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Output Formats
Aegean supports a number of output formats. There is the Aegean default, which is a set of columns separated by spaces, with header lines starting with #. The format is described within the output file itself.
The Aegean default output (which goes to STDOUT) does not contain all of the columns listed below.
Tables created with the --table option contain all the following columns, and as much meta-data as I can manage to pack in.
Columns included in output tables have the following columns:
- island - numerical indication of the island from which the source was fitted
- source - source number within that island
- background - background flux density in Jy/beam
- local_rms - local rms in Jy/beam
- ra_str - RA J2000 sexigecimal format
- dec_str - dec J2000 sexigecimal format
- ra - RA in degrees
- err_ra - source-finding fitting error on RA in degrees
- dec - dec in degrees
- err_dec - source-finding fitting error on dec in degrees
- peak_flux - peak flux density in Jy/beam
- err_peak_flux - source-finding fitting error on peak flux density in Jy/beam
- int_flux - integrated flux density in Jy. This is calcualted from a/b/peak_flux and the synthesized beam size. It is not fit directly.
- err_int_flux - source-finding fitting error on integrated flux density in Jy
- a - fitted semi-major axis in arcsec
- err_a - error on fitted semi-major axis in arcsec
- b - fitted semi-minor axis in arcsec
- err_b- error on fitted semi-minor axis in arcsec
- pa - fitted position angle in degrees
- err_pa - error on fitted position angle in degrees
- flags - fitting flags (should be all 0 for a good fit)
- residual_mean - mean of the residual flux remaining in the island after fitted Gaussian is subtracted
- residual_std - standard deviation of the residual flux remaining in the island after fitted Gaussian is subtracted
- uuid - a universally unique identifier for this component.
- psf_a - the semi-major axis of the point spread function at this location (arcsec)
- psf_b - the semi-minor axis of the point spread function at this location (arcsec)
- psf_pa - the position angle of the point spread function at this location (arcsec)
An island source will have the following columns:
- island - numerical indication of the island
- components - the number of components within this island
- background - background flux density in Jy/beam
- local_rms - local rms in Jy/beam
- ra_str - RA J2000 sexigecimal format
- dec_str - dec J2000 sexigecimal format
- ra - RA in degrees, of the brightest pixel in the island
- dec - dec in degrees, of the brightest pixel in the island
- peak_flux - peak flux density in Jy/beam, of the brightest pixel in the island
- int_flux - integrated flux density in Jy. Computed by summing pixels in the island, and dividing by the synthesized beam size.
- err_int_flux - Error in the above. Currently Null/None since I don't know how to calculate it.
- eta - a correction factor for int_flux that is meant to account for the flux that was not included because it was below the clipping limit. For a point source the true flux should be int_flux/eta. For extended sources this isn't always the case so use with caution.
- x_width - the extent of the island in the first pixel dimension, in pixels
- y_width - the extent of the island in the second pixel dimension, in pixels
- max_angular_size - the largest distance between to points on the boundary of the island, in degrees.
- pa - the position angle of the max_angular_size line
- pixels - the number of pixels within the island
- beam_area - the area of the synthesized beam (psf) in deg^2
- area - the area of the island in deg^2
- flags - fitting flags (should be all 0 for a good fit)
- uuid - a universally unique identifier for this island.
Note: Column names with 'ra/dec' will be replaced with a 'lat/lon' version if the input image has galactic coordinates in the WCS.
The most useful output is to use tables. Table output is supported by sqlite and astropy and there are three main types: database, votable, and ascii table. Additionally you can output ds9 region files by specifying a .reg file extension.
This format requires that the sqlite module is available. This is nearly always true by default, but if you get a crash then check that you can import sqlite3 from a python terminal before submitting a bug report.
Use --table out.db to create a database file containing one table for each source type that was discovered. The table names are 'components', 'islands', and 'simples'. Islands are created when --island is enabled. Components are elliptical gaussian fits and are the default type of source to create. Simples are sources that have been created by using the --measure option.
The columns of the database are self explanatory though they have no units. All fluxes are in Jy, major and minor axes are in arcseconds, and the position angle is in degrees. Errors that would normally be reported as -1 in other formats are stored as nulls in the database tables.
VOTables are difficult to work with as a human, but super awesome to work with when you have TopCat or some other VO enabled software.
VOTable output is supported by AstroPy (0.3+ I think). If you don't have the right version of AstroPy you can still run Aegean but will not be able to write VOTables. You will be told this when Aegean runs.
Use --table out.vot or --table out.xml to create a VOTable. Each type of sources that you find will be saved to a different file. Components are saved to out_comp.vot, islands are saved to out_isle.vot, and simple sources will be saved to out_simp.vot (or xml as appropriate). See above for a description of the source types.
ASCII tables are supported by AstroPy (0.4+ I think). As with VOTables, if you don't have the right version of AstroPy then Aegean will still run but it will tell you that you can't write ASCII tables.
There are currently four types of ascii tables that can be used:
- csv -> comma separated values
- tab -> tab separated values
- tex -> LaTeX formatted table
- html -> an html formatted table
Use --table out.html,out.tex etc.. for the type of table you are interested in. All tables have column headers that are the same as the variable names. These should be easily discernible. The units are Jy for fluxes, arcseconds for major/minor axes, and degrees for position angles.
As with other table formats the file names will be modified to out_comp.html, out_simp.csv, etc... to denote the different types of sources that are contained within.
use extension fits or FITS (but not fit or FIT) to write output tables.
Functionality supported by AstroPy.
These are binary tables and only the header is human readable.
Use extension reg for the output table to get DS9 region files.
Both components and islands are supported in this format with _comp.reg and _isle.reg being the corresponding filenames.
Component sources in the _comp.reg files will be shown as ellipses at the location of each component, with the fitted size/orientation. Each ellipse will be annotated with the island and component number such that Island 10, component 0 will appear as (10,0).
Island sources will appear as an outline of the pixels that comprise the island. Each island also has an annotation of the island number, and a diagonal line that represents the largest angular scale.
There are six different flags that can be set by Aegean during the source finding and fitting process.
In the STDOUT version of the Aegean catalog the flags column is written in binary format with a header that read WNCPES. These six flags correspond to:
| Abbreviation | Name | Numerical value | description |
|---|---|---|---|
| S | FITERRSMAL | 1 | This flag is set when islands are not able to be fit due to there being fewer pixels than free parameters. |
| E | FITERR | 2 | This flag is set when an error occurs during the fitting process. eg the fit doesn't converge. |
| P | FIXED2PSF | 4 | If a component is forced to have the shape of the local point spread function then this flag is set. This flag is often set at the same time as the FITERRSMALL, or FIXEDCRICULAR |
| C | FIXEDCRICULAR | 8 | If a source is forced to have a circular shape then this flag will be fit. |
| N | NOTFIT | 16 | If a component is not fit then this flag is set. This can because and island has reached the --maxsummits limit, or --measure mode has been invoked. |
| W | WCSERR | 32 | If the conversion from pixel to sky coordinates doesn't work then this flag will be set. This can happen for strange projections, but more likely when an image contains pixles that don't have valid sky coordinates. |
| Z | PRIORIZED | 64 | This flag is set when the source was fit using prorized fitting. |
Note that the flags column will be the summation of the numerical value of the above flags. So flags=7 means that flags P, E, and S have been set. This all makes more sense when you print the flags in binary format.