Boundary/finite element meshing from volumetric data with applications

Zhang, Yongjie
Journal Title
Journal ISSN
Volume Title

The main research work during my Ph.D. study is to extract adaptive and quality 2D (triangular or quadrilateral) meshes over isosurfaces and 3D (tetrahedral or hexahedral) meshes with isosurfaces as boundaries directly from volumetric imaging data. The software named LBIE-Mesher (Level Set Boundary Interior and Exterior Mesher) is developed. LBIE-Mesher generates 3D meshes for the volume interior to an isosurface, the volume exterior to an isosurface, or the interval volume between two isosurfaces. An algorithm has been developed to extract adaptive and quality 3D meshes directly from volumetric imaging data. The extracted tetrahedral meshes are extensively used in the Finite Element Method (FEM). A top-down octree subdivision coupled with the dual contouring method is used to rapidly extract adaptive 3D finite element meshes with correct topology from volumetric imaging data. The edge contraction and smoothing methods are used to improve the mesh quality. The main contribution is extending the dual contouring method to crack-free interval volume 3D meshing with feature sensitive adaptation. Compared to other tetrahedral extraction methods from imaging data, our method generates adaptive and quality 3D meshes without introducing any hanging nodes. Furthermore, another algorithm has been developed to extract adaptive and quality quadrilateral or hexahedral meshes directly from volumetric data. First, a bottom-up surface topology preserving octree-based algorithm is applied to select a starting octree level. Then the dual contouring method is used to extract a preliminary uniform quad/hex mesh, which is decomposed into finer quads/hexes adaptively without introducing any hanging nodes. The positions of all boundary vertices are recalculated to approximate the boundary surface more accurately. Mesh adaptivity can be controlled by a feature sensitive error function, the regions that users are interested in, or finite element calculation results. Finally, a relaxation based technique is deployed to improve mesh quality. Several demonstration examples are provided from a wide variety of application domains. An approach has been described to smooth the surface and improve the quality of surface/volume meshes with feature preserved using geometric flow. For triangular and quadrilateral surface meshes, the surface diffusion flow is selected to remove noise by relocating vertices in the normal direction, and the aspect ratio is improved with feature preserved by adjusting vertex positions in the tangent direction. For tetrahedral and hexahedral volume meshes, besides the surface vertex movement in the normal and tangent directions, interior vertices are relocated to improve the aspect ratio. Our method has the properties of noise removal, feature preservation and quality improvement of surface/volume meshes, and it is especially suitable for biomolecular meshes because the surface diffusion flow preserves sphere accurately if the initial surface is close to a sphere. A comprehensive approach has been proposed to construct quality meshes for imviii plicit solvation models of biomolecular structures starting from atomic resolution data in the Protein Data Bank (PDB). First, a smooth volumetric synthetic electron density map is constructed from parsed atomic location data of biomolecules in the PDB, using Gaussian isotropic kernels. An appropriate parameter selection is made for constructing an error bounded implicit solvation surface approximation to the Lee-Richards molecular surface. Next, a modified dual contouring method is used to extract triangular meshes for the molecular surface, and tetrahedral meshes for the volume inside or outside the molecule within a bounding sphere/box of influence. Finally, geometric flows are used to improve the mesh quality. Some of our generated meshes have been successfully used in finite element simulations. Techniques have been developed to generate an adaptive and quality tetrahedral finite element mesh of a human heart. An educational model and a patient-specific model are constructed. There are three main steps in our mesh generation: model acquisition, mesh extraction and boundary/material layer detection. (1) Model acquisition. Beginning from an educational polygonal model, we edit and convert it to volumetric gridded data. A component index for each cell edge and grid point is computed to assist the boundary and material layer detection. For the patient-specific model, some boundary points are selected from MRI images, and connected using cubic splines and lofting to segment the MRI data. Different components are identified. (2) Mesh extraction. We extract adaptive and quality tetrahedral meshes from the volumetric gridded data using our LBIE-Mesher. The mesh adaptivity is controlled by regions or using a feature sensitive error function. (3) Boundary/material layer detection. The boundary of each component and multiple material layers are identified and meshed. The extracted tetrahedral mesh of the educational model is being utilized in the analysis of cardiac fluid dynamics via immersed continuum method, and the generated patient-specific model will be used in simulating the electrical activity of the heart.