Merge pull request #281 from brainglobe/rotation-bug-fix

All examples rendering correctly with vedo 2023.5.0

brainrender/actor.py

@@ -45,7 +45,7 @@ def make_actor_label(
             color = [0.2, 0.2, 0.2]
 
         # Get mesh's highest point
-        points = actor.mesh.points().copy()
+        points = actor.mesh.vertices.copy()
         point = points[np.argmin(points[:, 1]), :]
         point += np.array(offset) + default_offset
         point[2] = -point[2]
@@ -58,7 +58,7 @@ def make_actor_label(
 
         # Create label
         txt = Text3D(
-            label, point * np.array([1, 1, -1]), s=size, c=color, depth=0.1
+            label, point * np.array([-1, -1, -1]), s=size, c=color, depth=0.1
         )
         new_actors.append(txt.rotate_x(180).rotate_y(180))
 

brainrender/actors/neurons.py

@@ -77,9 +77,12 @@ def __init__(
         self.mesh.c(color).alpha(alpha)
 
     def _from_morphapi_neuron(self, neuron: (MorphoNeuron)):
+        # Temporarily set cache to false as meshes were being corrupted
+        # on second load
         mesh = neuron.create_mesh(
             neurite_radius=self.neurite_radius,
             soma_radius=self.soma_radius,
+            use_cache=False,
         )[1]
         return mesh
 
@@ -95,4 +98,6 @@ def _from_file(self, neuron: (str, Path)):
 
         self.name = self.name or path.name
 
-        return self._from_morphapi_neuron(MorphoNeuron(data_file=neuron))
+        return self._from_morphapi_neuron(
+            MorphoNeuron(data_file=neuron, invert_dims=True)
+        )

brainrender/actors/points.py

@@ -134,7 +134,7 @@ def __init__(
         logger.debug("Creating a PointsDensity actor")
 
         # flip coordinates on XY axis to match brainrender coordinates system
-        # data[:, 2] = -data[:, 2]
+        data[:, 2] = -data[:, 2]
 
         # create volume and then actor
         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.rotate_z(180, around=midpoint)
     actors.append(lbl)
 
     # Add spheres add end
@@ -46,6 +46,7 @@ def ruler(p1, p2, unit_scale=1, units=None, s=50):
 
     act = Actor(merge(*actors), name="Ruler", br_class="Ruler")
     act.c((0.3, 0.3, 0.3)).alpha(1).lw(2)
+
     return act
 
 
@@ -66,7 +67,7 @@ def ruler_from_surface(
     p2 = p1.copy()
     p2[axis] = 0  # zero the chosen coordinate
 
-    pts = root.mesh.intersect_with_line(p1, p2)
+    pts = root._mesh.intersect_with_line(p1, p2)
     surface_point = pts[0]
 
     return ruler(p1, surface_point, unit_scale=unit_scale, units=units, s=s)

brainrender/render.py

@@ -8,6 +8,7 @@
 from rich import print
 from rich.syntax import Syntax
 from vedo import Plotter
+from vedo import Volume as VedoVolume
 from vedo import settings as vsettings
 
 from brainrender import settings
@@ -21,6 +22,7 @@
 
 # mtx used to transform meshes to sort axes orientation
 mtx = [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, -1, 0], [0, 0, 0, 1]]
+mtx_swap_x_z = [[0, 0, 1, 0], [0, 1, 0, 0], [1, 0, 0, 0], [0, 0, 0, 1]]
 
 
 class Render:
@@ -88,24 +90,24 @@ def _make_axes(self):
 
         # make custom axes dict
         axes = dict(
-            axesLineWidth=3,
-            tipSize=0,
+            axes_linewidth=3,
+            tip_size=0,
             xtitle="AP (μm)",
             ytitle="DV (μm)",
             ztitle="LR (μm)",
-            textScale=0.8,
-            xTitleRotation=180,
+            text_scale=0.8,
+            xtitle_rotation=180,
             zrange=z_range,
-            zValuesAndLabels=z_ticks,
-            xyGrid=False,
-            yzGrid=False,
-            zxGrid=False,
-            xUseBounds=True,
-            yUseBounds=True,
-            zUseBounds=True,
-            xLabelRotation=180,
-            yLabelRotation=180,
-            zLabelRotation=90,
+            z_values_and_labels=z_ticks,
+            xygrid=False,
+            yzgrid=False,
+            zxgrid=False,
+            x_use_bounds=True,
+            y_use_bounds=True,
+            z_use_bounds=True,
+            xlabel_rotation=180,
+            ylabel_rotation=180,
+            zlabel_rotation=90,
         )
 
         return axes
@@ -118,8 +120,8 @@ def _prepare_actor(self, actor):
 
         Once an actor is 'corrected' it spawns labels and silhouettes as needed
         """
-        # don't apply transforms to points density actors
-        if isinstance(actor, PointsDensity):
+        # don't apply transforms to points density actors or rulers
+        if isinstance(actor, PointsDensity) or actor.br_class == "Ruler":
             logger.debug(
                 f'Not transforming actor "{actor.name} (type: {actor.br_class})"'
             )
@@ -129,7 +131,16 @@ def _prepare_actor(self, actor):
         if not actor._is_transformed:
             try:
                 actor._mesh = actor.mesh.clone()
-                # actor._mesh.apply_transform(mtx)
+
+                if isinstance(actor._mesh, VedoVolume):
+                    actor._mesh.permute_axes(2, 1, 0)
+                    actor._mesh.apply_transform(mtx, True)
+                elif actor.br_class in ["None", "Gene Data"]:
+                    actor._mesh.apply_transform(mtx_swap_x_z)
+                    actor._mesh.apply_transform(mtx)
+                else:
+                    actor._mesh.apply_transform(mtx)
+
             except AttributeError:  # some types of actors don't transform
                 logger.debug(
                     f'Failed to transform actor: "{actor.name} (type: {actor.br_class})"'
@@ -256,6 +267,7 @@ def render(
                 bg=settings.BACKGROUND_COLOR,
                 camera=camera.copy() if update_camera else None,
                 rate=40,
+                axes=self.plotter.axes,
             )
         elif self.backend == "k3d":  # pragma: no cover
             # Remove silhouettes

examples/__init__.py

@@ -9,8 +9,8 @@
     cell_density,
     custom_camera,
     gene_expression,
-    # neurons,
-    # ruler,
+    neurons,
+    ruler,
     settings,
     slice,
     # streamlines,

examples/add_mesh_from_file.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from importlib.resources import files
 
 from myterial import orange
 from rich import print
@@ -14,7 +15,10 @@
 scene.add_brain_region("SCm", alpha=0.2)
 
 # Add from file
-scene.add("data/CC_134_1_ch1inj.obj", color="tomato")
+scene.add(
+    files("brainrender").joinpath("resources/CC_134_1_ch1inj.obj"),
+    color="tomato",
+)
 
 # Render!
 scene.render()

examples/neurons.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from importlib.resources import files
 
 from morphapi.api.mouselight import MouseLightAPI
 from myterial import orange
@@ -13,7 +14,7 @@
 scene = Scene(title="neurons")
 
 # Add a neuron from file
-scene.add(Neuron("data/neuron1.swc"))
+scene.add(Neuron(files("brainrender").joinpath("resources/neuron1.swc")))
 
 # Download neurons data with morphapi
 mlapi = MouseLightAPI()

examples/user_volumetric_data.py

@@ -28,9 +28,10 @@
 from bg_space import AnatomicalSpace
 from myterial import blue_grey, orange
 from rich import print
-from vedo import Volume
+from vedo import Volume as VedoVolume
 
 from brainrender import Scene
+from brainrender.actors import Volume
 
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
@@ -74,14 +75,14 @@
 
 # 3. create a Volume vedo actor and smooth
 print("Creating volume")
-vol = Volume(transformed_stack).permute_axes(2, 1, 0)
+vol = VedoVolume(transformed_stack)
 vol.smooth_median()
 
 
 # 4. Extract a surface mesh from the volume actor
 print("Extracting surface")
 mesh = vol.isosurface(value=20).c(blue_grey).decimate().clean()
-SHIFT = [-20, 15, 30]  # fine tune mesh position
+SHIFT = [30, 15, -20]  # fine tune mesh position
 current_position = mesh.pos()
 new_position = [SHIFT[i] + current_position[i] for i in range(3)]
 mesh.pos(*new_position)

examples/volumetric_data.py

@@ -9,24 +9,24 @@
 from brainrender import Scene, settings
 from brainrender.actors import Volume
 
-settings.SHOW_AXES = False
-
-
 from pathlib import Path
+from importlib.resources import files
 
 from myterial import orange
 from rich import print
 
+settings.SHOW_AXES = False
+
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
 scene = Scene(inset=False)
 
-data = np.load("data/volume.npy")
+data = np.load(files("brainrender").joinpath("resources/volume.npy"))
 print(data.shape)
 
 # make a volume actor and add
 actor = Volume(
-    "data/volume.npy",
+    data,
     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

pyproject.toml

@@ -10,7 +10,7 @@ dependencies = [
     "numpy",
     "pandas",
     "h5py<=3.9", # vedo requires hdf5 <=1.12.x but hdf5 is 1.14+ from h5py 3.10 onwards
-    "vedo",
+    "vedo>=2023.5.0",
     "k3d",
     "imio",
     "msgpack",
@@ -58,7 +58,8 @@ dev = [
   "pre-commit",
   "ruff",
   "setuptools_scm",
-  "pyside2"
+  "pyside2",
+  "imio",
 ]
 nb = ["jupyter", "k3d"]
         pyside2= ["PySide2"]