ctdam 1.0.0

Library to handle all steps when working with CTD data.

Intro

Welcome to the ctdam software package, a library to help with all the different stages in working with CTD data. For now, it focuses only on Sea-Bird CTD data, but we are open to extend to other CTD data types in the future. At the moment, the focus remains on fast and reliable conversion and processing of Sea-Birds .hex files. Data and metadata are stored inside python objects, with the possibility to export native .cnv files, as well as NetCDFs. In general, there are parsers for all the different Sea-Bird file formats: .hex, .xmlcon, .bl, .btl and .cnv .

To process CTD data, one needs to define workflow files, called ‘procedures’, .toml files which correspond to python dictionaries and e.g. look like this:

processing_config = {
    "output_type": "cnv",
    "output_dir": "somewhere",
    "modules": {
        "airpressure": {},
        "wildedit_geomar": {},
        "wfilter": {},
        "celltm": {},
        "alignctd": {},
        "Helmholtz_energy_ice": {},
        "binavg": {'bin_size': 0.1},
    },

}

All processing module behaviour can be modified via key-values, as seen for ‘binavg’. In the example config you can also see, that the native Sea-Bird processing modules can be mixed with custom ones (airpressure) and all gsw functions (Helmholtz_energy_ice). The Sea-Bird ones are either taken from seabirdscientific or are more efficient rewrites that stick to the same core logic. Its additionally possible to use the original Sea-Bird processing binaries, as long as they are installed on your machine.

Context

This software is developed for the German Marine Research Alliance (DAM) in the context of the Underway Research Data Project. The converter and parser are tested against a variety of data, acquired on different German research vessels. Because of the ongoing efforts to harmonise these infrastructures, the diversity of the test data may be smaller than thought and your data may pose problems to converter, parser or processing. Please feel free to contribute to this project in order to develop a toolkit, that is as general as possible.