mb7k2ss(1)

NAME
mb7k2ss - extracts sidescan sonar data from Reson 7k format data, bins and lays the sidescan onto the seafloor, and outputs files in the MBF_MBLDEOIH formst (MBIO format id 71).

VERSION
Version 5.0

SYNOPSIS
mb7k2ss [-Atype -Bbottompickmode/bottompickthreshold -C -Dinterpbins -Fformat -Ifile -Lstartline/lineroot -M -Ooutfile -Qroutetimefile -Rroutefile -Ttopogridfile -Urangethreshold -X -H -V]

DESCRIPTION
mb7k2ss is a utility that extracts Edgetech sidescan data from Reson 7k format (MBIO format 88) data and outputs in the MBF_MBLDEOIH format (MBIO format 71). Edgetech sonar systems may include dual frequency sidescans and a subbottom profiler. Users may use the -A option to specify whether low frequency or high frequency sidescan data are extracted. By default, low frequency sidescan is extracted. MB7k2ss can operate on a single input file or on a datalist referencing many input files. The raw sidescan consists of port and starboard channels, each with thousands of samples ordered uniformly in time from the sonar ping. MB7k2ss outputs a lower resolution single sidescan swath laid out onto the seafloor and ordered in pixels with uniform spacing in acrosstrack distance. Typically the output swath will have 4001 sidescan pixels, each representing an average of several raw samples. To achieve this result, the program calculates the location of each raw sample, and bins the samples into the output swath. By default, the program uses the sonar altitude and a flat bottom assumption to calculate the sample positions. If a topography grid covering the survey area is input using the -T option, then the sample positions will be calculated using that topography and the resulting sidescan will be properly located on the seafloor (that is, if the topography is accurate...). The method used to determine the sonar altitude is controlled using the -B option. By default, the program will use the altitude value recorded in the vehicle navigation records. Users may also specify use of nadir bathymetry from co-recorded multibeam bathymetry, or the altitude can be picked from the first arrival observed in the sidescan data itself. The extracted sidescan data file(s) can be organized three ways.By default there will be a separate output file for every input file. If the -O option is used to specify a single output file, then all of the specified sidescan data will be output to that file. If the -Q or -R option is used to specify a survey route file that includes the waypoints covered while collecting the data file(s) referenced by -Ifile, then the output sidescan data will be broken up by the sequential lines defined by the waypoints. The -R option requires a route file of the form exported by MBgrdviz. The -Q option requires a route file that includes the time at which each waypoint is reached in the data; this can be generated from a regular route file using mbroutetime. In either of these cases each output file will be named using the line root name specified by -Lstartline/lineroot with a sequential line number starting from startline. All output files will have a ".mb71" suffix. The program mbextractsegy is available to extract subbottom profiler data from Reson 7k data.

AUTHORSHIP
David W. Caress (caress@mbari.org)
  Monterey Bay Aquarium Research Institute
Dale N. Chayes (dale@ldeo.columbia.edu)
  Lamont-Doherty Earth Observatory

OPTIONS

-A  mode
    This option sets the types of data to be extracted and output. If -A1 is given, then any low frequency sidescan in the input will be extracted to the output. If -A2 is given, then any high frequency sidescan records are extracted. Default: Low frequency sidescan records are extracted.

-B  bottompickmode/bottompickthreshold
    This option sets the source of the sonar first arrival time used for laying out sidescan on the seafloor. If bottompickmode = 1, then mb7k2ss will use the altitude value associated with platform navigation. If bottompickmode = 2, then mb7k2ss will extract the first arrival time from multibeam bathymetry in the 7k data stream. If bottompickmode = 3, then mb7k2ss will pick the first arrival time in the sidescan sonar data by looking for the first sample with an amplitude > bottompickthreshold times the maximum amplitude in the trace. The altitude used will be the average of the first arrival times calculated for the port and starboard channels. Default: fIbottompickmode = 1.

-C
    This option causes mb7k2ss to print out any comment records encountered in the input Reson 7k data.

-D  interpbins
    Causes interpolation over gaps in the output sidescan resulting from draping the sidescan on topography. The interpbins values sets the maximum gap size over which interpolation will be applied.

-F  format
    Sets the data format used if the input is read from stdin or from a file. If format < 0, then the input file specified with the -I option will actually contain a list of input swath sonar data files. This program only reads Reson 7k format data files (MBIO format 88).

-H  This "help" flag cause the program to print out a description of its operation and then exit immediately.

-I  infile
    Sets the input file path. If format > 0 (set with the -f option or mbdefaults) then the swath sonar data contained in infile is read and processed. If format < 0, then infile is assumed to be an ascii file containing a list of the input swath sonar data files to be processed and their formats. The program will read the data in each one of these files. In the infile file, each data file should be followed by a data format identifier, e.g.:
         datafile1 88
         datafile2 88
    This program only reads Reson 7k format data files (MBIO format 88).

-L  startline/lineroot
    This option sets the starting line number and the output filename root used when -R is specified so that data are output according to planned survey lines. Default: startline = 1; lineroot = "jstar".

-M
    This option causes mb7k2ss to omit data during turns when extracting into line files according to a specified set of waypoints (-R option). The traces will not be output until the heading is within 15 degrees of the next survey line's bearing.

-O
    This option sets the output MBF_LDEOIH (MBIO format 71) format file path. If -O is not invoked, the output filename (or filenames if a datalist is being processed) will be the input swath filename with the ".s7k" or ".mb88" suffix replaced by a ".mb71) suffix. The record types to be extracted are set using the -A option.

-Q  routetimefile
    This option specifies a file containing the times that the survey reached the intended waypoints. This text file consists of lines of the form:
         count waypoint longitude latitude heading time_d
    where count is just an integer counter starting at 0, waypoint is the waypoint number starting at 0, longitude and latitude are the waypoint position in decimal degrees, heading is the heading in decimal degrees, and time_d is the unix or epoch time (time since 00:00:00 January 1, 1970) in decimal seconds that the survey reached this waypoint. This file can be generated from an mbgrdviz route file and survey data using the program mbroutetime. If routetimefile is specified, mb7k2ss will output data in files corresponding to the planned survey lines. The output file names will be based on lineroot and will include the line number starting with starline, both of which are specified using the -L options. If none of -O, -Q, or -R are invoked, the output filename (or files if a datalist is being processed) will be the input swath filename with an ".mb71" suffix appended.

-R  routefile
    This option specifies an mbgrdviz route file containing the intended waypoints of the survey. If routefile is specified, mb7k2ss will output sidescan data in files corresponding to the planned survey lines. The output file names will be based on lineroot and will include the line number starting with starline, both of which are specified using the -L options. If none of -O, -Q, or -R are invoked, the output filename (or files if a datalist is being processed) will be the input swath filename with an ".mb71" suffix appended.

-T  topogridfile
    This option specifies a GMT grid file containing a topography model of the survey area. When available, mb7k2ss, uses the topography to calculate the position of each raw sidescan sample on the seafloor prior to binning the sample into the swath data. This method is considerable improvement over the flat bottom assumption used when topography is unavailable. The grid file must contain topography (positive up) rather than bathymetry (positive down).

-U  rangethreshold
    If the -R option is specified, mb7k2ss breaks up the output into files corresponding to survey lines specified in a route file. This option sets the threshold distance in meters used to determine when a waypoint along the route has been reached; the program considers the next waypoint reached when the range to the waypoint becomes smaller than rangethreshold and then ceases to decrease. Default: rangethreshold = 50 m.

-V  This option increases the verbosity of mb7k2ss, causing it to print out messages regarding its progress to stdout.

-W  swathwidth This option sets the output sidescan swath width in meters. By default mb7k2ss calculates the swath width to use all of the samples available in the original data.

-X  This option switches port and starboard sidescan channels.

EXAMPLES
Suppose that we have collected two Reson 7k datafiles incorporating multibeam sonar data, sidescan data, and subbottom profiler data, and that the filenames are:
        20070809_173212.s7k
        20070809_175133.s7k After running mb7kpreprocess on these files to fix issues and prepare the data for processing, we will have two additional files named:
        20070809_173212.mb88
        20070809_175133.mb88 After editing the bathymetry in the ".mb88" files with mbedit, and running mbprocess to apply the edits, we will have two processed files that are, among other uses, suitable for sidescan extraction:
        20070809_173212p.mb88
        20070809_175133p.mb88 If we have two datalist files, one called datalist.mb-1 referencing the ".mb88" files with the following contents:
        20070809_173212p.mb88 88
        20070809_175133p.mb88 88 and another called datalistp.mb-1 referencing the first datalist with a $PROCESSED tag:
        $PROCESSED
        datalist.mb-1 -1 then we can extract the Edgetech sidescan from the processed files using:
        mb7k2ss -v -A1 -B2 -I datalistp.mb-1 \
            -M -X -R MAUV_Axial_1v4.rte -L1/Axial07SS \
            -T AxialCalderaMBARIAllTopo.grd Here the -R option specifies an MBgrdviz route file that was followed in collecting the data. By using this option, the output sidescan files will be broken into lines defined by the route waypoints, and the output filenames will be sequentially numbered. The -T option specifies a topography grid that is used by mb7k2ss to lay out the sidescan on the seafloor. The output appears as follows:
        Program mb7k2ss
     Version $Id: mb7k2ss.1 2096 2013-06-04 08:17:22Z caress $
     MB-system Version 5.1.1beta5
     Data records to extract:
          Low Sidescan
          Sidescan port and starboard exchanged
     Imported 45 waypoints from route file: MAUV_Axial_1v4.rte
     Grid read:
       Dimensions: 2072 3558
       Geographic Coordinate System Name: Geographic WGS84
       Geographic Coordinate System ID: 4326
       Longitude: 229.926767 230.060367 0.000065
       Latitude: 45.866667 46.026700 0.000045
       Internal Grid Projection Mode: 0
       Internal Grid Projection ID: epsg4326
     Data Read:
       grid_projection_mode: 0
       grid_projection_id: epsg4326
       nodatavalue: -10000000.000000
       nx: 2072
       ny: 3558
       min: -2302.588135
       max: -1382.877319
       xmin: 229.926767
       xmax: 230.060367
       ymin: 45.866667
       ymax: 46.026700
       dx: 0.000065
       dy: 0.000045
       data: 71467008
     Data records read from: 20070809_173212p.mb88
          Survey: 2330
          File Header: 2
          Bluefin CTD: 1152
          Bluefin Nav: 942
          Subbottom: 0
          Low Sidescan: 2328
          High Sidescan: 0
     Generating inf file for Axial07SS_0001_sslo.mb71
     Generating fnv file for Axial07SS_0001_sslo.mb71
     Data records written to: Axial07SS_0001_sslo.mb71
          Low Sidescan: 2759
          High Sidescan: 0
     Generating inf file for Axial07SS_0002_sslo.mb71
     Generating fnv file for Axial07SS_0002_sslo.mb71
     Data records written to: Axial07SS_0002_sslo.mb71
          Low Sidescan: 369
          High Sidescan: 0
     Data records read from: 20070809_175133p.mb88
          Survey: 2367
          File Header: 2
          Bluefin CTD: 1158
          Bluefin Nav: 942
          Subbottom: 0
          Low Sidescan: 2367
          High Sidescan: 0
     Generating inf file for Axial07SS_0003_sslo.mb71
     Generating fnv file for Axial07SS_0003_sslo.mb71
     Total data records read:
          Survey: 4697
          File Header: 4
          Bluefin CTD: 2310
          Bluefin Nav: 1884
          Subbottom: 0
          Low Sidescan: 4695
          High Sidescan: 0
      Total data records written:
           Low Sidescan: 4160
           High Sidescan: 0

SEE ALSO
mbsystem(1), mbformat(1), mbinfo(1), mb7kpreprocess(1), mb7k2jstar(1), mbextractsegy(1), mbbackangle(1), mbprocess(1)

BUGS
No doubt.