def test_compute_proj_ecg():
"""Test computation of ECG SSP projectors"""
raw = Raw(raw_fname).crop(0, 10, False)
raw.preload_data()
for average in [False, True]:
# For speed, let's not filter here (must also not reject then)
projs, events = compute_proj_ecg(raw, n_mag=2, n_grad=2, n_eeg=2,
ch_name='MEG 1531', bads=['MEG 2443'],
average=average, avg_ref=True,
no_proj=True, l_freq=None,
h_freq=None, reject=None,
tmax=dur_use, qrs_threshold=0.5)
assert_true(len(projs) == 7)
# heart rate at least 0.5 Hz, but less than 3 Hz
assert_true(events.shape[0] > 0.5 * dur_use and
events.shape[0] < 3 * dur_use)
# XXX: better tests
# without setting a bad channel, this should throw a warning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
projs, events = compute_proj_ecg(raw, n_mag=2, n_grad=2, n_eeg=2,
ch_name='MEG 1531', bads=[],
average=average, avg_ref=True,
no_proj=True, l_freq=None,
h_freq=None, tmax=dur_use)
assert_equal(len(w), 1)
assert_equal(projs, None)
def test_compute_proj_ecg(short_raw, average):
"""Test computation of ECG SSP projectors."""
raw = short_raw
# For speed, let's not filter here (must also not reject then)
with pytest.warns(RuntimeWarning, match='Attenuation'):
projs, events = compute_proj_ecg(raw,
n_mag=2,
n_grad=2,
n_eeg=2,
ch_name='MEG 1531',
bads=['MEG 2443'],
average=average,
avg_ref=True,
no_proj=True,
l_freq=None,
h_freq=None,
reject=None,
tmax=dur_use,
qrs_threshold=0.5,
filter_length=1000)
assert len(projs) == 7
# heart rate at least 0.5 Hz, but less than 3 Hz
assert (events.shape[0] > 0.5 * dur_use and events.shape[0] < 3 * dur_use)
ssp_ecg = [proj for proj in projs if proj['desc'].startswith('ECG')]
# check that the first principal component have a certain minimum
ssp_ecg = [proj for proj in ssp_ecg if 'PCA-01' in proj['desc']]
thresh_eeg, thresh_axial, thresh_planar = .9, .3, .1
for proj in ssp_ecg:
if 'planar' in proj['desc']:
assert proj['explained_var'] > thresh_planar
elif 'axial' in proj['desc']:
assert proj['explained_var'] > thresh_axial
elif 'eeg' in proj['desc']:
assert proj['explained_var'] > thresh_eeg
# XXX: better tests
# without setting a bad channel, this should throw a warning
with pytest.warns(RuntimeWarning, match='No good epochs found'):
projs, events, drop_log = compute_proj_ecg(
raw,
n_mag=2,
n_grad=2,
n_eeg=2,
ch_name='MEG 1531',
bads=[],
average=average,
avg_ref=True,
no_proj=True,
l_freq=None,
h_freq=None,
tmax=dur_use,
return_drop_log=True,
# XXX can be removed once
# XXX https://github.com/mne-tools/mne-python/issues/9273
# XXX has been resolved:
qrs_threshold=1e-15)
assert projs == []
assert len(events) == len(drop_log)
def test_compute_proj_ecg():
"""Test computation of ECG SSP projectors."""
raw = read_raw_fif(raw_fname).crop(0, 10)
raw.load_data()
for average in [False, True]:
# For speed, let's not filter here (must also not reject then)
projs, events = compute_proj_ecg(raw,
n_mag=2,
n_grad=2,
n_eeg=2,
ch_name='MEG 1531',
bads=['MEG 2443'],
average=average,
avg_ref=True,
no_proj=True,
l_freq=None,
h_freq=None,
reject=None,
tmax=dur_use,
qrs_threshold=0.5,
filter_length=6000)
assert len(projs) == 7
# heart rate at least 0.5 Hz, but less than 3 Hz
assert_true(events.shape[0] > 0.5 * dur_use
and events.shape[0] < 3 * dur_use)
ssp_ecg = [proj for proj in projs if proj['desc'].startswith('ECG')]
# check that the first principal component have a certain minimum
ssp_ecg = [proj for proj in ssp_ecg if 'PCA-01' in proj['desc']]
thresh_eeg, thresh_axial, thresh_planar = .9, .3, .1
for proj in ssp_ecg:
if 'planar' in proj['desc']:
assert proj['explained_var'] > thresh_planar
elif 'axial' in proj['desc']:
assert proj['explained_var'] > thresh_axial
elif 'eeg' in proj['desc']:
assert proj['explained_var'] > thresh_eeg
# XXX: better tests
# without setting a bad channel, this should throw a warning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
projs, events, drop_log = compute_proj_ecg(raw,
n_mag=2,
n_grad=2,
n_eeg=2,
ch_name='MEG 1531',
bads=[],
average=average,
avg_ref=True,
no_proj=True,
l_freq=None,
h_freq=None,
tmax=dur_use,
return_drop_log=True)
assert len(w) >= 1
assert projs is None
assert len(events) == len(drop_log)
def test_compute_proj_ecg_eog_deprecation_warning():
raw = read_raw_fif(raw_fname).crop(0, 10)
raw.load_data()
with pytest.warns(DeprecationWarning, match='average'):
_, _ = compute_proj_ecg(raw)
_, _ = compute_proj_eog(raw)
with pytest.warns(None):
for a in (True, False):
_, _ = compute_proj_ecg(raw, average=a)
_, _ = compute_proj_eog(raw, average=a)
def test_compute_proj_ecg():
"""Test computation of ECG SSP projectors"""
raw = Raw(raw_fname).crop(0, 10, False)
raw.preload_data()
for average in [False, True]:
# For speed, let's not filter here (must also not reject then)
projs, events = compute_proj_ecg(raw,
n_mag=2,
n_grad=2,
n_eeg=2,
ch_name='MEG 1531',
bads=['MEG 2443'],
average=average,
avg_ref=True,
no_proj=True,
l_freq=None,
h_freq=None,
reject=None,
tmax=dur_use,
qrs_threshold=0.5)
assert_true(len(projs) == 7)
# heart rate at least 0.5 Hz, but less than 3 Hz
assert_true(events.shape[0] > 0.5 * dur_use
and events.shape[0] < 3 * dur_use)
# XXX: better tests
# without setting a bad channel, this should throw a warning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
projs, events = compute_proj_ecg(raw,
n_mag=2,
n_grad=2,
n_eeg=2,
ch_name='MEG 1531',
bads=[],
average=average,
avg_ref=True,
no_proj=True,
l_freq=None,
h_freq=None,
tmax=dur_use)
assert_equal(len(w), 1)
assert_equal(projs, None)
def test_compute_proj_ctf():
"""Test to show that projector code completes on CTF data."""
raw = read_raw_ctf(ctf_fname)
raw.load_data()
# expected channels per projector type
n_mags = len(pick_types(raw.info, meg='mag', ref_meg=False,
exclude='bads'))
n_grads = len(
pick_types(raw.info, meg='grad', ref_meg=False, exclude='bads'))
n_eegs = len(
pick_types(raw.info,
meg=False,
eeg=True,
ref_meg=False,
exclude='bads'))
# Test with and without gradient compensation
for c in [0, 1]:
raw.apply_gradient_compensation(c)
for average in [False, True]:
n_projs_init = len(raw.info['projs'])
projs, events = compute_proj_eog(raw,
n_mag=2,
n_grad=2,
n_eeg=2,
average=average,
ch_name='EEG059',
avg_ref=True,
no_proj=False,
l_freq=None,
h_freq=None,
reject=None,
tmax=dur_use,
filter_length=6000)
_check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs)
assert len(projs) == (5 + n_projs_init)
projs, events = compute_proj_ecg(raw,
n_mag=1,
n_grad=1,
n_eeg=2,
average=average,
ch_name='EEG059',
avg_ref=True,
no_proj=False,
l_freq=None,
h_freq=None,
reject=None,
tmax=dur_use,
filter_length=6000)
_check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs)
assert len(projs) == (4 + n_projs_init)
def test_compute_proj_ecg():
"""Test computation of ECG SSP projectors."""
raw = read_raw_fif(raw_fname, add_eeg_ref=False).crop(0, 10, copy=False)
raw.load_data()
for average in [False, True]:
# For speed, let's not filter here (must also not reject then)
projs, events = compute_proj_ecg(raw, n_mag=2, n_grad=2, n_eeg=2,
ch_name='MEG 1531', bads=['MEG 2443'],
average=average, avg_ref=True,
no_proj=True, l_freq=None,
h_freq=None, reject=None,
tmax=dur_use, qrs_threshold=0.5,
filter_length=6000)
assert_true(len(projs) == 7)
# heart rate at least 0.5 Hz, but less than 3 Hz
assert_true(events.shape[0] > 0.5 * dur_use and
events.shape[0] < 3 * dur_use)
ssp_ecg = [proj for proj in projs if proj['desc'].startswith('ECG')]
# check that the first principal component have a certain minimum
ssp_ecg = [proj for proj in ssp_ecg if 'PCA-01' in proj['desc']]
thresh_eeg, thresh_axial, thresh_planar = .9, .3, .1
for proj in ssp_ecg:
if 'planar' in proj['desc']:
assert_true(proj['explained_var'] > thresh_planar)
elif 'axial' in proj['desc']:
assert_true(proj['explained_var'] > thresh_axial)
elif 'eeg' in proj['desc']:
assert_true(proj['explained_var'] > thresh_eeg)
# XXX: better tests
# without setting a bad channel, this should throw a warning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
projs, events = compute_proj_ecg(raw, n_mag=2, n_grad=2, n_eeg=2,
ch_name='MEG 1531', bads=[],
average=average, avg_ref=True,
no_proj=True, l_freq=None,
h_freq=None, tmax=dur_use)
assert_true(len(w) >= 1)
assert_equal(projs, None)
def test_compute_proj_ecg():
"""Test computation of ECG SSP projectors."""
raw = read_raw_fif(raw_fname).crop(0, 10)
raw.load_data()
for average in [False, True]:
# For speed, let's not filter here (must also not reject then)
projs, events = compute_proj_ecg(
raw, n_mag=2, n_grad=2, n_eeg=2, ch_name='MEG 1531',
bads=['MEG 2443'], average=average, avg_ref=True, no_proj=True,
l_freq=None, h_freq=None, reject=None, tmax=dur_use,
qrs_threshold=0.5, filter_length=6000)
assert len(projs) == 7
# heart rate at least 0.5 Hz, but less than 3 Hz
assert (events.shape[0] > 0.5 * dur_use and
events.shape[0] < 3 * dur_use)
ssp_ecg = [proj for proj in projs if proj['desc'].startswith('ECG')]
# check that the first principal component have a certain minimum
ssp_ecg = [proj for proj in ssp_ecg if 'PCA-01' in proj['desc']]
thresh_eeg, thresh_axial, thresh_planar = .9, .3, .1
for proj in ssp_ecg:
if 'planar' in proj['desc']:
assert proj['explained_var'] > thresh_planar
elif 'axial' in proj['desc']:
assert proj['explained_var'] > thresh_axial
elif 'eeg' in proj['desc']:
assert proj['explained_var'] > thresh_eeg
# XXX: better tests
# without setting a bad channel, this should throw a warning
with pytest.warns(RuntimeWarning, match='No good epochs found'):
projs, events, drop_log = compute_proj_ecg(
raw, n_mag=2, n_grad=2, n_eeg=2, ch_name='MEG 1531', bads=[],
average=average, avg_ref=True, no_proj=True, l_freq=None,
h_freq=None, tmax=dur_use, return_drop_log=True)
assert projs is None
assert len(events) == len(drop_log)
def test_compute_proj_ctf():
"""Test to show that projector code completes on CTF data."""
raw = read_raw_ctf(ctf_fname, preload=True)
# expected channels per projector type
mag_picks = pick_types(
raw.info, meg='mag', ref_meg=False, exclude='bads')[::10]
n_mags = len(mag_picks)
grad_picks = pick_types(raw.info, meg='grad', ref_meg=False,
exclude='bads')[::10]
n_grads = len(grad_picks)
eeg_picks = pick_types(raw.info, meg=False, eeg=True, ref_meg=False,
exclude='bads')[2::3]
n_eegs = len(eeg_picks)
ref_picks = pick_types(raw.info, meg=False, ref_meg=True)
raw.pick(np.sort(np.concatenate(
[mag_picks, grad_picks, eeg_picks, ref_picks])))
del mag_picks, grad_picks, eeg_picks, ref_picks
# Test with and without gradient compensation
raw.apply_gradient_compensation(0)
n_projs_init = len(raw.info['projs'])
with pytest.warns(RuntimeWarning, match='Attenuation'):
projs, _ = compute_proj_eog(
raw, n_mag=2, n_grad=2, n_eeg=2, average=True, ch_name='EEG059',
avg_ref=True, no_proj=False, l_freq=None, h_freq=None,
reject=None, tmax=dur_use, filter_length=1000)
_check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs)
assert len(projs) == (5 + n_projs_init)
raw.apply_gradient_compensation(1)
with pytest.warns(RuntimeWarning, match='Attenuation'):
projs, _ = compute_proj_ecg(
raw, n_mag=1, n_grad=1, n_eeg=2, average=True, ch_name='EEG059',
avg_ref=True, no_proj=False, l_freq=None, h_freq=None,
reject=None, tmax=dur_use, filter_length=1000)
_check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs)
assert len(projs) == (4 + n_projs_init)
def test_compute_proj_ctf():
"""Test to show that projector code completes on CTF data."""
raw = read_raw_ctf(ctf_fname)
raw.load_data()
# expected channels per projector type
n_mags = len(pick_types(raw.info, meg='mag', ref_meg=False,
exclude='bads'))
n_grads = len(pick_types(raw.info, meg='grad', ref_meg=False,
exclude='bads'))
n_eegs = len(pick_types(raw.info, meg=False, eeg=True, ref_meg=False,
exclude='bads'))
# Test with and without gradient compensation
for c in [0, 1]:
raw.apply_gradient_compensation(c)
for average in [False, True]:
n_projs_init = len(raw.info['projs'])
projs, events = compute_proj_eog(raw, n_mag=2, n_grad=2, n_eeg=2,
average=average,
ch_name='EEG059',
avg_ref=True, no_proj=False,
l_freq=None, h_freq=None,
reject=None, tmax=dur_use,
filter_length=6000)
_check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs)
assert len(projs) == (5 + n_projs_init)
projs, events = compute_proj_ecg(raw, n_mag=1, n_grad=1, n_eeg=2,
average=average,
ch_name='EEG059',
avg_ref=True, no_proj=False,
l_freq=None, h_freq=None,
reject=None, tmax=dur_use,
filter_length=6000)
_check_projs_for_expected_channels(projs, n_mags, n_grads, n_eegs)
assert len(projs) == (4 + n_projs_init)