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NoiseChisel - detect signal in a noisy image


astnoisechisel [OPTION...] ASTRdata


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:

HDU/extension of convolved image in file.
Convolved image file to avoid convolution.
-h, --hdu=STR/INT
Extension name or number of input data.
HDU containing kernel image.
-k, --kernel=STR
Filename of kernel to convolve with input
HDU containing wide kernel image.
-w, --widekernel=STR
Filename of wider kernel for better qthresh
Tessellation (tile grid):
Tile IDs in an image, the size of input.
-F, --remainderfrac=FLT
Fraction of remainder to split last tile.
Interpolation metric (radial, manhattan).
No. of neighbors to use for interpolation.
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).

Display 1 element/tile, not full input res.
Work (not tile) over channel edges.
-Z, --tilesize=INT[,INT]
Regular tile size on dim.s (FITS order).
-D, --dontdelete
Don't delete output if it exists.
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.
Output only detection labels & 1-elem/tile grid.
'txt', 'fits-ascii', 'fits-binary'.
Blanks are foreground in erosion and opening.
-B, --minskyfrac=FLT
Min. fraction of undetected area in tile.
Save all the detection steps to a file.
Save Sky value estimation for pseudo-dets.
Save quantile threshold estimation in file.
Final sky and its STD steps in a file.
Save pseudo-detection S/N values to a file.
Remove small S/N grown detections.
-c, --snquant=FLT
Quantile in pseudo-det. to define true.
Max. area of holes after growth to fill.
Depth of opening after dthresh.
4 or 8 connectivity for dthresh opening.
-d, --detgrowquant=FLT
Minimum quant. to expand true detections.
4 or 8 connectivity in erosion.
-e, --erode=INT
Number of erosions after thresholding.
4 or 8 connectivity for filling holes.
Minimum number for S/N estimation.
-m, --snminarea=INT
Min. pseudo-detection area for S/N dist.
Quantile for no erosion.
4 or 8 connectivity in opening.

--outliersclip=FLT,FLT Sigma-clip params for qthresh outliers.

Multiple of sigma to define outliers.
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.
No blanks in tile undetected frac. (minskyfrac).
Flat kernel width to smooth interpolated.
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
List all config files and variables read.
BibTeX citation for this program.
Read configuration file STR immediately.
-C, --continueaftercheck
Continue processing after checks.
Do not parse any more configuration files.
Minimum bytes in array to not use ram RAM.
-N, --numthreads=INT
Number of CPU threads to use.
Only run if the program version is STR.
-P, --printparams
Print parameter values to be used and abort.
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.
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:


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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


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