shipspy: ship campaign data processing and standardisation

With shipspy, data from ship campaigns can be processed and standardised. A number of instruments are included.

Setup

Install shipspy:

pip install shipspy

Using shipspy

The following processing options are available.

DShip

With the dship subcommand, data from the ship integrated system can be processed. For an exemplary order to download underway data, see [1]. The following steps are done:

• Fixing time stamps
• Averaging to minutely time stamps
• Removing unphysical values
• Renaming variables, changing units, and adding attributes
• Converting to netCDF

To process dship data run

shipspy dship -i <input file> -o <output file> -a <attribute dictionary> -s <ship>

with

• input file: downloaded data from BSH or GEOMAR (or directly from the ship) as txt or dat file with unix time stamp (seconds since 1970-01-01)
• output file: file name of netCDF output file
• attribute dictionary: yaml dictionary with variable names and attribute. For example dictionaries for the different research vessels see rv_information
• ship: name of the ship. Options are Merian, Sonne, and Meteor

Renaming

The rename command can be used to

• fix the time stamps
• rename variables and add attributes
• convert units to SI
• remove unphysical values
• Convert and save the file as netCDF

To rename a data file run

shipspy rename -i <input file> -o <output file> -a <attribute dictionary> -d <instrument>

with

• input file: input file, file format depends on the instrument
• output file: file name of netCDF output file
• attribute dictionary: yaml dictionary with variable names and attribute. For examples see [1]
• instrument: instrument name. Options are calitoo, ceilometer, ctd, hatpro, microtops, radiosondes, test, uav

Sections

The section command adds a new coordinate and specifies the time period of the campaign. To use it run

shipspy section -i <input file> -o <output file> -s <section file> -t <time dimension name> -a <global attribute dictionary>

with

• input file: input netCDF file
• output file: file name of netCDF output file
• section file: txt file specifying the campaign dates (start, end, break) and the sections in which it should be divided. For an example, see [1].
• time dimension name: name of the time dimension. Default is time but sometimes it can be something like start_time.
• global attribute dictionary: yaml file with global attributes if wanted. For example files see [1].

The repository [1] with the settings for the ARC and additional scripts can serve as a template.

References

[1] Köhler, L. (2023). ARC: Processing of atmospheric and oceanographic measurements (Version v1.0.0) [Computer software]. https://github.com/LauraKoehler/arc_processing