ImportError

[tmfoley24]

I recently had to uninstall then reinstall Ubuntu and Comp2Comp. After reinstalling I received the error below using the spine and liver_spleen_pancreas pipelines. Does anyone know how I might be able to fix this error?

Traceback (most recent call last):
File "/root/Comp2Comp/comp2comp/utils/process.py", line 131, in process_3d
pipeline(output_dir=output_dir, model_dir=model_dir)
File "/root/Comp2Comp/comp2comp/inference_pipeline.py", line 73, in call
output = inference_class(inference_pipeline=self, **output)
File "/root/Comp2Comp/comp2comp/liver_spleen_pancreas/liver_spleen_pancreas.py", line 27, in call
seg = self.organ_seg(
File "/root/Comp2Comp/comp2comp/liver_spleen_pancreas/liver_spleen_pancreas.py", line 51, in organ_seg
seg = totalsegmentator(
File "/root/miniconda3/envs/c2c_env/lib/python3.9/site-packages/totalsegmentatorv2/python_api.py", line 77, in totalsegmentator
from totalsegmentatorv2.nnunet import nnUNet_predict_image # this has to be after setting new env vars
File "/root/miniconda3/envs/c2c_env/lib/python3.9/site-packages/totalsegmentatorv2/nnunet.py", line 24, in
from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor
File "/root/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunetv2/inference/predict_from_raw_data.py", line 22, in
from nnunetv2.inference.data_iterators import PreprocessAdapterFromNpy, preprocessing_iterator_fromfiles,
File "/root/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunetv2/inference/data_iterators.py", line 12, in
from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor
File "/root/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 23, in
from nnunetv2.preprocessing.cropping.cropping import crop_to_nonzero
File "/root/miniconda3/envs/c2c_env/lib/python3.9/site-packages/nnunetv2/preprocessing/cropping/cropping.py", line 5, in
from acvl_utils.cropping_and_padding.bounding_boxes import get_bbox_from_mask, crop_to_bbox, bounding_box_to_slice
ImportError: cannot import name 'crop_to_bbox' from 'acvl_utils.cropping_and_padding.bounding_boxes' (/root/miniconda3/envs/c2c_env/lib/python3.9/site-packages/acvl_utils/cropping_and_padding/bounding_boxes.py)

[giemmecci]

I've had a similar issue two days ago, and my conclusion was that it probably has to do with recent changes introduced in the bounding_boxes.py file here:

https://github.com/MIC-DKFZ/acvl_utils/tree/master/acvl_utils/cropping_and_padding

And I think this discussion is related:

https://github.com/MIC-DKFZ/acvl_utils/issues/4

I put a temporary fix to it by replacing the whole acvl_utils folder at the location below from a previous installation of comp2comp:

/anaconda3/envs/c2c_env/lib/python3.9/site-packages/acvl_utils

Further discussion also here (it has the same error message I was getting):

https://github.com/MIC-DKFZ/nnUNet/issues/2589#issuecomment-2464528411

And this seems to be the solution that worked for most:

https://github.com/MIC-DKFZ/nnUNet/issues/2589#issuecomment-2464528411