astnoisechisel - Man Page

detect signal in a noisy image

NoiseChisel is part of GNU Astronomy Utilities 0.23. 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=FITS

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=FITS

Filename of kernel to convolve with input

--whdu=STR

HDU containing wide kernel image.

-w, --widekernel=FITS

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=STR

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.

--outfitsnocommit

No Git commit in 0-th HDU of output FITS.

--outfitsnoconfig

No metadata in 0-th HDU of output FITS.

--outfitsnodate

No 'DATE' in 0-th HDU of output FITS.

--outfitsnoversions

No versions in 0-th HDU of output FITS.

-o, --output=STR

Output file name.

--rawoutput

Output only detection labels & 1-elem/tile grid.

--tableformat=STR

'txt', 'fits-ascii', 'fits-binary'.

--wcslinearmatrix=STR

WCS linear matrix of output ('pc' or 'cd').

Detection:

-a, --outliernumngb=INT

Num neighboring tiles to look for outlier.

--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

Connectivity in erosion (number of ngbs).

-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

Connectivity in opening (number of ngbs).

--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.

--config-prefix=STR

Custom prefix of option names config files.

-C, --continueaftercheck

Continue processing after checks.

--lastconfig

Do not parse any more configuration files.

--minmapsize=INT

Min. bytes to avoid RAM automatically.

-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/

astnoisechisel - Man Page

Synopsis

Description

Reporting Bugs

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