Bathymetry of the Sandy Hook artificial reef (2-m resolution Esri binary grid and 32-bit GeoTIFF, Mercator, WGS 84)

Processing of the data at sea was carried out by USGS personnel with assistance from the Ocean Mapping Group at the University of New Brunswick (UNB), Canada. A suite of processing software, called SwathEd, developed by the Ocean Mapping Group was used to process, edit, and archive the bathymetric soundings. These routines are designed to be run on a Unix and/or Linux operating system.
The processing and editing steps carried out on board the ship were:
1. Demultiplex (unravel) the Simrad data files using RT to generate separate files for a given raw file (filename.raw_all) containing navigation (filename.nav), depth soundings (filename.merged), backscatter intensity values (filename.merged_ssdata), acquisition parameters (filename.param) sound velocity at the transducer (filename.sv_tdcr) and sound velocity profiler information (filename.svp).
Command line: RT -packdown -background -WRITE -em1000 -CnC -prefix RawFiles/ -suffix _raw.all -out ProcessedFiles/InputFilenamePrefix InputFilenamePrefix
2. Edit the navigation data on-screen using the SwathEd routine jview to remove undesirable points, including turns at the ends of survey lines. Jview also rejects stray GPS fixes outside of the survey area, as set by the operator.
Command line: jview -rejectnav -navedit filename.nav
3. Make a copy of the edited navigation, and then create a new navigation file that has the bad fixes deleted from it.
Command line: mv filename.nav filename.nav_all Command line: appendNav -goodonly -comp filename.nav filename.nav_all
4. Merge the edited navigation back into the file containing the depth soundings using just the prefix of the filename. The location of the antenna relative to the motion reference unit is also entered here, along with a maximum time gap (in seconds) allowed between navigation fixes.
Command line: mergeNav -ahead 5.379 -right 3.851 -below 4.244 -time_limit 300 filename
5. Edit the multibeam soundings for each trackline. SwathEd displays blocks of data across and along the trackline. Anomalous points were identified by comparison to other points and by an understanding of the sea floor geology and morphology. Anomalous soundings were removed.
Command line: swathed filename.merged

Map the bathymetric soundings from each processed data file onto a digital terrain model (DTM) in the Mercator projection using weigh_grid with grid nodes spaced at 2 meters. The weigh_grid program creates a DTM by summing up the weighted contributions of all the provided data into the DTM. The weighted contributions only extend to a user defined region around the true location of the estimate (the cutoff). The weight of an individual point contribution decays away from the node location based on the order of the Butterworth (inverse weighting) filter (-power n), the width of the flat topped radius of the weighting function (-lambda n.n), and the absolute cutoff limit (-cutoff) that will be used for data points contributing to a node. In addition, each beam/other value can be pre-weighted if required to account for its reliability. A custom weight file for each beam is created by hand and input into the weigh_grid program using the -custom_weight option. Three files are created which are used by the weigh_grid program. An ".r4" file, which contains the grid node values in binary format, an "r4_weights" file, and an "r4_weight_depth" file. To do the summing of the weights, the .r4_weights file contains the sums of the weights for each data point contributing to the node, and the .r4_weight_depth file contains the sum of the weights x the depths. The solution is: weight_depth/weights for each node.
First a blank binary grid and the weights and weight_depth files must be created (user specifies bounds of map sheet, floating point or integer, cell size) :
Command line: make_blank -float gridFile
This command commences a dialog to input the map boundaries and resolution. The program also prompts for the projection type and parameters to be used creating the binary map file (custom Mercator projection, central longitude of -75 degrees, latitude of true scale 40 degrees north). The next command creates the weights and weight_depth files associated with the binary grid:
Command line: tor4 gridFile
These two steps create all three files with a gridFile prefix.
Next, each individual data file (.merged suffix) is added to the grid using weigh_grid. The grid of the Sandy Hook reef data was created with a grid node spacing of 2 meters, a cutoff radius of 6 meters, and an inner radius to the weighting function of 2 meters:
Command line: weigh_grid -omg -tide -coeffs -mindep -2 -maxdep -800 -beam_mask -beam_weight -custom_weight EM1000_Weights -butter -power 2 -cutoff 6 -lambda 2 gridFile filename.merged

Data were edited and processed to produce final grids and images of the data. Steps included:
1. Correct errors in soundings due to sound refraction, caused by variations in sound velocity profile, using the SwathEd refraction tool. These artifacts can be recognized in a cross-swath profile of a relatively flat patch of sea floor. When viewing the swath data across a profile, the sea floor will appear to have a "frown" or "smile" when in fact the data should be flat across the profile. Insufficient and/or erroneous sound velocity information, which is usually due to widely spaced or non-existent velocity profiles within an area, results in an under or over-estimate of water depth which increases with distance from the center of the swath. For a discussion of how this effect can be recognized in a swath bathymetric data file, see < http://www.omg.unb.ca/AAAS/UNB_Seafloor_Mapping.html>.
2. Remove erroneous soundings that were not edited in the field using the SwathEd program.
3. The measured elevations were adjusted for tidal fluctuations by subtracting tidal elevations and mean sea level predicted by the ADCIRC tidal model (Westerink and others 1994; Luettich and Westerink, 1995; see cross reference). A MATLAB script was used to interpolate the ADCIRC constituents along the ship track and then calculate the tidal elevation and mean sea level at the time of the survey. The vertical datum of the ADCIRC correction is NAVD88.
Using the adjusted tidal elevations, create a binary tide file to be using in merging the tidal heights with the bathymetric soundings.
Command line: binTide -year YYYY asciiTideFile BinaryTideFile
The program mergeTide brings the swath soundings to NAVD88.
Command line (tides): mergeTide -tide BinaryTideFile filename.merged
4. Correct outer beams for depth offset caused by error in EEPROM programming (see Logical Consistency Report)
Command line: deHump -depscale 0.0105 filename.merged
5. Create a new 2 meter grid of the bathymetric soundings using the SwathEd routine weighgrid.
Command line: weigh_grid -fresh_start -omg -tide -coeffs -mindep -2 -maxdep -800 -beam_mask -beam_weight -custom_weight EM1000_Weights -butter -power 2 -cutoff 6 -lambda 2 gridFile filename.merged
6. Convert binary bathymetric grid to Esri ASCII raster format:
Command line: r4toASCII gridFile.r4
This creates a file called gridFile.asc.

An Esri bathymetry grid was created by importing data from ASCII raster format into Esri grid format using ArcToolbox (ArcGIS 9.3) conversion tool ASCII to Raster.

The SwathEd processing software produced depth as positive values. Change depth from positive to negative using the raster calculator in Spatial Analyst (ArcGIS 9.3). Multiply shreef_bath2m grid by -1.

The Esri binary grid was exported from an ArcMap 10.3.1 document as a 32-bit GeoTIFF image. The extent, spatial reference, and cell size were set to the original raster dataset.

Added keywords section with USGS persistent identifier as theme keyword.