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https://github.com/computationalphysiology/ldrb

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

https://github.com/computationalphysiology/ldrb

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

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Created over 7 years ago · Last pushed over 3 years ago
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README.md

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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/)

```python

Decide on the angles you want to use

angles = dict( alphaendolv=30, # Fiber angle on the LV endocardium alphaepilv=-30, # Fiber angle on the LV epicardium betaendolv=0, # Sheet angle on the LV endocardium betaepilv=0, # Sheet angle on the LV epicardium alphaendosept=60, # Fiber angle on the Septum endocardium alphaepisept=-60, # Fiber angle on the Septum epicardium betaendosept=0, # Sheet angle on the Septum endocardium betaepisept=0, # Sheet angle on the Septum epicardium alphaendorv=80, # Fiber angle on the RV endocardium alphaepirv=-80, # Fiber angle on the RV epicardium betaendorv=0, # Sheet angle on the RV endocardium betaepirv=0, # Sheet angle on the RV epicardium )

Choose space for the fiber fields

This is a string on the form {family}_{degree}

fiberspace = "P2"

Compute the microstructure

fiber, sheet, sheetnormal = ldrb.dolfinldrb( mesh=mesh, fiberspace=fiberspace, ffun=ffun, markers=markers, **angles )

Store files using a built in xdmf viewer that also works for functions

defined in quadrature spaces

ldrb.fibertoxdmf(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

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 (henriknf@simula.no)

Owner

  • Name: Computational Physiology at Simula Research Laboratory
  • Login: ComputationalPhysiology
  • Kind: organization
  • Location: Fornebu, Norway

GitHub organization for the computational physiology department at Simula Research Laboratory

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