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NKI-AI / ahcore

Ahcore is the AI for Oncology core computational pathology toolkit
Apache License 2.0
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Wrong typing in the initialization of H5 callback #57

Closed AjeyPaiK closed 7 months ago

AjeyPaiK commented 7 months ago

Describe the bug When we initialize the H5FileImageWriter callback, the default types for NormalizationType and InferencePrecison are set in this way:

https://github.com/NKI-AI/ahcore/blob/25cfc2c4d03ea351f2870288b1fba554bfd6adb8/ahcore/callbacks/h5_callback.py#L26-L27

This throws an error when the config files contain no values for these parameters:

image

To Reproduce Run either the segmentation training or the inference in ahcore without specifying values for InferencePrecision and NormalizationTypes in the callback config files.

Expected behavior NA

Environment dlup version: 0.3.35 How installed: pip Python version: 3.10 Operating System: Linux

Additional context NA