denseCRF3D import error

[rijobro]

In a clean conda environment, I did the following to install MONAILabel (wanted it from source so I could use my branch)

conda create -n monai-label python=3.9 -y
conda activate monai-label
conda install pytorch cudatoolkit=11.3 -c pytorch -y
cd <path/to/MONAILabel>
pip install -e .

Then the following line causes an error

python -c "monailabel start_server ..."

And more specifically, so does the following

python -c "from monailabel.scribbles.transforms import denseCRF3D"

Both times the error is as follows:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/rich/Documents/Code/MONAILabel/monailabel/scribbles/transforms.py", line 16, in <module>
    import denseCRF3D
ImportError: /home/rich/miniconda3/envs/monai-label/lib/python3.9/site-packages/denseCRF3D.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZSt28__throw_bad_array_new_lengthv

Any idea what's going on?

[SachidanandAlle]

@masadcv can you help and unblock @rijobro

[SachidanandAlle]

until @masadcv responds.. you can disable the scribbles

For example:
https://github.com/Project-MONAI/MONAILabel/blob/main/sample-apps/deepedit/main.py#L27
https://github.com/Project-MONAI/MONAILabel/blob/main/sample-apps/deepedit/main.py#L143-L146

[SachidanandAlle]

@masadcv can you handle the import error and automatically exclude scribbles in the app if import fails due to xyz reasons..

[diazandr3s]

Thanks, @rijobro for reporting this.
I agree with @SachidanandAlle. Please comment those lines out while this issue is solved.
There is another conversation around simpleCRF here.
Let's see how this progress :)

[masadcv]

Thanks @SachidanandAlle and @diazandr3s !
I am looking into this.

@rijobro this error is coming from SImpleCRF installation - I am unsure why it is causing this. As Andres mentioned, there is another ticket to resolve some installation issues with SimpleCRF on windows.

For now, the easiest and quickest solution would be to make these optional_import (unless I am missing something). This means you will lose Scribbles functionality, but be able to get around the errors and use everything else until we find a fix. I will add a PR to do this for all SimpleCRF imports

[rijobro]

Ok all will disable Scribbles for the time being, thanks for the help!