.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH MAKECATALOG "1" "October 2022" "GNU Astronomy Utilities 0.19" "User Commands"
.SH NAME
MakeCatalog \- Make a catalog from labeled input images
.SH SYNOPSIS
.B astmkcatalog
[\fI\,OPTION\/\fR...] \fI\,ASTRdata\/\fR
.SH DESCRIPTION
MakeCatalog is part of GNU Astronomy Utilities 0.19.
MakeCatalog will create a catalog from an input, labeled, and noise images.
.PP
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.
.TP
All options and their values:
$ astmkcatalog \fB\-P\fR
.TP
Inputs/Outputs and options:
$ info astmkcatalog
.TP
Full section in manual/book:
$ info MakeCatalog
.TP
Full Gnuastro manual/book:
$ info gnuastro
.PP
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:
.IP
\f(CW$ info help-gnuastro\fR
.PP
MakeCatalog options:
.IP
Input:
.TP
\fB\-\-clumpshdu\fR=\fI\,STR\/\fR
Clump labels extension name or number.
.TP
\fB\-\-forcereadstd\fR
Read STD even if no columns need it.
.TP
\fB\-h\fR, \fB\-\-hdu\fR=\fI\,STR\/\fR/INT
Extension name or number of input data.
.TP
\fB\-l\fR, \fB\-\-clumpsfile\fR=\fI\,FITS\/\fR
Dataset containing clump labels.
.TP
\fB\-\-sigmaclip\fR=\fI\,FLT\/\fR,FLT
Sigma\-clip column multiple and tolerance.
.TP
\fB\-\-skyhdu\fR=\fI\,STR\/\fR
Sky image extension name or number.
.TP
\fB\-\-stdhdu\fR=\fI\,STR\/\fR
Sky STD extension name or number.
.TP
\fB\-\-subtractsky\fR
Subtract the Sky dataset from the values.
.TP
\fB\-s\fR, \fB\-\-insky\fR=\fI\,FITS\/\fR/FLT
Input Sky value or file.
.TP
\fB\-t\fR, \fB\-\-instd\fR=\fI\,STR\/\fR/FLT
Sky standard deviation value or dataset.
.TP
\fB\-\-valueshdu\fR=\fI\,STR\/\fR
Name or number of extension containing values.
.TP
\fB\-\-variance\fR
STD input dataset is actually variance.
.TP
\fB\-v\fR, \fB\-\-valuesfile\fR=\fI\,FITS\/\fR
Values/brightness dataset.
.TP
\fB\-\-zeropoint\fR=\fI\,FLT\/\fR
Zeropoint magnitude of input dataset.
.IP
Tessellation (tile grid):
.TP
\fB\-\-checktiles\fR
Tile IDs in an image, the size of input.
.TP
\fB\-F\fR, \fB\-\-remainderfrac\fR=\fI\,FLT\/\fR
Fraction of remainder to split last tile.
.TP
\fB\-\-interpmetric\fR=\fI\,STR\/\fR
Interpolation metric (radial, manhattan).
.HP
\fB\-M\fR, \fB\-\-numchannels\fR=\fI\,INT[\/\fR,..] No. of channels in dim.s (FITS order).
.TP
\fB\-\-oneelempertile\fR
Display 1 element/tile, not full input res.
.TP
\fB\-Z\fR, \fB\-\-tilesize\fR=\fI\,INT[\/\fR,INT]
Regular tile size on dim.s (FITS order).
.IP
Output:
.TP
\fB\-C\fR, \fB\-\-clumpscat\fR
Make a clumps catalog also.
.TP
\fB\-D\fR, \fB\-\-dontdelete\fR
Don't delete output if it exists.
.TP
\fB\-\-inbetweenints\fR
Keep rows (integer ids) with no labels.
.TP
\fB\-K\fR, \fB\-\-keepinputdir\fR
Keep input directory for automatic output.
.TP
\fB\-\-noclumpsort\fR
Don't sort the clumps catalog by ID.
.TP
\fB\-o\fR, \fB\-\-output\fR=\fI\,STR\/\fR
Output file name.
.TP
\fB\-\-sfmagarea\fR=\fI\,FLT\/\fR
Surface brightness area (in arcseconds^2).
.TP
\fB\-\-sfmagnsigma\fR=\fI\,FLT\/\fR
Surface brightness multiple of Sky STD.
.TP
\fB\-\-spectrum\fR
Object spectrum for cube (3D) datasets.
.TP
\fB\-\-tableformat\fR=\fI\,STR\/\fR
Table fmt: 'fits\-ascii', 'fits\-binary', 'txt'.
.TP
\fB\-\-wcslinearmatrix\fR=\fI\,STR\/\fR
WCS linear matrix of output ('pc' or 'cd').
.IP
Upper limit magnitude settings:
.HP
\fB\-\-checkuplim\fR=\fI\,INT[\/\fR,INT] Check random distribution for one label.
.TP
\fB\-e\fR, \fB\-\-envseed\fR
Use GSL_RNG_SEED environment variable for seed.
.TP
\fB\-\-upmaskfile\fR=\fI\,FITS\/\fR
Mask image file name only for upper limit.
.TP
\fB\-\-upmaskhdu\fR=\fI\,STR\/\fR
Mask image HDU only for upper limit.
.TP
\fB\-\-upnsigma\fR=\fI\,FLT\/\fR
Multiple of sigma to define upperlimit.
.TP
\fB\-\-upnum\fR=\fI\,INT\/\fR
Number of randomly positioned samples
.TP
\fB\-\-uprange\fR=\fI\,INT\/\fR,INT
Range of random positions (pix) around target.
.TP
\fB\-\-upsigmaclip\fR=\fI\,FLT\/\fR,FLT
Sigma multiple and, tolerance or number.
.IP
Settings for other columns:
.TP
\fB\-\-fracmax\fR=\fI\,FLT[\/\fR,FLT]
Fraction(s) in \fB\-\-fracmaxarea1\fR or \fB\-\-fracmaxarea2\fR.
.TP
\fB\-\-spatialresolution\fR=\fI\,FLT\/\fR
Spatial resolution (for surface brightness
error).
.IP
Identifier columns
.TP
\fB\-\-idinhostobj\fR
ID of clump in host object.
.TP
\fB\-i\fR, \fB\-\-ids\fR
All IDs of objects and clumps.
.TP
\fB\-j\fR, \fB\-\-hostobjid\fR
ID of object hosting this clump.
.TP
\fB\-\-objid\fR
Object label/ID.
.IP
Positional columns (pixel)
.TP
\fB\-\-areamaxv\fR
Number of pixels with maximum value.
.TP
\fB\-\-areaminv\fR
Number of pixels with minimum value.
.TP
\fB\-\-clumpsgeox\fR
Geometric center of all clumps in obj. (X).
.TP
\fB\-\-clumpsgeoy\fR
Geometric center of all clumps in obj. (Y).
.TP
\fB\-\-clumpsgeoz\fR
Geometric center of all clumps in obj. (Z).
.TP
\fB\-\-clumpsx\fR
Flux.wht center of all clumps in obj. (X).
.TP
\fB\-\-clumpsy\fR
Flux.wht center of all clumps in obj. (Y).
.TP
\fB\-\-clumpsz\fR
Flux.wht center of all clumps in obj. (Z).
.TP
\fB\-\-geox\fR
Geometric center in first FITS axis.
.TP
\fB\-\-geoy\fR
Geometric center in second FITS axis.
.TP
\fB\-\-geoz\fR
Geometric center in third FITS axis.
.TP
\fB\-\-maxvx\fR
Maximum value's X axis position
.TP
\fB\-\-maxvy\fR
Maximum value's Y axis position
.TP
\fB\-\-maxvz\fR
Maximum value's Z axis position
.TP
\fB\-\-maxx\fR
Maximum X axis position.
.TP
\fB\-\-maxy\fR
Maximum Y axis position.
.TP
\fB\-\-maxz\fR
Maximum Z axis position.
.TP
\fB\-\-minvx\fR
Minimum value's X axis position
.TP
\fB\-\-minvy\fR
Minimum value's Y axis position
.TP
\fB\-\-minvz\fR
Minimum value's Z axis position
.TP
\fB\-\-minx\fR
Minimum X axis position.
.TP
\fB\-\-miny\fR
Minimum Y axis position.
.TP
\fB\-\-minz\fR
Minimum Z axis position
.TP
\fB\-x\fR, \fB\-\-x\fR
Flux weighted center in first FITS axis.
.TP
\fB\-y\fR, \fB\-\-y\fR
Flux weighted center in second FITS axis.
.TP
\fB\-z\fR, \fB\-\-z\fR
Flux weighted center in third FITS axis.
.IP
Positional columns (WCS)
.TP
\fB\-\-clumpsgeow1\fR
Geometric center of all clumps in 1st WCS.
.TP
\fB\-\-clumpsgeow2\fR
Geometric center of all clumps in 2nd WCS.
.TP
\fB\-\-clumpsgeow3\fR
Geometric center of all clumps in 3rd WCS.
.TP
\fB\-\-clumpsw1\fR
Flux.wht center of all clumps in 1st WCS.
.TP
\fB\-\-clumpsw2\fR
Flux.wht center of all clumps in 2nd WCS.
.TP
\fB\-\-clumpsw3\fR
Flux.wht center of all clumps in 3rd WCS.
.TP
\fB\-d\fR, \fB\-\-dec\fR
Flux weighted center declination.
.TP
\fB\-\-geow1\fR
Geometric center in first WCS axis.
.TP
\fB\-\-geow2\fR
Geometric center in second WCS axis.
.TP
\fB\-\-geow3\fR
Geometric center in third WCS axis.
.TP
\fB\-r\fR, \fB\-\-ra\fR
Flux weighted center right ascension.
.TP
\fB\-\-w1\fR
Flux weighted center in first WCS axis.
.TP
\fB\-\-w2\fR
Flux weighted center in second WCS axis.
.TP
\fB\-\-w3\fR
Flux weighted center in third WCS axis.
.IP
Brightness/magnitude related columns
.TP
\fB\-\-brightnesserr\fR
Error (1\-sigma) in measuring brightness.
.TP
\fB\-\-brightnessnoriver\fR
Sky (not river) subtracted clump brightness.
.TP
\fB\-b\fR, \fB\-\-brightness\fR
Brightness (sum of pixel values).
.TP
\fB\-\-clumpbrightness\fR
Brightness of clumps in an object.
.TP
\fB\-\-clumpsmagnitude\fR
Magnitude of all clumps in object.
.TP
\fB\-G\fR, \fB\-\-magnitudeerr\fR
Magnitude error of objects or clumps.
.TP
\fB\-\-maximum\fR
Maximum value (mean of top three pixels)
.TP
\fB\-\-mean\fR
Mean of values in object/clump.
.TP
\fB\-\-median\fR
Median of values in object/clump.
.TP
\fB\-m\fR, \fB\-\-magnitude\fR
Total magnitude of objects or clumps.
.TP
\fB\-n\fR, \fB\-\-sn\fR
Signal to noise ratio of objects or clumps.
.TP
\fB\-\-riverave\fR
Average river value surrounding a clump.
.TP
\fB\-\-rivernum\fR
Number of river pixels around a clump.
.TP
\fB\-\-sigclip\-mean\fR
Mean after Sigma\-clipping
.TP
\fB\-\-sigclip\-median\fR
Median after Sigma\-clipping
.TP
\fB\-\-sigclip\-number\fR
Number of pixels in Sigma\-clipped measurement.
.TP
\fB\-\-sigclip\-std\fR
Standard deviation after Sigma\-clipping
.TP
\fB\-\-sky\fR
Sky value (per pixel).
.TP
\fB\-\-skystd\fR
Sky standard deviation (per pixel).
.TP
\fB\-\-std\fR
Standard dev. of values in object/clump.
.TP
\fB\-\-upperlimit\fR
Upper\-limit value, use other options to config.
.TP
\fB\-\-upperlimitonesigma\fR
Upper\-limit one sigma value.
.TP
\fB\-\-upperlimitquantile\fR
Quantile in random distribution (max 1).
.TP
\fB\-\-upperlimitsb\fR
Upper\-limit surface brightness (mag/arcsec^2).
.TP
\fB\-\-upperlimitsigma\fR
Place in random distribution (sigma multiple).
.TP
\fB\-\-upperlimitskew\fR
(Mean\-Median)/STD of random distribution.
.TP
\fB\-u\fR, \fB\-\-upperlimitmag\fR
Upper\-limit mag. use other options to config.
.IP
Morphology/shape related columns
.TP
\fB\-\-areaarcsec2\fR
Area of labeled region in arcsec^2.
.TP
\fB\-\-areaxy\fR
Projected area in first two dimensions.
.TP
\fB\-a\fR, \fB\-\-area\fR
Number of non\-blank valued pixels.
.TP
\fB\-A\fR, \fB\-\-semimajor\fR
RMS along major axis (in pixels).
.TP
\fB\-B\fR, \fB\-\-semiminor\fR
RMS along minor axis (in pixels).
.TP
\fB\-\-clumpsarea\fR
Non\-blank area covered by clumps.
.TP
\fB\-c\fR, \fB\-\-numclumps\fR
Number of clumps in this object.
.TP
\fB\-\-fracmaxarea1\fR
Area containing 1st fraction of maximum.
.TP
\fB\-\-fracmaxarea2\fR
Area containing 2nd fraction of maximum.
.TP
\fB\-\-fracmaxradius1\fR
Radius calculated from \fB\-\-fracmaxarea1\fR.
.TP
\fB\-\-fracmaxradius2\fR
Radius calculated from \fB\-\-fracmaxarea2\fR.
.TP
\fB\-\-fracmaxsum1\fR
Sum of pixels brighter than 1st frac. of max.
.TP
\fB\-\-fracmaxsum2\fR
Sum of pixels brighter than 2nd frac. of max.
.TP
\fB\-\-fwhm\fR
Full width at half max (non\-parametric).
.TP
\fB\-\-geoarea\fR
Area labled region (irrespective of value).
.TP
\fB\-\-geoareaxy\fR
Projected geoarea in first two dimensions.
.TP
\fB\-\-geoaxisratio\fR
Geometric axis ratio.
.TP
\fB\-\-geopositionangle\fR
Geometric position angle.
.TP
\fB\-\-geosemimajor\fR
RMS along major axis (ignoring value).
.TP
\fB\-\-geosemiminor\fR
RMS along minor axis (ignoring value).
.TP
\fB\-\-halfmaxarea\fR
No. pixels valued above half the max.
.TP
\fB\-\-halfmaxradius\fR
Radius at half the maximum (non\-parametric).
.TP
\fB\-\-halfmaxsb\fR
Surface brightness within half the maximum.
.TP
\fB\-\-halfmaxsum\fR
Sum of pixels above half the maximum.
.TP
\fB\-\-halfsumarea\fR
Area containing half of \fB\-\-brightness\fR.
.TP
\fB\-\-halfsumradius\fR
Radius calculated from \fB\-\-halfsumarea\fR.
.TP
\fB\-\-halfsumsb\fR
Surface brightness within \fB\-\-halfsumarea\fR.
.TP
\fB\-p\fR, \fB\-\-positionangle\fR
Flux weighted position angle.
.TP
\fB\-Q\fR, \fB\-\-axisratio\fR
Flux weighted axis ratio.
.TP
\fB\-\-sberror\fR
Surface brightness error (mag/arcsec^2).
.TP
\fB\-\-surfacebrightness\fR
Surface brightness (mag/arcsec^2).
.TP
\fB\-\-weightarea\fR
Area used for value weighted positions.
.IP
Operating modes:
.TP
\-?, \fB\-\-help\fR
give this help list
.TP
\fB\-\-checkconfig\fR
List all config files and variables read.
.TP
\fB\-\-cite\fR
BibTeX citation for this program.
.TP
\fB\-\-config\fR=\fI\,STR\/\fR
Read configuration file STR immediately.
.TP
\fB\-\-lastconfig\fR
Do not parse any more configuration files.
.TP
\fB\-\-minmapsize\fR=\fI\,INT\/\fR
Min. bytes to avoid RAM automatically.
.TP
\fB\-N\fR, \fB\-\-numthreads\fR=\fI\,INT\/\fR
Number of CPU threads to use.
.TP
\fB\-\-onlyversion\fR=\fI\,STR\/\fR
Only run if the program version is STR.
.TP
\fB\-P\fR, \fB\-\-printparams\fR
Print parameter values to be used and abort.
.TP
\fB\-\-quietmmap\fR
Don't print mmap'd file's name and size.
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Only report errors, remain quiet about steps.
.TP
\fB\-S\fR, \fB\-\-setdirconf\fR
Set default values for this directory and abort.
.TP
\fB\-\-usage\fR
give a short usage message
.TP
\fB\-U\fR, \fB\-\-setusrconf\fR
Set default values for this user and abort.
.TP
\fB\-V\fR, \fB\-\-version\fR
print program version
.PP
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
.PP
GNU Astronomy Utilities home page: http://www.gnu.org/software/gnuastro/
.SH "REPORTING BUGS"
Report bugs to bug\-gnuastro@gnu.org.
.SH COPYRIGHT
Copyright \(co 2015\-2022 Free Software Foundation, Inc.
License GPLv3+: GNU General public license version 3 or later.
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
.PP
Written/developed by Mohammad Akhlaghi
.SH "SEE ALSO"
The full documentation for
.B MakeCatalog
is maintained as a Texinfo manual.  If the
.B info
and
.B MakeCatalog
programs are properly installed at your site, the command
.IP
.B info MakeCatalog
.PP
should give you access to the complete manual.