Description
Hi,
I can confirm that it is possible to install miniscoPy on Windows from within Miniconda environment. There are few differences and issues however. Regarding installation – the pyav package is easier to install than on Linux. In addition some package names are different, so you can use this command:
(miniscoPy) ... > conda install av scipy matplotlib jupyter pandas cython scikit-learn scikit-image h5py opencv tqdm future psutil
Another difference is that yaml is not available in conda (or I couldn’t find right name) so I end up installing PyYAML from pip:
(miniscoPy) ... > pip install PyYAML
The command above need to be executed from within Miniconda’s virtual environment you use for the miniscoPy.
The bigger problem however is that resulting environment and miniscoPy code (main_cnmf_e.py) doesn’t work under Windows beyond motion correction part. The cnm.fit(procs) call just hangs after some time consuming 100% CPU time and never returns even after 12 hours. By the way – CaImAn’s code doesn’t work on Windows too, with very similar problem. One possible reason is that code in the main_cnmf_e.py is not guarded by
if (__name__ == ‘__main__’):
which is essential for parallel processing. Unfortunately fixing that didn’t solve the problem…
I understand that you using Ubuntu as your development environment but different behavior on different platforms is a warning sign of somthing going not so well.
Also, I'd like to thank you for stripping down CaImAn which is itself one big mess.
Regards,
Denis