All resources used for examples and for testing are now in brainrende…

…r/resources, importlib.resources now used to fetch data
brainglobe · Nov 28, 2023 · b3fa6eb · b3fa6eb
1 parent 1c1f524
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Showing 16 changed files with 48 additions and 167,159 deletions.
diff --git a/examples/data/CC_134_1_ch1inj.obj → brainrender/resources/CC_134_1_ch1inj.obj b/examples/data/CC_134_1_ch1inj.obj → brainrender/resources/CC_134_1_ch1inj.obj
diff --git a/tests/files/CC_134_2_ch1inj.obj → brainrender/resources/CC_134_2_ch1inj.obj b/tests/files/CC_134_2_ch1inj.obj → brainrender/resources/CC_134_2_ch1inj.obj
diff --git a/examples/data/neuron1.swc → brainrender/resources/neuron1.swc b/examples/data/neuron1.swc → brainrender/resources/neuron1.swc
diff --git a/tests/files/random_cells.h5 → brainrender/resources/random_cells.h5 b/tests/files/random_cells.h5 → brainrender/resources/random_cells.h5
diff --git a/tests/files/random_cells.npy → brainrender/resources/random_cells.npy b/tests/files/random_cells.npy → brainrender/resources/random_cells.npy
diff --git a/examples/data/volume.npy → brainrender/resources/volume.npy b/examples/data/volume.npy → brainrender/resources/volume.npy
diff --git a/examples/add_mesh_from_file.py b/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()
diff --git a/examples/neurons.py b/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()

diff --git a/examples/volumetric_data.py b/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