--- name: "astmkcatalog" section: "1" platform: "linux" package: "gnuastro" version: "0.23-2+b3" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/astmkcatalog" --- # astmkcatalog(1) Make a catalog from labeled input images ## NAME MakeCatalog - Make a catalog from labeled input images ## SYNOPSIS **astmkcatalog** \[*OPTION*...\] *ASTRdata* ## DESCRIPTION MakeCatalog is part of GNU Astronomy Utilities 0.23. 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. - **--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. - **--sfmagarea**=*FLT* Surface brightness area (in arcseconds^2). - **--sfmagnsigma**=*FLT* Surface brightness multiple of Sky STD. - **--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. - **--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** Error (1-sigma) 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**. - **--num-clumps** Number of clumps in this object. - **--weight-area** Area used for value weighted positions. - Morphology/shape (elliptical) measurements - **--axis-ratio** Flux weighted axis ratio. - **--geo-axis-ratio** Geometric (ignoring values, only lab) axis ratio. - **--geo-position-angle** Geometric (ignoring values, only lab) pos. angle. - **--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. - **--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. - 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. - **--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 © 2015-2024 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.