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vholstein jackransomlovell konraddanielewski r-shruthi11

keypointmoseq's Issues

much slower s/it when run from CLI

Thanks for creating and sharing this codebase. I noticed a big difference in how both data loading and fitting it/s or s/it when I call load_data or fit_model from the command line as opposed to within a jupyter notebook. Could this be related to tdqm printing progress to stdout vs. in the notebook?
(Also please let me know if there is a different forum to raise issues or discuss bug fixes) - SR

fitting sLDS crashes on Windows

I'm trying to run the keypoint_moseq pipeline on some of my tracking data on a windows machine with a GPU. See below for specs:

Jax: 0.4.1
TensorFlow: 2.8.4
Numpy: 1.22.4
Python: 3.8.15
OS: Windows-10-10.0.19044-SP0

I've confirmed that jax sees my GPU.
I'm able to fit PCA, initialize and fit the AR-HMM but when I try to fit the SLDS my program crashes with no errors. I've tried running within a jupyter notebook and this step kills the kernel. I've tried running from the command line - same thing, the process just exists.
Any clues on how to troubleshoot this?

apply_model is either very slow or hangs

image

After fitting with SLDS, I'm trying to apply the model to the same coordinates that it was fit with to generate results.h5. However, I don't see any progress even after about 20 min on the model-fitting. Same thing happens when I use the example mouse data y'all provide.

deprecate?

you might want to make a big ol note that this repo is deprecated in favor of the new one!

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