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Joan Massich
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1 parent 1e41d1c commit bbb7c08

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Lines changed: 77 additions & 48 deletions

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‎mne/channels/_standard_montage_utils.py‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -104,16 +104,19 @@ def get_biosemi(basename):
104104
az = np.deg2rad(data[:, 2].astype(float))
105105
pol = np.deg2rad(data[:, 1].astype(float))
106106
rad = np.ones(len(az)) # spherical head model
107-
rad *= 85. # scale up to realistic head radius (8.5cm == 85mm)
107+
# rad *= 85. # scale up to realistic head radius (8.5cm == 85mm)
108108
pos = _sph_to_cart(np.array([rad, az, pol]).T)
109109

110+
pos *= 0.085 # XXX this should work out of the box with HEAD_SIZE
111+
110112
ch_pos, nasion, lpa, rpa = _split_eeg_fid(
111113
ch_pos=dict(zip(ch_names_, pos)),
112114
nz_str='Nz', lpa_str='LPA', rpa_str='RPA'
113115
)
114116

115117
return make_dig_montage(
116-
ch_pos=ch_pos, nasion=nasion, lpa=lpa, rpa=rpa, coord_frame='unknown',
118+
# ch_pos=ch_pos, nasion=nasion, lpa=lpa, rpa=rpa, coord_frame='unknown',
119+
ch_pos=ch_pos, nasion=nasion, lpa=lpa, rpa=rpa, coord_frame='head',
117120
)
118121

119122

‎mne/channels/tests/test_standard_montage.py‎

Lines changed: 72 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -117,47 +117,6 @@ def test_standard_montages_in_head(kind, tol):
117117
from mne.channels.montage import transform_to_head
118118
from pytest import approx
119119

120-
@pytest.mark.parametrize('kind, foo', [
121-
# XXX All should be 0.085 but they are not !!
122-
['EGI_256', 0.08500001],
123-
['easycap-M1', 0.08499999999999999],
124-
['easycap-M10', 0.08499999999999999],
125-
['GSN-HydroCel-128', 9.763325532616348],
126-
['GSN-HydroCel-129', 9.781833508100744],
127-
['GSN-HydroCel-256', 10.53120179308986],
128-
['GSN-HydroCel-257', 10.542564039112401],
129-
['GSN-HydroCel-32', 9.334690825727204],
130-
['GSN-HydroCel-64_1.0', 11.375727506868348],
131-
['GSN-HydroCel-65_1.0', 11.41411195568285],
132-
['biosemi128', 103.13293097944218],
133-
['biosemi16', 102.54836114601703],
134-
['biosemi160', 103.24734353529684],
135-
['biosemi256', 102.31834042785782],
136-
['biosemi32', 102.66433014370907],
137-
['biosemi64', 101.87617188729301],
138-
['mgh60', 0.11734227421583884],
139-
['mgh70', 0.11808759279592418],
140-
['standard_1005', 0.1171808880579489],
141-
['standard_1020', 0.11460403303216726],
142-
['standard_alphabetic', 0.12012639557866846],
143-
['standard_postfixed', 0.11887390168465949],
144-
['standard_prefixed', 0.11675854869450944],
145-
['standard_primed', 0.11887390168465949],
146-
])
147-
def test_foo(kind, foo):
148-
"""Test standard montage properties (ie: they form a head)."""
149-
montage = read_standard_montage(kind)
150-
# import pdb; pdb.set_trace()
151-
montage = transform_to_head(montage) if montage._coord_frame != 'head' else montage # noqa
152-
eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])
153-
154-
# assert_allclose(
155-
# actual=np.linalg.norm(eeg_loc, axis=1),
156-
# desired=np.full((eeg_loc.shape[0], ), EXPECTED_HEAD_SIZE),
157-
# atol=1e-2 # Use a high tolerance for now # tol,
158-
# )
159-
assert np.linalg.norm(eeg_loc, axis=1).mean() == approx(foo)
160-
161120

162121
import matplotlib.pyplot as plt
163122
from mne.channels._dig_montage_utils import _get_fid_coords
@@ -195,9 +154,10 @@ def _plot_fid_coord(renderer, data, color):
195154
center=np.array([0, 0, 0]),
196155
# color=(100, 100, 100), # XXX: is color (R,G,B) 0-255? doc needs rev.
197156
color=(1.0, 1.0, 1.0), # XXX: doc don't say [0-1 or 0-255] ??
198-
scale=EXPECTED_HEAD_SIZE, # XXX: why I cannot put radius a value in mm?? # noqa
199-
opacity=0.5,
200-
resolution=8, # XXX: why this is not callen n_poligons??
157+
# scale=EXPECTED_HEAD_SIZE, # XXX: why I cannot put radius a value in mm?? # noqa
158+
scale=0.17, # XXXX magic number!!
159+
opacity=0.3,
160+
resolution=20, # XXX: why this is not callen n_poligons??
201161
backface_culling=False,
202162
)
203163
N_RAND_PTS = 50
@@ -225,10 +185,10 @@ def _plot_fid_coord(renderer, data, color):
225185
)
226186

227187
_plot_fid_coord(ren, orig_data, (1.0, 0, 0))
228-
ren.sphere(center=orig_data.eeg, color=(1.0, .0, .0), scale=0.001)
188+
ren.sphere(center=orig_data.eeg, color=(1.0, .0, .0), scale=0.0022)
229189

230190
_plot_fid_coord(ren, trans_data, (0, 0, 1.0))
231-
ren.sphere(center=trans_data.eeg, color=(.0, .0, 1.0), scale=0.001)
191+
ren.sphere(center=trans_data.eeg, color=(.0, .0, 1.0), scale=0.0022)
232192

233193

234194
ren.show()
@@ -252,3 +212,69 @@ def test_bar():
252212
_plot_dig_transformation(trf_montage, montage)
253213

254214
import pdb; pdb.set_trace()
215+
216+
217+
@pytest.mark.parametrize('kind, foo', [
218+
# XXX All should be 0.085 but they are not !!
219+
# ['EGI_256', 0.08500001],
220+
# ['easycap-M1', 0.08499999999999999],
221+
# ['easycap-M10', 0.08499999999999999],
222+
# ['GSN-HydroCel-128', 9.763325532616348],
223+
# ['GSN-HydroCel-129', 9.781833508100744],
224+
# ['GSN-HydroCel-256', 10.53120179308986],
225+
# ['GSN-HydroCel-257', 10.542564039112401],
226+
# ['GSN-HydroCel-32', 9.334690825727204],
227+
# ['GSN-HydroCel-64_1.0', 11.375727506868348],
228+
# ['GSN-HydroCel-65_1.0', 11.41411195568285],
229+
# ['biosemi128', 103.13293097944218],
230+
# ['biosemi16', 102.54836114601703],
231+
# ['biosemi160', 103.24734353529684],
232+
# ['biosemi256', 102.31834042785782],
233+
# ['biosemi32', 102.66433014370907],
234+
# ['biosemi64', 101.87617188729301],
235+
['mgh60', 0.11734227421583884],
236+
# ['mgh70', 0.11808759279592418],
237+
# ['standard_1005', 0.1171808880579489],
238+
# ['standard_1020', 0.11460403303216726],
239+
# ['standard_alphabetic', 0.12012639557866846],
240+
# ['standard_postfixed', 0.11887390168465949],
241+
# ['standard_prefixed', 0.11675854869450944],
242+
# ['standard_primed', 0.11887390168465949],
243+
])
244+
def test_foo(kind, foo):
245+
"""Test standard montage properties (ie: they form a head)."""
246+
import pdb; pdb.set_trace()
247+
montage = read_standard_montage(kind)
248+
eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])
249+
dist_mean = np.linalg.norm(eeg_loc, axis=1).mean()
250+
# assert dist_mean == approx(0.085, atol=1e-2)
251+
montage = transform_to_head(montage) if montage._coord_frame != 'head' else montage # noqa
252+
eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])
253+
254+
# assert_allclose(
255+
# actual=np.linalg.norm(eeg_loc, axis=1),
256+
# desired=np.full((eeg_loc.shape[0], ), EXPECTED_HEAD_SIZE),
257+
# atol=1e-2 # Use a high tolerance for now # tol,
258+
# )
259+
assert np.linalg.norm(eeg_loc, axis=1).mean() == approx(foo)
260+
261+
262+
@pytest.mark.parametrize('kind, orig_mean, trans_mean', [
263+
['mgh60', 0.09797280213313385, 0.11734227421583884],
264+
])
265+
def test_foo(kind, orig_mean, trans_mean):
266+
"""Test standard montage properties (ie: they form a head)."""
267+
# import pdb; pdb.set_trace()
268+
montage = read_standard_montage(kind)
269+
eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])
270+
assert np.linalg.norm(eeg_loc, axis=1).mean() == approx(orig_mean, abs=1e-4)
271+
272+
trans_montage = transform_to_head(montage) if montage._coord_frame != 'head' else montage # noqa
273+
trans_eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(trans_montage.dig)])
274+
275+
# assert_allclose(
276+
# actual=np.linalg.norm(eeg_loc, axis=1),
277+
# desired=np.full((eeg_loc.shape[0], ), EXPECTED_HEAD_SIZE),
278+
# atol=1e-2 # Use a high tolerance for now # tol,
279+
# )
280+
assert np.linalg.norm(trans_eeg_loc, axis=1).mean() == approx(trans_mean, abs=1e-4)

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