astmkcatalog(1)

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 [email protected].

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.