Project-MONAI / Project-MONAI/tutorials
Kernel hangs in "TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb"
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Description
Describe the bug
Kernel hangs after itkwidgets visualization in jupyter notebook
https://github.com/Project-MONAI/tutorials/blob/main/model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
To Reproduce
- docker pull projectmonai/monai:latest
- create a new container
- run into container
pip install 'itkwidgets[notebook]>=1.0a49'
from monai.transforms import LoadImage
root_dir = "/opt/monai/workspace/Data"
data_dir = os.path.join(root_dir, "Task09_Spleen")
train_images = sorted(glob.glob(os.path.join(data_dir, "imagesTr", "*.nii.gz")))
out = LoadImage(ensure_channel_first=True)(train_images[0])
view(image=out)
Expected behavior
Kernal will not hangs after using view.
Screenshots
Additional context
- Look similar to this one:
https://github.com/InsightSoftwareConsortium/itkwidgets/issues/688 - 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.
Collecting pandas>=2.0.0 (from dask-image->ngff-zarr[dask-image]>=0.4.3->itkwidgets>=1.0a49->itkwidgets[notebook]>=1.0a49)
Downloading pandas-2.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
cudf 24.2.0 requires pandas<1.6.0dev0,>=1.3, but you have pandas 2.2.2 which is incompatible.
dask-cuda 24.2.0 requires pandas<1.6.0.dev0,>=1.3, but you have pandas 2.2.2 which is incompatible.
dask-cudf 24.2.0 requires pandas<1.6.0dev0,>=1.3, but you have pandas 2.2.2 which is incompatible.
- After install the itkwidgets and exiting the Jupyter notebook, trying to launch the notebook again leads to a configuration error. It appears that the installation of itkwidgets is causing a disruption in the configuration settings.
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 hang in model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb using the listed Docker, Jupyter, LoadImage, and view steps. Compare the itkwidgets-related behavior with issue 688 and check whether the pandas conflicts or notebook configuration error are involved; done means the notebook kernel remains usable after visualization and can be relaunched without the reported configuration error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- data-visualization, devtools
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100