108 of 508 rows in all_video_info_merged.xlsx were duplicates left over
from merging multiple source spreadsheets — same (date, machine, ROI)
appearing under two source_date values, identical data otherwise. The
`male` column was also using a mix of variants ('naïve', 'niave',
'naive', 'trained') with the canonical 'naive' a minority of 12/200.
scripts/cleanup_xlsx.py
Idempotent one-off: backs up the xlsx, dedupes preferring the row
whose source_date matches the experiment date, normalises `male`
spellings, strips whitespace from string columns. Re-running on a
clean file is a no-op.
scripts/export_video_db_index.py
New _validate_xlsx() runs first thing in main() and aborts the
export with an actionable error if duplicates or non-canonical
male values are present. Prevents silent regressions when the
xlsx is edited or re-merged in the future.
Result: TSV is now 400 rows (was 508), exactly 200 trained / 200
naive, no duplicates.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
build_video_inventory.py now opens each mp4 with cv2 to record
duration_s. Cached: a video already in the previous inventory keeps
its computed duration, so re-runs only pay the cv2 cost for new
recordings.
export_video_db_index.py looks up the matched video's duration and
writes it as training_video_duration_s / testing_video_duration_s
alongside the existing path columns. Useful for spotting unusually
short or long sessions and for sanity checks on the tracker output.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- export_video_db_index.py now writes a boolean `include` column
(default True). Flip it to False to drop a noisy/unusable row from
analysis without deleting it.
- load_roi_data filters on `include` automatically (back-compat:
missing column = load everything).
- flies_analysis_simple.ipynb section headers now explain *why* each
step exists (barrier alignment, body-area baseline, merged-blob
heuristic, Hungarian identity tracking) rather than just naming
the step.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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>
- 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>
