Pacific Coastal & Marine Science Center
Software for processing, analyzing, and visualizing time-series oceanographic data
Taken from USGS Open-File Report 02-19
During the past several years, the sediment transport group in the USGS Coastal and Marine Geology Program (CMGP) has made major revisions to its methodology of processing, analyzing, and maintaining the variety of oceanographic time-series data. First, CMGP completed the transition of the its oceanographic time-series database to a self-documenting NetCDF (Rew et al., 1997) data format. Second, CMGP’s oceanographic data variety and complexity have been greatly expanded from traditional 2-dimensional, single-point time-series measurements (e.g., Electro-magnetic current meters, transmissometers) to more advanced 3-dimensional and profiling time-series measurements due to many new acquisitions of modern instruments such as Acoustic Doppler Current Profiler (RDI, 1996), Acoustic Doppler Velocitimeter, Pulse-Coherence Acoustic Doppler Profiler (SonTek, 2001), Acoustic Bacscatter Sensor (Aquatec, 2001). In order to accommodate the NetCDF format of data from the new instruments, a software package of processing, analyzing, and visualizing time-series oceanographic data was developed. It is named CMGTooL.
The CMGTooL package contains two basic components: a user-friendly GUI for NetCDF file analysis, processing and manipulation; and a data analyzing program library. Most of the routines in the library are stand-alone programs suitable for batch processing.
CMGTooL is written in MATLAB computing language (The Mathworks, 1997), therefore users must have MATLAB installed on their computer in order to use this software package. In addition, MATLAB’s Signal Processing Toolbox is also required by some CMGTooL’s routines. Like most MATLAB programs, all CMGTooL codes are compatible with different computing platforms including PC, MAC, and UNIX machines.
The GUI and some of the library routines call low-level NetCDF file I/O, variable and attribute functions. These NetCDF exclusive functions are supported by a MATLAB toolbox named NetCDF, created by Dr. Charles Denham, which is included in the above zip file. As of release 2008b, Matlab includes native netCDF support, however you will still need the USGS netCDF toolbox for CMGTooL to function properly, as the syntax differs. In addition, the netCDF toolbox requires the mexnc gateway, which may be dependent up on your version of Matlab. See http://mexcdf.sourceforge.net/downloads/ for the correct version and more information.
The CMGTooL GUI calls several routines that were initially developed by others. The authors would like to acknowledge the following scientists for their ideas and codes: Dr. Rich Signell (USGS), Dr. Chris Sherwood (USGS), and Dr. Bob Beardsley (WHOI).
Many special terms that carry special meanings in either MATLAB or the NetCDF Toolbox are used in this manual. Users are encouraged to read the documents of MATLAB and NetCDF for references.