From f95c84760aae461179e8fab55034fa3dc0b5463d Mon Sep 17 00:00:00 2001 From: Guillaume Favelier Date: Thu, 13 Jan 2022 20:24:51 +0100 Subject: [PATCH] ENH: add helmet view option in coreg (#10200) * add helmet * update test * update changes --- doc/changes/latest.inc | 2 ++ mne/gui/_coreg.py | 32 ++++++++++++++++++++++++++++++-- mne/gui/tests/test_coreg_gui.py | 3 +++ mne/viz/_3d.py | 23 ++++++++++++++++------- 4 files changed, 51 insertions(+), 9 deletions(-) diff --git a/doc/changes/latest.inc b/doc/changes/latest.inc index 13499405d4d..b0e9c94c2c1 100644 --- a/doc/changes/latest.inc +++ b/doc/changes/latest.inc @@ -74,6 +74,8 @@ Enhancements - Annotations from a :class:`~mne.io.Raw` object are now preserved by the :class:`~mne.Epochs` constructor and are supported when saving Epochs (:gh:`9969` and :gh:`10019` by `Adam Li`_) +- Add a button to display the MEG helmet in the coregistration GUI (:gh:`10200` but `Guillaume Favelier`_) + Bugs ~~~~ diff --git a/mne/gui/_coreg.py b/mne/gui/_coreg.py index 4452c888fa3..49ff7abe946 100644 --- a/mne/gui/_coreg.py +++ b/mne/gui/_coreg.py @@ -18,8 +18,8 @@ from ..coreg import Coregistration, _is_mri_subject from ..viz._3d import (_plot_head_surface, _plot_head_fiducials, _plot_head_shape_points, _plot_mri_fiducials, - _plot_hpi_coils, _plot_sensors) -from ..transforms import (read_trans, write_trans, _ensure_trans, + _plot_hpi_coils, _plot_sensors, _plot_helmet) +from ..transforms import (read_trans, write_trans, _ensure_trans, _get_trans, rotation_angles, _get_transforms_to_coord_frame) from ..utils import (get_subjects_dir, check_fname, _check_fname, fill_doc, warn, verbose, logger) @@ -105,6 +105,7 @@ class CoregistrationUI(HasTraits): _eeg_channels = Bool() _head_resolution = Bool() _head_transparency = Bool() + _helmet = Bool() _grow_hair = Float() _scale_mode = Unicode() _icp_fid_match = Unicode() @@ -154,6 +155,7 @@ def _get_default(var, val): eeg_channels=_get_default(eeg_channels, True), head_resolution=_get_default(head_resolution, True), head_transparency=_get_default(head_transparency, False), + helmet=False, head_opacity=0.5, sensor_opacity=_get_default(sensor_opacity, 1.0), fiducials=("LPA", "Nasion", "RPA"), @@ -213,6 +215,7 @@ def _get_default(var, val): self._set_eeg_channels(self._defaults["eeg_channels"]) self._set_head_resolution(self._defaults["head_resolution"]) self._set_head_transparency(self._defaults["head_transparency"]) + self._set_helmet(self._defaults["helmet"]) self._set_grow_hair(self._defaults["grow_hair"]) self._set_omit_hsp_distance(self._defaults["omit_hsp_distance"]) self._set_icp_n_iterations(self._defaults["icp_n_iterations"]) @@ -324,6 +327,9 @@ def _set_head_resolution(self, state): def _set_head_transparency(self, state): self._head_transparency = bool(state) + def _set_helmet(self, state): + self._helmet = bool(state) + def _set_grow_hair(self, value): self._grow_hair = value @@ -497,6 +503,10 @@ def _head_transparency_changed(self, change=None): self._actors["head"].GetProperty().SetOpacity(self._head_opacity) self._renderer._update() + @observe("_helmet") + def _helmet_changed(self, change=None): + self._update_plot("helmet") + @observe("_grow_hair") def _grow_hair_changed(self, change=None): self._coreg.set_grow_hair(self._grow_hair) @@ -533,6 +543,7 @@ def _redraw(self, verbose=None): hpi=self._add_hpi_coils, eeg=self._add_eeg_channels, head_fids=self._add_head_fiducials, + helmet=self._add_helmet, ) with self._redraw_mutex: logger.debug(f'Redrawing {self._redraws_pending}') @@ -632,6 +643,7 @@ def _update_plot(self, changes="all"): 'head', 'mri_fids', # MRI first 'hair', # then hair 'hsp', 'hpi', 'eeg', 'head_fids', # then dig + 'helmet', ) if changes == 'all': changes = list(all_keys) @@ -828,6 +840,15 @@ def _add_head_hair(self): self._surfaces["head"].points = \ self._coreg._get_processed_mri_points(res) + def _add_helmet(self): + if self._helmet: + head_mri_t = _get_trans(self._coreg.trans, 'head', 'mri')[0] + helmet_actor, _, _ = _plot_helmet( + self._renderer, self._info, head_mri_t) + else: + helmet_actor = None + self._update_actor("helmet", helmet_actor) + def _fit_fiducials(self): if not self._lock_fids: self._display_message( @@ -1044,6 +1065,13 @@ def _configure_dock(self): tooltip="Enable/Disable high resolution head surface", layout=layout ) + self._widgets["helmet"] = self._renderer._dock_add_check_box( + name="Show helmet", + value=self._helmet, + callback=self._set_helmet, + tooltip="Enable/Disable helmet", + layout=layout + ) self._renderer._dock_add_stretch() self._renderer._dock_initialize(name="Parameters", area="right") diff --git a/mne/gui/tests/test_coreg_gui.py b/mne/gui/tests/test_coreg_gui.py index d6eca4fcfa5..b0af016e758 100644 --- a/mne/gui/tests/test_coreg_gui.py +++ b/mne/gui/tests/test_coreg_gui.py @@ -151,6 +151,9 @@ def test_coreg_gui_pyvista(tmp_path, renderer_interactive_pyvistaqt): assert coreg._grow_hair == 0.1 # visualization + assert not coreg._helmet + coreg._set_helmet(True) + assert coreg._helmet assert coreg._orient_glyphs assert coreg._scale_by_distance assert coreg._mark_inside diff --git a/mne/viz/_3d.py b/mne/viz/_3d.py index 6cc0375d27b..e844aa740b6 100644 --- a/mne/viz/_3d.py +++ b/mne/viz/_3d.py @@ -654,10 +654,6 @@ def plot_alignment(info=None, trans=None, subject=None, subjects_dir=None, skull['name'] = skull_name # set name for alpha surfs[skull_name] = skull - if 'helmet' in meg and pick_types(info, meg=True).size > 0: - surfs['helmet'] = get_meg_helmet_surf(info, head_mri_t) - assert surfs['helmet']['coord_frame'] == FIFF.FIFFV_COORD_MRI - # we've looked through all of them, raise if some remain if len(surfaces) > 0: raise ValueError(f'Unknown surface type{_pl(surfaces)}: {surfaces}') @@ -675,9 +671,8 @@ def plot_alignment(info=None, trans=None, subject=None, subjects_dir=None, head_alpha = max_alpha else: head_alpha = alpha_range[0] - alphas = dict(helmet=0.25, lh=hemi_val, rh=hemi_val) - colors = dict(helmet=DEFAULTS['coreg']['helmet_color'], - lh=(0.5,) * 3, rh=(0.5,) * 3) + alphas = dict(lh=hemi_val, rh=hemi_val) + colors = dict(lh=(0.5,) * 3, rh=(0.5,) * 3) for idx, name in enumerate(skulls): alphas[name] = alpha_range[idx + 1] colors[name] = (0.95 - idx * 0.2, 0.85, 0.95 - idx * 0.2) @@ -702,6 +697,11 @@ def plot_alignment(info=None, trans=None, subject=None, subjects_dir=None, renderer, head, subject, subjects_dir, bem, coord_frame, to_cf_t, alpha=head_alpha) + # plot helmet + if 'helmet' in meg and pick_types(info, meg=True).size > 0: + _, _, src_surf = _plot_helmet(renderer, info, head_mri_t) + assert src_surf['coord_frame'] == FIFF.FIFFV_COORD_MRI + # plot surfaces if brain and 'lh' not in surfs: # one layer sphere assert bem['coord_frame'] == FIFF.FIFFV_COORD_HEAD @@ -901,6 +901,15 @@ def _plot_head_surface(renderer, head, subject, subjects_dir, bem, return actor, dst_surf, src_surf +def _plot_helmet(renderer, info, head_mri_t, alpha=0.25, color=None): + color = DEFAULTS['coreg']['helmet_color'] if color is None else color + src_surf = get_meg_helmet_surf(info, head_mri_t) + actor, dst_surf = renderer.surface( + surface=src_surf, color=color, opacity=alpha, + backface_culling=False) + return actor, dst_surf, src_surf + + def _plot_axes(renderer, info, to_cf_t, head_mri_t): """Render different axes a 3D scene.""" axes = [(to_cf_t['head'], (0.9, 0.3, 0.3))] # always show head