Setting up
CODAS3 shipboard ADCP data processing software
Please let us know
if you are downloading zip files and want to be informed if there are
updates or bug fixes.
What you need from other
sources:
- Python 2.3
- Matlab R12 or R13 (Matlab R14 is not yet supported)
What you need from
us:
- cmat.zip:
for Matlab m-files. Some are of very general
usefulness
(see matlab/misc/read_asc.m, for example), some are specific to our
shipboard
ADCP data processing system.
- bin*.zip, where the * is one of the following:
- mgw:
mgw for Win95/NT/XP (command line)
- lnx:
linux for Intel processor
- sol:
Solaris 2.x (SunOs 5.x) for Sparc processor (May be out
of date, may be discontinued.)
- sgi:
IRIX for Silicon Graphics (May be out of date, may be
discontinued.)
- doc.zip
contains the documentation alone. It is not included in
any other zip file.
- qdemos.zip
contains examples of data processed using
quick_adcp.py. It is not included in any other zip file.
Optional but recommended:
- source.zip
for all source code; even if you don't want to modify
anything,
this can be useful for finding out what the programs really do. It
is not required, however, unless you need to recompile for your
particular system. This is advisable if you use anything other
than Windows or a recent Linux distribution. Compilation should
work for any reasonably Unix-like system, including OSX, but may
require some configuration changes.
- demo.zip
contains the directory tree of a completely processed dataset.
This is the dataset used in an extensively documented tutorial.
If you want to see what the final directory tree looks like after
processing manually, download this zip file. The descriptive text "process.txt" is contained in
doc.zip. A subset of the demo directory is included in bin*.zip
because it is used to create the processing directory. The zip
archive qdemos.zip (above) also contains complete directory structures
for processed data, one of which is the same pingdata used in
demo.zip.
Old examples or demos: (no longer supported, but probably work)
- tdemo.zip for the Broadband Transect demo, if you are so
unfortunate as
to be stuck with a shipboard BB instrument and have data acquired with
Transect. In this case you still need demo.zip also, and should
work
through the regular tutorial before the Transect version. The latter
covers only aspects that are specific to Transect files. Processing
of NB Transect files is very similar, so if you are stuck with them,
look at this demo. There will probably never be a NBTransect demo
(please
try not to collect any more NB Transect files). RDI's new software
(VmDAS) is far superior to Transect should you be using a BB instrument.
- vmdas_demos.zip for Ocean Surveyor and Broadband VmDAS demos.
These are examples of data processed using the older (no longer
supported) script: "quick_adcp'prl".
The corresponding *.lst files are just directory listings of the zip
files,
so you can see what is in each, including the directory structure.
download codas3
files
How to install:
Everything is archived using the "zip" utility from InfoZip, and should
be
installed using "unzip" or a Windows equivalent. You almost
certainly already have one of these, or, if using Linux, can add it
from your distribution. If you don't, see the Info-ZIP website for current
downloads. If you have access to ftp only, then go to
ftp.uu.net/pub/archiving/zip and find the subdirectory for your
particular system.
All zip files are intended to be unzipped in the
SAME DIRECTORY (denoted PROGRAMS in various documentation).
In our case, it is /home/noio/programs; unzipping then creates
/home/noio/programs/codas3 and /home/noio/programs/matlab, with many
subdirectories in each of these. Generally, these subdirectory trees
and the files they contain should not be changed by users. For example,
don't run the tutorial where it lands when you unzip it--see below for
instructions.
On the assumption that anyone processing ADCP data will have a
windowing system with a browser, there is a new and expanding
collection of HTML documentation. A list of documentation files will
land in
PROGRAMS/index.html, which contains a link to the starting point for
ADCP processing. This link is also accessible over
the internet.
FOR UNIX:
In your .cshrc (or .profile, or wherever you keep your shell setup
instructions) add to your path the location of the
executables for your machine: this includes the binary executables,
and the locations of csh and python scripts. We install everything
under
/home/noio/programs, so we add the following to our path:
- /home/noio/programs/codas3/bin/sol (if we are working on a Sun)
or
- /home/noio/programs/codas3/bin/lnx (if we are working on linux)
- /home/noio/programs/codas3/bin/scripts (for python scripts) and
- /home/noio/programs/py_common (for more general python scripts)
To use quick_adcp.py, you will need to add three locations to your
PYTHONPATH environment
variable:
- /home/noio/programs/codas3/bin/scripts
- /home/noio/programs/py_common
- /home/noio/programs/logging/parsing
You should also add the location of the matlab directory which was
extracted from cmat.zip (we would add /home/noio/programs/matlab to our
MATLABPATH environment variable). Any time you run matlab programs
you should type "adcppath; radcppath" to add the appropriate programs
to your path. Alternatively, you can put these commands in your
~/matlab/startup.m file.
To run a Python script: if it is on your path, you
can simply type its name to execute it. The permission should already
be set to executable, and the top line is "#!/usr/bin/python", which is
correct for Linux systems. If you are on another Unix-like
system, you will need to change this top line to give the correct path
to your python executable.
FOR WINDOWS
Suppose (for example) everything was extracted into c:\programs.
Then you would add these
to your path
- c:\programs\codas3\bin\mgw (for cygwin executables)
- c:\programs\codas3\bin\scripts (for .bat, .py scripts)
and set the following environment variable (for your case):
- SET PROGRAMDIR=c:\programs
You should also go into your matlab path editor and add
c:\programs\matlab to the path, and save it. Any time you run matlab
programs you should type "adcppath; radcppath" to add the appropriate
programs to your path. Alternatively, run the commands once, then go to
"Set Path" and "Save".
Note that you must restart your machine after
changing autoexect.bat or config.sys for the changes to become
effective. (More explict instructions are
contained here .
HINT: The path to your PROGRAMS
directory may be quite long. You can create a network share of the
folder containing
PROGRAMS (recommend "read only", and then "map network drive")
and
assign the folder a drive letter (such as "N"). Then the above
description would use "n:\programs" instead of "c:\programs".
Running python scripts is not as simple under Windows as under Unix;
you can't simply invoke the python script by name. Instead, we
provide batch files with similar names to invoke the scripts, as
described
here.
Documentation for processing data using CODAS software starts here.