Deeplabcut: Output scoremaps / render scoremap video

[fps]

Hi,

it would be awesome to be able to get the score maps from the inference process. Ideally it would be possible to render a scoremap video during analyze_video.

I looked at the code and it seems that the lower level inference functions do have an "outputall" parameter so it should be possible to get at those scoremaps. Before diving in though and producing a half-assed solution I reckoned it's smarter to maybe submit a feature request instead.

[AlexEMG]

While predict can indeed return the scoremap, the feature for creating videos is not implemented currently.

[fps]

OK, so I'll hack up my own solution then. Thanks for your comment!

[lambdaloop]

You can already get most of the valuable scoremap in DeepLabCut by setting the "num_outputs" parameter to something high, say 30, so that it outputs the top N points detected rather than the top 1. Beyond some point, the rest of the points have low probability and do not contribute much to the scoremap.

[fps]

That's a good point! Thanks!

[isaacrobinson2000]

Not sure if this is helpful, but I am currently working on bringing a back-end plugin system I wrote up to date with the latest DeepLabCut which already has a plugin that does this. I am hoping to have it done by the end of this month.

[MMathisLab]

^ this will be available in a upcoming package update (wanted to let others know so they don't spend dedicated time on this)

[MMathisLab]

Delighted to say this is possible in 2.2b5 ;) You can plot scoremaps, locref, and the new PAFs:

• please see the new fxn (see details under section “Evaluation”) https://github.com/DeepLabCut/DeepLabCut/blob/master/docs/functionDetails.md#h-evaluate-the-trained-network

[fps]

Oh cool! Thanks a bunch! :)