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SEGMENT(1)			 User Commands			    SEGMENT(1)

NAME
       Segment - segmentation based on signal structure

SYNOPSIS
       astsegment [OPTION...] ASTRdata

DESCRIPTION
       Segment	is part	of GNU Astronomy Utilities 0.15.  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	detec-
       tion.

       For more	information, please run	any of the following commands. In par-
       ticular the second contains a very comprehensive	 explanation  of  Seg-
       ment'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.

       --onlyclumps
	      Finish after finding true	clumps.

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

       --rawoutput
	      Output only object and clump labels.

       --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.

       -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/gnuas-
       tro/

REPORTING BUGS
       Report bugs to bug-gnuastro@gnu.org.

COPYRIGHT
       Copyright  (C)  2015-2021,  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.

GNU Astronomy Utilities	0.15	   May 2021			    SEGMENT(1)

NAME | SYNOPSIS | DESCRIPTION | REPORTING BUGS | COPYRIGHT | SEE ALSO

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