NAME

       NoiseChisel - detect signal in a noisy image

SYNOPSIS

       astnoisechisel [OPTION...] ASTRdata

DESCRIPTION

       NoiseChisel  is  part  of  GNU Astronomy Utilities 0.19.  NoiseChisel Detects 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 particular  the  second
       contains  a very comprehensive explanation of NoiseChisel's invocation: expected input(s),
       output(s), and a full description 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/gnuastro/

REPORTING BUGS

       Report bugs to bug-gnuastro@gnu.org.

COPYRIGHT

       Copyright © 2015-2022 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 manual.  If the info and
       NoiseChisel programs are properly installed at your site, the command

              info NoiseChisel

       should give you access to the complete manual.