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DMQC-fun

v0.9. J. Even Ø. Nilsen, Ingrid M. Angel-Benavides, Birgit Klein, Malgorzata Merchel, and Kjell Arne Mork. Last updated: Mon Oct 16 17:32:21 2023 by jan.even.oeie.nilsen@hi.no

DMQC-fun is a comprehensive toolbox for performing DMQC on and salinity calibration of core data from Argo floats. The toolbox provides a system for semi-automated work-flow through the stages of downloading reference and float data, general DMQC and preparation of float data for MATLAB_OWC, running of MATLAB_OWC, and production of updated D-files. Graphs, metadata and information from these stages are automaticly integrated into reports for each float.

The toolboxes to install are:

DMQC-fun also includes a LaTeX report template and the functions and scripts produce snippets of content linked into that template. You will need a working version of LaTeX, and for instance dviPDFm to make PDF reports. However, this is not necessary for DMQC-fun to be useful. (You might even be able to link the produced figures and text parts into some other word processor of choice.)

The files and directories in this toolbox are as follows:

Contents The Matlab help text for the toolbox.

README.md The Github version of Contents.m.

init_dmqc Both init-file and setup. Contains all installation and setup instructions, as well as list of your floats and set up for parameters that all functions use. Read that first!

work_log.txt Explains the whole workflow of DMQC and the use of this toolbox, and a good place to log your overall progress. Understand more there!

load_referencedata A script to ingest, quick-check and update the list of reference data for Argo DMQC and OWC.

check_referencedata A function to plot and check reference data files. Used by load_referencedata, but can also be used stand alone.

download_floats This script downloads Argo float NetCDF-files from the Coriolis server, as well as the altimetry comparison and current greylist.

prepare_floats Does general DMQC, including your visual checking of the profiles, and builds the mat-files for OWC.

plot_profiles Used by PREPARE_FLOATS to make overview plots of the positions and T&S data.

inpolygon_referencedata A function used to find reference data inside a lon/lat polygon.

operator_CPcor_new A tool for finding operator CPcor to correct for pressure dependent conductivity bias, using near float deployment ship CTD data.

argo_sbe_CPcor A function used by OPERATOR_CPCOR_NEW to recaclulate salinity with new CPcor.

run_ow_calibration Runs OWC on all selected floats.

pair_floats_with_referencedata Compares float profiles to individual reference data profiles in the vicinity of float. Alternative when OWC is not possible, but also useful for any float.

write_D Produces the D-files to deliver. The last thing you do.

rdtime Translates time format in Argo reference data to Matlab serial days. Used by several functions.

plot_diagnostics_ow This function is copied from the OWC toolbox and modified here because we felt it needed some improvements. It will be used instead of the original if you make sure the path to our version is first in Matlab's path list.

./tex/ The LaTeX part of the toolbox. You can ignore this directory. It will be automaticly distributed when you do your initial setup (see INIT_DMQC). And there's a sample-DMQC-report.pdf here.

./lib/ The good old oceans and seawater toolboxes are provided here since they are not easily found anymore. Some other necessary tools are here as well. Unzip and add paths as needed.

./doc/ Contains the odd presentation etc.

./old/ Ignore this directory.

The following files are only examples of how you can edit the two files from the OWC toolbox that you will copy to your working directory. But you can safely ignore this directory, and DO NOT add the path to it! See instructions in INIT_DMQC.

./bak/ow_config.txt Example of how to set the OWC paths and mapping parameters.

./bak/set_calseries.m Example of how to set the OWC calibration parameters.

Feedback is most welcome!