.csv output

[mooch443]

.csv output

[roaldarbol]

I actually use R too, and had to find a nice way to work with .npz files (they're getting increaslingly frequent, so I figured why not just work with them directly). As @mooch443 correctly mentions, the reticulate library is the way around it. I made a gist here which can be used to import and clean either a single file or even list all files in a folder, as well as removing Inf from the data frame (which was previously an issue, #21). I've got a few more snippets of code, e.g. for making moving averages/medians, so do let me know if I can help more. :-)

Here's the gist

[MarkJThomas]

@mooch443

Hiya, I don't suppose you have any guidance to the above please?

All the best,
Mark

[mooch443]

Hey,

yes - sorry. I was about to get around to issues just now.

You may use an R extension to load the npz files into R directly: https://rstudio.github.io/reticulate/
I haven't tried it myself (not an R user), but this is supposed to work.

As to how you can get to the trajectories of individuals, there is an example for handling the npz data (in Python), as well as an explanation of the format, here: https://trex.run/docs/formats.html#positional-data

I am sorry, again, for the delay and I hope this will help. Essentially, what you will have to do is open the npz file for an individual (e.g. data/video_fish0.npz) and then plot X#wcentroid and Y#wcentroid together in a 2D plot. The way you extracted them seems to have gotten rid of the _fishX.npz suffixes (which means you are probably losing information).

Best
-Tristan

[MarkJThomas]

Apologies for the delay in responding! Thank you so much for your help and the R script. It worked like a treat for the .npz files I have. You mentioned a few more snippets of code, I wondered if you had some to obtain movement speed/averages? I am quite new to this analysis so anything that can help me obtain output for the .npz files in R would be great :-)

@roaldarbol - I just noticed it says you are Brighton based, I am from Hassocks! - Small world