def test_how_to_deal_with_warnings():
"""Test filter some messages out of warning records."""
with pytest.warns(UserWarning, match='bb') as w:
warnings.warn("aa warning", UserWarning)
warnings.warn("bb warning", UserWarning)
warnings.warn("bb warning", RuntimeWarning)
warnings.warn("aa warning", UserWarning)
filter_out_warnings(w, category=UserWarning, match='aa')
filter_out_warnings(w, category=RuntimeWarning)
assert len(w) == 1
def test_how_to_deal_with_warnings():
"""Test filter some messages out of warning records."""
with pytest.warns(UserWarning, match='bb') as w:
warnings.warn("aa warning", UserWarning)
warnings.warn("bb warning", UserWarning)
warnings.warn("bb warning", RuntimeWarning)
warnings.warn("aa warning", UserWarning)
filter_out_warnings(w, category=UserWarning, match='aa')
filter_out_warnings(w, category=RuntimeWarning)
assert len(w) == 1
def test_io_set_raw(fnames, tmpdir):
"""Test importing EEGLAB .set files."""
tmpdir = str(tmpdir)
raw_fname, raw_fname_onefile = fnames
with pytest.warns(RuntimeWarning) as w:
_test_raw_reader(read_raw_eeglab,
input_fname=raw_fname,
montage=montage)
_test_raw_reader(read_raw_eeglab,
input_fname=raw_fname_onefile,
montage=montage)
for want in ('Events like', 'could not be mapped',
'string preload is not supported'):
assert (any(want in str(ww.message) for ww in w))
with pytest.warns(RuntimeWarning) as w:
# test finding events in continuous data
event_id = {'rt': 1, 'square': 2}
raw0 = read_raw_eeglab(input_fname=raw_fname,
montage=montage,
event_id=event_id,
preload=True)
raw1 = read_raw_eeglab(input_fname=raw_fname,
montage=montage,
event_id=event_id,
preload=False)
raw2 = read_raw_eeglab(input_fname=raw_fname_onefile,
montage=montage,
event_id=event_id)
raw3 = read_raw_eeglab(input_fname=raw_fname,
montage=montage,
event_id=event_id)
raw4 = read_raw_eeglab(input_fname=raw_fname, montage=montage)
assert raw0.filenames[0].endswith('.fdt') # .set with additional .fdt
assert raw2.filenames[0].endswith('.set') # standalone .set
raw0_events = find_events(raw0)
assert raw0_events.size
Epochs(raw0, raw0_events, event_id)
epochs = Epochs(raw1, find_events(raw1), event_id)
assert len(find_events(raw4)) == 0 # no events without event_id
assert epochs["square"].average().nave == 80 # 80 with
assert_array_equal(raw0[:][0], raw1[:][0], raw2[:][0], raw3[:][0])
assert_array_equal(raw0[:][-1], raw1[:][-1], raw2[:][-1], raw3[:][-1])
# 1 for preload=False / str with fname_onefile, 3 for dropped events
raw0.filter(1,
None,
l_trans_bandwidth='auto',
filter_length='auto',
phase='zero') # test that preloading works
filter_out_warnings(w, category=FutureWarning)
filter_out_warnings(w, category=ImportWarning)
assert len(w) == 3 # check `preload=False` raises RuntimeWarning
# test that using uint16_codec does not break stuff
raw0 = read_raw_eeglab(input_fname=raw_fname,
montage=montage,
event_id=event_id,
preload=False,
uint16_codec='ascii')
# test old EEGLAB version event import (read old version)
eeg = io.loadmat(raw_fname_mat, struct_as_record=False,
squeeze_me=True)['EEG']
for event in eeg.event: # old version allows integer events
event.type = 1
with pytest.warns(DeprecationWarning, match="read_events_eeglab"):
assert read_events_eeglab(eeg)[-1, -1] == 1
eeg.event = eeg.event[0] # single event
eeg.event.latency = float(eeg.event.latency) - .1 # test rounding
with pytest.warns(DeprecationWarning, match="read_events_eeglab"):
assert read_events_eeglab(eeg)[-1, -1] == 1
# test reading file with one event (read old version)
eeg = io.loadmat(raw_fname_mat, struct_as_record=False,
squeeze_me=True)['EEG']
one_event_fname = op.join(tmpdir, 'test_one_event.set')
io.savemat(one_event_fname, {
'EEG': {
'trials': eeg.trials,
'srate': eeg.srate,
'nbchan': eeg.nbchan,
'data': 'test_one_event.fdt',
'epoch': eeg.epoch,
'event': eeg.event[0],
'chanlocs': eeg.chanlocs,
'pnts': eeg.pnts
}
},
appendmat=False,
oned_as='row')
shutil.copyfile(op.join(base_dir, 'test_raw.fdt'),
one_event_fname.replace('.set', '.fdt'))
event_id = {eeg.event[0].type: 1}
test_raw = read_raw_eeglab(input_fname=one_event_fname,
montage=montage,
event_id=event_id,
preload=True)
# test that sample indices are read python-wise (zero-based)
assert find_events(test_raw)[0, 0] == round(eeg.event[0].latency) - 1
# test negative event latencies
negative_latency_fname = op.join(tmpdir, 'test_negative_latency.set')
evnts = deepcopy(eeg.event[0])
evnts.latency = 0
io.savemat(negative_latency_fname, {
'EEG': {
'trials': eeg.trials,
'srate': eeg.srate,
'nbchan': eeg.nbchan,
'data': 'test_negative_latency.fdt',
'epoch': eeg.epoch,
'event': evnts,
'chanlocs': eeg.chanlocs,
'pnts': eeg.pnts
}
},
appendmat=False,
oned_as='row')
shutil.copyfile(op.join(base_dir, 'test_raw.fdt'),
negative_latency_fname.replace('.set', '.fdt'))
event_id = {eeg.event[0].type: 1}
with pytest.warns(RuntimeWarning, match="has a sample index of -1."):
read_raw_eeglab(input_fname=negative_latency_fname,
preload=True,
event_id=event_id,
montage=montage)
evnts.latency = -1
io.savemat(negative_latency_fname, {
'EEG': {
'trials': eeg.trials,
'srate': eeg.srate,
'nbchan': eeg.nbchan,
'data': 'test_negative_latency.fdt',
'epoch': eeg.epoch,
'event': evnts,
'chanlocs': eeg.chanlocs,
'pnts': eeg.pnts
}
},
appendmat=False,
oned_as='row')
with pytest.raises(ValueError, match='event sample index is negative'):
with pytest.warns(RuntimeWarning, match="has a sample index of -1."):
read_raw_eeglab(input_fname=negative_latency_fname,
preload=True,
event_id=event_id,
montage=montage)
# test overlapping events
overlap_fname = op.join(tmpdir, 'test_overlap_event.set')
io.savemat(overlap_fname, {
'EEG': {
'trials': eeg.trials,
'srate': eeg.srate,
'nbchan': eeg.nbchan,
'data': 'test_overlap_event.fdt',
'epoch': eeg.epoch,
'event': [eeg.event[0], eeg.event[0]],
'chanlocs': eeg.chanlocs,
'pnts': eeg.pnts
}
},
appendmat=False,
oned_as='row')
shutil.copyfile(op.join(base_dir, 'test_raw.fdt'),
overlap_fname.replace('.set', '.fdt'))
event_id = {'rt': 1, 'square': 2}
with pytest.warns(RuntimeWarning, match='will be dropped'):
raw = read_raw_eeglab(input_fname=overlap_fname,
montage=montage,
event_id=event_id,
preload=True)
events_stimchan = find_events(raw)
with pytest.warns(DeprecationWarning, match="read_events_eeglab"):
events_read_events_eeglab = read_events_eeglab(overlap_fname, event_id)
assert (len(events_stimchan) == 1)
assert (len(events_read_events_eeglab) == 2)
# test reading file with one channel
one_chan_fname = op.join(tmpdir, 'test_one_channel.set')
io.savemat(one_chan_fname, {
'EEG': {
'trials': eeg.trials,
'srate': eeg.srate,
'nbchan': 1,
'data': np.random.random((1, 3)),
'epoch': eeg.epoch,
'event': eeg.epoch,
'chanlocs': {
'labels': 'E1',
'Y': -6.6069,
'X': 6.3023,
'Z': -2.9423
},
'times': eeg.times[:3],
'pnts': 3
}
},
appendmat=False,
oned_as='row')
with pytest.warns(None) as w:
read_raw_eeglab(input_fname=one_chan_fname, preload=True)
# no warning for 'no events found'
assert len(w) == 0
# test reading file with 3 channels - one without position information
# first, create chanlocs structured array
ch_names = ['F3', 'unknown', 'FPz']
x, y, z = [1., 2., np.nan], [4., 5., np.nan], [7., 8., np.nan]
dt = [('labels', 'S10'), ('X', 'f8'), ('Y', 'f8'), ('Z', 'f8')]
chanlocs = np.zeros((3, ), dtype=dt)
for ind, vals in enumerate(zip(ch_names, x, y, z)):
for fld in range(4):
chanlocs[ind][dt[fld][0]] = vals[fld]
if LooseVersion(np.__version__) == '1.14.0':
# There is a bug in 1.14.0 (or maybe with SciPy 1.0.0?) that causes
# this write to fail!
raise SkipTest('Need to fix bug in NumPy 1.14.0!')
# save set file
one_chanpos_fname = op.join(tmpdir, 'test_chanpos.set')
io.savemat(one_chanpos_fname, {
'EEG': {
'trials': eeg.trials,
'srate': eeg.srate,
'nbchan': 3,
'data': np.random.random((3, 3)),
'epoch': eeg.epoch,
'event': eeg.epoch,
'chanlocs': chanlocs,
'times': eeg.times[:3],
'pnts': 3
}
},
appendmat=False,
oned_as='row')
# load it
with pytest.warns(RuntimeWarning, match='did not have a position'):
raw = read_raw_eeglab(input_fname=one_chanpos_fname, preload=True)
# position should be present for first two channels
for i in range(2):
assert_array_equal(
raw.info['chs'][i]['loc'][:3],
np.array([-chanlocs[i]['Y'], chanlocs[i]['X'], chanlocs[i]['Z']]))
# position of the last channel should be zero
assert_array_equal(raw.info['chs'][-1]['loc'][:3], [np.nan] * 3)
# test reading channel names from set and positions from montage
with pytest.warns(RuntimeWarning, match='did not have a position'):
raw = read_raw_eeglab(input_fname=one_chanpos_fname,
preload=True,
montage=montage)
# when montage was passed - channel positions should be taken from there
correct_pos = [[-0.56705965, 0.67706631, 0.46906776], [np.nan] * 3,
[0., 0.99977915, -0.02101571]]
for ch_ind in range(3):
assert_array_almost_equal(raw.info['chs'][ch_ind]['loc'][:3],
np.array(correct_pos[ch_ind]))
# test reading channel names but not positions when there is no X (only Z)
# field in the EEG.chanlocs structure
nopos_chanlocs = chanlocs[['labels', 'Z']]
nopos_fname = op.join(tmpdir, 'test_no_chanpos.set')
io.savemat(nopos_fname, {
'EEG': {
'trials': eeg.trials,
'srate': eeg.srate,
'nbchan': 3,
'data': np.random.random((3, 2)),
'epoch': eeg.epoch,
'event': eeg.epoch,
'chanlocs': nopos_chanlocs,
'times': eeg.times[:2],
'pnts': 2
}
},
appendmat=False,
oned_as='row')
# load the file
raw = read_raw_eeglab(input_fname=nopos_fname, preload=True)
# test that channel names have been loaded but not channel positions
for i in range(3):
assert_equal(raw.info['chs'][i]['ch_name'], ch_names[i])
assert_array_equal(raw.info['chs'][i]['loc'][:3],
np.array([np.nan, np.nan, np.nan]))