Hi,
To install the JupyterNotebook extension on Slicer and to add a Slicer kernel on Jupyter I followed the steps on https://github.com/Slicer/SlicerJupyter/blob/master/README.md#setup .
After I tried in the new Slicer kernel import JupyterNotebooksLib as slicernbModuleNotFoundError: No module named ‘JupyterNotebooksLib’ .
I’m using Slicer 4.11, Windows10, Anaconda with different version of Python (3.7) than which is used by Slicer (3.6).
During the installation steps I encountered a problem with installing the jupyter lab:PS C:\User> conda install -c conda-forge nodejs
Is this a Python version or a path problem?
lassoan
June 9, 2020, 9:15pm
2
Can you post a screenshot?
Ponyo2311:
During the installation steps I encountered a problem with installing the jupyter lab:PS C:\User> conda install -c conda-forge nodejs
This error is not related to Slicer, but to your conda install. Make sure you activate your virtual environment before you attempt to run any script (simply starting a command prompt in the Scripts folder is not enough).
Thanks for the reply.
I created and activated a python virtual environment via command prompt (run as admin) and have run all lines from the tutorial, including:
conda install -c conda-forge nodejs@jupyter-widgets /jupyterlab-manager@jupyter-widgets /jupyterlab-manager ipycanvas@jupyter-widgets /jupyterlab-manager ipyevents
This time it seemed to be installed, but I still get the same error message when trying to import the module in a new kernel:
lassoan
June 10, 2020, 12:29pm
4
Did you choose the “Slicer-4.11” kernel in the notebook?
Yes, I did.
Could it be that my python virtual environment wasn’t in the Slicer directory?
lassoan
June 10, 2020, 12:34pm
6
Are other Slicer features available? For example, do you have access to slicer.util.getNode function? When you started the kernel, did a Slicer application instance start? Can you post a screenshot of your entire browser window (not just a single cell)?
Slicer application does start with kernel.
lassoan
June 10, 2020, 3:25pm
8
Which Slicer version are you using? Can you copy here the full application log (menu: Help / Report a bug) here?
[DEBUG][Qt] 10.06.2020 17:37:35 [] (unknown:0) - Session start time …: 2020-06-10 17:37:35
lassoan
June 10, 2020, 4:31pm
10
Can you do this in the Slicer instance that Jupyter started? (it shows a read message in the status bar that this instance is controlled by Jupyter)
Does this file exist on your computer?c:\Users\Domi\AppData\Roaming\NA-MIC\Extensions-29031\SlicerJupyter\Lib\Slicer-4.11\qt-scripted-modules\JupyterNotebooksLib\__init__.py
You may also try to reinstall SlicerJupyter and extension and make sure that installation is completed (do not press “Close” button while the extension is being installed but wait for the “Restart” button to appear and click that).
I reinstalled the extension properly waiting for the restart button to pop up when I tried to figure out what was wrong.
On the other hand the whole qt-scripted-modules folder is missing.
The bug report with the Kernel open:
lassoan
June 10, 2020, 5:23pm
12
Yes, please install the latest Slicer Preview Release, I cannot check it anymore what the extension package contained in the 2020-05-04 version, there might have been some problem with the nightly build that day.
I installed the latest Slicer 4.11 release and the problem’s solved!
Thank you so much for your help.
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