SPASSO (Software Package for Adaptive Satellite-based Sampling for Oceanographic cruises is a Python code designed to compute daily maps of ocean state, based on available satellite data, to help guiding oceanographic cruise sampling. It can be used during oceanographic campaigns (near-real-time mode) or pre- and post-cruise to prepare sampling strategy and analyze observations. SPASSO code includes an independant Lagrangian diagnostic package (LAMTA) available here.

SPASSO website: https://spasso.mio.osupytheas.fr/

SPASSO automatically and independently download daily satellite-derived data such as surface height, velocity, temperature, salinity and chlorophyll-a concentration (freely distributed on CMEMS with support from CNES). Data are mapped over the studied region and diagnostics for lagrangian analysis are computed. SPASSO outputs (figures and data files) can be directly send to user’s email and can be gathered in a daily bulletin (.tex file).

Installation

Requirements

SPASSO is a package designed for Python >= 3.9, tested on Linux and Mac systems. It also requires a LaTeX compiler (latexmk or pdflatex).

Dependencies are listed in the pyproject.toml file.

Tip

Run check_modules.py in Python to get a list of required Python packages missing.
Python packages can be installed using the pip3 install <package_name> or python -m pip install <package_name> commands. How to install and use pip3.

Download

There are different options too clone the SPASSO repository from GitHub:

• Above the list of files, click <> Code, and then Download ZIP.
• Open a terminal, change the working directory to the location of the local cloned directory

git clone https://github.com/OceanCruises/SPASSO.git 

Directory tree

• Cruises/: contains the different cruise directories.
  • CruiseName#1/: contains the configuration file and all SPASSO outputs organized in the corresponding directories.
• Data/: contains data downloaded from CMEMS.
  • BATHY/: must contain a NETCDF  le including global bathymetry that can be downloaded from NOAA.
• Doc/: contains user manual and useful documents such as references.
• src/: contains all source code:
  • Bulletin.py: code preparing a tex and pdf bulletin file including all maps computed with SPASSO.
  • colormaps.py: contains some useful colormaps.
  • Diagnostics.py: code computing Eulerian and Lagrangian diagnostics.
  • Fields.py: code to download, load and create netcdf for all the fields used by SPASSO such as satellite, diagnostics and bathymetry.
  • Functions.py: additional useful functions (ex: climatologies).
  • GlobalVars.py: code loading all the global variables such as directory paths, dates, diagnostic parameters, emailing parameters, and bulletin parameters.
  • Library.py: code for SPASSO run functions to print messages, write in a log fille, send email, copy files, clean directories, execute shell requests.. .
  • PlotField.py: plot maps.
• Spasso.py: main code launching SPASSO software.

How to run SPASSO: test case

1. Open a terminal
2. Define the name of the Cruise:

cr=WMedSeaExample

If the cruise name contains space but it must be defined in the terminal with a backslash: cr=Med\ Sea

3. Edit the configuration file Cruises/WMedSeaExample/config_WMedSeaExample.ini and modify the motuclient library and LaTeX compiler paths to your local path:

4. Change working directory to the source code repository:

cd spasso2.0/src/

5. Launch SPASSO:

clear; python3 Spasso.py $cr

How to set up a new configuration

1. Create a new Cruise directory:

cd spasso2.0/Cruises/
mkdir <NameOfMyCruise>

2. Create a config_<NameOfMyCruise>.ini file:

cp /$localdir/spasso2.0/Cruises/WMedSeaExample/config_WMedSeaExample.ini /localdir/spasso2.0/Cruises/<NameOfMyCruise>/config_<NameOfMyCruise>.ini

3. Modify the config_<NameOfMyCruise>.ini file for the new configuration

Tip

A full description of the configuration file parameters is available in the config.ini.

More detailed information on how to set up a new SPASSO configuration can be found in the user manual. Section 5 of the manual is a Tutorial on the western Mediterranean Sea.

How to cite

The manuscript detailing the first release of SPASSO, version 2.0, is currently in revision for JTECH:

Louise Rousselet, Francesco d’Ovidio, Lloyd Izard, Alice Della Penna, Anne Petrenko, et al.. A Software Package for an Adaptive Satellite-based Sampling for Oceanographic cruises (SPASSOv2.0): tracking fine scale features for physical and biogeochemical studies. 2024. hal-04705438 preprint

SPASSO fundings and supports

SPASSO development has been supported by the following organisations:

• LOCEAN (Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques), Sorbonne University
• MIO (Mediterranean Institute of Oceanography), Aix-Marseille University
• CNES (Centre National d'Études Spatiales)