3D on a realistic cardiac geometry

Getting the data

Download and save the attached file Propagation3d.tgz​. Either use an Archive Manager to extract the content to disk or save it and then unpack it with 

tar xvfz  Propagation3d.tgz

Running the simulation

Change directory to Propagation3d 

cd Propagation3d

In this folder you will find the following files:

  • ChasteParameters.xml -- this file describes the simulation, and can be used to override the default parameter values (in releases of the executable up to and including version 2.0, the default parameters were read in from another xml file, ChasteDefaults.xml).
  • ChasteParameters_2_1.xsd -- XML schema for input validation (in general never has to be altered or touched).

Run the simulation by doing 

<path_to_chaste>/Chaste.sh ChasteParameters.xml

Note: in releases up to and including version 2.0, the executable would be called directly (ie: <path_to_chaste>/Chaste ChasteParameters.xml), in release 2.1 the executable should be called via the shell script Chaste.sh; as above.

A folder called testoutput will appear once the simulation has finished.

Visualising the results

Move into the newly created output folder 

cd testoutput/ChasteResults

In this folder you will find the following files and folders:

  • progress_status.txt -- this file can be viewed whilst the simulation is running to gauge how long it will take
  • 3dResults.h5 -- the output of the simulation, in HDF5 format
  • output (folder) -- contains the output converted into Meshalyzer format
  • cmgui_output (folder) -- contains the output converted into CMGUI format
  • vtk_output (folder) -- contains the output converted into Paraview (VTK) format

There are more details on visualising your results at ChasteGuides/VisualisationGuides.

Visualising with Meshalyzer

For Meshalyzer visualisation, now move into the Meshalyzer-compatible output folder 

cd output

Launch Meshalyzer with 

<path_to_meshalyzer>/meshalyzer 3dResults_mesh

and visualise the results by loading the 3dResults_V.dat file.

Visualising with Cmgui

For Cmgui visualisation, now move into the Cmgui-compatible output folder 

cd cmgui_output

Launch the cmgui visualiser with 

<path_to_cmgui>/cmgui script.com

The script will ensure that all the time-step files are loaded into Cmgui.

Visualising the VTK data with Paraview

For Paraview visualisation, now move into the VTK output folder 

cd vtk_output

For easy animation of cardiac simulations, we have written a Python script to add Paraview-specific time annotation features to the standard VTK output. Run this with 

<path_to_Chaste>/python/utils/AddVtuTimeAnnotations.py 3dResults.vtu 3dResultsAnnotated.vtu

Launch Paraview with 

paraview --data=3dResultsAnnotated.vtu

Understanding the XML parameters file

Open ChasteParameters.xml (it is sensible to do this in a web-browser or XML editor in order to get syntax highlighting). The file should be reasonably readable; it defines:

  • a 3D simulation that lasts for 5ms
  • the use of the monodomain model
    • to use bidomain, the only thing that needs to be done is to change Mono to Bi
  • a LuoRudyIBackwardEuler cell model as the default cell model
  • a 3D mesh generated from an anatomical geometry. The are three files defining the mesh OxfordRabbitHeart_482um(.node, .ele, .face) representing respectively nodes elements and faces files.
  • an axisymmetric orientation of the fibres is used and is given in the file OxfordRabbitHeart_482um.axi where the longitudinal direction of the fibres is defined in each element.
  • a stimulated region is defined in the apex. It starts at the beginning of the simulation and its duration is 2ms.
  • output directory and filenames
  • an OutputVisualizer element giving which visualiser formats to write
  • physiological parameters: conductivities, capacitance, surface-area-to-volume ratio
    • in monodomain problems, the defined intracellular conductivity is used, not a harmonic mean of intra and extracellular conductivities.
  • Numerical parameters including ODE, PDE and printing timesteps