pySAP-etomo

Python Sparse data Analysis Package external electron tomography (etomo) plugin.

Pysap-etomo is a plugin of the open-source Python library called PySAP (https://github.com/cea-cosmic/pySAP) for compressed sensing tomographic reconstruction using gradient-based and wavelet-based regularizations. It was developed in the context of an interdisciplinary project involving CEA-Leti (Martin Jacob, Jyh-Miin Lin, Guillaume Biagi, Zineb Saghi), CEA-NeuroSpin (Loubna El Gueddari, Philippe Ciuciu) and CEA-CosmoStat (Samuel Farrens, Jean-Luc Starck). We acknowledge the financial support of the Cross-Disciplinary Program on Numerical Simulation of CEA, the French Alternative Energies and Atomic Energy Commission.

The current version of pysap-etomo contains 2D and 3D implementations of:

• Total variation (TV)
• Higher order TV (HOTV)
• Wavelets from PyWavelets library.
• Radon operators
• Fourier operators using the projection-slice theorem

Installation instructions

Install python-pySAP using:

pip install python-pysap

This will install pysap and its current plugins (except pysapp-etomo).

To install pysap-etomo, clone the repository or download it locally with the following command:

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

python setup.py install

Special Installations

For Radon operators in 2D/3D (both CPU & GPU implementations astratoolbox

Linux/Mac:

git clone github: https://github.com/astra-toolbox/astra-toolbox

cd build/linux

./autogen.sh # when building a git version

./configure --with-cuda=/usr/local/cuda --with-python --with-install-type=module

make

make install

Windows:

conda install -c astra-toolbox/label/dev astra-toolbox