astsegment - Man Page

astsegment [OPTION...] ASTRdata

Segment is part of GNU Astronomy Utilities 0.23. 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/

Report bugs to bug-gnuastro@gnu.org.

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

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.