NES-LTER Stingray

📌 Overview

This repository contains code and data processing scripts for the In-situ Ichthyoplankton Imaging System (ISIIS), also known as Stingray.

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📦 Installation

Clone this repository

bash git clone https://github.com/anhph95/nes-lter-stingray.git cd nes-lter-stingray

Create Python virtual environment (venv):

bash sudo apt update sudo apt install python3-venv -y python3 -m venv venv source venv/bin/activate pip install -r requirements.txt

Or create Conda environment:

bash wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh source ~/.bashrc conda env create -f environment.yml conda activate venv

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🚀 Usage

Merge sensor data

``` usage: datamerge.py [-h] [--path PATH] [--calyear CALYEAR] --cruise CRUISE --startdate STARTDATE --enddate END_DATE

Merge sensor data from multiple CSV files.

options: -h, --help show this help message and exit --path PATH Path to the sensor data, default is /mnt/vast/nes-lter/Stingray/data/sensordata --calyear CALYEAR Sensor calibration year, default is 2021 --cruise CRUISE Cruise ID, required, e.g. EN706 --startdate STARTDATE Cruise start date (YYYY-MM-DD), required --enddate END_DATE Cruise end date (YYYY-MM-DD), required ```

(Optional) Get media list and Tator link (not recommended for real-time, requires tator, opencv)

``` usage: media_list.py [-h] [--cruise CRUISE] [--host HOST] [--project-id PROJECT_ID] [--token TOKEN] [--media-dir MEDIA_DIR]

options: -h, --help show this help message and exit --cruise CRUISE Cruise ID, required, e.g. EN706 --host HOST Tator host IP address, default is https://tator.whoi.edu --project-id PROJECTID Project ID --token TOKEN Tator login token, string or token file --media-dir MEDIADIR Path to the media data ```

Bin data and compute mean, standard deviation

``` usage: databin.py [-h] --cruise CRUISE [--sensordir SENSORDIR] [--mediadir MEDIADIR] [--bincols BINCOLS [BINCOLS ...]] [--binsteps BINSTEPS [BIN_STEPS ...]]

Process sensor and media data for a given cruise.

options: -h, --help show this help message and exit --cruise CRUISE Cruise ID --sensordir SENSORDIR Path to the sensor data --mediadir MEDIADIR Path to the media data --bincols BINCOLS [BINCOLS ...] Columns to bin (space-separated list, e.g., "matdate depth") --binsteps BINSTEPS [BINSTEPS ...] Steps to bin (space-separated list, e.g., "0.000347 1" [30 seconds/86400, 1 meter]) ```

Visualize data

Data from dash_data/data can be copied into: \\vast.whoi.edu\proj\nes-lter\stingray_dashboard\dash_data\data

The dashboard can then be accessed via:
👉 https://stingraydash.whoi.edu/

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OR run the visualization app locally (requires plotly, dash)

``` usage: dashapp.py [-h] [--host HOST] [--port PORT]

Stingray Dashboard

options: -h, --help show this help message and exit --host HOST Host IP address for the Dash app, default is 0.0.0.0 --port PORT Port number for the Dash app, default is 8050 ```

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🐳 Running via Docker

The recommended way to run the Stingray Dashboard is with Docker Compose.

🛠 Prerequisites

• Docker installed
  
• Docker Compose (bundled with Docker Desktop on most systems)
  

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1. Start the app (build if first time or code changed)

bash docker compose up --build

This will: - Build the Docker image (if not already built or if code changed)
- Mount the dash_data/ folder so new data is available without rebuilding
- Run the dashboard on http://localhost:8050

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2. Stop the app

bash docker compose down

This stops and removes the running container(s).

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3. Start in background (detached mode)

bash docker compose up -d

The dashboard will run in the background.
Stop it anytime with: bash docker compose down

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4. Update data

Because dash_data/ is mounted as a bind volume, any changes to CSVs or input files in dash_data/ on your machine are immediately reflected inside the container.

👉 No rebuild is required when updating data.

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5. Rebuild when code changes

You only need to rebuild the image if you: - Modify dashapp.py
- Change code in the assets/ folder
- Update requirements.txt

Rebuild with: bash docker compose up --build

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6. Access the dashboard

After startup, visit in your browser:
👉 http://localhost:8050

Or, from another computer on the same network (LAN):
👉 http://<your-computer-ip>:8050

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📚 License

This project is licensed under the MIT License. See the LICENSE file for details.

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✨ Contributors

• Anh Pham
  
• Sidney Batchelder
  
• Heidi Sosik
  

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🔗 GitHub Repository: https://github.com/anhph95/nes-lter-stingray