One Fish, Two Fish

further explorations will take place soon-ish... :)

This repo contains code used for post processing + analysis in the SLEAP fish tracking project. Feel free to read my thesis or view the poster to learn more about it.

• models: folder with the SLEAP centroid and centered-instance models used for tracking (not required for running analysis)
• allcsvs: folder of SLEAP csv output for all groups of tracked fish (each file labeled by group_id)
• constants.py: constants used throughout the project
• erikas_1min.csv & erikas_t2_4s.csv: sample datasets for testing code
• extras.ipynb: some explorations with DTW + some interactive plotly graphs
• find_center_demo.ipynb: walkthrough tutorial for finding center of tank (least squares + midpoint methods)
• fish_utils.py: all core utilities for preprocessing, data analysis, calculations + some extra functions
• total_dists.ipynb: main processing loop for calculating total distances traveled on full dataset (+ size estimation)
• total_dists_with_sizes_.csv: output of total_dists.ipynb (includes total dists + size est)
• visuals_demo.ipynb & visuals_demo_2.html/Rmd: contain all visuals from the project (+ some extra plots)
• visuals.py script for automating visualizations in visuals_demo.ipynb

Recommendations:

1. Run fish_utils.py and visuals.py for the core analysis + plotting functions.
2. See find_center_demo.ipynb and total_dists.ipynb for some analysis examples.
3. Generate visualizations with visuals_demo.ipynb and visuals_demo_2.Rmd (also has HTML).

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Repository URL: https://github.com/erikamoore/onefishtwofish.git