MRG, ENH: Add cortex, fix sensors

doc/changes/latest.inc

@@ -133,6 +133,8 @@ Enhancements
 
 - Add :func:`mne.viz.Brain.add_volume_labels` to plot subcortical surfaces and other regions of interest (:gh:`9540` by `Alex Rockhill`_ and `Eric Larson`_)
 
+- Add custom cortex curvature colors in :class:`mne.viz.Brain` via the ``cortex`` argument (:gh:`9750` by `Eric Larson`_)
+
 - Add :meth:`mne.channels.DigMontage.apply_trans` to apply a transform directly to a montage (:gh:`9601` by `Alex Rockhill`_)
 
 - :meth:`mne.preprocessing.ICA.fit` now emits a warning if any of the ``start``, ``stop``, ``reject``, and ``flat`` parameters are passed when performing ICA on `~mne.Epochs`. These parameters only have an effect on `~mne.io.Raw` data and were previously silently ignored in the case of `~mne.Epochs` (:gh:`9605` by `Richard Höchenberger`_)

examples/visualization/eeg_on_scalp.py

@@ -28,3 +28,12 @@
                      coord_frame='head', subjects_dir=subjects_dir)
 # Set viewing angle
 set_3d_view(figure=fig, azimuth=135, elevation=80)
+
+# %%
+# A similar effect can be achieved using :class:`mne.viz.Brain`:
+
+brain = mne.viz.Brain(
+    'sample', 'both', 'pial', 'frontal', background='w',
+    subjects_dir=subjects_dir)
+brain.add_head()
+brain.add_sensors(raw.info, trans, meg=False, eeg=('original', 'projected'))

mne/tests/test_cov.py

@@ -5,6 +5,7 @@
 
 import os.path as op
 import itertools as itt
+import sys
 
 from numpy.testing import (assert_array_almost_equal, assert_array_equal,
                            assert_equal, assert_allclose)
@@ -87,7 +88,7 @@ def test_compute_whitener(proj, pca):
     W3, _, C3 = compute_whitener(cov3, raw.info, pca=pca, return_colorer=True,
                                  picks=None, verbose='error')
     # this tol is not great, but Windows needs it
-    rtol = 3e-5 if pca in (True, 'white') and proj is True else 1e-11
+    rtol = 3e-5 if sys.platform.startswith('win') else 1e-11
     assert_allclose(W, W2, rtol=rtol)
     assert_allclose(C, C2, rtol=rtol)
     n_channels = len(raw.ch_names) - len(raw.info['bads'])

mne/utils/__init__.py

@@ -20,7 +20,7 @@
                     _on_missing, _check_on_missing, int_like, _safe_input,
                     _check_all_same_channel_names, path_like, _ensure_events,
                     _check_eeglabio_installed, _check_dict_keys,
-                    _check_edflib_installed)
+                    _check_edflib_installed, _to_rgb)
 from .config import (set_config, get_config, get_config_path, set_cache_dir,
                      set_memmap_min_size, get_subjects_dir, _get_stim_channel,
                      sys_info, _get_extra_data_path, _get_root_dir,

mne/utils/check.py

@@ -826,3 +826,15 @@ def _ensure_events(events):
         raise ValueError(
             f'events must be of shape (N, 3), got {events.shape}')
     return events
+
+
+def _to_rgb(*args, name='color', alpha=False):
+    from matplotlib.colors import colorConverter
+    func = colorConverter.to_rgba if alpha else colorConverter.to_rgb
+    try:
+        return func(*args)
+    except ValueError:
+        args = args[0] if len(args) == 1 else args
+        raise ValueError(
+            f'Invalid RGB{"A" if alpha else ""} argument(s) for {name}: '
+            f'{repr(args)}') from None

mne/viz/_3d.py

@@ -41,7 +41,7 @@
 from ..utils import (get_subjects_dir, logger, _check_subject, verbose, warn,
                      has_nibabel, check_version, fill_doc, _pl, get_config,
                      _ensure_int, _validate_type, _check_option, deprecated,
-                     CONNECTIVITY_DEPRECATION_MSG)
+                     CONNECTIVITY_DEPRECATION_MSG, _to_rgb)
 from .utils import (mne_analyze_colormap, _get_color_list,
                     plt_show, tight_layout, figure_nobar, _check_time_unit)
 from ..bem import ConductorModel, _bem_find_surface, _ensure_bem_surfaces
@@ -1030,6 +1030,7 @@ def _plot_sensors(renderer, info, to_cf_t, picks, meg, eeg, fnirs,
 
     actors = dict(meg=list(), ref_meg=list(), eeg=list(), fnirs=list(),
                   ecog=list(), seeg=list(), dbs=list())
+    scalar = 1 if units == 'm' else 1e3
     for ch_name, ch_coord in ch_pos.items():
         ch_type = channel_type(info, info.ch_names.index(ch_name))
         # for default picking
@@ -1041,7 +1042,6 @@ def _plot_sensors(renderer, info, to_cf_t, picks, meg, eeg, fnirs,
         plot_sensors = (ch_type != 'fnirs' or 'channels' in fnirs) and \
             (ch_type != 'eeg' or 'original' in eeg)
         color = defaults[ch_type + '_color']
-        scalar = 1 if units == 'm' else 1e3
         # plot sensors
         if isinstance(ch_coord, tuple):  # is meg, plot coil
             verts, triangles = ch_coord
@@ -1071,7 +1071,8 @@ def _plot_sensors(renderer, info, to_cf_t, picks, meg, eeg, fnirs,
                 'pairs' in fnirs:
             actor, _ = renderer.tube(  # array of origin and dest points
                 origin=sources[ch_name][np.newaxis] * scalar,
-                destination=detectors[ch_name][np.newaxis] * scalar)
+                destination=detectors[ch_name][np.newaxis] * scalar,
+                radius=0.001 * scalar)
             actors[ch_type].append(actor)
 
     # add projected eeg
@@ -1080,17 +1081,19 @@ def _plot_sensors(renderer, info, to_cf_t, picks, meg, eeg, fnirs,
         logger.info('Projecting sensors to the head surface')
         eeg_loc = np.array([
             ch_pos[info.ch_names[idx]] for idx in eeg_indices])
-        eeg_loc = apply_trans(to_cf_t['head'], eeg_loc)
         eegp_loc, eegp_nn = _project_onto_surface(
             eeg_loc, head_surf, project_rrs=True,
             return_nn=True)[2:4]
+        del eeg_loc
+        eegp_loc *= scalar
+        scale = defaults['eegp_scale'] * scalar
         actor, _ = renderer.quiver3d(
             x=eegp_loc[:, 0], y=eegp_loc[:, 1], z=eegp_loc[:, 2],
             u=eegp_nn[:, 0], v=eegp_nn[:, 1], w=eegp_nn[:, 2],
             color=defaults['eegp_color'], mode='cylinder',
-            scale=defaults['eegp_scale'], opacity=0.6,
+            scale=scale, opacity=0.6,
             glyph_height=defaults['eegp_height'],
-            glyph_center=(0., -defaults['eegp_height'], 0),
+            glyph_center=(0., -defaults['eegp_height'] / 2., 0),
             glyph_resolution=20,
             backface_culling=True)
         actors['eeg'].append(actor)
@@ -2650,7 +2653,6 @@ def plot_sparse_source_estimates(src, stcs, colors=None, linewidth=2,
         The triangular mesh surface.
     """
     import matplotlib.pyplot as plt
-    from matplotlib.colors import ColorConverter
     # Update the backend
     from .backends.renderer import _get_renderer
 
@@ -2713,8 +2715,6 @@ def plot_sparse_source_estimates(src, stcs, colors=None, linewidth=2,
                for stc in stcs]
     unique_vertnos = np.unique(np.concatenate(vertnos).ravel())
 
-    color_converter = ColorConverter()
-
     renderer = _get_renderer(bgcolor=bgcolor, size=(600, 600), name=fig_name)
     surface = renderer.mesh(x=points[:, 0], y=points[:, 1],
                             z=points[:, 2], triangles=use_faces,
@@ -2756,7 +2756,7 @@ def plot_sparse_source_estimates(src, stcs, colors=None, linewidth=2,
         x, y, z = points[v]
         nx, ny, nz = normals[v]
         renderer.quiver3d(x=x, y=y, z=z, u=nx, v=ny, w=nz,
-                          color=color_converter.to_rgb(c),
+                          color=_to_rgb(c),
                           mode=mode, scale=scale_factor)
 
         for k in ind:
@@ -3169,8 +3169,6 @@ def _plot_dipole(ax, data, vox, idx, dipole, gridx, gridy, ori, coord_frame,
                  show_all, pos, color, highlight_color, title):
     """Plot dipoles."""
     import matplotlib.pyplot as plt
-    from matplotlib.colors import ColorConverter
-    color_converter = ColorConverter()
     xidx, yidx, zidx = np.round(vox[idx]).astype(int)
     xslice = data[xidx]
     yslice = data[:, yidx]
@@ -3179,8 +3177,9 @@ def _plot_dipole(ax, data, vox, idx, dipole, gridx, gridy, ori, coord_frame,
     ori = ori[idx]
     if color is None:
         color = 'y' if show_all else 'r'
-    color = np.array(color_converter.to_rgba(color))
-    highlight_color = np.array(color_converter.to_rgba(highlight_color))
+    color = np.array(_to_rgb(color, alpha=True))
+    highlight_color = np.array(_to_rgb(
+        highlight_color, name='highlight_color', alpha=True))
     if show_all:
         colors = np.repeat(color[np.newaxis], len(vox), axis=0)
         colors[idx] = highlight_color