This repository contains code for generating data of an idealized bi-ventricular geometry with microstructure (fiber, sheets, and sheet normal directions) as well as a purkinje system.
It uses cardiac-geometries to create the idealized BiV geometry, ldrb to generate the fiber orientations, and fractal-tree to generate the Purkinje system.
In order to generate the mesh you need to install gmsh and to run the the ldrb algorithm you would need FEniCS. These are both packages that can be quite complicated to install. The easiest way to install all the necessary dependencies is therefore by using docker To start a docker container that comes with gmsh and fenics pre-installed, run the following command
docker run --name cardiac -w /home/shared -v $PWD:/home/shared -it ghcr.io/scientificcomputing/fenics-gmsh:2023-08-16
This will start a new docker container and also share your current working directory ($PWD) with the container (at /home/shared). This means that any files you generate inside the container can be shared with your local machine an vica-versa.
Next, you need to install the rest of the dependencies. This can be done with pip
python3 -m pip install -r requirements.txt
To generate the mesh with correctly marked boundaries, the microstructure and the Purkinje system you can run generate_data.py
python3 generate_data.py
Once you have run this script a folder called data will be created that will contain mesh, boundaries, fibers and purkinje system.
The folder will contain the following files
data
├── biv_ellipsoid.msh - Mesh generated from gmsh
├── ffun.h5 - Data for facet markers
├── ffun.xdmf - File for visualizing facet markers in Paraview
├── fiber.h5 - Data for fiber fields
├── fiber.xdmf - File for visualizing fibers in Paraview
├── info.json - Parameter used for generating mesh
├── lv_tree.vtu - File for visualizing purkinje system in the LV in Paraview
├── lv_tree_endnodes.txt - List of leaf nodes in the purkinje system in the LV
├── lv_tree_lines.txt - Connectivity to create lines for purkinje system in the LV
├── lv_tree_xyz.txt - Coordinates of all points in the purkinje system in the LV
├── markers.json - List of markers for the facets
├── mesh.h5 - Data of the mesh
├── mesh.xdmf - File for visualizing mesh in Paraview
├── rv_tree.vtu - File for visualizing purkinje system in the RV in Paraview
├── rv_tree_endnodes.txt - List of leaf nodes in the purkinje system in the RV
├── rv_tree_lines.txt - Connectivity to create lines for purkinje system in the RV
├── rv_tree_xyz.txt - Coordinates of all points in the purkinje system in the RV
├── sheet.h5 - Data for sheet fields
├── sheet.xdmf - File for visualizing sheets in Paraview
├── sheet_normal.h5 - Data for sheet normal fields
├── sheet_normal.xdmf - File for visualizing sheet normals in Paraview
├── triangle_mesh.h5 - Surface mesh (essentially same as ffun)
└── triangle_mesh.xdmf - Surface mesh (essentially same as ffun)
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