Cardiac Benchmark Toolkit

This repository contains basic scripts that allow you to reproduce the mesh as well as the fibers in the cardiac mechanics benchmark in dolfin (legacy).

For the dolfinx implementation of the tools, check here

Installation

Docker (Recommended) Run the following command to start a container with all the required dependencies:

docker run --name dolfin-stable -v $(pwd):/home/shared -w /home/shared -ti ghcr.io/scientificcomputing/fenics-gmsh:2023-04-21

In order to enter the shell, use:

docker exec -ti dolfin-stable /bin/bash -l

Note docker image is courtesy of Simula Lab.

Local Installation

If your system has already fenics version 2019.1.0.post0, you can install this package typing:

pip3 install .

Quickstart

To have an overview of the options available through this package, execute it your terminal

cardiac-benchmark-toolkit --help

It the installation was succesfull you should be prompted with the following:

Mesh Generation

Ellipsoid domain

The ellipsoid domain can be created with a characteristic element size (default is 0.005 [m]) using the script mesh_generation.py. It will create a folder structure ./results to stores xdmf as well as pvd formats for further usage.

To execute it, consider the following command:

cardiac-benchmark-toolkit create-ellipsoid --char-length 0.007

Its command details can be seen with:

cardiac-benchmark-toolkit create-ellipsoid --help

It will create an ellipsoid mesh with characteristic element size of 0.007 [m]. You can use it in conjuntion with the ellipsoid_fiber_generation to create the fiber directions for your specific simulation (and benchmark).

Examples of mesh at two different element sizes can be seen below:

Biventricular domain

The biventricular domain is provided in the ./data/ including source files in vtk, pvd for fine and coarse sizes. Example of a fine geometry is depicted below:

Ellipsoid Fiber Generation

This repository provides a tagged ellipsoid geometry for reference purposes in the folder ./data/monoventricle_mesh/. Using the mesh ./monoventricle_mesh/ellipsoid_0.005.xdmf, you can create the fibers as follows:

cardiac-benchamrk-toolkit create-fibers-for-ellipsoid-mesh ./monoventricle_mesh/ellipsoid_0.005.xdmf

If succesfull, the script will create fibers in xdmf and vtk files in a ./results/ folder.

Further options can be found with:

cardiac-benchmark-toolkit create-fibers-for-ellipsoid-mesh --help

Biventricular Fiber Generation (LifeX -> FEniCS)

Reference fibers created using the lifex can be found in the subfolder in ./data/ as fiber_biv.vtk. This repository includes options to generate FEniCS-compatible h5 format for fiber directions.

To crate fibers for the fine mesh in P2, run in your shell:

cardiac-benchmark-toolkit create-biv-domain-from-mesh-and-fibers data/biv_mesh_and_fibers_fine_p2/ --element_degree 2

The command line above will create fiber, sheet and sheet-normal directions from the vtk source files in ./data/biv_mesh_and_fibers_fine_p2.

Depicted below are fiber (left) and sheet (right) directions created from this procedure.