Anisotropic geometry-conforming d-simplicial meshing via isometric embeddings

We develop a dimension-independent, Delaunay-based anisotropic mesh generation algorithm suitable for integration with adaptive numerical solvers. As such, the mesh produced by our algorithm conforms to an anisotropic metric prescribed by the solver as well as the domain geometry, given as a piecewise smooth complex. Motivated by the work of Lévy and Dassi [10-12,20], we use a discrete manifold embedding algorithm to transform the anisotropic problem to a uniform one. This work differs from previous approaches in several ways. First, the embedding algorithm is driven by a Riemannian metric field instead of the Gauss map, lending itself to general anisotropic mesh generation problems. Second we describe our method for computing restricted Voronoi diagrams in a dimension-independent manner which is used to compute constrained centroidal Voronoi tessellations. In particular, we compute restricted Voronoi simplices using exact arithmetic and use data structures based on convex polytope theory. Finally, since adaptive solvers require geometry-conforming meshes, we offer a Steiner vertex insertion algorithm for ensuring the extracted dual Delaunay triangulation is homeomorphic to the input geometries. The two major contributions of this paper are: a method for isometrically embedding arbitrary mesh-metric pairs in higher dimensional Euclidean spaces and a dimension-independent vertex insertion algorithm for producing geometry-conforming Delaunay meshes. The former is demonstrated on a two-dimensional anisotropic problem whereas the latter is demonstrated on both 3d and 4d problems. Keywords: Anisotropic mesh generation; metric; Nash embedding theorem; isometric; geometry-conforming; restricted Voronoi diagram; constrained centroidal Voronoi tessellation; Steiner vertices; dimension-independen

Surface fluid registration of conformal representation: Application to detect disease burden and genetic influence on hippocampus

abstract: In this paper, we develop a new automated surface registration system based on surface conformal parameterization by holomorphic 1-forms, inverse consistent surface fluid registration, and multivariate tensor-based morphometty (mTBM). First, we conformally map a surface onto a planar rectangle space with holomorphic 1-forms. Second, we compute surface conformal representation by combining its local conformal factor and mean curvature and linearly scale the dynamic range of the conformal representation to form the feature image of the surface. Third, we align the feature image with a chosen template image via the fluid image registration algorithm, which has been extended into the curvilinear coordinates to adjust for the distortion introduced by surface parameterization. The inverse consistent image registration algorithm is also incorporated in the system to jointly estimate the forward and inverse transformations between the study and template images. This alignment induces a corresponding deformation on the surface. We tested the system on Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline dataset to study AD symptoms on hippocampus. In our system, by modeling a hippocampus as a 3D parametric surface, we nonlinearly registered each surface with a selected template surface. Then we used mTBM to analyze the morphometry difference between diagnostic groups. Experimental results show that the new system has better performance than two publicly available subcortical surface registration tools: FIRST and SPHARM. We also analyzed the genetic influence of the Apolipoprotein E(is an element of)4 allele (ApoE4), which is considered as the most prevalent risk factor for AD. Our work successfully detected statistically significant difference between ApoE4 carriers and non-carriers in both patients of mild cognitive impairment (MCI) and healthy control subjects. The results show evidence that the ApoE genotype may be associated with accelerated brain atrophy so that our work provides a new MRI analysis tool that may help presymptomatic AD research.NOTICE: this is the author’s version of a work that was accepted for publication in NEUROIMAGE. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Neuroimage, 78, 111-134 [2013] http://dx.doi.org/10.1016/j.neuroimage.2013.04.01

Numerical Methods in Shape Spaces and Optimal Branching Patterns

The contribution of this thesis is twofold. The main part deals with numerical methods in the context of shape space analysis, where the shape space at hand is considered as a Riemannian manifold. In detail, we apply and extend the time-discrete geodesic calculus (established by Rumpf and Wirth [WBRS11, RW15]) to the space of discrete shells, i.e. triangular meshes with fixed connectivity. The essential building block is a variational time-discretization of geodesic curves, which is based on a local approximation of the squared Riemannian distance on the manifold. On physical shape spaces this approximation can be derived e.g. from a dissimilarity measure. The dissimilarity measure between two shell surfaces can naturally be defined as an elastic deformation energy capturing both membrane and bending distortions. Combined with a non-conforming discretization of a physically sound thin shell model the time-discrete geodesic calculus applied to the space of discrete shells is shown to be suitable to solve important problems in computer graphics and animation. To extend the existing calculus, we introduce a generalized spline functional based on the covariant derivative along a curve in shape space whose minimizers can be considered as Riemannian splines. We establish a corresponding time-discrete functional that fits perfectly into the framework of Rumpf and Wirth, and prove this discretization to be consistent. Several numerical simulations reveal that the optimization of the spline functional—subject to appropriate constraints—can be used to solve the multiple interpolation problem in shape space, e.g. to realize keyframe animation. Based on the spline functional, we further develop a simple regression model which generalizes linear regression to nonlinear shape spaces. Numerical examples based on real data from anatomy and botany show the capability of the model. Finally, we apply the statistical analysis of elastic shape spaces presented by Rumpf and Wirth [RW09, RW11] to the space of discrete shells. To this end, we compute a Fréchet mean within a class of shapes bearing highly nonlinear variations and perform a principal component analysis with respect to the metric induced by the Hessian of an elastic shell energy. The last part of this thesis deals with the optimization of microstructures arising e.g. at austenite-martensite interfaces in shape memory alloys. For a corresponding scalar problem, Kohn and Müller [KM92, KM94] proved existence of a minimizer and provided a lower and an upper bound for the optimal energy. To establish the upper bound, they studied a particular branching pattern generated by mixing two different martensite phases. We perform a finite element simulation based on subdivision surfaces that suggests a topologically different class of branching patterns to represent an optimal microstructure. Based on these observations we derive a novel, low dimensional family of patterns and show—numerically and analytically—that our new branching pattern results in a significantly better upper energy bound

Fixtureless geometric inspection of nonrigid parts using "generalized numerical inspection fixture"

Free-form nonrigid parts form the substance of today’s automotive and aerospace industries. These parts have different shapes in free state due to their dimensional and geometric variations, gravity and residual strains. For the geometric inspection of such compliant parts, special inspection fixtures, in combination with coordinate measuring systems (CMM) and/or optical data acquisition devices (scanners) are used. This inevitably causes additional costs and delays that result in a lack of competitiveness in the industry. The goal of this thesis is to facilitate the dimensional and geometrical inspection of flexible components from a point cloud without using a jig or secondary conformation operation. More specifically, we aim to develop a methodology to localize and quantify the profile defects in the case of thin shells which are typical to the aerospace and automotive industries. The presented methodology is based on the fact that the interpoint geodesic distance between any two points of a shape remains unchangeable during an isometric deformation. This study elaborates on the theory and general methods for the metrology of nonrigid parts. We have developed a Generalized Numerical Inspection Fixture (GNIF), a robust methodology which merges existing technologies in metric and computational geometry, nonlinear dimensionality reduction techniques, and finite element methods to introduce a general approach to the fixtureless geometrical inspection of nonrigid parts

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Principal manifolds are defined as lines or surfaces passing through ``the middle'' of data distribution. Linear principal manifolds (Principal Components Analysis) are routinely used for dimension reduction, noise filtering and data visualization. Recently, methods for constructing non-linear principal manifolds were proposed, including our elastic maps approach which is based on a physical analogy with elastic membranes. We have developed a general geometric framework for constructing ``principal objects'' of various dimensions and topologies with the simplest quadratic form of the smoothness penalty which allows very effective parallel implementations. Our approach is implemented in three programming languages (C++, Java and Delphi) with two graphical user interfaces (VidaExpert http://bioinfo.curie.fr/projects/vidaexpert and ViMiDa http://bioinfo-out.curie.fr/projects/vimida applications). In this paper we overview the method of elastic maps and present in detail one of its major applications: the visualization of microarray data in bioinformatics. We show that the method of elastic maps outperforms linear PCA in terms of data approximation, representation of between-point distance structure, preservation of local point neighborhood and representing point classes in low-dimensional spaces.Comment: 35 pages 10 figure

Orthogonally Constrained Sparse Approximations with Applications to Geometry Processing

Compressed manifold modes are solutions to an optimisation problem involving the $\ell_1$ norm and the orthogonality condition $X^TMX=I$. Such functions can be used in geometry processing as a basis for the function space of a mesh and are related to the Laplacian eigenfunctions. Compressed manifold modes and other alternatives to the Laplacian eigenfunctions are all special cases of generalised manifold harmonics, introduced here as solutions to a more general problem. An important property of the Laplacian eigenfunctions is that they commute with isometry. A definition for isometry between meshes is given and it is proved that compressed manifold modes also commute with isometry. The requirements for generalised manifold harmonics to commute with isometry are explored. A variety of alternative basis functions are tested for their ability to reconstruct specific functions -- it is observed that the function type has more impact than the basis type. The bases are also tested for their ability to reconstruct functions transformed by functional map -- it is observed that some bases work better for different shape collections. The Stiefel manifold is given by the set of matrices $X \in \mathbb{R}^{n \times k}$ such that $X^TMX = I$, with $M=I$. Properties and results are generalised for the $M \neq I$ case. A sequential algorithm for optimisation on the generalised Stiefel manifold is given and applied to the calculation of compressed manifold modes. This involves a smoothing of the $\ell_1$ norm. Laplacian eigenfunctions can be approximated by solving an eigenproblem restricted to a subspace. It is proved that these restricted eigenfunctions also commute with isometry. Finally, a method for the approximation of compressed manifold modes is given. This combines the method of fast approximation of Laplacian eigenfunctions with the ADMM solution to the compressed manifold mode problem. A significant improvement is made to the speed of calculation

Elastic shape analysis of geometric objects with complex structures and partial correspondences

In this dissertation, we address the development of elastic shape analysis frameworks for the registration, comparison and statistical shape analysis of geometric objects with complex topological structures and partial correspondences. In particular, we introduce a variational framework and several numerical algorithms for the estimation of geodesics and distances induced by higher-order elastic Sobolev metrics on the space of parametrized and unparametrized curves and surfaces. We extend our framework to the setting of shape graphs (i.e., geometric objects with branching structures where each branch is a curve) and surfaces with complex topological structures and partial correspondences. To do so, we leverage the flexibility of varifold fidelity metrics in order to augment our geometric objects with a spatially-varying weight function, which in turn enables us to indirectly model topological changes and handle partial matching constraints via the estimation of vanishing weights within the registration process. In the setting of shape graphs, we prove the existence of solutions to the relaxed registration problem with weights, which is the main theoretical contribution of this thesis. In the setting of surfaces, we leverage our surface matching algorithms to develop a comprehensive collection of numerical routines for the statistical shape analysis of sets of 3D surfaces, which includes algorithms to compute Karcher means, perform dimensionality reduction via multidimensional scaling and tangent principal component analysis, and estimate parallel transport across surfaces (possibly with partial matching constraints). Moreover, we also address the development of numerical shape analysis pipelines for large-scale data-driven applications with geometric objects. Towards this end, we introduce a supervised deep learning framework to compute the square-root velocity (SRV) distance for curves. Our trained network provides fast and accurate estimates of the SRV distance between pairs of geometric curves, without the need to find optimal reparametrizations. As a proof of concept for the suitability of such approaches in practical contexts, we use it to perform optical character recognition (OCR), achieving comparable performance in terms of computational speed and accuracy to other existing OCR methods. Lastly, we address the difficulty of extracting high quality shape structures from imaging data in the field of astronomy. To do so, we present a state-of-the-art expectation-maximization approach for the challenging task of multi-frame astronomical image deconvolution and super-resolution. We leverage our approach to obtain a high-fidelity reconstruction of the night sky, from which high quality shape data can be extracted using appropriate segmentation and photometric techniques