Error using picai_prep v2

Hi, I was trying to preprocess the data using https://github.com/DIAGNijmegen/picai_baseline/blob/main/src/picai_baseline/prepare_data_semi_supervised.py, but this script currently doesn't work because of the new version of picai_prep. I tried adapting the picai_baseline script mentioned above but there is an error when passing the annotation_preprocess_func as an option in the settings (previosly that was the lbl_preprocess_func argument): jsonschema.exceptions.ValidationError: Additional properties are not allowed ('options' was unexpected) The way I am passing the argument option is directly after the task like this: mha2nnunet_settings["dataset_json"]["task"] = task #(this was not modified) mha2nnunet_settings['options'] = {'annotation_preprocess_func': preprocess_picai_annotation}

And when creating the MHA2nnUNetConverter im passing that object instead of the json path to the mha2nnunet_settings argument and using the new argument names. Those are the only things that I've modified. Is there something i'm doing wrong here?

Thank you for your help!

Hi Jorge,

Thanks for raising this issue! Unfortunately, we indeed broke the preprocessing scripts with the update to picai_prep>=2.0.0. The steps you performed to fix this issue are indeed correct, and I will add the same to the picai_baseline documentation as well.

The error you got after patching prepare_data_semi_supervised.py traces back to the picai_prep>=2.0.0 module. I have proposed a bugfix for this issue, and will update you once this is finished!

Kind regards, Joeran

Hi Jorge,

We have updated the picai_prep module to version 2.0.1, which fixes this issue. I have also updated the Docker container joeranbosma/picai_nnunet:latest to install the updated picai_prep module. I tested this locally, and for me the conversion works again.

To run your preprocessing script, please ensure you pull the latest Docker container (docker pull joeranbosma/picai_nnunet:latest) or install the updated picai_prep module (pip install picai_prep==2.0.1).

The updated scripts (prepare_data.py and prepare_data_semi_supervised.py) are under review by my colleage, and can be found here: https://github.com/DIAGNijmegen/picai_baseline/pull/13.

Please let me know if you run into any other issues!

Kind regards, Joeran