How to make animated gif images

Animated GIF images are a good choice for creating animations of model results because the files are relatively small and portable compared to other movie formats. You make an animated GIF using, for example, gifsicle, as such:

gifsicle --colors 256 -O1 -l0 -d20 frames*.gif > movie.gif

The options are -O1 stores only the changed pixels, -l0 loops forever, and -d20 sets the delay to 20 hundreths of a second between frames. The trick is creating a bunch of GIF frames. I do this in MATLAB by first outputting to TIFF files, like this:

print -dtiff -r100 -zbuffer frame03.tiff

In matlab, use the eval function to write a series of frames like this:

frame = 1;
for n = 1:TOTALFRAMES;
plot commands;
eval(['print -dtiff -r100 -zbuffer frame',num2str(frame,'%2.2i'),'.tiff']);
frame=frame+1;
end

I make the figure as big in inches as I want it in hundreds of pixles (the -r100 gives me 100 pixels per inch). Then convert these images to GIFS using convert by ImageMagick like this:

convert frame03.tiff frame03.gif

Here is a script that gets you from a bunch of numbered TIFF frames to an animated GIF. Go knock yourself out.

The TGLO/TABS Current Prediction System: 2003 Annual Report

A year late, but still hot off the presses: the The TGLO/TABS Current Prediction System: 2003 Annual Report. This document covers basic information about the TGLO TABS modeling effort, covering input fields, model and grid information, output data styles and formats, and visualization techniques. Enjoy.

TAMU GCOOS Wiki

A new 'superblog' has been created to cover ongoing GCOOS and TABS developments, the TAMU GCOOS Wiki found at http://pong.tamu.edu/tiki

Interesting web visualization techniques

At style.org, there are a number of interesting visualization techniques.

How to get OpenDAP working for ROMS model output

Rich Signell sent me this advice on getting DODS/OpenDAP working for my model output:

The 5 step program to a blissful OpenDAP Life

• Inspiration: grab the mexcdf_dap binary for your platform
  and "get_roms_dap.m" at:
  http://cove.whoi.edu/~rsignell/mexcdf_dap Make sure that
  "which mexcdf53" points to your new OpenDAP-enabled mexcdf53
  mex file, and then run the "get_roms_dap" demo script.
  
  
• Kick Ass: Get the IDV http://my.unidata.ucar.edu/content/software/idv/.
  Replace the "idv.jar" file in your IDV installation
  directory with this updated "idv.jar":
  ftp://ftp.unidata.ucar.edu/pub/idv/untested/idv.jar
  Then get http://cove.whoi.edu/~rsignell/john/DefaultIdv_rps.tar.gz
  and unpack it from your "~/.metapps" directory so that it
  overwrites the files in the ~/.metapps/DefaultIdv directory. Start IDV,
  and in the Displays menu, select: Displays=>Favorite
  Bundles=>Adriatic=Test01
  
  
• Good Citizen: Serve your netcdf data via OpenDAP: Grab the "CGI Server
  Base" and "CGI Server NetCDF module" for your web server from
  http://opendap.org/download/index.html and then follow the install
  instructions at: http://opendap.org/server/install-html/install.html
  Basically all you do is unpack the binaries into your cgi-bin directory, edit
  a conf file to point to the places where you have netcdf files, and who can
  have access. It took me 35 minutes to get our OpenDAP server going!
  
  
• Ultimate Citizen: Make a THREDDS catalog
  http://my.unidata.ucar.edu/content/projects/THREDDS
  of your DODS-served data so folks can view it with tools like the IDV.
  These are simple XML files that just tell tools like IDV the protocol and
  location of the data. Check out an example at:
  http://cove.whoi.edu/~rsignell/adria-models.xml
  
  
• Go Uptown: If you want to get a bit fancier, install an aggregation server.
  http://www.opendap.org/server/agg-html/, which just makes it possible for
  groups of files to appear as one.
  

Office of Coast Survey - Historical Maps and Charts

A huge array of historical charts are available online:

Office of Coast Survey - Historical Maps and Charts

They use a goofy format, called MrSid, that must be decoded into something more sensible to use. I use the linux decoder created by Lizardtech found here. Once you decompress the image, you see why they use this format which compresses the image using wavelets.

Below is an image of a historical chart of the Mississippi River Delta first published in 1874 found by searching for key word 'Mississippi'. Click the image for a higher resolution image (still only 1/4 of full resolution).

TGLO skill estimates

Skill estimates for the mooring locations were calculated from a simulation lasting one year: summer 2001 to summer 2002. The largest skill is for buoy D, away from the Mississippi, and near the coast. Most of the skill estimates are around, or beneath zero, indicating that the model error is of a similar magnitude to the variance. The first two columns of numbers are the skill for the east-west and north-south velocities. The third column is the skill for speed. This particular model run had no buoyancy forcing, and represents the 'base' model skill, to which future, improved runs will be compared.

All timeseries use the mean of the data for the 'climatology', which produces the lowest skill estimates (see paper on skill linked below). Also, if the timeseries are filtered more, say with a 3-day boxcar, the skill is increased so that 4 to 5 of the skill estimates are positive.

B : -1.3335 : -0.3682 :-1.4042
D : -0.5348 : 0.2566 :-0.2602
F : -1.2726 : -2.9699 : -2.0598
J : -4.2723 : -0.9684 : -3.1124
K : -0.5815 : -1.4996 : -1.5841
N : -2.9575 : -1.5863 : -0.5991
R : -0.0772 : -0.5407 : -0.3376
S : -2.9290 : -1.9349 : -9.9881
V : -3.6531 : -5.8301 : -0.9598
W : -0.4621 : -0.3207 : -0.3583