mednist_app:latest -- No module named 'nibabel'

[Leengit]

I am trying to run the Jupyter lab notebook 02_mednist_app.ipynb on my local machine but the invocation of

!monai-deploy run mednist_app:latest input output

is giving me ModuleNotFoundError: No module named 'nibabel'. Thoughts?

To reproduce:

sudo apt install cuda=11.3.1-1 libcudnn8-dev=8.2.1.32-1+cuda11.3 libcudnn8=8.2.1.32-1+cuda11.3
python3 -m venv ~/venv/mednist
source ~/venv/mednist/bin/activate
pip install -U pip setuptools wheel ipykernel
python -m ipykernel install --user --name=mednist
pip install -U torch torchvision torchaudio ipywidgets 'monai[pillow, tqdm, ignite, gdown, nibabel]' \
    monailabel monai-deploy-app-sdk pandas transformers mlflow \
    --extra-index-url https://download.pytorch.org/whl/cu113
# Then run the whole notebook using the `mednist` kernel

The full output from !monai-deploy run mednist_app:latest input output is

Checking dependencies...
--> Verifying if "docker" is installed...

--> Verifying if "mednist_app:latest" is available...

Checking for MAP "mednist_app:latest" locally
"mednist_app:latest" found.

Reading MONAI App Package manifest...
--> Verifying if "nvidia-docker" is installed...

Traceback (most recent call last):
  File "/opt/monai/app/mednist_classifier_monaideploy.py", line 13, in <module>
    import monai.deploy.core as md  # 'md' stands for MONAI Deploy (or can use 'core' instead)
  File "/root/.local/lib/python3.8/site-packages/monai/__init__.py", line 43, in <module>
    load_submodules(sys.modules[__name__], False, exclude_pattern=excludes)
  File "/root/.local/lib/python3.8/site-packages/monai/utils/module.py", line 187, in load_submodules
    mod = import_module(name)
  File "/opt/conda/lib/python3.8/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/root/.local/lib/python3.8/site-packages/monai/deploy/operators/__init__.py", line 39, in <module>
    from .stl_conversion_operator import STLConversionOperator, STLConverter
  File "/root/.local/lib/python3.8/site-packages/monai/deploy/operators/stl_conversion_operator.py", line 19, in <module>
    import nibabel as nib
ModuleNotFoundError: No module named 'nibabel'

ERROR: MONAI Application "mednist_app:latest" failed.

Versions are:

Python 3.8.10
MONAI version: 0.8.1
Numpy version: 1.22.4
Pytorch version: 1.11.0+cu113
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 71ff399a3ea07aef667b23653620a290364095b1
Pytorch Ignite version: 0.4.8
Nibabel version: 3.2.2
scikit-image version: 0.19.2
Pillow version: 9.1.1
Tensorboard version: 2.9.0
gdown version: 4.4.0
TorchVision version: 0.12.0+cu113
tqdm version: 4.64.0
lmdb version: 1.3.0
psutil version: 5.9.1
pandas version: 1.4.2
einops version: 0.3.2
transformers version: 4.19.2
mlflow version: 1.26.1

REPOSITORY               TAG         IMAGE ID       CREATED          SIZE
mednist_app              latest      361424005b6f   17 minutes ago   15.5GB
<none>                   <none>      114e7e0380f6   20 hours ago     15.5GB
nvcr.io/nvidia/pytorch   21.07-py3   7beec3ff8d35   10 months ago    15GB

Thanks in advance!

[dbericat]

Thanks for your question. I created issue #302 and assigned a couple people. Will find the problem soon!

Did you try to run any of the other Jupyter tutorials? Were you successful?

[Leengit]

I did not look at the other Jupyter tutorials. Thank you @dbericat for creating #302. Let's continue any discussion there.