Sequential Inference (Non-MP)

[LennyN95]

This PR resolves #2556.
Improved implementation following #2614.

• Implementation of preprocessing based on a single process
• Introduce new environment variables nnUNet_npp and nnUNet_nps to set -npp and -nps
• Using the new use predict_from_files_sequential function

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

[LennyN95]

@FabianIsensee, did you find a moment to look into this? The changes are minimal but necessary to use your new sequential function from the CLI. Let me know if there's anything I can do to expedite the process or assist in any other way.

Once resolved, we can proceed with implementing the following models:

• BAMF NNUnet Lung and Nodules (v2) MHubAI/models#92
• BAMF MR Brain tumor segmentation MHubAI/models#93
• BAMF Liver and Tumor segmentation MHubAI/models#84
• [FEAT]: BAMF nnUNet Breast MR Model MHubAI/models#82

[LennyN95]

@FabianIsensee Hi Fabian, I know times are busy. This PR includes minimal changes to enable the use of your new non-parallel inference from the CLI. I would appreciate it if you could take a quick look or suggest a rough timeline.

Thank you and best, Leo.

[FabianIsensee]

Hey, sorry for being so slow 😅. Looks great, thank you for this addition! Many will be happy to have this!