Comments (11)
Thank you for the detailed report on the itkwidget repo. Matt and Brianna are looking into it!
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Hello ๐ ,
With itkwidgets 1.0a50
, itkwidgets supports JupyterLab 4 and Jupyter Notebook 7. The Jupyter project made these versions major breaking changes. So, there are a few approaches:
a) Update the JupyterLab and Jupyter Notebook version
b) Set the itkwidgets dependency to itkwidgets==1.0a49
until a) can be performed.
After install itkwidgets[notebook]>=1.0a49, look like there will be a requirement compatibility issues for pandas, not sure whether it's related the issue.
This seems to be unrelated in the transitive dependency arena, but a patch is here:
Testing and feedback to see if it addresses your use cause are appreciated. ๐ Thanks!
from tutorials.
Hi @thewtex, thanks for the quick response.
I update the notebook version but the same issue occurred.
Step to reproduce:
docker run -it --ipc=host --rm --net host --gpus all nvcr.io/nvidia/pytorch:24.03-py3
pip install -U notebook
Then run this notebook: https://github.com/InsightSoftwareConsortium/itkwidgets/blob/v1.0a50/examples/integrations/MONAI/transform_visualization.ipynb
You can see from the screen shot after view even import numpy as not be executed. Also can see the output from view.
BTW, where can I find the requirement for the notebook, I didn't find it in the requirement. Perhaps I want to try the version which can run in notebook 6.
Thanks!
from tutorials.
Hi @KumoLiu , these improvements have now been released in itkwidgets 1.0a51.
Please try:
docker run -it --ipc=host --rm --net host --gpus all nvcr.io/nvidia/pytorch:24.03-py3
pip install -U notebook
pip install 'itkwidgets[notebook]==1.0a51'
# Start the notebook
from tutorials.
cc @kirbyju @aylward and @thewtex, in case you can shed any light on this issue, it would be greatly appreciated.
Also created a ticket here InsightSoftwareConsortium/itkwidgets#743
Thanks.
from tutorials.
Also tried this notebook with pytorch container: nvcr.io/nvidia/pytorch:24.03-py3.
See the same issue.
https://github.com/InsightSoftwareConsortium/itkwidgets/blob/v1.0a50/examples/integrations/MONAI/transform_visualization.ipynb
from tutorials.
@KumoLiu thanks for the reproducible example!
Addressed here:
InsightSoftwareConsortium/itkwidgets#745
After it is released, it will be better to install itkwidgets in the containers so all javascript is loaded at startup.
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BTW, where can I find the requirement for the notebook, I didn't find it in the requirement. Perhaps I want to try the version which can run in notebook 6.
The dependencies are here:
We keep them as small and light and universal as possible.
from tutorials.
Hi @thewtex, thanks for the quick fix.
I tried with 1.0a51, and the same issue occurred.
In addition, after this command pip install 'itkwidgets[notebook]==1.0a51'
and jupyter notebook
can not even launched correctly.
from tutorials.
@KumoLiu thanks for testing.
I also observed that error in my testing when I tried installing widgetsnbextension
(a different, unrelated package), made for notebook==6 when notebook==7 was installed.
I am wondering if there is something else in your installation?
Could you please try:
docker run -it -p 8888:8888 --ipc=host --rm --net host --gpus all thewtex/monai-1694
or simply build and run the following Dockerfile:
FROM nvcr.io/nvidia/pytorch:24.03-py3
RUN pip install -U notebook
RUN pip install 'itkwidgets[notebook]==1.0a51'
RUN curl -L -o /transform_visualization.ipynb https://raw.github.com/InsightSoftwareConsortium/itkwidgets/main/examples/integrations/MONAI/transform_visualization.ipynb
CMD jupyter notebook /transform_visualization.ipynb
?
You should see:
(there is an issue with the last cell, but I have a fix in progress for that).
from tutorials.
(there is an issue with the last cell, but I have a fix in progress for that).
This was a side-effect of fixing the pandas dependency issue, but it has been addressed in itkwidgets 1.0a52.
from tutorials.
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