MB-System Unix Manual Page

mbextractsegy

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



 

NAME


mbextractsegy - extracts subbottom profiler, center beam reflection,
or seismic reflection data from swath data supported by MB-System and
rewrites it as a SEGY file.


 

VERSION


Version 5.0


 

SYNOPSIS


mbextractsegy [-Byr/mo/da/hr/mn/sc -Eyr/mo/da/hr/mn/sc
-Fformat -Ifile -Jxscale/yscale/maxwidth
-Lstartline/lineroot -M -Osegyfile -Qroutetimefile
-Rroutefile -Ssampleformat
-Ttimeshift -Urangethreshold -Zplotmax -V -H]


 

DESCRIPTION


MBextractsegy is a utility for reading a swath sonar data file
or files, extracting subbottom profiler, center beam reflection,
or seismic reflection data, and outputting that selected data
as a SEGY file. Parameters such as sonar depth, seafloor depth, and
position are embedded into the SEGY data. The SEGY files are
output in a form used by the seismic reflection processing package
SIOSEIS. A "sinf" file containing statistics about the content
of the SEGY file is created automatically by MBextractsegy; this
file is named by adding a ".sinf" suffix to the SEGY filename.


At present, the only swath data formats from which subbottom data
can be extracted are format 88 (Reson 7k format), format 132
(Edgetech Jstar format), and format 133 (Edgetech Jstar format).


The extracted segy data file(s) can be organized three ways. If the -O
option is used to specify a single segy output file, then all of the
segy data will be output to that single file. If either the -Q or
-R options are used to specify a survey route file that includes
the waypoints covered while collecting the data file(s) referenced by
-Ifile, then the output segy data will be broken up by the
sequential lines defined by the waypoints. The -Q option specifies a
route file that includes the time at which each waypoint is reached in the
data, and the -R option specifies a route file of the form exported by
MBgrdviz. In the waypoint-driven case each output segy 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
segy output file with the ".segy" suffix added to the original filename.


MBextractsegy also generates a "first cut plot" script that will generate
grayscale section plots in Postscript of each segy file using the programs
MBsegygrid and mbm_grdplot. The -Z sets the trace value
corresponding to the maximum grayscale (black) in the section plots.


 

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



yr/mo/da/hr/mn/sc



This option sets the starting time for data allowed in the input data.
The -E option sets the ending time for data. If the
starting time is before the ending time, then any data
with a time stamp before the starting time or after the
ending time is ignored. If instead the starting time is
after the ending time, then any data between the ending
and starting time will be ignored. This scheme allows time
windowing both inside and outside a specified interval.
Default: yr/mo/da/hr/mn/sc = 1962/2/21/10/30/0.
-E

yr/mo/da/hr/mn/sc



This option sets the ending time for data allowed in the input data.
The -B option sets the starting time for data. If the
starting time is before the ending time, then any data
with a time stamp before the starting time or after the
ending time is ignored. If instead the starting time is
after the ending time, then any data between the ending
and starting time will be ignored. This scheme allows time
windowing both inside and outside a specified interval.
Default: yr/mo/da/hr/mn/sc = 2062/2/21/10/30/0.

-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. The default format is set
using the program mbdefaults..

-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 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 = "stdin".

-J



xscale/yscale/maxwidth



Sets the scale of the default section plots. The xscale value is
in inches per shot, and the yscale value is in inches per second.
The maxwidth value sets the maximum plot width in inches. If
xscale and the shot range imply a width greater than maxwidth,
then the section will be broken up into multiple plots.
Default: xscale = 0.01; yscale = 75; maxwidth = 45.0

-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 = "sbp".

-M






This option causes mbextractsegy 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 SEGY file path. If neither -O nore -R are invoked,
the output SEGY filename (or files if a datalist is being processed) will
be the input swath filename with ".segy" appended.

-Q



routetimefile



This option specifies route file containing the times that the survey reached
the intended waypoints. This text file consists of lines of the form:

        count waypoint longitude latitude heading time_d




where count is just an integer counter starting at 0, waypoint is the waypoint
number starting at 0, longitude and latitude are the waypoint position in
decimal degrees, heading is the heading in decimal degrees, and time_d is
the unix or epoch time (time since 00:00:00 January 1, 1970) in decimal
seconds that the survey reached this waypoint. This file can be generated from
an mbgrdviz route file and survey data using the program mbroutetime.
If routetimefile is specified, mbextractsegy
will output SEGY data in files corresponding to the planned survey lines.
The output SEGY 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 SEGY filename (or files if a datalist is being processed) will
be the input swath filename with ".segy" appended.

-R



routefile



This option specifies an mbgrdviz route file containing the intended
waypoints of the survey. If routefile is specified, mbextractsegy
will output SEGY data in files corresponding to the planned survey lines.
The output SEGY 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 SEGY filename (or files if a datalist is being processed) will
be the input swath filename with ".segy" appended.

-S



sampleformat



Sets the sample format desired for use in the output SEGY file. Options include:

        MB_SEGY_SAMPLEFORMAT_NONE           1


        MB_SEGY_SAMPLEFORMAT_TRACE          2


        MB_SEGY_SAMPLEFORMAT_ENVELOPE       3


        MB_SEGY_SAMPLEFORMAT_ANALYTIC       4




MB_SEGY_SAMPLEFORMAT_TRACE implies that the seismic trace is in the original,
most raw form with both positive and negative values.
MB_SEGY_SAMPLEFORMAT_ANALYTIC implies that the trace has been
been transformed from the original time series to an analytic signal containing
both real and imaginary parts. Both the real and imaginary signals
are stored in the SEGY file. MB_SEGY_SAMPLEFORMAT_ENVELOPE implies that the
analytic signal has been reduced back to a single real, positive-only envelope
signal by taking the magnitude of the real and imaginary parts at every sample.
It is important to note that this option only sets the desired sample format, and
the program may find it necessary to store the data in an alternate form. For
instance, if the user specifies MB_SEGY_SAMPLEFORMAT_TRACE or
MB_SEGY_SAMPLEFORMAT_ANALYTIC but the swath file only contains envelope data,
the data will be written in the envelope form. The default value of
MB_SEGY_SAMPLEFORMAT_NONE allows the program to choose the most appropriate
sample format.

-U



rangethreshold



If the -R option is specified, mbextractsegy breaks up the
output into files corresponding to survey lines specified in a route file.
This option sets the threshold distance in meters used to determine when
a waypoint along the route has been reached; the program considers the
next waypoint reached when the range to the waypoint becomes smaller
than rangethreshold and then ceases to decrease.
Default: rangethreshold = 25 m.

-Z



plotmax



Specifies the trace value corresponding to the maximum grayscale (black)
in the section plots. Default: plotmax = 50.

-V



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




 

EXAMPLES


Suppose that one has collected a set of Reson 7k datafiles incorporating
multibeam sonar data, sidescan data, and subbottom profiler data, and
that the filenames are:

        20040722_152111.s7k


        20040722_154429.s7k


        20040722_160809.s7k






In order to extract the subbottom data into segy files, one can use
mbextractsegy on each file in turn, for example:

        mbextractsegy -I 20040722_152111.s7k




which yields the following output:

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




In this command the 7k file format id of 88 is inferred from the
".7k" filename suffix.


One may also input a datalist file referencing all of the 7k files. The
contents of a datalist file (typically named datalist.mb-1) would look like:

        20040722_152111.s7k 88


        20040722_154429.s7k 88


        20040722_160809.s7k 88




where the second column is the data format id (see the mbsystem man page
for a discussion of datalist files). To operate on all the files in
a single command, use:

        mbextractsegy -I datalist.mb-1


 which yields the following output:

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


        2568 records output to segy file 20040722_160809.s7k.segy


        2569 records output to segy file 20040722_163148.s7k.segy




In this command the datalist format id of -1 is inferred from the
".mb-1" filename suffix.


Use of the -V option causes mbextractsegy to output information
about every tenth record written to a segy file. So:

        mbextractsegy -I 20040722_152111.s7k -V




which yields the following output:

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





        Outputting subbottom data to segy file 20040722_152111.s7k.segy


        file:20040722_152111.s7k record:10 shot:65  2004/204 15:20:42.083 samples:8330 interval:64 usec  minmax: 0.000000 17487.244141


        file:20040722_152111.s7k record:20 shot:75  2004/204 15:20:47.698 samples:8330 interval:64 usec  minmax: 0.000000 16525.875000


        ......... lines omitted ..........


        file:20040722_152111.s7k record:2510 shot:2565  2004/204 15:44:05.893 samples:8330 interval:64 usec  minmax: 0.000000 17616.189453


        file:20040722_152111.s7k record:2520 shot:2575  2004/204 15:44:11.507 samples:8330 interval:64 usec  minmax: 0.000000 31888.093750


        2527 records output to segy file 20040722_152111.s7k.segy




MBextractsegy also generates a "sinf" file containing statistics about the data in the segy
file 20040722_152111.s7k.segy. The contents of the sinf file 20040722_152111.s7k.segy.sinf are:

        SEGY Data File:      20040722_152111.s7k.segy




        File Header Info:


          Channels:                          1


          Auxiliary Channels:                0


          Sample Interval (usec):           64


          Number of Samples in Trace:     8330


          Trace length (sec):         0.533120


          Data Format:                IEEE 32 bit integer


          CDP Fold:                          0




        Data Totals:


          Number of Traces:               2527


          Min Max Delta:


            Shot number:                    56     2582     2527


            Shot trace:                      1        1        1


            RP number:                      56     2582     2527


            RP trace:                        1        1        1


            Delay (sec):              0.000000 0.000000 0.000000


            Range (m):                0.000000 0.000000 0.000000


            Receiver Elevation (m):   -224.030000 -2.860000 -221.170000


            Source Elevation (m):     -224.030000 -2.860000 -221.170000


            Source Depth (m):         2.860000 224.030000 -221.170000


            Receiver Water Depth (m): 51.510000 487.670000 -436.160000


            Source Water Depth (m):   51.510000 487.670000 -436.160000




        Navigation Totals:




          Start of Data:


            Time:  07 22 2004 15:20:37.029000  JD204


            Lon: -121.8573     Lat:   36.7755




          End of Data:


            Time:  07 22 2004 15:44:15.438000  JD204


            Lon: -121.8572     Lat:   36.7952




        Limits:


          Minimum Longitude:    -121.8574   Maximum Longitude:    -121.8572


          Minimum Latitude:       36.7755   Maximum Latitude:       36.7952







 

SEE ALSO


mbsystem(1), mbsegyinfo(1), mbsegylist(1), mbsegygrid(1),
SIOSEIS(http://sioseis.ucsd.edu/ )


 

BUGS


Doesn't support all of the data formats containing subbottom or center beam
reflection data..





 
Index




NAME


VERSION


SYNOPSIS


DESCRIPTION


AUTHORSHIP


OPTIONS


EXAMPLES


SEE ALSO


BUGS


Last Updated: 3 June 2013

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