opentps-core 1.1.2

Open source TPS for advanced proton therapy

opentps-core

Core library of opentps, a Python application for treatment planning in proton therapy, based on the MCsquare Monte Carlo dose engine.

Installation (Linux):

Requirements are listed in pyproject.toml. To install all required dependencies:

poetry install

Additional system libraries (Ubuntu 19 or more recent):

sudo apt install libmkl-rt

Additional system libraries (Ubuntu 18):

cd /tmp
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
sudo sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
sudo apt-get update
sudo apt-get install intel-mkl-64bit-2020.1-102
echo 'export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH' | sudo tee -a /etc/profile.d/mkl_lib.sh

# adapted from: http://dirk.eddelbuettel.com/blog/2018/04/15/

Optional python modules:

pip3 install --user tensorflow
pip3 install --user keras
pip3 install --user cupy

Installation (Windows):

Note: VTK is only compatible with Python version <= 3.9. Do not use Python 3.10

1. Install anaconda on your Windows computer

2. Open Anaconda Prompt (via the Anaconda application)

3. Create a new Anaconda environment:

conda create --name OpenTPS python=3.8

4. Activate the new environment:

conda activate OpenTPS

5. Install the following python modules: Python modules:

pip3 install --upgrade pip
pip3 install pydicom
pip3 install numpy
pip3 install scipy
pip3 install matplotlib
pip3 install Pillow
pip3 install sparse_dot_mkl
pip3 install SimpleITK
pip3 install pandas
pip3 install scikit-image
pip3 install pymedphys==0.39.3
pip3

Optional python modules:

pip3 install tensorflow
pip3 install keras
pip3 install cupy