This toolbox contains a variety of functions for accessing, processing, and visualizing Biogeochemical Argo data. Functions are designed to be maximally efficient, to provide access to the most up-to-date data available, and to allow for downloading and plotting of those data based on numerous user-defined conditions.
This repository can be cloned using the command line or the GitHub Desktop application. The files can also be downloaded directly in zipped format.
Before use, make sure the files from this repository are placed in a directory that is in the MATLAB search path. Or add the directory where they are located to the search path (https://www.mathworks.com/help/matlab/matlab_env/add-remove-or-reorder-folders-on-the-search-path.html). Or run it in the directory where the main_workshop script was placed.
For an overview of how to use this toolbox, step through the 'main_workshop' script (using the "Run and Advance" button of the MATLAB editor window), a tutorial that was developed for the 2021 GO-BGC Scientific Workshop (6/30/21).
initialize_argo.m : defines standard settings and paths and downloads synthetic profile index file
load_float_data.m : loads data of one or more specified float(s) into memory
select_profiles.m : returns profiles and corresponding floats based on input criteria
show_profiles.m : downloads float data and calls plot_profiles to create plot
show_sections.m : downloads float data and calls plot_sections to create plot
show_trajectories.m : downloads float data and calls plot_trajectories to create plot
main_workshop.m : tutorial script for GO-BGC Scientific Workshop (6/30/21)
calc_auxil.m : calculates various auxiliary variables from Argo float data
check_dir.m : determines if a directory needs to be created and does so if necessary
depth_interp.m : interpolates values for BGC-Argo parameters against depth
do_download.m : determines if a file should be downloaded or not
do_pause.m : pauses execution of main_workshop (if used without desktop)
download_float.m : downloads the Sprof NetCDF file for one float
download_multi_floats.m : calls download_float to download Sprof NetCDF files for multiple floats
get_lon_lat_lims.m : obtains maximum/minimum latitude and longitude values from input data
get_multi_profile_mean : calculates the mean profile of multiple profiles
get_var_name_units.m : returns the long variable name and units name for a given short parameter name input
plot_profiles.m : plots profiles of one or more specified float(s) for the specified variable(s)
plot_sections.m : plots sections of one or more specified float(s) for the specified variable(s)
plot_trajectories.m : plots trajectories of one or more specified float(s)
try_download.m : attempts to download a file from any of the specified GDACs
Use "help function_name" in the MATLAB command window to see a full description of input and output parameters for these functions.
At least MATLAB R2016b (or any newer release) is needed to use these functions without modifications.
An Internet connection is needed to get the latest versions of index and Sprof files; but the repository includes versions of these files so that it can be run offline.
Memory requirements depend on the number of profiles and variables that are simultaneously loaded into memory.
Please feel free to use the GitHub Issues and Pull Requests features to report any problems with this code and to suggest bug fixes.
More detailed information about quality control flags, raw and adjusted modes, etc., can be found in H. C. Bittig et al., 2019. Front. Mar. Sci. https://doi.org/10.3389/fmars.2019.00502.
Please cite this toolbox as:
H. Frenzel*, J. Sharp*, A. Fassbender, J. Plant, T. Maurer, Y. Takeshita, D. Nicholson, A. Gray, 2021. BGC-Argo-Mat: A MATLAB toolbox for accessing and visualizing Biogeochemical Argo data. Zenodo. https://doi.org/10.5281/zenodo.4971318.
*These authors contributed equally to the code.
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