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Optional Torch Multiprocessing in nnUNet for Improved Security and Compatibility #2614

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Optional Torch Multiprocessing in nnUNet for Improved Security and Compatibility #2614

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@LennyN95 LennyN95 commented Nov 22, 2024 •
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This PR resolves #2556.

  • Implementation of preprocessing based on a single process
  • Introduce new environment variables to set -npp and -nps

We have done some internal testing and get identical results between the latest nnunetv2==2.5.1 and with our proposed patch.

surajpaib and others added 6 commits November 21, 2024 08:15
@surajpaib
Non-mp predict support [WIP]
69fd9a7
@LennyN95
add torchification
a595f64
@LennyN95
update preprocess_fromfiles_noqueue
6cb4e7a
@LennyN95
dev-only: remove enforced num_processes = 1
b570e8a
@LennyN95
add env to overwrite npp and nps
3628055 
New environment variables:
- nnUNet_npp
- nnUNet_nps

Default values remain unchanged, cli parameter -npp and -nps overwrite environment variables if set.
@surajpaib
Fix preprocessor initialization order
6bcec21
@LennyN95
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@FabianIsensee I have noticed some (significant) differences between nnunetv2==2.0 and nnunetv2==2.5.1. This is beyond the scope of this topic / PR, but since some of our contributors have used this version, we'd like to see if and to what extent we can offer them a solution as well. In general, I am curious if you have any idea what changes might have led to these differences (we are talking about a Dice score of 0.9451 between these versions for a lung nodule segmentation task).

@FabianIsensee FabianIsensee self-assigned this Nov 22, 2024
@LennyN95 LennyN95 mentioned this pull request Nov 29, 2024
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Optional Torch Multiprocessing in nnUNet for Improved Security and Compatibility
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@LennyN95 @FabianIsensee @surajpaib