Acoustic Doppler Current Meter (ADCP) Data
Data from ADCPs are processed using the ADCP Toolbox, a collection of MATLAB® routines written at the USGS Science Center in Woods Hole (WHSC), described in Coté and others (2005). We compare data from the four beams in pairs for symmetry and check for high-intensity reflection indicative of fish or other beam obstructions. "Bad" values are masked both manually and automatically and, where possible, a three-beam solution is used to fill in gaps caused by one compromised beam. Averages replace short-duration spikes in the data, with pad values replacing bad data points to maintain timebase consistency. Profiles are trimmed at the surface (6 percent of depth) using software provided by the manufacturer. However, bins that are out of the water at low tide are retained because during higher tides to retain the full tidal range. We remove data collected by the instrument before and after the deployment using the instrument's tilt and compass data to define when the tripod was stably settled on the ocean floor. Finally, we rotate the data to compensate for magnetic variation from true north at the site and convert from the beam coordinates recorded by the ADCP into earth coordinates. Processed versions of these data files are stored in EPIC-compliant netCDF files.
The WHSC commonly configures ADCPs to collect wave data simultaneously with current data. The software provided by manufacturer is used to split the raw file and compute the wave statistics and spectra. MATLAB® programs written at WHSC are used subsequently to create EPIC-compliant netCDF files from the individual waves file. The waves processing software is described in Sullivan and others (2006).
Acoustic Doppler Velocimeter (ADV) and Pulse Coherent Acoustic Doppler Profiler (PCADP) Data
Binary files logged by ADVs and PCADPs are processed using a series of MATLAB® routines in the Hydratools toolbox developed at the USGS WHSC (Martini and others, 2007). TheADV and PCADP both employ burst sampling at high frequency to characterize the water flow, so these data types have one time series for each burst logged, and each file contains as many bursts as were logged during the deployment. Statistics, including mean and standard deviation, maxima, minima, and medians are computed on the bursts as part of the initial conversion from binary to netCDF format and stored in a separate file.
In some ADVs, the instrument firmware from Sontek had a faulty Digital Signal Processing (DSP) chip that corrupted part, but not all, of the data from many bursts. Other sources of data degradation included fouling and flow obstacles such as seaweed and animals. To handle data flaws and retain as much viable data as possible, a system to vary the cutoff for minimum beam correlation and maximum standard deviation across each burst was developed to use with software for flagging bad sections. Small data gaps are interpolated over and larger sections of unusable data are replaced with pad values to maintain the timebase. Pressure and range to seabed data are despiked, and pad values substituted for obviously faulty records. After questionable data records are treated, the raw velocities are rotated into east-north-up coordinates, and the mean and standard deviation statistics are recalculated and data are low-pass filtered. Separate files are written for raw burst data and for time series of the averaged statistics of the bursts. The mean current velocities in the statistics files are comparable to the current data from mechanical current meters.
Optical Backscatter Sensor (OBS) Data
The Sontek Hydra datalogger converts raw OBS voltage measurements to counts with a 14-bit analog-digital converter. A linear conversion is used to convert counts back to volts so the data can be calibrated to sediment concentration using laboratory-derived calibration coefficients. After the point at which biological fouling significantly degrades the returns, data are replaced with the fill value. The OBS data are stored in the file with other data from the instrument that logged it (either an ADV or PCADP).
The Sontek Hydra dataloggers also log transmissometer data in counts, so a linear conversion is necessary to convert counts to volts. The SeaCAT, however, logs the raw voltage, so no conversion is required. The transmissometer data can also be presented either as percent light transmission (from 0 to 100, where 0 indicates complete occlusion). Beam attenuation coefficients (units of m-1) were computed from the light transmission observations as -4(ln(T/100)), where T is percent light transmission over a beam length of 0.25 meters. The beam attenuation coefficient is linearly proportional to the concentration of suspended material in the water if the particles are of uniform size and composition (Moody and others,1987). However, the size of the particles in the water changes with time, especially during resuspension events; therefore, the beam attenuation measurements must be interpreted with care. The processed data are usually stored in the file with other data from the logger to which the transmissometer was connected (MIDAS, ADV, PCADP, or SeaCAT).
Acoustic Backscatter Sensor (ABS) Data
Aquatec ABS raw data are logged in a set of binary files and processed with a MATLAB®-based toolbox that truncates files to include in-water times only, flags questionable points, and transforms the data to NetCDF format. The ABS data are not subject to the normal conversion to scientific units and quality-control procedures because calibration protocols are not yet in place. When in doubt, we prefer to preserve all samples rather than remove potentially useful data. These data are distributed as provisional.
Laser In Situ Suspended Scattering and Transmissometry (LISST) Data
LISST raw data are extracted from the logger and stored in the native
format. Sequoia Scientific Inc., the manufacturer, supplies processing software.
Calibration methods and additional software for working with the data and converting to NetCDF are under development at WHSC; and until they are completed, the raw data may be distributed as provisional.
MicroCAT (MC), SeaCAT (SC)
Software provided by Sea-Bird Electronics (SeaSoft) is used to validate the raw data and compute salinity from time series of temperature and conductivity measurements recorded by SeaBird sensors. Water density is ordinarily computed from the temperature, salinity and pressure measurements. Transmissometers and fluorometers are commonly logged by the SeaCats and MicroCats, so other variables may be present. Data processed with SeaSoft are stored in ASCII files so the final step is conversion to EPIC-compliant NetCDF using a program called asc2epic.
The logger for Imagenex sonar data stores each scan in a separate file, so after a 10-day deployment with hourly sampling, 240 files should exist. Those files are decoded to determine the signal amplitude for a series of pings or sweeps. The data are then converted for display in a polar view, with scaling for the radius of the sweep or ping. Both the raw data and radial images are stored in netCDF files. The sonar images are considered provisional, since processing and quality-control methods are still under development.