BUG: Fix STC limit bug (mne-tools#8202)

marsipu · Oct 14, 2020 · 4d1c398 · 4d1c398
1 parent ce1649f
commit 4d1c398
Show file tree

Hide file tree

Showing 5 changed files with 12 additions and 6 deletions.
diff --git a/doc/changes/latest.inc b/doc/changes/latest.inc
@@ -232,6 +232,8 @@ Bug
 
 - Fix bug with :func:`mne.viz.plot_vector_source_estimates` using the PyVista backend with ``time_viewer=True`` when updating the arrow colormaps by `Eric Larson`_
 
+- Fix bug with :func:`mne.viz.plot_vector_source_estimates` where ``clim='auto'`` and ``clim=dict(..., kind='percent')`` did not take into account the magnitude of the activation, by `Eric Larson`_
+
 - The default plotting mode for :func:`mne.io.Raw.plot` and :ref:`mne browse_raw` has been changed to ``clipping=3.`` to facilitate data analysis with large deflections, by `Eric Larson`_
 
 - PSD plots will now show non-data channels (e.g., ``misc``) if those channels are explicitly passed to ``picks``, by `Daniel McCloy`_.

diff --git a/examples/inverse/plot_vector_mne_solution.py b/examples/inverse/plot_vector_mne_solution.py
@@ -15,7 +15,7 @@
 It can also be instructive to visualize the actual dipole/activation locations
 in 3D space in a glass brain, as opposed to activations imposed on an inflated
 surface (as typically done in :meth:`mne.SourceEstimate.plot`), as it allows
-you to get a better sense of the true underlying source geometry.
+you to get a better sense of the underlying source geometry.
 """
 # Author: Marijn van Vliet <w.m.vanvliet@gmail.com>
 #

diff --git a/mne/viz/_3d.py b/mne/viz/_3d.py
@@ -1781,7 +1781,8 @@ def _plot_stc(stc, subject, surface, hemi, colormap, time_label,
     time_label, times = _handle_time(time_label, time_unit, stc.times)
 
     # convert control points to locations in colormap
-    mapdata = _process_clim(clim, colormap, transparent, stc.data,
+    use = stc.magnitude().data if vec else stc.data
+    mapdata = _process_clim(clim, colormap, transparent, use,
                             allow_pos_lims=not vec)
 
     stc_surf, stc_vol, src_vol = _triage_stc(

diff --git a/mne/viz/_brain/_brain.py b/mne/viz/_brain/_brain.py
@@ -1381,7 +1381,9 @@ def _update_glyphs(self, hemi, vectors):
                 glyph_mapper = hemi_data['glyph_mapper']
             if add:
                 glyph_actor = _create_actor(glyph_mapper)
-                glyph_actor.GetProperty().SetLineWidth(2.)
+                prop = glyph_actor.GetProperty()
+                prop.SetLineWidth(2.)
+                prop.SetOpacity(vector_alpha)
                 self._renderer.plotter.add_actor(glyph_actor)
                 hemi_data['glyph_actor'].append(glyph_actor)
             else:

diff --git a/tutorials/source-modeling/plot_visualize_stc.py b/tutorials/source-modeling/plot_visualize_stc.py
@@ -1,10 +1,11 @@
 """
 .. _tut_viz_stcs:
 
-Visualize source time courses
-=============================
+Visualize source time courses (stcs)
+====================================
 
-This tutorial focuses on visualization of stcs.
+This tutorial focuses on visualization of
+:term:`stcs <source estimates (abbr. stc)>`.
 
 .. contents:: Table of Contents
    :local: