October 2014 bathymetry collected near Dumbarton Bridge in south San Francisco Bay, California

Sonar Data Collection. Bathymetry data were collected using a 234.5 kHz SEA (Systems Engineering and Assessment Ltd.) SWATHplus-M phase-differencing sidescan sonar. The sonar was pole-mounted on the 34-foot USGS mapping vessel R/V Parke Snavely and affixed to a hull brace. GPS position data were passed through an Applanix Position and Motion Compensation System for Marine Vessels POS/MV inertial measurement unit (IMU) to the sonar hardware and data-collection software. Sonar heads, GPS antennae, and the IMU were surveyed in place to a common reference frame with a Geodimeter 640 Total Station. The R/V Parke Snavely was outfitted with three networked workstations and a navigation computer for use by the captain and survey crew for data collection and initial processing.

Vessel Position and Attitude. An Applanix Position and Motion Compensation System for Marine Vessels (POS/MV) was used to accurately determine the position of the survey vessel. The POS/MV utilizes Global Navigation Satellite System (GNSS) data in combination with angular rate and acceleration data from the IMU and heading data from the GPS Azimuth Measurement Systems (GAMS) to produce accurate position and orientation information through a virtual network of base stations. As opposed to receiving high-accuracy Real-Time Kinematic (RTK) corrections, the POS records raw inertial and GNSS data while surveying, which are later refined through post processing to incorporate publicly available GPS data from nearby base stations. During post processing the POS/MV data is run through POSPac software to produce a Smoothed Best Estimate of Trajectory (SBET) file, which is then imported back into Swath Processor to produce high-accuracy positions relative to the WGS84 ellipsoid. The RMS results from our POS/MV surveys show positional errors of less than 5 cm in X, Y, and Z.

Sound Velocity Measurements. Sound velocity measurements were collected continuously with an Applied Micro Systems Micro SV deployed on the transducer frame for real-time sound velocity adjustments at the transducer-water interface. The Micro SV is accurate to +/- 0.03 m/s. In addition, sound velocity profiles (SVP) were collected with an Applied MicroSystems, SvPlus 3472. This instrument provides time-of-flight sound-velocity measurements by using invar rods with a sound-velocity accuracy of +/- 0.06 m/s, pressure measured by a semiconductor bridge strain gauge to an accuracy of 0.15 percent (Full Scale) and temperature measured by thermistor to an accuracy of 0.05 degrees Celsius (Applied Microsystems Ltd., 2005).

Sonar Sounding Processing. GPS data and measurements of vessel motion (heave, pitch, and roll) were combined in the POS/MV hardware to produce a high-precision vessel attitude packet. This packet was transmitted to the Swath Processor acquisition software in post-processing and combined with instantaneous sound velocity measurements at the transducer head before each ping. Up to 20 pings per second were transmitted with each ping consisting of 2048 samples per side (port and starboard). The returned samples were projected to the seafloor using a ray-tracing algorithm working with the previously measured sound velocity profiles in SEA Swath Processor (version 3.12.7). A series of statistical filters were applied to the raw samples to isolate the seafloor returns from other uninteresting targets in the water column. Finally, the processed data were stored line-by-line in both raw (.sxr) and processed (.sxp) trackline files.

Digital Elevation Model Production. The raw bathymetry data were filtered in SEA Swath Processor (version 3.12.7) and imported into CARIS HIPS and SIPS (version 9.1) for post-processing. Within CARIS a swath angle BASE (Bathymetric with Associated Statistical Error) surface was created at 1-m resolution and the subset editor used to manually eliminate any remaining outliers or artifacts. The average depth within each 1 by 1 m cell was exported as an ASCII text file and imported into Surfer (version 10) for interpolation using a linear kriging algorithm with a 1-simga nugget of 0.07 m and a 5 by 5 m search radius. The resultant grid was exported to ESRI ArcMap (version 10.7.1) for display and further analyses.

Datum Conversions. To convert the bathymetry from WGS84 ellipsoid heights to the tidal datum of MLLW the data were first transformed from WGS84(ITRF2000) to the NAD83(CORS96) ellipsoid using a 14-point Helmert transformation described by Soler and Snay (2004) using the command line tool CS2CS in the Proj4 library (http://trac.osgeo.org/proj/). A fixed Geoid09 offset of -32.58 m was then applied to convert the NAD83 ellipsoid heights to orthometric heights NAD83(CORS96)/NAVD88. The orthometric NAVD88 elevations were converted to MLLW (1983–2001 tidal epoch) by adding 0.37 m to the surface, the conversion provided by the CO-OPS division of NOAA for a 2005 bathymetric survey of south San Francisco Bay (Foxgrover and others, 2007).