marisco 0.2.0

MARIS companion package and tutorials

Marisco

The IAEA Marine Radioactivity Information System (MARIS) allows free access to users to search and download the results of measurements of radioactivity in seawater, biota, sediment and suspended matter. MARIS is maintained and developed by the IAEA Environmental Laboratories in Monaco.

The current Python package offers command-line utilities for encoding MARIS harvested datasets into NetCDF or .csv formats. This allows to convert MARIS data into a format that is compatible with a wide range of scientific and data analysis tools.

Install

Now, to install marisco simply run

pip install marisco

Once successfully installed, run the following command:

maris_init

This command:

1. creates a .marisco/ directory containing various configuration/configurable files ((below)) in your /home directory
2. creates a configs.toml file containing default but configurable settings (default paths, …)
3. creates a configurable cdl.toml file used to generate a MARIS NetCDF4 CDL (Common Data Language) template;
4. downloads several MARIS DB nomenclature/lookup table into .marisco/lut/ directory
5. generate maris-template.nc, the MARIS NetCDF4 template generated from cdl.toml and use to encode MARIS datasets

[!TIP]

For inexperienced Python users, please refers to How to setup Marisco with Anaconda or How to setup Marisco with Windows Subsystem for Linux (WSL) and Visual Studio Code editor.

Getting started

Command line utilities

All commands accept a -h argument to get access to its documentation.

maris_init

Create configuration files, MARIS NetCDF CDL (Common Data Language) and donwload required lookup tables (nomenclatures).

maris_create_nc_template

Generate MARIS NetCDF template to be used when encoding datasets

maris_netcdfy

Encode MARIS dataset as NetCDF

Positional arguments:

• handler_name: Handler’s name (e.g helcom, …)
• str: Path to dataset to encode
• dest: Path to converted NetCDF4

Example:

maris_netcdfy helcom _data/accdb/mors/csv _data/output/helcom.nc

Development

FAQ

How is cdl.toml created & what it is used for?

A Python dictionary named CONFIGS_CDL specifying MARIS NetCDF attributes, variables, dimensions, … is defined in nbs/api/configs.ipynb in the first instance. Running the command maris_init will generate a toml version of it named .marisco/cdl.toml further used to create a MARIS NetCDF template named in .marisco/maris-template.nc.

Once marisco installed, further customization of the MARIS NetCDF template can be done directly through .marisco/cdl.toml file then running the command maris_create_nc_template.