Metadata-Version: 2.1
Name: ctdfjorder
Version: 0.3.0
Summary: A package for processing and analyzing CTD data.
License: MIT
Keywords: CTD
Author: Nikolas Yanek-Chrones
Author-email: research@icarai.io
Requires-Python: >=3.11
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: colorlog (>=6.8.2)
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Requires-Dist: gsw (>=3.6.18)
Requires-Dist: matplotlib (>=3.9.1)
Requires-Dist: numpy (>=2.0.0)
Requires-Dist: openpyxl (>=3.1.4)
Requires-Dist: pandas (>=2.2.2)
Requires-Dist: plotly (>=5.20.0,<6.0.0)
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Requires-Dist: psutil (>=6.0.0,<7.0.0)
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Requires-Dist: setuptools (>=70.3.0)
Requires-Dist: statsmodels (>=0.14.2)
Requires-Dist: torch (>=2.1.7)
Project-URL: homepage, https://github.com/nikothomas/ctdfjorder
Project-URL: issues, https://github.com/nikothomas/ctdfjorder/issues
Description-Content-Type: text/markdown

# CTDFjorder

CTDFjorder is a Python package for processing and analyzing CTD (Conductivity, Temperature, Depth) data.
Documentation: [Read the docs](https://nikothomas.github.io/ctdfjorder/)

## 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.
```shell
conda create --name ctdfjorder python=3.12
conda activate ctdfjorder
```
To install ctdfjorder you can use pip:
```shell
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](https://www.mapbox.com).


## 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](https://nikothomas.github.io/ctdfjorder/Getting%20Started.html).

## Contributing

Contributions to CTDFjorder are welcome! If you find any issues or have suggestions for improvements, please open an issue on the [GitHub repository](https://github.com/nikothomas/CTDFjorder).

## 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.


