Exposed the invert_dim parameter

brainrender/actors/neurons.py

@@ -41,6 +41,7 @@ def __init__(
         alpha=1,
         neurite_radius=8,
         soma_radius=15,
+        invert_dims=True,
         name=None,
     ):
         """
@@ -50,6 +51,7 @@ def __init__(
         :param color: str,
         :param neuron_radius: float, radius of axon/dendrites
         :param soma_radius: float, radius of soma
+        :param invert_dims: bool, invert dimensions of neuron
         :param name: str, actor name
         """
         logger.debug("Creating a Neuron actor")
@@ -61,7 +63,7 @@ def __init__(
         self.name = None
 
         if isinstance(neuron, (str, Path)):
-            mesh = self._from_file(neuron)
+            mesh = self._from_file(neuron, invert_dims)
         elif isinstance(neuron, (Mesh)):
             mesh = neuron
         elif isinstance(neuron, Actor):
@@ -86,7 +88,7 @@ def _from_morphapi_neuron(self, neuron: MorphoNeuron):
         )[1]
         return mesh
 
-    def _from_file(self, neuron: (str, Path)):
+    def _from_file(self, neuron: (str, Path), invert_dims):
         path = Path(neuron)
         if not path.exists():
             raise FileExistsError(f"Neuron file doesn't exist: {path}")
@@ -99,5 +101,5 @@ def _from_file(self, neuron: (str, Path)):
         self.name = self.name or path.name
 
         return self._from_morphapi_neuron(
-            MorphoNeuron(data_file=neuron, invert_dims=True)
+            MorphoNeuron(data_file=neuron, invert_dims=invert_dims)
         )

brainrender/atlas_specific/allen_brain_atlas/gene_expression/api.py

@@ -1,7 +1,9 @@
 import os
 import sys
+from time import sleep
 
 import pandas as pd
+import requests
 from loguru import logger
 
 from brainrender import base_dir
@@ -86,7 +88,18 @@
         :param gene_symbol: str
         """
         url = self.gene_experiments_url.replace("-GENE_SYMBOL-", gene)
-        data = request(url).json()["msg"]
+        max_retries = 8
+        delay = 4
+        data = None
+
+        for i in range(max_retries):
+            try:
+                data = request(url).json()["msg"]
+                break
+            except requests.exceptions.JSONDecodeError:
+                print(f"Unable to connect to Allen API, retrying in {delay}")
+                sleep(delay)
+                delay *= 2
 
         if not len(data):
             print(f"No experiment found for gene {gene}")

examples/neurons.py

@@ -4,6 +4,7 @@
 from morphapi.api.mouselight import MouseLightAPI
 from myterial import orange
 from rich import print
+from urllib3.exceptions import NewConnectionError, MaxRetryError
 
 from brainrender import Scene
 from brainrender.actors import Neuron, make_neurons
@@ -28,7 +29,12 @@
     to_add = [neurons_metadata[47], neurons_metadata[51]]
     neurons = mlapi.download_neurons(to_add)
     neurons = scene.add(*make_neurons(*neurons, neurite_radius=12))
-except ConnectionError or requests.exceptions.ReadTimeout as e:
+except (
+    NewConnectionError,
+    MaxRetryError,
+    requests.exceptions.ConnectionError,
+    requests.exceptions.ReadTimeout,
+) as e:
     print("Failed to download neurons data from neuromorpho.org.")
 
 # Render!