Merge pull request #345 from brainglobe/resources

Move resources to top level

.gitignore

@@ -16,6 +16,8 @@ brainrender/atlas_specific/gene_expression/__pycache__
 brainrender/atlas_specific/gene_expression/__pycache__/*
 brainrender/atlas_specific/__pycache__
 
+example_brainrender_shot*
+
 workspace.py
 workspace.ipynb
 brexport.html

MANIFEST.in

@@ -7,6 +7,7 @@ prune tests
 prune examples
 prune imgs
 prune videos
+prune resources
 
 graft brainrender
 

brainrender/_colors.py

@@ -1,6 +1,6 @@
 import random
 
-import matplotlib.cm as cm_mpl
+import matplotlib as mpl
 import numpy as np
 from vedo.colors import colors as vcolors
 from vedo.colors import get_color as getColor
@@ -20,7 +20,7 @@ def map_color(value, name="jet", vmin=None, vmax=None):
     if vmax < vmin:
         raise ValueError("vmax should be larger than vmin")
 
-    mp = cm_mpl.get_cmap(name=name)
+    mp = mpl.colormaps.get_cmap(name)
 
     value -= vmin
     value /= vmax - vmin

examples/add_mesh_from_file.py

@@ -1,11 +1,12 @@
 from pathlib import Path
-from importlib.resources import files
 
 from myterial import orange
 from rich import print
 
 from brainrender import Scene
 
+obj_file = Path(__file__).parent.parent / "resources" / "CC_134_1_ch1inj.obj"
+
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
 # Create a brainrender scene
@@ -15,10 +16,7 @@
 scene.add_brain_region("SCm", alpha=0.2)
 
 # Add from file
-scene.add(
-    files("brainrender").joinpath("resources/CC_134_1_ch1inj.obj"),
-    color="tomato",
-)
+scene.add(obj_file, color="tomato")
 
 # Render!
 scene.render()

examples/neurons.py

@@ -8,13 +8,15 @@
 from brainrender import Scene
 from brainrender.actors import Neuron, make_neurons
 
+neuron_file = Path(__file__).parent.parent / "resources" / "neuron1.swc"
+
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
 # Create a brainrender scene
 scene = Scene(title="neurons")
 
 # Add a neuron from file
-scene.add(Neuron(files("brainrender").joinpath("resources/neuron1.swc")))
+scene.add(Neuron(neuron_file))
 
 # Download neurons data with morphapi
 mlapi = MouseLightAPI()

examples/notebook_workflow.ipynb

@@ -35,7 +35,6 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [],
    "source": [
     "import vedo\n",
     "vedo.settings.default_backend= 'vtk'\n",
@@ -46,7 +45,8 @@
     "popup_scene.add_brain_region('VISp')\n",
     "\n",
     "popup_scene.render()  # press 'Esc' to close"
-   ]
+   ],
+   "outputs": []
   },
   {
    "cell_type": "markdown",
@@ -73,7 +73,6 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "# Set the backend\n",
     "import vedo\n",
@@ -94,7 +93,8 @@
     "from vedo import Plotter  # <- this will be used to render an embedded scene \n",
     "plt = Plotter()\n",
     "plt.show(*scene.renderables)  # same as vedo.show(*scene.renderables)"
-   ]
+   ],
+   "outputs": []
   }
  ],
  "metadata": {

examples/probe_tracks.py

@@ -8,7 +8,7 @@
 from brainrender import Scene
 from brainrender.actors import Points
 
-data_path = Path(__file__).parent.parent / "brainrender" / "resources"
+resource_path = Path(__file__).parent.parent / "resources"
 
 scene = Scene(title="Silicon Probe Visualization")
 
@@ -21,15 +21,15 @@
 # part of the probe.
 scene.add(
     Points(
-        np.load(data_path / "probe_1_striatum.npy"),
+        np.load(resource_path / "probe_1_striatum.npy"),
         name="probe_1",
         colors="darkred",
         radius=50,
     )
 )
 scene.add(
     Points(
-        np.load(data_path / "probe_2_RSP.npy"),
+        np.load(resource_path / "probe_2_RSP.npy"),
         name="probe_2",
         colors="darkred",
         radius=50,

examples/volumetric_data.py

@@ -11,18 +11,19 @@
 from brainrender.actors import Volume
 
 from pathlib import Path
-from importlib.resources import files
 
 from myterial import orange
 from rich import print
 
 settings.SHOW_AXES = False
+volume_file = Path(__file__).parent.parent / "resources" / "volume.npy"
+
 
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
 scene = Scene(inset=False)
 
-data = np.load(files("brainrender").joinpath("resources/volume.npy"))
+data = np.load(volume_file)
 print(data.shape)
 
 # make a volume actor and add

tests/test_aba_gene.py

@@ -12,7 +12,6 @@
 
 #     return geapi
 
-
 # @pytest.mark.xfail
 # def test_gene_expression_api(geapi):
 

tests/test_integration.py

@@ -1,4 +1,3 @@
-from importlib.resources import files
 from pathlib import Path
 
 import numpy as np
@@ -19,6 +18,8 @@
 )
 from brainrender.atlas_specific import GeneExpressionAPI
 
+resources_dir = Path(__file__).parent.parent / "resources"
+
 
 def get_n_points_in_region(region, N):
     """
@@ -109,7 +110,7 @@ def test_add_labels(scene):
 
 
 def test_add_mesh_from_file(scene):
-    data_path = files("brainrender").joinpath("resources/CC_134_1_ch1inj.obj")
+    data_path = resources_dir / "CC_134_1_ch1inj.obj"
     scene.add_brain_region("SCm", alpha=0.2)
     file_mesh = scene.add(data_path, color="tomato")
 
@@ -236,7 +237,7 @@ def test_gene_expression(scene):
 
 
 def test_neurons(scene, pytestconfig):
-    data_path = files("brainrender").joinpath("resources/neuron1.swc")
+    data_path = resources_dir / "neuron1.swc"
 
     neuron = Neuron(data_path)
     scene.add(neuron)
@@ -368,7 +369,7 @@ def test_video(scene, pytestconfig):
 
 
 def test_volumetric_data(scene):
-    data_path = files("brainrender").joinpath("resources/volume.npy")
+    data_path = resources_dir / "volume.npy"
     data = np.load(data_path)
     actor = Volume(
         data,

tests/test_neuron.py

@@ -1,4 +1,4 @@
-from importlib.resources import files
+from pathlib import Path
 
 import pytest
 from vedo import Sphere
@@ -7,12 +7,12 @@
 from brainrender.actor import Actor
 from brainrender.actors import Neuron, make_neurons
 
+resources_dir = Path(__file__).parent.parent / "resources"
+
 
 def test_neuron():
     s = Scene(title="BR")
-    neuron = s.add(
-        Neuron(files("brainrender").joinpath("resources/neuron1.swc"))
-    )
+    neuron = s.add(Neuron(resources_dir / "neuron1.swc"))
     s.add(Neuron(Actor(neuron.mesh)))
     s.add(Neuron(neuron.mesh))
     Neuron(Sphere())
@@ -21,13 +21,13 @@ def test_neuron():
         Neuron(1)
 
     with pytest.raises(FileExistsError):
-        Neuron(files("brainrender").joinpath("resources/neuronsfsfs.swc"))
+        Neuron(resources_dir / "neuronsfsfs.swc")
     with pytest.raises(NotImplementedError):
-        Neuron(files("brainrender").joinpath("resources/random_cells.h5"))
+        Neuron(resources_dir / "random_cells.h5")
 
     del s
 
 
 def test_make_neurons():
-    data_path = files("brainrender").joinpath("resources/neuron1.swc")
+    data_path = resources_dir / "neuron1.swc"
     make_neurons(data_path, data_path)

tests/test_points.py

@@ -1,5 +1,5 @@
 import random
-from importlib.resources import files
+from pathlib import Path
 
 import numpy as np
 import pytest
@@ -8,6 +8,8 @@
 from brainrender.actor import Actor
 from brainrender.actors import Point, Points, PointsDensity
 
+resources_dir = Path(__file__).parent.parent / "resources"
+
 
 def get_n_random_points_in_region(region, N):
     """
@@ -26,7 +28,7 @@ def get_n_random_points_in_region(region, N):
 
 def test_points_working():
     s = Scene(title="BR")
-    data_path = files("brainrender").joinpath("resources/random_cells.npy")
+    data_path = resources_dir / "random_cells.npy"
     act = Points(np.load(data_path))
     act2 = Points(data_path, colors="k")
     act3 = Points(data_path, name="test")
@@ -59,11 +61,11 @@ def test_points_density():
 def test_points_error():
     with pytest.raises(FileExistsError):
         Points(
-            files("brainrender").joinpath("resources/testsfsdfs.npy"),
+            resources_dir / "testsfsdfs.npy",
             colors="k",
         )
     with pytest.raises(NotImplementedError):
         Points(
-            files("brainrender").joinpath("resources/random_cells.h5"),
+            resources_dir / "random_cells.h5",
             colors="k",
         )

tests/test_volume.py

@@ -1,15 +1,17 @@
-from importlib.resources import files
+from pathlib import Path
 
 import numpy as np
 
 from brainrender import Scene
 from brainrender.actors import Volume
 
+resources_dir = Path(__file__).parent.parent / "resources"
+
 
 def test_volume():
     s = Scene(inset=False, root=True)
 
-    data = np.load(files("brainrender").joinpath("resources/volume.npy"))
+    data = np.load(resources_dir / "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"))
     del s