SoFiA, the Source Finding Application, is a new HI source finding pipeline intended to find and parametrise galaxies in HI data cubes. SoFiA can be launched from the command line, but it also comes with an easy-to-use graphical user interface that allows control parameters to be manipulated interactively. While the software is still under development, several stable versions of SoFiA have already been released and can be obtained from the SoFiA webpage on GitHub.
The following packages and libraries will be required to install and run SoFiA:
Operating system:
Linux or Unix (e.g. Ubuntu, Mac OS, etc.)
Terminal with bash or tcsh (other shells should work as well)
Packages (Python):
Python (≥ 2.4)
numpy (≥ 1.8)
scipy (≥ 0.7)
astropy (≥ 0.2.5)
matplotlib (≥ 1.1; optional, only needed for reliability plot)
Packages (C++):
GCC (≥ 4.6)
GNU Scientific Library (≥ 1.15; including dev files)
Qt (≥ 4.7; including dev files and qmake)
All of the above packages must be installed before SoFiA can be compiled and run. It is recommended that you install them through your operating system’s package manager. Please ensure that the development packages of the GNU Scientific Library and the Qt library are installed as well.
To install SoFiA on your computer, open a terminal window and change into the folder where the downloaded file was saved. Then follow the steps below.
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Unpack all files
Download and unpack the zipped archive into a directory of your choice:
unzip SoFiA-[version].zip
or
tar -xzvf SoFiA-[version].tar.gz
where [version] is the downloaded version of SoFiA, e.g. 0.2. This will unpack all files into a directory called SoFiA-[version].
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Enter the installation directory
cd SoFiA-[version]
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Compile and install the SoFiA pipeline and user interface
python setup.py build --force
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Set up environment variables
Follow the instructions given at the end of the installation process to define the required environment variables and paths in your .bashrc or .cshrc file.
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Launch SoFiA
Open a new terminal window and type:
SoFiA &
If you encounter problems when running the setup script, it is likely that you are either missing one of the required packages and libraries or that some of the packages are outdated. Please check that the required versions of all packages are installed and properly set up such that they can be found by Python and the GCC. On some systems it may be necessary to explicitly install the GNU C++ compiler (g++, should normally be part of the GCC) as well as the development packages (dev) of Qt and the GNU Scientific Library. Please also see the trouble shooting page on the SoFiA wiki for more information on a few commonly encountered problems:
SoFiA comes with its own built-in help browser that can be launched from the help menu in the user interface. Alternatively, you can use your web browser to open the index.html file located in the gui/doc/ sub-folder. Please note that the user manual is still work in progress, and only basic help is available at this stage.
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SoFiA 0.4.0
- Released 22/12/2014
- Adds several new features, including 2D–1D wavelet filtering, the CNHI finder, and optically motivated source finding.
- Fixes a few bugs and greatly improves the graphical user interface and documentation.
- See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v0.4.0
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SoFiA 0.3.2
- Released 25/08/2014
- Adds several new features, including subcube processing and separate output directory.
- Fixes a bug that limited the number of detected sources to 10,000.
- See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v0.3.2
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SoFiA 0.3.1
- Released 14/07/2014
- Adds several new features, including weights functions, flagging, and Qt 5 support.
- Fixes several bugs, including reduction of memory footprint and removal of a security vulnerability.
- See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v0.3.1
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SoFiA 0.3
- Released 20/05/2014
- Adds several new features, including WCS support, PV diagrams, and handling of units.
- Fixes a few bugs related to FITS import and handling of blanked pixels.
- See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v0.3
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SoFiA 0.2.1
- Released 25/02/2014
- Some more bug fixes, including fixing the threshold finder.
- Implementation of VO table output.
- See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v0.2.1
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SoFiA 0.2
- Released 10/02/2014
- Fixes several bugs that were still present in the initial beta version.
- See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v0.2
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SoFiA 0.1 beta
- Released 14/11/2013
- Initial beta release of the package with basic functionality and built-in help system; may still contain bugs and errors.
SoFiA was created by the following people: Lars Flöer, Nadine Giese, Russell Jurek, Martin Meyer, Attila Popping, Paolo Serra, Tobias Westmeier, and Benjamin Winkel.
© 2014 The SoFiA Authors
This programme 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 programme 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 programme. If not, see http://www.gnu.org/licenses/.