730 retinal oct rpd segmentation

[ybagdasa]

Fixes # .

Description

This is a proposed segmentation model to add to the model zoo.

Status

Ready for review/work in progress.

Please ensure all the checkboxes:

• Codeformat tests passed locally by running ./runtests.sh --codeformat.
• In-line docstrings updated.
• Update version and changelog in metadata.json if changing an existing bundle.
• [ x] Please ensure the naming rules in config files meet our requirements (please refer to: CONTRIBUTING.md).
• [x ] Ensure versions of packages such as monai, pytorch and numpy are correct in metadata.json.
• [x ] Descriptions should be consistent with the content, such as eval_metrics of the provided weights and TorchScript modules.
• [x ] Files larger than 25MB are excluded and replaced by providing download links in large_file.yml.
• [ x] Avoid using path that contains personal information within config files (such as use /home/your_name/ for "bundle_root").

[ybagdasa]

@yiheng-wang-nv here is my draft PR

[yiheng-wang-nv]

Hi @ybagdasa , could you fix the commit for the detectron2 installation?

[ybagdasa]

@yiheng-wang-nv Thanks for considering the contribution. For the detectron2 installation, what is the command I should run to replicate the error you're getting? I know that the install works for python<3.10. Could this be the source of the issue for the ci install checks?

[yiheng-wang-nv]

Hi @ybagdasa ,

For the comment of this line (python -m pip install 'git+https://github.com/facebookresearch/detectron2.git'),
based on https://github.com/Project-MONAI/model-zoo/pull/748/files#diff-6d26dc7c0d9fa894d66c944bd9d0a7c970f95371163c70631b8d6b0ed790fc81R19 detectron2 0.6 is used, thus here we can modify the install command into:

python -m pip install 'git+https://github.com/facebookresearch/detectron2.git@v0.6'

Otherwise, the command will install the latest commit, which may have incompatible issues in the future.

[yiheng-wang-nv]

For the python version, can you confirm if python 3.9 is necessary?
I'm not 100% sure, but based on https://detectron2.readthedocs.io/en/latest/tutorials/install.html#requirements , it only requires to use python >= 3.7.

Currently, our repo uses python 3.10 in default for CI tests. If we do need python 3.9 for this bundle, I may consider some changes in the CI to support multiple python versions.

[yiheng-wang-nv]

For the CI error: https://github.com/Project-MONAI/model-zoo/actions/runs/14742610327/job/42137993317?pr=748#step:7:510 Let me push a commit to your branch to fix it. Since detectron2 cannot simply be installed via pip install detectron2, we should consider some changes in:
https://github.com/Project-MONAI/model-zoo/blob/dev/ci/get_bundle_requirements.py#L54

[yiheng-wang-nv]

Since I don't have the permission to push to your forked repo directly, I pushed the changes into: https://github.com/Project-MONAI/model-zoo/tree/730-retinalOCT_RPD_segmentation, could you help to merge it?
The branch also fixed the pre-commit ci errors.

Then we can see if there are other issues in the dependencies.

[ybagdasa]

For the python version, can you confirm if python 3.9 is necessary? I'm not 100% sure, but based on https://detectron2.readthedocs.io/en/latest/tutorials/install.html#requirements , it only requires to use python >= 3.7.

Currently, our repo uses python 3.10 in default for CI tests. If we do need python 3.9 for this bundle, I may consider some changes in the CI to support multiple python versions.

My attempts to build the detectron2 wheel failed with python 3.10 and it unfortunately seems to be a common issue with their repo: facebookresearch/detectron2#5445

[yiheng-wang-nv]

Thanks, let me enable py3.9 in the CI

[yiheng-wang-nv]

Hi @ybagdasa , thanks for the PR contribution. For pre-commit CI errors, could you fix them? The auto-push seems cannot work since the branch is pushed from an organization account.

[yiheng-wang-nv]

Format test can be fixed according to: https://github.com/Project-MONAI/model-zoo/actions/runs/14742610314/job/42137993243?pr=748#step:7:67

[yiheng-wang-nv]

I will look at this PR later this week

[ybagdasa]

Format test can be fixed according to: https://github.com/Project-MONAI/model-zoo/actions/runs/14742610314/job/42137993243?pr=748#step:7:67

@yiheng-wang-nv When running flake8 on the code it flags a lot of mixed-case naming conventions (N800 flags). A lot of the naming comes from the pycocotools api which used mixed-case naming for functions and variables. Having everything lowercase will probably hinder the readability of the code at this point. Is this a strict requirement or can I somehow skip it?

[yiheng-wang-nv]

We may not need the requirements.txt file in the bundle, it's content is included in the metadata.json.
Our CI can generate the requirements file directly via: https://github.com/Project-MONAI/model-zoo/blob/dev/ci/get_bundle_requirements.py#L54

[yiheng-wang-nv]

Format test can be fixed according to: https://github.com/Project-MONAI/model-zoo/actions/runs/14742610314/job/42137993243?pr=748#step:7:67

@yiheng-wang-nv When running flake8 on the code it flags a lot of mixed-case naming conventions (N800 flags). A lot of the naming comes from the pycocotools api which used mixed-case naming for functions and variables. Having everything lowercase will probably hinder the readability of the code at this point. Is this a strict requirement or can I somehow skip it?

Hi @ybagdasa , sorry I cannot see the error you mentioned, the error I saw is from isort, could you fix it first? Then we can see the other checks like black and flake8

[ybagdasa]

@yiheng-wang-nv
I merged your changes with my fixes on my organization repo and gave you write privileges for the repo. I fixed all the formatting issues detected by runtests.sh except for the mixed-case ones from flake8. I also added torchvision to metadata.json since that is required.

[yiheng-wang-nv]

Hi @ybagdasa , thanks for the updates and providing me the permissions. I pushed a commit to fix the black and pre-commit issues. Now, our CI can reach to the flake8 errors: https://github.com/Project-MONAI/model-zoo/actions/runs/15105923819/job/42454628204?pr=748

I think we can skip N802, N803 and N806 errors, but others may need to be solved

[yiheng-wang-nv]

Hi @ybagdasa , thanks for the updates and providing me the permissions. I pushed a commit to fix the black and pre-commit issues. Now, our CI can reach to the flake8 errors: https://github.com/Project-MONAI/model-zoo/actions/runs/15105923819/job/42454628204?pr=748

I think we can skip N802, N803 and N806 errors, but others may need to be solved

Hi @ybagdasa , I updated, and could you help to resolve other issues? Like line too long (https://github.com/Project-MONAI/model-zoo/actions/runs/15106735909/job/42456940644?pr=748)

[ybagdasa]

Hi @ybagdasa , thanks for the updates and providing me the permissions. I pushed a commit to fix the black and pre-commit issues. Now, our CI can reach to the flake8 errors: https://github.com/Project-MONAI/model-zoo/actions/runs/15105923819/job/42454628204?pr=748
I think we can skip N802, N803 and N806 errors, but others may need to be solved

Hi @ybagdasa , I updated, and could you help to resolve other issues? Like line too long (https://github.com/Project-MONAI/model-zoo/actions/runs/15106735909/job/42456940644?pr=748)

@yiheng-wang-nv I was able to do ./runtests.sh up through pytype. The error popped up here:
[163/167] check models.maisi_ct_generative.scripts.rectified_flow