Input files for ExportOneAnimal.py

[croneal]

Hi,

I encountered an issue while following your pipeline. Specifically, I'm stuck at the ExportOneAnimal.py script, which requires a data_file generated from ExportScaledSeg.py, along with a timestamp file.

I attempted to create a timestamp file by generating a txt file with a single line of time, such as 20240604100000. However, upon execution, I encountered the following error:

NameError: free variable 'sync_skip' referenced before assignment in enclosing scope

Additionally, I'm unsure about the requirements for the EEG files.

It would be helpful if you could provide some demo files or further guidance on generating the feather format file.

Thanks a lot.

[SkepticRaven]

It looks like that's a bug!

I had created a csv file with 2 columns.

• Video filename without extension
• Frame index when alignment occurs.

While it is an optional input (with --timesyncfile), it appears that I never wrote the case when it isn't provided. It should be a relatively easy fix. I should be able to write a minor patch for this pretty quickly (possibly today).

As for getting demo files... that may take a bit longer.

I can also in the patch for the exclusion of timesyncfile also try and write down more details about the structure of the files.

Briefly to give you some insight into what we did ---
Although we describe the data collection being Raspberry-Pi-based in the paper, I never shared the exact command here (which for stability reasons, we needed to separate the video stream and the time logging stream). The timestamps were written out to a plain text file. This code (that is producing this error) reads in those timestamps (which are formatted as seconds relative to system boot) and adjusts them to be a localized time.

[SkepticRaven]

Just added https://github.com/KumarLabJax/MouseSleep/tree/issue%232

It adds documentation in the main file alongside patching the exact error you ran into above. Hopefully this helps!