Compatibility with vedo 2023.5.0 (#277)

* Added to changes to conform to vedo 2023.5.0+dev26a

* Further compatibility updates

* Changed function name in bm_cells from camel case to snake case

* Fixed colormap related issue

* Cleaned up return from volume.py::_from_numpy()

* Fixed failing volume test by removing mode=2 for now

benchmark/bm_cells.py

@@ -19,7 +19,7 @@ def get_n_random_points_in_region(region, N):
     Z = np.random.randint(region_bounds[4], region_bounds[5], size=10000)
     pts = [[x, y, z] for x, y, z in zip(X, Y, Z)]
 
-    ipts = region.mesh.insidePoints(pts).points()
+    ipts = region.mesh.inside_points(pts).coordinates
     return np.vstack(random.choices(ipts, k=N))
 
 

benchmark/bm_napari.py

@@ -21,7 +21,7 @@
 surfaces = []
 for act in scene.clean_actors:
     surfaces.append(
-        (act.points(), act.faces(), np.ones(len(act.points())) * 0.5)
+        (act.vertices, act.cells, np.ones(len(act.vertices)) * 0.5)
     )
 
 # render stuff in napar

benchmark/timer.py

@@ -37,7 +37,7 @@ def __rich_console__(self, console, dimension):
         )
         for act in self.scene.clean_actors:
             try:
-                points = len(act.points())
+                points = act.npoints
             except AttributeError:
                 points = 0
             actors.add(
@@ -71,7 +71,7 @@ def __rich_console__(self, console, dimension):
         points = []
         for act in self.scene.clean_actors:
             try:
-                points.append(len(act.points()))
+                points.append(act.npoints)
             except AttributeError:
                 pass
         tot_points = sum(points)

brainrender/_colors.py

@@ -3,7 +3,7 @@
 import matplotlib.cm as cm_mpl
 import numpy as np
 from vedo.colors import colors as vcolors
-from vedo.colors import getColor
+from vedo.colors import get_color as getColor
 
 
 def map_color(value, name="jet", vmin=None, vmax=None):

brainrender/actor.py

@@ -24,7 +24,7 @@ def make_actor_label(
     zoffset=0,
 ):
     """
-    Adds a 2D text ancored to a point on the actor's mesh
+    Adds a 2D text anchored to a point on the actor's mesh
     to label what the actor is
 
     :param kwargs: keyword arguments can be passed to determine
@@ -64,12 +64,12 @@ def make_actor_label(
 
         # Mark a point on Mesh that corresponds to the label location
         if radius is not None:
-            pt = actor.closestPoint(point)
+            pt = actor.closest_point(point)
             pt[2] = -pt[2]
             sphere = Sphere(pt, r=radius, c=color, res=8)
             sphere.ancor = pt
             new_actors.append(sphere)
-            sphere.computeNormals()
+            sphere.compute_normals()
 
     return new_actors
 
@@ -159,7 +159,7 @@ def center(self):
         """
         Returns the coordinates of the mesh's center
         """
-        return self.mesh.points().mean(axis=0)
+        return self.mesh.center_of_mass()
 
     @classmethod
     def make_actor(cls, mesh, name, br_class):
@@ -218,7 +218,7 @@ def __rich_console__(self, *args):
             f"[{orange}]center of mass:[/{orange}][{amber}] {self.mesh.center_of_mass().astype(np.int32)}"
         )
         rep.add(
-            f"[{orange}]number of vertices:[/{orange}][{amber}] {len(self.mesh.points())}"
+            f"[{orange}]number of vertices:[/{orange}][{amber}] {self.mesh.npoints}"
         )
         rep.add(
             f"[{orange}]dimensions:[/{orange}][{amber}] {np.array(self.mesh.bounds()).astype(np.int32)}"

brainrender/actors/cylinder.py

@@ -20,7 +20,7 @@ def __init__(self, pos, root, color="powderblue", alpha=1, radius=350):
 
         # Get pos
         if isinstance(pos, Mesh):
-            pos = pos.points().mean(axis=0)
+            pos = pos.center_of_mass()
         elif isinstance(pos, Actor):
             pos = pos.center
         logger.debug(f"Creating Cylinder actor at: {pos}")

brainrender/actors/points.py

@@ -140,7 +140,7 @@ def __init__(
         volume = (
             vPoints(data)
             .density(dims=dims, radius=radius, **kwargs)
-            .c("Dark2")
+            .cmap("Dark2")
             .alpha([0, 0.9])
             .mode(1)
         )  # returns a vedo Volume

brainrender/actors/ruler.py

@@ -37,7 +37,7 @@ def ruler(p1, p2, unit_scale=1, units=None, s=50):
     dist = mag(p2 - p1) * unit_scale
     label = precision(dist, 3) + " " + units
     lbl = Text3D(label, pos=midpoint, s=s + 100, justify="center")
-    lbl.SetOrientation([0, 0, 180])
+    # lbl.SetOrientation([0, 0, 180])
     actors.append(lbl)
 
     # Add spheres add end

brainrender/actors/volume.py

@@ -78,12 +78,12 @@ def _from_numpy(self, griddata, voxel_size, color, **volume_kwargs):
         Creates a vedo.Volume actor from a 3D numpy array
         with volume data
         """
+
         return VedoVolume(
             griddata,
             spacing=[voxel_size, voxel_size, voxel_size],
-            c=color,
             **volume_kwargs,
-        )
+        ).cmap(color)
 
     def _from_file(self, filepath, voxel_size, color, **volume_kwargs):
         """

examples/add_cells.py

@@ -22,7 +22,7 @@ def get_n_random_points_in_region(region, N):
     Z = np.random.randint(region_bounds[4], region_bounds[5], size=10000)
     pts = [[x, y, z] for x, y, z in zip(X, Y, Z)]
 
-    ipts = region.mesh.inside_points(pts).points()
+    ipts = region.mesh.inside_points(pts).coordinates
     return np.vstack(random.choices(ipts, k=N))
 
 

examples/add_mesh_from_file.py

@@ -14,7 +14,7 @@
 scene.add_brain_region("SCm", alpha=0.2)
 
 # Add from file
-scene.add("examples/data/CC_134_1_ch1inj.obj", color="tomato")
+scene.add("data/CC_134_1_ch1inj.obj", color="tomato")
 
 # Render!
 scene.render()

examples/cell_density.py

@@ -27,7 +27,7 @@ def get_n_random_points_in_region(region, N):
     Z = np.random.randint(region_bounds[4], region_bounds[5], size=10000)
     pts = [[x, y, z] for x, y, z in zip(X, Y, Z)]
 
-    ipts = region.mesh.inside_points(pts).points()
+    ipts = region.mesh.inside_points(pts).vertices
     return np.vstack(random.choices(ipts, k=N))
 
 

examples/neurons.py

@@ -13,7 +13,7 @@
 scene = Scene(title="neurons")
 
 # Add a neuron from file
-scene.add(Neuron("examples/data/neuron1.swc"))
+scene.add(Neuron("data/neuron1.swc"))
 
 # Download neurons data with morphapi
 mlapi = MouseLightAPI()

examples/screenshot.py

@@ -32,7 +32,7 @@
     "focalPoint": (7718, 4290, -3507),
     "distance": 40610,
 }
-zoom = 1.5
+zoom = 2.5
 
 # If you only want a screenshot and don't want to move the camera
 # around the scene, set interactive to False.

examples/user_volumetric_data.py

@@ -74,7 +74,8 @@
 
 # 3. create a Volume vedo actor and smooth
 print("Creating volume")
-vol = Volume(transformed_stack, origin=scene.root.origin()).smooth_median()
+vol = Volume(transformed_stack).permute_axes(2, 1, 0)
+vol.smooth_median()
 
 
 # 4. Extract a surface mesh from the volume actor

examples/volumetric_data.py

@@ -21,12 +21,12 @@
 
 scene = Scene(inset=False)
 
-data = np.load("examples/data/volume.npy")
+data = np.load("data/volume.npy")
 print(data.shape)
 
 # make a volume actor and add
 actor = Volume(
-    "examples/data/volume.npy",
+    "data/volume.npy",
     voxel_size=200,  # size of a voxel's edge in microns
     as_surface=False,  # if true a surface mesh is rendered instead of a volume
     c="Reds",  # use matplotlib colormaps to color the volume

tests/test_volume.py

@@ -9,5 +9,5 @@ def test_volume():
 
     data = np.load("examples/data/volume.npy")
     s.add(Volume(data, voxel_size=200, as_surface=False, c="Reds"))
-    s.add(Volume(data, voxel_size=200, as_surface=True, c="Reds", mode=2))
+    s.add(Volume(data, voxel_size=200, as_surface=True, c="Reds"))
     del s