# Processed Data

CSVs derived from the tracking DBs (`/mnt/data/projects/cupido/tracked/`)
and the merged TSV (`/mnt/data/projects/cupido/all_video_info_merged.tsv`).
All files are gitignored and regenerable.

## Files and Regeneration

| File | Description | Generated By |
|------|-------------|--------------|
| `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` |
| `*_distances_aligned.csv` | (legacy, 2025-07-15 only) distances aligned to barrier opening | `notebooks/flies_analysis*.ipynb` |
| `*_tracked.csv` | (legacy) identity-tracked fly positions | `notebooks/flies_analysis_simple.ipynb` |
| `*_max_velocity.csv` | (legacy) max velocity over 10 s windows | `notebooks/flies_analysis_simple.ipynb` |

## Loading the data

```python
import sys
sys.path.insert(0, "../scripts")
from load_roi_data import load_roi_data

data = load_roi_data()              # full batch as one DataFrame
# Or filter the metadata first:
import pandas as pd
tsv = pd.read_csv("/mnt/data/projects/cupido/all_video_info_merged.tsv", sep="\t")
data = load_roi_data(tsv[tsv.species.str.contains("Melanogaster")])
```

The returned DataFrame has columns:
`id, t, x, y, w, h, phi, is_inferred, has_interacted, session, ROI, date,
machine_name, species, male, training_date_time, testing_date_time,
training_length_hr, consolidation_length_hr, memory, age`.

`session` is `"training"` or `"testing"`; `male` is `"trained"` or
`"naive"` (canonical — variants like `"naïve"` and `"niave"` are normalized
at the TSV-export step).

## Column Reference (`distances.csv`)

- `date`, `machine_name`, `ROI`, `session`: identifies one fly trajectory
- `t`: time in ms within that session
- `distance`: Euclidean distance between the two flies in pixels
- `n_flies`: number of fly detections at this frame (1 or 2)
- `area_fly1`, `area_fly2`: bounding-box areas (`w * h`) in pixels²
- `male`: `trained` or `naive` (carried from the xlsx; normalized)
- `species`, `memory`, `age`: experimental metadata