The HI Source Finding Application
This repository has been archived and is not being maintained any more. Hence, we will no longer be responding to any bug reports or user enquiries. SoFiA has been replaced by the more advanced SoFiA 2, and existing SoFiA users are strongly advised to switch to SoFiA 2. We thank all SoFiA users for their help and support over many years.
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.
If you would like to stay informed about new stable releases of SoFiA and
other important updates, you can sign up to the SoFiA mailing list. To do
so, simply send an e-mail to sofia-request [at] atnf.csiro.au
with the
word subscribe
in the e-mail body (note that the e-mail subject will be
ignored).
The following packages and libraries will be required to install and run SoFiA:
bash
or tcsh
(other shells should work as well)Python
(≥ 3.0; including dev package; note that Python 2.7 is no
longer supported at this point.)NumPy
(≥ 1.8)SciPy
(≥ 0.7)Astropy
(≥ 0.2.5)matplotlib
(≥ 1.1; optional, needed for reliability plots)GCC
(≥ 4.8; including g++
)Clang
(≥ 3.3; Xcode version ≥ 5.0.0 (clang-500.2.75))zlib
(≥ 1.2.8; including dev package)Qt
(≥ 4.7; including dev packages and qmake
)All of the above packages, unless marked as optional, must be installed before SoFiA can be compiled and run. It is recommended that you install them through your operating system’s package manager.
Installation of the GUI, and hence of zlib
and Qt
, is optional and can be
disabled during installation using the --no-gui=True
option (see below for
installation instructions). If you want the GUI to be installed, please ensure
that the development packages of zlib and the Qt library are installed as
well.
Just as an example, on an Ubuntu system with Qt4 the zlib1g-dev
,
libqt4-dev
and qt4-qmake
packages must be 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.
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. 1.0. This will
unpack all files into a directory called SoFiA-[version]
.
Enter the installation directory
cd SoFiA-[version]
Delete any existing build
folder if necessary, then compile and install
the SoFiA pipeline and user interface
rm -rf build
python setup.py build --force
(Note: add --no-gui=True
to the setup call to install SoFiA without
the graphical user interface.)
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.
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. 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.
Further information about SoFiA is available from the SoFiA description papers:
SoFiA: a flexible source finder for 3D spectral line data
Serra, P., Westmeier, T., Giese, N., et al., 2015, MNRAS, 448, 1922
http://adsabs.harvard.edu/abs/2015MNRAS.448.1922S
SoFiA 2 – An automated, parallel HI source finding pipeline for the WALLABY survey
Westmeier, T., Kitaeff, S., Pallot, D., et al., 2021, MNRAS, 506, 3962
http://adsabs.harvard.edu/abs/2021MNRAS.506.3962W
If you find SoFiA useful and intend to use it in your own research, we would appreciate a reference to the two SoFiA papers in any publication that results from your work.
SoFiA 1.3.2
SoFiA 1.3.0
SoFiA 1.2.0
SoFiA 1.1.0
SoFiA 1.0.0
SoFiA 0.5.0
SoFiA 0.4.0
SoFiA 0.3.2
SoFiA 0.3.1
SoFiA 0.3
SoFiA 0.2.1
SoFiA 0.2
SoFiA 0.1 beta
SoFiA was created by the following people: Lars Flöer, Nadine Giese, Russell Jurek, Martin Meyer, Attila Popping, Paolo Serra, Tobias Westmeier, and Benjamin Winkel.
© 2020 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/.