Add SW_FastEdit code

[matt3o]

See this discussion for details, also @diazandr3s

Paper link Link to the full code base.

Current limitations:

• all parameter are currently tuned for AutoPET
• currently inference only, I'll see if I can get training to work
• Pretrained weights only available for AutoPET, can be found here: https://bwsyncandshare.kit.edu/s/Yky4x6PQbtxLj2H , rename it to pretrained_sw_fastedit.pt and put them into the folder radiology/model/. This model was pretrained on tumor-only AutoPET volumes. (where do can upload the weights?)
• main code is not integrated into MONAI, thus some additional transforms have been added

[SachidanandAlle]

Can you fix the precommit checks.. you can run locally to identify the issues..

Please check the contrib guidelines to know the command to run the same locally

[matt3o]

Sure! The code also still contains some debug code which I will remove as well.

On May 13, 2024 12:04:23 AM GMT+02:00, SACHIDANAND ALLE @.***> wrote:

Can you fix the precommit checks.. you can run locally to identify the issues..

Please check the contrib guidelines to know the command to run the same locally

-- Reply to this email directly or view it on GitHub: https://github.com/Project-MONAI/MONAILabel/pull/1689#issuecomment-2106388112 You are receiving this because you authored the thread.

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[matt3o]

@SachidanandAlle Should work with this commit. If you want to try it yourself, use the following weights file https://drive.google.com/file/d/1p59s-ehEyp39vlqULAd1eB8gV4hkmxR0/view?usp=drive_link (I changed the code to use the newer, AutoPET 3rd place ScaleIntensityRangePercentilesd, which helps to make the results more robust)

Please tell me if there is anything else you need.

[SachidanandAlle]

Assigning to @diazandr3s to verify and merge