astmkcatalog

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 arcseconds^2).

--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/arcsec^2).

--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 arcsec^2.

--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/arcsec^2).

--surfacebrightness: Surface brightness (mag/arcsec^2).

--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 [email protected].

COPYRIGHT

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