Chaste File Formats

General

.dat
Primarily used for the fixed-width space-separated column data file format, written by the ColumnDataWriter class, and compatible with Gnuplot. Other parts of the code do write files with a .dat extension which don't follow this rigid format. They are all, however, data files with a similar structure suitable for plotting with Gnuplot.
.edge
Edge file for Triangle or Tetgen format meshes.
.ele
Element file for Triangle or Tetgen format meshes.
.exnode
CMGUI node format, see the Cmgui guide.
.exelem
CMGUI element format, see the Cmgui guide.
.face
Faces file for Tetgen format meshes.
.h5
HDF5 format used for cardiac simulation results. HDF5 represents data in a hierarchical way. Each file contains different datasets, with each dataset containing dataspaces and attributes. Every HDF5 file generated by Chaste defines two main datasets: The program h5dump (if installed) can be used to view the contents of small HDF5 files. Larger datasets can be converted to Meshalyzer, CMGUI or VTK readable files using the classes Hdf5ToMeshalyzerConverter, Hdf5ToCmguiConverter or Hdf5ToVtkConverter. One of these is generally called at the end of a cardiac simulation that writes HDF5 data.
.info
There are 3 different sorts of .info file:
  1. archive.info is read and written by the cardiac archiving code, and is not for user consumption.
  2. The ColumnDataWriter also creates a .info file, to tell it how many variables of different types there are.
  3. The final kind, named "something_times.info", is created by the cardiac post-processing code, to give a human readable summary of the timesteps used.
.log
Used for test output.
.ncl
Node connectivity file for Triangle or Tetgen format meshes. For each mesh node, records which elements contain the node. Note that this file format is not part of the standard Triangle or Tetgen format, but can be created by Chaste and then used to make the mesh load faster in parallel.
.node
Nodes file for Triangle or Tetgen format meshes.
.vtu
An XML file format used to visualize simulation results in a VTK visualizer. The file format represents a Chaste mesh as a vtkUnstructuredGrid, with each variable represented as point data. The file consists of:

Cardiac

.axi
Defines the fibre direction for each element (used for setting up axisymmetric (transversely isotropic) conductivity tensors).
.epi
Used to specify a list of node numbers (one column) of the nodes belonging to the epicardial surface.
.endo
Used to specify a list of node numbers (one column) of the nodes belonging to the endocardial surface.
.mid
Used to specify a list of node numbers (one column) of the nodes belonging to the midmyocardial surface.
.ortho
Defines the fibre, sheet and normal directions for each element (used for setting up orthotropic (anisotropic) conductivity tensors).
.pts
Meshalyzer (used for visualisation) nodes format. First line is <number of nodes>. Following lines are the nodal coordinates.
.tri
Meshalyzer (used for visualisation) triangles format. Represents elements in 2D, and boundary elements in 3D.
.tetra
Meshalyzer (used for visualisation) elements format.

Cell-based

.viz*
General format of results files written by cell_based chaste for the Visualize2dCells.java program.
.vizancestors
The ancestor index of each cell at each time step in a TissueSimulation. Each line has the form time ancestor_1 ancestor_2 ... ancestor_n.
.vizbetacatenin
The levels of membrane-bound, cytoplasmic and nuclear beta-catenin in each cell at each time step in a CryptSimulation2d. Each line has the form time location_index_1 x_1 y_1 b_cat_membrane_1 b_cat_cytoplasm_1 b_cat_nuclear_1 ... location_index_n x_n y_n b_cat_membrane_n b_cat_cytoplasm_n b_cat_nuclear_n.
.vizboundarynodes
Whether each node at each time step in a TissueSimulation is a boundary node. Each line has the form time bool_1 bool_2 ... bool_n.
.vizcelltypes
The cell type of each cell at each time step in a TissueSimulation. Each line has the form time c_1 c_2 ... c_n.
.vizelements
The nodes associated with each element at each time step in a TissueSimulation. Each line has the form time element1_node1 element1_node2 element1_node3 ... elementn_node1 elementn_node2 elementn_node3.
.viznodes
The position of each node at each time step in a TissueSimulation. Each line has the form time x_1 ... x_n in 1D, time x_1 y_1 ... x_n y_n in 2D and time x_1 y_1 z_1... x_n y_n z_n in 3D.
.vizsetup
The cell_based visualiser setup file. This contains such things as mesh_width for periodic simulations.