KeyError when trying to train in toy_exp

MIC-DKFZ / medicaldetectiontoolkit

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

Apache License 2.0

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KeyError when trying to train in toy_exp #125

Open 17alia opened 3 years ago

17alia commented 3 years ago

I am trying to train using the donuts_shape dataset in the toy_exp and I am getting the following error:

How can I fix this? it looks like the dictionary "batch" has keys 'data', 'seg', 'pid', 'class_target', 'bb_target', and 'roi_masks', but not 'roi_labels'.

Thanks for any help you can provide.

themantalope commented 3 years ago

I'm also having a similar issue.

themantalope commented 3 years ago

I think this is an issue with the batchgenerators repository. The medicaldetectiontoolkit repository expects batchgenerators to be version 0.19.3. If you install the latest version, the output of the generator doesn't include the 'roi_labels' key. Might be worth submitting an issue over there.

themantalope commented 3 years ago

@17alia

pip uninstall batchgenerators
pip install batchgenerators==0.19.3