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NOISECHISEL(1) User Commands NOISECHISEL(1)

NAME

NoiseChisel - detect signal in a noisy image

SYNOPSIS

astnoisechisel [OPTION...] ASTRdata

DESCRIPTION

NoiseChisel is part of GNU Astronomy Utilities 0.14. 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=STR
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=STR
Filename of kernel to convolve with input
--whdu=STR
HDU containing wide kernel image.
-w, --widekernel=STR
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=INT
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'.
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
4 or 8 connectivity in erosion.
-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
4 or 8 connectivity in opening.

--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
Minimum bytes in array to not use ram RAM.
-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 © 2015-2021, 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

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.

January 2021 GNU Astronomy Utilities 0.14