Saved movie looks completely black

[vambrosi]

Bug description: If you try to use the save_movie=True parameter in the movie.play() function you get the correct preview, but the saved AVI file looks completely black. This happens with both opencv backends.

Minimal working example:

import numpy as np
import caiman as cm

movie = cm.movie(np.random.rand(150, 300, 300))
movie.play(save_movie=True, plot_text=True)

Possible Fix: Before playing the movie, the code seems to normalize the frame range to be between 0 and 1 (for offset=0 and gain=1). And afterwards, at least in the embed_opencv backend, it scales the data back to span the uint8 range.

However, this is not done when saving the file. So changing this line to

frame = np.clip((frame * 255.), 0, 255).astype('u1')

seems to fix the problem. This uses the same scaling and clipping as used to display the preview (I was not sure what the expected behavior would be when gain != 1 or offset != 0).

@pgunn is there any chance I could get an early release with this fix? Thanks! (I can submit a pull request.)

[pgunn]

@vambrosi Hi, sorry for the delay in getting back to you - been busy with some surprising real-life things over the break. I'll get you an answer on this soon.

[pgunn]

@vambrosi I can do this, or you can; either works for me. I know some people really care about getting in the contributors to github repos, while others don't care at all (some other people had to explain this to me as I'm in the latter camp); just let me know which you prefer.

[vambrosi]

Thanks for checking everything!

And I'll submit the PR, if you don't mind. I just started working on some neuroscience projects, so this might be relevant for the future. Also, I think I might have another simple bug fix, so submitting the PR might be good for practice.

Do you prefer it as a branch of main or dev (since it is a quick fix)?

[pgunn]

dev please; all changes to main come through dev only as part of our release process.

Thanks!