Visualising simulation results¶
There are a number of approaches for visualising simulation results from OpenCMISS-Iron.
Cmgui¶
OpenCMISS-Iron support export of meshes and fields in .exelem and .exnode files for visualisation in the Cmgui 3D visualisation software package. This isdemonstrated in the Basics tutorial.
Installing Cmgui¶
The latest standalone and installer versions of Cmgui (cmgui-3.0.1.r11315) can be downloaded from the following links:
- x86_64-Ubuntu-12.04.5-LTS.deb
- x86_64-Ubuntu-12.04.5-LTS.tar.gz
- i386-Mac-OS-X-10.6.8.dmg
- i386-Mac-OS-X-10.6.8.tar.gz
- amd64-Windows.exe
- amd64-Windows.zip
Previous versions can be found on the Physiome Software website. An extensive list of all previous versions can be found on the following Auckland Bioengineering Institute ftp link (only accessible within the Unviersity of Auckland).
Cmgui documentation¶
Documentation for cmgui can be found from the following sources:
Note
For OpenCMISS-Iron Docker installations, install cmgui on your host machine. The meshes exported from running python scripts/Jupyter notebooks in the OpenCMISS-Iron Docker containers will be accessible from the host machine for visualisation. See the Docker installation Section of the documentation for more information about how to access folders mounted within Docker container from the host machine.
Pythreejs¶
The OpenCMISS-Iron tutorials provide basic support for visualising simulation results in html using Pythreejs. These html visualisations can be embedded in Jupyter notebooks, or generate standalone html files when run through a python interpreter. This is demonstrated in the Basics tutorial.
VTK¶
The OpenCMISS-Iron tutorials provide basic scripts for creating VTK objects from OpenCMISS-Iron meshes. These VTK files can then be visualised in almost all visualisation software (e.g. paraview) The python meshio module can then be used to convert these to a number of different mesh formats. meshio 4.3.5 is already installed within the OpenCMISS-Iron Docker containers, and supports the following mesh output formats:
- Abaqus,
- ANSYS msh,
- AVS-UCD,
- CGNS,
- DOLFIN XML,
- Exodus,
- FLAC3D,
- H5M,
- Kratos/MDPA,
- Medit,
- MED/Salome,
- Nastran (bulk data),
- Neuroglancer precomputed format,
- Gmsh (format versions 2.2, 4.0, and 4.1),
- OBJ,
- OFF,
- PERMAS,
- PLY,
- STL,
- Tecplot .dat,
- TetGen .node/.ele,
- SVG (2D only, output only),
- SU2,
- UGRID,
- VTK,
- VTU,
- WKT (TIN),
- XDMF.
Note
Exporting higher order elements, e.g. cubic Hermite elements, in these formats using the meshio python module is not supported. If you want to visualise higher order elements, please use Cmgui.
Note
The meshio python module: 1) only supports specific element interpolations that can be described in VTK format, and 2) has to conform to the capabilities of these file formats. Therefore, it may not be possible to export your mesh in a paricular format. For more information, consult the [meshio source code](https://github.com/nschloe/meshio/tree/master/meshio). You can browse the soruce code for the format of interest to determine what element interporlations are supported.