Windows Installation: OpenCV Configuration File Missing

[FlynnOConnell]

Following the new(ish) caiman install steps for Windows on miniforge3:

conda create -n caiman python=3.11 pip vs2019_win-64 && conda activate caiman
conda activate caiman
git clone <caiman url> 
cd caiman
pip install .

Importing caiman results in an error with opencv:

In [2]: import caiman as cm
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[2], line 1
----> 1 import caiman as cm

File ~\repos\CaImAn\caiman\__init__.py:4
      1 #!/usr/bin/env python
      3 import pkg_resources
----> 4 from caiman.base.movies import movie, load, load_movie_chain, _load_behavior, play_movie
      5 from caiman.base.timeseries import concatenate
      6 from caiman.cluster import start_server, stop_server

File ~\repos\CaImAn\caiman\base\movies.py:9
      1 #!/usr/bin/env python
      3 """ Suite of functions that help manage movie data
      4
      5 Contains the movie class.
      6
      7 """
----> 9 import cv2
     10 from functools import partial
     11 import h5py

File ~\miniforge3\envs\caiman\Lib\site-packages\cv2\__init__.py:181
    176             if DEBUG: print("Extra Python code for", submodule, "is loaded")
    178     if DEBUG: print('OpenCV loader: DONE')
--> 181 bootstrap()

File ~\miniforge3\envs\caiman\Lib\site-packages\cv2\__init__.py:112, in bootstrap()
    109         raise ImportError('OpenCV loader: missing configuration file: {}. Check OpenCV installation.'.format(fnames))
    111 load_first_config(['config.py'], True)
--> 112 load_first_config([
    113     'config-{}.{}.py'.format(sys.version_info[0], sys.version_info[1]),
    114     'config-{}.py'.format(sys.version_info[0])
    115 ], True)
    117 if DEBUG: print('OpenCV loader: PYTHON_EXTENSIONS_PATHS={}'.format(str(l_vars['PYTHON_EXTENSIONS_PATHS'])))
    118 if DEBUG: print('OpenCV loader: BINARIES_PATHS={}'.format(str(l_vars['BINARIES_PATHS'])))

File ~\miniforge3\envs\caiman\Lib\site-packages\cv2\__init__.py:109, in bootstrap.<locals>.load_first_config(fnames, required)
    107     return True
    108 if required:
--> 109     raise ImportError('OpenCV loader: missing configuration file: {}. Check OpenCV installation.'.format(fnames))

ImportError: OpenCV loader: missing configuration file: ['config-3.11.py', 'config-3.py']. Check OpenCV installation.

---

I've tried installing opencv with conda install conda-forge::opencv, then I get partially initialized module:

Traceback (most recent call last)
Cell In[1], line 1
----> 1 import caiman as cm

File ~\repos\CaImAn\caiman\__init__.py:4
      1 #!/usr/bin/env python
      3 import pkg_resources
----> 4 from caiman.base.movies import movie, load, load_movie_chain, _load_behavior, play_movie
      5 from caiman.base.timeseries import concatenate
      6 from caiman.cluster import start_server, stop_server

File ~\repos\CaImAn\caiman\base\movies.py:36
     34 import caiman.base.traces
     35 import caiman.mmapping
---> 36 import caiman.summary_images
     37 import caiman.utils.sbx_utils
     38 import caiman.utils.visualization

File ~\repos\CaImAn\caiman\summary_images.py:18
     16 import caiman
     17 import caiman.base.movies
---> 18 from caiman.source_extraction.cnmf.pre_processing import get_noise_fft
     20 def max_correlation_image(Y, bin_size: int = 1000, eight_neighbours: bool = True, swap_dim: bool = True) -> np.ndarray:
     21     """Computes the max-correlation image for the input dataset Y with bin_size
     22
     23     Args:
   (...)
     40             max correlation image
     41     """

File ~\repos\CaImAn\caiman\source_extraction\cnmf\__init__.py:12
     10 from . import spatial
     11 from . import temporal
---> 12 from . import oasis
     13 from . import params
     14 from . import online_cnmf

ImportError: cannot import name 'oasis' from partially initialized module 'caiman.source_extraction.cnmf' (most likely due to a circular import) (C:\Users\RBO\repos\CaImAn\caiman\source_extraction\cnmf\__init__.py)

conda setup:

$ conda info

     active environment : caiman
    active env location : C:\Users\RBO\miniforge3\envs\caiman
            shell level : 8
       user config file : C:\Users\RBO\.condarc
 populated config files : C:\Users\RBO\miniforge3\.condarc
                          C:\Users\RBO\.condarc
          conda version : 24.11.3
    conda-build version : not installed
         python version : 3.12.6.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake
                          __conda=24.11.3=0
                          __cuda=12.6=0
                          __win=0=0
       base environment : C:\Users\RBO\miniforge3  (writable)
      conda av data dir : C:\Users\RBO\miniforge3\etc\conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
                          https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : C:\Users\RBO\miniforge3\pkgs
                          C:\Users\RBO\.conda\pkgs
                          C:\Users\RBO\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\RBO\miniforge3\envs
                          C:\Users\RBO\.conda\envs
                          C:\Users\RBO\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/24.11.3 requests/2.32.3 CPython/3.12.6 Windows/10 Windows/10.0.19045 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.10
          administrator : True
             netrc file : None
           offline mode : False

[pgunn]

I think that "partially initialized module" thing is very close to working; the only thing you need to change is to leave the source directory (run caimanmanager install and then enter the caiman_data directory under your homedir; THEN start your scripts or jupyter and it will probably work).

Give this a go; if that doesn't work we can look more deeply. The compile route on Windows has been messy for a long time, but we should be able to get you through it (maybe even with a videochat).

[FlynnOConnell]

Giving this a go now. I'm right downstairs at the workshop so I could pop in and say hi.

[pgunn]

We're probably on the same floor if you're on the 3rd floor. I'm in room 304 and will be free until about 2:30; come over if you have a sec.

[FlynnOConnell]

caimanmanager install fixed this issue, but I did need to add opencv to the conda install (or install it manually after creating the env as shown in the readme).

I won't have time to make it by 230, can you let me know if you have any time in the afternoon?

[pgunn]

I may be free sometime around 4:30, maybe sooner. I'm meeting with someone else at 4pm, but that may be a fairly brief meeting - not sure.

Drop me an email at [email protected] and I'll ping you when I'm free.

[FlynnOConnell]

Resolved, thank you!