fenicsx-ldrb 0.1.19

Laplace-Dirichlet Rule-based algorithm for assigning myocardial fiber orientations.

Laplace-Dirichlet Rule-Based (LDRB) algorithm for assigning myocardial fiber orientations

A software for assigning myocardial fiber orientations based on the Laplace Dirichlet Ruled-Based algorithm based on FEniCSx.

Bayer, J.D., Blake, R.C., Plank, G. and Trayanova, N.A., 2012. A novel rule-based algorithm for assigning myocardial fiber orientation to computational heart models. Annals of biomedical engineering, 40(10), pp.2243-2254.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518842/)

Getting started

For example if you have a bi-ventricular geometry (e.g from cardiac-geometries), you can generate fibers as follows

import cardiac_geometries
import ldrb
import dolfinx

# Generate an idealized BiV geometry
geo = cardiac_geometries.mesh.biv_ellipsoid(outdir=geodir)
# Generate fibers with 60/-60 fibers angles on the endo- and epicardium
system = ldrb.dolfinx_ldrb(mesh=geo.mesh, ffun=geo.ffun, markers=geo.markers, alpha_endo_lv=60, alpha_epi_lv=-60, beta_endo_lv=0, beta_epi_lv=0, fiber_space="P_2")
# Visualize fibers in Paraview
with dolfinx.io.VTXWriter(
    geo.mesh.comm, outdir / f"microstructure-viz.bp", [system.f0, system.s0, system.n0], engine="BP4"
) as vtx:
    vtx.write(0.0)

If you now open the file microstructure-viz.bp in Paraview (using the ADIOS2VTXReader), select Glyph and choose f0 as orientation array you can see the fiber orientations similar to the following figure (here I have also added a Calculator to compute the fiber angle)

Note that you can achieve the the same results using the command line interface

ldrb mesh.xdmf --markers-file markers.json --fiber-space P_2 --alpha-endo-lv 60 --alpha-epi-lv -60 --beta-endo-lv 0 --beta-epi-lv 0

Note that if you don't specify a different angle for the RV or Septum, then the same angle as the LV will be used.

Installation

pip

Note that you can install the package with pip, but then you need to install FEniCSx separatly, see download

python3 -m pip install fenicsx-ldrb

conda

The package can also be installed with conda, i.e

conda install -c conda-forge fenicsx-ldrb

Docker

To pull the latest docker image you can do

docker pull ghcr.io/finsberg/fenicsx-ldrb:main

or choose a specific version e.g

docker pull ghcr.io/finsberg/fenicsx-ldrb:v0.1.4

Note that you can also run the cli directly using docker e.g

docker run --rm -v $PWD:/home/shared -w /home/shared -it ghcr.io/finsberg/fenicsx-ldrb ldrb --help

Documentation

See https://finsberg.github.io/fenicsx-ldrb

License

MIT

Contributors

Henrik Finsberg ([e-mail])