mbneptune2esfSection: MB-System 5.0 (1)
Updated: 3 June 2013
NAMEmbneptune2esf - Tool to import beam flags from Simrad's Neptune system.
SYNOPSISmbneptune2esf [-Fformat -Iinfile -Ooutfile -Mmode -Rrules_file -V -H]
DESCRIPTIONmbneptune2esf 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.
ls *raw.all | while (read file) ; do
echo $file 56 1 >> datalist.mb-1
cat $PROCHOME/old_survey/binstat_*.rules | mbneptune2esf -m3
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.
AUTHORSHIPGordon Keith (email@example.com)
David W. Caress (firstname.lastname@example.org)
Monterey Bay Aquarium Research Institute
Dale N. Chayes (email@example.com)
Lamont-Doherty Earth Observatory
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 | \
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:
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 \
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
Probably plenty of others.
Last Updated: 3 June 2013
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