def test_auto_topomap_coords():
"""Test mapping of coordinates in 3D space to 2D"""
info = Raw(fif_fname).info.copy()
picks = pick_types(info, meg=False, eeg=True, eog=False, stim=False)
# Remove extra digitization point, so EEG digitization points match up
# with the EEG channels
del info['dig'][85]
# Remove head origin from channel locations, so mapping with digitization
# points yields the same result
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL,
FIFF.FIFFV_POINT_EEG,
FIFF.FIFFV_POINT_EXTRA)
_, origin_head, _ = fit_sphere_to_headshape(info, dig_kinds)
origin_head /= 1000. # to meters
for ch in info['chs']:
ch['loc'][:3] -= origin_head
# Use channel locations
l0 = _auto_topomap_coords(info, picks)
# Remove electrode position information, use digitization points from now
# on.
for ch in info['chs']:
ch['loc'] = np.zeros(12)
l1 = _auto_topomap_coords(info, picks)
assert_allclose(l1, l0)
# Test plotting mag topomap without channel locations: it should fail
mag_picks = pick_types(info, meg='mag')
assert_raises(ValueError, _auto_topomap_coords, info, mag_picks)
# Test function with too many EEG digitization points: it should fail
info['dig'].append({'r': [1, 2, 3], 'kind': FIFF.FIFFV_POINT_EEG})
assert_raises(ValueError, _auto_topomap_coords, info, picks)
# Test function with too little EEG digitization points: it should fail
info['dig'] = info['dig'][:-2]
assert_raises(ValueError, _auto_topomap_coords, info, picks)
# Electrode positions must be unique
info['dig'].append(info['dig'][-1])
assert_raises(ValueError, _auto_topomap_coords, info, picks)
# Test function without EEG digitization points: it should fail
info['dig'] = [d for d in info['dig'] if d['kind'] != FIFF.FIFFV_POINT_EEG]
assert_raises(RuntimeError, _auto_topomap_coords, info, picks)
# Test function without any digitization points, it should fail
info['dig'] = None
assert_raises(RuntimeError, _auto_topomap_coords, info, picks)
info['dig'] = []
assert_raises(RuntimeError, _auto_topomap_coords, info, picks)
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points."""
# Create points of various kinds
rad = 0.09
big_rad = 0.12
center = np.array([0.0005, -0.01, 0.04])
dev_trans = np.array([0., -0.005, -0.01])
dev_center = center - dev_trans
dig = [
# Left auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])},
# Nasion
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])},
# Right auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])},
# Top of the head (extra point)
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])},
# F3
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])},
# F4
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])},
# Cz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])},
# Pz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])},
]
for d in dig:
d['r'] *= rad
d['r'] += center
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
info = Info(dig=dig, dev_head_t=dev_head_t)
# Degenerate conditions
pytest.raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds=(FIFF.FIFFV_POINT_HPI,))
pytest.raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds='foo', units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
pytest.raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-5)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
kwargs = dict(rtol=1e-3, atol=1e-3)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = 'eeg'
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-2)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
# Test big size
dig_kinds = ('cardinal', 'extra')
info_big = deepcopy(info)
for d in info_big['dig']:
d['r'] -= center
d['r'] *= big_rad / rad
d['r'] += center
with pytest.warns(RuntimeWarning, match='Estimated head size'):
r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
units='mm')
assert_allclose(oh, center * 1000, atol=1e-3)
assert_allclose(r, big_rad * 1000, atol=1e-3)
del info_big
# Test offcenter
dig_kinds = ('cardinal', 'extra')
info_shift = deepcopy(info)
shift_center = np.array([0., -0.03, 0.])
for d in info_shift['dig']:
d['r'] -= center
d['r'] += shift_center
with pytest.warns(RuntimeWarning, match='from head frame origin'):
r, oh, od = fit_sphere_to_headshape(
info_shift, dig_kinds=dig_kinds, units='m')
assert_allclose(oh, shift_center, atol=1e-6)
assert_allclose(r, rad, atol=1e-6)
# Test "auto" mode (default)
# Should try "extra", fail, and go on to EEG
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, units='m')
kwargs = dict(rtol=1e-3, atol=1e-3)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
assert_allclose(r, r2, atol=1e-7)
assert_allclose(oh, oh2, atol=1e-7)
assert_allclose(od, od2, atol=1e-7)
# this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = Info(dig=dig[:7], dev_head_t=dev_head_t)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, units='m')
# this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = Info(dig=dig[:6], dev_head_t=dev_head_t)
pytest.raises(ValueError, fit_sphere_to_headshape, info, units='m')
pytest.raises(TypeError, fit_sphere_to_headshape, 1, units='m')
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points."""
# Create points of various kinds
rad = 0.09
big_rad = 0.12
center = np.array([0.0005, -0.01, 0.04])
dev_trans = np.array([0., -0.005, -0.01])
dev_center = center - dev_trans
dig = [
# Left auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])},
# Nasion
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])},
# Right auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])},
# Top of the head (extra point)
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'ident': 0,
'r': np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'ident': 0,
'r': np.array([0, .72, .69])},
# F3
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'ident': 1,
'r': np.array([-.55, .67, .50])},
# F4
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'ident': 2,
'r': np.array([.55, .67, .50])},
# Cz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'ident': 3,
'r': np.array([0.0, 0.0, 1.0])},
# Pz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'ident': 4,
'r': np.array([0, -.72, .69])},
]
for d in dig:
d['r'] *= rad
d['r'] += center
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
info = Info(dig=dig, dev_head_t=dev_head_t)
# Degenerate conditions
pytest.raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds=(FIFF.FIFFV_POINT_HPI,))
pytest.raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds='foo', units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
pytest.raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-5)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
kwargs = dict(rtol=1e-3, atol=1e-3)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = 'eeg'
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-2)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
# Test big size
dig_kinds = ('cardinal', 'extra')
info_big = deepcopy(info)
for d in info_big['dig']:
d['r'] -= center
d['r'] *= big_rad / rad
d['r'] += center
with pytest.warns(RuntimeWarning, match='Estimated head size'):
r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
units='mm')
assert_allclose(oh, center * 1000, atol=1e-3)
assert_allclose(r, big_rad * 1000, atol=1e-3)
del info_big
# Test offcenter
dig_kinds = ('cardinal', 'extra')
info_shift = deepcopy(info)
shift_center = np.array([0., -0.03, 0.])
for d in info_shift['dig']:
d['r'] -= center
d['r'] += shift_center
with pytest.warns(RuntimeWarning, match='from head frame origin'):
r, oh, od = fit_sphere_to_headshape(
info_shift, dig_kinds=dig_kinds, units='m')
assert_allclose(oh, shift_center, atol=1e-6)
assert_allclose(r, rad, atol=1e-6)
# Test "auto" mode (default)
# Should try "extra", fail, and go on to EEG
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, units='m')
kwargs = dict(rtol=1e-3, atol=1e-3)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
assert_allclose(r, r2, atol=1e-7)
assert_allclose(oh, oh2, atol=1e-7)
assert_allclose(od, od2, atol=1e-7)
# this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = Info(dig=dig[:7], dev_head_t=dev_head_t)
with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
r, oh, od = fit_sphere_to_headshape(info, units='m')
# this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = Info(dig=dig[:6], dev_head_t=dev_head_t)
pytest.raises(ValueError, fit_sphere_to_headshape, info, units='m')
pytest.raises(TypeError, fit_sphere_to_headshape, 1, units='m')
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
rad = 90. # mm
center = np.array([0.5, -10., 40.]) # mm
dev_trans = np.array([0., -0.005, -10.])
dev_center = center - dev_trans
dig = [
# Left auricular
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])
},
# Nasion
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])
},
# Right auricular
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])
},
# Top of the head (extra point)
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])
},
# EEG points
# Fz
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])
},
# F3
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])
},
# F4
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])
},
# Cz
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])
},
# Pz
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])
},
]
for d in dig:
d['r'] *= rad / 1000.
d['r'] += center / 1000.
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))
info = {'dig': dig, 'dev_head_t': dev_head_t}
# Degenerate conditions
assert_raises(ValueError,
fit_sphere_to_headshape,
info,
dig_kinds=(FIFF.FIFFV_POINT_HPI, ))
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
assert_raises(RuntimeError, fit_sphere_to_headshape, info)
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=1e-2) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = (FIFF.FIFFV_POINT_EEG, )
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=10.) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
dig = [dict(coord_frame=FIFF.FIFFV_COORD_DEVICE, )]
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
rad = 0.09
big_rad = 0.12
center = np.array([0.0005, -0.01, 0.04])
dev_trans = np.array([0., -0.005, -0.01])
dev_center = center - dev_trans
dig = [
# Left auricular
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])
},
# Nasion
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])
},
# Right auricular
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])
},
# Top of the head (extra point)
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])
},
# EEG points
# Fz
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])
},
# F3
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])
},
# F4
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])
},
# Cz
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])
},
# Pz
{
'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])
},
]
for d in dig:
d['r'] *= rad
d['r'] += center
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
info = {'dig': dig, 'dev_head_t': dev_head_t}
# Degenerate conditions
with warnings.catch_warnings(record=True) as w:
assert_raises(ValueError,
fit_sphere_to_headshape,
info,
dig_kinds=(FIFF.FIFFV_POINT_HPI, ))
assert_equal(len(w), 1)
assert_true(w[0].category == DeprecationWarning)
assert_raises(ValueError,
fit_sphere_to_headshape,
info,
dig_kinds='foo',
units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
assert_raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info,
dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-5)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
kwargs = dict(rtol=1e-3, atol=1e-3)
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info,
dig_kinds=dig_kinds,
units='m')
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = 'eeg'
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info,
dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-2)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
# Test big size
dig_kinds = ('cardinal', 'extra')
info_big = deepcopy(info)
for d in info_big['dig']:
d['r'] -= center
d['r'] *= big_rad / rad
d['r'] += center
with warnings.catch_warnings(record=True): # fit
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_big,
dig_kinds=dig_kinds,
verbose='warning',
units='mm')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 2)
assert_true('Estimated head size' in log_file)
assert_allclose(oh, center * 1000, atol=1e-3)
assert_allclose(r, big_rad * 1000, atol=1e-3)
del info_big
# Test offcenter
dig_kinds = ('cardinal', 'extra')
info_shift = deepcopy(info)
shift_center = np.array([0., -0.03, 0.])
for d in info_shift['dig']:
d['r'] -= center
d['r'] += shift_center
with warnings.catch_warnings(record=True):
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_shift,
dig_kinds=dig_kinds,
verbose='warning',
units='m')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 2)
assert_true('from head frame origin' in log_file)
assert_allclose(oh, shift_center, atol=1e-6)
assert_allclose(r, rad, atol=1e-6)
# Test "auto" mode (default)
# Should try "extra", fail, and go on to EEG
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info, units='m')
kwargs = dict(rtol=1e-3, atol=1e-3)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
with warnings.catch_warnings(record=True): # not enough points
r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
assert_allclose(r, r2, atol=1e-7)
assert_allclose(oh, oh2, atol=1e-7)
assert_allclose(od, od2, atol=1e-7)
# this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = {'dig': dig[:7], 'dev_head_t': dev_head_t}
with warnings.catch_warnings(record=True): # bad fit
r, oh, od = fit_sphere_to_headshape(info, units='m')
# this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = {'dig': dig[:6], 'dev_head_t': dev_head_t}
assert_raises(ValueError, fit_sphere_to_headshape, info, units='m')
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
dig = [
# Left auricular
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])
},
# Nasion
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])
},
# Right auricular
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])
},
# Top of the head (extra point)
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])
},
# EEG points
# Fz
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])
},
# F3
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])
},
# F4
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])
},
# Cz
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])
},
# Pz
{
'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])
},
]
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = {
'from': FIFF.FIFFV_COORD_DEVICE,
'to': FIFF.FIFFV_COORD_HEAD,
'trans': rotation(x=0.2),
}
info = {'dig': dig, 'dev_head_t': dev_head_t}
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_almost_equal(r / 1000, 1.0, decimal=10)
assert_almost_equal(oh / 1000, [0.0, 0.0, 0.0], decimal=10)
assert_almost_equal(od / 1000, [0.0, 0.0, 0.0], decimal=10)
# Test with all points. Digitization points are no longer perfect, so
# allow for a wider margin of error.
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_almost_equal(r / 1000, 1.0, decimal=3)
assert_almost_equal(oh / 1000, [0.0, 0.0, 0.0], decimal=3)
assert_almost_equal(od / 1000, [0.0, 0.0, 0.0], decimal=3)
# Test with some noisy EEG points only.
dig_kinds = (FIFF.FIFFV_POINT_EEG, )
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_almost_equal(r / 1000, 1.0, decimal=2)
assert_almost_equal(oh / 1000, [0.0, 0.0, 0.0], decimal=2)
assert_almost_equal(od / 1000, [0.0, 0.0, 0.0], decimal=2)
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
rad = 90. # mm
big_rad = 120.
center = np.array([0.5, -10., 40.]) # mm
dev_trans = np.array([0., -0.005, -10.])
dev_center = center - dev_trans
dig = [
# Left auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])},
# Nasion
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])},
# Right auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])},
# Top of the head (extra point)
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])},
# F3
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])},
# F4
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])},
# Cz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])},
# Pz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])},
]
for d in dig:
d['r'] *= rad / 1000.
d['r'] += center / 1000.
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))
info = {'dig': dig, 'dev_head_t': dev_head_t}
# Degenerate conditions
assert_raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds=(FIFF.FIFFV_POINT_HPI,))
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
assert_raises(RuntimeError, fit_sphere_to_headshape, info)
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=1e-2) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
FIFF.FIFFV_POINT_EEG)
kwargs = dict(rtol=1e-3, atol=1.) # in mm
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = (FIFF.FIFFV_POINT_EEG,)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=10.) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
# Test big size
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
info_big = deepcopy(info)
for d in info_big['dig']:
d['r'] -= center / 1000.
d['r'] *= big_rad / rad
d['r'] += center / 1000.
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
verbose='warning')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 1)
assert_true(log_file.startswith('Estimated head size'))
assert_allclose(oh, center, atol=1e-3)
assert_allclose(r, big_rad, atol=1e-3)
del info_big
# Test offcenter
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
info_shift = deepcopy(info)
shift_center = np.array([0., -30, 0.])
for d in info_shift['dig']:
d['r'] -= center / 1000.
d['r'] += shift_center / 1000.
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_shift, dig_kinds=dig_kinds,
verbose='warning')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 1)
assert_true('from head frame origin' in log_file)
assert_allclose(oh, shift_center, atol=1e-3)
assert_allclose(r, rad, atol=1e-3)
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
rad = 90. # mm
big_rad = 120.
center = np.array([0.5, -10., 40.]) # mm
dev_trans = np.array([0., -0.005, -10.])
dev_center = center - dev_trans
dig = [
# Left auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])},
# Nasion
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])},
# Right auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])},
# Top of the head (extra point)
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])},
# F3
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])},
# F4
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])},
# Cz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])},
# Pz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])},
]
for d in dig:
d['r'] *= rad / 1000.
d['r'] += center / 1000.
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))
info = {'dig': dig, 'dev_head_t': dev_head_t}
# Degenerate conditions
assert_raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds=(FIFF.FIFFV_POINT_HPI,))
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
assert_raises(RuntimeError, fit_sphere_to_headshape, info)
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=1e-2) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
FIFF.FIFFV_POINT_EEG)
kwargs = dict(rtol=1e-3, atol=1.) # in mm
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = (FIFF.FIFFV_POINT_EEG,)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=10.) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
# Test big size
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
info_big = deepcopy(info)
for d in info_big['dig']:
d['r'] -= center / 1000.
d['r'] *= big_rad / rad
d['r'] += center / 1000.
with warnings.catch_warnings(record=True): # fit
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
verbose='warning')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 1)
assert_true(log_file.startswith('Estimated head size'))
assert_allclose(oh, center, atol=1e-3)
assert_allclose(r, big_rad, atol=1e-3)
del info_big
# Test offcenter
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
info_shift = deepcopy(info)
shift_center = np.array([0., -30, 0.])
for d in info_shift['dig']:
d['r'] -= center / 1000.
d['r'] += shift_center / 1000.
with warnings.catch_warnings(record=True):
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(
info_shift, dig_kinds=dig_kinds, verbose='warning')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 1)
assert_true('from head frame origin' in log_file)
assert_allclose(oh, shift_center, atol=1e-3)
assert_allclose(r, rad, atol=1e-3)
def test_fit_sphere_to_headshape():
""" Test fitting a sphere to digitization points. """
# Create points of various kinds
dig = [
# Left auricular
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])},
# Nasion
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])},
# Right auricular
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])},
# Top of the head (extra point)
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])},
# F3
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])},
# F4
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])},
# Cz
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])},
# Pz
{'coord_frame': FIFF.FIFFV_COORD_DEVICE,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])},
]
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = {
'from': FIFF.FIFFV_COORD_DEVICE,
'to': FIFF.FIFFV_COORD_HEAD,
'trans': rotation(x=0.2),
}
info = {'dig': dig, 'dev_head_t': dev_head_t}
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
verbose=logging.ERROR)
assert_almost_equal(r / 1000, 1.0, decimal=10)
assert_almost_equal(oh / 1000, [0.0, 0.0, 0.0], decimal=10)
assert_almost_equal(od / 1000, [0.0, 0.0, 0.0], decimal=10)
# Test with all points. Digitization points are no longer perfect, so
# allow for a wider margin of error.
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
verbose=logging.ERROR)
assert_almost_equal(r / 1000, 1.0, decimal=3)
assert_almost_equal(oh / 1000, [0.0, 0.0, 0.0], decimal=3)
assert_almost_equal(od / 1000, [0.0, 0.0, 0.0], decimal=3)
# Test with some noisy EEG points only.
dig_kinds = (FIFF.FIFFV_POINT_EEG,)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
verbose=logging.ERROR)
assert_almost_equal(r / 1000, 1.0, decimal=2)
assert_almost_equal(oh / 1000, [0.0, 0.0, 0.0], decimal=2)
assert_almost_equal(od / 1000, [0.0, 0.0, 0.0], decimal=2)
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
rad = 90.0 # mm
big_rad = 120.0
center = np.array([0.5, -10.0, 40.0]) # mm
dev_trans = np.array([0.0, -0.005, -10.0])
dev_center = center - dev_trans
dig = [
# Left auricular
{
"coord_frame": FIFF.FIFFV_COORD_HEAD,
"ident": FIFF.FIFFV_POINT_LPA,
"kind": FIFF.FIFFV_POINT_CARDINAL,
"r": np.array([-1.0, 0.0, 0.0]),
},
# Nasion
{
"coord_frame": FIFF.FIFFV_COORD_HEAD,
"ident": FIFF.FIFFV_POINT_NASION,
"kind": FIFF.FIFFV_POINT_CARDINAL,
"r": np.array([0.0, 1.0, 0.0]),
},
# Right auricular
{
"coord_frame": FIFF.FIFFV_COORD_HEAD,
"ident": FIFF.FIFFV_POINT_RPA,
"kind": FIFF.FIFFV_POINT_CARDINAL,
"r": np.array([1.0, 0.0, 0.0]),
},
# Top of the head (extra point)
{"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EXTRA, "r": np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0, 0.72, 0.69])},
# F3
{"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([-0.55, 0.67, 0.50])},
# F4
{"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0.55, 0.67, 0.50])},
# Cz
{"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0.0, 0.0, 1.0])},
# Pz
{"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0, -0.72, 0.69])},
]
for d in dig:
d["r"] *= rad / 1000.0
d["r"] += center / 1000.0
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform("meg", "head", translation(*(dev_trans / 1000.0)))
info = {"dig": dig, "dev_head_t": dev_head_t}
# Degenerate conditions
assert_raises(ValueError, fit_sphere_to_headshape, info, dig_kinds=(FIFF.FIFFV_POINT_HPI,))
info["dig"][0]["coord_frame"] = FIFF.FIFFV_COORD_DEVICE
assert_raises(RuntimeError, fit_sphere_to_headshape, info)
info["dig"][0]["coord_frame"] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=1e-2) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA, FIFF.FIFFV_POINT_EEG)
kwargs = dict(rtol=1e-3, atol=1.0) # in mm
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = (FIFF.FIFFV_POINT_EEG,)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=10.0) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
# Test big size
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
info_big = deepcopy(info)
for d in info_big["dig"]:
d["r"] -= center / 1000.0
d["r"] *= big_rad / rad
d["r"] += center / 1000.0
with warnings.catch_warnings(record=True): # fit
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds, verbose="warning")
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split("\n")), 1)
assert_true(log_file.startswith("Estimated head size"))
assert_allclose(oh, center, atol=1e-3)
assert_allclose(r, big_rad, atol=1e-3)
del info_big
# Test offcenter
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
info_shift = deepcopy(info)
shift_center = np.array([0.0, -30, 0.0])
for d in info_shift["dig"]:
d["r"] -= center / 1000.0
d["r"] += shift_center / 1000.0
with warnings.catch_warnings(record=True):
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_shift, dig_kinds=dig_kinds, verbose="warning")
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split("\n")), 1)
assert_true("from head frame origin" in log_file)
assert_allclose(oh, shift_center, atol=1e-3)
assert_allclose(r, rad, atol=1e-3)
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
rad = 0.09
big_rad = 0.12
center = np.array([0.0005, -0.01, 0.04])
dev_trans = np.array([0., -0.005, -0.01])
dev_center = center - dev_trans
dig = [
# Left auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])},
# Nasion
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])},
# Right auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])},
# Top of the head (extra point)
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])},
# F3
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])},
# F4
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])},
# Cz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])},
# Pz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])},
]
for d in dig:
d['r'] *= rad
d['r'] += center
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
info = {'dig': dig, 'dev_head_t': dev_head_t}
# Degenerate conditions
with warnings.catch_warnings(record=True) as w:
assert_raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds=(FIFF.FIFFV_POINT_HPI,))
assert_equal(len(w), 1)
assert_true(w[0].category == DeprecationWarning)
assert_raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds='foo', units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
assert_raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-5)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
kwargs = dict(rtol=1e-3, atol=1e-3)
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = 'eeg'
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
units='m')
kwargs = dict(rtol=1e-3, atol=1e-2)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
# Test big size
dig_kinds = ('cardinal', 'extra')
info_big = deepcopy(info)
for d in info_big['dig']:
d['r'] -= center
d['r'] *= big_rad / rad
d['r'] += center
with warnings.catch_warnings(record=True): # fit
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
verbose='warning', units='mm')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 2)
assert_true('Estimated head size' in log_file)
assert_allclose(oh, center * 1000, atol=1e-3)
assert_allclose(r, big_rad * 1000, atol=1e-3)
del info_big
# Test offcenter
dig_kinds = ('cardinal', 'extra')
info_shift = deepcopy(info)
shift_center = np.array([0., -0.03, 0.])
for d in info_shift['dig']:
d['r'] -= center
d['r'] += shift_center
with warnings.catch_warnings(record=True):
with catch_logging() as log_file:
r, oh, od = fit_sphere_to_headshape(
info_shift, dig_kinds=dig_kinds, verbose='warning', units='m')
log_file = log_file.getvalue().strip()
assert_equal(len(log_file.split('\n')), 2)
assert_true('from head frame origin' in log_file)
assert_allclose(oh, shift_center, atol=1e-6)
assert_allclose(r, rad, atol=1e-6)
# Test "auto" mode (default)
# Should try "extra", fail, and go on to EEG
with warnings.catch_warnings(record=True): # not enough points
r, oh, od = fit_sphere_to_headshape(info, units='m')
kwargs = dict(rtol=1e-3, atol=1e-3)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
with warnings.catch_warnings(record=True): # not enough points
r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
assert_allclose(r, r2, atol=1e-7)
assert_allclose(oh, oh2, atol=1e-7)
assert_allclose(od, od2, atol=1e-7)
# this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = {'dig': dig[:7], 'dev_head_t': dev_head_t}
with warnings.catch_warnings(record=True): # bad fit
r, oh, od = fit_sphere_to_headshape(info, units='m')
# this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
info = {'dig': dig[:6], 'dev_head_t': dev_head_t}
assert_raises(ValueError, fit_sphere_to_headshape, info, units='m')
fnum_raw = "%02d" % ii_raw
mfp["input_file"] = raw_fname
if len(session_input_files) > 1:
output_name_base = output_folder + "/" + session + "-" + fnum_raw
else:
output_name_base = output_folder + "/" + session
if not "empt" in session.lower(): #### TYPO IN ONE SESSION NAME: emptRy!!
# change this to test existence of initial HPI measurement...
mfp["output_file"] = output_name_base + mf_fname_suffix + ".fif"
mfp["mv_hp"] = output_name_base + mf_fname_suffix + ".pos"
mfp["logfile"] = output_name_base + mf_fname_suffix + ".log"
if radius_head is None: # only needed once per study (same HPI digs)
raw = Raw(raw_fname)
radius_head, origin_head, origin_devive = fit_sphere_to_headshape(raw.info, verbose=VERBOSE)
raw.close()
mfp["origin_head"] = origin_head
mfp["radius_head"] = radius_head
else:
mfp["output_file"] = output_name_base + mf_fname_suffix + ".fif"
mfp["mv_hp"] = None
mfp["logfile"] = output_name_base + mf_fname_suffix + ".log"
mfp["movecomp"] = False
mfp["hpicons"] = False
mfp["origin_head"] = False # Must be False, if None, will try to estimate it!
mfp["radius_head"] = False
# Since both session_input and session_output_files are lists, they
# will now remain ordered 1-to-1
def test_fit_sphere_to_headshape():
"""Test fitting a sphere to digitization points"""
# Create points of various kinds
rad = 90. # mm
center = np.array([0.5, -10., 40.]) # mm
dev_trans = np.array([0., -0.005, -10.])
dev_center = center - dev_trans
dig = [
# Left auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([-1.0, 0.0, 0.0])},
# Nasion
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([0.0, 1.0, 0.0])},
# Right auricular
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': np.array([1.0, 0.0, 0.0])},
# Top of the head (extra point)
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': np.array([0.0, 0.0, 1.0])},
# EEG points
# Fz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, .72, .69])},
# F3
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([-.55, .67, .50])},
# F4
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([.55, .67, .50])},
# Cz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0.0, 0.0, 1.0])},
# Pz
{'coord_frame': FIFF.FIFFV_COORD_HEAD,
'kind': FIFF.FIFFV_POINT_EEG,
'r': np.array([0, -.72, .69])},
]
for d in dig:
d['r'] *= rad / 1000.
d['r'] += center / 1000.
# Device to head transformation (rotate .2 rad over X-axis)
dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))
info = {'dig': dig, 'dev_head_t': dev_head_t}
# Degenerate conditions
assert_raises(ValueError, fit_sphere_to_headshape, info,
dig_kinds=(FIFF.FIFFV_POINT_HPI,))
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
assert_raises(RuntimeError, fit_sphere_to_headshape, info)
info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD
# # Test with 4 points that match a perfect sphere
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=1e-2) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with all points
dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
FIFF.FIFFV_POINT_EXTRA)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, dev_center, **kwargs)
# Test with some noisy EEG points only.
dig_kinds = (FIFF.FIFFV_POINT_EEG,)
r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
kwargs = dict(rtol=1e-3, atol=10.) # in mm
assert_allclose(r, rad, **kwargs)
assert_allclose(oh, center, **kwargs)
assert_allclose(od, center, **kwargs)
dig = [dict(coord_frame=FIFF.FIFFV_COORD_DEVICE, )]
mfp['input_file'] = raw_fname
if len(session_input_files) > 1:
output_name_base = output_folder + '/' + session + '-' + fnum_raw
else:
output_name_base = output_folder + '/' + session
if not 'empt' in session.lower(
): #### TYPO IN ONE SESSION NAME: emptRy!!
# change this to test existence of initial HPI measurement...
mfp['output_file'] = output_name_base + mf_fname_suffix + '.fif'
mfp['mv_hp'] = output_name_base + mf_fname_suffix + '.pos'
mfp['logfile'] = output_name_base + mf_fname_suffix + '.log'
if radius_head is None: # only needed once per study (same HPI digs)
raw = Raw(raw_fname)
radius_head, origin_head, origin_devive = fit_sphere_to_headshape(
raw.info, verbose=VERBOSE)
raw.close()
mfp['origin_head'] = origin_head
mfp['radius_head'] = radius_head
else:
mfp['output_file'] = output_name_base + mf_fname_suffix + '.fif'
mfp['mv_hp'] = None
mfp['logfile'] = output_name_base + mf_fname_suffix + '.log'
mfp['movecomp'] = False
mfp['hpicons'] = False
mfp['origin_head'] = False # Must be False, if None, will try to estimate it!
mfp['radius_head'] = False
# Since both session_input and session_output_files are lists, they
# will now remain ordered 1-to-1
