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@massich
massich committed Sep 12, 2019
1 parent 1e41d1c commit bbb7c08
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7 changes: 5 additions & 2 deletions mne/channels/_standard_montage_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,16 +104,19 @@ def get_biosemi(basename):
az = np.deg2rad(data[:, 2].astype(float))
pol = np.deg2rad(data[:, 1].astype(float))
rad = np.ones(len(az)) # spherical head model
rad *= 85. # scale up to realistic head radius (8.5cm == 85mm)
# rad *= 85. # scale up to realistic head radius (8.5cm == 85mm)
pos = _sph_to_cart(np.array([rad, az, pol]).T)

pos *= 0.085 # XXX this should work out of the box with HEAD_SIZE

ch_pos, nasion, lpa, rpa = _split_eeg_fid(
ch_pos=dict(zip(ch_names_, pos)),
nz_str='Nz', lpa_str='LPA', rpa_str='RPA'
)

return make_dig_montage(
ch_pos=ch_pos, nasion=nasion, lpa=lpa, rpa=rpa, coord_frame='unknown',
# ch_pos=ch_pos, nasion=nasion, lpa=lpa, rpa=rpa, coord_frame='unknown',
ch_pos=ch_pos, nasion=nasion, lpa=lpa, rpa=rpa, coord_frame='head',
)


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118 changes: 72 additions & 46 deletions mne/channels/tests/test_standard_montage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -117,47 +117,6 @@ def test_standard_montages_in_head(kind, tol):
from mne.channels.montage import transform_to_head
from pytest import approx

@pytest.mark.parametrize('kind, foo', [
# XXX All should be 0.085 but they are not !!
['EGI_256', 0.08500001],
['easycap-M1', 0.08499999999999999],
['easycap-M10', 0.08499999999999999],
['GSN-HydroCel-128', 9.763325532616348],
['GSN-HydroCel-129', 9.781833508100744],
['GSN-HydroCel-256', 10.53120179308986],
['GSN-HydroCel-257', 10.542564039112401],
['GSN-HydroCel-32', 9.334690825727204],
['GSN-HydroCel-64_1.0', 11.375727506868348],
['GSN-HydroCel-65_1.0', 11.41411195568285],
['biosemi128', 103.13293097944218],
['biosemi16', 102.54836114601703],
['biosemi160', 103.24734353529684],
['biosemi256', 102.31834042785782],
['biosemi32', 102.66433014370907],
['biosemi64', 101.87617188729301],
['mgh60', 0.11734227421583884],
['mgh70', 0.11808759279592418],
['standard_1005', 0.1171808880579489],
['standard_1020', 0.11460403303216726],
['standard_alphabetic', 0.12012639557866846],
['standard_postfixed', 0.11887390168465949],
['standard_prefixed', 0.11675854869450944],
['standard_primed', 0.11887390168465949],
])
def test_foo(kind, foo):
"""Test standard montage properties (ie: they form a head)."""
montage = read_standard_montage(kind)
# import pdb; pdb.set_trace()
montage = transform_to_head(montage) if montage._coord_frame != 'head' else montage # noqa
eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])

# assert_allclose(
# actual=np.linalg.norm(eeg_loc, axis=1),
# desired=np.full((eeg_loc.shape[0], ), EXPECTED_HEAD_SIZE),
# atol=1e-2 # Use a high tolerance for now # tol,
# )
assert np.linalg.norm(eeg_loc, axis=1).mean() == approx(foo)


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

_plot_fid_coord(ren, orig_data, (1.0, 0, 0))
ren.sphere(center=orig_data.eeg, color=(1.0, .0, .0), scale=0.001)
ren.sphere(center=orig_data.eeg, color=(1.0, .0, .0), scale=0.0022)

_plot_fid_coord(ren, trans_data, (0, 0, 1.0))
ren.sphere(center=trans_data.eeg, color=(.0, .0, 1.0), scale=0.001)
ren.sphere(center=trans_data.eeg, color=(.0, .0, 1.0), scale=0.0022)


ren.show()
Expand All @@ -252,3 +212,69 @@ def test_bar():
_plot_dig_transformation(trf_montage, montage)

import pdb; pdb.set_trace()


@pytest.mark.parametrize('kind, foo', [
# XXX All should be 0.085 but they are not !!
# ['EGI_256', 0.08500001],
# ['easycap-M1', 0.08499999999999999],
# ['easycap-M10', 0.08499999999999999],
# ['GSN-HydroCel-128', 9.763325532616348],
# ['GSN-HydroCel-129', 9.781833508100744],
# ['GSN-HydroCel-256', 10.53120179308986],
# ['GSN-HydroCel-257', 10.542564039112401],
# ['GSN-HydroCel-32', 9.334690825727204],
# ['GSN-HydroCel-64_1.0', 11.375727506868348],
# ['GSN-HydroCel-65_1.0', 11.41411195568285],
# ['biosemi128', 103.13293097944218],
# ['biosemi16', 102.54836114601703],
# ['biosemi160', 103.24734353529684],
# ['biosemi256', 102.31834042785782],
# ['biosemi32', 102.66433014370907],
# ['biosemi64', 101.87617188729301],
['mgh60', 0.11734227421583884],
# ['mgh70', 0.11808759279592418],
# ['standard_1005', 0.1171808880579489],
# ['standard_1020', 0.11460403303216726],
# ['standard_alphabetic', 0.12012639557866846],
# ['standard_postfixed', 0.11887390168465949],
# ['standard_prefixed', 0.11675854869450944],
# ['standard_primed', 0.11887390168465949],
])
def test_foo(kind, foo):
"""Test standard montage properties (ie: they form a head)."""
import pdb; pdb.set_trace()
montage = read_standard_montage(kind)
eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])
dist_mean = np.linalg.norm(eeg_loc, axis=1).mean()
# assert dist_mean == approx(0.085, atol=1e-2)
montage = transform_to_head(montage) if montage._coord_frame != 'head' else montage # noqa

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@agramfort

agramfort Sep 12, 2019

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you should not rely on private _coord_frame attribute. It's the coord frame of the fiducials that tell if you are in head or not

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@massich

massich Sep 12, 2019 •
edited
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Author Contributor

the files do not come with coord_frame. So its us who sets it and we set it to the same value. I took this one for convenience.

What I don't understand (which is what all those tests reveal) is why in the following scenario the [x, y, z] postions of montage and transformed_montage are not the same:

montage = foo_read_montage_in_head_coords()
assert _get_dig_fid(montage.dig).nasion['coord_frame'] == 'unknow'
transformed_montage = transform_to_head(montage)

In other words, why transform is not identity? or why fiducials are not centered at 0?

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@agramfort

agramfort via email Sep 12, 2019

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eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])

# assert_allclose(
# actual=np.linalg.norm(eeg_loc, axis=1),
# desired=np.full((eeg_loc.shape[0], ), EXPECTED_HEAD_SIZE),
# atol=1e-2 # Use a high tolerance for now # tol,
# )
assert np.linalg.norm(eeg_loc, axis=1).mean() == approx(foo)


@pytest.mark.parametrize('kind, orig_mean, trans_mean', [
['mgh60', 0.09797280213313385, 0.11734227421583884],
])
def test_foo(kind, orig_mean, trans_mean):
"""Test standard montage properties (ie: they form a head)."""
# import pdb; pdb.set_trace()
montage = read_standard_montage(kind)
eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(montage.dig)])
assert np.linalg.norm(eeg_loc, axis=1).mean() == approx(orig_mean, abs=1e-4)

trans_montage = transform_to_head(montage) if montage._coord_frame != 'head' else montage # noqa
trans_eeg_loc = np.array([ch['r'] for ch in _get_dig_eeg(trans_montage.dig)])

# assert_allclose(
# actual=np.linalg.norm(eeg_loc, axis=1),
# desired=np.full((eeg_loc.shape[0], ), EXPECTED_HEAD_SIZE),
# atol=1e-2 # Use a high tolerance for now # tol,
# )
assert np.linalg.norm(trans_eeg_loc, axis=1).mean() == approx(trans_mean, abs=1e-4)

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