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. Required software and libraries, and their minimum supported versions, are listed below. The build system will attempt to automatically download and build the automatically included libraries. (an internet connection is required for this).
C++ dependencies:
- CMake v3.5.1 A free software that allows cross-platform compilation
- GCC v7.3.0 GNU compiler for
C++ - OpenMP v4.8.4 - Optional - Speeds up some of the operations.
- MPI v3.1.1 - Optional - Parallelisation paradigm to speed up operations.
- astro-informatics/sopt v4.1.0: Sparse Optimization Compressed Sensing library.
- Boost v1.78.0: A set of free peer-reviewed portable C++ libraries.
- fftw3 v3.3.9: Fastest Fourier Transform in the West.
- Eigen3 v3.3.7: Modern
C++linear algebra. - tiff v4.0.9: Tag Image File Format library.
- cfitsio: v4.0.0: Library of
CandFortransubroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. - yaml-cpp v0.6.3: YAML parser and emitter in
C++. - casacore - Optional - Needed to interface with measurement
- ONNXruntime v1.17.1 - Optional - a cross-platform runtime engine based on the Open Neural Network eXchange format. sets.
- Catch2 v2.13.9: Optional - A
C++unit-testing framework only needed for testing. - google/benchmark v1.6.0: Optional - A
C++micro-benchmarking framework only needed for benchmarks.
For examples on how to install dependencies on Ubuntu and MacOS, see the cmake.yml.
If the dependencies are already available on your system, you can also install PURIFY manually like so
cd /path/to/code
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../local
make -j
make -j installOn MacOS, you can also install most of the dependencies with Homebrew e.g.
brew install boost fftw eigen yaml-cpp catch2 [onnxruntime]The SOPT library includes an interface to ONNXrt for using trained models
as priors in the Forward-Backward optimization algorithm. To build PURIFY with
ONNXrt capability, you need to enable ONNXrt support also in SOPT using
the onnxrt option when running the cmake command.
To check everything went all right, run the test suite:
cd /path/to/purify/build
ctest .
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.
The CI workflow has a manual dispatch trigger which allows you to log into the job while it's running. You can trigger it in
actions.
Run the workflow and set debug_enabled=true to enable the tmate step in the CI workflow. Once the workflow is running, open the job in actions.
You should see it printing out a line with a ssh command. Run it in terminal to log into the GitHub Actions runner.
A Dockerfile is available on DockerHub. We are currently not maintaining it, and cannot guarantee it is up to date. Use the below documentation at your own risk.
If you want to use Docker instead, you can build an image using the Dockerfile available in the repository or pulling it from DockerHub.
docker build -t purify .
or
docker pull uclrits/purify
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:
docker run -it --name purify -v /full/path/to/data:/mydata uclrits/purify
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](@ref purify_contributors) page (github).
If you use PURIFY for work that results in publication, please reference the webpage and our related academic papers:
- L. Pratley, et al. "Distributed convex optimization for Radio Interferometry with PURIFY". Link will be here soon!
- L. Pratley, M. Johnston-Hollitt, J. D. McEwen, "A fast and exact w-stacking and w-projection hybrid algorithm for wide-field interferometric imaging". Submitted to ApJ arXiv:1807.09239
- L. Pratley, J. D. McEwen, M. d'Avezac, R. E. Carrillo, A. Onose, Y. Wiaux. "Robust sparse image reconstruction of radio interferometric observations with PURIFY". Accepted (2016) arxiv:1610.02400
- A. Onose, R. E. Carrillo, A. Repetti, J. D. McEwen, J.-P. Thiran, J.-C. Pesquet, and Y. Wiaux. "Scalable splitting algorithms for big-data interferometric imaging in the SKA era" Mon. Not. Roy. Astron. Soc. 462(4):4314-4335 (2016) arXiv:1601.04026
- R. E. Carrillo, J. D. McEwen and Y. Wiaux. "PURIFY: a new approach to radio-interferometric imaging". Mon. Not. Roy. Astron. Soc. 439(4):3591-3604 (2014) arXiv:1307.4370
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.