astnoisechisel(1)

NAME

   NoiseChisel - detect signal in a noisy image

SYNOPSIS

   astnoisechisel [OPTION...] ASTRdata

DESCRIPTION

   NoiseChisel   is   part   of   GNU   Astronomy  Utilities  0.2.33-8a3b.
   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. They
   will respectively show you the `Invoking NoiseChisel'  subsection,  the
   complete  `NoiseChisel'  section,  or  the full GNU Astronomy Utilities
   manual. In particular the first contains a very complete explanation of
   each option.

          info astnoisechisel

          info NoiseChisel

          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:

   -B, --minbfrac=FLT
          Minimum fraction of undetected area in a mesh.

   -E, --skysubtracted
          Input is already sky subtracted.

   -F, --minnumfalse=INT
          Min No. of false detection/segments for quantile.

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

   -H, --mhdu=STR
          Mask image header name.

   -k, --kernel=STR
          Kernel image file name.

   -M, --mask=STR
          Mask image file name.

   -U, --khdu=STR
          Kernel image header name.

          Output:

   -C, --grownclumps
          Save grownclumps instead of original clumps.

   --detectonly
          Do not do any segmentation.

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

   -K, --keepinputdir
          Do not remove input's dir info for output.

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

          Mesh grid:

   -a, --nch1=INT
          Number of channels along first FITS axis.

   -b, --nch2=INT
          Number of channels along second FITS axis.

   --checkmesh
          Store mesh IDs in `_mesh.fits' file.

   -d, --mirrordist=FLT
          Distance beyond mirror point. Multiple of std.

   --fullconvolution
          Ignore channels in convolution.

   --fullinterpolation
          Ignore channels in interpolation.

   --fullsmooth
          Ignore channels in smoothing.

   --interponlyblank
          Only interpolate over the blank pixels.

   -l, --lmeshsize=INT
          Size of each large mesh (tile) in the grid.

   -L, --lastmeshfrac=INT
          Fraction of last mesh area to add new.

   --meshbasedcheck
          Each mesh in one pixel in mesh check images.

   -n, --numnearest=INT
          Number of nearest neighbors to interpolate.

   -Q, --minmodeq=FLT
          Minimum acceptable quantile for the mode.

   -s, --smeshsize=INT
          Size of each small mesh (tile) in the grid.

   -T, --smoothwidth=INT
          Width of smoothing kernel (odd number).

          Detection:

   -c, --detquant=FLT
          False detections S/N quantile to find the true.

   --checkdetection
          False detection steps in file `_det.fits'.

   --checkdetectionsky
          Sky for false detections in file `_detsky.fits'.

   --checkmaskdet
          Mask detections and sky, `_maskdet.fits'.

   --checksky
          Final sky and its STD per pixel `_sky.fits'.

   --checkthreshold
          Threshold value on each mesh `_thresh.fits'.

   --detsnhistnbins=INT
          Det. S/N histogram bins, suffix `_detsn.txt'.

   -e, --erode=INT
          Num. erosions to apply after thresholding.

   --erodengb=4or8
          Use 4 or 8 connectivity in erosion.

   -i, --detsnminarea=INT
          Minimum area to calculate S/N in detection.

   -I, --dilate=INT
          Number of times to dilate true detections.

   --noerodequant=FLT
          Quantile for no erosion.

   --openingngb=4or8
          Use 4 or 8 connectivity in opening.

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

   -r,   --sigcliptolerance=FLT   Difference  in  STD  tolerance  to  halt
          iteration.

   -R, --dthresh=FLT
          Threshold (STD multiple) for false detections.

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

   -u, --sigclipmultip=FLT
          Multiple of standard deviation in sigma-clipping.

          Segmentation:

   --checksegmentation
          Store segmentation steps in file `_seg.fits'.

   --clumpsnhistnbins=INT Clump S/N histogram bins, suffix `_clumpsn.txt'.

   -g, --segquant=FLT
          Signal to noise ratio quantile for clumps.

   -G, --gthresh=FLT
          Threshold (STD multiple) to stop growing clumps.

   -m, --segsnminarea=INT
          Minimum area to find clumps S/N.

   -O, --objbordersn=FLT
          Minimum S/N for grown clumps to be one object.

   -v, --keepmaxnearriver
          Keep clumps with max touching river.

   -y, --minriverlength
          Minimum length of useful rivers in grown clumps.

          Operating modes:

   -?, --help
          give this help list

   --cite BibTeX citation for NoiseChisel.

   --nolog
          No log file for programs which make one.

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

   --onlydirconf
          Only read current directory configuration file.

   --onlyversion=STR
          Only run if the program version is this.

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

   -q, --quiet
          Only report errors, remain quiet about steps.

   --setusrconf
          Set default values for this user and abort.

   -S, --setdirconf
          Set default values for this directory and abort.

   --usage
          give a short usage message

   -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/

AUTHOR

   Written by Mohammad Akhlaghi

REPORTING BUGS

   Report bugs to [email protected].

COPYRIGHT

   Copyright  2015-2016, 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.

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.

GNU Astronomy Utilities 0.2.33-8aOctober 2016                   NOISECHISEL(1)

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