def test_set_bipolar_reference():
"""Test bipolar referencing"""
raw = Raw(fif_fname, preload=True)
reref = set_bipolar_reference(
raw, "EEG 001", "EEG 002", "bipolar", {"kind": FIFF.FIFFV_EOG_CH, "extra": "some extra value"}
)
assert_true(reref.info["custom_ref_applied"])
# Compare result to a manual calculation
a = raw.pick_channels(["EEG 001", "EEG 002"], copy=True)
a = a._data[0, :] - a._data[1, :]
b = reref.pick_channels(["bipolar"], copy=True)._data[0, :]
assert_allclose(a, b)
# Original channels should be replaced by a virtual one
assert_true("EEG 001" not in reref.ch_names)
assert_true("EEG 002" not in reref.ch_names)
assert_true("bipolar" in reref.ch_names)
# Check channel information
bp_info = reref.info["chs"][reref.ch_names.index("bipolar")]
an_info = reref.info["chs"][raw.ch_names.index("EEG 001")]
for key in bp_info:
if key == "loc":
assert_array_equal(bp_info[key], 0)
elif key == "coil_type":
assert_equal(bp_info[key], FIFF.FIFFV_COIL_EEG_BIPOLAR)
elif key == "kind":
assert_equal(bp_info[key], FIFF.FIFFV_EOG_CH)
else:
assert_equal(bp_info[key], an_info[key])
assert_equal(bp_info["extra"], "some extra value")
# Minimalist call
reref = set_bipolar_reference(raw, "EEG 001", "EEG 002")
assert_true("EEG 001-EEG 002" in reref.ch_names)
# Test creating a bipolar reference that doesn't involve EEG channels:
# it should not set the custom_ref_applied flag
reref = set_bipolar_reference(raw, "MEG 0111", "MEG 0112", ch_info={"kind": FIFF.FIFFV_MEG_CH})
assert_true(not reref.info["custom_ref_applied"])
assert_true("MEG 0111-MEG 0112" in reref.ch_names)
# Test a battery of invalid inputs
assert_raises(ValueError, set_bipolar_reference, raw, "EEG 001", ["EEG 002", "EEG 003"], "bipolar")
assert_raises(ValueError, set_bipolar_reference, raw, ["EEG 001", "EEG 002"], "EEG 003", "bipolar")
assert_raises(ValueError, set_bipolar_reference, raw, "EEG 001", "EEG 002", ["bipolar1", "bipolar2"])
assert_raises(
ValueError,
set_bipolar_reference,
raw,
"EEG 001",
"EEG 002",
"bipolar",
ch_info=[{"foo": "bar"}, {"foo": "bar"}],
)
assert_raises(ValueError, set_bipolar_reference, raw, "EEG 001", "EEG 002", ch_name="EEG 003")
def test_set_bipolar_reference():
"""Test bipolar referencing"""
raw = Raw(fif_fname, preload=True)
reref = set_bipolar_reference(raw, 'EEG 001', 'EEG 002', 'bipolar',
{'kind': FIFF.FIFFV_EOG_CH,
'extra': 'some extra value'})
assert_true(reref.info['custom_ref_applied'])
# Compare result to a manual calculation
a = raw.pick_channels(['EEG 001', 'EEG 002'], copy=True)
a = a._data[0, :] - a._data[1, :]
b = reref.pick_channels(['bipolar'], copy=True)._data[0, :]
assert_allclose(a, b)
# Original channels should be replaced by a virtual one
assert_true('EEG 001' not in reref.ch_names)
assert_true('EEG 002' not in reref.ch_names)
assert_true('bipolar' in reref.ch_names)
# Check channel information
bp_info = reref.info['chs'][reref.ch_names.index('bipolar')]
an_info = reref.info['chs'][raw.ch_names.index('EEG 001')]
for key in bp_info:
if key == 'loc':
assert_array_equal(bp_info[key], 0)
elif key == 'coil_type':
assert_equal(bp_info[key], FIFF.FIFFV_COIL_EEG_BIPOLAR)
elif key == 'kind':
assert_equal(bp_info[key], FIFF.FIFFV_EOG_CH)
else:
assert_equal(bp_info[key], an_info[key])
assert_equal(bp_info['extra'], 'some extra value')
# Minimalist call
reref = set_bipolar_reference(raw, 'EEG 001', 'EEG 002')
assert_true('EEG 001-EEG 002' in reref.ch_names)
# Test creating a bipolar reference that doesn't involve EEG channels:
# it should not set the custom_ref_applied flag
reref = set_bipolar_reference(raw, 'MEG 0111', 'MEG 0112',
ch_info={'kind': FIFF.FIFFV_MEG_CH})
assert_true(not reref.info['custom_ref_applied'])
assert_true('MEG 0111-MEG 0112' in reref.ch_names)
# Test a battery of invalid inputs
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', ['EEG 002', 'EEG 003'], 'bipolar')
assert_raises(ValueError, set_bipolar_reference, raw,
['EEG 001', 'EEG 002'], 'EEG 003', 'bipolar')
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', 'EEG 002', ['bipolar1', 'bipolar2'])
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', 'EEG 002', 'bipolar',
ch_info=[{'foo': 'bar'}, {'foo': 'bar'}])
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', 'EEG 002', ch_name='EEG 003')
def test_set_bipolar_reference():
"""Test bipolar referencing"""
raw = Raw(fif_fname, preload=True)
reref = set_bipolar_reference(raw, 'EEG 001', 'EEG 002', 'bipolar',
{'kind': FIFF.FIFFV_EOG_CH,
'extra': 'some extra value'})
assert_true(reref.info['custom_ref_applied'])
# Compare result to a manual calculation
a = raw.copy().pick_channels(['EEG 001', 'EEG 002'])
a = a._data[0, :] - a._data[1, :]
b = reref.copy().pick_channels(['bipolar'])._data[0, :]
assert_allclose(a, b)
# Original channels should be replaced by a virtual one
assert_true('EEG 001' not in reref.ch_names)
assert_true('EEG 002' not in reref.ch_names)
assert_true('bipolar' in reref.ch_names)
# Check channel information
bp_info = reref.info['chs'][reref.ch_names.index('bipolar')]
an_info = reref.info['chs'][raw.ch_names.index('EEG 001')]
for key in bp_info:
if key == 'loc':
assert_array_equal(bp_info[key], 0)
elif key == 'coil_type':
assert_equal(bp_info[key], FIFF.FIFFV_COIL_EEG_BIPOLAR)
elif key == 'kind':
assert_equal(bp_info[key], FIFF.FIFFV_EOG_CH)
else:
assert_equal(bp_info[key], an_info[key])
assert_equal(bp_info['extra'], 'some extra value')
# Minimalist call
reref = set_bipolar_reference(raw, 'EEG 001', 'EEG 002')
assert_true('EEG 001-EEG 002' in reref.ch_names)
# Test creating a bipolar reference that doesn't involve EEG channels:
# it should not set the custom_ref_applied flag
reref = set_bipolar_reference(raw, 'MEG 0111', 'MEG 0112',
ch_info={'kind': FIFF.FIFFV_MEG_CH})
assert_true(not reref.info['custom_ref_applied'])
assert_true('MEG 0111-MEG 0112' in reref.ch_names)
# Test a battery of invalid inputs
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', ['EEG 002', 'EEG 003'], 'bipolar')
assert_raises(ValueError, set_bipolar_reference, raw,
['EEG 001', 'EEG 002'], 'EEG 003', 'bipolar')
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', 'EEG 002', ['bipolar1', 'bipolar2'])
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', 'EEG 002', 'bipolar',
ch_info=[{'foo': 'bar'}, {'foo': 'bar'}])
assert_raises(ValueError, set_bipolar_reference, raw,
'EEG 001', 'EEG 002', ch_name='EEG 003')
def set_eog_ecg_channels(raw):
"""Set the HCP ECG and EOG channels
Operates in place.
Parameters
----------
raw : instance of Raw
the hcp raw data.
"""
for kind in ['ECG', 'VEOG', 'HEOG']:
set_bipolar_reference(
raw, anode=kind + '-', cathode=kind + '+', ch_name=kind,
copy=False)
raw.set_channel_types({'ECG': 'ecg', 'VEOG': 'eog', 'HEOG': 'eog'})
def set_eog_ecg_channels(raw):
"""Set the HCP ECG and EOG channels
.. note::
Operates in place.
Parameters
----------
raw : instance of Raw
the hcp raw data.
"""
for kind in ['ECG', 'VEOG', 'HEOG']:
set_bipolar_reference(
raw, anode=kind + '-', cathode=kind + '+', ch_name=kind,
copy=False)
raw.set_channel_types({'ECG': 'ecg', 'VEOG': 'eog', 'HEOG': 'eog'})