ctdfjorder 0.4.0

A package for processing and analyzing CTD data.

CTDFjorder

CTDFjorder is a Python package for processing and analyzing CTD (Conductivity, Temperature, Depth) data. Documentation: Read the docs

Features

• Read RSK (.rsk) and Castaway (.csv) files and extract CTD data
• Process CTD data, including removing non-positive samples and cleaning data
• Calculate derived quantities such as absolute salinity, density, and potential density
• Determine mixed layer depth (MLD) using different methods
• Generate plots for visualizing CTD profiles and derived quantities
• Command-line interface (CLI) for easy processing and merging of CTD data files

Installation

It's recommended that you create a new environment just for CTDFjorder. This can be done in conda with the following command.

conda create --name ctdfjorder python=3.12
conda activate ctdfjorder

To install ctdfjorder you can use pip:

pip install ctdfjorder

Map plots

If you want to enable map plotting at the end of the pipeline you'll need a default token from MapBox.

Usage

CTDFjorder provides a command-line interface (CLI) for processing and analyzing CTD data in addition to serving as a library for other bio-informaticians. A tutorial has been setup here.

Contributing

Contributions to CTDFjorder are welcome! If you find any issues or have suggestions for improvements, please open an issue on the GitHub repository.

License

CTDFjorder is released under the MIT License.

Acknowledgments

CTDFjorder was developed by Nikolas Yanek-Chrones for the Fjord Phyto project. The gsw library was used for certain dervied calculations.

Citations

McDougall, T. J., & Barker, P. M. (2011). Getting started with TEOS-10 and the Gibbs Seawater (GSW) Oceanographic Toolbox. SCOR/IAPSO WG127.