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tiny cosmetic improvements to BEM code #8404

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Merged
larsoner merged 2 commits into from
Oct 22, 2020
Merged

tiny cosmetic improvements to BEM code #8404

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50f7597
Cleanup
jasmainak Oct 9, 2020
eedf9a4
DOC: clarify doc + code
jasmainak Oct 21, 2020
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30 changes: 15 additions & 15 deletions mne/bem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,8 +197,8 @@ def _fwd_bem_lin_pot_coeff(surfs):
# if sidx1 == sidx2 and (tri == j).any():
# continue
# Otherwise do the hard job
coeffs = _lin_pot_coeff(surf1['rr'], tri_rr[k], tri_nn[k],
tri_area[k])
coeffs = _lin_pot_coeff(fros=surf1['rr'], tri_rr=tri_rr[k],
tri_nn=tri_nn[k], tri_area=tri_area[k])
coeffs[skip_idx] = 0.
submat[:, tri] -= coeffs
if si_1 == si_2:
Expand Down Expand Up @@ -233,7 +233,7 @@ def _fwd_bem_multi_solution(solids, gamma, nps):

def _fwd_bem_homog_solution(solids, nps):
"""Make a homogeneous solution."""
return _fwd_bem_multi_solution(solids, None, nps)
return _fwd_bem_multi_solution(solids, gamma=None, nps=nps)


def _fwd_bem_ip_modify_solution(solution, ip_solution, ip_mult, n_tri):
Expand Down Expand Up @@ -273,33 +273,33 @@ def _check_complete_surface(surf, copy=False, incomplete='raise', extra=''):
return surf


def _fwd_bem_linear_collocation_solution(m):
def _fwd_bem_linear_collocation_solution(bem):
"""Compute the linear collocation potential solution."""
# first, add surface geometries
for surf in m['surfs']:
for surf in bem['surfs']:
_check_complete_surface(surf)

logger.info('Computing the linear collocation solution...')
logger.info(' Matrix coefficients...')
coeff = _fwd_bem_lin_pot_coeff(m['surfs'])
m['nsol'] = len(coeff)
coeff = _fwd_bem_lin_pot_coeff(bem['surfs'])
bem['nsol'] = len(coeff)
logger.info(" Inverting the coefficient matrix...")
nps = [surf['np'] for surf in m['surfs']]
m['solution'] = _fwd_bem_multi_solution(coeff, m['gamma'], nps)
if len(m['surfs']) == 3:
ip_mult = m['sigma'][1] / m['sigma'][2]
nps = [surf['np'] for surf in bem['surfs']]
bem['solution'] = _fwd_bem_multi_solution(coeff, bem['gamma'], nps)
if len(bem['surfs']) == 3:
ip_mult = bem['sigma'][1] / bem['sigma'][2]
if ip_mult <= FWD.BEM_IP_APPROACH_LIMIT:
logger.info('IP approach required...')
logger.info(' Matrix coefficients (homog)...')
coeff = _fwd_bem_lin_pot_coeff([m['surfs'][-1]])
coeff = _fwd_bem_lin_pot_coeff([bem['surfs'][-1]])
logger.info(' Inverting the coefficient matrix (homog)...')
ip_solution = _fwd_bem_homog_solution(coeff,
[m['surfs'][-1]['np']])
[bem['surfs'][-1]['np']])
logger.info(' Modify the original solution to incorporate '
'IP approach...')
_fwd_bem_ip_modify_solution(m['solution'], ip_solution, ip_mult,
_fwd_bem_ip_modify_solution(bem['solution'], ip_solution, ip_mult,
nps)
m['bem_method'] = FWD.BEM_LINEAR_COLL
bem['bem_method'] = FWD.BEM_LINEAR_COLL
logger.info("Solution ready.")


Expand Down
8 changes: 4 additions & 4 deletions mne/forward/_compute_forward.py
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Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,7 @@ def _bem_specify_coils(bem, coils, coord_frame, mults, n_jobs):

Parameters
----------
bem : dict
bem : instance of ConductorModel
BEM information
coils : list of dict, len(n_MEG_sensors)
MEG sensor information dicts
Expand Down Expand Up @@ -231,7 +231,7 @@ def _bem_specify_els(bem, els, mults):

Parameters
----------
bem : dict
bem : instance of ConductorModel
BEM information
els : list of dict, len(n_EEG_sensors)
List of EEG sensor information dicts
Expand Down Expand Up @@ -732,7 +732,7 @@ def _prep_field_computation(rr, bem, fwd_data, n_jobs, verbose=None):
----------
rr : ndarray, shape (n_dipoles, 3)
3D dipole source positions in head coordinates
bem : dict
bem : instance of ConductorModel
Boundary Element Model information
fwd_data : dict
Dict containing sensor information. Gets updated here with BEM and
Expand Down Expand Up @@ -893,7 +893,7 @@ def _compute_forwards(rr, bem, coils_list, ccoils_list, infos, coil_types,
----------
rr : ndarray, shape (n_sources, 3)
3D dipole in head coordinates
bem : dict
bem : instance of ConductorModel
Boundary Element Model information for all surfaces
coils_list : list
List of MEG and/or EEG sensor information dicts
Expand Down