Sample data

[roaldarbol]

Hi there, hope all's well!
I'm writing an R package for analysis of movement data (animovement), and I'm about to write a reader for SLEAP CSV data.
However, I don't have any exported sample data right at hand - would you happen to have some laying around? It would be great to have both single-2D, single-3D and multianimal data to allow import of them all. I mostly need to get snippets of all the headers and maybe the first 10 lines of data to run the tests I need.
Thanks!

[talmo]

Hi @roaldarbol,

For sure -- here's an example dataset and associated notebook that walks through it.

The movement folks also have example datasets you can check out.

Finally, I'd recommend checking out sleap-io if you want to do any sort of I/O related things. This is a standalone library that has much less annoying dependencies than core SLEAP (e.g., DL and GUI deps).

---

Those datasets are all 2D/multi-animal in SLP or Analysis HDF5 formats, but you're welcome to poke around our test fixtures for other formats (e.g., CSV).

For 3D specifically: we haven't quite converged on a stable format for this yet since we're still actively developing it, but sleap-anipose has the current backend for our aniposelib-based implementation of 3D. The tests folder there has example files and keypoint-moseq has a loader for it.

Let me know if there's anything we can help with!

Talmo

[roaldarbol]

Thanks for the reply @talmo!

I'm already using the h5 files that movement uses; it was more for the natively exported csv files. Does that mean that https://github.com/talmolab/sleap/blob/develop/tests/data/csv_format/minimal_instance.000_centered_pair_low_quality.analysis.csv is a representative csv SLEAP exported file? What would look different if it was a multi-animal project?

It's a pure R package, so I can't rely on sleap-io for this (other than making my own test files 😉). I'm currently also implementing a reader for the h5 files - I'll give you a heads-up when I have; then R folks should have a good place to go when wanting to works with your h5 or csv files.

I can't quite recall, are your .slp files simply stringent h5 files? I.e. would it be possible to load them with a generic h5 parser?

Good to know regarding 3D! I'll probably come back to them at a later point!

Thanks, and for now I think I'm all good - you're being super helpful answering questions, can't ask for more! 😃
Cheers,
Mikkel

[roaldarbol]

Didn't take as long as expected - now the h5 reader is implemented! roaldarbol/animovement#50
Just got the csv reader to go then!