def _deface(t1w, mri_landmarks, deface, trans, raw):
if not has_nibabel(): # pragma: no cover
raise ImportError('This function requires nibabel.')
import nibabel as nib
inset, theta = (20, 35.)
if isinstance(deface, dict):
if 'inset' in deface:
inset = deface['inset']
if 'theta' in deface:
theta = deface['theta']
if not _is_numeric(inset):
raise ValueError('inset must be numeric (float, int). '
'Got %s' % type(inset))
if not _is_numeric(theta):
raise ValueError('theta must be numeric (float, int). '
'Got %s' % type(theta))
if inset < 0:
raise ValueError('inset should be positive, ' 'Got %s' % inset)
if not 0 < theta < 90:
raise ValueError('theta should be between 0 and 90 '
'degrees. Got %s' % theta)
# x: L/R L+, y: S/I I+, z: A/P A+
t1w_data = t1w.get_data().copy()
idxs_vox = np.meshgrid(np.arange(t1w_data.shape[0]),
np.arange(t1w_data.shape[1]),
np.arange(t1w_data.shape[2]),
indexing='ij')
idxs_vox = np.array(idxs_vox) # (3, *t1w_data.shape)
idxs_vox = np.transpose(idxs_vox, [1, 2, 3, 0]) # (*t1w_data.shape, 3)
idxs_vox = idxs_vox.reshape(-1, 3) # (n_voxels, 3)
mri_landmarks_ras = apply_trans(t1w.affine, mri_landmarks)
ras_meg_t = \
get_ras_to_neuromag_trans(*mri_landmarks_ras[[1, 0, 2]])
idxs_ras = apply_trans(t1w.affine, idxs_vox)
idxs_meg = apply_trans(ras_meg_t, idxs_ras)
# now comes the actual defacing
# 1. move center of voxels to (nasion - inset)
# 2. rotate the head by theta from the normal to the plane passing
# through anatomical coordinates
trans_y = -mri_landmarks_ras[1, 1] + inset
idxs_meg = apply_trans(translation(y=trans_y), idxs_meg)
idxs_meg = apply_trans(rotation(x=-np.deg2rad(theta)), idxs_meg)
coords = idxs_meg.reshape(t1w.shape + (3, )) # (*t1w_data.shape, 3)
mask = (coords[..., 2] < 0) # z < 0
t1w_data[mask] = 0.
# smooth decided against for potential lack of anonymizaton
# https://gist.github.com/alexrockhill/15043928b716a432db3a84a050b241ae
t1w = nib.Nifti1Image(t1w_data, t1w.affine, t1w.header)
return t1w
def test_set_dig_montage():
"""Test applying DigMontage to inst."""
# Extensive testing of applying `dig` to info is done in test_meas_info
# with `test_make_dig_points`.
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
hsp_points = _read_dig_points(hsp)
elp_points = _read_dig_points(elp)
nasion, lpa, rpa = elp_points[:3]
nm_trans = get_ras_to_neuromag_trans(nasion, lpa, rpa)
elp_points = apply_trans(nm_trans, elp_points)
nasion, lpa, rpa = elp_points[:3]
hsp_points = apply_trans(nm_trans, hsp_points)
montage = read_dig_montage(hsp,
hpi,
elp,
names,
transform=True,
dev_head_t=True)
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'test.fif')
montage.save(fname_temp)
montage_read = read_dig_montage(fif=fname_temp)
for use_mon in (montage, montage_read):
info = create_info(['Test Ch'], 1e3, ['eeg'])
with warnings.catch_warnings(record=True) as w: # test ch pos not set
_set_montage(info, use_mon)
assert_true(all('not set' in str(ww.message) for ww in w))
hs = np.array([
p['r'] for i, p in enumerate(info['dig'])
if p['kind'] == FIFF.FIFFV_POINT_EXTRA
])
nasion_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_NASION, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
lpa_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_LPA, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
rpa_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_RPA, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
hpi_dig = np.array(
[p['r'] for p in info['dig'] if p['kind'] == FIFF.FIFFV_POINT_HPI])
assert_allclose(hs, hsp_points, atol=1e-7)
assert_allclose(nasion_dig.ravel(), nasion, atol=1e-7)
assert_allclose(lpa_dig.ravel(), lpa, atol=1e-7)
assert_allclose(rpa_dig.ravel(), rpa, atol=1e-7)
assert_allclose(hpi_dig, elp_points[3:], atol=1e-7)
def test_set_dig_montage():
"""Test applying DigMontage to inst."""
# Extensive testing of applying `dig` to info is done in test_meas_info
# with `test_make_dig_points`.
names = ["nasion", "lpa", "rpa", "1", "2", "3", "4", "5"]
hsp_points = _read_dig_points(hsp)
elp_points = _read_dig_points(elp)
nasion, lpa, rpa = elp_points[:3]
nm_trans = get_ras_to_neuromag_trans(nasion, lpa, rpa)
elp_points = apply_trans(nm_trans, elp_points)
nasion, lpa, rpa = elp_points[:3]
hsp_points = apply_trans(nm_trans, hsp_points)
montage = read_dig_montage(hsp, hpi, elp, names, transform=True, dev_head_t=True)
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, "test.fif")
montage.save(fname_temp)
montage_read = read_dig_montage(fif=fname_temp)
for use_mon in (montage, montage_read):
info = create_info(["Test Ch"], 1e3, ["eeg"])
with warnings.catch_warnings(record=True) as w: # test ch pos not set
_set_montage(info, use_mon)
assert_true(all("not set" in str(ww.message) for ww in w))
hs = np.array([p["r"] for i, p in enumerate(info["dig"]) if p["kind"] == FIFF.FIFFV_POINT_EXTRA])
nasion_dig = np.array(
[
p["r"]
for p in info["dig"]
if all([p["ident"] == FIFF.FIFFV_POINT_NASION, p["kind"] == FIFF.FIFFV_POINT_CARDINAL])
]
)
lpa_dig = np.array(
[
p["r"]
for p in info["dig"]
if all([p["ident"] == FIFF.FIFFV_POINT_LPA, p["kind"] == FIFF.FIFFV_POINT_CARDINAL])
]
)
rpa_dig = np.array(
[
p["r"]
for p in info["dig"]
if all([p["ident"] == FIFF.FIFFV_POINT_RPA, p["kind"] == FIFF.FIFFV_POINT_CARDINAL])
]
)
hpi_dig = np.array([p["r"] for p in info["dig"] if p["kind"] == FIFF.FIFFV_POINT_HPI])
assert_allclose(hs, hsp_points, atol=1e-7)
assert_allclose(nasion_dig.ravel(), nasion, atol=1e-7)
assert_allclose(lpa_dig.ravel(), lpa, atol=1e-7)
assert_allclose(rpa_dig.ravel(), rpa, atol=1e-7)
assert_allclose(hpi_dig, elp_points[3:], atol=1e-7)
def test_set_dig_montage():
"""Test applying DigMontage to inst
Extensive testing of applying `dig` to info is done in test_meas_info
with `test_make_dig_points`.
"""
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
hsp_points = _read_dig_points(hsp)
elp_points = _read_dig_points(elp)
hpi_points = read_mrk(hpi)
p0, p1, p2 = elp_points[:3]
nm_trans = get_ras_to_neuromag_trans(p0, p1, p2)
elp_points = apply_trans(nm_trans, elp_points)
nasion_point, lpa_point, rpa_point = elp_points[:3]
hsp_points = apply_trans(nm_trans, hsp_points)
montage = read_dig_montage(hsp, hpi, elp, names, unit='m', transform=True)
info = create_info(['Test Ch'], 1e3, ['eeg'])
_set_montage(info, montage)
hs = np.array([
p['r'] for i, p in enumerate(info['dig'])
if p['kind'] == FIFF.FIFFV_POINT_EXTRA
])
nasion_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_NASION, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
lpa_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_LPA, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
rpa_dig = np.array([
p['r'] for p in info['dig'] if all([
p['ident'] == FIFF.FIFFV_POINT_RPA, p['kind'] ==
FIFF.FIFFV_POINT_CARDINAL
])
])
hpi_dig = np.array(
[p['r'] for p in info['dig'] if p['kind'] == FIFF.FIFFV_POINT_HPI])
assert_array_equal(hs, hsp_points)
assert_array_equal(nasion_dig.ravel(), nasion_point)
assert_array_equal(lpa_dig.ravel(), lpa_point)
assert_array_equal(rpa_dig.ravel(), rpa_point)
assert_array_equal(hpi_dig, hpi_points)
assert_array_equal(montage.dev_head_t, info['dev_head_t']['trans'])
def test_set_dig_montage():
"""Test applying DigMontage to inst."""
# Extensive testing of applying `dig` to info is done in test_meas_info
# with `test_make_dig_points`.
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
hsp_points = _read_dig_points(hsp)
elp_points = _read_dig_points(elp)
nasion, lpa, rpa = elp_points[:3]
nm_trans = get_ras_to_neuromag_trans(nasion, lpa, rpa)
elp_points = apply_trans(nm_trans, elp_points)
nasion, lpa, rpa = elp_points[:3]
hsp_points = apply_trans(nm_trans, hsp_points)
montage = read_dig_montage(hsp, hpi, elp, names, transform=True,
dev_head_t=True)
temp_dir = _TempDir()
fname_temp = op.join(temp_dir, 'test.fif')
montage.save(fname_temp)
montage_read = read_dig_montage(fif=fname_temp)
for use_mon in (montage, montage_read):
info = create_info(['Test Ch'], 1e3, ['eeg'])
with pytest.warns(None): # warns on one run about not all positions
_set_montage(info, use_mon)
hs = np.array([p['r'] for i, p in enumerate(info['dig'])
if p['kind'] == FIFF.FIFFV_POINT_EXTRA])
nasion_dig = np.array([p['r'] for p in info['dig']
if all([p['ident'] == FIFF.FIFFV_POINT_NASION,
p['kind'] == FIFF.FIFFV_POINT_CARDINAL])
])
lpa_dig = np.array([p['r'] for p in info['dig']
if all([p['ident'] == FIFF.FIFFV_POINT_LPA,
p['kind'] == FIFF.FIFFV_POINT_CARDINAL])])
rpa_dig = np.array([p['r'] for p in info['dig']
if all([p['ident'] == FIFF.FIFFV_POINT_RPA,
p['kind'] == FIFF.FIFFV_POINT_CARDINAL])])
hpi_dig = np.array([p['r'] for p in info['dig']
if p['kind'] == FIFF.FIFFV_POINT_HPI])
assert_allclose(hs, hsp_points, atol=1e-7)
assert_allclose(nasion_dig.ravel(), nasion, atol=1e-7)
assert_allclose(lpa_dig.ravel(), lpa, atol=1e-7)
assert_allclose(rpa_dig.ravel(), rpa, atol=1e-7)
assert_allclose(hpi_dig, elp_points[3:], atol=1e-7)
def test_get_ras_to_neuromag_trans():
"""Test the coordinate transformation from ras to neuromag"""
# create model points in neuromag-like space
anterior = [0, 1, 0]
left = [-1, 0, 0]
right = [0.8, 0, 0]
up = [0, 0, 1]
rand_pts = np.random.uniform(-1, 1, (3, 3))
pts = np.vstack((anterior, left, right, up, rand_pts))
# change coord system
rx, ry, rz, tx, ty, tz = np.random.uniform(-2 * np.pi, 2 * np.pi, 6)
trans = np.dot(translation(tx, ty, tz), rotation(rx, ry, rz))
pts_changed = apply_trans(trans, pts)
# transform back into original space
nas, lpa, rpa = pts_changed[:3]
hsp_trans = get_ras_to_neuromag_trans(nas, lpa, rpa)
pts_restored = apply_trans(hsp_trans, pts_changed)
err = "Neuromag transformation failed"
assert_array_almost_equal(pts_restored, pts, 6, err)
def test_get_ras_to_neuromag_trans():
"""Test the coordinate transformation from ras to neuromag"""
# create model points in neuromag-like space
anterior = [0, 1, 0]
left = [-1, 0, 0]
right = [.8, 0, 0]
up = [0, 0, 1]
rand_pts = np.random.uniform(-1, 1, (3, 3))
pts = np.vstack((anterior, left, right, up, rand_pts))
# change coord system
rx, ry, rz, tx, ty, tz = np.random.uniform(-2 * np.pi, 2 * np.pi, 6)
trans = np.dot(translation(tx, ty, tz), rotation(rx, ry, rz))
pts_changed = apply_trans(trans, pts)
# transform back into original space
nas, lpa, rpa = pts_changed[:3]
hsp_trans = get_ras_to_neuromag_trans(nas, lpa, rpa)
pts_restored = apply_trans(hsp_trans, pts_changed)
err = "Neuromag transformation failed"
assert_array_almost_equal(pts_restored, pts, 6, err)
def test_set_dig_montage():
"""Test applying DigMontage to inst
Extensive testing of applying `dig` to info is done in test_meas_info
with `test_make_dig_points`.
"""
names = ['nasion', 'lpa', 'rpa', '1', '2', '3', '4', '5']
hsp_points = _read_dig_points(hsp)
elp_points = _read_dig_points(elp)
hpi_points = read_mrk(hpi)
p0, p1, p2 = elp_points[:3]
nm_trans = get_ras_to_neuromag_trans(p0, p1, p2)
elp_points = apply_trans(nm_trans, elp_points)
nasion_point, lpa_point, rpa_point = elp_points[:3]
hsp_points = apply_trans(nm_trans, hsp_points)
montage = read_dig_montage(hsp, hpi, elp, names, unit='m', transform=True)
info = create_info(['Test Ch'], 1e3, ['eeg'])
_set_montage(info, montage)
hs = np.array([p['r'] for i, p in enumerate(info['dig'])
if p['kind'] == FIFF.FIFFV_POINT_EXTRA])
nasion_dig = np.array([p['r'] for p in info['dig']
if all([p['ident'] == FIFF.FIFFV_POINT_NASION,
p['kind'] == FIFF.FIFFV_POINT_CARDINAL])])
lpa_dig = np.array([p['r'] for p in info['dig']
if all([p['ident'] == FIFF.FIFFV_POINT_LPA,
p['kind'] == FIFF.FIFFV_POINT_CARDINAL])])
rpa_dig = np.array([p['r'] for p in info['dig']
if all([p['ident'] == FIFF.FIFFV_POINT_RPA,
p['kind'] == FIFF.FIFFV_POINT_CARDINAL])])
hpi_dig = np.array([p['r'] for p in info['dig']
if p['kind'] == FIFF.FIFFV_POINT_HPI])
assert_array_equal(hs, hsp_points)
assert_array_equal(nasion_dig.ravel(), nasion_point)
assert_array_equal(lpa_dig.ravel(), lpa_point)
assert_array_equal(rpa_dig.ravel(), rpa_point)
assert_array_equal(hpi_dig, hpi_points)
assert_array_equal(montage.dev_head_t, info['dev_head_t']['trans'])
def test_montage():
"""Test making montages"""
tempdir = _TempDir()
# no pep8
input_str = [
"""FidNz 0.00000 10.56381 -2.05108
FidT9 -7.82694 0.45386 -3.76056
FidT10 7.82694 0.45386 -3.76056""",
"""// MatLab Sphere coordinates [degrees] Cartesian coordinates
// Label Theta Phi Radius X Y Z off sphere surface
E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011
E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000
E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000""", # noqa
"""# ASA electrode file
ReferenceLabel avg
UnitPosition mm
NumberPositions= 68
Positions
-86.0761 -19.9897 -47.9860
85.7939 -20.0093 -48.0310
0.0083 86.8110 -39.9830
Labels
LPA
RPA
Nz
""",
"""Site Theta Phi
Fp1 -92 -72
Fp2 92 72
F3 -60 -51
""",
"""346
EEG F3 -62.027 -50.053 85
EEG Fz 45.608 90 85
EEG F4 62.01 50.103 85
""",
"""
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
"""
]
kinds = [
'test.sfp', 'test.csd', 'test.elc', 'test.txt', 'test.elp', 'test.hpts'
]
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
assert_equal(len(montage.ch_names), 3)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (3, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2, montage.pos, 4)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
"""
kind = 'test_fid.hpts'
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index('2')
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index('1')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index('3')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, 'test_fid.hpts')
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
evoked = EvokedArray(data=np.zeros((len(montage.ch_names), 1)),
info=info,
tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
inputs = dict(
sfp='FidNz 0 9.071585155 -2.359754454\n'
'FidT9 -6.711765 0.040402876 -3.251600355\n'
'very_very_very_long_name -5.831241498 -4.494821698 4.955347697\n'
'Cz 0 0 8.899186843',
csd='// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E31 90.000 -11.000 1.000 0.0000 0.9816 -0.1908 0.00000000000000000\n' # noqa: E501
'E61 158.000 -17.200 1.000 -0.8857 0.3579 -0.2957 -0.00000000000000022', # noqa: E501
mm_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n' # noqa:E501
'NumberPositions= 68\n'
'Positions\n'
'-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n'
'0.0083 86.8110 -39.9830\n'
'-86.0761 -24.9897 -67.9860\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
m_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n' # noqa:E501
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
txt='Site Theta Phi\n'
'Fp1 -92 -72\n'
'Fp2 92 72\n'
'very_very_very_long_name -92 72\n'
'O2 92 -90\n',
elp='346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n'
'EEG\t FCz\t 68.01\t 58.103\t 85\n',
hpts='eeg Fp1 -95.0 -3. -3.\n'
'eeg AF7 -1 -1 -3\n'
'eeg A3 -2 -2 2\n'
'eeg A 0 0 0',
bvef='<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n'
'<!-- Generated by EasyCap Configurator 19.05.2014 -->\n'
'<Electrodes defaults="false">\n'
' <Electrode>\n'
' <Name>Fp1</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-72</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>1</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>Fz</Name>\n'
' <Theta>45</Theta>\n'
' <Phi>90</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>2</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F3</Name>\n'
' <Theta>-60</Theta>\n'
' <Phi>-51</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>3</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F7</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-36</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>4</Number>\n'
' </Electrode>\n'
'</Electrodes>',
)
# Get actual positions and save them for checking
# csd comes from the string above, all others come from commit 2fa35d4
poss = dict(
sfp=[[0.0, 9.07159, -2.35975], [-6.71176, 0.0404, -3.2516],
[-5.83124, -4.49482, 4.95535], [0.0, 0.0, 8.89919]],
mm_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.08681, -0.03998], [-0.08608, -0.02499, -0.06799]],
m_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.00868, -0.03998], [0.08, -0.02, -0.04]],
txt=[[-26.25044, 80.79056, -2.96646], [26.25044, 80.79056, -2.96646],
[-26.25044, -80.79056, -2.96646], [0.0, -84.94822, -2.96646]],
elp=[[-48.20043, 57.55106, 39.86971], [0.0, 60.73848, 59.4629],
[48.1426, 57.58403, 39.89198], [41.64599, 66.91489, 31.8278]],
hpts=[[-95, -3, -3], [-1, -1., -3.], [-2, -2, 2.], [0, 0, 0]],
bvef=[[-26.266444, 80.839803, 5.204748e-15],
[3.680313e-15, 60.104076, 60.104076],
[-46.325632, 57.207392, 42.500000],
[-68.766444, 49.961746, 5.204748e-15]],
)
for key, text in inputs.items():
kind = key.split('_')[-1]
fname = op.join(tempdir, 'test.' + kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if kind in ('sfp', 'txt'):
assert ('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, 'test')
if kind == 'csd':
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
poss['csd'] = np.c_[table['x'], table['y'], table['z']]
if kind == 'elc':
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(
np.linalg.norm, 1,
montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
assert_array_almost_equal(poss[key], montage.pos, 4, err_msg=key)
# Test reading in different letter case.
ch_names = ["F3", "FZ", "F4", "FC3", "FCz", "FC4", "C3", "CZ", "C4", "CP3",
"CPZ", "CP4", "P3", "PZ", "P4", "O1", "OZ", "O2"]
montage = read_montage('standard_1020', ch_names=ch_names)
assert_array_equal(ch_names, montage.ch_names)
# test transform
input_strs = ["""
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
""", """
Fp1 -95.0 -31.0 -3.0
AF7 -81 -59 -3
AF3 -87 -41 28
FidNz -91 0 -42
FidT9 0 -91 -42
FidT10 0 91 -42
"""]
# sfp files seem to have Nz, T9, and T10 as fiducials:
# https://github.com/mne-tools/mne-python/pull/4482#issuecomment-321980611
kinds = ['test_fid.hpts', 'test_fid.sfp']
for kind, input_str in zip(kinds, input_strs):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, kind), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
assert_array_equal(montage.nasion[[0, 2]], [0, 0])
assert_array_equal(montage.lpa[[1, 2]], [0, 0])
assert_array_equal(montage.rpa[[1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, kind)
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3,
['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(
montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
evoked = EvokedArray(
data=np.zeros((len(montage.ch_names), 1)), info=info, tmin=0)
# test return type as well as set montage
assert (isinstance(evoked.set_montage(montage), type(evoked)))
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in montage
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage)
# Channel names can be treated case insensitive
info = create_info(['FP1', 'af7', 'AF3'], 1e3, ['eeg'] * 3)
_set_montage(info, montage)
# Unless there is a collision in names
info = create_info(['FP1', 'Fp1', 'AF3'], 1e3, ['eeg'] * 3)
assert (info['dig'] is None)
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage)
assert len(info['dig']) == 5 # 2 EEG w/pos, 3 fiducials
montage.ch_names = ['FP1', 'Fp1', 'AF3']
info = create_info(['fp1', 'AF3'], 1e3, ['eeg', 'eeg'])
assert (info['dig'] is None)
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage, set_dig=False)
assert (info['dig'] is None)
# test get_pos2d method
montage = read_montage("standard_1020")
c3 = montage.get_pos2d()[montage.ch_names.index("C3")]
c4 = montage.get_pos2d()[montage.ch_names.index("C4")]
fz = montage.get_pos2d()[montage.ch_names.index("Fz")]
oz = montage.get_pos2d()[montage.ch_names.index("Oz")]
f1 = montage.get_pos2d()[montage.ch_names.index("F1")]
assert (c3[0] < 0) # left hemisphere
assert (c4[0] > 0) # right hemisphere
assert (fz[1] > 0) # frontal
assert (oz[1] < 0) # occipital
assert_allclose(fz[0], 0, atol=1e-2) # midline
assert_allclose(oz[0], 0, atol=1e-2) # midline
assert (f1[0] < 0 and f1[1] > 0) # left frontal
# test get_builtin_montages function
montages = get_builtin_montages()
assert (len(montages) > 0) # MNE should always ship with montages
assert ("standard_1020" in montages) # 10/20 montage
assert ("standard_1005" in montages) # 10/05 montage
def test_montage():
"""Test making montages"""
tempdir = _TempDir()
# no pep8
input_str = ["""FidNz 0.00000 10.56381 -2.05108
FidT9 -7.82694 0.45386 -3.76056
FidT10 7.82694 0.45386 -3.76056""",
"""// MatLab Sphere coordinates [degrees] Cartesian coordinates
// Label Theta Phi Radius X Y Z off sphere surface
E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011
E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000
E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000""", # noqa
"""# ASA electrode file
ReferenceLabel avg
UnitPosition mm
NumberPositions= 68
Positions
-86.0761 -19.9897 -47.9860
85.7939 -20.0093 -48.0310
0.0083 86.8110 -39.9830
Labels
LPA
RPA
Nz
""",
"""Site Theta Phi
Fp1 -92 -72
Fp2 92 72
F3 -60 -51
""",
"""346
EEG F3 -62.027 -50.053 85
EEG Fz 45.608 90 85
EEG F4 62.01 50.103 85
""",
"""
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
"""]
kinds = ['test.sfp', 'test.csd', 'test.elc', 'test.txt', 'test.elp',
'test.hpts']
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
assert_equal(len(montage.ch_names), 3)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (3, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2, montage.pos, 4)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal nasion -91 0 -42
cardinal lpa 0 -91 -42
cardinal rpa 0 91 -42
"""
kind = 'test_fid.hpts'
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index('nasion')
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index('lpa')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index('rpa')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
apply_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
pos3 = np.array([c['eeg_loc'][:, 0] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
inputs = dict(
sfp='FidNz 0 9.071585155 -2.359754454\n'
'FidT9 -6.711765 0.040402876 -3.251600355\n'
'very_very_very_long_name -5.831241498 -4.494821698 4.955347697\n'
'Cz 0 0 8.899186843',
csd='// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E31 90.000 -11.000 1.000 0.0000 0.9816 -0.1908 0.00000000000000000\n' # noqa: E501
'E61 158.000 -17.200 1.000 -0.8857 0.3579 -0.2957 -0.00000000000000022', # noqa: E501
mm_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n' # noqa:E501
'NumberPositions= 68\n'
'Positions\n'
'-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n'
'0.0083 86.8110 -39.9830\n'
'-86.0761 -24.9897 -67.9860\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
m_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n' # noqa:E501
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
txt='Site Theta Phi\n'
'Fp1 -92 -72\n'
'Fp2 92 72\n'
'very_very_very_long_name -92 72\n'
'O2 92 -90\n',
elp='346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n'
'EEG\t FCz\t 68.01\t 58.103\t 85\n',
hpts='eeg Fp1 -95.0 -3. -3.\n'
'eeg AF7 -1 -1 -3\n'
'eeg A3 -2 -2 2\n'
'eeg A 0 0 0',
)
# Get actual positions and save them for checking
# csd comes from the string above, all others come from commit 2fa35d4
poss = dict(
sfp=[[0.0, 9.07159, -2.35975], [-6.71176, 0.0404, -3.2516],
[-5.83124, -4.49482, 4.95535], [0.0, 0.0, 8.89919]],
mm_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.08681, -0.03998], [-0.08608, -0.02499, -0.06799]],
m_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.00868, -0.03998], [0.08, -0.02, -0.04]],
txt=[[-26.25044, 80.79056, -2.96646], [26.25044, 80.79056, -2.96646],
[-26.25044, -80.79056, -2.96646], [0.0, -84.94822, -2.96646]],
elp=[[-48.20043, 57.55106, 39.86971], [0.0, 60.73848, 59.4629],
[48.1426, 57.58403, 39.89198], [41.64599, 66.91489, 31.8278]],
hpts=[[-95, -3, -3], [-1, -1., -3.], [-2, -2, 2.], [0, 0, 0]],
)
for key, text in inputs.items():
kind = key.split('_')[-1]
fname = op.join(tempdir, 'test.' + kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if kind in ('sfp', 'txt'):
assert_true('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, 'test')
if kind == 'csd':
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
poss['csd'] = np.c_[table['x'], table['y'], table['z']]
if kind == 'elc':
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(
np.linalg.norm, 1,
montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
assert_array_almost_equal(poss[key], montage.pos, 4, err_msg=key)
# Test reading in different letter case.
ch_names = ["F3", "FZ", "F4", "FC3", "FCz", "FC4", "C3", "CZ", "C4", "CP3",
"CPZ", "CP4", "P3", "PZ", "P4", "O1", "OZ", "O2"]
montage = read_montage('standard_1020', ch_names=ch_names)
assert_array_equal(ch_names, montage.ch_names)
# test transform
input_strs = ["""
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
""", """
Fp1 -95.0 -31.0 -3.0
AF7 -81 -59 -3
AF3 -87 -41 28
nasion -91 0 -42
lpa 0 -91 -42
rpa 0 91 -42
"""]
all_fiducials = [['2', '1', '3'], ['nasion', 'lpa', 'rpa']]
kinds = ['test_fid.hpts', 'test_fid.sfp']
for kind, fiducials, input_str in zip(kinds, all_fiducials, input_strs):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, kind), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index(fiducials[0])
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index(fiducials[1])
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index(fiducials[2])
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, kind)
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3,
['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(
montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
evoked = EvokedArray(
data=np.zeros((len(montage.ch_names), 1)), info=info, tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in montage
with warnings.catch_warnings(record=True) as w:
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
_set_montage(info, montage)
assert_true(len(w) == 1)
# Channel names can be treated case insensitive
with warnings.catch_warnings(record=True) as w:
info = create_info(['FP1', 'af7', 'AF3'], 1e3, ['eeg'] * 3)
_set_montage(info, montage)
assert_true(len(w) == 0)
# Unless there is a collision in names
with warnings.catch_warnings(record=True) as w:
info = create_info(['FP1', 'Fp1', 'AF3'], 1e3, ['eeg'] * 3)
_set_montage(info, montage)
assert_true(len(w) == 1)
with warnings.catch_warnings(record=True) as w:
montage.ch_names = ['FP1', 'Fp1', 'AF3']
info = create_info(['fp1', 'AF3'], 1e3, ['eeg', 'eeg'])
_set_montage(info, montage)
assert_true(len(w) == 1)
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
inputs = dict(
sfp="FidNz 0 9.071585155 -2.359754454\n"
"FidT9 -6.711765 0.040402876 -3.251600355\n"
"very_very_very_long_name -5.831241498 -4.494821698 4.955347697\n"
"Cz 0 0 8.899186843",
csd="// MatLab Sphere coordinates [degrees] Cartesian coordinates\n" # noqa: E501
"// Label Theta Phi Radius X Y Z off sphere surface\n" # noqa: E501
"E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n" # noqa: E501
"E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n" # noqa: E501
"E31 90.000 -11.000 1.000 0.0000 0.9816 -0.1908 0.00000000000000000\n" # noqa: E501
"E61 158.000 -17.200 1.000 -0.8857 0.3579 -0.2957 -0.00000000000000022", # noqa: E501
mm_elc="# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n" # noqa:E501
"NumberPositions= 68\n"
"Positions\n"
"-86.0761 -19.9897 -47.9860\n"
"85.7939 -20.0093 -48.0310\n"
"0.0083 86.8110 -39.9830\n"
"-86.0761 -24.9897 -67.9860\n"
"Labels\nLPA\nRPA\nNz\nDummy\n",
m_elc="# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n"
"NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n" # noqa:E501
".0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n"
".08 -.02 -.04\n"
"Labels\nLPA\nRPA\nNz\nDummy\n",
txt="Site Theta Phi\n"
"Fp1 -92 -72\n"
"Fp2 92 72\n"
"very_very_very_long_name -92 72\n"
"O2 92 -90\n",
elp="346\n"
"EEG\t F3\t -62.027\t -50.053\t 85\n"
"EEG\t Fz\t 45.608\t 90\t 85\n"
"EEG\t F4\t 62.01\t 50.103\t 85\n"
"EEG\t FCz\t 68.01\t 58.103\t 85\n",
hpts="eeg Fp1 -95.0 -3. -3.\n" "eeg AF7 -1 -1 -3\n" "eeg A3 -2 -2 2\n" "eeg A 0 0 0",
)
# Get actual positions and save them for checking
# csd comes from the string above, all others come from commit 2fa35d4
poss = dict(
sfp=[[0.0, 9.07159, -2.35975], [-6.71176, 0.0404, -3.2516], [-5.83124, -4.49482, 4.95535], [0.0, 0.0, 8.89919]],
mm_elc=[
[-0.08608, -0.01999, -0.04799],
[0.08579, -0.02001, -0.04803],
[1e-05, 0.08681, -0.03998],
[-0.08608, -0.02499, -0.06799],
],
m_elc=[
[-0.08608, -0.01999, -0.04799],
[0.08579, -0.02001, -0.04803],
[1e-05, 0.00868, -0.03998],
[0.08, -0.02, -0.04],
],
txt=[
[-26.25044, 80.79056, -2.96646],
[26.25044, 80.79056, -2.96646],
[-26.25044, -80.79056, -2.96646],
[0.0, -84.94822, -2.96646],
],
elp=[
[-48.20043, 57.55106, 39.86971],
[0.0, 60.73848, 59.4629],
[48.1426, 57.58403, 39.89198],
[41.64599, 66.91489, 31.8278],
],
hpts=[[-95, -3, -3], [-1, -1.0, -3.0], [-2, -2, 2.0], [0, 0, 0]],
)
for key, text in inputs.items():
kind = key.split("_")[-1]
fname = op.join(tempdir, "test." + kind)
with open(fname, "w") as fid:
fid.write(text)
montage = read_montage(fname)
if kind in ("sfp", "txt"):
assert_true("very_very_very_long_name" in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, "test")
if kind == "csd":
dtype = [
("label", "S4"),
("theta", "f8"),
("phi", "f8"),
("radius", "f8"),
("x", "f8"),
("y", "f8"),
("z", "f8"),
("off_sph", "f8"),
]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
poss["csd"] = np.c_[table["x"], table["y"], table["z"]]
if kind == "elc":
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(np.linalg.norm, 1, montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
assert_array_almost_equal(poss[key], montage.pos, 4, err_msg=key)
# Test reading in different letter case.
ch_names = [
"F3",
"FZ",
"F4",
"FC3",
"FCz",
"FC4",
"C3",
"CZ",
"C4",
"CP3",
"CPZ",
"CP4",
"P3",
"PZ",
"P4",
"O1",
"OZ",
"O2",
]
montage = read_montage("standard_1020", ch_names=ch_names)
assert_array_equal(ch_names, montage.ch_names)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
"""
fname = op.join(tempdir, "test_fid.hpts")
with open(fname, "w") as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, "test_fid.hpts"), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index("2")
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index("1")
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index("3")
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, "test_fid.hpts")
montage = read_montage(montage_fname, unit="mm")
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ["eeg"] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c["loc"][:3] for c in info["chs"]])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info["ch_names"])
info = create_info(montage.ch_names, 1e3, ["eeg"] * len(montage.ch_names))
evoked = EvokedArray(data=np.zeros((len(montage.ch_names), 1)), info=info, tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c["loc"][:3] for c in evoked.info["chs"]])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info["ch_names"])
# Warning should be raised when some EEG are not specified in the montage
with warnings.catch_warnings(record=True) as w:
info = create_info(montage.ch_names + ["foo", "bar"], 1e3, ["eeg"] * (len(montage.ch_names) + 2))
_set_montage(info, montage)
assert_true(len(w) == 1)
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
inputs = dict(
sfp='FidNz 0 9.071585155 -2.359754454\n'
'FidT9 -6.711765 0.040402876 -3.251600355\n'
'very_very_very_long_name -5.831241498 -4.494821698 4.955347697\n'
'Cz 0 0 8.899186843',
csd=
'// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E31 90.000 -11.000 1.000 0.0000 0.9816 -0.1908 0.00000000000000000\n' # noqa: E501
'E61 158.000 -17.200 1.000 -0.8857 0.3579 -0.2957 -0.00000000000000022', # noqa: E501
mm_elc=
'# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n' # noqa:E501
'NumberPositions= 68\n'
'Positions\n'
'-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n'
'0.0083 86.8110 -39.9830\n'
'-86.0761 -24.9897 -67.9860\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
m_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n' # noqa:E501
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
txt='Site Theta Phi\n'
'Fp1 -92 -72\n'
'Fp2 92 72\n'
'very_very_very_long_name -92 72\n'
'O2 92 -90\n',
elp='346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n'
'EEG\t FCz\t 68.01\t 58.103\t 85\n',
hpts='eeg Fp1 -95.0 -3. -3.\n'
'eeg AF7 -1 -1 -3\n'
'eeg A3 -2 -2 2\n'
'eeg A 0 0 0',
)
# Get actual positions and save them for checking
# csd comes from the string above, all others come from commit 2fa35d4
poss = dict(
sfp=[[0.0, 9.07159, -2.35975], [-6.71176, 0.0404, -3.2516],
[-5.83124, -4.49482, 4.95535], [0.0, 0.0, 8.89919]],
mm_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.08681, -0.03998], [-0.08608, -0.02499, -0.06799]],
m_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.00868, -0.03998], [0.08, -0.02, -0.04]],
txt=[[-26.25044, 80.79056, -2.96646], [26.25044, 80.79056, -2.96646],
[-26.25044, -80.79056, -2.96646], [0.0, -84.94822, -2.96646]],
elp=[[-48.20043, 57.55106, 39.86971], [0.0, 60.73848, 59.4629],
[48.1426, 57.58403, 39.89198], [41.64599, 66.91489, 31.8278]],
hpts=[[-95, -3, -3], [-1, -1., -3.], [-2, -2, 2.], [0, 0, 0]],
)
for key, text in inputs.items():
kind = key.split('_')[-1]
fname = op.join(tempdir, 'test.' + kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if kind in ('sfp', 'txt'):
assert_true('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, 'test')
if kind == 'csd':
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
poss['csd'] = np.c_[table['x'], table['y'], table['z']]
if kind == 'elc':
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(
np.linalg.norm, 1, montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
assert_array_almost_equal(poss[key], montage.pos, 4, err_msg=key)
# Test reading in different letter case.
ch_names = [
"F3", "FZ", "F4", "FC3", "FCz", "FC4", "C3", "CZ", "C4", "CP3", "CPZ",
"CP4", "P3", "PZ", "P4", "O1", "OZ", "O2"
]
montage = read_montage('standard_1020', ch_names=ch_names)
assert_array_equal(ch_names, montage.ch_names)
# test transform
input_strs = [
"""
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
""", """
Fp1 -95.0 -31.0 -3.0
AF7 -81 -59 -3
AF3 -87 -41 28
nasion -91 0 -42
lpa 0 -91 -42
rpa 0 91 -42
"""
]
all_fiducials = [['2', '1', '3'], ['nasion', 'lpa', 'rpa']]
kinds = ['test_fid.hpts', 'test_fid.sfp']
for kind, fiducials, input_str in zip(kinds, all_fiducials, input_strs):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, kind), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index(fiducials[0])
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index(fiducials[1])
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index(fiducials[2])
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, kind)
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3,
['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(montage.ch_names, 1e3,
['eeg'] * len(montage.ch_names))
evoked = EvokedArray(data=np.zeros((len(montage.ch_names), 1)),
info=info,
tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in montage
with warnings.catch_warnings(record=True) as w:
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
_set_montage(info, montage)
assert_true(len(w) == 1)
def test_montage():
"""Test making montages"""
tempdir = _TempDir()
# no pep8
input_str = [
'FidNz 0.00000 10.56381 -2.05108\nFidT9 -7.82694 0.45386 -3.76056\n'
'very_very_very_long_name 7.82694 0.45386 -3.76056',
'// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa
'E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000\n' # noqa
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000', # noqa
'# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n'
'NumberPositions= 68\nPositions\n-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n0.0083 86.8110 -39.9830\n'
'Labels\nLPA\nRPA\nNz\n',
'Site Theta Phi\nFp1 -92 -72\nFp2 92 72\n'
'very_very_very_long_name -60 -51\n',
'346\n'
'EEG F3 -62.027 -50.053 85\n'
'EEG Fz 45.608 90 85\n'
'EEG F4 62.01 50.103 85\n',
'eeg Fp1 -95.0 -31.0 -3.0\neeg AF7 -81 -59 -3\neeg AF3 -87 -41 28\n'
]
kinds = ['test.sfp', 'test.csd', 'test.elc', 'test.txt', 'test.elp',
'test.hpts']
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if ".sfp" in kind or ".txt" in kind:
assert_true('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 3)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (3, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2, montage.pos, 4)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
"""
kind = 'test_fid.hpts'
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index('2')
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index('1')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index('3')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, 'test_fid.hpts')
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(
montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
evoked = EvokedArray(
data=np.zeros((len(montage.ch_names), 1)), info=info, tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in the montage
with warnings.catch_warnings(record=True) as w:
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
_set_montage(info, montage)
assert_true(len(w) == 1)
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
# no pep8
input_str = [
'FidNz 0.00000 10.56381 -2.05108\nFidT9 -7.82694 0.45386 -3.76056\n'
'very_very_very_long_name 7.82694 0.45386 -3.76056\nDmy 7.0 0.0 1.0',
'// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E4 52.700 12.000 1.000 0.7084 0.7504 0.1508 0.00000000000000000', # noqa: E501; dummy line
'# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n'
'NumberPositions= 68\nPositions\n-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n0.0083 86.8110 -39.9830\n'
'85 -20 -48\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
'# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n'
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
'Site Theta Phi\nFp1 -92 -72\nFp2 92 72\n'
'very_very_very_long_name -60 -51\n'
'dummy -60 -52\n',
'346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n'
'EEG\t FCz\t 68.01\t 58.103\t 85\n',
'eeg Fp1 -95.0 -3. -3.\neeg AF7 -1 -1 -3\neeg A3 -2 -2 2\neeg A 0 0 0'
]
kinds = [
'test.sfp', 'test.csd', 'test_mm.elc', 'test_m.elc', 'test.txt',
'test.elp', 'test.hpts'
]
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if ".sfp" in kind or ".txt" in kind:
assert_true('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2[:-1, :], montage.pos[:-1, :], 4)
if kind.endswith('elc'):
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(
np.linalg.norm, 1, montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
# Test reading in different letter case.
ch_names = [
"F3", "FZ", "F4", "FC3", "FCz", "FC4", "C3", "CZ", "C4", "CP3", "CPZ",
"CP4", "P3", "PZ", "P4", "O1", "OZ", "O2"
]
montage = read_montage('standard_1020', ch_names=ch_names)
assert_array_equal(ch_names, montage.ch_names)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
"""
kind = 'test_fid.hpts'
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index('2')
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index('1')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index('3')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, 'test_fid.hpts')
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
evoked = EvokedArray(data=np.zeros((len(montage.ch_names), 1)),
info=info,
tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in the montage
with warnings.catch_warnings(record=True) as w:
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
_set_montage(info, montage)
assert_true(len(w) == 1)
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
inputs = dict(
sfp='FidNz 0 9.071585155 -2.359754454\n'
'FidT9 -6.711765 0.040402876 -3.251600355\n'
'very_very_very_long_name -5.831241498 -4.494821698 4.955347697\n'
'Cz 0 0 8.899186843',
csd=
'// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E31 90.000 -11.000 1.000 0.0000 0.9816 -0.1908 0.00000000000000000\n' # noqa: E501
'E61 158.000 -17.200 1.000 -0.8857 0.3579 -0.2957 -0.00000000000000022', # noqa: E501
mm_elc=
'# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n' # noqa:E501
'NumberPositions= 68\n'
'Positions\n'
'-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n'
'0.0083 86.8110 -39.9830\n'
'-86.0761 -24.9897 -67.9860\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
m_elc='# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n' # noqa:E501
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
txt='Site Theta Phi\n'
'Fp1 -92 -72\n'
'Fp2 92 72\n'
'very_very_very_long_name -92 72\n'
'O2 92 -90\n',
elp='346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n'
'EEG\t FCz\t 68.01\t 58.103\t 85\n',
hpts='eeg Fp1 -95.0 -3. -3.\n'
'eeg AF7 -1 -1 -3\n'
'eeg A3 -2 -2 2\n'
'eeg A 0 0 0',
bvef='<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n'
'<!-- Generated by EasyCap Configurator 19.05.2014 -->\n'
'<Electrodes defaults="false">\n'
' <Electrode>\n'
' <Name>Fp1</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-72</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>1</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>Fz</Name>\n'
' <Theta>45</Theta>\n'
' <Phi>90</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>2</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F3</Name>\n'
' <Theta>-60</Theta>\n'
' <Phi>-51</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>3</Number>\n'
' </Electrode>\n'
' <Electrode>\n'
' <Name>F7</Name>\n'
' <Theta>-90</Theta>\n'
' <Phi>-36</Phi>\n'
' <Radius>1</Radius>\n'
' <Number>4</Number>\n'
' </Electrode>\n'
'</Electrodes>',
)
# Get actual positions and save them for checking
# csd comes from the string above, all others come from commit 2fa35d4
poss = dict(
sfp=[[0.0, 9.07159, -2.35975], [-6.71176, 0.0404, -3.2516],
[-5.83124, -4.49482, 4.95535], [0.0, 0.0, 8.89919]],
mm_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.08681, -0.03998], [-0.08608, -0.02499, -0.06799]],
m_elc=[[-0.08608, -0.01999, -0.04799], [0.08579, -0.02001, -0.04803],
[1e-05, 0.00868, -0.03998], [0.08, -0.02, -0.04]],
txt=[[-26.25044, 80.79056, -2.96646], [26.25044, 80.79056, -2.96646],
[-26.25044, -80.79056, -2.96646], [0.0, -84.94822, -2.96646]],
elp=[[-48.20043, 57.55106, 39.86971], [0.0, 60.73848, 59.4629],
[48.1426, 57.58403, 39.89198], [41.64599, 66.91489, 31.8278]],
hpts=[[-95, -3, -3], [-1, -1., -3.], [-2, -2, 2.], [0, 0, 0]],
bvef=[[-26.266444, 80.839803, 5.204748e-15],
[3.680313e-15, 60.104076, 60.104076],
[-46.325632, 57.207392, 42.500000],
[-68.766444, 49.961746, 5.204748e-15]],
)
for key, text in inputs.items():
kind = key.split('_')[-1]
fname = op.join(tempdir, 'test.' + kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if kind in ('sfp', 'txt'):
assert ('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, 'test')
if kind == 'csd':
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
poss['csd'] = np.c_[table['x'], table['y'], table['z']]
if kind == 'elc':
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(
np.linalg.norm, 1, montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
assert_array_almost_equal(poss[key], montage.pos, 4, err_msg=key)
# Test reading in different letter case.
ch_names = [
"F3", "FZ", "F4", "FC3", "FCz", "FC4", "C3", "CZ", "C4", "CP3", "CPZ",
"CP4", "P3", "PZ", "P4", "O1", "OZ", "O2"
]
montage = read_montage('standard_1020', ch_names=ch_names)
assert_array_equal(ch_names, montage.ch_names)
# test transform
input_strs = [
"""
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
""", """
Fp1 -95.0 -31.0 -3.0
AF7 -81 -59 -3
AF3 -87 -41 28
FidNz -91 0 -42
FidT9 0 -91 -42
FidT10 0 91 -42
"""
]
# sfp files seem to have Nz, T9, and T10 as fiducials:
# https://github.com/mne-tools/mne-python/pull/4482#issuecomment-321980611
kinds = ['test_fid.hpts', 'test_fid.sfp']
for kind, input_str in zip(kinds, input_strs):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, kind), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
assert_array_equal(montage.nasion[[0, 2]], [0, 0])
assert_array_equal(montage.lpa[[1, 2]], [0, 0])
assert_array_equal(montage.rpa[[1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, kind)
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3,
['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(montage.ch_names, 1e3,
['eeg'] * len(montage.ch_names))
evoked = EvokedArray(data=np.zeros((len(montage.ch_names), 1)),
info=info,
tmin=0)
# test return type as well as set montage
assert (isinstance(evoked.set_montage(montage), type(evoked)))
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in montage
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage)
# Channel names can be treated case insensitive
info = create_info(['FP1', 'af7', 'AF3'], 1e3, ['eeg'] * 3)
_set_montage(info, montage)
# Unless there is a collision in names
info = create_info(['FP1', 'Fp1', 'AF3'], 1e3, ['eeg'] * 3)
assert (info['dig'] is None)
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage)
assert len(info['dig']) == 5 # 2 EEG w/pos, 3 fiducials
montage.ch_names = ['FP1', 'Fp1', 'AF3']
info = create_info(['fp1', 'AF3'], 1e3, ['eeg', 'eeg'])
assert (info['dig'] is None)
with pytest.warns(RuntimeWarning, match='position specified'):
_set_montage(info, montage, set_dig=False)
assert (info['dig'] is None)
# test get_pos2d method
montage = read_montage("standard_1020")
c3 = montage.get_pos2d()[montage.ch_names.index("C3")]
c4 = montage.get_pos2d()[montage.ch_names.index("C4")]
fz = montage.get_pos2d()[montage.ch_names.index("Fz")]
oz = montage.get_pos2d()[montage.ch_names.index("Oz")]
f1 = montage.get_pos2d()[montage.ch_names.index("F1")]
assert (c3[0] < 0) # left hemisphere
assert (c4[0] > 0) # right hemisphere
assert (fz[1] > 0) # frontal
assert (oz[1] < 0) # occipital
assert_allclose(fz[0], 0, atol=1e-2) # midline
assert_allclose(oz[0], 0, atol=1e-2) # midline
assert (f1[0] < 0 and f1[1] > 0) # left frontal
# test get_builtin_montages function
montages = get_builtin_montages()
assert (len(montages) > 0) # MNE should always ship with montages
assert ("standard_1020" in montages) # 10/20 montage
assert ("standard_1005" in montages) # 10/05 montage
def test_montage():
"""Test making montages."""
tempdir = _TempDir()
# no pep8
input_str = [
'FidNz 0.00000 10.56381 -2.05108\nFidT9 -7.82694 0.45386 -3.76056\n'
'very_very_very_long_name 7.82694 0.45386 -3.76056\nDmy 7.0 0.0 1.0',
'// MatLab Sphere coordinates [degrees] Cartesian coordinates\n' # noqa: E501
'// Label Theta Phi Radius X Y Z off sphere surface\n' # noqa: E501
'E1 37.700 -14.000 1.000 0.7677 0.5934 -0.2419 -0.00000000000000011\n' # noqa: E501
'E2 44.600 -0.880 1.000 0.7119 0.7021 -0.0154 0.00000000000000000\n' # noqa: E501
'E3 51.700 11.000 1.000 0.6084 0.7704 0.1908 0.00000000000000000\n' # noqa: E501
'E4 52.700 12.000 1.000 0.7084 0.7504 0.1508 0.00000000000000000', # noqa: E501; dummy line
'# ASA electrode file\nReferenceLabel avg\nUnitPosition mm\n'
'NumberPositions= 68\nPositions\n-86.0761 -19.9897 -47.9860\n'
'85.7939 -20.0093 -48.0310\n0.0083 86.8110 -39.9830\n'
'85 -20 -48\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
'# ASA electrode file\nReferenceLabel avg\nUnitPosition m\n'
'NumberPositions= 68\nPositions\n-.0860761 -.0199897 -.0479860\n'
'.0857939 -.0200093 -.0480310\n.0000083 .00868110 -.0399830\n'
'.08 -.02 -.04\n'
'Labels\nLPA\nRPA\nNz\nDummy\n',
'Site Theta Phi\nFp1 -92 -72\nFp2 92 72\n'
'very_very_very_long_name -60 -51\n'
'dummy -60 -52\n',
'346\n'
'EEG\t F3\t -62.027\t -50.053\t 85\n'
'EEG\t Fz\t 45.608\t 90\t 85\n'
'EEG\t F4\t 62.01\t 50.103\t 85\n'
'EEG\t FCz\t 68.01\t 58.103\t 85\n',
'eeg Fp1 -95.0 -3. -3.\neeg AF7 -1 -1 -3\neeg A3 -2 -2 2\neeg A 0 0 0'
]
kinds = ['test.sfp', 'test.csd', 'test_mm.elc', 'test_m.elc', 'test.txt',
'test.elp', 'test.hpts']
for kind, text in zip(kinds, input_str):
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(text)
montage = read_montage(fname)
if ".sfp" in kind or ".txt" in kind:
assert_true('very_very_very_long_name' in montage.ch_names)
assert_equal(len(montage.ch_names), 4)
assert_equal(len(montage.ch_names), len(montage.pos))
assert_equal(montage.pos.shape, (4, 3))
assert_equal(montage.kind, op.splitext(kind)[0])
if kind.endswith('csd'):
dtype = [('label', 'S4'), ('theta', 'f8'), ('phi', 'f8'),
('radius', 'f8'), ('x', 'f8'), ('y', 'f8'), ('z', 'f8'),
('off_sph', 'f8')]
try:
table = np.loadtxt(fname, skip_header=2, dtype=dtype)
except TypeError:
table = np.loadtxt(fname, skiprows=2, dtype=dtype)
pos2 = np.c_[table['x'], table['y'], table['z']]
assert_array_almost_equal(pos2[:-1, :], montage.pos[:-1, :], 4)
if kind.endswith('elc'):
# Make sure points are reasonable distance from geometric centroid
centroid = np.sum(montage.pos, axis=0) / montage.pos.shape[0]
distance_from_centroid = np.apply_along_axis(
np.linalg.norm, 1,
montage.pos - centroid)
assert_array_less(distance_from_centroid, 0.2)
assert_array_less(0.01, distance_from_centroid)
# Test reading in different letter case.
ch_names = ["F3", "FZ", "F4", "FC3", "FCz", "FC4", "C3", "CZ", "C4", "CP3",
"CPZ", "CP4", "P3", "PZ", "P4", "O1", "OZ", "O2"]
montage = read_montage('standard_1020', ch_names=ch_names)
assert_array_equal(ch_names, montage.ch_names)
# test transform
input_str = """
eeg Fp1 -95.0 -31.0 -3.0
eeg AF7 -81 -59 -3
eeg AF3 -87 -41 28
cardinal 2 -91 0 -42
cardinal 1 0 -91 -42
cardinal 3 0 91 -42
"""
kind = 'test_fid.hpts'
fname = op.join(tempdir, kind)
with open(fname, 'w') as fid:
fid.write(input_str)
montage = read_montage(op.join(tempdir, 'test_fid.hpts'), transform=True)
# check coordinate transformation
pos = np.array([-95.0, -31.0, -3.0])
nasion = np.array([-91, 0, -42])
lpa = np.array([0, -91, -42])
rpa = np.array([0, 91, -42])
fids = np.vstack((nasion, lpa, rpa))
trans = get_ras_to_neuromag_trans(fids[0], fids[1], fids[2])
pos = apply_trans(trans, pos)
assert_array_equal(montage.pos[0], pos)
idx = montage.ch_names.index('2')
assert_array_equal(montage.pos[idx, [0, 2]], [0, 0])
idx = montage.ch_names.index('1')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
idx = montage.ch_names.index('3')
assert_array_equal(montage.pos[idx, [1, 2]], [0, 0])
pos = np.array([-95.0, -31.0, -3.0])
montage_fname = op.join(tempdir, 'test_fid.hpts')
montage = read_montage(montage_fname, unit='mm')
assert_array_equal(montage.pos[0], pos * 1e-3)
# test with last
info = create_info(montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
_set_montage(info, montage)
pos2 = np.array([c['loc'][:3] for c in info['chs']])
assert_array_equal(pos2, montage.pos)
assert_equal(montage.ch_names, info['ch_names'])
info = create_info(
montage.ch_names, 1e3, ['eeg'] * len(montage.ch_names))
evoked = EvokedArray(
data=np.zeros((len(montage.ch_names), 1)), info=info, tmin=0)
evoked.set_montage(montage)
pos3 = np.array([c['loc'][:3] for c in evoked.info['chs']])
assert_array_equal(pos3, montage.pos)
assert_equal(montage.ch_names, evoked.info['ch_names'])
# Warning should be raised when some EEG are not specified in the montage
with warnings.catch_warnings(record=True) as w:
info = create_info(montage.ch_names + ['foo', 'bar'], 1e3,
['eeg'] * (len(montage.ch_names) + 2))
_set_montage(info, montage)
assert_true(len(w) == 1)
