.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH SEGMENT "1" "October 2022" "GNU Astronomy Utilities 0.19" "User Commands"
.SH NAME
Segment \- segmentation based on signal structure
.SH SYNOPSIS
.B astsegment
[\fI\,OPTION\/\fR...] \fI\,ASTRdata\/\fR
.SH DESCRIPTION
Segment is part of GNU Astronomy Utilities 0.19.
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.
.PP
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.
.TP
All options and their values:
$ astsegment \fB\-P\fR
.TP
Inputs/Outputs and options:
$ info astsegment
.TP
Full section in manual/book:
$ info Segment
.TP
Full Gnuastro manual/book:
$ info gnuastro
.PP
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:
.IP
\f(CW$ info help-gnuastro\fR
.PP
Segment options:
.IP
Input:
.TP
\fB\-\-chdu\fR=\fI\,STR\/\fR
HDU/extension of convolved image in file.
.TP
\fB\-\-convolved\fR=\fI\,FITS\/\fR
Convolved image file to avoid convolution.
.TP
\fB\-\-dhdu\fR=\fI\,STR\/\fR
HDU containing detection image.
.TP
\fB\-d\fR, \fB\-\-detection\fR=\fI\,FITS\/\fR
Filename of detection image (to segment).
.TP
\fB\-h\fR, \fB\-\-hdu\fR=\fI\,STR\/\fR/INT
HDU containing values (science image).
.TP
\fB\-\-khdu\fR=\fI\,STR\/\fR
HDU containing kernel image.
.TP
\fB\-k\fR, \fB\-\-kernel\fR=\fI\,FITS\/\fR
Filename of kernel to convolve with input.
.TP
\fB\-\-sky\fR=\fI\,STR\/\fR/FLT
Filename of Sky values image to subtract.
.TP
\fB\-\-skyhdu\fR=\fI\,STR\/\fR
HDU containing Sky value to subtract.
.TP
\fB\-\-std\fR=\fI\,STR\/\fR/FLT
Filename of Sky standard deviation.
.TP
\fB\-\-stdhdu\fR=\fI\,STR\/\fR
HDU containing Sky standard deviation.
.TP
\fB\-\-variance\fR
STD input is actually variance.
.IP
Tessellation (tile grid):
.TP
\fB\-\-checktiles\fR
Tile IDs in an image, the size of input.
.TP
\fB\-F\fR, \fB\-\-remainderfrac\fR=\fI\,FLT\/\fR
Fraction of remainder to split last tile.
.TP
\fB\-\-interpmetric\fR=\fI\,STR\/\fR
Interpolation metric (radial, manhattan).
.TP
\fB\-\-interpnumngb\fR=\fI\,INT\/\fR
No. of neighbors to use for interpolation.
.TP
\fB\-\-interponlyblank\fR
Only interpolate over the blank tiles.
.TP
\fB\-L\fR, \fB\-\-largetilesize\fR=\fI\,INT[\/\fR,INT]
Sim. to \fB\-\-tilesize\fR, but for larger tiles.
.HP
\fB\-M\fR, \fB\-\-numchannels\fR=\fI\,INT[\/\fR,..] No. of channels in dim.s (FITS order).
.TP
\fB\-\-oneelempertile\fR
Display 1 element/tile, not full input res.
.TP
\fB\-\-workoverch\fR
Work (not tile) over channel edges.
.TP
\fB\-Z\fR, \fB\-\-tilesize\fR=\fI\,INT[\/\fR,INT]
Regular tile size on dim.s (FITS order).
.IP
Output:
.TP
\fB\-D\fR, \fB\-\-dontdelete\fR
Don't delete output if it exists.
.TP
\fB\-K\fR, \fB\-\-keepinputdir\fR
Keep input directory for automatic output.
.TP
\fB\-\-noobjects\fR
Finish with true clumps, don't create objects.
.TP
\fB\-o\fR, \fB\-\-output\fR=\fI\,STR\/\fR
Output file name.
.TP
\fB\-\-rawoutput\fR
Output contains only CLUMPS and/or OBJECTS HDUs.
.TP
\fB\-\-tableformat\fR=\fI\,STR\/\fR
\&'txt', 'fits\-ascii', 'fits\-binary'.
.TP
\fB\-\-wcslinearmatrix\fR=\fI\,STR\/\fR
WCS linear matrix of output ('pc' or 'cd').
.IP
Segmentation:
.TP
\fB\-B\fR, \fB\-\-minskyfrac\fR=\fI\,FLT\/\fR
Min. fraction of undetected area in tile.
.TP
\fB\-\-checksegmentation\fR
Store segmentation steps in a file.
.TP
\fB\-\-checksn\fR
Save clump S/N values into a file.
.TP
\fB\-c\fR, \fB\-\-snquant\fR=\fI\,FLT\/\fR
S/N Quantile of true sky clumps.
.TP
\fB\-\-grownclumps\fR
Save grown clumps instead of original.
.TP
\fB\-G\fR, \fB\-\-gthresh\fR=\fI\,FLT\/\fR
Multiple of STD to stop growing clumps.
.TP
\fB\-\-minima\fR
Built internal clumps from minima.
.TP
\fB\-\-minnumfalse\fR=\fI\,INT\/\fR
Minimum number for S/N estimation.
.TP
\fB\-m\fR, \fB\-\-snminarea\fR=\fI\,INT\/\fR
Minimum area of clumps for S/N estimation.
.TP
\fB\-O\fR, \fB\-\-objbordersn\fR=\fI\,FLT\/\fR
Min. S/N for grown clumps as one object.
.TP
\fB\-s\fR, \fB\-\-clumpsnthresh\fR=\fI\,FLT\/\fR
S/N threshold of true clumps.
.TP
\fB\-v\fR, \fB\-\-keepmaxnearriver\fR
Keep clumps with peak touching a river.
.TP
\fB\-y\fR, \fB\-\-minriverlength\fR=\fI\,INT\/\fR
Minimum len of useful grown clump rivers.
.IP
Operating modes:
.TP
\-?, \fB\-\-help\fR
give this help list
.TP
\fB\-\-checkconfig\fR
List all config files and variables read.
.TP
\fB\-\-cite\fR
BibTeX citation for this program.
.TP
\fB\-\-config\fR=\fI\,STR\/\fR
Read configuration file STR immediately.
.TP
\fB\-C\fR, \fB\-\-continueaftercheck\fR
Continue processing after checks.
.TP
\fB\-\-lastconfig\fR
Do not parse any more configuration files.
.TP
\fB\-\-minmapsize\fR=\fI\,INT\/\fR
Min. bytes to avoid RAM automatically.
.TP
\fB\-N\fR, \fB\-\-numthreads\fR=\fI\,INT\/\fR
Number of CPU threads to use.
.TP
\fB\-\-onlyversion\fR=\fI\,STR\/\fR
Only run if the program version is STR.
.TP
\fB\-P\fR, \fB\-\-printparams\fR
Print parameter values to be used and abort.
.TP
\fB\-\-quietmmap\fR
Don't print mmap'd file's name and size.
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Only report errors, remain quiet about steps.
.TP
\fB\-S\fR, \fB\-\-setdirconf\fR
Set default values for this directory and abort.
.TP
\fB\-\-usage\fR
give a short usage message
.TP
\fB\-U\fR, \fB\-\-setusrconf\fR
Set default values for this user and abort.
.TP
\fB\-V\fR, \fB\-\-version\fR
print program version
.PP
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
.PP
GNU Astronomy Utilities home page: http://www.gnu.org/software/gnuastro/
.SH "REPORTING BUGS"
Report bugs to bug\-gnuastro@gnu.org.
.SH COPYRIGHT
Copyright \(co 2015\-2022 Free Software Foundation, Inc.
License GPLv3+: GNU General public license version 3 or later.
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
.PP
Written/developed by Mohammad Akhlaghi
.SH "SEE ALSO"
The full documentation for
.B Segment
is maintained as a Texinfo manual.  If the
.B info
and
.B Segment
programs are properly installed at your site, the command
.IP
.B info Segment
.PP
should give you access to the complete manual.