def test_apply_reference():
"""Test base function for rereferencing"""
raw = Raw(fif_fname, preload=True)
# Rereference raw data by creating a copy of original data
reref, ref_data = _apply_reference(raw,
ref_from=['EEG 001', 'EEG 002'],
copy=True)
assert_true(reref.info['custom_ref_applied'])
_test_reference(raw, reref, ref_data, ['EEG 001', 'EEG 002'])
# The CAR reference projection should have been removed by the function
assert_true(not _has_eeg_average_ref_proj(reref.info['projs']))
# Test that disabling the reference does not break anything
reref, ref_data = _apply_reference(raw, [])
assert_array_equal(raw._data, reref._data)
# Test that data is modified in place when copy=False
reref, ref_data = _apply_reference(raw, ['EEG 001', 'EEG 002'], copy=False)
assert_true(raw is reref)
# Test re-referencing Epochs object
raw = Raw(fif_fname, preload=False, add_eeg_ref=False)
events = read_events(eve_fname)
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
epochs = Epochs(raw,
events=events,
event_id=1,
tmin=-0.2,
tmax=0.5,
picks=picks_eeg,
preload=True)
reref, ref_data = _apply_reference(epochs,
ref_from=['EEG 001', 'EEG 002'],
copy=True)
assert_true(reref.info['custom_ref_applied'])
_test_reference(epochs, reref, ref_data, ['EEG 001', 'EEG 002'])
# Test re-referencing Evoked object
evoked = epochs.average()
reref, ref_data = _apply_reference(evoked,
ref_from=['EEG 001', 'EEG 002'],
copy=True)
assert_true(reref.info['custom_ref_applied'])
_test_reference(evoked, reref, ref_data, ['EEG 001', 'EEG 002'])
# Test invalid input
raw_np = Raw(fif_fname, preload=False)
assert_raises(RuntimeError, _apply_reference, raw_np, ['EEG 001'])
def test_apply_reference():
"""Test base function for rereferencing"""
raw = Raw(fif_fname, preload=True)
# Rereference raw data by creating a copy of original data
reref, ref_data = _apply_reference(raw, ref_from=['EEG 001', 'EEG 002'],
copy=True)
assert_true(reref.info['custom_ref_applied'])
_test_reference(raw, reref, ref_data, ['EEG 001', 'EEG 002'])
# The CAR reference projection should have been removed by the function
assert_true(not _has_eeg_average_ref_proj(reref.info['projs']))
# Test that disabling the reference does not break anything
reref, ref_data = _apply_reference(raw, [])
assert_array_equal(raw._data, reref._data)
# Test that data is modified in place when copy=False
reref, ref_data = _apply_reference(raw, ['EEG 001', 'EEG 002'],
copy=False)
assert_true(raw is reref)
# Test re-referencing Epochs object
raw = Raw(fif_fname, preload=False, add_eeg_ref=False)
events = read_events(eve_fname)
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
epochs = Epochs(raw, events=events, event_id=1, tmin=-0.2, tmax=0.5,
picks=picks_eeg, preload=True)
reref, ref_data = _apply_reference(epochs, ref_from=['EEG 001', 'EEG 002'],
copy=True)
assert_true(reref.info['custom_ref_applied'])
_test_reference(epochs, reref, ref_data, ['EEG 001', 'EEG 002'])
# Test re-referencing Evoked object
evoked = epochs.average()
reref, ref_data = _apply_reference(evoked, ref_from=['EEG 001', 'EEG 002'],
copy=True)
assert_true(reref.info['custom_ref_applied'])
_test_reference(evoked, reref, ref_data, ['EEG 001', 'EEG 002'])
# Test invalid input
raw_np = Raw(fif_fname, preload=False)
assert_raises(RuntimeError, _apply_reference, raw_np, ['EEG 001'])
def test_apply_reference():
"""Test base function for rereferencing."""
raw = read_raw_fif(fif_fname, preload=True)
# Rereference raw data by creating a copy of original data
reref, ref_data = _apply_reference(raw.copy(),
ref_from=['EEG 001', 'EEG 002'])
assert (reref.info['custom_ref_applied'])
_test_reference(raw, reref, ref_data, ['EEG 001', 'EEG 002'])
# The CAR reference projection should have been removed by the function
assert (not _has_eeg_average_ref_proj(reref.info['projs']))
# Test that data is modified in place when copy=False
reref, ref_data = _apply_reference(raw, ['EEG 001', 'EEG 002'])
assert (raw is reref)
# Test that disabling the reference does not change anything
reref, ref_data = _apply_reference(raw.copy(), [])
assert_array_equal(raw._data, reref._data)
# Test re-referencing Epochs object
raw = read_raw_fif(fif_fname, preload=False)
events = read_events(eve_fname)
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
epochs = Epochs(raw,
events=events,
event_id=1,
tmin=-0.2,
tmax=0.5,
picks=picks_eeg,
preload=True)
reref, ref_data = _apply_reference(epochs.copy(),
ref_from=['EEG 001', 'EEG 002'])
assert (reref.info['custom_ref_applied'])
_test_reference(epochs, reref, ref_data, ['EEG 001', 'EEG 002'])
# Test re-referencing Evoked object
evoked = epochs.average()
reref, ref_data = _apply_reference(evoked.copy(),
ref_from=['EEG 001', 'EEG 002'])
assert (reref.info['custom_ref_applied'])
_test_reference(evoked, reref, ref_data, ['EEG 001', 'EEG 002'])
# Referencing needs data to be preloaded
raw_np = read_raw_fif(fif_fname, preload=False)
pytest.raises(RuntimeError, _apply_reference, raw_np, ['EEG 001'])
# Test having inactive SSP projections that deal with channels involved
# during re-referencing
raw = read_raw_fif(fif_fname, preload=True)
raw.add_proj(
Projection(
active=False,
data=dict(col_names=['EEG 001', 'EEG 002'],
row_names=None,
data=np.array([[1, 1]]),
ncol=2,
nrow=1),
desc='test',
kind=1,
))
# Projection concerns channels mentioned in projector
with pytest.raises(RuntimeError, match='Inactive signal space'):
_apply_reference(raw, ['EEG 001'])
# Projection does not concern channels mentioned in projector, no error
_apply_reference(raw, ['EEG 003'], ['EEG 004'])
# CSD cannot be rereferenced
raw.info['custom_ref_applied'] = FIFF.FIFFV_MNE_CUSTOM_REF_CSD
with pytest.raises(RuntimeError, match="Cannot set.* type 'CSD'"):
raw.set_eeg_reference()
def test_apply_reference():
"""Test base function for rereferencing."""
raw = read_raw_fif(fif_fname, preload=True)
# Rereference raw data by creating a copy of original data
reref, ref_data = _apply_reference(
raw.copy(), ref_from=['EEG 001', 'EEG 002'])
assert (reref.info['custom_ref_applied'])
_test_reference(raw, reref, ref_data, ['EEG 001', 'EEG 002'])
# The CAR reference projection should have been removed by the function
assert (not _has_eeg_average_ref_proj(reref.info['projs']))
# Test that data is modified in place when copy=False
reref, ref_data = _apply_reference(raw, ['EEG 001', 'EEG 002'])
assert (raw is reref)
# Test that disabling the reference does not change anything
reref, ref_data = _apply_reference(raw.copy(), [])
assert_array_equal(raw._data, reref._data)
# Test re-referencing Epochs object
raw = read_raw_fif(fif_fname, preload=False)
events = read_events(eve_fname)
picks_eeg = pick_types(raw.info, meg=False, eeg=True)
epochs = Epochs(raw, events=events, event_id=1, tmin=-0.2, tmax=0.5,
picks=picks_eeg, preload=True)
reref, ref_data = _apply_reference(
epochs.copy(), ref_from=['EEG 001', 'EEG 002'])
assert (reref.info['custom_ref_applied'])
_test_reference(epochs, reref, ref_data, ['EEG 001', 'EEG 002'])
# Test re-referencing Evoked object
evoked = epochs.average()
reref, ref_data = _apply_reference(
evoked.copy(), ref_from=['EEG 001', 'EEG 002'])
assert (reref.info['custom_ref_applied'])
_test_reference(evoked, reref, ref_data, ['EEG 001', 'EEG 002'])
# Referencing needs data to be preloaded
raw_np = read_raw_fif(fif_fname, preload=False)
pytest.raises(RuntimeError, _apply_reference, raw_np, ['EEG 001'])
# Test having inactive SSP projections that deal with channels involved
# during re-referencing
raw = read_raw_fif(fif_fname, preload=True)
raw.add_proj(
Projection(
active=False,
data=dict(
col_names=['EEG 001', 'EEG 002'],
row_names=None,
data=np.array([[1, 1]]),
ncol=2,
nrow=1
),
desc='test',
kind=1,
)
)
# Projection concerns channels mentioned in projector
pytest.raises(RuntimeError, _apply_reference, raw, ['EEG 001'])
# Projection does not concern channels mentioned in projector, no error
_apply_reference(raw, ['EEG 003'], ['EEG 004'])
