ModuleNotFoundError: No module named 'blosc2'

[ASHISRAVINDRAN]

Hi @wasserth
I am from the MITK development team working to update TotalSegmentator to v2.4 for our upcoming release.
I am testing out installing TotalSegmentator via MITK and I see that TotalSegmentator has stopped working due to import errors.
Error log:

Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Scripts\TotalSegmentator.exe\__main__.py", line 7, in <module>
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py", line 138, in main
    totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\site-packages\totalsegmentator\python_api.py", line 126, in totalsegmentator
    from totalsegmentator.nnunet import nnUNet_predict_image  # this has to be after setting new env vars
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\site-packages\totalsegmentator\nnunet.py", line 30, in <module>
    from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 22, in <module>
    from nnunetv2.inference.data_iterators import PreprocessAdapterFromNpy, preprocessing_iterator_fromfiles, \
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\site-packages\nnunetv2\inference\data_iterators.py", line 12, in <module>
    from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\site-packages\nnunetv2\preprocessing\preprocessors\default_preprocessor.py", line 25, in <module>
    from nnunetv2.preprocessing.cropping.cropping import crop_to_nonzero
  File "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\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 "C:\DKFZ\TotalSegmentator_work\.venv_7Nov\Lib\site-packages\acvl_utils\cropping_and_padding\bounding_boxes.py", line 5, in <module>
    import blosc2
ModuleNotFoundError: No module named 'blosc2'

Merely pip installing blosc2 leads to even more import errors.
It would be great if you can take a look.

[krekiehn]

same for me

Win10 & Ubuntu
TotalSegmentator 2.4.0
python 3.9

pip freeze:
acvl_utils==0.2.1
batchgenerators==0.25.1
batchgeneratorsv2==0.2.1
certifi==2024.8.30
charset-normalizer==2.0.12
connected-components-3d==3.19.0
contourpy==1.3.0
cycler==0.12.1
dataclasses==0.6
dicom2nifti==2.5.0
dill==0.3.9
dynamic_network_architectures==0.3.1
einops==0.8.0
fft-conv-pytorch==1.2.0
filelock==3.16.1
fonttools==4.54.1
fsspec==2024.10.0
future==1.0.0
graphviz==0.20.3
idna==3.10
imagecodecs==2024.9.22
imageio==2.36.0
importlib_resources==6.4.5
Jinja2==3.1.4
joblib==1.4.2
kiwisolver==1.4.7
lazy_loader==0.4
linecache2==1.0.0
MarkupSafe==3.0.2
matplotlib==3.9.2
mpmath==1.3.0
multiprocess==0.70.17
networkx==3.2.1
nibabel==5.3.2
nnunetv2==2.5.1
numpy==1.26.4
nvidia-cublas-cu12==12.4.5.8
nvidia-cuda-cupti-cu12==12.4.127
nvidia-cuda-nvrtc-cu12==12.4.127
nvidia-cuda-runtime-cu12==12.4.127
nvidia-cudnn-cu12==9.1.0.70
nvidia-cufft-cu12==11.2.1.3
nvidia-curand-cu12==10.3.5.147
nvidia-cusolver-cu12==11.6.1.9
nvidia-cusparse-cu12==12.3.1.170
nvidia-nccl-cu12==2.21.5
nvidia-nvjitlink-cu12==12.4.127
nvidia-nvtx-cu12==12.4.127
opencv-python==4.10.0.84
p_tqdm==1.4.2
packaging==24.2
pandas==2.2.3
pathos==0.3.3
pillow==11.0.0
pkg_resources==0.0.0
pox==0.3.5
ppft==1.7.6.9
pyarrow==18.0.0
pydicom==2.4.4
pyparsing==3.2.0
python-dateutil==2.9.0.post0
python-gdcm==3.0.24.1
pytz==2024.2
PyYAML==6.0.2
requests==2.27.1
rt-utils==1.2.7
scikit-image==0.24.0
scikit-learn==1.5.2
scipy==1.13.1
seaborn==0.13.2
SimpleITK==2.4.0
six==1.16.0
sympy==1.13.1
threadpoolctl==3.5.0
tifffile==2024.8.30
torch==2.5.1
torchaudio==2.5.1
torchvision==0.20.1
TotalSegmentator==2.4.0
tqdm==4.67.0
traceback2==1.4.0
triton==3.1.0
typing_extensions==4.12.2
tzdata==2024.2
unittest2==1.1.0
urllib3==1.26.20
xvfbwrapper==0.2.9
yacs==0.1.8
zipp==3.20.2

[krekiehn]

here is a solution from nnunet repo:

MIC-DKFZ/nnUNet#2589 (comment)

[mibadev]

Do you have blosc2 installed in your venv? Activate your venv than check
pip install blosc2
test install
python -c "import blosc2"

[ASHISRAVINDRAN]

I see this issue is mostly fixed now, except on Python 3.9.
I believe this comes from acvl_utils v0.2.2. See: MIC-DKFZ/acvl_utils@4cad0de
where the blosc2>=3.0.0b4 is needed as dependency. A pip wheel doesn't seem exist for blosc>2.5 on Python 3.9.
This renders TotalSegmentator not working on python 3.9