Giorgio Gilestro
9f3ee24a23
- 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>
51 lines
2.3 KiB
Markdown
51 lines
2.3 KiB
Markdown
# Processed Data
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CSVs derived from the tracking DBs (`/mnt/data/projects/cupido/tracked/`)
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and the merged TSV (`/mnt/data/projects/cupido/all_video_info_merged.tsv`).
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All files are gitignored and regenerable.
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## Files and Regeneration
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| File | Description | Generated By |
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|------|-------------|--------------|
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| `distances.csv` | Per-frame inter-fly distances for every (date, machine, ROI, session). Includes metadata columns to filter trained vs naïve, training phase, species, etc. | `scripts/calculate_distances.py` |
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| `*_distances_aligned.csv` | (legacy, 2025-07-15 only) distances aligned to barrier opening | `notebooks/flies_analysis*.ipynb` |
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| `*_tracked.csv` | (legacy) identity-tracked fly positions | `notebooks/flies_analysis_simple.ipynb` |
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| `*_max_velocity.csv` | (legacy) max velocity over 10 s windows | `notebooks/flies_analysis_simple.ipynb` |
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## Loading the data
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```python
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import sys
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sys.path.insert(0, "../scripts")
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from load_roi_data import load_roi_data
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data = load_roi_data() # full batch as one DataFrame
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# Or filter the metadata first:
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import pandas as pd
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tsv = pd.read_csv("/mnt/data/projects/cupido/all_video_info_merged.tsv", sep="\t")
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data = load_roi_data(tsv[tsv.species.str.contains("Melanogaster")])
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```
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The returned DataFrame has columns:
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`id, t, x, y, w, h, phi, is_inferred, has_interacted, session, ROI, date,
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machine_name, species, male, training_date_time, testing_date_time,
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training_length_hr, consolidation_length_hr, memory, age`.
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`session` is `"training"` or `"testing"`; `male` is `"trained"` or
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`"naive"` (canonical — variants like `"naïve"` and `"niave"` are normalized
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at the TSV-export step).
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The TSV also has a per-row boolean `include` column (default `True`).
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Flip it to `False` to drop a noisy / unusable fly+session from analysis
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without deleting the row. `load_roi_data` honors this flag automatically.
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## Column Reference (`distances.csv`)
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- `date`, `machine_name`, `ROI`, `session`: identifies one fly trajectory
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- `t`: time in ms within that session
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- `distance`: Euclidean distance between the two flies in pixels
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- `n_flies`: number of fly detections at this frame (1 or 2)
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- `area_fly1`, `area_fly2`: bounding-box areas (`w * h`) in pixels²
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- `male`: `trained` or `naive` (carried from the xlsx; normalized)
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- `species`, `memory`, `age`: experimental metadata
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