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https://github.com/finsberg/cardiac-biv-purkinje
Idealized BiV geometry with purkinje system
https://github.com/finsberg/cardiac-biv-purkinje
Last synced: 3 days ago
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Idealized BiV geometry with purkinje system
- Host: GitHub
- URL: https://github.com/finsberg/cardiac-biv-purkinje
- Owner: finsberg
- License: mit
- Created: 2023-10-10T06:04:05.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2023-10-10T09:34:56.000Z (about 1 year ago)
- Last Synced: 2023-10-10T10:38:31.564Z (about 1 year ago)
- Language: Python
- Size: 5.86 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Sandbox for creating idealized BiV geometry with fibers and purkinje system.
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](https://github.com/ComputationalPhysiology/cardiac_geometries) to create the idealized BiV geometry, [ldrb](https://github.com/finsberg/ldrb) to generate the fiber orientations, and [fractal-tree](https://github.com/finsberg/fractal-tree) to generate the Purkinje system.
## Install
In order to generate the mesh you need to install [gmsh](https://gmsh.info) and to run the the ldrb algorithm you would need [FEniCS](https://fenicsproject.org/download/archive/). 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](https://www.docker.com/get-started/)
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
```
## Generate data
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)
```