Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add unet++ notebook #1476

Merged
merged 7 commits into from
Aug 4, 2023

Conversation

nhhung1810
Copy link
Contributor

@nhhung1810 nhhung1810 commented Aug 2, 2023

Fixes #1475.

Description

A few sentences describing the changes proposed in this pull request.

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>

@review-notebook-app
Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

@wyli
Copy link
Contributor

wyli commented Aug 2, 2023

thanks, please follow this https://github.com/Project-MONAI/tutorials/blob/main/CONTRIBUTING.md#create-a-notebook to create the necessary cells, I think you can copy them from https://github.com/Project-MONAI/tutorials/blob/main/modules/UNet_input_size_constrains.ipynb

@nhhung1810 nhhung1810 force-pushed the 1475-unetplusplus-input-shape branch from 5ec357b to ac68e50 Compare August 2, 2023 13:10
@nhhung1810
Copy link
Contributor Author

After several trial, I finally understand the basic process, hope you guy can check on the notebook content :D

@mingxin-zheng
Copy link
Contributor

Thank you @nhhung1810 for the PR. I just started to read the notebook. I noticed that there are many commented code, and the last cell has outputs from all-commented code block. May I know what the commented code is for?

@nhhung1810
Copy link
Contributor Author

Hey @mingxin-zheng , that commented code is for exploration on the implementation of UNET++. I'll delete it after the other things resolved

@wyli
Copy link
Contributor

wyli commented Aug 4, 2023

thanks! would be great to have a conclusion section to recommend the usage, for example, about how to set number of downsampling layers and input spatial sizes, and the normalisation argument might require a tuple for additional parameters https://github.com/Project-MONAI/MONAI/blob/6f5cea3795278c20568261ebb38907d94b576b98/monai/networks/nets/daf3d.py#L490-L491. the current notebook explores many tests but it's unclear to me what are the suitable configurations for this model.

@nhhung1810
Copy link
Contributor Author

Sure @wyli, I'll dig into the original papers and others papers to write the conclusion. Also, I'll include a network image for reference

@nhhung1810
Copy link
Contributor Author

Just add some conclusions to the normalization (also an example of passing norm's argument) and up/down-sampling sections. I also comment about the features argument as I found it have a small difference compare to the paper.

Copy link
Contributor

@wyli wyli left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks, it looks good to me.

@wyli wyli enabled auto-merge (squash) August 4, 2023 17:12
@wyli wyli merged commit 7dfeaec into Project-MONAI:main Aug 4, 2023
5 checks passed
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
Fixes Project-MONAI#1475.

### Description
A few sentences describing the changes proposed in this pull request.

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [x] 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
- [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: nhhung1810 <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

UNET++: input constraint vs. networks configurations
3 participants