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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
..
README.md Initial commit: organized project structure for student handoff 2026-03-05 16:08:36 +00:00

README.md

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"