ENH: Add white matter fiber tracking to sEEG tutorial

doc/changes/devel/12555.newfeature.rst

@@ -0,0 +1 @@
+Add diffusion imaging to :ref:`tut-working-with-seeg` including adding :meth:`mne.viz.Brain.add_streamline` and :meth:`mne.viz.Brain.remove_streamlines` to visualize the fiber tracts, by `Alex Rockhill`_.

mne/datasets/config.py

@@ -90,7 +90,7 @@
 # here: ↓↓↓↓↓↓↓↓
 RELEASES = dict(
     testing="0.152",
-    misc="0.27",
+    misc="0.29",
     phantom_kit="0.2",
     ucl_opm_auditory="0.2",
 )
@@ -131,7 +131,7 @@
 )
 MNE_DATASETS["misc"] = dict(
     archive_name=f"{MISC_VERSIONED}.tar.gz",  # 'mne-misc-data',
-    hash="md5:e343d3a00cb49f8a2f719d14f4758afe",
+    hash="md5:19535192331d9e4e99d8886028c1f447",
     url=(
         "https://codeload.github.com/mne-tools/mne-misc-data/tar.gz/"
         f'{RELEASES["misc"]}'

mne/viz/_brain/_brain.py

@@ -225,6 +225,8 @@ class Brain:
        +-------------------------------------+--------------+---------------+
        | :meth:`add_skull`                   |              | ✓             |
        +-------------------------------------+--------------+---------------+
+       | :meth:`add_streamline`              |              | ✓             |
+       +-------------------------------------+--------------+---------------+
        | :meth:`add_text`                    | ✓            | ✓             |
        +-------------------------------------+--------------+---------------+
        | :meth:`add_volume_labels`           |              | ✓             |
@@ -253,6 +255,8 @@ class Brain:
        +-------------------------------------+--------------+---------------+
        | :meth:`remove_skull`                |              | ✓             |
        +-------------------------------------+--------------+---------------+
+       | :meth:`remove_streamlines`          |              | ✓             |
+       +-------------------------------------+--------------+---------------+
        | :meth:`remove_text`                 |              | ✓             |
        +-------------------------------------+--------------+---------------+
        | :meth:`remove_volume_labels`        |              | ✓             |
@@ -2535,6 +2539,66 @@ def remove_skull(self):
         """Remove skull objects from the rendered scene."""
         self._remove("skull", render=True)
 
+    @fill_doc
+    def add_streamline(
+        self,
+        streamline,
+        line_width=1,
+        color="red",
+        scalars=None,
+        colormap=None,
+        vmin=None,
+        vmax=None,
+        alpha=1,
+    ):
+        """Add a streamlines to render fiber tracts.
+
+        Parameters
+        ----------
+        streamline : array shape=(n_points, 3)
+           An array with 3D points forming a line in units of m.
+        line_width : int
+            The width of the line.
+        color : list
+            A list with entries of anything matplotlib accepts:
+            string, RGB, hex, etc.
+        scalars : list
+            A list of scalar values associated with each vertex of
+            the streamline.
+        %(colormap)s
+        vmin : None | float
+            The minimum value for color scaling.
+        vmax : None | float
+            The maximum value for color scaling.
+        %(alpha)s
+
+        Notes
+        -----
+        .. versionadded:: 0.24
+        """
+        color = _to_rgb(color)
+
+        for _ in self._iter_views("vol"):
+            actor, _ = self._renderer.line(
+                streamline * (1e3 if self._units == "mm" else 1),
+                color=color,
+                opacity=alpha,
+                line_width=line_width,
+                scalars=scalars,
+                colormap=colormap,
+                vmin=vmin,
+                vmax=vmax,
+                reset_camera=False,
+                render=False,
+            )
+            self._add_actor("streamlines", actor)
+
+        self._renderer._update()
+
+    def remove_streamlines(self):
+        """Remove streamline objects from the rendered scene."""
+        self._remove("streamlines", render=True)
+
     @fill_doc
     def add_volume_labels(
         self,

mne/viz/backends/_abstract.py

@@ -194,6 +194,66 @@ def mesh(
         """
         pass
 
+    @abstractclassmethod
+    def line(
+        self,
+        line,
+        colors,
+        opacity=1.0,
+        backface_culling=False,
+        scalars=None,
+        colormap=None,
+        vmin=None,
+        vmax=None,
+        interpolate_before_map=True,
+        line_width=1.0,
+        polygon_offset=None,
+        **kwargs,
+    ):
+        """Add a mesh in the scene.
+
+        Parameters
+        ----------
+        line : list
+            A list of array-like points defining the lines.
+        color : tuple | str
+            The color of the mesh as a tuple (red, green, blue) of float
+            values between 0 and 1 or a valid color name (i.e. 'white'
+            or 'w').
+        opacity : float
+            The opacity of the mesh.
+        shading : bool
+            If True, enable the mesh shading.
+        backface_culling : bool
+            If True, enable backface culling on the mesh.
+        scalars : ndarray, shape (n_vertices,)
+            The scalar valued associated to the vertices.
+        vmin : float | None
+            vmin is used to scale the colormap.
+            If None, the min of the data will be used.
+        vmax : float | None
+            vmax is used to scale the colormap.
+            If None, the max of the data will be used.
+        colormap : str | np.ndarray | matplotlib.colors.Colormap | None
+            The colormap to use.
+        interpolate_before_map :
+            Enabling makes for a smoother scalars display. Default is True.
+            When False, OpenGL will interpolate the mapped colors which can
+            result is showing colors that are not present in the color map.
+        line_width : int
+            The width of the line.
+        polygon_offset : float
+            If not None, the factor used to resolve coincident topology.
+        kwargs : args
+            The arguments to pass to triangular_mesh
+
+        Returns
+        -------
+        line :
+            Handle of the line in the scene.
+        """
+        pass
+
     @abstractclassmethod
     def contour(
         self,

mne/viz/backends/_pyvista.py

@@ -458,6 +458,37 @@ def mesh(
             **kwargs,
         )
 
+    def line(
+        self,
+        line,
+        color,
+        opacity=1.0,
+        backface_culling=False,
+        scalars=None,
+        colormap=None,
+        vmin=None,
+        vmax=None,
+        interpolate_before_map=True,
+        line_width=1.0,
+        polygon_offset=None,
+        **kwargs,
+    ):
+        return self.polydata(
+            mesh=pyvista.MultipleLines(line),
+            color=color,
+            opacity=opacity,
+            normals=np.zeros_like(np.array(line)),
+            backface_culling=backface_culling,
+            scalars=scalars,
+            colormap=colormap,
+            vmin=vmin,
+            vmax=vmax,
+            interpolate_before_map=interpolate_before_map,
+            line_width=line_width,
+            polygon_offset=polygon_offset,
+            **kwargs,
+        )
+
     def contour(
         self,
         surface,

mne/viz/backends/tests/test_renderer.py

@@ -101,6 +101,9 @@ def test_3d_backend(renderer):
     txt_text = "renderer"
     txt_size = 14
 
+    line_data = [[0, 0, 0], [1, 1, 1]]
+    line_color = "red"
+
     cam_distance = 5 * tet_size
 
     # init scene
@@ -123,6 +126,14 @@ def test_3d_backend(renderer):
     )
     rend.remove_mesh(mesh_data)
 
+    # use lines
+    line_actor = rend.line(
+        line_data,
+        color=line_color,
+        line_width=5,
+    )
+    rend.remove_mesh(line_actor)
+
     # use contour
     rend.contour(
         surface=ct_surface, scalars=ct_scalars, contours=ct_levels, kind="line"