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PURIFY
Next-generation radio interferometric imaging
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PURIFY is an open-source collection of routines written in C++
available under the license below. It implements different tools and high-level to perform radio interferometric imaging, i.e. to recover images from the Fourier measurements taken by radio interferometric telescopes.
PURIFY leverages recent developments in the field of compressive sensing and convex optimization. Low-level functionality to solve the resulting convex optimisation is factored into the open-source companion code, SOPT, also written by the authors of PURIFY. For further background please see the reference section.
This documentation outlines the necessary and optional dependencies upon which PURIFY should be built, before describing installation, testing and usage details. Contributors, references and license information then follows.
PURIFY is written in C++11
. Pre-requisites and dependencies are listed in following and minimal versions required are tested against Travis CI
meaning that they come natively with OSX and the Ubuntu Trusty release. These are also the default ones fetched by CMake
(an internet connection is required for this).
C++
minimal dependencies:
cmake3
) A free software that allows cross-platform compilationC++
CMake
recipes. Downloaded automatically if absentC++
linear algebra. Downloaded automatically if absent.C
and Fortran
subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Downloaded automatically if absent.C++
unit-testing framework only needed for testing. Downloaded automatically if absent.v1.3.0
- Optional - A C++
micro-benchmarking framework only needed for benchmarks. Downloaded automatically if absent.PURIFY can be installed through the software packet manager on Linux Debian distributions:
Alternatively, you can build PURIFY entirely from the source code. Once the mandatory dependencies are present, git clone
from the GitHub repository:
Then, the program can be built with standard CMake
command:
To test everything went all right:
To install in directory /X
, with libraries going to ‘X/’ do:
To check everything went all right, run the test suite:
The main purify executable lives either in the build directory or in the in the bin
subdirectory of the installation directory. purify
has one required argument, it a string for the file path of the config file containing the settings.
purify path/to/config.yaml
.
A template with a description of the settings is included in the data/config
directory. When
purify` runs a directory will be created, and the output images will be saved and time-stamped. Additionally, a config file with the settings used will be saved and time-stamped, helping for reproducibility and book-keeping.
If you want to use Docker instead, you can build an image using the Dockerfile available in the repository or pulling it from DockerHub.
or
Then to use it, you should mount the directory with your data and config files to /mydata
in the container. To run the container and mount the directory is with:
That will start a shell inside the container in the /mydata
directory where you can see all the files from your /full/path/to/data
. There you can run purify
as shown above.`
Check the contributors page (github).
If you use PURIFY for work that results in publication, please reference the webpage and our related academic papers:
It is possible to tell CMake
exactly which libraries to compile and link against. The general idea is to add -DVARIABLE=something
to the command-line arguments of CMake. CMake can be called any number of times: previous settings will not be overwritten unless specifically requested. Some of the more common options are the following:
CMAKE_PREFIX_PATH
: CMake will look in "CMAKE_PREFIX_PATH/lib" for libraries, "CMAKE_PREFIX_PATH/include" for headers, etc.FFTW3_LIBRARIES
, FFTW3_INCLUDE_DIR
BLAS_INCLUDE_DIRS
, BLAS_LIBRARIES
All these variables and more can be found and modified in the CMakeCache.txt
file in the build directory. There are extra CMake options sepcific to purify. -Ddompi=ON
will turn MPI on in the build, -Dopenmp=ON
will turn openmp on for the build. -Dtests=ON
will make sure tests are built.
ctest
should be run to make sure the unit tests pass.
PURIFY Copyright (C) 2013-2019
This program 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 2 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 (LICENSE.txt).
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
For any questions or comments, feel free to contact Jason McEwen, or add an issue to the issue tracker.
The code is given for educational purpose. The code is in beta and still under development.