Rich Pawlowicz's Matlab Stuff

Matlab toolboxes available here:

Other people's useful Matlab stuff

1. M_Map home page

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1. T_Tide Harmonic Analysis Toolbox

 

 
 

One widely-used program for performing harmonic analysis of oceanic tides is the FORTRAN  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: https://www.eoas.ubc.ca/~rich/t_tide/t_tide_v1.1.zip

Enjoy!

A newer version (Jan/2003) is available as a zip file here: https://www.eoas.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 obsolet signal 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: https://www.eoas.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.




WARNING:   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.

(2014) If you want to do something that stretches the bounds of T_Tide, why not try Dan Codiga's UTIDE, which builds on T_TIDE by incorporating some of the things mentioned above. 


(2019) I've modified v1.3b by running it through the matlab editor and fixing a lot of the suggestions (removing semicolons after end, etc.), removing the call to a (nonexistent) t_get18consts, and changing the plotting in t_demo and t_equilib so that colours match between legends and lines (since MATLAB changed the default color order some of these no longer matched). The latest version is available here: https://www.eoas.ubc.ca/~rich/t_tide/t_tide_v1.4beta.zip.

(2022) As per the suggestion of R. Ray (see his note in the Journal "Ocean Science" at https://doi.org/10.5194/os-18-1073-2022) I have renamed the annual sidebars to M2 from H1/H2 to ALP2/BET2 (Alpha_2/Beta_2) for consistency with current naming standards. The latest version is available here: https://www.eoas.ubc.ca/~rich/t_tide/t_tide_v1.5beta.zip.


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2. LIM Toolbox

  Are you a limnologist? Do you want to compute the conductivity 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:


• limcond.m   - conductivity, specific conductivity, and salinity using my all-new algorithm that outperforms the following:
  
• limcondw.m - same using algorithm of Wuest et al. (1996)
• limSMEWW.m - same using algorithms of Standard Methods for the Examination of Water and Waste Water (American Public Health Association, 1998 and earlier)
• limR75 - same using Rossum (1975)
• limk25.m - standard composition-independent reference conductivity
• limexample.m - examples file
• limstate.m - limnological equation of state (Chen and Millero, 1986)
• limsal - convert g/l salinity from limcond to g/kg salinity using limstate
• limPESC.m - converts from mg/l to molar concentrations
• limcarbonate.m - carbonate chemistry: converts from alkalinity/ph to ionic concentrations
• limconsts.m - utility function with useful constants.
  

...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


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!

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2. RDADCP


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 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? evolving?) the format of their files as new instruments and instrument firmwares are developed. over time I have been keeping track of these changes....so...presenting:

RDADCP_Oct23v0.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 many 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.
 

 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.
Jun/2017 - WINRIVER II, VMDAS, Sentinel V-series, some bug fixes...
Jan/2018 - newer VMDAS
Sep/2021 - Sentinel V firmware 66 support
Oct/2023 - Pioneer DVL Support added

2015 - - These ADCP Processing Tools with a GUI written by Marius Becker were announced Sep 2007, but no longer seem to be available.


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3. RDDTX 

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).








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4. CTD_RD 

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.


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5. OCEANS toolbox


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 .



6. Extcontour


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/.

 

 

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!