After recovery of the instruments, proprietary software from each specific instrument manufacturer was used to download sensor measurements from each instrument and decode those measurments to instrument-specific data formats. The data were then converted from instrument-specific formats and calibrated. Units were modified to scientific EPIC-standard units (http://www.pmel.noaa.gov/epic/), and the data were stored in network common data format (NetCDF). EPIC is a set of standards that allow researchers from different organizations to share oceanographic data without having to translate "foreign" data types into the local vernacular. NetCDF is a very general, self-documenting, machine-transportable data format created and supported by the University Corporation for Atmospheric Research (UCAR) (http://www.unidata.ucar.edu/software/netcdf/). After the conversion, the data were carefully checked for inconsistencies due to instrument malfunctions and biological fouling and then edited to remove these spurious points. Also, the beginning and end of each data series were truncated to remove data collected out-of-water. The data were carefully checked at each stage of processing. After final editing, the data are considered to be the "best basic version" and include all variables recorded at the basic sampling interval. Best basic versions of most data files in NetCDF format are included in this report (see the Digital Data Files page).

Details below describe the conversion and calibration process for the equipment deployed by the USGS specific to this deployment. Additional documentation of the data processing for all instruments, as well as a description of the quality-control and review process, can be found in Montgomery and others (2008).

Data and processing descriptions for site N13, the lighthouse camera system, WERA, nearshore surveys and BUG are not included in this report. For inquiries regarding site N13, the lighthouse camera system, WERA, nearshore surveys and BUG data please see the contact information on the Digital Data Files page.

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            Nortek Aquadopp Acoustic Profiler

Teledyne RD Instruments Acoustic Doppler Current Profiler

The Teledyne RD Instruments (T-RDI) acoustic Doppler current profiler (ADCP) water flow observations were processed using Matlab®-based USGS software the ADCP Toolbox (available at http://woodshole.er.usgs.gov/operations/stg/Pubs/ADCPtools/adcp_index.htm). The ADCPs were normally configured to record data in beam coordinates (rather than earth coordinates). Upon recovery, the ADCP data were transferred to a personal computer using a PCMCIA flash memory card. These data were converted to NetCDF format using software available from the ADCP Toolbox. Matlab® routines were used to check for data quality, flag wild values, truncate the data to remove out-of-water data at the beginning and end of the deployment, and discard bins that were always exposed above the water surface. Some near-surface bins were not discarded even though the side-beam reflection at times of low tide renders these data invalid, so near-surface ADCP data must be interpreted with care. Normally, a 4-beam solution was used to rotate the data to earth coordinates. When one beam was flagged as bad, a 3-beam solution was used. If two or more beams were bad, the output file has a fill value. The end result of processing is an EPIC-standard NetCDF data file.

The ADCP wave observations were processed using the T-RDI proprietary software, WavesMon (see T-RDI Waves Primer), and Matlab®-based Wave Data Processing Toolbox software (available at http://pubs.usgs.gov/of/2005/1211/). The WavesMon software package was used to process the raw binary ADCP file and produce a series of data files from which the directional and nondirectional wave energy spectra were calculated. These spectra, in addition to the time series of wave parameters, were output as a series of ASCII files. These files were converted to NetCDF format using the Wave Data Processing Toolbox. This toolbox used a series of Matlab® routines to load the data from the WavesMon-generated ASCII files, flag wild values, truncate data to remove out-of-water data at the beginning and end of the deployment, and convert the data to an EPIC-standard NetCDF file.

Nortek Aquadopp Acoustic Profiler

Nortek Aquadopp acoustic profiler water flow observations were processed using the proprietary AquaPro software from Nortek (see www.nortek-as.com) and Matlab®-based software developed by the USGS. AquaPro was used to read the raw binary data file from the instrument and export a series of ASCII files containing instrument setup information, sensor altimetry information, and water flow and pressure data. Matlab® routines were used to check for data quality, flag wild values, convert data from beam to geographical coordinates, truncate data to remove out-of-water data at the beginning and end of the deployment, and convert the data to an EPIC-standard NetCDF file.

The Wave Data Processing Toolbox (available at http://pubs.usgs.gov/of/2005/1211/) was used to process wave observations from the Aquadopp. This toolbox loaded the ASCII data generated in AquaPro into Matlab® and performed PUV analysis (Gordon and Lohrmann, 2001) to estimate wave parameters. Errant data values were flagged, the data were truncated to remove out-of-water data at the beginning and end of the deployment, and the data were converted to an EPIC-standard NetCDF file.