ldrb 2022.0.0

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.

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/)

# Decide on the angles you want to use
angles = dict(
    alpha_endo_lv=30,  # Fiber angle on the LV endocardium
    alpha_epi_lv=-30,  # Fiber angle on the LV epicardium
    beta_endo_lv=0,  # Sheet angle on the LV endocardium
    beta_epi_lv=0,  # Sheet angle on the LV epicardium
    alpha_endo_sept=60,  # Fiber angle on the Septum endocardium
    alpha_epi_sept=-60,  # Fiber angle on the Septum epicardium
    beta_endo_sept=0,  # Sheet angle on the Septum endocardium
    beta_epi_sept=0,  # Sheet angle on the Septum epicardium
    alpha_endo_rv=80,  # Fiber angle on the RV endocardium
    alpha_epi_rv=-80,  # Fiber angle on the RV epicardium
    beta_endo_rv=0,  # Sheet angle on the RV endocardium
    beta_epi_rv=0,  # Sheet angle on the RV epicardium
)

# Choose space for the fiber fields
# This is a string on the form {family}_{degree}
fiber_space = "Quadrature_2"

# Compute the microstructure
fiber, sheet, sheet_normal = ldrb.dolfin_ldrb(
    mesh=mesh, fiber_space=fiber_space, ffun=ffun, markers=markers, **angles
)
# Store files using a built in xdmf viewer that also works for functions
# defined in quadrature spaces
ldrb.fiber_to_xdmf(fiber, "fiber")
# And visualize it in Paraview

Installation

Install with pip

In order to install the software you need to have installed FEniCS (versions older than 2016 are not supprted)

The package can be installed with pip.

python -m pip install ldrb

or if you need the most recent version you can install the source

python -m pip install git+https://github.com/finsberg/ldrb.git

Install with conda

Alternatively you can install with conda

conda install -c conda-forge ldrb

which will also install FEniCS through conda.

Documetation

Documentation is hosted at http://finsberg.github.io/ldrb

Getting started

Check out the demos

License

ldrb is licensed under the GNU LGPL, version 3 or (at your option) any later version. ldrb is Copyright (2011-2019) by the authors and Simula Research Laboratory.

Contributors

Henrik Finsberg ([e-mail])