))
if isinstance(raw.info['dig'], list):
for di, d in enumerate(raw.info['dig']):
assert isinstance(d, DigPoint), (di, d)
# gh-5604
assert _handle_meas_date(raw.info['meas_date']) >= 0
# test resetting raw
if test_kwargs:
raw2 = reader(**raw._init_kwargs)
assert set(raw.info.keys()) == set(raw2.info.keys())
assert_array_equal(raw.times, raw2.times)
# Test saving and reading
out_fname = op.join(tempdir, 'test_raw.fif')
raw = concatenate_raws([raw])
raw.save(out_fname, tmax=raw.times[-1], overwrite=True, buffer_size_sec=1)
raw3 = read_raw_fif(out_fname)
assert set(raw.info.keys()) == set(raw3.info.keys())
assert_allclose(raw3[0:20][0], full_data[0:20], rtol=1e-6,
atol=1e-20) # atol is very small but > 0
assert_array_almost_equal(raw.times, raw3.times)
assert not math.isnan(raw3.info['highpass'])
assert not math.isnan(raw3.info['lowpass'])
assert not math.isnan(raw.info['highpass'])
assert not math.isnan(raw.info['lowpass'])
assert raw3.info['kit_system_id'] == raw.info['kit_system_id']
# Make sure concatenation works
first_samp = raw.first_samp
last_samp = raw.last_samp
concat_raw = concatenate_raws([raw.copy(), raw])
assert concat_raw.n_times == 2 * raw.n_times
assert concat_raw.first_samp == first_samp
assert concat_raw.last_samp - last_samp + first_samp == last_samp + 1
idx = np.where(concat_raw.annotations.description == 'BAD boundary')[0]
if concat_raw.info['meas_date'] is None:
expected_bad_boundary_onset = ((last_samp - first_samp) /
raw.info['sfreq'])
else:
expected_bad_boundary_onset = raw._last_time
assert_array_almost_equal(concat_raw.annotations.onset[idx],
expected_bad_boundary_onset,
decimal=boundary_decimal)
if raw.info['meas_id'] is not None:
for key in ['secs', 'usecs', 'version']:
assert raw.info['meas_id'][key] == raw3.info['meas_id'][key]
assert_array_equal(raw.info['meas_id']['machid'],
raw3.info['meas_id']['machid'])
assert isinstance(raw.annotations, Annotations)
# Make a "soft" test on units: They have to be valid SI units as in
# mne.io.meas_info.valid_units, but we accept any lower/upper case for now.
valid_units = _get_valid_units()
valid_units_lower = [unit.lower() for unit in valid_units]
if raw._orig_units is not None:
assert isinstance(raw._orig_units, dict)
for ch_name, unit in raw._orig_units.items():
assert unit.lower() in valid_units_lower, ch_name
return raw
def test_handle_meas_date(meas_date, out):
"""Test meas date formats."""
if out is not None:
assert out >= 0 # otherwise it'll break on Windows
out = datetime.fromtimestamp(out, timezone.utc)
assert _handle_meas_date(meas_date) == out
