NAME

       Segment - segmentation based on signal structure

SYNOPSIS

       astsegment [OPTION...] ASTRdata

DESCRIPTION

       Segment  is  part  of  GNU  Astronomy  Utilities  0.22.  Segment will segment an initially
       labeled region based on structure with the signal. It will first find true  clumps  (local
       maxima), estimate which ones have strong connections, and then grow them to cover the full
       area of each detection.

       For more information, please run any of the following commands. In particular  the  second
       contains  a  very  comprehensive  explanation  of Segment's invocation: expected input(s),
       output(s), and a full description of all the options.

       All options and their values:
              $ astsegment -P

       Inputs/Outputs and options:
              $ info astsegment

       Full section in manual/book:
              $ info Segment

       Full Gnuastro manual/book:
              $ info gnuastro

       If you couldn't find your answer in the manual, you can get direct help  from  experienced
       Gnuastro users and developers. For more information, please run:

              $ info help-gnuastro

       Segment options:

              Input:

       --chdu=STR
              HDU/extension of convolved image in file.

       --convolved=FITS
              Convolved image file to avoid convolution.

       --dhdu=STR
              HDU containing detection image.

       -d, --detection=FITS
              Filename of detection image (to segment).

       -h, --hdu=STR/INT
              HDU containing values (science image).

       --khdu=STR
              HDU containing kernel image.

       -k, --kernel=FITS
              Filename of kernel to convolve with input.

       --sky=STR/FLT
              Filename of Sky values image to subtract.

       --skyhdu=STR
              HDU containing Sky value to subtract.

       --std=STR/FLT
              Filename of Sky standard deviation.

       --stdhdu=STR
              HDU containing Sky standard deviation.

       --variance
              STD input is actually variance.

              Tessellation (tile grid):

       --checktiles
              Tile IDs in an image, the size of input.

       -F, --remainderfrac=FLT
              Fraction of remainder to split last tile.

       --interpmetric=STR
              Interpolation metric (radial, manhattan).

       --interpnumngb=INT
              No. of neighbors to use for interpolation.

       --interponlyblank
              Only interpolate over the blank tiles.

       -L, --largetilesize=INT[,INT]
              Sim. to --tilesize, but for larger tiles.

       -M, --numchannels=INT[,..] No. of channels in dim.s (FITS order).

       --oneelempertile
              Display 1 element/tile, not full input res.

       --workoverch
              Work (not tile) over channel edges.

       -Z, --tilesize=INT[,INT]
              Regular tile size on dim.s (FITS order).

              Output:

       -D, --dontdelete
              Don't delete output if it exists.

       -K, --keepinputdir
              Keep input directory for automatic output.

       --noobjects
              Finish with true clumps, don't create objects.

       --outfitsnocommit
              No Git commit in 0-th HDU of output FITS.

       --outfitsnoconfig
              No metadata in 0-th HDU of output FITS.

       --outfitsnodate
              No 'DATE' in 0-th HDU of output FITS.

       --outfitsnoversions
              No versions in 0-th HDU of output FITS.

       -o, --output=STR
              Output file name.

       --rawoutput
              Output contains only CLUMPS and/or OBJECTS HDUs.

       --tableformat=STR
              'txt', 'fits-ascii', 'fits-binary'.

       --wcslinearmatrix=STR
              WCS linear matrix of output ('pc' or 'cd').

              Segmentation:

       -B, --minskyfrac=FLT
              Min. fraction of undetected area in tile.

       --checksegmentation
              Store segmentation steps in a file.

       --checksn
              Save clump S/N values into a file.

       -c, --snquant=FLT
              S/N Quantile of true sky clumps.

       --grownclumps
              Save grown clumps instead of original.

       -G, --gthresh=FLT
              Multiple of STD to stop growing clumps.

       --minima
              Built internal clumps from minima.

       --minnumfalse=INT
              Minimum number for S/N estimation.

       -m, --snminarea=INT
              Minimum area of clumps for S/N estimation.

       -O, --objbordersn=FLT
              Min. S/N for grown clumps as one object.

       -s, --clumpsnthresh=FLT
              S/N threshold of true clumps.

       -v, --keepmaxnearriver
              Keep clumps with peak touching a river.

       -y, --minriverlength=INT
              Minimum len of useful grown clump rivers.

              Operating modes:

       -?, --help
              give this help list

       --checkconfig
              List all config files and variables read.

       --cite BibTeX citation for this program.

       --config=STR
              Read configuration file STR immediately.

       --config-prefix=STR
              Custom prefix of option names config files.

       -C, --continueaftercheck
              Continue processing after checks.

       --lastconfig
              Do not parse any more configuration files.

       --minmapsize=INT
              Min. bytes to avoid RAM automatically.

       -N, --numthreads=INT
              Number of CPU threads to use.

       --onlyversion=STR
              Only run if the program version is STR.

       -P, --printparams
              Print parameter values to be used and abort.

       --quietmmap
              Don't print mmap'd file's name and size.

       -q, --quiet
              Only report errors, remain quiet about steps.

       -S, --setdirconf
              Set default values for this directory and abort.

       --usage
              give a short usage message

       -U, --setusrconf
              Set default values for this user and abort.

       -V, --version
              print program version

       Mandatory  or  optional  arguments  to long options are also mandatory or optional for any
       corresponding short options.

       GNU Astronomy Utilities home page: http://www.gnu.org/software/gnuastro/

REPORTING BUGS

       Report bugs to bug-gnuastro@gnu.org.

COPYRIGHT

       Copyright © 2015-2024 Free Software Foundation, Inc.  License GPLv3+: GNU  General  public
       license version 3 or later.
       This  is free software: you are free to change and redistribute it.  There is NO WARRANTY,
       to the extent permitted by law.

       Written/developed by Mohammad Akhlaghi

SEE ALSO

       The full documentation for Segment is maintained as a Texinfo manual.   If  the  info  and
       Segment programs are properly installed at your site, the command

              info Segment

       should give you access to the complete manual.