Meshed and processed artery model. A variable density volumetric mesh (left), with corresponding inlet flow rate, outlet flow splits, and probes for velocity and pressure sampling (middle), generated by the pre-processing tools. Following the fluid simulation, temporal wall shear stress gradient (right) is one of the hemodynamic indices computed by the post-processing scripts.
The Vascular Modeling Pypeline (VaMPy) is a collection of scripts used to prepare, run, and analyze cardiac and atrial morphologies. This includes pre-processing scripts for meshing and probe sampling, a Oasis problem file for simulating flow in the internal carotid artery, and a variety of post-processing scripts for computing WSS-based metrics, more advanced turbulence metrics, and a variety of morphological parameters in patient-specific geometries.
VaMPy has been developed by
- Aslak Wigdahl Bergersen
- Christophe Chnafa
- Henrik A. Kjeldsberg
VaMPy is licensed under the GNU GPL, version 3 or (at your option) any later version.
VaMPy is Copyright (2018-2021) by the authors.
For detailed installation notes and an introduction to VaMPy, please refer to the documentation.
For reference, VaMPy requires the following dependencies: morphMan, FEniCS, and Paramiko.
If you are on Windows, macOS or Linux you can install all the general dependencies through Anaconda.
First install Anaconda or Miniconda (preferably the Python 3.6 version).
Then create two environments, one for morphMan and one for FEniCS by executing the following in a terminal
conda create -n morphman -c vmtk -c morphman morphman python=3.6 paramiko
conda create -n fenics -c conda-forge fenics
You might run into a problem with the morphMan dependency VMTK 1.4 if using Python 3, or if you are a Linux user, and we have therefore provided a set of temporary fixes for these known issues here.
Next, you need to install Oasis. You can do so with the following commands:
conda activate fenics
git clone https://github.com/mikaem/Oasis
cd Oasis
pip install . && pip install cppimport
Finally, you are ready to clone and use the Vascular Modeling Pypeline:
git clone https://github.com/KVSLab/VaMPy.git
cd VaMPy
Please report bugs and other issues through the issue tracker at: