mbextractsegy(1)

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 -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.

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  routefile
    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. 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.

-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.

-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
       Auxilliary 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(l), mbsegyinfo(l), mbsegylist(l), mbsegygrid(l), SIOSEIS(http://sioseis.ucsd.edu/ )

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