Spline-based structured conformal hexahedral meshing

A Python package for generating GMSH meshes from SCANCO HR-pQCT images.

👷🏼 Simone Poncioni

🦴 Musculoskeletal Biomechanics Group

🎓 ARTORG Center for Biomedical Engineering Research, University of Bern

📝 Introduction

A Python package for generating GMSH meshes from SCANCO HR-pQCT images. Import a voxel-based model and convert it to a geometrical simplified representation through the use of splines for each slice in the transverse plane.

💡 Method

• Structured Mesh: Provides greater simplicity, efficiency, and lower memory usage due to implicit connectivity with neighboring elements. Ensures topologically identical models for easy comparison between patients or across longitudinal 
• Contour Extraction & Smoothing: Utilizes scikit-image for periosteal and endosteal contour extraction, followed by Douglas-Ramer-Peucker simplification and 3rd-order periodic BSplines for smooth geometry 
• Sanity Check: Ensures a minimum cortical thickness of 0.5 mm, allowing space for at least three elements and continuity in thin 
• Mesh Generation: The simplified geometry is imported into GMSH via the OpenCASCADE kernel. Transfinite techniques and the Winslow untangler are used for optimal mesh 
• Quality Assessment: Mesh quality is evaluated using the Dice similarity coefficient (DSC) with a minimum value of 95%, and the (signed-) inverse conditioning number ((S-) ICN) to ensure matrix conditioning and simulation stability.

For more examples, please refer to the Documentation: https://artorg-unibe-ch.github.io/spline_mesher/

🔧 Installation

To get a local copy up and running follow these simple example steps.

1. Clone the repo

git clone https://github.com/artorg-unibe-ch/spline_mesher.git

2. Install dependencies

conda create -n meshenv python=3.9 --file requirements.txt
conda activate meshenv
python setup.py build_ext --inplace
python setup.py install

3. For developers: install the package in editable mode and install requirements for testing

 
pip install -e .
pip install -r requirements-dev.txt