About

How to cite

If you use ciclope please cite:

Iori et al., (2023). Ciclope: micro Computed Tomography to Finite Elements. Journal of Open Source Software, 8(84), 4952, https://doi.org/10.21105/joss.04952 

@article{Iori2023, doi = {10.21105/joss.04952}, url = {https://doi.org/10.21105/joss.04952}, year = {2023}, publisher = {The Open Journal}, volume = {8}, number = {84}, pages = {4952}, author = {Gianluca Iori and Gianluigi Crimi and Enrico Schileo and Fulvia Taddei and Giulia Fraterrigo and Martino Pani}, title = {Ciclope: micro Computed Tomography to Finite Elements}, journal = {Journal of Open Source Software} }

Statement of need

Micro Finite Element (microFE) models are often derived from volumetric stacks of micro Computed Tomography (microCT) images to non-destructively assess mechanical properties of biological or artificial specimens. However, the general absence of reproducible image-to-model pipelines and the use of proprietary or non-open-source software strongly limit validation and comparison of results across studies. Ciclope is a fully open-source pipeline, allowing to preprocess microCT data and obtain a corresponding microFE model, solve and postprocess it.

Design

A typical pipeline for FE model generation from 3D microCT data is shown in the picture below. ciclope_design

  • Ciclope is composed of a core module containing methods for voxel and tetrahedra FE model generation, and a module utils containing utilities for image and FE model pre- and post-processing. Both modules can be imported and used within Python.

  • Pipelines of FE model generation can be launched from the commandline using the ciclope.py script generated during installation. See the section usage for more details.

Ecosystem

Ciclope requires several dependencies. The following is a list of the main external packages required for FE model generation and solution:

  • All mesh exports (voxel and tetrahedra Finite Elements) are performed with the meshio module.

  • Tetrahedra meshes are generated with pygalmesh (a Python frontend to CGAL).

  • High-resolution surface meshes for visualization are generated with the PyMCubes module.

  • Ciclope generates Finite Element .INP files that can be solved using both CalculiX and Abaqus.

  • The definition of material properties and of the FE analysis parameters (e.g. boundary conditions, simulation steps..) is handled through separate template files. The folders material_properties and input_templates contain a library of template files that can be used to generate FE simulations.

  • Additional libraries of CalculiX examples and template files can be found here and here

  • For the post-processing of FE results, Ciclope uses ParaView and the CalculiX to ParaView converter ccx2paraview.