MB-System Unix Manual Page: mbareaclean

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    mbareaclean
    Section:  MB-System 5.0  (1)
    Updated:  29 September 2013
    Index

    NAME

    mbareaclean - Tool to automatically flag bad beams in swath
    sonar bathymetry data within a specified area.

    VERSION

    Version 5.0

    SYNOPSIS

    mbareaclean  -Rwest/east/south/north  -Sbinsize
    [-Dthreshold -Fformat -Iinfile
    -B -G -H -Mthreshold[/nmin[/nmax]]
    -N[-]min_beam[/maxbeam] -Ttype -V]

    DESCRIPTION

    mbareaclean identifies and flags artifacts in swath sonar
    bathymetry data within a specified area of interest.
    The input data are one swath file or a datalist referencing multiple
    swath files. The user may specify the work area in longitude and latitude
    bounds, along with a bin size in meters. If these are not specified, the
    program will attempt to set useful values. The area is divided into a grid with
    square cells of the specified bin size. As the data are read, each of
    the soundings that fall within one of the bins is stored. Once all of
    data are read, one or more statistical tests are performed on the soundings
    within each bin, providing there are a sufficient number of soundings.

    The user may specify one or both of the following actions:

      1) Previously unflagged soundings that fail a test are
    flagged as bad

      2) Previously flagged soundings that pass all tests are
    unflagged (the -G option)..

    The edit events are output to edit save files which can be applied
    to the data by the program mbprocess. These are the same edit save
    files created and/or modified by mbclean and mbedit.
    If a sounding's flag status is changed, that flagging action is output
    to the edit save file of the swath file containing that sounding. This
    program will create edit save files if necessary, or append to those that
    already exist.

    At present only two algorithms for identifying good and bad beams is
    implemented. The first is a simple median filter controlled by the
    -Mthreshold/nmin[/nmax] option. Soundings that differ from the
    median depth by a value greater than threshold times the sonar
    altitude will be considered "bad". So, if threshold = 0.05, then
    any sounding that is 5% greater or less than the median depth will be
    considered bad. The nmin parameter sets the minimum number of
    soundings required to use the median filter. The nmax parameter
    sets the maximum number of soundings allowed within a cell. If the number
    of initially good beams in a cell exceeds nmax, then only the nmax
    soundings nearest the median value remain unflagged, and the rest are
    flagged even if they meet the threshold test. The default values are
    threshold = 0.25, nmin = 10, and nmax = infinite.

    The second algorithm is a simple standard deviation filter controlled by the
    -Dthreshold/nmin option. Soundings that differ from the
    mean depth by a value greater than threshold times the standard deviation
    of the bin will be considered "bad". So, if threshold = 2, then
    any sounding that is more than 2 standard deviations greater or less than the mean depth will be
    considered bad. The nmin parameter sets the minimum number of
    soundings required to use the filter, The default values are
    threshold = 2.0 and nmin = 10.

    Two options allow limiting the soundings that may be flagged.
    -N[-]min_beam/maxbeam limits flagging to only those beams in
    (or out) of the given range.
    -Ttype limits flagging to soundings using the specified bottom
    detection algorithm.
    Many sounders use amplitude detection algorithms for the central beams
    and phase detection algorithms for the outer beams, falling back to
    amplitude detection when phase detection fails.
    Amplitude detections in the outer beams are second rate soundings and
    frequently have a higher range of errors than other soundings.
    Using -N and -T together allows stricter cleaning algorithms
    to be applied to these lower quality data. For example to flag bad all
    amplitude detections in the outer thirty beams which are more than one standard deviation
    from the mean: -N-30 -T1 -D1.

    AUTHORSHIP

    David W. Caress (caress@mbari.org)

      Monterey Bay Aquarium Research Institute

    Dale N. Chayes (dale@ldeo.columbia.edu)

      Lamont-Doherty Earth Observatory

    OPTIONS

    -B

    This option causes mbareaclean to flag as bad any previously unflagged
    soundings that fail one of the specified statistical tests. If neither -B
    or -G are specified, then the program will by default use this option.
    -D

    threshold[/nmin]

    Turns on use of a standard deviation filter test for the soundings.
    Soundings that differ from the
    mean depth by a value greater than threshold times the standard deviation
    will be considered "bad". So, if threshold = 2.0, then
    any sounding that is twice the standard deviation from the mean depth will be
    considered bad. The nmin parameter sets the minimum number of
    soundings required to use the standard deviation filter. The default values are
    threshold = 2.0 and nmin = 10.
    -F

    format

    Sets the data format used to read infile.
    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 uses the MBIO library
    and will read or write any swath sonar
    format supported by MBIO. A list of the swath sonar data formats
    currently supported by MBIO and their identifier values
    is given in the MBIO manual page. Default: format = 11.
    -G

    This option cause mbarealcean to unflag (set good) any previously flagged
    soundings that pass all of the specified statistical tests. If neither -B
    or -G are specified, then the program will by default apply the  -B
    option.
    -H

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

    infile

    Sets the input filename. If format > 0 (set with the
    -F option) 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
    and process the data in all of these files. Each input file will
    have an associated output file with either the ".esf" suffix.
    In the infile file, each
    data file should be followed by a data format identifier, e.g.:

            datafile1 11

            datafile2 24

    This program uses the MBIO library and will read or write any swath sonar
    format supported by MBIO. A list of the swath sonar data formats
    currently supported by MBIO and their identifier values
    is given in the MBIO manual page. Default: infile = "datalist.mb-1".
    -M

    threshold[/nmin]

    Turns on use of a median filter test for the soundings. If no other test is
    specified, the median filter test is used by default. Soundings that differ from the
    median depth by a value greater than threshold times the sonar
    altitude will be considered "bad". So, if threshold = 0.05, then
    any sounding that is 5% greater or less than the median depth will be
    considered bad. The nmin parameter sets the minimum number of
    soundings required to use the median filter, The default values are
    threshold = 0.25 and nmin = 10.
    -N

    [-]min_beam[/max_beam]

    Limits the beams to which flagging will be applied.
    Only soundings for beams from min_beam to max_beam, inclusive, will have flags applied.
    If min_beam is preceded by a - then only beams outside the range will be flagged.
    If max_beam is not given it will be set so that an equal number of beams lay above it as
    lay below min_beam. So for a Simrad EM1002 sounder with 111 beams -N-30 will only flag
    beam numbers 1 to 29 and 82 to 111.
    All good soundings, regardless of beam, will be included in the calculations of median, mean
    and standard deviation for the bin.
    -R

    west/east/south/north

    Sets the longitude and latitude bounds within which swath sonar
    data will be read, binned, and tested. Soundings lying outside these
    bounds will be ignored.

    Default: The program will determine and use a square area encompassing
    all of the data contained in the input files.
    -S

    binsize

    Sets the size of the bins to be used in meters. The area specified
    with the -R option will be broken into a grid with cells that
    are roughly binsize meters east-west and north-south.

    Default: A binsize equal to 0.2 times the maximum sonar altitude
    will be used.
    -T

    detect_type

    Limits the soundings to which flagging will be applied to only those which
    use the specified bottom detection algorithm.
    detect_type must be one of:

          0 - unknown algorithm

          1 - amplitude detection

          2 - phase detection
    -V

    Normally, mbareaclean works "silently" without outputting
    anything to the stderr stream.  If the
    -V flag is given, then mbareaclean works in a "verbose" mode and
    outputs the program version being used, all error status messages,
    and the number of beams flagged as bad.

    EXAMPLES

    Suppose we are working with a set of 5 Reson 8101 multibeam data files comprising a
    shallow water survey. One of these files has previously been edited with mbedit,
    so an esf file exists and contains a number of pre-existing edits.
    If we know that this survey is contained in the area specified
    by -R-122.42556/-122.41974/47.67111/47.67529, then we can invoke mbareaclean
    using:

            mbareaclean -Idatalist.mb-1 \

                    -B -M0.1/10 -S2.5 \

                    -R-122.42556/-122.41974/47.67111/47.67529  \

                    -V

    where the bin size is 2.5 meters, the median filter threshold is 0.1 (or 10%)
    of the sonar altitude, and the minimum number of sounding required for
    filtering is 10. The results look like:

     Program MBAREACLEAN

     Version $Id: mbareaclean.1 2155 2013-10-13 20:55:57Z caress $

     MB-system Version 5.0.beta29

     Area of interest:

          Minimum Longitude: -122.425560 Maximum Longitude: -122.419740

          Minimum Latitude:  47.671110 Maximum Latitude:  47.675290

          Bin Size:   2.500000

          Dimensions: 175 186

     Cleaning algorithms:

          Median filter: ON

          Plane fit:     OFF

     Output:

          Flag unflagged soundings identified as bad:  ON

          Unflag flagged soundings identified as good: OFF

     Processing 001_1730.fbt

     Sorting 41580 old edits...

     10000 of 41580 old edits sorted...

     20000 of 41580 old edits sorted...

     30000 of 41580 old edits sorted...

     40000 of 41580 old edits sorted...

     pings:1169  beams:   20233 good   41686 flagged   56150 null

     Processing 003_1733.fbt

     pings: 991  beams:   52439 good     159 flagged   47493 null

     Processing 005_1736.fbt

     pings:1011  beams:   53080 good     588 flagged   48443 null

     Processing 007_1739.fbt

     pings: 922  beams:   48854 good     212 flagged   44056 null

     Processing 009_1741.fbt

     pings:1017  beams:   53416 good     586 flagged   48715 null

     MBareaclean Processing Totals:

     -------------------------

     5 total swath data files processed

     5110 total pings processed

     271253 total soundings processed

     -------------------------

       0 soundings:  61919 flagged:      0 unflagged:      0  file:001_1730

       1 soundings:  52598 flagged:      0 unflagged:      0  file:003_1733

       2 soundings:  53668 flagged:      0 unflagged:      0  file:005_1736

       3 soundings:  49066 flagged:      0 unflagged:      0  file:007_1739

       4 soundings:  54002 flagged:      0 unflagged:      0  file:009_1741

    SEE ALSO

    mbsystem(1), mbclean(1), mbedit(1),
    mbinfo(1) mbprocess(1),

    BUGS

    The algorithms implemented in mbareaclean simply
    don't detect all bathymetric artifacts that
    are obvious to the eye on contour charts.  Although
    the autofiltering tools mbareaclean and mbclean
    often do a credible first pass at
    flagging obvious artifacts, we strongly recommend that
    any swath bathymetry processing stream include
    interactive editing of the
    bathymetry data (e.g. mbedit).

     Index

    NAME
    VERSION
    SYNOPSIS
    DESCRIPTION
    AUTHORSHIP
    OPTIONS
    EXAMPLES
    SEE ALSO
    BUGS

Last Updated: 29 September 2013

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