MRG: Recreate our helmet graphic

examples/visualization/plot_mne_helmet.py

@@ -0,0 +1,32 @@
+"""
+Plot the MNE brain and helmet
+=============================
+
+This tutorial shows how to make the MNE helmet + brain image.
+"""
+
+import os.path as op
+import mne
+
+sample_path = mne.datasets.sample.data_path()
+subjects_dir = op.join(sample_path, 'subjects')
+fname_evoked = op.join(sample_path, 'MEG', 'sample', 'sample_audvis-ave.fif')
+fname_inv = op.join(sample_path, 'MEG', 'sample',
+                    'sample_audvis-meg-oct-6-meg-inv.fif')
+fname_trans = op.join(sample_path, 'MEG', 'sample',
+                      'sample_audvis_raw-trans.fif')
+inv = mne.minimum_norm.read_inverse_operator(fname_inv)
+evoked = mne.read_evokeds(fname_evoked, baseline=(None, 0),
+                          proj=True, verbose=False, condition='Left Auditory')
+maps = mne.make_field_map(evoked, trans=fname_trans, ch_type='meg',
+                          subject='sample', subjects_dir=subjects_dir)
+time = 0.083
+fig = mne.viz.create_3d_figure((256, 256))
+mne.viz.plot_alignment(
+    evoked.info, subject='sample', subjects_dir=subjects_dir, fig=fig,
+    trans=fname_trans, meg='sensors', eeg=False, surfaces='pial',
+    coord_frame='mri')
+evoked.plot_field(maps, time=time, fig=fig, time_label=None, vmax=5e-13)
+mne.viz.set_3d_view(
+    fig, azimuth=40, elevation=87, focalpoint=(0., -0.01, 0.04), roll=-100,
+    distance=0.48)

mne/evoked.py

@@ -336,10 +336,11 @@ def plot_topomap(self, times="auto", ch_type=None, vmin=None,
 
     @copy_function_doc_to_method_doc(plot_evoked_field)
     def plot_field(self, surf_maps, time=None, time_label='t = %0.0f ms',
-                   n_jobs=1, fig=None, verbose=None):
+                   n_jobs=1, fig=None, vmax=None, n_contours=21, verbose=None):
         return plot_evoked_field(self, surf_maps, time=time,
                                  time_label=time_label, n_jobs=n_jobs,
-                                 fig=fig, verbose=verbose)
+                                 fig=fig, vmax=vmax, n_contours=n_contours,
+                                 verbose=verbose)
 
     @copy_function_doc_to_method_doc(plot_evoked_white)
     def plot_white(self, noise_cov, show=True, rank=None, time_unit='s',

mne/viz/_3d.py

@@ -304,7 +304,8 @@ def _set_aspect_equal(ax):
 
 @verbose
 def plot_evoked_field(evoked, surf_maps, time=None, time_label='t = %0.0f ms',
-                      n_jobs=1, fig=None, verbose=None):
+                      n_jobs=1, fig=None, vmax=None, n_contours=21,
+                      verbose=None):
     """Plot MEG/EEG fields on head surface and helmet in 3D.
 
     Parameters
@@ -316,14 +317,22 @@ def plot_evoked_field(evoked, surf_maps, time=None, time_label='t = %0.0f ms',
     time : float | None
         The time point at which the field map shall be displayed. If None,
         the average peak latency (across sensor types) is used.
-    time_label : str
+    time_label : str | None
         How to print info about the time instant visualized.
     %(n_jobs)s
     fig : instance of mayavi.core.api.Scene | None
         If None (default), a new figure will be created, otherwise it will
         plot into the given figure.
 
         .. versionadded:: 0.20
+    vmax : float | None
+        Maximum intensity. Can be None to use the max(abs(data)).
+
+        .. versionadded:: 0.21
+    n_contours : int
+        The number of contours.
+
+        .. versionadded:: 0.21
     %(verbose)s
 
     Returns
@@ -334,6 +343,8 @@ def plot_evoked_field(evoked, surf_maps, time=None, time_label='t = %0.0f ms',
     # Update the backend
     from .backends.renderer import _get_renderer
     types = [t for t in ['eeg', 'grad', 'mag'] if t in evoked]
+    _validate_type(vmax, (None, 'numeric'), 'vmax')
+    n_contours = _ensure_int(n_contours, 'n_contours')
 
     time_idx = None
     if time is None:
@@ -382,23 +393,27 @@ def plot_evoked_field(evoked, surf_maps, time=None, time_label='t = %0.0f ms',
         data = np.dot(map_data, evoked.data[pick, time_idx])
 
         # Make a solid surface
-        vlim = np.max(np.abs(data))
+        if vmax is None:
+            vmax = np.max(np.abs(data))
+        vmax = float(vmax)
         alpha = alphas[ii]
         renderer.surface(surface=surf, color=colors[ii],
                          opacity=alpha)
 
         # Now show our field pattern
-        renderer.surface(surface=surf, vmin=-vlim, vmax=vlim,
-                         scalars=data, colormap=colormap)
+        renderer.surface(surface=surf, vmin=-vmax, vmax=vmax,
+                         scalars=data, colormap=colormap,
+                         polygon_offset=-1)
 
         # And the field lines on top
-        renderer.contour(surface=surf, scalars=data, contours=21,
-                         vmin=-vlim, vmax=vlim, opacity=alpha,
+        renderer.contour(surface=surf, scalars=data, contours=n_contours,
+                         vmin=-vmax, vmax=vmax, opacity=alpha,
                          colormap=colormap_lines)
 
-    if '%' in time_label:
-        time_label %= (1e3 * evoked.times[time_idx])
-    renderer.text2d(x_window=0.01, y_window=0.01, text=time_label)
+    if time_label is not None:
+        if '%' in time_label:
+            time_label %= (1e3 * evoked.times[time_idx])
+        renderer.text2d(x_window=0.01, y_window=0.01, text=time_label)
     renderer.set_camera(azimuth=10, elevation=60)
     renderer.show()
     return renderer.scene()

mne/viz/_brain/_brain.py

@@ -632,13 +632,13 @@ def _add_surface_data(self, hemi):
             z=self.geo[hemi].coords[:, 2],
             triangles=self.geo[hemi].faces,
             normals=self.geo[hemi].nn,
+            polygon_offset=-2,
             **kwargs,
         )
         if isinstance(mesh_data, tuple):
             actor, mesh = mesh_data
             # add metadata to the mesh for picking
             mesh._hemi = hemi
-            self.resolve_coincident_topology(actor)
         else:
             actor, mesh = mesh_data, None
         return actor, mesh
@@ -865,10 +865,8 @@ def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
                     color=None,
                     colormap=ctable,
                     backface_culling=False,
+                    polygon_offset=-2,
                 )
-                if isinstance(mesh_data, tuple):
-                    actor, _ = mesh_data
-                    self.resolve_coincident_topology(actor)
             self._label_data.append(mesh_data)
             self._renderer.set_camera(**views_dicts[hemi][v])
 
@@ -1077,6 +1075,7 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
                 vmax=np.max(ids),
                 scalars=ids,
                 interpolate_before_map=False,
+                polygon_offset=-2,
             )
             if isinstance(mesh_data, tuple):
                 from ..backends._pyvista import _set_colormap_range
@@ -1085,17 +1084,9 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
                 mesh._hemi = hemi
                 _set_colormap_range(actor, cmap.astype(np.uint8),
                                     None)
-                self.resolve_coincident_topology(actor)
 
         self._update()
 
-    def resolve_coincident_topology(self, actor):
-        """Resolve z-fighting of overlapping surfaces."""
-        mapper = actor.GetMapper()
-        mapper.SetResolveCoincidentTopologyToPolygonOffset()
-        mapper.SetRelativeCoincidentTopologyPolygonOffsetParameters(
-            -1., -1.)
-
     def close(self):
         """Close all figures and cleanup data structure."""
         self._closed = True

mne/viz/backends/_pysurfer_mayavi.py

@@ -99,8 +99,11 @@ def mesh(self, x, y, z, triangles, color, opacity=1.0, shading=False,
              backface_culling=False, scalars=None, colormap=None,
              vmin=None, vmax=None, interpolate_before_map=True,
              representation='surface', line_width=1., normals=None,
-             pickable=None, **kwargs):
+             polygon_offset=None, **kwargs):
         # normals and pickable are unused
+        kwargs.pop('pickable', None)
+        del normals
+
         if color is not None:
             color = _check_color(color)
         if color is not None and isinstance(color, np.ndarray) \
@@ -162,7 +165,7 @@ def contour(self, surface, scalars, contours, width=1.0, opacity=1.0,
     def surface(self, surface, color=None, opacity=1.0,
                 vmin=None, vmax=None, colormap=None,
                 normalized_colormap=False, scalars=None,
-                backface_culling=False):
+                backface_culling=False, polygon_offset=None):
         if color is not None:
             color = _check_color(color)
         if normalized_colormap:

mne/viz/backends/_pyvista.py

@@ -292,7 +292,8 @@ def set_interaction(self, interaction):
     def polydata(self, mesh, color=None, opacity=1.0, normals=None,
                  backface_culling=False, scalars=None, colormap=None,
                  vmin=None, vmax=None, interpolate_before_map=True,
-                 representation='surface', line_width=1., **kwargs):
+                 representation='surface', line_width=1.,
+                 polygon_offset=None, **kwargs):
         with warnings.catch_warnings():
             warnings.filterwarnings("ignore", category=FutureWarning)
             rgba = False
@@ -325,12 +326,19 @@ def polydata(self, mesh, color=None, opacity=1.0, normals=None,
                 style=representation, line_width=line_width, **kwargs,
             )
 
+            if polygon_offset is not None:
+                mapper = actor.GetMapper()
+                mapper.SetResolveCoincidentTopologyToPolygonOffset()
+                mapper.SetRelativeCoincidentTopologyPolygonOffsetParameters(
+                    polygon_offset, polygon_offset)
+
             return actor, mesh
 
     def mesh(self, x, y, z, triangles, color, opacity=1.0, shading=False,
              backface_culling=False, scalars=None, colormap=None,
              vmin=None, vmax=None, interpolate_before_map=True,
-             representation='surface', line_width=1., normals=None, **kwargs):
+             representation='surface', line_width=1., normals=None,
+             polygon_offset=None, **kwargs):
         with warnings.catch_warnings():
             warnings.filterwarnings("ignore", category=FutureWarning)
             vertices = np.c_[x, y, z]
@@ -349,6 +357,7 @@ def mesh(self, x, y, z, triangles, color, opacity=1.0, shading=False,
             interpolate_before_map=interpolate_before_map,
             representation=representation,
             line_width=line_width,
+            polygon_offset=polygon_offset,
             **kwargs,
         )
 
@@ -366,7 +375,7 @@ def contour(self, surface, scalars, contours, width=1.0, opacity=1.0,
             triangles = np.c_[np.full(n_triangles, 3), triangles]
             mesh = PolyData(vertices, triangles)
             mesh.point_arrays['scalars'] = scalars
-            contour = mesh.contour(isosurfaces=contours, rng=(vmin, vmax))
+            contour = mesh.contour(isosurfaces=contours)
             line_width = width
             if kind == 'tube':
                 contour = contour.tube(radius=width, n_sides=self.tube_n_sides)
@@ -377,6 +386,7 @@ def contour(self, surface, scalars, contours, width=1.0, opacity=1.0,
                 show_scalar_bar=False,
                 line_width=line_width,
                 color=color,
+                rng=[vmin, vmax],
                 cmap=colormap,
                 opacity=opacity,
                 smooth_shading=self.figure.smooth_shading
@@ -386,7 +396,7 @@ def contour(self, surface, scalars, contours, width=1.0, opacity=1.0,
     def surface(self, surface, color=None, opacity=1.0,
                 vmin=None, vmax=None, colormap=None,
                 normalized_colormap=False, scalars=None,
-                backface_culling=False):
+                backface_culling=False, polygon_offset=None):
         with warnings.catch_warnings():
             warnings.filterwarnings("ignore", category=FutureWarning)
             normals = surface.get('nn', None)
@@ -407,6 +417,7 @@ def surface(self, surface, color=None, opacity=1.0,
             colormap=colormap,
             vmin=vmin,
             vmax=vmax,
+            polygon_offset=polygon_offset,
         )
 
     def sphere(self, center, color, scale, opacity=1.0,
@@ -743,8 +754,6 @@ def _set_3d_view(figure, azimuth, elevation, focalpoint, distance, roll=None):
         phi = _deg2rad(azimuth)
     if elevation is not None:
         theta = _deg2rad(elevation)
-    if roll is not None:
-        roll = _deg2rad(roll)
 
     renderer = figure.plotter.renderer
     bounds = np.array(renderer.ComputeVisiblePropBounds())

mne/viz/backends/base_renderer.py

@@ -36,7 +36,8 @@ def set_interaction(self, interaction):
     def mesh(self, x, y, z, triangles, color, opacity=1.0, shading=False,
              backface_culling=False, scalars=None, colormap=None,
              vmin=None, vmax=None, interpolate_before_map=True,
-             representation='surface', line_width=1., normals=None, **kwargs):
+             representation='surface', line_width=1., normals=None,
+             polygon_offset=None, **kwargs):
         """Add a mesh in the scene.
 
         Parameters
@@ -79,6 +80,8 @@ def mesh(self, x, y, z, triangles, color, opacity=1.0, shading=False,
             The width of the lines when representation='wireframe'.
         normals: array, shape (n_vertices, 3)
             The array containing the normal of each vertex.
+        polygon_offset: float
+            If not None, the factor used to resolve coincident topology.
         kwargs: args
             The arguments to pass to triangular_mesh
 
@@ -128,8 +131,9 @@ def contour(self, surface, scalars, contours, width=1.0, opacity=1.0,
 
     @abstractclassmethod
     def surface(self, surface, color=None, opacity=1.0,
-                vmin=None, vmax=None, colormap=None, scalars=None,
-                backface_culling=False):
+                vmin=None, vmax=None, colormap=None,
+                normalized_colormap=False, scalars=None,
+                backface_culling=False, polygon_offset=None):
         """Add a surface in the scene.
 
         Parameters
@@ -154,6 +158,8 @@ def surface(self, surface, color=None, opacity=1.0,
             The scalar valued associated to the vertices.
         backface_culling: bool
             If True, enable backface culling on the surface.
+        polygon_offset: float
+            If not None, the factor used to resolve coincident topology.
         """
         pass
 

mne/viz/backends/renderer.py

@@ -200,7 +200,7 @@ def _use_test_3d_backend(backend_name, interactive=False):
 
 
 def set_3d_view(figure, azimuth=None, elevation=None,
-                focalpoint=None, distance=None):
+                focalpoint=None, distance=None, roll=None):
     """Configure the view of the given scene.
 
     Parameters
@@ -215,10 +215,12 @@ def set_3d_view(figure, azimuth=None, elevation=None,
         The focal point of the view: (x, y, z).
     distance : float
         The distance to the focal point.
+    roll : float
+        The view roll.
     """
     backend._set_3d_view(figure=figure, azimuth=azimuth,
                          elevation=elevation, focalpoint=focalpoint,
-                         distance=distance)
+                         distance=distance, roll=roll)
 
 
 def set_3d_title(figure, title, size=40):