Update modules notebooks to match format requirements

[Nic-Ma]

Description

This PR updated several modules tutorials to match the format requirements of contribution guideline.
CC @mingxin-zheng .

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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[mingxin-zheng]

In tutorials/modules/layer_wise_learning_rate.ipynb, the RSNA Bone Age Challenge link

http://rsnachallenges.cloudapp.net/competitions/4

isn't working for me.

[mingxin-zheng]

In modules/image_dataset.ipynb, there is an extra . after seg in this line:

print("seg. shape:", img_dataset[0][1].shape)

[mingxin-zheng]

In modules/integrate_3rd_party_transforms.ipynb, there is a pip install for itk:

!python -c "import itk" || pip install -q itk==5.1.0

Can it be merged with pip install monai as the following?

!python -c "import monai" || pip install -q "monai-weekly[nibabel, itk]"

Thanks

[mingxin-zheng]

In modules/inverse_transforms_and_test_time_augmentations.ipynb, there are a few duplicated %matplotlib inline and %matplotlib inline (for example, under Display some examples)

[mingxin-zheng]

In Appendix: layers of DenseNet 121 network of modules/layer_wise_learning_rate.ipynb, the network structure is printed out as text outputs. There are 621 lines and is this necessary to keep in the notebook?

[mingxin-zheng]

In modules/mednist_GAN_tutorial.ipynb, the RSNA Bone Age Challenge link needs to be fixed. Also, the notebook has the following line and it seems a bit weird to me. Should it be https://medmnist.com/?

If you use the MedNIST dataset, please acknowledge the source, e.g.
https://github.com/Project-MONAI/tutorials/blob/main/2d_classification/mednist_tutorial.ipynb.

[mingxin-zheng]

In modules/mednist_GAN_workflow_array.ipynb, the following line can use a relative path to the mednist_GAN_tutorial notebook:

"Read the [MONAI Mednist GAN Tutorial](https://github.com/Project-MONAI/tutorials/blob/main/modules/mednist_GAN_tutorial.ipynb) for details about the network architecture and loss functions.\n",

[mingxin-zheng]

In modules/mednist_GAN_workflow_dict.ipynb, the following lines need to use relative path, or replace the link with external site (MedNIST.com)

Read the [MONAI Mednist GAN Tutorial](https://github.com/Project-MONAI/tutorials/blob/main/modules/mednist_GAN_tutorial.ipynb) for details about the network architecture and loss functions.

If you use the MedNIST dataset, please acknowledge the source, e.g.
https://github.com/Project-MONAI/tutorials/blob/main/2d_classification/mednist_tutorial.ipynb.

And the RSNA links is invalid

The MedNIST dataset was gathered from several sets from [TCIA](https://wiki.cancerimagingarchive.net/display/Public/Data+Usage+Policies+and+Restrictions), [the RSNA Bone Age Challenge](http://rsnachallenges.cloudapp.net/competitions/4), and [the NIH Chest X-ray dataset](https://cloud.google.com/healthcare/docs/resources/public-datasets/nih-chest).

[Nic-Ma]

Hi @mingxin-zheng ,

Thanks for your suggestion, I think we need fixed version of ITK in this tutorial, so I didn't change it.

[Nic-Ma]

Hi @mingxin-zheng ,

I have updated the PR according to all your comments.

Thanks for the review.

[mingxin-zheng]

Hi @Nic-Ma , can you try to merge the main branch and see if the relevant notebooks in the PR can pass copyright and guideline tests? Thanks!

[Nic-Ma]

Hi @Nic-Ma , can you try to merge the main branch and see if the relevant notebooks in the PR can pass copyright and guideline tests? Thanks!

I don't see error related to this PR.

Thanks.

[mingxin-zheng]

Hi @Nic-Ma , thanks for the update. I think the pep8 test shows there is an import error in the jupyter_util.ipynb. Can you fix it when you have time?

[mingxin-zheng]

@Nic-Ma a minor fix is needed here:

Running ./modules/jupyter_utils.ipynb
Checking PEP8 compliance...
stdin:45:1: F401 'monai' imported but unused
import monai

I don't see any other issues. Please feel free to merge after the fix if there is no more pep8 failures