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SoFiA

Introduction

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).

Requirements

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 (= 2.7; including dev package)
    • NumPy (≥ 1.8)
    • SciPy (≥ 0.7)
    • Astropy (≥ 0.2.5)
    • matplotlib (≥ 1.1; optional, needed for reliability plots)
  • Packages (C/C++):
    • Compiler:
      • Preferred: GCC (≥ 4.8; including g++)
      • Alternative: Clang (≥ 3.3; Xcode version ≥ 5.0.0 (clang-500.2.75))
    • Graphical user interface (optional):
      • 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.

Installation

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.

  1. 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].

  2. Enter the installation directory

    cd SoFiA-[version]

  3. Compile and install the SoFiA pipeline and user interface

    python setup.py build --force

    (add --no-gui=True to install SoFiA without graphical user interface)

  4. 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.

  5. Launch SoFiA

    Open a new terminal window and type:

    SoFiA &

Problems

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:

Documentation

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.

Version history

  • SoFiA 1.2.0

    • Released 24/05/2018
    • Adds several new features, including better handling of reliability calculation, the option to discard negative signals, and a new image viewer built into the GUI that allows output data products from SoFiA to be inspected in situ.
    • Fixes a large number of bugs across the entire pipeline that have led to frequent crashes in the past, including bugs in the linker module, cubelet and moment map generation, and the handling of 4-D FITS cubes.
    • See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v1.2.0

  • SoFiA 1.1.0

    • Released 25/10/2017
    • Adds several new features, including better handling of reliability calculation, the option to discard negative signals, and a new image viewer built into the GUI that allows output data products from SoFiA to be inspected in situ.
    • Fixes a large number of bugs across the entire pipeline that have led to frequent crashes in the past, including bugs in the linker module, cubelet and moment map generation, and the handling of 4-D FITS cubes.
    • See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v1.1.0

  • SoFiA 1.0.0

    • Released 13/07/2016
    • Adds several new features, including improvements in reliability calculation, the inclusion of new source parameters aimed at exteded galaxies, and the introduction of basic GUI configuration options.
    • Fixes a large number of bugs across the entire pipeline that have led to frequent crashes in the past.
    • See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v1.0.0

  • SoFiA 0.5.0

    • Released 22/09/2015
    • Adds several new features, including GUI sessions, automated kernel size determination in reliability calculation and Unified Content Descriptors for source parameters (UCDs).
    • Fixes a few bugs in handling WCS information and merging detections into sources.
    • See release notes for details: https://github.com/SoFiA-Admin/SoFiA/releases/tag/v0.5.0

  • 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

  • SoFiA 0.3.2

  • SoFiA 0.3.1

  • SoFiA 0.3

  • SoFiA 0.2.1

  • SoFiA 0.2

  • 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.

Copyright and licence

SoFiA was created by the following people: Lars Flöer, Nadine Giese, Russell Jurek, Martin Meyer, Attila Popping, Paolo Serra, Tobias Westmeier, and Benjamin Winkel.

© 2018 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/.

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