matplotlib / matplotlib/ipympl
key error in jupyter notebook using brainrender
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Description
Hello,
I am very new to these things thus sorry if I am not giving you enough informations about the issue !
to resume
I am trying to plot the coordinate of a group of cells in a 3D brain by using brainrender with jupyter notebook
I am using an anaconda environnement with the version 3.7.0 of python and the version of my anaconda navigator is 1.9.6.
my scirpt is working until this entry :
```
#Get a numpy array coordinates of some labelled cells
scene = Scene(title='area_cell')
MOx = scene.add_brain_region("MO", alpha=0.15)
SSx = scene.add_brain_region("SS", alpha=0.15)
VISx = scene.add_brain_region("VIS", alpha=0.15)
#STRx = scene.add_brain_region("STR", alpha=0.15)
```
```
KeyError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_16228\2284008602.py in
1 #Get a numpy array coordinates of some labelled cells
----> 2 scene = Scene(title='area_cell')
3 MOx = scene.add_brain_region("MO", alpha=0.15)
4 SSx = scene.add_brain_region("SS", alpha=0.15)
5 VISx = scene.add_brain_region("VIS", alpha=0.15)
~\Anaconda2\envs\plot3Dbrain\lib\site-packages\brainrender\scene.py in __init__(self, root, atlas_name, inset, title, screenshots_folder, plotter, title_color)
48 f"Creating scene with parameters: root: {root}, atlas_name: '{atlas_name}'', inset: {inset}, screenshots_folder: {screenshots_folder}"
49 )
---> 50 JupyterMixIn.__init__(self)
51
52 self.actors = [] # stores all actors in the scene
~\Anaconda2\envs\plot3Dbrain\lib\site-packages\brainrender\_jupyter.py in __init__(self)
10 def __init__(self): # pragma: no cover
11 # keep track if we are in a jupyter notebook
---> 12 if vedo.settings.notebookBackend == "k3d":
13 self.backend = "k3d"
14 elif vedo.settings.notebookBackend == "itkwidgets":
~\Anaconda2\envs\plot3Dbrain\lib\site-packages\vedo\utils.py in __getattr__(self, k)
236
237 def __getattr__(self, k):
--> 238 return self[k]
239
240 def __setattr__(self, k, v):
KeyError: 'notebookBackend'
```
I tried unsuccessfully to understand what was going wrong and to find someonne with the same issue, thus if you have idea it would be great !
also let me know if you need more informations,
Thanks !
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the traceback in the reported Anaconda/Jupyter setup, then inspect brainrender/scene.py and brainrender/_jupyter.py where vedo.settings.notebookBackend is accessed. Done means Scene(...) initializes without the reported KeyError in the notebook path, with a regression check for this setup.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- anaconda, jupyter-notebook, python
- Domain
- developer-experience
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 18/100