cichlid-tracking

Raspberry Pi data collection for the McGrathLab bower-tracking fleet. This is the tracking-only half of the former CichlidBowerTracking monolith; post-hoc analysis lives in a separate repo. Both build on cichlid-file-management.

Layout

src/cichlid_tracking/
    cichlid_tracker.py     # CichlidTracker: per-Pi capture + command loop
    file_manager.py        # FileManager(BowerFileManager): credentials + Pi dirs
    cli.py                 # `cichlid-tracker` entry point
    helper_modules/        # log_parser, google_controller (control sheet)

FileManager layering

BaseFileManager      (cichlid-file-management)  cloud I/O, env detection, branch_name
    -> BowerFileManager  (cichlid-file-management)  project + analysis-state dirs
        -> FileManager   (this repo)                 credentials + Pi-capture dirs

Install

This package is pip-installable. conda is optional and only for dev machines — the Pi fleet uses pip only.

Raspberry Pi (and any machine without conda)

picamera2 (apt) and pyrealsense2 (built from source) live in the system Python, so create the virtual environment with access to system packages, then pip-install:

python3 -m venv --system-site-packages ~/cichlid-env
source ~/cichlid-env/bin/activate
pip install -e ".[pi]"      # or: pip install "git+ssh://git@github.com/McGrathLab/cichlid-tracking.git"

venv is Python's built-in environment tool (apt python3-venv) — no conda is involved. rclone is a separate binary, not a pip package: install it via apt and configure the Dropbox remote (see the Raspberry Pi setup guide).

Development machine (optional, conda)

If you prefer conda on your workstation:

conda env create -f environment.yml
conda activate cichlid-tracking

The hardware extras ([pi]: picamera2, pyrealsense2) are Pi-only and are not installed on a dev machine. Runtime dependencies are declared once in pyproject.toml; both paths pull them from there.

Status

Core port complete: command loop, command dispatch, recording (picamera2 → direct MP4), depth capture (pyrealsense2), background upload, crash reporting, and log versioning. LogParser and GoogleController are ported (LogParser lives in cichlid-file-management, shared with post-hoc analysis).

Remaining:

• Hardware shakeout on a real Pi 4 (picamera2 segment lifecycle, MP4 finalization, power-loss behavior on the day-long file)
• Confirm every Pi has a unique bt-<tankID> hostname