Bathymetry of the Historic Area Remediation Site in 2000 (3-m resolution Esri binary grid and 32-bit GeoTIFF, Mercator, WGS 84)

Processing of the data 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 (Clarke, 1998; see cross reference) 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), sidescan sonar backscatter 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 3 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. Naturally the solution is: weight_depth/weights for each node. For more information, visit the OMG website at <http://www.omg.unb.ca>.
First a blank binary grid and the weights and weight_depth files must be created:
Command line: make_blank -float gridFile
This command commences a dialog to enable an 8-bit image and 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 HARS data were created with a grid node spacing of 3 meters, a cutoff radius of 6 meters, and an inner radius to the weighting function of 1.5 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 1.5 gridFile filename.merged

Processing steps 1 and 2 produced a preliminary bathymetry data set. An error in the University of New Brunswick (Clarke, 1998, see cross reference) processing software that resulted in the multibeam observations not being properly projected onto a plane was discovered in 2003. A second error in the gridding algorithm was discovered in 2007, requiring a shift of 1/2 grid cell to northwest. This processing step uses the corrected software. Processing to further edit the data, correct for tides, and to produce the final grid of the data 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. Reference the bathymetric data to mean lower low water using the observed tidal data at Sandy Hook, NJ (NOAA tide station 8531680). The measured elevations were adjusted for fluctuations in sea level during the survey by subtracting tidal elevations predicted by a tidal model and low-frequency sea level observed at the National Oceanic and Atmospheric Administration Sandy Hook tide station located at 40 degrees 28 minutes N., 74 degrees 0.6 minutes W. The tidal model utilized nine constituents derived from a 4-month bottom pressure record obtained at Station A, located at 40 degrees 23.4 minutes N., 73 degrees 47.1 minutes W. in 38 m water depth about 2.7 km east of the HARS, during the winter of 1999-2000 (Butman, Alexander, and others, 2003; see cross references). An estimate of the error due to sea level remaining in the multibeam observations after the sea level correction is about 3 cm.
Using the adjusted tidal elevations, create a binary tide file to be used in merging the tidal heights with the bathymetric soundings.
Command line: binTide -year YYYY asciiTideFile BinaryTideFile
The program mergeTide brings the swath soundings to the MLLW vertical tidal datum:
Command line (tides): mergeTide -tide BinaryTideFile filename.merged
4. Create a new 3-meter grid of the edited bathymetric soundings from each line file (filename.merged) using the SwathEd routine weigh_grid.
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 1.5 gridFile filename.merged
5. Convert binary bathymetric grid to ESRI ASCII raster format:
Command line: r4toASCII gridFile.r4
This creates a file called gridFile.asc.

Create Esri bathymetry grid by importing data from ASCII raster format into Esri grid format.

ArcGIS 10.3.1 was used to export the grid to a 32-bit TIFF image. The extent and spatial reference were set to the original dataset, as was the cell size. The compression type was set to LZW. The NoData value is the default -3.40282306074e+38. The process also creates the TIFF world file automatically.

Removed the link to the TIFF image in the distribution section. The link was invalid.

Added keywords section with USGS persistent identifier as theme keyword.