The nnUNet team has released a new version of the nnUNet, called nnUNetv2 python code. Currently, in beta, this needs to be tested with MITK.
Code: https://phabricator.mitk.org/source/nnunet/browse/nnunet_remake/
Interface-wise, the commands like nnUNet_predict etc. are expected to remain the same. Nevertheless, this would require a sanity test.
Main points to test:
- The concept of .pkl will be migrated to JSON files in the new nnUNet(v2). Currently, MITK contains a python snippet to look into .pkl files and dump the necessary info in an arbitrary mitk_export.json file. We need to test and probably, adapt to the change from the nnUNet side.
- Currently, MITK asks nnUnet to dump available models' information (to download) as a JSON file and then, parses from the file. Test if this is dumped correctly.