PyEPRI

A CPU & GPU compatible Python package for Electron Paramagnetic Resonance Imaging.

Package documentation and tutorials are available here.

If you have any comments, questions, or suggestions regarding this code, don't hesitate to open a discussion or a bug issue.

Installation

System requirements

PyEPRI can be installed on all plateforms (Linux, MacOs or Windows). However, GPU support is currently only available for systems equipped with an NVIDIA graphics card and a working installation of the CUDA drivers (which excludes MAC systems).

The following installation guidelines assume that you have the following libraries installed on your system:

• [mandatory] python3 (the Python 3 programming language)
• [mandatory] python3-pip (to install Python packages using the pip command)
• [mandatory] python3-venv (for the creation of virtual environment)
• [recommended] python3-tk (to avoid display issues on Linux systems)
• [optional] git (if you want to install the PyEPRI package via the github repository)

Install latest stable version using pip (recommended)

Open a terminal and execute the following steps in order to create a virtual environment, and install the latest stable version of pyepri from the PyPi repository.

###################################################
# Create and activate a fresh virtual environment #
###################################################
python3 -m venv ~/.venv/pyepri
source ~/.venv/pyepri/bin/activate

#########################################################
# Install the `pyepri` package from the PyPi repository #
#########################################################
pip install pyepri

###########################################################
# Optional: enable {torch-cpu, torch-cuda, cupy} backends #
###########################################################

# enable `torch-cpu` backend
pip install pyepri[torch-cpu]

# enable `torch-cuda` backend (requires a NVIDIA graphics card with CUDA installed)
pip install pyepri[torch-cuda]

# enable `cupy` backend (requires a NVIDIA graphics card with CUDA installed)
# (please uncomment the appropriate line depending on your CUDA installation)
# pip install pyepri[cupy-cuda12x] # For CUDA 12.x
# pip install pyepri[cupy-cuda11x] # For CUDA 11.x

Install latest version from Github

Open a terminal and execute the following steps in order to checkout the current code release, create a virtual environment, and install pyepri from the github repository.

##################
# Clone the code #
##################
git clone https://github.com/remy-abergel/pyepri.git
cd pyepri

###################################################
# Create and activate a fresh virtual environment #
###################################################
python3 -m venv ~/.venv/pyepri
source ~/.venv/pyepri/bin/activate
	 
##########################################################
# Install the `pyepri` package from the checked out code #
# (do not forget the . at the end of the command line)   #
##########################################################
pip install -e .

###########################################################
# Optional: enable {torch-cpu, torch-cuda, cupy} backends #
###########################################################

# enable `torch-cpu` backend
pip install -e ".[torch-cpu]"

# enable `torch-cuda` backend (requires a NVIDIA graphics card with CUDA installed)
pip install -e ".[torch-cuda]"

# enable `cupy` backend (requires a NVIDIA graphics card with CUDA installed)
# (please uncomment the appropriate line depending on your CUDA installation)
# pip install -e ".[cupy-cuda12x]" # For CUDA 12.x
# pip install -e ".[cupy-cuda11x]" # For CUDA 11.x

################################################################
# If you want to compile the documentation by yourself, you    #
# must install the [doc] optional dependencies of the package, #
# compilation instructions are provided next                   #
################################################################
pip install -e ".[doc]" # install some optional dependencies
make -C docs html # build the documentation in html format
firefox docs/_build/html/index.html # open the built documentation (you can replace firefox by any other browser)

Because this installation was done in editable mode (thanks to the -e option of pip), any further update of the repository (e.g., using the syncing commang git pull) will also update the current installation of the package.

Troubleshooting

• Mac users are strongly recommended to use bash shell instead of zsh to avoid slow copy-paste issues (type chsh -s /bin/bash in a terminal).

• Display issues related to matplotlib interactive mode were reported on Linux systems and were solved by installing python3-tk (type sudo apt-get install python3-tk in a terminal).

• If the installation of the package or one of its optional dependency fails, you may have more chance with miniconda (or conda).

• If you still encounter difficulties, feel free to open a bug issue.

License

PyEPRI was created by Rémy Abergel (Centre National de la Recherche Scientifique, Université Paris Cité, Laboratoire MAP5). It is licensed under the terms of the MIT license.