small fixes following #21

brainglobe_heatmap/heatmaps.py

@@ -19,10 +19,10 @@
 
 # Set settings for transparent background
 # vedo for transparent bg
-# settings.vsettings.screenshotTransparentBackground = True
+# settings.vsettings.screenshot_transparent_background = True
 
 # This needs to be false for transparent bg
-# settings.vsettings.useFXAA = False
+# settings.vsettings.use_fxaa = False
 
 
 def check_values(values: dict, atlas: Atlas) -> Tuple[float, float]:
@@ -157,7 +157,7 @@ def render(self, **kwargs) -> Scene:
                 camera = self.orientation
         else:
             self.orientation = np.array(self.orientation)
-            com = self.slicer.plane0.centerOfMass()
+            com = self.slicer.plane0.center_of_mass()
             camera = {
                 "pos": com - self.orientation * 2 * np.linalg.norm(com),
                 "viewup": (0, -1, 0),

brainglobe_heatmap/plane.py

@@ -4,42 +4,10 @@
 import vedo as vd
 import vtkmodules.all as vtk
 from brainrender.actor import Actor
-from vtkmodules.vtkFiltersCore import vtkPolyDataPlaneCutter
 
-np.float = float  # for compatibility with old vedo
-vtk.vtkLogger.SetStderrVerbosity(vtk.vtkLogger.VERBOSITY_OFF)
-
-
-# from vedo 2023.4.6
-def intersect_with_plane(mesh: vd.Mesh, origin=(0, 0, 0), normal=(1, 0, 0)):
-    """
-    Intersect this Mesh with a plane to return a set of lines.
-
-    Example:
-        ```python
-        from vedo import *
-        sph = Sphere()
-        mi = sph.clone().intersect_with_plane().join()
-        print(mi.lines())
-        show(sph, mi, axes=1).close()
-        ```
-        ![](https://vedo.embl.es/images/feats/intersect_plane.png)
-    """
-    plane = vtk.vtkPlane()
-    plane.SetOrigin(origin)
-    plane.SetNormal(normal)
-
-    cutter = vtkPolyDataPlaneCutter()
-    cutter.SetInputData(mesh.dataset)
-    cutter.SetPlane(plane)
-    cutter.InterpolateAttributesOn()
-    cutter.ComputeNormalsOff()
-    cutter.Update()
-
-    msh = vd.Mesh(cutter.GetOutput(), "k", 1).lighting("off")
-    msh.properties.SetLineWidth(3)
-    msh.name = "PlaneIntersection"
-    return msh
+vtk.vtkLogger.SetStderrVerbosity(
+    vtk.vtkLogger.VERBOSITY_OFF
+)  # remove logger's prints during intersect_with_plane()
 
 
 class Plane:
@@ -57,7 +25,7 @@ def __init__(
         self.M = np.vstack([u, v]).T
 
     @staticmethod
-    def from_norm(origin: np.ndarray, norm: np.ndarray) -> vd.Plane:
+    def from_norm(origin: np.ndarray, norm: np.ndarray):
         u = np.zeros(3)
         m = np.where(norm != 0)[0][0]  # orientation can't be all-zeros
         n = (m + 1) % 3
@@ -85,35 +53,33 @@ def to_mesh(self, actor: Actor):
         plane_mesh.width = length
         return plane_mesh
 
-    def centerOfMass(self):
+    def center_of_mass(self):
         return self.center
 
-    def P3toP2(self, ps):
+    def p3_to_p2(self, ps):
         # ps is a list of 3D points
         # returns a list of 2D point mapped on
         # the plane (u -> x axis, v -> y axis)
         return (ps - self.center) @ self.M
 
-    def intersectWith(self, mesh: vd.Mesh):
-        # mesh.intersect_with_plane(
-        # origin=self.center, normal=self.normal) in newer vedo
-        return intersect_with_plane(
-            mesh, origin=self.center, normal=self.normal
+    def intersect_with(self, mesh: vd.Mesh):
+        return mesh.intersect_with_plane(
+            origin=self.center, normal=self.normal
         )
 
     # for Slicer.get_structures_slice_coords()
     def get_projections(self, actors: List[Actor]) -> Dict[str, np.ndarray]:
         projected = {}
         for actor in actors:
             mesh: vd.Mesh = actor._mesh
-            intersection = self.intersectWith(mesh)
+            intersection = self.intersect_with(mesh)
             if not intersection.vertices.shape[0]:
                 continue
             pieces = intersection.split()  # intersection.split() in newer vedo
             for piece_n, piece in enumerate(pieces):
                 # sort coordinates
                 points = piece.join(reset=True).vertices
-                projected[actor.name + f"_segment_{piece_n}"] = self.P3toP2(
+                projected[actor.name + f"_segment_{piece_n}"] = self.p3_to_p2(
                     points
                 )
         return projected

brainglobe_heatmap/slicer.py

@@ -36,7 +36,7 @@ def __init__(
         3D vector) + thickness (spacing between the two planes)
         """
         if position is None:
-            position = root.centerOfMass()
+            position = root.center_of_mass()
 
         if isinstance(position, (float, int)):
             if isinstance(orientation, str):
@@ -123,7 +123,7 @@ def show_plane_intersection(
         to the brainrender scene.
         """
         for region in regions + [root]:
-            intersection = self.plane0.intersectWith(region._mesh)
+            intersection = self.plane0.intersect_with(region._mesh)
 
             if len(intersection.vertices):
                 scene.add(intersection, transform=False)