.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH NOISECHISEL "1" "December 2018" "GNU Astronomy Utilities 0.8" "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 0.8.
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. 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.
.TP
All options and their values:
$ astnoisechisel \fB\-P\fR
.TP
Inputs/Outputs and options:
$ info astnoisechisel
.TP
Full section in manual/book:
$ info NoiseChisel
.TP
Full Gnuastro manual/book:
$ 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
\f(CW$ info help-gnuastro\fR
.PP
NoiseChisel options:
.IP
Input:
.TP
\fB\-\-chdu\fR=\fI\,STR\/\fR
HDU/extension of convolved image in file.
.TP
\fB\-\-convolved\fR=\fI\,STR\/\fR
Convolved image file to avoid convolution.
.TP
\fB\-h\fR, \fB\-\-hdu\fR=\fI\,STR\/\fR/INT
Extension name or number of input data.
.TP
\fB\-k\fR, \fB\-\-kernel\fR=\fI\,STR\/\fR
Filename of kernel to convolve with input
.TP
\fB\-\-khdu\fR=\fI\,STR\/\fR
HDU containing kernel image.
.TP
\fB\-w\fR, \fB\-\-widekernel\fR=\fI\,STR\/\fR
Filename of wider kernel for better qthresh
.TP
\fB\-\-whdu\fR=\fI\,STR\/\fR
HDU containing wide kernel image.
.IP
Tessellation (tile grid):
.TP
\fB\-\-checktiles\fR
Tile IDs in an image, the size of input.
.TP
\fB\-F\fR, \fB\-\-remainderfrac\fR=\fI\,FLT\/\fR
Fraction of remainder to split last tile.
.TP
\fB\-\-interpnumngb\fR=\fI\,INT\/\fR
No. of neighbors to use for interpolation.
.TP
\fB\-\-interponlyblank\fR
Only interpolate over the blank tiles.
.TP
\fB\-L\fR, \fB\-\-largetilesize\fR=\fI\,INT[\/\fR,INT]
Sim. to \fB\-\-tilesize\fR, but for larger tiles.
.HP
\fB\-M\fR, \fB\-\-numchannels\fR=\fI\,INT[\/\fR,..] No. of channels in dim.s (FITS order).
.TP
\fB\-\-oneelempertile\fR
Display 1 element/tile, not full input res.
.TP
\fB\-\-workoverch\fR
Work (not tile) over channel edges.
.TP
\fB\-Z\fR, \fB\-\-tilesize\fR=\fI\,INT[\/\fR,INT]
Regular tile size on dim.s (FITS order).
.IP
Output:
.TP
\fB\-D\fR, \fB\-\-dontdelete\fR
Don't delete output if it exists.
.TP
\fB\-\-ignoreblankinsky\fR
Don't write input's blanks in the Sky output.
.TP
\fB\-K\fR, \fB\-\-keepinputdir\fR
Keep input directory for automatic output.
.TP
\fB\-l\fR, \fB\-\-label\fR
Label/count detected pixels that are connected.
.TP
\fB\-o\fR, \fB\-\-output\fR=\fI\,STR\/\fR
Output file name.
.TP
\fB\-\-rawoutput\fR
Output only detection labels & 1\-elem/tile grid.
.TP
\fB\-\-tableformat\fR=\fI\,STR\/\fR
`txt', `fits\-ascii', `fits\-binary'.
.IP
Detection:
.TP
\fB\-\-blankasforeground\fR
Blanks are foreground in erosion and opening.
.TP
\fB\-B\fR, \fB\-\-minskyfrac\fR=\fI\,FLT\/\fR
Min. fraction of undetected area in tile.
.TP
\fB\-\-checkdetection\fR
Save all the detection steps to a file.
.TP
\fB\-\-checkdetsky\fR
Save Sky value estimation for pseudo\-dets.
.TP
\fB\-\-checkqthresh\fR
Save quantile threshold estimation in file.
.TP
\fB\-\-checksky\fR
Final sky and its STD steps in a file.
.TP
\fB\-\-checksn\fR
Save pseudo\-detection S/N values to a file.
.TP
\fB\-c\fR, \fB\-\-snquant\fR=\fI\,FLT\/\fR
Quantile in pseudo\-det. to define true.
.TP
\fB\-\-cleangrowndet\fR
Remove small S/N grown detections.
.TP
\fB\-d\fR, \fB\-\-detgrowquant\fR=\fI\,FLT\/\fR
Minimum quant. to expand true detections.
.TP
\fB\-\-detgrowmaxholesize\fR=\fI\,INT\/\fR
Max. area of holes after growth to fill.
.TP
\fB\-e\fR, \fB\-\-erode\fR=\fI\,INT\/\fR
Number of erosions after thresholding.
.TP
\fB\-\-erodengb\fR=\fI\,INT\/\fR
4 or 8 connectivity in erosion.
.TP
\fB\-\-holengb\fR=\fI\,INT\/\fR
4 or 8 connectivity for filling holes.
.TP
\fB\-m\fR, \fB\-\-snminarea\fR=\fI\,INT\/\fR
Min. pseudo\-detection area for S/N dist.
.TP
\fB\-\-minnumfalse\fR=\fI\,INT\/\fR
Minimum number for S/N estimation.
.TP
\fB\-\-noerodequant\fR=\fI\,FLT\/\fR
Quantile for no erosion.
.TP
\fB\-\-openingngb\fR=\fI\,INT\/\fR
4 or 8 connectivity in opening.
.HP
\fB\-\-outliersclip\fR=\fI\,FLT\/\fR,FLT Sigma\-clip params for qthresh outliers.
.TP
\fB\-\-outliersigma\fR=\fI\,FLT\/\fR
Multiple of sigma to define outliers.
.TP
\fB\-p\fR, \fB\-\-opening\fR=\fI\,INT\/\fR
Depth of opening after erosion.
.TP
\fB\-Q\fR, \fB\-\-meanmedqdiff\fR=\fI\,FLT\/\fR
Max. mean and median quant diff. per tile.
.TP
\fB\-R\fR, \fB\-\-dthresh\fR=\fI\,FLT\/\fR
Sigma threshold for Pseudo\-detections.
.TP
\fB\-\-skyfracnoblank\fR
No blanks in tile undetected frac. (minskyfrac).
.TP
\fB\-\-smoothwidth\fR=\fI\,INT\/\fR
Flat kernel width to smooth interpolated.
.TP
\fB\-s\fR, \fB\-\-sigmaclip\fR=\fI\,FLT\/\fR,FLT
Sigma multiple and, tolerance or number.
.TP
\fB\-t\fR, \fB\-\-qthresh\fR=\fI\,FLT\/\fR
Quantile threshold on convolved image.
.IP
Operating modes:
.TP
\-?, \fB\-\-help\fR
give this help list
.TP
\fB\-\-cite\fR
BibTeX citation for this program.
.TP
\fB\-\-config\fR=\fI\,STR\/\fR
Read configuration file STR immediately.
.TP
\fB\-C\fR, \fB\-\-continueaftercheck\fR
Continue processing after checks.
.TP
\fB\-\-lastconfig\fR
Do not parse any more configuration files.
.TP
\fB\-\-minmapsize\fR=\fI\,INT\/\fR
Minimum bytes in array to not use ram RAM.
.TP
\fB\-N\fR, \fB\-\-numthreads\fR=\fI\,INT\/\fR
Number of CPU threads to use.
.TP
\fB\-\-onlyversion\fR=\fI\,STR\/\fR
Only run if the program version is STR.
.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\-S\fR, \fB\-\-setdirconf\fR
Set default values for this directory and abort.
.TP
\fB\-\-usage\fR
give a short usage message
.TP
\fB\-U\fR, \fB\-\-setusrconf\fR
Set default values for this user and abort.
.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 "REPORTING BUGS"
Report bugs to bug\-gnuastro@gnu.org.
.SH COPYRIGHT
Copyright \(co 2015\-2018, 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.
.PP
Written/developed by Mohammad Akhlaghi
.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.