lab/cupido

Giorgio e7e4db264d Initial commit: organized project structure for student handoff

Reorganized flat 41-file directory into structured layout with:
- scripts/ for Python analysis code with shared config.py
- notebooks/ for Jupyter analysis notebooks
- data/ split into raw/, metadata/, processed/
- docs/ with analysis summary, experimental design, and bimodal hypothesis tutorial
- tasks/ with todo checklist and lessons learned
- Comprehensive README, PLANNING.md, and .gitignore

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

2026-03-05 16:08:36 +00:00

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Processed Data

Large CSV files generated from the analysis pipeline. All files are gitignored (~370MB total) and can be regenerated.

Files and Regeneration

File	Description	Generated By
`trained_roi_data.csv`	Raw tracking data for trained ROIs	`scripts/load_roi_data.py` or notebook step 1
`untrained_roi_data.csv`	Raw tracking data for untrained ROIs	`scripts/load_roi_data.py` or notebook step 1
`trained_distances.csv`	Pairwise distances (unaligned)	`scripts/calculate_distances.py`
`untrained_distances.csv`	Pairwise distances (unaligned)	`scripts/calculate_distances.py`
`trained_distances_aligned.csv`	Distances aligned to barrier opening	Notebook step 4
`untrained_distances_aligned.csv`	Distances aligned to barrier opening	Notebook step 4
`trained_tracked.csv`	Identity-tracked fly positions	Notebook step 7
`untrained_tracked.csv`	Identity-tracked fly positions	Notebook step 7
`trained_max_velocity.csv`	Max velocity over 10s windows	Notebook step 7
`untrained_max_velocity.csv`	Max velocity over 10s windows	Notebook step 7

To Regenerate All Data

Run the full notebook notebooks/flies_analysis_simple.ipynb with:

recalculate_distances = True
recalculate_tracking = True

Warning: Identity tracking and velocity calculations take significant time (~30+ minutes).

Column Reference

Distance CSVs (`*_distances_aligned.csv`)

machine_name: Ethoscope machine ID (string)
ROI: ROI number (1-6)
aligned_time: Time in ms relative to barrier opening (0 = opening)
distance: Euclidean distance between flies in pixels
n_flies: Number of flies detected at this time point
area_fly1, area_fly2: Bounding box areas (w*h) in pixels^2
group: "trained" or "untrained"

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