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ENH: Add helmet deformation for OPMs
1 parent da8c794 commit ac43da0

4 files changed

Lines changed: 252 additions & 6 deletions

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‎mne/data/helmets/Kernel_Flux.fif.gz‎

-5.89 KB
Binary file not shown.

‎mne/data/helmets/Kernel_Flux_ch_pos.txt‎

Lines changed: 202 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,202 @@
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‎mne/surface.py‎

Lines changed: 44 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,13 @@
88
# Many of the computations in this code were derived from Matti Hämäläinen's
99
# C code.
1010

11+
from collections import OrderedDict
1112
from copy import deepcopy
1213
from functools import partial, lru_cache
13-
from collections import OrderedDict
1414
from glob import glob
15+
import json
1516
from os import path as op
17+
from pathlib import Path
1618
import time
1719
import warnings
1820

@@ -33,6 +35,9 @@
3335
_get_trans,
3436
apply_trans,
3537
Transform,
38+
_fit_matched_points,
39+
_MatchedDisplacementFieldInterpolator,
40+
_angle_between_quats,
3641
)
3742
from .utils import (
3843
logger,
@@ -52,6 +57,8 @@
5257
_import_nibabel,
5358
)
5459

60+
_helmet_path = Path(__file__).parent / "data" / "helmets"
61+
5562

5663
###############################################################################
5764
# AUTOMATED SURFACE FINDING
@@ -205,10 +212,11 @@ def get_meg_helmet_surf(info, trans=None, *, verbose=None):
205212
system, have_helmet = _get_meg_system(info)
206213
if have_helmet:
207214
logger.info("Getting helmet for system %s" % system)
208-
fname = op.join(op.split(__file__)[0], "data", "helmets", system + ".fif.gz")
215+
fname = _helmet_path / f"{system}.fif.gz"
209216
surf = read_bem_surfaces(
210217
fname, False, FIFF.FIFFV_MNE_SURF_MEG_HELMET, verbose=False
211218
)
219+
surf = _scale_helmet_to_sensors(system, surf, info)
212220
else:
213221
rr = np.array(
214222
[
@@ -248,6 +256,40 @@ def get_meg_helmet_surf(info, trans=None, *, verbose=None):
248256
return surf
249257

250258

259+
def _scale_helmet_to_sensors(system, surf, info):
260+
fname = _helmet_path / f"{system}_ch_pos.txt"
261+
if not fname.is_file():
262+
return surf
263+
with open(fname) as fid:
264+
ch_pos_from = json.load(fid)
265+
# find correspondence
266+
fro, to = list(), list()
267+
for key, f_ in ch_pos_from.items():
268+
t_ = [ch["loc"][:3] for ch in info["chs"] if ch["ch_name"].startswith(key)]
269+
if not len(t_):
270+
continue
271+
fro.append(f_)
272+
to.append(np.mean(t_, axis=0))
273+
if len(fro) < 4:
274+
logger.info("Using CAD helmet because fewer than 4 sensors found")
275+
return surf
276+
fro = np.array(fro, float)
277+
to = np.array(to, float)
278+
interp = _MatchedDisplacementFieldInterpolator(fro, to)
279+
new_rr = interp(surf["rr"])
280+
quat, sc = _fit_matched_points(surf["rr"], new_rr)
281+
rot = np.rad2deg(_angle_between_quats(quat[:3]))
282+
tr = 1000 * np.linalg.norm(quat[3:])
283+
logger.info(f" Deforming to match info using {len(fro)} matched points:")
284+
logger.info(f" 1. Affine: {rot:0.1f}°, {tr:0.1f} mm, {sc:0.2f}× scale")
285+
deltas = interp._last_deltas * 1000
286+
mu, mx = np.mean(deltas), np.max(deltas)
287+
logger.info(f" 2. Nonlinear displacement: " f"mean={mu:0.1f}, max={mx:0.1f} mm")
288+
surf["rr"] = new_rr
289+
complete_surface_info(surf, copy=False, verbose=False)
290+
return surf
291+
292+
251293
def _reorder_ccw(rrs, tris):
252294
"""Reorder tris of a convex hull to be wound counter-clockwise."""
253295
# This ensures that rendering with front-/back-face culling works properly

‎mne/transforms.py‎

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2095,9 +2095,9 @@ def __init__(self, fro, to):
20952095
assert fro.shape[1] == 3
20962096

20972097
# Prealign using affine + uniform scaling
2098-
trans, scale = _fit_matched_points(fro, to, scale=True)
2099-
trans = _quat_to_affine(trans)
2100-
trans[:3, :3] *= scale
2098+
self._quat, self._scale = _fit_matched_points(fro, to, scale=True)
2099+
trans = _quat_to_affine(self._quat)
2100+
trans[:3, :3] *= self._scale
21012101
self._affine = trans
21022102
fro = apply_trans(trans, fro)
21032103

@@ -2114,6 +2114,8 @@ def __init__(self, fro, to):
21142114
def __call__(self, x):
21152115
assert x.ndim in (1, 2) and x.shape[-1] == 3
21162116
singleton = x.ndim == 1
2117-
out = self._interp(apply_trans(self._affine, x))
2117+
x = apply_trans(self._affine, x)
2118+
out = self._interp(x)
2119+
self._last_deltas = np.linalg.norm(x - out, axis=1)
21182120
out = out[0] if singleton else out
21192121
return out

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