Import MisalignTransform fails with current version

[ndebs]

Hi,

I followed the instructions for installing misalignement depedencies with:

https://github.com/MIC-DKFZ/misalignment_DA.git
cd misalignment-DA
pip install -e .

but it failed when I launch nnUNet with nnUNetTrainer_Misalign trainer:
nnUNetv2_train 001 3d_fullres 0 -tr nnUNetTrainer_Misalign --npz

MisalignTransform could not be imported from /batchgenerators/transforms/spatial_transforms.py. Actually, spatial_transforms.py was exactly the same as the one on nnUNet_v2 master branch, and did not contain 'MisalignTransform' class.

I tried then to force the installation of batchgenerators with a recent version (v 0.23.2 should contain Misalignment data augmentation), but it didn't worked either.

Best regards,

Noëlie

[Kobalt93]

Hi Noëlie,
strange, I will doublecheck it, could you please try this command?: pip install --upgrade --force-reinstall git+https://github.com/MIC-DKFZ/batchgenerators.git
Let me know it it doesnt work.

[ndebs]

Hi,
Thanks for your answer! by forcing batchgenerator install it worked !

[Kobalt93]

Happy for hearing that :))

[alexandreroutier]

Hi @Kobalt93,

I had the same issue than Noëlie and I was wondering if MIC-DKFZ/batchgenerators#122 would solve this issue?

Best,
Alex