PySAP

PySAP (Python Sparse data Analysis Package) is a Python module for sparse data analysis that offers:

• A common API for astronomical and neuroimaging datasets.
• Access to Sparse2D executables with both wrappers and bindings.
• Access to application specific plugins.
• A graphical user interface to play with the provided functions.

This package is the result of the COSMIC project, which is a collaboration between the CEA Neurospin UNATI and CEA CosmoStat laboratories.

Important links

• Official source code repo: https://github.com/cea-cosmic/pysap
• API documentation (last stable release): https://python-pysap.readthedocs.io/
• PySAP paper: https://arxiv.org/abs/1910.08465

Dependencies

PySAP will automatically install all of the required dependencies, however issues may arise on some operating systems. If you encounter any problems please ensure that you have all of the following dependencies installed before opening a new issue.

1. PySAP requires that the COSMIC package ModOpt be installed.

2. PySAP also requires the installation of the following third party software packages:

• astropy
• matplotlib
• nibabel
• numpy
• scipy
• progressbar2
• pyqtgraph
• PyWavelets
• scikit-learn

Installation

The installation of PySAP has been extensively tested on Ubuntu and macOS, however we cannot guarantee it will work on every operating system (e.g. Windows).

If you encounter any installation issues be sure to go through the following steps before opening a new issue:

1. Check that that all of the installed all the dependencies listed above have been installed.
2. Read through all of the documentation provided, including the troubleshooting suggestions.
3. Check if you problem has already been addressed in a previous issue.

Further instructions are available here.

From PyPi

To install PySAP simply run:

$ pip install python-pysap

Depending on your Python setup you may need to provide the --user option.

$ pip install --user python-pysap

Locally

To build PySAP locally, clone the repository:

$ git clone https://github.com/CEA-COSMIC/pysap.git

and run:

$ python setup.py install

or:

$ python setup.py develop

As before, use the --user option if needed.

macOS

Help with installation on macOS is available here.

Linux

Please refer to the PyQtGraph homepage for issues regarding the installation of pyqtgraph.

Contributing

If you want to contribute to pySAP, be sure to review the contribution guidelines and follow to the code of conduct.

Citation

If you use PySAP in a scientific publication, we would appreciate citations to the following paper: PySAP: Python Sparse Data Analysis Package for multidisciplinary image processing, S. Farrens et al., Astronomy and Computing 32, 2020

The bibtex citation is the following: k:

@Article{farrens2020pysap,
  title={{PySAP: Python Sparse Data Analysis Package for multidisciplinary image processing}},
  author={Farrens, S and Grigis, A and El Gueddari, L and Ramzi, Z and Chaithya, GR and Starck, S and Sarthou, B and Cherkaoui, H and Ciuciu, P and Starck, J-L},
  journal={Astronomy and Computing},
  volume={32},
  pages={100402},
  year={2020},
  publisher={Elsevier}
}