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NOISECHISEL(1)			 User Commands			NOISECHISEL(1)

NAME
       NoiseChisel - detect signal in a	noisy image

SYNOPSIS
       astnoisechisel [OPTION...] ASTRdata

DESCRIPTION
       NoiseChisel  is	part of	GNU Astronomy Utilities	0.15.  NoiseChisel De-
       tects and segments signal that is deeply	burried	in noise. It employs a
       noise-based  detection  and  segmentation method	enabling it to be very
       resilient to the	rich diversity of shapes in astronomical targets.

       For more	information, please run	any of the following commands. In par-
       ticular	the  second  contains  a  very	comprehensive  explanation  of
       NoiseChisel's invocation: expected input(s), output(s), and a full  de-
       scription of all	the options.

       All options and their values:
	      $	astnoisechisel -P

       Inputs/Outputs and options:
	      $	info astnoisechisel

       Full section in manual/book:
	      $	info NoiseChisel

       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

       NoiseChisel options:

	      Input:

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

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

       -h, --hdu=STR/INT
	      Extension	name or	number of input	data.

       --khdu=STR
	      HDU containing kernel image.

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

       --whdu=STR
	      HDU containing wide kernel image.

       -w, --widekernel=FITS
	      Filename of wider	kernel for better qthresh

	      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.

       --ignoreblankintiles
	      Don't write input's blanks in tiled output.

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

       -l, --label
	      Label/count detected pixels that are connected.

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

       --rawoutput
	      Output only detection labels & 1-elem/tile grid.

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

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

	      Detection:

       --blankasforeground
	      Blanks are foreground in erosion and opening.

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

       --checkdetection
	      Save all the detection steps to a	file.

       --checkdetsky
	      Save Sky value estimation	for pseudo-dets.

       --checkqthresh
	      Save quantile threshold estimation in file.

       --checksky
	      Final sky	and its	STD steps in a file.

       --checksn
	      Save pseudo-detection S/N	values to a file.

       --cleangrowndet
	      Remove small S/N grown detections.

       -c, --snquant=FLT
	      Quantile in pseudo-det. to define	true.

       --detgrowmaxholesize=INT
	      Max. area	of holes after growth to fill.

       --dopening=INT
	      Depth of opening after dthresh.

       --dopeningngb=INT
	      4	or 8 connectivity for dthresh opening.

       -d, --detgrowquant=FLT
	      Minimum quant. to	expand true detections.

       --erodengb=INT
	      Connectivity in erosion (number of ngbs).

       -e, --erode=INT
	      Number of	erosions after thresholding.

       --holengb=INT
	      4	or 8 connectivity for filling holes.

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

       -m, --snminarea=INT
	      Min. pseudo-detection area for S/N dist.

       --noerodequant=FLT
	      Quantile for no erosion.

       --openingngb=INT
	      Connectivity in opening (number of ngbs).

       --outliersclip=FLT,FLT Sigma-clip params	for qthresh outliers.

       --outliersigma=FLT
	      Multiple of sigma	to define outliers.

       --pseudoconcomp=INT
	      4	or 8 neighbors for labeling pseudo-dets.

       -p, --opening=INT
	      Depth of opening after erosion.

       -Q, --meanmedqdiff=FLT
	      Max. mean	and median quant diff. per tile.

       -R, --dthresh=FLT
	      Sigma threshold for Pseudo-detections.

       --skyfracnoblank
	      No blanks	in tile	undetected frac. (minskyfrac).

       --smoothwidth=INT
	      Flat kernel width	to smooth interpolated.

       --snthresh=FLT
	      Manually input pseudo-det	S/N threshold.

       -s, --sigmaclip=FLT,FLT
	      Sigma multiple and, tolerance or number.

       -t, --qthresh=FLT
	      Quantile threshold on convolved image.

	      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 NoiseChisel is maintained as	a Texinfo man-
       ual.  If	the info and NoiseChisel programs are  properly	 installed  at
       your site, the command

	      info NoiseChisel

       should give you access to the complete manual.

GNU Astronomy Utilities	0.15	   May 2021			NOISECHISEL(1)

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

Want to link to this manual page? Use this URL:
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