SSL Tutorial updated as being notebooks

[finalelement]

Signed-off-by: Vishwesh Nath [email protected]

Converts the python scripts to being jupyter notebooks that are reflected in MONAI Toolkit.

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See visual diffs & provide feedback on Jupyter Notebooks.

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[mingxin-zheng]

Thank you @finalelement for the PR!

• Regarding the license header, we slightly modify the template to fit Jupyter notebooks. Please copy it from here for the exact format.
• The Contributing guidelines require "## Setup environment" and "Setup imports" cells to standardize the notebook, and ease the packing of the toolkit. Can we ensure the notebooks following the guidelines here?
• Because there is no automatic download of the dataset, the notebooks needs to be excluded from the CI/CD papermill test. Can you refer to here for how to fix it?

[finalelement]

@mingxin-zheng I've tried addressing all the comments. Please see if there is anything more that I can do from my side.

[mingxin-zheng]

The comments above should fix these relevant check failures in build/guidelines:

• Error: Missing the "Setup imports" after the first code cell of file: /home/runner/work/tutorials/tutorials/self_supervised_pretraining/ssl_finetune.ipynb.
• Error: print_config() cannot be found after the "Setup imports" markdown cell in file: /home/runner/work/tutorials/tutorials/self_supervised_pretraining/ssl_finetune.ipynb.
• Error: Missing the "Setup imports" after the first code cell of file: /home/runner/work/tutorials/tutorials/self_supervised_pretraining/ssl_train.ipynb.
• Error: print_config() cannot be found after the "Setup imports" markdown cell in file: /home/runner/work/tutorials/tutorials/self_supervised_pretraining/ssl_train.ipynb.

But there are some errors in build/pep8 that needs attention:

Checking PEP8 compliance...
stdin:290:13: B007 Loop control variable 'step' not used within the loop body. If this is intended, start the name with an underscore.
        for step, batch in enumerate(epoch_iterator_val):
            ^
Error: Try running with autofixes: --autofix.

Check failed!
Running ./self_supervised_pretraining/ssl_train.ipynb
Checking PEP8 compliance...
stdin:88:10: B007 Loop control variable 'each_d' not used within the loop body. If this is intended, start the name with an underscore.
for idx, each_d in enumerate(train_data):
         ^
stdin:91:10: B007 Loop control variable 'each_d' not used within the loop body. If this is intended, start the name with an underscore.
for idx, each_d in enumerate(val_data):
         ^
Error: Try running with autofixes: --autofix.

[mingxin-zheng]

Because the SSL notebooks are created in this PR, the notebook list in README.md should also be updated.

[finalelement]

Addressed all comments again, lets see if the tests work out this time.

[finalelement]

The 2 failing tests are from other prior notebooks. Let me know if more changes are needed to the SSL notebooks.

[mingxin-zheng]

Thank you @finalelement . It looks good to me!