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 0.22. 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 bug-gnuastro@gnu.org.

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

Source file:	astmkcatalog.1.en.gz (from gnuastro 0.22-3)
Source last updated:	2024-02-20T08:43:34Z
Converted to HTML:	2024-03-15T23:17:37Z

NAME¶

SYNOPSIS¶

DESCRIPTION¶

REPORTING BUGS¶

COPYRIGHT¶

SEE ALSO¶