astmkcatalog(1)

Make a catalog from labeled input images

Section 1 gnuastro bookworm source

Description

MAKECATALOG

NAME

MakeCatalog - Make a catalog from labeled input images

SYNOPSIS

astmkcatalog [OPTION...] ASTRdata

DESCRIPTION

MakeCatalog is part of GNU Astronomy Utilities 0.19. MakeCatalog will create a catalog from an input, labeled, and noise images.

For more information, please run any of the following commands. In particular the second contains a very comprehensive explanation of MakeCatalog’s invocation: expected input(s), output(s), and a full description of all the options.
All options and their values:

$ astmkcatalog -P

Inputs/Outputs and options:

$ info astmkcatalog

Full section in manual/book:

$ info MakeCatalog

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

MakeCatalog options:

Input:

--clumpshdu=STR

Clump labels extension name or number.

--forcereadstd

Read STD even if no columns need it.

-h, --hdu=STR/INT

Extension name or number of input data.

-l, --clumpsfile=FITS

Dataset containing clump labels.

--sigmaclip=FLT,FLT

Sigma-clip column multiple and tolerance.

--skyhdu=STR

Sky image extension name or number.

--stdhdu=STR

Sky STD extension name or number.

--subtractsky

Subtract the Sky dataset from the values.

-s, --insky=FITS/FLT

Input Sky value or file.

-t, --instd=STR/FLT

Sky standard deviation value or dataset.

--valueshdu=STR

Name or number of extension containing values.

--variance

STD input dataset is actually variance.

-v, --valuesfile=FITS

Values/brightness dataset.

--zeropoint=FLT

Zeropoint magnitude of input dataset.

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).

-M, --numchannels=INT[,..] No. of channels in dim.s (FITS order).

--oneelempertile

Display 1 element/tile, not full input res.

-Z, --tilesize=INT[,INT]

Regular tile size on dim.s (FITS order).

Output:

-C, --clumpscat

Make a clumps catalog also.

-D, --dontdelete

Don’t delete output if it exists.

--inbetweenints

Keep rows (integer ids) with no labels.

-K, --keepinputdir

Keep input directory for automatic output.

--noclumpsort

Don’t sort the clumps catalog by ID.

-o, --output=STR

Output file name.

--sfmagarea=FLT

Surface brightness area (in arcsecondsˆ2).

--sfmagnsigma=FLT

Surface brightness multiple of Sky STD.

--spectrum

Object spectrum for cube (3D) datasets.

--tableformat=STR

Table fmt: ’fits-ascii’, ’fits-binary’, ’txt’.

--wcslinearmatrix=STR

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

Upper limit magnitude settings:

--checkuplim=INT[,INT] Check random distribution for one label.

-e, --envseed

Use GSL_RNG_SEED environment variable for seed.

--upmaskfile=FITS

Mask image file name only for upper limit.

--upmaskhdu=STR

Mask image HDU only for upper limit.

--upnsigma=FLT

Multiple of sigma to define upperlimit.

--upnum=INT

Number of randomly positioned samples

--uprange=INT,INT

Range of random positions (pix) around target.

--upsigmaclip=FLT,FLT

Sigma multiple and, tolerance or number.

Settings for other columns:

--fracmax=FLT[,FLT]

Fraction(s) in --fracmaxarea1 or --fracmaxarea2.

--spatialresolution=FLT

Spatial resolution (for surface brightness error).

Identifier columns

--idinhostobj

ID of clump in host object.

-i, --ids

All IDs of objects and clumps.

-j, --hostobjid

ID of object hosting this clump.

--objid

Object label/ID.

Positional columns (pixel)

--areamaxv

Number of pixels with maximum value.

--areaminv

Number of pixels with minimum value.

--clumpsgeox

Geometric center of all clumps in obj. (X).

--clumpsgeoy

Geometric center of all clumps in obj. (Y).

--clumpsgeoz

Geometric center of all clumps in obj. (Z).

--clumpsx

Flux.wht center of all clumps in obj. (X).

--clumpsy

Flux.wht center of all clumps in obj. (Y).

--clumpsz

Flux.wht center of all clumps in obj. (Z).

--geox

Geometric center in first FITS axis.

--geoy

Geometric center in second FITS axis.

--geoz

Geometric center in third FITS axis.

--maxvx

Maximum value’s X axis position

--maxvy

Maximum value’s Y axis position

--maxvz

Maximum value’s Z axis position

--maxx

Maximum X axis position.

--maxy

Maximum Y axis position.

--maxz

Maximum Z axis position.

--minvx

Minimum value’s X axis position

--minvy

Minimum value’s Y axis position

--minvz

Minimum value’s Z axis position

--minx

Minimum X axis position.

--miny

Minimum Y axis position.

--minz

Minimum Z axis position

-x, --x

Flux weighted center in first FITS axis.

-y, --y

Flux weighted center in second FITS axis.

-z, --z

Flux weighted center in third FITS axis.

Positional columns (WCS)

--clumpsgeow1

Geometric center of all clumps in 1st WCS.

--clumpsgeow2

Geometric center of all clumps in 2nd WCS.

--clumpsgeow3

Geometric center of all clumps in 3rd WCS.

--clumpsw1

Flux.wht center of all clumps in 1st WCS.

--clumpsw2

Flux.wht center of all clumps in 2nd WCS.

--clumpsw3

Flux.wht center of all clumps in 3rd WCS.

-d, --dec

Flux weighted center declination.

--geow1

Geometric center in first WCS axis.

--geow2

Geometric center in second WCS axis.

--geow3

Geometric center in third WCS axis.

-r, --ra

Flux weighted center right ascension.

	--w1		Flux weighted center in first WCS axis.
	--w2		Flux weighted center in second WCS axis.
	--w3		Flux weighted center in third WCS axis.

Brightness/magnitude related columns

--brightnesserr

Error (1-sigma) in measuring brightness.

--brightnessnoriver

Sky (not river) subtracted clump brightness.

-b, --brightness

Brightness (sum of pixel values).

--clumpbrightness

Brightness of clumps in an object.

--clumpsmagnitude

Magnitude of all clumps in object.

-G, --magnitudeerr

Magnitude error of objects or clumps.

--maximum

Maximum value (mean of top three pixels)

--mean

Mean of values in object/clump.

--median

Median of values in object/clump.

-m, --magnitude

Total magnitude of objects or clumps.

-n, --sn

Signal to noise ratio of objects or clumps.

--riverave

Average river value surrounding a clump.

--rivernum

Number of river pixels around a clump.

--sigclip-mean

Mean after Sigma-clipping

--sigclip-median

Median after Sigma-clipping

--sigclip-number

Number of pixels in Sigma-clipped measurement.

--sigclip-std

Standard deviation after Sigma-clipping

--sky

Sky value (per pixel).

--skystd

Sky standard deviation (per pixel).

--std

Standard dev. of values in object/clump.

--upperlimit

Upper-limit value, use other options to config.

--upperlimitonesigma

Upper-limit one sigma value.

--upperlimitquantile

Quantile in random distribution (max 1).

--upperlimitsb

Upper-limit surface brightness (mag/arcsecˆ2).

--upperlimitsigma

Place in random distribution (sigma multiple).

--upperlimitskew

(Mean-Median)/STD of random distribution.

-u, --upperlimitmag

Upper-limit mag. use other options to config.

Morphology/shape related columns

--areaarcsec2

Area of labeled region in arcsecˆ2.

--areaxy

Projected area in first two dimensions.

-a, --area

Number of non-blank valued pixels.

-A, --semimajor

RMS along major axis (in pixels).

-B, --semiminor

RMS along minor axis (in pixels).

--clumpsarea

Non-blank area covered by clumps.

-c, --numclumps

Number of clumps in this object.

--fracmaxarea1

Area containing 1st fraction of maximum.

--fracmaxarea2

Area containing 2nd fraction of maximum.

--fracmaxradius1

Radius calculated from --fracmaxarea1.

--fracmaxradius2

Radius calculated from --fracmaxarea2.

--fracmaxsum1

Sum of pixels brighter than 1st frac. of max.

--fracmaxsum2

Sum of pixels brighter than 2nd frac. of max.

--fwhm

Full width at half max (non-parametric).

--geoarea

Area labled region (irrespective of value).

--geoareaxy

Projected geoarea in first two dimensions.

--geoaxisratio

Geometric axis ratio.

--geopositionangle

Geometric position angle.

--geosemimajor

RMS along major axis (ignoring value).

--geosemiminor

RMS along minor axis (ignoring value).

--halfmaxarea

No. pixels valued above half the max.

--halfmaxradius

Radius at half the maximum (non-parametric).

--halfmaxsb

Surface brightness within half the maximum.

--halfmaxsum

Sum of pixels above half the maximum.

--halfsumarea

Area containing half of --brightness.

--halfsumradius

Radius calculated from --halfsumarea.

--halfsumsb

Surface brightness within --halfsumarea.

-p, --positionangle

Flux weighted position angle.

-Q, --axisratio

Flux weighted axis ratio.

--sberror

Surface brightness error (mag/arcsecˆ2).

--surfacebrightness

Surface brightness (mag/arcsecˆ2).

--weightarea

Area used for value weighted positions.

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.

--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/

REPORTING BUGS

Report bugs to bug-gnuastro@gnu.org.

COPYRIGHT

Copyright © 2015-2022 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