astmkcatalog1

Usage

Overview

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.

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/