ldrb 2020.0.0

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.

pip install ldrb

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

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

Install with conda

Alternatively you can install with conda

conda install -c finsberg ldrb

Documetation

Documentation is hosted at https://ldrb.readthedocs.io.

Getting started

Check out the demos and the documentation

Known issues

If you encounter the following error:

ImportError: numpy.core.multiarray failed to import

see https://github.com/moble/quaternion/issues/72 for how to troubleshoot.

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])