Rich Pawlowicz's Matlab Stuff


(changes Mar/2011)


Matlab toolboxes available here:

  • M_Map - mapping toolbox - Version 1.4 now available.
  • T_Tide - classical harmonic analysis with error estimates.
  • LIM - limnological conductivities, salinities, and densities.
  • AIR_SEA - air-sea heat flux estimates from standard observations

  • RDADCP - Reads RDI (now Teledyne RDI) binary and processed Acoustic Doppler Current Profiler files
  • RDDTX - Reads the .dt4 binaries produces by a BIOSONICS DTX digital echosounder (single beam, single tranducer systems only - not split or dual-beam systems).
  • CTD_RD- Reads Seabird Electronics CTD .cnv files.


  •  
  • Extcontour (obsolete) - extended contouring capabilities for matlab v4.
  • OCEANS (obsolete) - once handy oceanography stuff

  •  

    Other people's useful Matlab stuff

  • SEAMAT - Matlab for oceanographers: A central index and database for Matlab tools useful to oceanographers.

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    1. M_Map home page

    M_Map is a collection of routines that allow you to draw publication-quality maps in 18 different projections. M_Map includes a simple coastline and elevation database, and allows you to add your own data to those maps. Requires Matlab version 5 (or higher).

    Now available for downloading - version 1.4g  (released Oct 2013), as tar or zip file (if you are unpacking the zip, REMEMBER TO UNZIP SUBDIRECTORIES AS WELL - this is by far the most common problem people have).




       
       
    1. T_Tide Harmonic Analysis Toolbox

    2.  

       
       

      One widely-used program for performing harmonic analysis of oceanic tides is the FORTRAN Demonstration of tidal analysis package created by Mike Foreman (IOS), available at http://www.pac.dfo-mpo.gc.ca/sci/osap/projects/tidpack/tidpack_e.htm. However, the code is old, and difficult to understand and modify. Together with Steve Lentz and Bob Beardsley, I have rewritten that package in MATLAB, incorporating many useful extras. Currently the code is apparently trustworthy for performing a complete analysis.  Confidence intervals for the analysis can also be calculated.

      (1 Dec 2001) a new function "t_xtide" now provides tidal predictions in matlab for many stations worldwide using the XTIDE database!!

        (Oct 2002) T_tide described in:
       

      1. R. Pawlowicz, B. Beardsley, and S. Lentz, "Classical tidal harmonic analysis including error estimates in MATLAB using T_TIDE", Computers and Geosciences 28 (2002), 929-937.


       Please cite this article if you find T_Tide useful!

      The original version of the package (1/Dec/2001) is available as a zip file here: http://www.eos.ubc.ca/~rich/t_tide/t_tide_v1.1.zip

      Enjoy!

      A newer version (Jan/2003) is available as a zip file here: http://www.eos.ubc.ca/~rich/t_tide/t_tide_v1.2beta.zip. This includes a way of handling time series with many points (e.g. every minute for a year) without running out of memory, and a really preliminary attempt at analyzing 18.6+ year time series (which is really not right, so don't use it for this purpose!). Note: the recommended way of handling time series longer than one year but less than 18.6 years in length is to do it in one-year chunks - do not just suck in a 3 year time series.

      (Feb/2007) An experimental version of T_Tide that includes support for robust rather than the usual least-squares fitting is available from David Jay and Keith Leffler (who spend far more time thinking about tides than I do, these days). Their modifications will be incorporated into the current version at some point.

      (Mar/2011) I've modified v1.2b by changing finite to isfinite and call to obsoletsignal processing toolbox functions psd and csd to the newer functions pwelch and cpsd , which stops a list of annoying warnings. This newer version is available as a zip file here: http://www.eos.ubc.ca/~rich/t_tide/t_tide_v1.3beta.zip. This includes a way of handling time series with many points (e.g. every minute for a year) without running out of memory, and a really preliminary attempt at analyzing 18.6+ year time series (which is really not right, so don't use it for this purpose!). Note: the recommended way of handling time series longer than one year but less than 18.6 years in length is to do it in one-year chunks - do not just suck in a 3 year time series.



    3. LIM Toolbox

    4.   Are you a limnologist? Do you want to compute the conductivityNZ waters of lake water (or seawater at salinities less than about 4) from its chemical composition? Do you want to compute lake salinity from conductivity (to get density?). Then THIS is the toolbox for you! Contents are:


      ...and Pawlowicz (2008), Calculating the conductivity of natural waters, Limnology and Oceanography:Methods, 6:489-501 describes what is being done.



    1. Air-Sea Toolbox v1.1

    2. This is an updated version of the air-sea interaction toolbox originally developed by Bob Beardsley et al. (available through the SEAMAT page). This toolbox is useful if you want to compute the fluxes of heat and stress across the oceans surface (and assorted related things) from standard measurements of temperature, wind, etc. The update (v1.1) available here as a tar-file (or here as a gzipped tar file ) contains many additions and enhancements to the original code.

        The air-sea toolbox has been upgraded to v2.0 and is no longer distributed here - go to the SEAMAT page to get the new version!



       
       
    3. RDADCP

    4. Although the RDI binary and P-file formats are compact and efficient for storing data, it would be handy to be able to read that data into MATLAB. There are in fact various existing toolboxes that purport to do this, but I have found that they are  a) much too complicated for what I want (requiring netcdf, etc.), b) or they don't work, or c) both. One reason why these programs often don't work is because RDI is constantly changing (improving?) the format of their files. After several years of off-and-on development I think I have all (well, most) of the various firmware/version dependencies sorted out....so...presenting:

      RDADCP_mar10v0.zip - Two functions (rdpadcp.m and rdradcp.m) designed to read RDI binaries!

      Also included is a demo script (adcpdemo) so you can see how it works.

      These functions have been tested on datafiles from about half a dozen different instruments, with various firmware and software versions, and with consultation from RDI. However,  I know that YOUR instrument is some weird custom job that will immediately break it...if so please let me know. If it works fine...I'd appreciate knowing about it as well.
       
      Sep 2007 - Try some of these ADCP Processing Tools with a GUI written by Marius Becker.


       Changes:
      Nov/2003 - added support for navigation data in VMDAS and WINRIVER r-files.
      Aug/2004 - Some handling of junk data at beginning and end of file (apparently required for moored ADCPS using several flash cards)
      Sep/2005 - If your data was very, very, very noisy then the default median cleaning could bias results slightly negative due to a bug. This is now fixed.
      Dec/2005 - better handling of corrupted data blocks.
      Mar/2006 - OS/OO and WH-navigators now handled.
      Oct/2006 - WINRIVER R-file handling fixed.
      Mar/2010 - a lot of minor updates.



    5. RDDTX 
    6. BIOSONICS now has a nice digital echosounder that writes files in a binary format "for later use". This binary format has files ending in '.dt4'. If you want to read this stuff into matlab, use RDDTX.m (note - currently it only works for a single beam, single transducer system - NOT dual or split-beam systems).

      Nice picture


    7. CTD_RD 
    8. Seabird CTD processing software creates a nice self-describing data file in which the various header lines describe the contents. ctd_rd.m can read this format to produce a data structure containing the profile data, with field names taken from the column labels.



    9. OCEANS toolbox

    10. A collection of routines useful for oceanographers, including the UNESCO routines (specific heat capacity, the equation of state, etc.), various sound-speed equations, T/S diagrams, distances on an ellipsoidal earth, and more.

      As of 2010, I would heartily recommend going somewhere instead of using this old, obsolete, and superceded toolbox. For equation of state and thermodynamics stuff, go to the TEOS-10 website. Ellipsoidal distance are best handled by an algorithm in M_Map .

    11. Extcontour

    12. Extended contouring capabilities for Matlab. Can handle parametric surfaces, filled contours, publication-quality labelling and more.

      1. Original version , intended for v4.2. No longer really supported, but if you find a bug let me know and I will still try to help you!
      2. Original version of extcontour, with the minimal modifications necessary to make it run under Matlab5.0 (click on either the gzipped tar-file or the .zip archive ). I DO NOT RECOMMEND USING THIS FOR ANYTHING OTHER THAN V4 PROGRAMS YOU NEED TO GET RUNNING UNDER V5. For future use, the code of option 3 is a better choice.
      3. Most of the code from the original version is incorporated into matlab v5.0. However, there are a few bugs in the 5.0 implementation of contourf.m, contours.m, and clabel.m. Also, all capability to change font name/size/colour/rotation and label spacing was also left out of the 5.0 implementation of clabel.m. Updated and corrected versions of these m-files are available here (click on either the gzipped tar-file or the .zip archive ). These files should be placed in $MATLAB/toolbox/matlab/specgraph/.

      4.  

         

        As of v5.2 contourf.m and contours.m are satisfactory. However, clabel.m is still missing a few things which should (hopefully) be available in 5.3, when that comes out. A version of clabel.m for 5.2 that allows for such things as changing the font size and label spacing is available here .

        By v5.3 you don't need to come here any more!


    Last changed 10/Mar/2010. Questions and comments to Rich Pawlowicz , mailto:rich@eos.ubc.ca