MB-System Unix Manual Page: mbneptune2esf

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    mbneptune2esf
    Section:  MB-System 5.0  (1)
    Updated:  3 June 2013
    Index

    NAME

    mbneptune2esf - Tool to import beam flags from Simrad's Neptune system.

    VERSION

    Version 5.0

    SYNOPSIS

    mbneptune2esf [-Fformat
    -Iinfile -Ooutfile
    -Mmode -Rrules_file -V -H]

    DESCRIPTION

    mbneptune2esf imports manual data flagging performed using Simrad's NEPTUNE
    software and flags those beams in the corresponding MB-System files.

    The binstat tool in Simrad's NEPTUNE software has a number of advantages over mbedit
    as a tool for flagging bad data, including access to a variety of statistics from gridding
    the data. MB-System is generally more flexible and powerful in a number of other areas.
    mbneptune2esf tries to give you the best of both worlds.

    mbneptune2esf reads a binstat_?.rules file generated by manually cleaning
    data using the correlation plot in the binstat tool of the neptune sofware
    written by Kongsberg Simrad and writes these edits in a mbsystem esf file.
    The purpose of this tool is to allow data cleaning done using neptune to
    be carried into the mbsystem environment - thus making neptune a more useful
    tool.

    mbneptune2esf applies all the manual edits in the rules file given to those
    of the input files it recognises as matching the original lines.
    A line is considered to match if the line name contained in the rules file
    (e.g. 0002_20000408_221415) is part of the file name of the data file
    (e.g. 0002_20000408_221415.mb57).

    Swath line files should be converted to format 57 using mbcopy before
    using this program, as format 56 does not have the ability to flag data
    (although data can be zeroed - but zero may be a valid depth).

    Data flagged by rules generated in binstat is not flagged by this program -
    only manually flagged data is flagged.

    mbneptune2esf can also be used to transfer processing done in neptune to other surveys.
    Neptune breaks a survey up into a number of blocks and records all the
    processing done in these blocks. Changing a block results in a loss of
    all the existing processing information. When adding data to an existing
    survey that falls outside any existing block, all of the existing blocks
    must be removed, and therefore all of the processing is lost.
    mbneptune2esf and mbprocess
    can be used to zero all the beams flagged during neptune processing and
    the processed files can then be used as the basis for a new survey, preserving
    the manual flagging (but losing the flagged data).
    The zero data can then be easily flagged in neptune.

            cd $RAWDATAHOME

            ls *raw.all | while (read file) ; do

                            echo $file 56 1 >> datalist.mb-1

                    done

            cat $PROCHOME/old_survey/binstat_*.rules | mbneptune2esf -m3

            mbprocess

            cat *p.mb56 | handleEmX new_survey op

    This program flags beams by outputting the flags as
    edit events to an "edit save file", like that produced
    by mbedit. If an "edit save file" (named by adding
    a ".esf" suffix to the input swath filename) already
    exists, the edits are read in and applied before the
    mbneptune2esf flagging algorithms are used.
    Once generated, the edit events can be applied
    to the data using the program mbprocess, which
    outputs a processed swath data file.
    The mbprocess program is also used to merge
    edited navigation, recalculate bathymetry, and apply
    other corrections to swath bathymetry data.

    AUTHORSHIP

    Gordon Keith (gordon.keith@csiro.au)

      CSIRO Australia

    David W. Caress (caress@mbari.org)

      Monterey Bay Aquarium Research Institute

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

      Lamont-Doherty Earth Observatory

    OPTIONS

    -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 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.
    Only formats 56 and 57 files are affected by this program. Other files are
    ignored.
    -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 each one of these files. Each input file will
    have an associated output file with 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.
    Only formats 56 and 57 files are affected by this program. Other files are ignored.
    Default: infile = "datalist.mb-1".
    -M

    mode

    Sets the manner in which flagged by neptune are handled.

            mode = 1:       Flags the flagged beam.

            mode = 3:       Zeros the flagged beam.

    Default: mode = 1.
    -O

    outfile

    Specifies a file to write a copy of the beam information extracted from the
    rules file. Mostly for debugging purposes.
    -R

    rules_file

    The binstat rules file containing the manual flagging rules to be
    applied. Rules files are normally $PROCHOME/survey/binstat_block.rules.
    The LINES_PING_BEAM_RULE rules from this file will be applied to the
    matching line(s) in the input file.
    Default: rules_file = stdin.
    -V

    Normally, mbneptune2esf works "silently" without outputting
    anything to the stderr stream.  If the
    -V flag is given, then mbneptune2esf 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

    The normal use of mbneptune2esf would be to apply all the manual edits
    in a Neptune survey to the coresponding MB-System survey represented by a
    datalist:

            cat $PROCHOME/Broken_Reef/binstat_*.rules | \

                    mbneptune2esf -I/data/mbproc/Broken_Reef/datalist.mb-1

    Since the default input file is the datalist in the current directory,
    the following is equivalent if the Neptune environment variable PROCHOME
    evaluates to /data/proc:

            cd /data/mbproc/Broken_Reef

            cat /data/proc/Broken_Reef/binstat_*.rules | mbneptune2esf

    To apply the manual edits from a particular block of a Neptune survey
    to only one of the related data files:

            mbneptune2esf -R $PROCHOME/Broken_Reef/binstat_1.rules \

                    -F57 -I0032_20000408_221201.mb57

    To use the manual edits from a particular block of a Neptune survey
    to zero the beams of one of the related data files:

            mbneptune2esf -R $PROCHOME/Broken_Reef/binstat_2.rules

                    -M3  -F56 -I0002_20000408_153940_raw.all

    SEE ALSO

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

    BUGS

    mbneptune2esf does not flag beams flagged by rules in binstat,
    only beams that are flagged manually using the correlation plot.

    Probably plenty of others.

     Index

    NAME
    VERSION
    SYNOPSIS
    DESCRIPTION
    AUTHORSHIP
    OPTIONS
    EXAMPLES
    SEE ALSO
    BUGS

Last Updated: 3 June 2013

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