1090-enhance-tutorials

[binliunls]

Signed-off-by: binliu [email protected]

Fixes #1090 .

Description

Fix some basic problems occured during test.

Checks

• Reconstruction tutorial:

  • some typo and grammar problems in the readme file.
  • fastmri_ssim.py absents in varnet_demo folder.
  • the checkpoint device directly map to 'cpu' in unet_demo/inference.ipynb.

• Detection tutorial:

  • some typo, link and grammar problems in the readme file.

• CAI tutorial:

  • add explanation for opencv codec error in the video_seg tutorial.
  • use EnsureChannelFirst instead of AsChannelFirst in endoscopic inbody classification tutorial.
  • accuracy in endoscopic inbody classfication tutorial should be a number instead of tensor.

• Pathology tutorial:

  • some useless cell output in nuclick tutorial.

• Add license to above tutorials

• Check license in other tutorials

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[mingxin-zheng]

Hi @binliunls . Thank you for the PR and making changes on so many files. Below are my comments.

For paired_lung_ct.ipynb:

• I suggest to re-run the notebook to get rid of the warning message

  UserWarning: This DataLoader will create 4 worker processes in total. Our suggested max number of worker in current system is 2,
  

  /usr/local/lib/python3.7/dist-packages/monai/networks/blocks/warp.py:69: UserWarning: monai.networks.blocks.Warp: Using PyTorch native grid_sample.
  warnings.warn("monai.networks.blocks.Warp: Using PyTorch native grid_sample.")
  

• The last markdown should be ## Cleanup data directory
• There is a difference between toolkit and tutorial on the extract_level of the LocalNet

[binliunls]

• There is a difference between toolkit and tutorial on the extract_level of the LocalNet

Hi @wyli,
I saw you updat this extract_level parameter in the last commit of the paired_lung_ct tutorial. I think we need to update the toolkit with this change. Could you please help me to double check that? cc: @mingxin-zheng

Thanks,
Bin

[wyli]

• There is a difference between toolkit and tutorial on the extract_level of the LocalNet

Hi @wyli, I saw you updat this extract_level parameter in the last commit of the paired_lung_ct tutorial. I think we need to update the toolkit with this change. Could you please help me to double check that? cc: @mingxin-zheng

sure, in monai v1.1.0 we released a bug fix (Project-MONAI/MONAI@c8ef7fe ), and the fix broke the tutorial (ticket #1056), then I fixed the tutorial with this update (5d490ea).

[binliunls]

In video_seg.ipynb, does the Video work in general settings? @binliunls

Video(inferred_vid, embed=True, height=300)

Hi @mingxin-zheng ,
In all cases I have met, this Video part doesn't work. However, this feature is added by @rijobro . We'd better confirm this with him. If it's not necessary we can delete this part. How do you think about this @rijobro .

Thanks,
Bin

[rijobro]

Hi, video doesn't appear to be working for me, either. This stackoverflow post has a few ideas on how to fix if anyone wants to give those a go: https://stackoverflow.com/a/68381044/12411867.

[mingxin-zheng]

Hi, video doesn't appear to be working for me, either. This stackoverflow post has a few ideas on how to fix if anyone wants to give those a go: https://stackoverflow.com/a/68381044/12411867.

Hi @rijobro @binliunls , if it needs some tweaking to get it work, how about removing this code cell, or replace it by other solutions, such as writing a video file?

[rijobro]

I'd be grateful if someone wanted to invest some time to get it working in some capacity. The purpose of the notebook is to segment a video, so it's a shame to not then show the segmented video at the end.

We could save it to file and allow the user to view externally, but this requires more effort from the user, so fewer people will review the video, especially if using Google Colab or jupyter notebook over SSH.

[mingxin-zheng]

@binliunls did you try to resolve this issue? I remember we had similar conversations a month or two ago about this Video plugin.

@rijobro
We can make this in a new bug fix PR and assign/volunteer ourselves to fix this. One thing that worries me is that we can't keep a code block in the executable area of the notebook when we know it doesn't work for most cases... So I'd prefer to make this a plan in a PR rather than keeping a bug in a notebook....

[rijobro]

I'm definitely ok to have a separate issue/pr to fix the video playback! Don't think it should be deleted from the source code in this pr though - - it'll mess up the diff to delete something and then add it back in.