Python wrapper script for catalogue-based source finding with SoFiA 2. Note that the installation of SoFiA 2 is a prerequisite for OptiFind. SoFiA 2 can be obtained from https://github.com/SoFiA-Admin/SoFiA-2.

OptiFind depends on the following software packages:

• SoFiA 2
• Python 3
• Astropy

optifind.py <par_file> <source_list> <r_spat> <r_spec> [<sofia_exe>]

• <par_file> Name of the SoFiA 2 control parameter file to be used.
• <source_list> Name of the input source catalogue file.
• <r_spat> Spatial radius of the sub-region in pixels.
• <r_spec> Spectral radius of the sub-region in channels.
• <sofia_exe> Optional name of the SoFiA 2 executable. Default: sofia.

OptiFind serves as a wrapper script around the SoFiA 2 source finding pipeline to allow source finding on multiple sub-regions of a data cube centred on the positions from a user-supplied source catalogue. The user will need to provide a template SoFiA 2 parameter file that will be used in each source finding run spawned by OptiFind.

The template file must specify the input data cube to be searched and can also define an output file name which will be used as the base name for all output. In addition, the user must specify a source catalogue containing the position of each source to be searched. The catalogue must specify the world coordinate position of each source on a separate line. The following, comma-separated parameters must be supplied with each source:

id, coord_1, coord_2, coord_3, ...

Here, id is a unique source ID that will be used as an identifier for output products, while coord_n denotes the coordinates in each dimension of the data cube. The coordinate must be specified in the raw units of the data cube as specified in the FITS header. A coordinate value must be given for each axis of the cube in the correct order.

For example, if a cube has four axes (right ascension, declination, frequency and Stokes), then four coordinate values need to be provided for each source, and they must be given in the native units specified in the header, e.g. degrees for right ascension and Hz for frequency. An example for a 3D data cube with RA, declination and velocity axis might look like this:

# Example catalogue
Source 1, 180.7, 62.0, 1300000.0
Source 2, 180.9, 62.3, 1200000.0

Here, RA and declination are in degrees, while velocity is specified in m/s, which are the default units defined by the FITS standard.

Separate output catalogues and products will be created for each SoFiA 2 run. Their base name will be either optifind + suffix or output.filename + suffix depending on whether or not an output file name was defined in the parameter file. The suffix will be an underscore followed by the source ID provided in the catalogue file.

In addition to the individual output catalogues from each run, OptiFind will also create a single, merged catalogue called optifind_merged_catalogue.txt in the same output directory. Note that this feature is currently only available for plain-text ASCII catalogues, but not for XML or SQL catalogues.

Copyright (C) 2020 Tobias Westmeier

OptiFind is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.