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MAKECATALOG(1) User Commands MAKECATALOG(1)

NAME

MakeCatalog - Make a catalog from labeled input images

SYNOPSIS

astmkcatalog [OPTION...] ASTRdata

DESCRIPTION

MakeCatalog is part of GNU Astronomy Utilities 0.14. 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=STR
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=STR/FLT
Input Sky value or dataset.
-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=STR
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=INT
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'.
Upper limit magnitude settings:

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

-e, --envseed
Use GSL_RNG_SEED environment variable for seed.
--upmaskfile=STR
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.
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).
--std
Sky standard deviation (per pixel).
--upperlimit
Upper-limit value, use other options to config.
--upperlimitonesigma
Upper-limit one sigma value.
--upperlimitquantile
Quantile in random distribution (max 1).
--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.
--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
Minimum bytes in array to not use ram RAM.
-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 © 2015-2021, 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.

January 2021 GNU Astronomy Utilities 0.14