actor getattr and tests fiz

.pre-commit-config.yaml

@@ -1,8 +1,4 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.3.0  # Use the ref you want to point at
-    hooks:
-      - id: check-added-large-files
 -   repo: https://github.com/python/black
     rev: 19.10b0
     hooks:

brainrender/Utils/actors_funcs.py

@@ -134,7 +134,7 @@ def edit_actor(
     if color:
         actor.color(c=color)
     if line:
-        set_line(actor, **line_kwargs)
+        set_line(actor.mesh, **line_kwargs)
     if upsample:
         actor.subdivide(N=1)
     if downsample:

brainrender/Utils/scene_utils.py

@@ -1,9 +1,7 @@
 import numpy as np
-import inspect
 from vedo import Mesh, Text, Sphere
 import random
 
-from brainrender.atlases.atlas import Atlas
 import brainrender
 from brainrender.Utils.camera import check_camera_param
 from brainrender.colors import get_random_colors
@@ -38,24 +36,6 @@ def parse_add_actors_inputs(actors, name, br_class):
     return actors, names, br_classes
 
 
-def get_scene_atlas(atlas, base_dir, atlas_kwargs={}, **kwargs):
-    """
-        Return an instance of an Atlas class. 
-
-    """
-    if atlas is None:
-        atlas = brainrender.DEFAULT_ATLAS
-
-    if isinstance(atlas, str):
-        return Atlas(atlas, base_dir=base_dir, **atlas_kwargs, **kwargs,)
-    elif inspect.isclass(atlas):
-        return atlas(**atlas_kwargs)
-    else:
-        raise ValueError(
-            "The `atlas` argument should be None, a string with atlas name or a class"
-        )
-
-
 def get_scene_camera(camera, atlas):
     """
         Gets a working camera. 

brainrender/actor.py

@@ -1,5 +1,4 @@
 import pyinspect as pi
-from vedo import Mesh
 from io import StringIO
 from rich.console import Console
 from pyinspect._colors import orange, mocassin, salmon
@@ -8,7 +7,7 @@
 from brainrender.Utils.scene_utils import make_actor_label
 
 
-class Actor(Mesh):
+class Actor(object):
     _skip = ["Ruler", "silhouette"]
 
     _needs_label = False
@@ -20,6 +19,18 @@ def __init__(self, mesh, name=None, br_class=None):
         self.name = name
         self.br_class = br_class
 
+    def __getattr__(self, attr):
+        """
+            If an unknown attribute is called, try `self.mesh.attr`
+        """
+        if attr == "__rich__":
+            return None
+        print(attr)
+        if hasattr(self.__dict__["mesh"], attr):
+            return getattr(self.__dict__["mesh"], attr)
+        else:
+            raise AttributeError(f"{self} doesn not have attribute {attr}")
+
     def __repr__(self):
         return f"brainrender.Actor: {self.name}-{self.br_class}"
 

brainrender/atlases/atlas.py

@@ -4,7 +4,7 @@
 import os
 from bg_atlasapi.bg_atlas import BrainGlobeAtlas
 from pyinspect.classes import Enhanced
-
+import inspect
 import brainrender
 from brainrender.Utils.paths_manager import Paths
 from brainrender.atlases.aba import ABA
@@ -18,6 +18,25 @@
 from brainrender.colors import check_colors
 from brainrender.Utils.atlases_utils import parse_neurons_colors
 from brainrender.morphology.utils import get_neuron_actors_with_morphapi
+from brainrender.actor import Actor
+
+
+def get_scene_atlas(atlas, base_dir, atlas_kwargs={}, **kwargs):
+    """
+        Return an instance of an Atlas class. 
+
+    """
+    if atlas is None:
+        atlas = brainrender.DEFAULT_ATLAS
+
+    if isinstance(atlas, str):
+        return Atlas(atlas, base_dir=base_dir, **atlas_kwargs, **kwargs,)
+    elif inspect.isclass(atlas):
+        return atlas(**atlas_kwargs)
+    else:
+        raise ValueError(
+            "The `atlas` argument should be None, a string with atlas name or a class"
+        )
 
 
 class Atlas(BrainGlobeAtlas, Paths, ABA, Enhanced):
@@ -289,9 +308,16 @@ def get_neurons(
         if not isinstance(neurons, (list, tuple)):
             neurons = [neurons]
 
+        clean_neurons = []
+        for n in neurons:
+            if isinstance(n, (tuple, list)):
+                clean_neurons.extend(list(n))
+            else:
+                clean_neurons.append(n)
+
         # ---------------------------------- Render ---------------------------------- #
         _neurons_actors = []
-        for neuron in neurons:
+        for neuron in clean_neurons:
             neuron_actors = {"soma": None, "dendrites": None, "axon": None}
 
             # Deal with neuron as filepath
@@ -314,7 +340,7 @@ def get_neurons(
                     )
 
             # Deal with neuron as single actor
-            elif isinstance(neuron, Mesh):
+            elif isinstance(neuron, (Actor, Mesh)):
                 # A single actor was passed, maybe it's the entire neuron
                 neuron_actors["soma"] = neuron  # store it as soma
                 pass
@@ -357,7 +383,7 @@ def get_neurons(
             # Check that we don't have anything weird in neuron_actors
             for key, act in neuron_actors.items():
                 if act is not None:
-                    if not isinstance(act, Mesh):
+                    if not isinstance(act, (Actor, Mesh)):
                         raise ValueError(
                             f"Neuron actor {key} is {type(act)} but should be a vedo Mesh. Not: {act}"
                         )

brainrender/render.py

@@ -102,6 +102,14 @@ def __init__(
             vedosettings.screenshotTransparentBackground = False
             vedosettings.useFXAA = True
 
+    @property
+    def to_render(self):
+        return [
+            a.mesh
+            for a in flatten(self.actors) + flatten(self.actors_labels)
+            if a.mesh is not None
+        ]
+
     def _make_custom_axes(self):
         """
             When using `ruler` axes (vedy style 7), we need to 
@@ -137,7 +145,7 @@ def _make_custom_axes(self):
         plt.renderer.AddActor(rulax)
         plt.axes_instances[0] = rulax
 
-        return
+        return plt
 
     def _correct_axes(self):
         """
@@ -246,7 +254,7 @@ def render(
             args_dict["offscreen"] = True
 
         if self.make_custom_axes:
-            self._make_custom_axes()
+            self.plotter = self._make_custom_axes()
             self.make_custom_axes = False
 
         # Correct axes orientations
@@ -259,10 +267,7 @@ def render(
         self.apply_render_style()
 
         self.is_rendered = True
-        to_render = [
-            a.mesh for a in flatten(self.actors) + flatten(self.actors_labels)
-        ]
-        show(*to_render, **args_dict)
+        show(*self.to_render, **args_dict)
 
     def close(self):
         closePlotter()
@@ -281,7 +286,7 @@ def export_for_web(self, filepath="brexport.html"):
 
         # Create new plotter and save to file
         plt = Plotter()
-        plt.add(self.actors)
+        plt.add(self.to_render)
         plt = plt.show(interactive=False)
         plt.camera[-2] = -1
 

brainrender/scene.py

@@ -7,16 +7,15 @@
     Text2D,
     closePlotter,
     Plane,
-    Mesh,
 )
 import numpy as np
 import pyinspect as pi
 from pyinspect._colors import dimorange, orange, mocassin, salmon
 from rich import print as rprint
 import sys
 
+from brainrender.atlases.atlas import get_scene_atlas
 from brainrender.Utils.scene_utils import (
-    get_scene_atlas,
     get_cells_colors_from_metadata,
     parse_add_actors_inputs,
 )
@@ -124,7 +123,7 @@ def __repr__(self):
         return f"A `brainrender.scene.Scene` with {len(self)} actors."
 
     def __add__(self, other):
-        if isinstance(other, Mesh):
+        if isinstance(other, Actor):
             self.add_actor(other)
         elif isinstance(other, (Path, str)):
             self.add_from_file(str(other))
@@ -813,7 +812,7 @@ def render(self, _interactive=True):
         for scene in self.scenes:
             scene.apply_render_style()
             actors.append(scene.actors)
-            mv.add(scene.actors)
+            mv.add([act.mesh for act in scene.actors])
 
         mv.show(
             actors[0],
@@ -884,8 +883,8 @@ def render(self, _interactive=True, **kwargs):
         actors = []
         for i, scene in enumerate(self.scenes):
             scene.apply_render_style()
-            actors.append(scene.actors)
-            mv.add(scene.actors)
+            actors.append(scene.to_render)
+            mv.add(scene.to_render)
 
         for i, scene.actors in enumerate(actors):
             mv.show(scene.actors, at=i, interactive=False)

tests/test_scene.py

@@ -306,7 +306,7 @@ def test_get_random_points(scene):
     get_n_random_points_in_region(scene.atlas, "MOs", 100)
     get_n_random_points_in_region(scene.atlas, "MOp", 100, hemisphere="right")
     ca1 = scene.add_brain_regions("CA1")
-    get_n_random_points_in_region(scene.atlas, ca1, 100)
+    get_n_random_points_in_region(scene.atlas, ca1.mesh, 100)
 
 
 def test_add_from_file(scene):

tests/test_scene_io.py

@@ -10,16 +10,13 @@
     sagittal_camera,
     top_camera,
 )
-from brainrender.colors import colorMap
 
 import pytest
 
 
 @pytest.mark.slow
 def test_animated_scene():
     # --------------------------------- Variables -------------------------------- #
-    minalpha = 0.01  # transparency of background neurons
-    darkcolor = "lightgray"  # background neurons color
 
     N_FRAMES = 50
     N_neurons = 4  # number of neurons to show in total, if -1 all neurons are shown but it might take a while to render them at first
@@ -86,21 +83,11 @@ def test_animated_scene():
         if step % N_frames_for_change == 0:  # change neurons every N framse
 
             # reset neurons from previous set of neurons
-            for neuron in prev_neurons:
-                for component, actor in neuron.items():
-                    actor.alpha(minalpha)
-                    actor.color(darkcolor)
             prev_neurons = []
 
             # highlight new neurons
             neurons = choices(neurons_actors, k=N_neurons_in_frame)
             for n, neuron in enumerate(neurons):
-                color = colorMap(
-                    n, "Greens_r", vmin=-2, vmax=N_neurons_in_frame + 3
-                )
-                for component, actor in neuron.items():
-                    actor.alpha(1)
-                    actor.color(color)
                 prev_neurons.append(neuron)
 
         # Move scene camera between 3 cameras