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SLEAP csv import error for multiple identities #408

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JuneAMeans opened this issue Jan 24, 2025 · 6 comments
Open

SLEAP csv import error for multiple identities #408

JuneAMeans opened this issue Jan 24, 2025 · 6 comments

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@JuneAMeans
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Describe the bug
I created a script that filled in missing identities and corrected jumps on a csv file from SLEAP and exported it in the same format as released by SLEAP. I attempted to import the file to SIMBA with the following entries into the import section:

Image

Then the following error occurred:

Image

To confirm this was an issue with the SLEAP csv structure and not the script I wrote I directly exported the csv for a single video in the SLEAP project and directly imported into SIMBA where the same error occurred.

Desktop (please complete the following information):

  • OS: Windows
  • Python: 3.6.13
  • Anaconda used. Conda version: 25.1.0

Additional context

  • The SLEAP file is for two distinct tracked identities consisting of 6 body parts each(custom skeleton).
@sronilsson
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sronilsson commented Jan 24, 2025

Thanks for reporting @JuneAMeans - would you mind sharing the sleep tracking data and I can see if I can recreate the error? You should be able to zip it and drop it in this thread.

EDIT PS. also, which version of simba do you run and see when typing pip show simba-uw-tf-dev ?

@JuneAMeans
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Simba version: 2.5.4

Here are the two csv files mentioned before:

SLEAPcsvFiles.zip

Here is the SLEAP file itself:

SLEAPslpFile.zip

Let me know if you would need the video as well it is too big for github.

@sronilsson
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sronilsson commented Jan 25, 2025

One more ask for now, could you share two files:

(i) the project_config.ini associated with the SimBA project?

(ii) the project_folder\logs\measures\pose_configs\bp_names\project_bp_names.csv located in the simba project directory?

@JuneAMeans
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Sorry for the weekend delay. Here are the files
(i):
project_config.zip
(ii)
project_bp_names.csv

The latter is unusual since it only has three of the 12 points but replacing it seemed to lead to the same error

@sronilsson
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Hi @JuneAMeans - can you give me a little more info on the unusual part:

I see in the project_bp_names.csv that your SimBA project has 3 defined body-parts from single animal. In the CSV I see six body-parts per animal and two animals. Did the import fail both when the project_bp_names.csv file had 3 entries and when it had 12 entries?

Also, in your project_config.ini, I se the project is set up to handle tracking data for 1 animal:

Image

... but the CSV data suggests that there are two animals.

If you update the project_config.ini to specify 2 animals, and you list the 12 body-parts in the project_bp_names.csv, does it still fail?

@JuneAMeans
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I think that resolved the issue. Thanks!

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