Add maisi mask aug example

Project-MONAI / tutorials

MONAI Tutorials

https://monai.io/started.html

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Add maisi mask aug example #1748

Closed guopengf closed 1 month ago

guopengf commented 1 month ago

Fixes # .

Description

Add notebook example for tumor mask augmentation.

Checks

[ ] Avoid including large-size files in the PR.
[ ] Clean up long text outputs from code cells in the notebook.
[ ] For security purposes, please check the contents and remove any sensitive info such as user names and private key.
[ ] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the ./figure folder
[ ] Notebook runs automatically ./runner.sh -t <path to .ipynb file>

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guopengf commented 1 month ago

Hi @KumoLiu, I plan to add an example mask as tutorials/generative/maisi/data/example_mask.nii.gz. Where should I host this file? Shall I put it into https://github.com/Project-MONAI/MONAI-extra-test-data/releases/tag/0.8.1?

KumoLiu commented 1 month ago

Hi @KumoLiu, I plan to add an example mask as tutorials/generative/maisi/data/example_mask.nii.gz. Where should I host this file? Shall I put it into https://github.com/Project-MONAI/MONAI-extra-test-data/releases/tag/0.8.1?

Yes, you can host it there.

guopengf commented 1 month ago

I think we have this error (https://github.com/Project-MONAI/tutorials/actions/runs/9764583292/job/26953264670?pr=1748) because some utility functions have not been merged. So I make it a draft PR first.

guopengf commented 1 month ago

This PR is ready for review once https://github.com/Project-MONAI/tutorials/pull/1749 is merged.

KumoLiu commented 1 month ago

@guopengf seems premerge can not pass, did you run the notebook locally?

guopengf commented 1 month ago

@guopengf seems premerge can not pass, did you run the notebook locally?

Yeah, I can successfully run it locally, as you can see those cell outputs. However, the augmentation functions rely on latest monai core dev branch. I don’t know if this causes problems.

KumoLiu commented 1 month ago

Hi @guopengf, Could you please add the file here https://github.com/Project-MONAI/tutorials/blob/main/runner.sh#L79 to exclude max_epochs check? Thanks. https://github.com/Project-MONAI/tutorials/actions/runs/9788615557/job/27026970836?pr=1748#step:5:610

guopengf commented 1 month ago

Hi @guopengf, Could you please add the file here https://github.com/Project-MONAI/tutorials/blob/main/runner.sh#L79 to exclude max_epochs check? Thanks. https://github.com/Project-MONAI/tutorials/actions/runs/9788615557/job/27026970836?pr=1748#step:5:610

Hi @KumoLiu, thanks for the instruction! All tests are passed.