matplotlib / matplotlib/ipympl

key error in jupyter notebook using brainrender

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Jupyter Notebook
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描述

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 !

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调研方向

在报告的 Anaconda/Jupyter 环境中重现 traceback,然后检查访问 vedo.settings.notebookBackend 的 brainrender/scene.py 和 brainrender/_jupyter.py。完成的标准是 Scene(...) 在 notebook 路径中能够初始化且不会出现报告的 KeyError,并为此环境添加回归检查。

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评估

技术栈
anaconda, jupyter-notebook, python
领域
developer-experience
Issue 类型
缺陷
难度
4/5
预计耗时
3-5 天
活跃度
停滞
描述清晰度
需要澄清
新手友好度
18/100

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