https://github.com/ctroupin/alborex-data-python
Python code to read the netCDF files and produce the figures of the paper.
https://github.com/ctroupin/alborex-data-python
data-visualization mediterranean mediterraneansea mesoscale ocean-modelling ocean-sciences oceanography python submesoscale
Last synced: 7 months ago
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Python code to read the netCDF files and produce the figures of the paper.
- Host: GitHub
- URL: https://github.com/ctroupin/alborex-data-python
- Owner: ctroupin
- License: mit
- Created: 2018-04-30T09:37:53.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-01-12T14:21:18.000Z (almost 7 years ago)
- Last Synced: 2025-04-11T18:07:24.581Z (7 months ago)
- Topics: data-visualization, mediterranean, mediterraneansea, mesoscale, ocean-modelling, ocean-sciences, oceanography, python, submesoscale
- Language: Jupyter Notebook
- Homepage:
- Size: 42.3 MB
- Stars: 5
- Watchers: 1
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: readme.md
- License: LICENSE
Awesome Lists containing this project
README
This repository contains the python code in the form of [jupyter](https://jupyter.org/) notebooks to reproduce the figures of the paper:
> Troupin, C.; Pascual, A.; Ruiz, S.; Olita, A.; Casas, B.; Margirier, F.; Poulain, P.-M.; Notarstefano, G.; Torner, M.; Fernández, J. G.; Rújula, M. Muñoz, C.; Allen, J. T.; Mahadevan, A. & Tintoré, J. The AlborEX dataset: sampling of submesoscale features in the Alboran Sea Earth System Science Data Discussions, 2018, 1-21.
and to provide examples of the data from the netCDF files can be read, processed and displayed.
## Directories
* __data__: contains data files used for the plots and not available through [OPeNDAP](https://www.opendap.org/) protocol.
* __figures__: default directory where the figures are saved.
* __leaflet__: contains the source (html) to generate a [Leaflet](https://leafletjs.com/) interactive map showing the deployments and the sea surface temperature in the area of study.
* __python__: contains
1. the main module [`alborexdata.py`](./python/alborexdata.py) that defines the different classes
2. the jupyter notebooks and
## Usage
### Configuration
The file [`alborexpaths.py`](./python/alborexpaths.py) stores the OPEnDAP URLs of all the data files (so they don't have to be downloaded locally), the extension of the domain and the path to the figure directory.
__Note:__ the URLs were hard-coded but can be obtained using the [SOCIB Data API](http://api.socib.es/home/) (see the [API Examples](https://github.com/socib/API_examples)).
The SST files are not available in this repository but are automatically download from [OceanColor](http://oceancolor.gsfc.nasa.gov/) web when needed.
### Reading files
Each platform (drifters, Argo floats, gliders, ...) has a class defined in [`alborexdata.py`](./python/alborexdata.py), and the corresponding class has a method to read the data from the netCDF file.
For example, for the CTD data:
1. We create an object CTD:
```python
ctd = alborexdata.CTD()
```
2. We read the data from the correspond files, whose URL comes from `alborexpaths`:
```python
ctd.get_from_netcdf(alborexpaths.ctdfile)
```
### Plotting data
There are many different types of plots used here.
For the maps, we used the [Basemap Toolkit](https://matplotlib.org/basemap/) but in the future we will switch to [Cartopy](https://scitools.org.uk/cartopy/docs/latest/), once all the Basemap's features have been implemented.
We also work with the [cmocean](https://matplotlib.org/cmocean/) module in order to obtain perceptually uniform colormaps.
## How to cite?
This module:
> Charles Troupin. (2019, January 12). ctroupin/AlborEx-Data-Python: V1.1.0 (Version V1.1.0). Zenodo. DOI: [10.5281/zenodo.2538348](http://doi.org/10.5281/zenodo.2538348)
The AlborEx paper in [Earth System Science Data](https://www.earth-system-science-data.net/) (the reference will be updated):
> Troupin, C.; Pascual, A.; Ruiz, S.; Olita, A.; Casas, B.; Margirier, F.; Poulain, P.-M.; Notarstefano, G.; Torner, M.; Fernández, J. G.; Rújula, M. Muñoz, C.; Allen, J. T.; Mahadevan, A. & Tintoré, J. The AlborEX dataset: sampling of submesoscale features in the Alboran Sea. *Earth System Science Data Discussions*, 2018, 1-21. DOI: [10.5194/essd-2018-104](https://doi.org/10.5194/essd-2018-104)
Other related papers:
> Pascual, A.; Ruiz, S.; Olita, A.; Troupin, C.; Claret, M.; Casas, B.; Mourre, B.; Poulain, P.-M.; Tovar-Sanchez, A.; Capet, A.; Mason, E.; Allen, John T..; Mahadevan, A. & Tintoré, J. A multiplatform experiment to unravel meso- and submesoscale processes in an intense front (AlborEx). *Frontiers in Marine Science*, 2017, **4**, 1-16. DOI: [10.3389/fmars.2017.00039](https://doi.org/10.3389/fmars.2017.00039)
> Olita, A.; Capet, A.; Claret, M.; Mahadevan, A.; Poulain, P. M.; Ribotti, A.; Ruiz, S.; Tintoré, J.; Tovar-Sánchez, A. & Pascual, A. Frontal dynamics boost primary production in the summer stratified Mediterranean Sea. *Ocean Dynamics*, 2017, **67**, 767-782. DOI: [10.1007/s10236-017-1058-z](https://doi.org/10.1007/s10236-017-1058-z)
## Acknowledgments
The 3 anonymous reviewers made an outstanding work with a lot of comments that helped us improve
the initial manuscript, and also motivated me to improve and update the present project.
I am also thankful to the SOCIB Data Center for corrections and improvements made on the
data file. Their [Data API](http://api.socib.es/home/) is very cool and I really invite everybody to try and use it.