Seapopym-data

Standardize the observation data used by SeapoPym.

Folder structure

Data folder is organized as follows:

• data
  • <location>
    • 1_raw : raw data extracted from the source + metadata as markdown file.
    • 2_preprocessed: data pre-processed in CSV format and netcdf (including metadata), cleaned and normalized. No loss of information (round, ceiling, etc...).
    • 3_post_processed: union of all pre-processed data in a single HDF5 style file. Usable by Seapopym.
    • scripts
      • 0_request : When the data is available on the Web we can request it using an API.
      • 1_preprocessed : Clean the data in each dataset.
      • 2_post_processed : Gather the data in a single usable product.
  • zooplankton_product : This is where you will find the product in a complient format. The format is NetCDF and all necessary metadata are available for the integration of the Pint and CF_xarray libraries.

What data should be included in the Seapopym data?

Not all data is always available. SeapoPym-data will try to standardize the available data to make them usable by SeapoPym.

List of data to include :

• Temperature
• Surface wind
• Dissolved oxygen
• Chlorophyll a
• Primary production
• Phytoplankton groups
• Zooplankton groups

Output resolution

• Temporal resolution: daily
• Spatial resolution: 1 degree

How to vizualize the process

Open the notebook in the data/stations/<location>/scripts folder and run the cells.

You can also use the voila command to run the notebook as a standalone web application.

voila <notebook>.ipynb