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https://github.com/finsberg/cardiac_benchmark
https://github.com/finsberg/cardiac_benchmark
Last synced: 3 days ago
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- Host: GitHub
- URL: https://github.com/finsberg/cardiac_benchmark
- Owner: finsberg
- Created: 2021-11-26T19:05:20.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-03-26T09:47:59.000Z (8 months ago)
- Last Synced: 2024-03-26T10:52:45.191Z (8 months ago)
- Language: Python
- Homepage: https://finsberg.github.io/cardiac_benchmark
- Size: 4.64 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://zenodo.org/doi/10.5281/zenodo.10875817)
# Cardiac benchmark
This is the contribution to the cardiac mechanics benchmark from Simula Research Laboratory
## Installation
### Docker (recommended)
Run the following command to start the container interactively and mount the current directory
```
docker run --rm -v $PWD:/home/shared -w /home/shared -it ghcr.io/finsberg/cardiac_benchmark:latest
```
This should spin up a container with everything installed. You will also find the [Dockerfile](docker/Dockerfile) used for creating this image in this repo.
### Conda
Create the conda environment using the `environment.yml` file
```
conda env create -f environment.yml
```
Activate the environment
```
conda activate cardiac-benchmark
```
and finally install the `cardiac-benchmark` package (from the root of the repository)
```
python3 -m pip install .
```
#### Note for M1 Mac
FEniCS is currently not available through conda for M1 mac (unless you use Rosetta 2). If you are using M1 mac then you can use the provided docker image.
### For developers
Developers should also install the pre-commit hook
```
python -m pip install pre-commit
pre-commit install
```
## Quick start
### Get the geometry
Before running the benchmark you need to first get a geometry. For benchmark 1 you can either use the provided geometry or create your own. To create your own geometry you can do
```
cardiac-benchmark create-geometry lv_ellipsoid.h5
```
which will save the geometry together with the fibers in a file called `lv_ellipsoid.h5`. You can also specify the mesh resolution and the fiber angles see `cardiac-benchmark create-geometry --help` for more info. Note that this requires `fenics` and `gmsh` to be be installed. To get this you can e.g use the `fenics-gmsh` docker image that we have created here: https://github.com/scientificcomputing/packages/pkgs/container/fenics-gmsh
To use the provided benchmark you first need to download the files to a folder. For benchmark 1 you can download the data to a folder called `data_benchmark1` using the following command
```
cardiac-benchmark download-data-benchmark1 --fiber-space=P2 --outdir=data_benchmark1
```
Here we also specify which space to use for the fibers (P1 or P2). Next we need to convert all the files to a single file containing both the mesh, markers and the microstructure using the command
```
cardiac-benchmark convert-data-benchmark1 data_benchmark1 --outpath="lv_ellipsoid.h5"
```
This will also generate some files in the same folder that can be visualized in paraview. You can use the same procedure to download the data for benchmark 2, e.g
```
cardiac-benchmark download-data-benchmark2 coarse --outdir=data_coarse
```
and
```
cardiac-benchmark convert-data-benchmark2 data_benchmark2_coarse --outpath="biv_ellipsoid_coarse.h5"
```
However, note that here we need to specify whether we want the *fine* or *coarse* resolution.
### Running the benchmark
You can run the command line interface directly, e.g
```
cardiac-benchmark benchmark1-step1
```
To see all steps that you can run, do
```
cardiac-benchmark --help
```
and to see the specific options for a given step you can do (for e.g `step1`)
```
cardiac-benchmark benchmark1-step1 --geometry-path="lv_ellipsoid.h5"
```
It is also possible to run the scripts using
```
python3 -m cardiac-benchmark --help
```
if you prefer that.
You can also use the python API
```python
import cardiac_benchmark
cardiac_benchmark.benchmark1.run(geometry_path="lv_ellipsoid.h5")
```
which by default will run benchmark 1 - step 1.
### Options
- Create geometry for benchmark 1 (save lv ellipsoidal geometry to `lv_ellipsoid.h5`). Note: requires `gmsh`
```
cardiac-benchmark create-geometry lv_ellipsoid.h5
```
- Download provided for benchmark 1 to a folder called `data_benchmark1` with P2 fibers
```
cardiac-benchmark download-data-benchmark1 --fiber-space=P2 --outdir=data_benchmark1
```
- Convert data for benchmark1 with P2 fiber space into a single file and files to be viewed in Paraview
```
cardiac-benchmark convert-data-benchmark1 data_benchmark1 --outpath="lv_ellipsoid.h5"
```
- Run benchmark 1 step 0 case A
```
cardiac-benchmark benchmark1-step0 a --geometry-path="lv_ellipsoid.h5"
```
- Run benchmark 1 step 0 case B
```
cardiac-benchmark benchmark1-step0 b --geometry-path="lv_ellipsoid.h5"
```
- Run benchmark 1 step 1
```
cardiac-benchmark benchmark1-step1 --geometry-path="lv_ellipsoid.h5"
```
- Run benchmark 1 step 2 case A
```
cardiac-benchmark benchmark1-step2 a --geometry-path="lv_ellipsoid.h5"
```
- Run benchmark 1 step 2 case B
```
cardiac-benchmark benchmark1-step2 b --geometry-path="lv_ellipsoid.h5"
```
- Run benchmark 1 step 2 case C
```
cardiac-benchmark benchmark1-step2 c --geometry-path="lv_ellipsoid.h5"
```
- Download coarse data for benchmark 2 to a folder called `data_coarse`
```
cardiac-benchmark download-data-benchmark2 coarse --outdir=data_coarse
```
- Download fine data for benchmark 2 to a folder called `data_fine`
```
cardiac-benchmark download-data-benchmark2 fine --outdir=data_fine
```
- Convert data for benchmark 2 into a single file and files to be viewed in Paraview
```
cardiac-benchmark convert-data-benchmark2 data_benchmark2_coarse --outpath="biv_ellipsoid_coarse.h5"
```
- Run benchmark 2 with fine data
```
cardiac-benchmark benchmark2 --geometry-path="biv_ellipsoid_coarse.h5"
```
## License
MIT
## Citing
```
@software{Finsberg_A_software_benchmark_2024,
author = {Finsberg, Henrik and Sundnes, Joakim},
doi = {10.5281/zenodo.10875818},
month = mar,
title = {{A software benchmark for cardiac elastodynamics}},
url = {https://github.com/finsberg/cardiac_benchmark.},
version = {1.0.0},
year = {2024}
}
```
## Authors
- Henrik Finsberg ([email protected])
- Joakim Sundnes ([email protected])