Contents
Target Outcome
Finite element mesh of the full knee OR compartments of interest, e.g. cruciate complex, patellofemoral joint, ready for model development:
- node definitions
- element definitions
- node set definitions
- element set definitions
- surface set definitions
Prerequisites
Infrastructure
Python. Python is a programming language (GPL compatible license, http://www.python.org/). Python is the default scripting environment for Open Knee(s); for more details, please refer to Infrastructure/ScriptingEnvironment.
SciPy. SciPy is a Python based open-source software for mathematics, science, and engineering (BSD license, see http://www.scipy.org/).
Spyder. Spyder is an interactive development environment for Python with advanced editing, interactive testing, debugging and introspection features (MIT license, see http://code.google.com/p/spyderlib/).
npTDMS. npTDMS is Cross-platform, NumPy based module for reading TDMS files produced by LabVIEW. TDMS files are the binary files used for the robotic testing raw data. (LGPL license, see https://pypi.python.org/pypi/npTDMS/).
Previous Protocols
For more details, see Specifications/MeshGeneration.
Protocols
Input
Finite element mesh of ALL tissues of interest (within the compartment or in the whole knee); in human readable format, e.g., Abaqus input (INP) file, XML file, or as open format binary files, e.g., MED file, including
- node definitions (numbering and coordinates)
- element definitions (numbering, element-specific node numbers and connectivity)
- node set definitions (set name(s) and relevant node numbers)
- element set definitions (set name(s) and relevant element numbers)
- face definitions (numbering, face-specific node numbers and connectivity)
- surface set definitions (set name(s) and relevant face numbers)
Overview
The template model is a generalized model with mesh definitions for rigid and deformable bodies. It includes the contacts and ties between the bodies. Boundary conditions related to knee mechanics are not included in the template model.
The script MedToFebio.py will convert mesh contents from .med files including groups (e.g. element, node, face sets) to FEBio model file. The script requires a Connectivity File as input (see Specifications/MeshGeneration for details on creating this file)
Scripted Procedure for Mesh Assembly
This python script will read the xml file with the connectivity of several med files in the same coordinate system including groups of nodes, elements, faces, etc. It will then create an FEBio model file (.feb, version 2.5) containing all the groups, and the ties/contacts as specified in the Connectivity File.
The directions for running the script from Salome are identical to those for running the script StlToMed.py, as described in Specifications/MeshGeneration. The script uses the same connectivity file as well.
Output
Assembled finite element mesh of the compartment OR the complete knee with all relevant tissues; in FEBio model file (.feb, version 2.5) including:
- node definitions (numbering and coordinates)
- element definitions (numbering, element-specific node numbers and connectivity)
- node set definitions (set name(s) and relevant node numbers)
- element set definitions (set name(s) and relevant element numbers)
- face definitions (numbering, face-specific node numbers and connectivity)
- surface set definitions (set name(s) and relevant face numbers)