Consolidates everything bulky (tracking DBs, targets, metadata
spreadsheet) under a single DATA_VOLUME root outside the ownCloud-synced
repo. Notebooks now use a visible DATA_DIR = Path(...) idiom rather than
walking up the filesystem with PROJECT_ROOT.parent — easier for students
with no Python background to follow.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Four guided notebooks under notebooks/getting_started/ aimed at someone
new to Python and data science. The series progresses: project orientation
→ Python/pandas crash course → exploring one tracking DB → first
trained-vs-naive comparison using load_roi_data + Mann-Whitney U.
Each notebook leans heavily on markdown explanations, includes exercises
with empty cells, and links out to canonical references (JupyterLab,
official Python tutorial, pandas 10-min guide, Wikipedia for stats
concepts).
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- Tracked DBs now live at /mnt/data/projects/cupido/tracked/ (out of
ownCloud to avoid sync conflicts and bandwidth churn). config.py
TRACKING_OUTPUT_DIR points there; the docker-compose for ethoscope-lab
mounts it world-readable for JupyterHub users.
- New scripts/export_video_db_index.py joins all_video_info_merged.xlsx
with the video inventory and the on-disk DBs, producing a TSV that has
one row per fly/ROI plus training/testing video and DB paths. Handles
approximate xlsx times, cross-day training/testing, the 12 AM/PM
ambiguity, and date typos.
- scripts/load_roi_data.py rewritten as a TSV-driven loader returning a
single DataFrame with session and metadata columns. calculate_distances
and the two flies_analysis notebooks migrated to use it; downstream
trained/naive splits remain available via simple equality filters.
- Metadata vocabulary canonicalized: {naïve, niave, untrained, test} all
resolve to {trained, naive}. Normalization happens at the TSV-export
boundary (idempotent); the xlsx and the 2025-07-15 legacy CSV were
edited in place to remove the worst variants.
- scripts/monitor_tracking.py rate calculation fixed: with N parallel
workers, completions arrive in bursts; the old formula divided by burst
width and reported nonsense rates. Now uses a 6 h window denominator.
- scripts/track_videos.py: BGRMovieCamera retries cv2.read on transient
NFS hiccups and a post-tracking completeness gate (≥ 90 % of expected
duration via MAX(t) across all 6 ROIs) deletes silent partial DBs.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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>
