def test_read_dig_polhemus_isotrak_eeg(isotrak_eeg):
"""Test reading Polhemus IsoTrak EEG positions."""
N_CHANNELS = 5
_SEED = 42
EXPECTED_FID_IN_POLHEMUS = {
'nasion': np.array([1.1056e-01, -5.4210e-19, 0]),
'lpa': np.array([-2.1075e-04, 8.0793e-02, -7.5894e-19]),
'rpa': np.array([2.1075e-04, -8.0793e-02, -2.8731e-18]),
}
ch_names = ['eeg {:01d}'.format(ii) for ii in range(N_CHANNELS)]
EXPECTED_CH_POS = dict(zip(
ch_names, np.random.RandomState(_SEED).randn(N_CHANNELS, 3)))
montage = read_dig_polhemus_isotrak(fname=isotrak_eeg, ch_names=ch_names)
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 0 HPIs, 3 fiducials, 5 channels>'
)
fiducials, fid_coordframe = _get_fid_coords(montage.dig)
assert fid_coordframe == FIFF.FIFFV_COORD_UNKNOWN
for kk, val in fiducials.items():
assert_array_equal(val, EXPECTED_FID_IN_POLHEMUS[kk])
for kk, dig_point in zip(montage.ch_names, _get_dig_eeg(montage.dig)):
assert_array_equal(dig_point['r'], EXPECTED_CH_POS[kk])
assert dig_point['coord_frame'] == FIFF.FIFFV_COORD_UNKNOWN
def test_read_dig_captrak(tmpdir):
"""Test reading a captrak montage file."""
EXPECTED_CH_NAMES_OLD = [
'AF3', 'AF4', 'AF7', 'AF8', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'CP1',
'CP2', 'CP3', 'CP4', 'CP5', 'CP6', 'CPz', 'Cz', 'F1', 'F2', 'F3', 'F4',
'F5', 'F6', 'F7', 'F8', 'FC1', 'FC2', 'FC3', 'FC4', 'FC5', 'FC6',
'FT10', 'FT7', 'FT8', 'FT9', 'Fp1', 'Fp2', 'Fz', 'GND', 'O1', 'O2',
'Oz', 'P1', 'P2', 'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'PO10', 'PO3',
'PO4', 'PO7', 'PO8', 'PO9', 'POz', 'Pz', 'REF', 'T7', 'T8', 'TP10',
'TP7', 'TP8', 'TP9'
]
EXPECTED_CH_NAMES = [
'T7', 'FC5', 'F7', 'C5', 'FT7', 'FT9', 'TP7', 'TP9', 'P7', 'CP5',
'PO7', 'C3', 'CP3', 'P5', 'P3', 'PO3', 'PO9', 'O1', 'Oz', 'POz', 'O2',
'PO4', 'P1', 'Pz', 'P2', 'CP2', 'CP1', 'CPz', 'Cz', 'C1', 'FC1', 'FC3',
'REF', 'F3', 'F1', 'Fz', 'F5', 'AF7', 'AF3', 'Fp1', 'GND', 'F2', 'AF4',
'Fp2', 'F4', 'F8', 'F6', 'AF8', 'FC2', 'FC6', 'FC4', 'C2', 'C4', 'P4',
'CP4', 'PO8', 'P8', 'P6', 'CP6', 'PO10', 'TP10', 'TP8', 'FT10', 'T8',
'C6', 'FT8'
]
assert set(EXPECTED_CH_NAMES) == set(EXPECTED_CH_NAMES_OLD)
montage = read_dig_captrak(
fname=op.join(data_path, 'montage', 'captrak_coords.bvct'))
# XXX: remove with 0.22 once captrCK is deprecated
with pytest.warns(DeprecationWarning,
match='read_dig_captrack is deprecated'):
montage2 = read_dig_captrack(
fname=op.join(data_path, 'montage', 'captrak_coords.bvct'))
assert repr(montage) == repr(montage2)
assert montage.ch_names == EXPECTED_CH_NAMES
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 0 HPIs, 3 fiducials, 66 channels>')
montage = transform_to_head(montage) # transform_to_head has to be tested
_check_roundtrip(montage=montage, fname=str(tmpdir.join('bvct_test.fif')))
fid, _ = _get_fid_coords(montage.dig)
assert_allclose(
actual=np.array([fid.nasion, fid.lpa, fid.rpa]),
desired=[[0, 0.11309, 0], [-0.09189, 0, 0], [0.09240, 0, 0]],
atol=1e-5,
)
raw_bv = read_raw_brainvision(bv_raw_fname)
raw_bv.set_channel_types({"HEOG": 'eog', "VEOG": 'eog', "ECG": 'ecg'})
raw_bv.set_montage(montage)
test_raw_bv = read_raw_fif(bv_fif_fname)
# compare after set_montage using chs loc.
for actual, expected in zip(raw_bv.info['chs'], test_raw_bv.info['chs']):
assert_allclose(actual['loc'][:3], expected['loc'][:3])
if actual['kind'] == FIFF.FIFFV_EEG_CH:
assert_allclose(actual['loc'][3:6], [-0.005103, 0.05395, 0.144622],
rtol=1e-04)
def test_standard_montages_have_fids(kind):
"""Test standard montage are all in unknown coord (have fids)."""
montage = make_standard_montage(kind)
fids, coord_frame = _get_fid_coords(montage.dig)
for k, v in fids.items():
assert v is not None, k
for d in montage.dig:
assert d['coord_frame'] == FIFF.FIFFV_COORD_UNKNOWN
def test_egi_dig_montage():
"""Test EGI MFF XML dig montage support."""
dig_montage = read_dig_egi(egi_dig_montage_fname)
fid, coord = _get_fid_coords(dig_montage.dig)
assert coord == FIFF.FIFFV_COORD_UNKNOWN
assert_allclose(
actual=np.array([fid[key] for key in ['nasion', 'lpa', 'rpa']]),
desired=[
[0., 10.564, -2.051], # noqa
[-8.592, 0.498, -4.128], # noqa
[8.592, 0.498, -4.128]
], # noqa
)
# Test accuracy and embedding within raw object
raw_egi = read_raw_egi(egi_raw_fname, channel_naming='EEG %03d')
raw_egi.set_montage(dig_montage)
test_raw_egi = read_raw_fif(egi_fif_fname)
assert_equal(len(raw_egi.ch_names), len(test_raw_egi.ch_names))
for ch_raw, ch_test_raw in zip(raw_egi.info['chs'],
test_raw_egi.info['chs']):
assert_equal(ch_raw['ch_name'], ch_test_raw['ch_name'])
assert_equal(ch_raw['coord_frame'], FIFF.FIFFV_COORD_HEAD)
assert_allclose(ch_raw['loc'], ch_test_raw['loc'], atol=1e-7)
assert_dig_allclose(raw_egi.info, test_raw_egi.info)
dig_montage_in_head = transform_to_head(dig_montage.copy())
fid, coord = _get_fid_coords(dig_montage_in_head.dig)
assert coord == FIFF.FIFFV_COORD_HEAD
assert_allclose(
actual=np.array([fid[key] for key in ['nasion', 'lpa', 'rpa']]),
desired=[[0., 10.278, 0.], [-8.592, 0., 0.], [8.592, 0., 0.]],
atol=1e-4,
)
# test round-trip IO
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'egi_test.fif')
_check_roundtrip(dig_montage_in_head, fname_temp) # XXX: write forces head
def test_standard_montages_have_fids(kind):
"""Test standard montage are all in unknown coord (have fids)."""
montage = make_standard_montage(kind)
fids, coord_frame = _get_fid_coords(montage.dig)
for k, v in fids.items():
assert v is not None, k
for d in montage.dig:
if kind.startswith(('artinis', 'standard', 'mgh')):
want = FIFF.FIFFV_COORD_MRI
else:
want = FIFF.FIFFV_COORD_UNKNOWN
assert d['coord_frame'] == want
def test_read_dig_polhemus_isotrak_elp():
"""Test reading Polhemus IsoTrak ELP file."""
EXPECTED_FID_IN_POLHEMUS = {
'nasion': np.array([1.1056e-01, -5.4210e-19, 0]),
'lpa': np.array([-2.1075e-04, 8.0793e-02, -7.5894e-19]),
'rpa': np.array([2.1075e-04, -8.0793e-02, -2.8731e-18]),
}
montage = read_dig_polhemus_isotrak(fname=op.join(kit_dir, 'test.elp'),
ch_names=None)
assert repr(montage) == (
'<DigMontage | '
'0 extras (headshape), 5 HPIs, 3 fiducials, 0 channels>')
fiducials, fid_coordframe = _get_fid_coords(montage.dig)
assert fid_coordframe == FIFF.FIFFV_COORD_UNKNOWN
for kk, val in fiducials.items():
assert_array_equal(val, EXPECTED_FID_IN_POLHEMUS[kk])
def test_read_dig_montage_using_polhemus_fastscan():
"""Test FastScan."""
N_EEG_CH = 10
my_electrode_positions = read_polhemus_fastscan(
op.join(kit_dir, 'test_elp.txt')
)
montage = make_dig_montage(
# EEG_CH
ch_pos=dict(zip(ascii_lowercase[:N_EEG_CH],
np.random.RandomState(0).rand(N_EEG_CH, 3))),
# NO NAMED points
nasion=my_electrode_positions[0],
lpa=my_electrode_positions[1],
rpa=my_electrode_positions[2],
hpi=my_electrode_positions[3:],
hsp=read_polhemus_fastscan(op.join(kit_dir, 'test_hsp.txt')),
# Other defaults
coord_frame='unknown'
)
assert repr(montage) == (
'<DigMontage | '
'500 extras (headshape), 5 HPIs, 3 fiducials, 10 channels>'
) # XXX: is this wrong? extra is not in headspace, is it?
assert set([d['coord_frame'] for d in montage.dig]) == {
FIFF.FIFFV_COORD_UNKNOWN
} # XXX: so far we build everything in 'unknown'
EXPECTED_FID_IN_POLHEMUS = {
'nasion': [0.001393, 0.0131613, -0.0046967],
'lpa': [-0.0624997, -0.0737271, 0.07996],
'rpa': [-0.0748957, 0.0873785, 0.0811943],
}
fiducials, fid_coordframe = _get_fid_coords(montage.dig)
assert fid_coordframe == FIFF.FIFFV_COORD_UNKNOWN
for kk, val in fiducials.items():
assert_allclose(val, EXPECTED_FID_IN_POLHEMUS[kk])
def test_transform_to_head_and_compute_dev_head_t():
"""Test transform_to_head and compute_dev_head_t."""
EXPECTED_DEV_HEAD_T = \
[[-3.72201691e-02, -9.98212167e-01, -4.67667497e-02, -7.31583414e-04],
[8.98064989e-01, -5.39382685e-02, 4.36543170e-01, 1.60134431e-02],
[-4.38285221e-01, -2.57513699e-02, 8.98466990e-01, 6.13035748e-02],
[0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]]
EXPECTED_FID_IN_POLHEMUS = {
'nasion': np.array([0.001393, 0.0131613, -0.0046967]),
'lpa': np.array([-0.0624997, -0.0737271, 0.07996]),
'rpa': np.array([-0.0748957, 0.0873785, 0.0811943]),
}
EXPECTED_FID_IN_HEAD = {
'nasion': np.array([-8.94466792e-18, 1.10559624e-01, -3.85185989e-34]),
'lpa': np.array([-8.10816716e-02, 6.56321671e-18, 0]),
'rpa': np.array([8.05048781e-02, -6.47441364e-18, 0]),
}
hpi_dev = np.array(
[[ 2.13951493e-02, 8.47444056e-02, -5.65431188e-02], # noqa
[ 2.10299433e-02, -8.03141101e-02, -6.34420259e-02], # noqa
[ 1.05916829e-01, 8.18485672e-05, 1.19928083e-02], # noqa
[ 9.26595105e-02, 4.64804385e-02, 8.45141253e-03], # noqa
[ 9.42554419e-02, -4.35206589e-02, 8.78999363e-03]] # noqa
)
hpi_polhemus = np.array(
[[-0.0595004, -0.0704836, 0.075893 ], # noqa
[-0.0646373, 0.0838228, 0.0762123], # noqa
[-0.0135035, 0.0072522, -0.0268405], # noqa
[-0.0202967, -0.0351498, -0.0129305], # noqa
[-0.0277519, 0.0452628, -0.0222407]] # noqa
)
montage_polhemus = make_dig_montage(
**EXPECTED_FID_IN_POLHEMUS, hpi=hpi_polhemus, coord_frame='unknown'
)
montage_meg = make_dig_montage(hpi=hpi_dev, coord_frame='meg')
# Test regular worflow to get dev_head_t
montage = montage_polhemus + montage_meg
fids, _ = _get_fid_coords(montage.dig)
for kk in fids:
assert_allclose(fids[kk], EXPECTED_FID_IN_POLHEMUS[kk], atol=1e-5)
with pytest.raises(ValueError, match='set to head coordinate system'):
_ = compute_dev_head_t(montage)
montage = transform_to_head(montage)
fids, _ = _get_fid_coords(montage.dig)
for kk in fids:
assert_allclose(fids[kk], EXPECTED_FID_IN_HEAD[kk], atol=1e-5)
dev_head_t = compute_dev_head_t(montage)
assert_allclose(dev_head_t['trans'], EXPECTED_DEV_HEAD_T, atol=1e-7)
# Test errors when number of HPI points do not match
EXPECTED_ERR_MSG = 'Device-to-Head .*Got 0 .*device and 5 points in head'
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = compute_dev_head_t(transform_to_head(montage_polhemus))
EXPECTED_ERR_MSG = 'Device-to-Head .*Got 5 .*device and 0 points in head'
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = compute_dev_head_t(transform_to_head(
montage_meg + make_dig_montage(**EXPECTED_FID_IN_POLHEMUS)
))
EXPECTED_ERR_MSG = 'Device-to-Head .*Got 3 .*device and 5 points in head'
with pytest.raises(ValueError, match=EXPECTED_ERR_MSG):
_ = compute_dev_head_t(transform_to_head(
DigMontage(dig=_format_dig_points(montage_meg.dig[:3])) +
montage_polhemus
))
