Simple usage

Suggested basic usage (with mostly default parameters):

aegean RadioImage.fits --table=Catalog.fits

Usage and short description can be obtained via aegean, which is replicated below.

This is Aegean 2.2.2-(2020-06-07)
usage: aegean [-h] [--find] [--cores CORES] [--hdu HDU_INDEX]
              [--beam BEAM BEAM BEAM] [--telescope TELESCOPE] [--lat LAT]
              [--slice SLICE] [--forcerms RMS] [--forcebkg BKG]
              [--noise NOISEIMG] [--background BACKGROUNDIMG] [--psf IMGPSF]
              [--autoload] [--out OUTFILE] [--table TABLES] [--tformats]
              [--blankout] [--colprefix COLUMN_PREFIX]
              [--maxsummits MAX_SUMMITS] [--seedclip INNERCLIP]
              [--floodclip OUTERCLIP] [--island] [--nopositive] [--negative]
              [--region REGION] [--nocov] [--condon] [--priorized PRIORIZED]
              [--ratio RATIO] [--noregroup] [--input INPUT] [--catpsf CATPSF]
              [--save] [--outbase OUTBASE] [--debug] [--versions] [--cite]
              [image]

positional arguments:
  image

optional arguments:
  -h, --help            show this help message and exit

Configuration Options:
  --find                Source finding mode. [default: true, unless --save or
                        --measure are selected]
  --cores CORES         Number of CPU cores to use for processing [default:
                        all cores]
  --hdu HDU_INDEX       HDU index (0-based) for cubes with multiple images in
                        extensions. [default: 0]
  --beam BEAM BEAM BEAM
                        The beam parameters to be used is "--beam major minor
                        pa" all in degrees. [default: read from fits header].
  --telescope TELESCOPE
                        DEPRECATED
  --lat LAT             DEPRECATED
  --slice SLICE         If the input data is a cube, then this slice will
                        determine the array index of the image which will be
                        processed by aegean

Input Options:                                                                                                                                                                      [29/99695]
  --forcerms RMS        Assume a single image noise of rms. [default: None]
  --forcebkg BKG        Assume a single image background of bkg. [default:
                        None]
  --noise NOISEIMG      A .fits file that represents the image noise (rms),
                        created from Aegean with --save or BANE. [default:
                        none]
  --background BACKGROUNDIMG
                        A .fits file that represents the background level,
                        created from Aegean with --save or BANE. [default:
                        none]
  --psf IMGPSF          A .fits file that represents the local PSF.
  --autoload            Automatically look for background, noise, region, and
                        psf files using the input filename as a hint.
                        [default: don't do this]

Output Options:
  --out OUTFILE         Destination of Aegean catalog output. [default: No
                        output]
  --table TABLES        Additional table outputs, format inferred from
                        extension. [default: none]
  --tformats            Show a list of table formats supported in this
                        install, and their extensions
  --blankout            Create a blanked output image. [Only works if
                        cores=1].
  --colprefix COLUMN_PREFIX
                        Prepend each column name with "prefix_". Default =
                        prepend nothing

Source finding/fitting configuration options:
  --maxsummits MAX_SUMMITS
                        If more than *maxsummits* summits are detected in an
                        island, no fitting is done, only estimation. [default:
                        no limit]
  --seedclip INNERCLIP  The clipping value (in sigmas) for seeding islands.
                        [default: 5]
  --floodclip OUTERCLIP
                        The clipping value (in sigmas) for growing islands.
                        [default: 4]
  --island              Also calculate the island flux in addition to the
                        individual components. [default: false]
  --nopositive          Don't report sources with positive fluxes. [default:
                        false]
  --negative            Report sources with negative fluxes. [default: false]
  --region REGION       Use this regions file to restrict source finding in
                        this image. Use MIMAS region (.mim) files.
  --nocov               Don't use the covariance of the data in the fitting
                        proccess. [Default = False]
  --condon              replace errors with those suggested by Condon'97.
                        [Default = False]

Priorized Fitting config options:
  in addition to the above source fitting options

  --priorized PRIORIZED
                        Enable priorized fitting level n=[1,2,3]. 1=fit flux,
                        2=fit flux/position, 3=fit flux/position/shape. See
                        the GitHub wiki for more details.
  --ratio RATIO         The ratio of synthesized beam sizes (image psf / input
                        catalog psf). For use with priorized.
  --noregroup           Do not regroup islands before priorized fitting.
  --input INPUT         If --priorized is used, this gives the filename for a
                        catalog of locations at which fluxes will be measured.
  --catpsf CATPSF       A psf map corresponding to the input catalog. This
                        will allow for the correct resizing of sources when
                        the catalog and image psfs differ.

Extra options:
  --save                Enable the saving of the background and noise images.
                        Sets --find to false. [default: false]
  --outbase OUTBASE     If --save is True, then this specifies the base name
                        of the background and noise images. [default: inferred
                        from input image]
  --debug               Enable debug mode. [default: false]
  --versions            Show the file versions of relevant modules. [default:
                        false]
  --cite                Show citation information.

Example usage:

The following commands can be run from the Aegean directory right out of the box, since they use the test images that are included with Aegean.

• Blind source finding on a test image and report results to stdout
  • aegean tests/test_files/1904-66_SIN.fits
• As above but put the results into a text file
  • aegean tests/test_files1904-66_SIN.fits --table out.csv
  • The above creates a file out_comp.csv for the components that were fit
• Do source finding using a catalog input as the initial parameters for the sources
  • aegean --priorized 1 --input out_comp.csv tests/test_files/1904-66_SIN.fits
• Source-find an image and save results to multiple tables
  • aegean --table catalog.csv,catalog.vot,catalog.fits tests/test_files1904-66_SIN.fits
• Source-find an image and report the components and islands that were found
  • aegean --table catalog.vot --island tests/test_files1904-66_SIN.fits
  • The above creates two files: catalog_comp.vot for the components, and catalog_isle.vot for the islands. The island column of the components maps to the island column of the islands.
• Source-find a sub-region of an image
  • aegean --region=region.mim tests/test_files1904-66_SIN.fits
  • The region.mim is a region file in the format created by MIMAS