MAKECATALOG(1)

📦
version 0.24 · 5 versions
, in epel 10, epel 9, nixos 26.05, nixpkgs unstable, ubuntu resolute, ubuntu stonking

💖 MAKECATALOG 💖

okay so bestie, this is the manual page for MakeCatalog (you'll also hear it called astmkcatalog), and it lives in User Commands — section 1 of the manual, iykyk. It ships with GNU Astronomy Utilities 0.24 and it is literally the glow-up step where your pixels become a whole catalog. Let's get into it. 🦋

✨ NAME ✨

MakeCatalog — Make a catalog from labeled input images

🌸 SYNOPSIS 🌸

astmkcatalog [OPTION...] ASTRdata

💅 DESCRIPTION 💅

MakeCatalog is part of GNU Astronomy Utilities 0.24. What it does, bestie, is create a catalog from an input image, a labeled image, and a noise image. That's the whole vibe. 👑

For more info, you can run any of these commands. And fr fr, that second one is the main character here — it has a very comprehensive explanation of how MakeCatalog gets invoked: what inputs it expects, what outputs it makes, and a full rundown of every single option.

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

And if the manual just isn't giving what you need, you can get direct help from experienced Gnuastro users and developers. For more info, run:

$ info help-gnuastro

🫶 MakeCatalog options 🫶

🎀 Input 🎀

  • --clumpshdu=STR — Clump labels extension name or number.
  • -h, --hdu=STR/INT — Extension name or number of input data.
  • -l, --clumpsfile=FITS — Dataset containing clump labels.
  • --novalinerror — Ignore pixel values when estimating errors.
  • --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.
  • --meta-measures — Measures on/about indiv. measures (e.g., limits).
  • --noclumpsort — Don't sort the clumps catalog by ID.
  • --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.
  • --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 💜

  • --frac-max=FLT[,FLT] — Fraction(s) in --frac-max* options.
  • --spatialresolution=FLT — Spatial resolution (for surf. brightness err).

⭐ Identifier columns ⭐

  • --id-in-host-obj — ID of clump in host object.
  • -i, --ids — All IDs of objects and clumps.
  • -j, --host-obj-id — ID of object hosting this clump.
  • --obj-id — Object label/ID.

🦋 Positional (pixel/image) measurements 🦋

  • --area-max-val — Number of pixels used in '--max-val-*'.
  • --area-min-val — Number of pixels used in '--min-val-*'.
  • --clumps-geo-x — Geometric center of all clumps in obj. (X).
  • --clumps-geo-y — Geometric center of all clumps in obj. (Y).
  • --clumps-geo-z — Geometric center of all clumps in obj. (Z).
  • --clumps-x — Flux.wht center of all clumps in obj. (X).
  • --clumps-y — Flux.wht center of all clumps in obj. (Y).
  • --clumps-z — Flux.wht center of all clumps in obj. (Z).
  • --geo-x — Geometric center in first FITS axis.
  • --geo-y — Geometric center in second FITS axis.
  • --geo-z — Geometric center in third FITS axis.
  • --max-val-x — Maximum value's X axis position.
  • --max-val-y — Maximum value's Y axis position.
  • --max-val-z — Maximum value's Z axis position
  • --max-x — Maximum X axis position.
  • --max-y — Maximum Y axis position.
  • --max-z — Maximum Z axis position.
  • --min-val-x — Minimum value's X axis position.
  • --min-val-y — Minimum value's Y axis position.
  • --min-val-z — Minimum value's Z axis position.
  • --min-x — Minimum X axis position.
  • --min-y — Minimum Y axis position.
  • --min-z — 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 (WCS) measurements 🌸

  • --clumps-geo-w1 — Geometric center of all clumps in 1st WCS.
  • --clumps-geo-w2 — Geometric center of all clumps in 2nd WCS.
  • --clumps-geo-w3 — Geometric center of all clumps in 3rd WCS.
  • --clumps-w1 — Flux.wht center of all clumps in 1st WCS.
  • --clumps-w2 — Flux.wht center of all clumps in 2nd WCS.
  • --clumps-w3 — Flux.wht center of all clumps in 3rd WCS.
  • -d, --dec — Flux weighted center declination.
  • --geo-w1 — Geometric center in first WCS axis.
  • --geo-w2 — Geometric center in second WCS axis.
  • --geo-w3 — 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 (only using pixel value/error) measurements 🔥

  • --clumps-magnitude — Magnitude of all clumps in object.
  • --clumps-sum — Brightness of clumps in an object.
  • --magnitude-error — Magnitude error of objects or clumps.
  • --maximum — Maximum value (mean of top three pixels)
  • --mean — Mean of values in object/clump.
  • --mean-error — Error of the mean in object/clump.
  • --median — Median of values in object/clump.
  • -m, --magnitude — Total magnitude of objects or clumps.
  • --river-max — Maximum river value around clump.
  • --river-mean — Mean river value surrounding a clump.
  • --river-min — Minimum river value around clump.
  • --river-num — 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).
  • --sky-std — Sky standard deviation (per pixel).
  • --sn — Signal to noise ratio of objects or clumps.
  • --std — Standard dev. of values in object/clump.
  • --sum — Sum of pixel values in each label.
  • --sum-error — Standard deviation (error) in measuring sum.
  • --sum-no-river — Sky (not river) subtracted clump sum.
  • --upperlimit — Upper-limit value, use other options to config.
  • --upperlimit-mag — Upper-limit mag. use other options to config.
  • --upperlimit-onesigma — Upper-limit one sigma value.
  • --upperlimit-quantile — Quantile in random distribution (max 1).
  • --upperlimit-sigma — Place in random distribution (sigma multiple).
  • --upperlimit-skew — (Mean-Median)/STD of random distribution.

💖 Surface brightness measurements (all: mag/arcsec^2) 💖

  • --half-max-sb — Surface brightness within half the maximum.
  • --half-sum-sb — Surface brightness within --halfsumarea.
  • --sb — Surface brightness.
  • --sb-error — Surface brightness error from STD/VAR image.
  • --sigclip-mean-sb — Surface brightness of sigclip-mean (1 pix area).
  • --sigclip-mean-sb-delta — sigclip-mean-sb delta from sigclip'd STD.
  • --sigclip-std-sb — Surface brightness of sigclip-std (1 pix area).
  • --upperlimit-sb — Upper-limit surface brightness.

👑 Morphology/shape (non-parametric) measurements 👑

  • --area — Number of non-blank valued pixels.
  • --area-arcsec2 — Area of labeled region in arcsec^2.
  • --area-xy — Projected area in first two dimensions.
  • --clumps-area — Non-blank area covered by clumps.
  • --frac-max1-area — Area containing 1st fraction of maximum.
  • --frac-max1-radius — Radius calculated from --fracmaxarea1.
  • --frac-max1-sum — Sum of pixels brighter than 1st frac. of max.
  • --frac-max2-area — Area containing 2nd fraction of maximum.
  • --frac-max2-radius — Radius calculated from --fracmaxarea2.
  • --frac-max2-sum — Sum of pixels brighter than 2nd frac. of max.
  • --fwhm — Full width at half max (non-parametric).
  • --geo-area — Area labled region (irrespective of value).
  • --geo-area-xy — Projected geo-area in first two dimensions.
  • --half-max-area — No. pixels valued above half the max.
  • --half-max-radius — Radius at half the maximum (non-parametric).
  • --half-max-sum — Sum of pixels above half the maximum.
  • --half-sum-area — Area containing half of --brightness.
  • --half-sum-radius — Radius calculated from --halfsumarea. That's it, that's the whole math bestie. 💖
  • --num-clumps — Number of clumps in this object. Count 'em. 🦋
  • --weight-area — Area used for value weighted positions. This is the area that gets the weighted-position glow-up. ✨

✨ Morphology/shape (elliptical) measurements ✨

  • --axis-ratio — Flux weighted axis ratio. The shape ratio but make it flux-weighted. 💅
  • --geo-axis-ratio — Geometric (ignoring values, only lab) axis ratio. No value drama, just label geometry. 🎀
  • --geo-position-angle — Geometric (ignoring values, only lab) pos. angle. Position angle, geometric style. 🌸
  • --geo-semi-major — Geometric RMS along major axis (ignoring value). 🌈
  • --geo-semi-minor — Geometric RMS along minor axis (ignoring value). 🌈
  • --position-angle — Flux weighted position angle. Angle, but flux-weighted. ⭐
  • --semi-major — RMS along major axis (in pixels). 📏
  • --semi-minor — RMS along minor axis (in pixels). 📏

🌈 Vector (multi-valued) measurements 🌈

  • --area-in-slice — [3D input] Number of labeled in each slice. 🍰
  • --area-other-in-slice — [3D input] Area of other lab. in projected area. 🫶
  • --area-proj-in-slice — [3D input] Num. voxels in --sum-proj-in-slice. 🧊
  • --sum-err-in-slice — [3D input] Error in --sum-in-slice. 😭
  • --sum-in-slice — [3D input] Sum of values in each slice. ➕
  • --sum-other-err-in-slice — [3D input] Area in --sum-other-in-slice. 🫠
  • --sum-other-in-slice — [3D input] Sum of other lab. in projected area. 🫶
  • --sum-proj-err-in-slice — [3D input] Error of --sum-proj-in-slice. 💀
  • --sum-proj-in-slice — [3D input] Sum of projected area in each slice. 🧮

🔥 Metameasurements (e.g., limits): 🔥

  • --cnl-check — Table as extra HDU in output with all matches. Extra HDU, all matches, periodt. 💖
  • --cnl-with-objects — Use objects for confusion limit, not clumps. Objects only, no clumps. 👑
  • --nml-area=FLT — Noise-based mag. lim area (in arcsec^2). 📐
  • --nml-sigma=FLT — Noise-based mag. lim multip. of Sky STD. 🌌
  • --sbl-area=FLT — Surf. bright. limit area (in arcseconds^2). 📐
  • --sbl-sigma=FLT — Surf. bright. limit multiple of Sky STD. 🌌

🎛️ Operating modes: 🎛️

  • -?, --help — give this help list 🙋
  • --checkconfig — List all config files and variables read. 🔍
  • --cite — BibTeX citation for this program. Cite me bestie. 📚
  • --config=STR — Read configuration file STR immediately. 🗂️
  • --config-prefix=STR — Custom prefix of option names config files. ✨
  • --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. iykyk 💅

GNU Astronomy Utilities home page: http://www.gnu.org/software/gnuastro/ 🌐

🐛 REPORTING BUGS 🐛

Report bugs to bug-gnuastro@gnu.org. 💖

Copyright © 2015-2025 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 MakeCatalog is maintained as a Texinfo manual. If the info and MakeCatalog programs are properly installed at your site, the command

info MakeCatalog

should give you access to the complete manual.

💖 And that's a wrap, bestie — this page is from GNU Astronomy Utilities 0.24, November 2025, and it's the MAKECATALOG(1) manual. Stay iconic. ✨

📦 where this page comes from