Ubuntu Manpage: MakeCatalog - 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 0.18. 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 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

NAME

SYNOPSIS

DESCRIPTION

REPORTING BUGS

COPYRIGHT

SEE ALSO