MB-System Unix Manual Page: mb7k2jstar

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    mb7k2jstar
    Section:  MB-System 5.0  (1)
    Updated:  26 October 2009
    Index

    NAME

    mb7k2jstar - extracts subbottom profiler and/or sidescan sonar
    data from Reson 7k format data files into Edgetech Jstar format data files.

    VERSION

    Version 5.0

    SYNOPSIS

    mb7k2jstar [-Ifile -Atype
    -Bbottompickmode/bottompickthreshold -C
    -Fformat -Lstartline/lineroot
    -M -Ooutfile -Rroutefile -X -H -V]

    DESCRIPTION

    MB7k2jstar is a utility that extracts Edgetech subbottom
    profiler and sidescan data from Reson 7k format (MBIO format 88) data and
    outputs in the Edgetech Jstar format (MBIO formats 132 and 133).
    By default, mb7k2jstar extracts all channels of
    sonar data from the Reson 7k file to the Edgetech Jstar file.
    Edgetech sonar systems may include dual frequency sidescans and a
    subbottom profiler. Users may use the -A option to specify
    which channels are extracted. MB7k2jstar operates on single
    input files or on datalists. By default there will be a separate
    output file for every input file, but if the -O option
    is used to specify an output file, data from all input files will
    be directed to that single output file.

    The extracted Jstar data file(s) can be organized three ways. If the -O
    option is used to specify a single Jstar output file, then all of the
    Jstar data will be output to that single file. If the -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 Jstar data will be broken up by the sequential lines defined by
    the waypoints. In this case each output Jstar file will be named using the
    line root name specified by -Lstartline/lineroot with a sequential line
    number starting from startline. If neither the -O or -L
    options are used, each input swath file will have a corresponding Jstar output
    file.

    When the user specifies that all Edgetech sidescan and subbottom
    data be extracted but does not specify the output file name, the
    output files will have the "*.jsf" suffix recognized by Edgetech
    software. If the -A1 option is used to specify that only
    low frequency sidescan be extracted, the output files will have
    an "*.mb132" suffix. If the -A1 option is used to specify that only
    high frequency sidescan be extracted, the output files will have
    an "*.mb133" suffix.

    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.
    The -A3 option causes subbottom profiler records to
    be extracted. Default: All Edgetech sidescan and subbottom
    profiler 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 mb7k2jstar will use the altitude value associated with
    platform navigation. If bottompickmode = 2, then mb7k2jstar
    will extract the first arrival time from multibeam bathymetry in the
    7k data stream. If bottompickmode = 3, then mb7k2jstar
    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.
    Default: fIbottompickmode = 1.
    -C

    This option causes  mb7k2jstar to print out any comment records
    encountered in the input Reson 7k data.
    -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 mb7k2jstar 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 Edgetech Jstar (MBIO format 132/133) format file path.
    If -O is not invoked,
    the output jstar filename (or files if a datalist is being processed) will
    be the input swath filename with the ".s7k" or ".mb88" suffix replaced by a new suffix.
    An ".jsf" suffix is used when all Edgetech record types are extracted
    to the output, ".mb132" is used when the low frequency sidescan records are extracted,
    and ".mb133" is used when the high frequency sidescan records are extracted. The record
    types to be extracted are set using the -A option.
    -R

    routefile

    This option specifies an mbgrdviz route file containing the intended
    waypoints of the survey. If routefile is specified, mb7k2jstar
    will output Jstar data in files corresponding to the planned survey lines.
    The output Jstar 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 neither -O nore -R are invoked,
    the output Jstar filename (or files if a datalist is being processed) will
    be the input swath filename with an appropriate suffix appended (".jsf" for
    mixed Jstar files, ".mb132" for low frequency sidescan only files, and ".mb133"
    for high frequency sidescan only files).
    -V

    This option increases the verbosity of mb7k2jstar, causing it
    to print out messages regarding its progress to stdout.
    -X

    This option switches port and starboard sidescan channels.

    EXAMPLES

    Suppose that one has collected a Reson 7k datafile incorporating
    multibeam sonar data, sidescan data, and subbottom profiler data, and
    that the filename is:

            20050418_150155.s7k

    In order to extract all of the Edgetech sonar data into a Jstar file, one can use
    mb7k2jstar with no special arguments:

            mb7k2jstar -I 20040722_152111.s7k

    which yields the following output:

            Data records read from: 20050418_150155.s7k

                 Survey:        990

                 File Header:   1

                 Bluefin CTD:   989

                 Bluefin Nav:   760

                 Subbottom:     989

                 Low Sidescan:  990

                 High Sidescan: 989

            Data records written to: 20050418_150155.jsf

                 Subbottom:     989

                 Low Sidescan:  990

                 High Sidescan: 989

    One may also extract just the low frequency sidescan by using the -A1 option:

            mb7k2jstar -I 20040722_152111.s7k -A1

    which yields the following output:

            Data records read from: 20050418_150155.s7k

                 Survey:        990

                 File Header:   1

                 Bluefin CTD:   989

                 Bluefin Nav:   760

                 Subbottom:     989

                 Low Sidescan:  990

                 High Sidescan: 989

            Data records written to: 20050418_150155.mb132

                 Subbottom:     0

                 Low Sidescan:  990

                 High Sidescan: 0

    One may also extract just the high frequency sidescan by using the -A2 option:

            mb7k2jstar -I 20040722_152111.s7k -A2

    which yields the following output:

            Data records read from: 20050418_150155.s7k

                 Survey:        990

                 File Header:   1

                 Bluefin CTD:   989

                 Bluefin Nav:   760

                 Subbottom:     989

                 Low Sidescan:  990

                 High Sidescan: 989

            Data records written to: 20050418_150155.mb132

                 Subbottom:     0

                 Low Sidescan:  990

                 High Sidescan: 0

            2527 records output to segy file 20040722_154429.s7k.segy

    Users may process multiple Reson 7k files by inputting a datalist, or list of
    swath data files. All of the extracted data records can be output to a single
    file by specifying the output file with the -O option. For example, if
    one has a datalist file called datalistp.mb-1 that references three Reson 7k files:

            20050418_150155p.mb88 88

            20050418_151812p.mb88 88

    and one wants all the low frequency sidescan data collated into a single
    Jstar data file called 20050418_sslow.mb132, then use the following command:

            mb7k2jstar -A1 -I datalistp.mb-1 -O 20050418_sslow.mb132

    which yields the following output:

            Data records to extract:

                 Low Sidescan

            Data records read from: 20050418_150155p.mb88

                 Survey:        990

                 File Header:   2

                 Bluefin CTD:   989

                 Bluefin Nav:   760

                 Subbottom:     989

                 Low Sidescan:  990

                 High Sidescan: 989

            Data records written to: 20050418_sslow.mb132

                 Subbottom:     0

                 Low Sidescan:  990

                 High Sidescan: 0

            Data records read from: 20050418_151812p.mb88

                 Survey:        741

                 File Header:   2

                 Bluefin CTD:   741

                 Bluefin Nav:   563

                 Subbottom:     741

                 Low Sidescan:  742

                 High Sidescan: 741

            Data records written to: 20050418_sslow.mb132

                 Subbottom:     0

                 Low Sidescan:  742

                 High Sidescan: 0

            Total data records read from: 20050418_151812p.mb88

                 Survey:        1731

                 File Header:   4

                 Bluefin CTD:   1730

                 Bluefin Nav:   1323

                 Subbottom:     1730

                 Low Sidescan:  1732

                 High Sidescan: 1730

            Total data records written to: 20050418_sslow.mb132

                 Subbottom:     0

                 Low Sidescan:  1732

                 High Sidescan: 0

    SEE ALSO

    mbsystem(l), mbformat(l), mbinfo(l)

    BUGS

    No doubt.

     Index

    NAME
    VERSION
    SYNOPSIS
    DESCRIPTION
    AUTHORSHIP
    OPTIONS
    EXAMPLES
    SEE ALSO
    BUGS

Last Updated: 26 October 2009

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