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

See pysap documentation for more informations about the install options. As of v0.0.6 of pysap, the following will install only what is necessary (from pysap setup.py directly):

python setup.py install --nosparse2d --only=pysap-etomo

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