Copyright (c) 2020 lnferris
ocean_data_tools simplifies the process of extracting, formatting, and visualizing freely-available oceanographic data. While there is a wealth of oceanographic data accessible online, some end-users may be dissuaded from utilizing this data due to the overhead associated with batch downloading it and formatting it into usable data structures. ocean_data_tools solves this problem by allowing the user to transform common oceanographic data sources into uniform structs (e.g. argo, cruise, hycom, mercator, woa, wod), call generalized functions on these structs, easily perform custom calculations, and make graphics.
Find a bug? Open an issue or contact lnferris@alum.mit.edu.
nctoolbox (https://github.com/nctoolbox/nctoolbox)
- Download bathymetry (see below).
- Download the nctoolbox (https://github.com/nctoolbox/nctoolbox).
- Run each demonstration in demos/demos.m.
Functions are named using a two-part system. The prefix (argo_, bathymetry_, general_, etc.) indicates the appropriate data source, while the suffix (_build, _profiles, _section, etc.) indicates the action performed. Functions with the _build suffix are special because they load raw data into uniform structs (e.g. argo, cruise, hycom, mercator, woa, wod). Uniform structs created by _build functions are compatable with any general_ function.
Main functions are located in ocean_data_tools/. Demonstrations are located in demos/. Test datas are located in data/. Shell scripts for batch downloading data are located in shell_scripts/. While shell scripts can be run directly in a macOS Terminal, running them in Windows requires Cygwin (https://www.cygwin.com/) or similar. Python syntax examples are located in python/, which might be expanded at a later date.
Download argo (www.argo.ucsd.edu) data directly from GDAC FTP servers using either the Coriolis selection tool (http://www.argodatamgt.org/Access-to-data/Argo-data-selection), or the US GDAC (http://www.usgodae.org/cgi-bin/argo_select.pl).
Alternatively run shell_scripts/download_argo to download data via File Transfer Protocol.
To get bathymetry data (for bathymetry_dir), download Smith & Sandwell under "Global Topography V19.1" (https://topex.ucsd.edu/marine_topo/) in netcdf form (topo_20.1.nc).
The url for MOCHA Mid-Atlantic Bight climatology is embedded. See Rutgers Marine catalog (http://tds.marine.rutgers.edu/thredds/catalog.html).
For HYCOM, download subsetted data directly using NCSS. Get the data url by visiting https://www.hycom.org/dataserver/gofs-3pt1/analysis. For example, click Access Data Here -> GLBv0.08/expt_57.7 (Jun-01-2017 to Sep-30-2017)/ -> Hindcast Data: Jun-01-2017 to Sep-30-2017. Click on the NetcdfSubset link. Set constraints and copy the NCSS Request URL at the bottom of the page. Run shell_scripts/download_hycom_lite. To download multiple months or years, run shell_scripts/download_hycom_bulk_daily (partition files by day) or shell_scripts/download_hycom_bulk_monthly (partition files by month). Please use responsibly.
For Mercator, download Copernicus Marine data directly from FTP servers. Go to http://marine.copernicus.eu/services-portfolio/access-to-products/ and make a Copernicus account. Use the selection tool to download GLOBAL_ANALYSIS_FORECAST_PHY_001_024. Alternatively run shell_scripts/download_mercator. Before running the script, follow the instructions for modifying your ~/.netrc file in the comments of the script.
For GO-SHIP (https://usgoship.ucsd.edu/hydromap/) data, get CTD data (for ctdo_dir) by choosing a GO-SHIP cruise (https://cchdo.ucsd.edu/search?q=GO-SHIP) and downloading the CTD data in whp_netcdf format. Visit https://exchange-format.readthedocs.io/en/latest/index.html# for information about whp_netcdf parameters, specific to GO-SHIP. Get LADCP data (for uv_dir, wke_dir) at https://currents.soest.hawaii.edu/go-ship/ladcp/. There is information about LACDP processing at https://www.ldeo.columbia.edu/~ant/LADCP.html.
Functions build the World Ocean Atlas url based on arguments, but coarser resolutions and seasonal climatologies are available at https://www.nodc.noaa.gov/OC5/woa18/woa18data.html. Note NCEI is scheduled to update data urls in the near future. Functions will be updated as such.
Search and select World Ocean Database data at https://www.nodc.noaa.gov/OC5/SELECT/dbsearch/dbsearch.html.