TotalSegmentator Failed to compute results....returned non-zero exit status 1

jamesobutler · November 9, 2024, 5:04pm

It appears MIC-DFZ has messed up their packages with a recent new dependency release. See the following link below for details:

github.com/MIC-DKFZ/acvl_utils

broken nnunetv2 import

opened 12:44PM - 07 Nov 24 UTC

jeandre-db

ImportError: cannot import name 'crop_to_bbox' from 'acvl_utils.cropping_and_pad…ding.bounding_boxes' (/local_disk0/.ephemeral_nfs/cluster_libraries/python/lib/python3.11/site-packages/acvl_utils/cropping_and_padding/bounding_boxes.py) File <command-1458388170907476>, line 7 5 import pyspark.sql.functions as f 6 from nnunetv2.imageio.simpleitk_reader_writer import SimpleITKIO ----> 7 from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor 8 from nnunetv2.paths import nnUNet_results, nnUNet_raw 9 import torch It seems that the update to acvl broke nnunetv2 imports. locking the version to 0.2 fixes this issue.

github.com/MIC-DKFZ/nnUNet

`nnunetv2.inference` crashes on import (`No module named 'blosc2'`) due to buggy `acvl_utils` release

opened 05:31PM - 07 Nov 24 UTC

joshuacwnewton

Traceback: ``` File "/home/runner/sct_0.0/spinalcordtoolbox/deepseg/infere…nce.py", line 27, in <module> import spinalcordtoolbox.deepseg.nnunet as ds_nnunet File "/home/runner/sct_0.0/spinalcordtoolbox/deepseg/nnunet.py", line 13, in <module> from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor # noqa: E402 File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/inference/predict_from_raw_data.py", line 22, in <module> from nnunetv2.inference.data_iterators import PreprocessAdapterFromNpy, preprocessing_iterator_fromfiles, \ File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/inference/data_iterators.py", line 12, in <module> from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 23, in <module> from nnunetv2.preprocessing.cropping.cropping import crop_to_nonzero File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/preprocessing/cropping/cropping.py", line 5, in <module> from acvl_utils.cropping_and_padding.bounding_boxes import get_bbox_from_mask, crop_to_bbox, bounding_box_to_slice File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/acvl_utils/cropping_and_padding/bounding_boxes.py", line 5, in <module> import blosc2 ModuleNotFoundError: No module named 'blosc2' ``` This is a duplicate of https://github.com/MIC-DKFZ/acvl_utils/issues/2, but I'm re-reporting here just in case anyone else runs into this bug and tries to find it by checking nnUNet's issues.

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TotalSegmentator Failed to compute results....returned non-zero exit status 1

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