.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH NOISECHISEL "1" "October 2016" "GNU Astronomy Utilities 0.2.33-8a3b" "User Commands"
.SH NAME
NoiseChisel \- detect signal in a noisy image
.SH SYNOPSIS
.B astnoisechisel
[\fI\,OPTION\/\fR...] \fI\,ASTRdata\/\fR
.SH 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.
.PP
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.
.IP
info astnoisechisel
.IP
info NoiseChisel
.IP
info gnuastro
.PP
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:
.IP
info help\-gnuastro
.PP
NoiseChisel options:
.IP
Input:
.TP
\fB\-B\fR, \fB\-\-minbfrac\fR=\fI\,FLT\/\fR
Minimum fraction of undetected area in a mesh.
.TP
\fB\-E\fR, \fB\-\-skysubtracted\fR
Input is already sky subtracted.
.TP
\fB\-F\fR, \fB\-\-minnumfalse\fR=\fI\,INT\/\fR
Min No. of false detection/segments for quantile.
.TP
\fB\-h\fR, \fB\-\-hdu\fR=\fI\,STR\/\fR
Extension name or number of input data.
.TP
\fB\-H\fR, \fB\-\-mhdu\fR=\fI\,STR\/\fR
Mask image header name.
.TP
\fB\-k\fR, \fB\-\-kernel\fR=\fI\,STR\/\fR
Kernel image file name.
.TP
\fB\-M\fR, \fB\-\-mask\fR=\fI\,STR\/\fR
Mask image file name.
.TP
\fB\-U\fR, \fB\-\-khdu\fR=\fI\,STR\/\fR
Kernel image header name.
.IP
Output:
.TP
\fB\-C\fR, \fB\-\-grownclumps\fR
Save grownclumps instead of original clumps.
.TP
\fB\-\-detectonly\fR
Do not do any segmentation.
.TP
\fB\-D\fR, \fB\-\-dontdelete\fR
Don't delete output if it exists.
.TP
\fB\-K\fR, \fB\-\-keepinputdir\fR
Do not remove input's dir info for output.
.TP
\fB\-o\fR, \fB\-\-output\fR=\fI\,STR\/\fR
Output file or directory name.
.IP
Mesh grid:
.TP
\fB\-a\fR, \fB\-\-nch1\fR=\fI\,INT\/\fR
Number of channels along first FITS axis.
.TP
\fB\-b\fR, \fB\-\-nch2\fR=\fI\,INT\/\fR
Number of channels along second FITS axis.
.TP
\fB\-\-checkmesh\fR
Store mesh IDs in `_mesh.fits' file.
.TP
\fB\-d\fR, \fB\-\-mirrordist\fR=\fI\,FLT\/\fR
Distance beyond mirror point. Multiple of std.
.TP
\fB\-\-fullconvolution\fR
Ignore channels in convolution.
.TP
\fB\-\-fullinterpolation\fR
Ignore channels in interpolation.
.TP
\fB\-\-fullsmooth\fR
Ignore channels in smoothing.
.TP
\fB\-\-interponlyblank\fR
Only interpolate over the blank pixels.
.TP
\fB\-l\fR, \fB\-\-lmeshsize\fR=\fI\,INT\/\fR
Size of each large mesh (tile) in the grid.
.TP
\fB\-L\fR, \fB\-\-lastmeshfrac\fR=\fI\,INT\/\fR
Fraction of last mesh area to add new.
.TP
\fB\-\-meshbasedcheck\fR
Each mesh in one pixel in mesh check images.
.TP
\fB\-n\fR, \fB\-\-numnearest\fR=\fI\,INT\/\fR
Number of nearest neighbors to interpolate.
.TP
\fB\-Q\fR, \fB\-\-minmodeq\fR=\fI\,FLT\/\fR
Minimum acceptable quantile for the mode.
.TP
\fB\-s\fR, \fB\-\-smeshsize\fR=\fI\,INT\/\fR
Size of each small mesh (tile) in the grid.
.TP
\fB\-T\fR, \fB\-\-smoothwidth\fR=\fI\,INT\/\fR
Width of smoothing kernel (odd number).
.IP
Detection:
.TP
\fB\-c\fR, \fB\-\-detquant\fR=\fI\,FLT\/\fR
False detections S/N quantile to find the true.
.TP
\fB\-\-checkdetection\fR
False detection steps in file `_det.fits'.
.TP
\fB\-\-checkdetectionsky\fR
Sky for false detections in file `_detsky.fits'.
.TP
\fB\-\-checkmaskdet\fR
Mask detections and sky, `_maskdet.fits'.
.TP
\fB\-\-checksky\fR
Final sky and its STD per pixel `_sky.fits'.
.TP
\fB\-\-checkthreshold\fR
Threshold value on each mesh `_thresh.fits'.
.TP
\fB\-\-detsnhistnbins\fR=\fI\,INT\/\fR
Det. S/N histogram bins, suffix `_detsn.txt'.
.TP
\fB\-e\fR, \fB\-\-erode\fR=\fI\,INT\/\fR
Num. erosions to apply after thresholding.
.TP
\fB\-\-erodengb\fR=\fI\,4or8\/\fR
Use 4 or 8 connectivity in erosion.
.TP
\fB\-i\fR, \fB\-\-detsnminarea\fR=\fI\,INT\/\fR
Minimum area to calculate S/N in detection.
.TP
\fB\-I\fR, \fB\-\-dilate\fR=\fI\,INT\/\fR
Number of times to dilate true detections.
.TP
\fB\-\-noerodequant\fR=\fI\,FLT\/\fR
Quantile for no erosion.
.TP
\fB\-\-openingngb\fR=\fI\,4or8\/\fR
Use 4 or 8 connectivity in opening.
.TP
\fB\-p\fR, \fB\-\-opening\fR=\fI\,INT\/\fR
Depth of opening to apply after erosion.
.HP
\fB\-r\fR, \fB\-\-sigcliptolerance\fR=\fI\,FLT\/\fR Difference in STD tolerance to halt iteration.
.TP
\fB\-R\fR, \fB\-\-dthresh\fR=\fI\,FLT\/\fR
Threshold (STD multiple) for false detections.
.TP
\fB\-t\fR, \fB\-\-qthresh\fR=\fI\,FLT\/\fR
Quantile threshold on convolved image.
.TP
\fB\-u\fR, \fB\-\-sigclipmultip\fR=\fI\,FLT\/\fR
Multiple of standard deviation in sigma\-clipping.
.IP
Segmentation:
.TP
\fB\-\-checksegmentation\fR
Store segmentation steps in file `_seg.fits'.
.HP
\fB\-\-clumpsnhistnbins\fR=\fI\,INT\/\fR Clump S/N histogram bins, suffix `_clumpsn.txt'.
.TP
\fB\-g\fR, \fB\-\-segquant\fR=\fI\,FLT\/\fR
Signal to noise ratio quantile for clumps.
.TP
\fB\-G\fR, \fB\-\-gthresh\fR=\fI\,FLT\/\fR
Threshold (STD multiple) to stop growing clumps.
.TP
\fB\-m\fR, \fB\-\-segsnminarea\fR=\fI\,INT\/\fR
Minimum area to find clumps S/N.
.TP
\fB\-O\fR, \fB\-\-objbordersn\fR=\fI\,FLT\/\fR
Minimum S/N for grown clumps to be one object.
.TP
\fB\-v\fR, \fB\-\-keepmaxnearriver\fR
Keep clumps with max touching river.
.TP
\fB\-y\fR, \fB\-\-minriverlength\fR
Minimum length of useful rivers in grown clumps.
.IP
Operating modes:
.TP
\-?, \fB\-\-help\fR
give this help list
.TP
\fB\-\-cite\fR
BibTeX citation for NoiseChisel.
.TP
\fB\-\-nolog\fR
No log file for programs which make one.
.TP
\fB\-N\fR, \fB\-\-numthreads\fR=\fI\,INT\/\fR
Number of CPU threads to use.
.TP
\fB\-\-onlydirconf\fR
Only read current directory configuration file.
.TP
\fB\-\-onlyversion\fR=\fI\,STR\/\fR
Only run if the program version is this.
.TP
\fB\-P\fR, \fB\-\-printparams\fR
Print parameter values to be used and abort.
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Only report errors, remain quiet about steps.
.TP
\fB\-\-setusrconf\fR
Set default values for this user and abort.
.TP
\fB\-S\fR, \fB\-\-setdirconf\fR
Set default values for this directory and abort.
.TP
\fB\-\-usage\fR
give a short usage message
.TP
\fB\-V\fR, \fB\-\-version\fR
print program version
.PP
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
.PP
GNU Astronomy Utilities home page: http://www.gnu.org/software/gnuastro/
.SH AUTHOR
Written by Mohammad Akhlaghi
.SH "REPORTING BUGS"
Report bugs to bug\-gnuastro@gnu.org.
.SH COPYRIGHT
Copyright \(co 2015\-2016, Free Software Foundation, Inc.
License GPLv3+: GNU General public license version 3 or later.
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
.SH "SEE ALSO"
The full documentation for
.B NoiseChisel
is maintained as a Texinfo manual.  If the
.B info
and
.B NoiseChisel
programs are properly installed at your site, the command
.IP
.B info NoiseChisel
.PP
should give you access to the complete manual.