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SEA-MAT

Matlab Tools for Oceanographic Analysis

A collaborative effort to organize and distribute Matlab tools for the Oceanographic Community

Mailing list

Submitting M-files

Master Index of LOCAL M-files

Time Series Tools

Numerical Modeling Tools

Mapping Tools

Hydrographic Data Tools

Data Interface Tools

Miscellaneous Tools

Time Series Tools

• UTide: M-functions for unified tidal analysis of sea level or currents, with the ability to handle irregularly distributed and/or gappy times; accurate nodal/satellite corrections for multi-year records; confidence intervals based on residual spectra; and constituent selection diagnostics. From Dan Codiga (September 2011).
• T_Tide: A full-featured tidal analysis package written in Matlab! By Rich Pawlowicz, Bob Beardsley and Steve Lentz.
• Air-Sea: Compute surface wind stress and heat flux components from buoy and shipboard atmospheric and near-surface oceanographic time series measurements. Developed by Bob Beardlsley and Rick Pawlowicz. This is version 2.0.
• Timeplt: Stacked x-y and vector stick plots with Gregorian time labeling from Rich Signell. See also Timeplt5
• Bobstuff Vector Correlation, Complex Correlation, and other tools from Bob Beardsley (WHOI)
• RPS Stuff Miscellaneous time series tools from Rich Signell, a PPM image reader and writer, a program to read SeaBird CTD .CNV files, and more.
• ADCP i/o package Simple but robust tools to read RDI raw and processed binary data into MATLAB. Tested for a number of different WH, NB, and BB instruments with various firmware versions. From Rich Pawlowicz.
• RDI Workhorse ADCP==>NetCDF: This toolbox is for fixed platform self-contained Workhorse data collection. Developed by Jessica Cote, Marinna Martini, Fran Hotchkiss, and Chuck Denham at the USGS Woods Hole Field Center.
• ADCP Tool Box: This toolbox is a set of documented Matlab scripts that convert RDI data into NetCDF format. From Andree Ramsey.
• Cross Wavelet and Wavelet Coherence - for examining relationships in time frequency space between two time series. From Aslak Grinsted,Arctic Centre, University of Lapland.
• JLAB: Matlab freeware for data analysis by J. M. Lilly. 300+ heavily tested functions including industrial stength wavelet and time series analysis tools.

Numerical Modeling Tools

• NetCDF-Java Toolbox (njTBX) for Matlab: - njTBX implements the Unidata Common Data Model (a generalization of the NetCDF, OpenDAP and HDF5 data models), so can read both local and remote NetCDF-3 and NetCDF-4 files, data from OPeNDAP and ADDE servers, as well as GRIB, GRIB2, HDF4, HDF5, BUFR, URF and TDWR files. njTBX also uses high-level methods to return geospatial coordinate data (lon, lat, z and time) from “CF Compliant data” (uniform, rectilinear, or curvilinear horizontal coordinates, and fixed level or terrain-following vertical coordinates), which allows standardized access to a variety of local and remote bathymetry, remote sensing, atmospheric and oceanic modeling results.
• OM-Viz:Visualization and Analysis tools for SCRUM, ECOM and POM Ocean Models from Rich Signell.
• HOPS GUI: - Visualization tools for the Harvard Ocean Prediction System (HOPS) by Pedro Velez.
• HISWA-Viz:Visualization and Analysis tools for the HISWA wave model from Jeff list.
• Ocean Processes Numerical Modeling Laboratory (OPNML) Matlab library: Tools for working with the Dartmouth Finite Element Circulation Models.
• RSliCE - a nice GUI for ROMS model visualization, including horizontal z or s level slicing, arbitrary vertical slices along splined paths, velocity vector overlays, and more. Can access netcdf files locally or remotely via OpenDAP.

Mapping Tools

• Mapping tools : Projections, inverse-projections, coastline & elevation databases and more. From - who else? Rich Pawlowicz!
• Map Stuff: Coastline and lon/lon labeling stuff from Rich Signell. Check out this sample image. If you need coastline data, you might want to check out the Coastline Extractor.
• Read Global Topographic Data: Two Matlab functions to extract the data from two global topographic data base, ETOPO2v2 and GEOBEC.

Hydrographic Tools

• EasyKrig2.0 Toolkit: A gui-driven collection of routines to make Kriging of hydrographic and other spatial data a simple process, by Dr. Dezhang Chu.
• OCEANS toolbox (obsolete): A collection of routines using the EOS-80 "equation of state", including distances on an ellipsoidal earth. This OCEANS toolbox is now obsolete because the EOS-80 "equation of state" has been superseded by the Thermodynamic Equation Of Seawater - 2010 (TEOS-10), see www.TEOS-10.org. Evaluating distances on an ellipsoidal earth is now available from M_Map.
• GSW Oceanographic Toolbox: routines to compute the TEOS-10 thermodynamic properties of seawater, and other oceanographic properties. The TEOS-10 "equation of state" has been endorsed by the Intergovernmental Oceanographic Commission to replace the previous oceanographic standard of 1980, EOS-80. TEOS-10 has Absolute Salinity (instead of Practical Salinity) as its salinity argument. The GSW Oceanographic Toolbox has almost 100 functions, such as density, entropy, enthalpy, Conservative Temperature, buoyancy frequency, and various geostrophic streamfunctions. The SeaWater library of EOS-80, CSIRO Seawater Toolkit (obsolete), has now been superseded by the GSW Oceanographic Toolbox of TEOS-10.
• Dynamic Normal Modes routine from John Klinck.
• Optimal Multi-Parameter (OMP) Water Mass Mixing Analysis from the University of Hamburg. These m-files facilitate water mass mixing analysis for hydrographic data. The analysis is an inverse method looking for the best linear fit in a n-dimensional parameter space of tracers. A Users Guide is included!
• STAPLOT : A simple and flexible package designed to facilitate graphical analysis of hydrographic or other irregularly spaced data.
• WOCE tools A collection of WOCE water property data utilities from Paul Robbins (WHOI).
• FloatAxis: Plot data with different units (eg. temperature, salinity and density versus depth) on the same axes having the x-axis for the parameters "floating" below. The number of parameters plotted is not limited. From Blair Greenan.
  
• Temperature-Salinity Plot: The tsplot toolbox builds on the tsdiagram function found in the OCEANS toolbox at the Woods Hole Oceanographic Institution. You can produce TS plots using either a command line function (tsdiagram) or a Graphical User Interface (tsplot). From Blair Greenan.
• RPS Stuff Miscellaneous time series tools from Rich Signell, a PPM image reader and writer, a program to read SeaBird CTD .CNV files, and more.

Data Interface Tools

• NetCDF-Java Toolbox (njTBX) for Matlab: - njTBX implements the Unidata Common Data Model (a generalization of the NetCDF, OpenDAP and HDF5 data models), so can read both local and remote NetCDF-3 and NetCDF-4 files, data from OPeNDAP and ADDE servers, as well as GRIB, GRIB2, HDF4, HDF5, BUFR, URF and TDWR files. njTBX also uses high-level methods to return geospatial coordinate data (lon, lat, z and time) from “CF Compliant data” (uniform, rectilinear, or curvilinear horizontal coordinates, and fixed level or terrain-following vertical coordinates), which allows standardized access to a variety of local and remote bathymetry, remote sensing, atmospheric and oceanic modeling results.
• MEXCDF: A complete and efficient interface between MATLAB and NetCDF files, implemented through a mex file.
• NetCDF toolbox for Matlab 5. An powerful and elegant syntax for working with NetCDF data from within Matlab 5.
• MEXEPS: An interface between MATLAB and EPIC, NOAA PMEL's system for management, display, and analysis of oceanographic data.
• CSIRO NetCDF access tools. These tools allow simplified extraction of data from NetCDF files using either an interactive or command line interface.
• MSQUERY enables you to transfer the results of a query in the Microsoft Access 97 database program directly into your Matlab workspace using MS Windows ActiveX technology. The columns headings from the Access query are parsed and assigned as the variable names of the appropriate columns in your Matlab workspace. From Blair Greenan.

Miscellaneous Other Tools

• Float tracking software for Matlab 5 from Eurofloat.
• Mooring dynamics and design tools: A MATLAB 5 package to design, analyze and model oceanographic moorings, from Richard Dewey.
• Tidal Ellipse Tools from Zhigang Xu. These convert between u and v amplitude and phase parameters and tidal ellipse parameters (major axis, ellipticity, inclination and phase). There is also a program to estimate vertical profiles of tidal ellipse parameters, given sea-elevation gradients. Postscript documentation is provided.
• Spatial and Geometric Analysis (SaGA) toolkit. Gridding, tesselation, and more.
• EasyKrig2.0 Toolkit: A gui-driven collection of routines to make Kriging of hydrographic and other spatial data a simple process, by Dr. Dezhang Chu.
• EXTCONTOUR Extended contouring capabilities for Matlab 4 & 5. Can handle parametric surfaces, filled contours, publication-quality labelling and more.
• COLORBARF Produces a colorbar for a filled contour plot with the appropriate colors and tick marks. From Blair Greenan.
• Carter corrects single-beam echosounder depths using Carter's tables. (As you undoubtedly know, most ship's echosounders assume sound velocity to be 1500m/s, which is only very approximate. Carter's tables were thus produced to enable a correction to a more realistic depth, using an assumed mean sound speed that depends on latitude and longitude.) From Mike Meredith.
• Schlee makes a ternary diagram for sand, mud and gravel, assuming that mud=(silt+clay).
• Shepard_Ternary_Plot plots sand, silt and clay fraction data on a ternary plot that is marked with the Shepard classification scheme labels .
• Sand/Silt/Clay plotting routine based on a different classification scheme (Folk, 1954)
• MATHEMATICA-based Wavelet tidal analysis software (No longer active) - Tidal analysis tools for non-stationary tidal processes (e.g., barotropic river tides and continental shelf internal tides). Developed by David Jay and Ed Flinchem. Note: although this software isn't in Matlab, it seemed useful enough to link here anyway!
• Sturges - For some purposes we want to remove the annual cycle in a long data set, particularly for cross spectra with other data. Trivial for monthly data, but less so for weekly or daily data.
• TSG-QC - is a software for interactive analysis and validation of underway SST / SSS (Sea Surface Temperature and Sea Surface Salinity) measurements from a SeaBird Thermosalinograph (TSG). It has been developed under Matlab.

Related Web sites

• Mathworks link Exchange: links to User-contributed and Mathworks-contributed m-files.
• Mathworks File Exchange: library of files contributed by users and developers of MATLAB, Simulink and related products.
• Mat2html
• MathTools list of Matlab toolboxes: A surprisingly long list, and most toolboxes are free!
• Matlab Snack Bar from Chuck Denham at USGS.
• MACE is a MATLAB toolbox collects MATLAB .m functions for coastal engineers and researchers. The main purpose of this site is exchange our resources between the people in the coastal research area.