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NOISECHISEL(1)			 User Commands			NOISECHISEL(1)

       NoiseChisel - detect signal in a	noisy image

       astnoisechisel [OPTION...] ASTRdata

       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:


	      HDU/extension of convolved image in file.

	      Convolved	image file to avoid convolution.

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

	      HDU containing kernel image.

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

	      HDU containing wide kernel image.

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

	      Tessellation (tile grid):

	      Tile IDs in an image, the	size of	input.

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

	      Interpolation metric (radial, manhattan).

	      No. of neighbors to use for interpolation.

	      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).

	      Display 1	element/tile, not full input res.

	      Work (not	tile) over channel edges.

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


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

	      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.

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

	      'txt', 'fits-ascii', 'fits-binary'.

	      WCS linear matrix	of output ('pc'	or 'cd').


	      Blanks are foreground in erosion and opening.

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

	      Save all the detection steps to a	file.

	      Save Sky value estimation	for pseudo-dets.

	      Save quantile threshold estimation in file.

	      Final sky	and its	STD steps in a file.

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

	      Remove small S/N grown detections.

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

	      Max. area	of holes after growth to fill.

	      Depth of opening after dthresh.

	      4	or 8 connectivity for dthresh opening.

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

	      Connectivity in erosion (number of ngbs).

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

	      4	or 8 connectivity for filling holes.

	      Minimum number for S/N estimation.

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

	      Quantile for no erosion.

	      Connectivity in opening (number of ngbs).

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

	      Multiple of sigma	to define outliers.

	      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.

	      No blanks	in tile	undetected frac. (minskyfrac).

	      Flat kernel width	to smooth interpolated.

	      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

	      List all config files and	variables read.

       --cite BibTeX citation for this program.

	      Read configuration file STR immediately.

       -C, --continueaftercheck
	      Continue processing after	checks.

	      Do not parse any more configuration files.

	      Min. bytes to avoid RAM automatically.

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

	      Only run if the program version is STR.

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

	      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.

	      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:

       Report bugs to

       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

       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)


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