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

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