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Geometric and Topological Mesh Feature
Extraction for 3D Shape Analysis
 Geometric Modeling and Applications Set
coordinated by
Marc Daniel

Volume 3

Geometric and Topological

Mesh Feature Extraction for
3D Shape Analysis

Jean-Luc Mari
Franck Hétroy-Wheeler
Gérard Subsol
First published 2019 in Great Britain and the United States by ISTE Ltd and John Wiley & Sons, Inc.

Apart from any fair dealing for the purposes of research or private study, or criticism or review, as
permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced,
stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers,
or in the case of reprographic reproduction in accordance with the terms and licenses issued by the
CLA. Enquiries concerning reproduction outside these terms should be sent to the publishers at the
undermentioned address:

ISTE Ltd John Wiley & Sons, Inc.

27-37 St George’s Road 111 River Street
London SW19 4EU Hoboken, NJ 07030
UK USA

www.iste.co.uk www.wiley.com

© ISTE Ltd 2019

The rights of Jean-Luc Mari, Franck Hétroy-Wheeler and Gérard Subsol to be identified as the authors of
this work have been asserted by them in accordance with the Copyright, Designs and Patents Act 1988.

Library of Congress Control Number: 2019946683

British Library Cataloguing-in-Publication Data

A CIP record for this book is available from the British Library
ISBN 978-1-78630-041-6
 Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Chapter 1. Geometric Features based on Curvatures . . . . . . 1

1.1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2. Some mathematical reminders of the differential geometry
of surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2.1. Fundamental forms and normal curvature . . . . . . . . . . . 2
1.2.2. Principal curvatures and shape index . . . . . . . . . . . . . 5
1.2.3. Principal directions and lines of curvature . . . . . . . . . . 6
1.2.4. Weingarten equations and shape operator . . . . . . . . . . . 9
1.2.5. Practical computation of differential parameters . . . . . . . 12
1.2.6. Euler’s theorem . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.2.7. Meusnier’s theorem . . . . . . . . . . . . . . . . . . . . . . . 15
1.2.8. Local approximation of the surface . . . . . . . . . . . . . . 16
1.2.9. Focal surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.3. Computation of differential parameters on a discrete
3D mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.3.1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.3.2. Some notations . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.3.3. Computing normal vectors . . . . . . . . . . . . . . . . . . . 20
1.3.4. Locally fitting a parametric surface . . . . . . . . . . . . . . 22
1.3.5. Discrete differential geometry operators . . . . . . . . . . . 22
1.3.6. Integrating 2D curvatures . . . . . . . . . . . . . . . . . . . . 28
vi Geometric and Topological Mesh Feature Extraction for 3D Shape Analysis

1.3.7. Tensor of curvature: Taubin’s formula . . . . . . . . . . . . . 28

1.3.8. Tensor of curvature based on the normal cycle
theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
1.3.9. Integral estimators . . . . . . . . . . . . . . . . . . . . . . . . 34
1.3.10. Processing unstructured 3D point clouds . . . . . . . . . . 38
1.3.11. Discussion of the methods . . . . . . . . . . . . . . . . . . . 38
1.4. Feature line extraction . . . . . . . . . . . . . . . . . . . . . . . . 46
1.4.1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
1.4.2. Lines of curvature . . . . . . . . . . . . . . . . . . . . . . . . 47
1.4.3. Crest/ridge lines . . . . . . . . . . . . . . . . . . . . . . . . . 55
1.4.4. Feature lines based on homotopic thinning . . . . . . . . . . 79
1.5. Region-based approaches . . . . . . . . . . . . . . . . . . . . . . 84
1.5.1. Mesh segmentation . . . . . . . . . . . . . . . . . . . . . . . 84
1.5.2. Shape description based on graphs . . . . . . . . . . . . . . . 87
1.6. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

Chapter 2. Topological Features . . . . . . . . . . . . . . . . . . . 99

2.1. Mathematical background . . . . . . . . . . . . . . . . . . . . . 99
2.1.1. A topological view on surfaces . . . . . . . . . . . . . . . . . 100
2.1.2. Algebraic topology . . . . . . . . . . . . . . . . . . . . . . . 103
2.2. Computation of global topological features . . . . . . . . . . . . 106
2.2.1. Connected components and genus . . . . . . . . . . . . . . . 106
2.2.2. Homology groups . . . . . . . . . . . . . . . . . . . . . . . . 107
2.3. Combining geometric and topological features . . . . . . . . . . 111
2.3.1. Persistent homology . . . . . . . . . . . . . . . . . . . . . . . 112
2.3.2. Reeb graph and Morse–Smale complex . . . . . . . . . . . . 115
2.3.3. Homology generators . . . . . . . . . . . . . . . . . . . . . . 118
2.3.4. Measuring holes . . . . . . . . . . . . . . . . . . . . . . . . . 121
2.4. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

Chapter 3. Applications . . . . . . . . . . . . . . . . . . . . . . . . . 131

3.1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
3.2. Medicine: lines of curvature for polyp detection in virtual
colonoscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
3.3. Paleo-anthropology: crest/ridge lines for shape analysis of
human fossils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
3.4. Geology: extraction of fracture lines on virtual outcrops . . . . 137
 Contents vii

3.5. Planetary science: detection of feature lines for the extraction

of impact craters on asteroids and rocky planets . . . . . . . . . . . . 140
3.6. Botany: persistent homology to recover the branching
structure of plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
 Preface

Three-dimensional surface meshes, composed of collections of planar

polygons, are the most common discrete representation of the surface of a
virtual shape. These 3D surface meshes need to be inspected in order to
understand or evaluate their overall structure or some details. This can be
done by extracting relevant geometric or topological features. Such shape
characteristics can simplify the way the object is looked at, can help
recognition and can describe and categorize it according to specific criteria.

Shape characteristics can be defined in many ways. This book takes the
point of view of discrete mathematics, which aims to propose discrete
counterparts to concepts mathematically defined in continuous terms. More
specifically, in this book, we review how standard geometric and topological
notions of surfaces can be defined and computed for a 3D surface mesh, as
well as their use for shape analysis. In particular, recent methods are
described to extract feature lines having a meaning related to either geometry
or topology. Differential estimators such as discrete principal curvatures are
detailed as they play a critical role in the computation of salient structures. An
emphasis is then placed on topology since the global structure and the
connectivity of features play an important role in the understanding of a
shape. Several applications are finally developed, showing that each of them
needs specific adjustments to generic approaches. These applications are
related to medicine, geology, botany and other sciences.

Focusing on shape features, the topic of this book is narrower but more
detailed than other shape analysis books, which do not, or only briefly, refer
to feature definition and computation. It is intended not only for students,
x Geometric and Topological Mesh Feature Extraction for 3D Shape Analysis

researchers and engineers in computer science and shape analysis, but also
numerical geologists, anthropologists, biologists and other scientists looking
for practical solutions to their shape analysis, understanding or recognition
problems. We hope that our book will be a useful review of existing work for
all of them.

Finally, we would like to thank Marc Daniel for giving us the opportunity
to write this book and Aldo Gonzalez-Lorenzo for his reading of chapter 2 and
for his constructive remarks.

Jean-Luc M ARI
Franck H ÉTROY-W HEELER
Gérard S UBSOL
August 2019
 Introduction

I.1. Context: 3D shape analysis

Shapes, whether from the natural world or manufactured, are more and
more often digitized for visualization or measurement purposes, among
others. This process generally results in 3D surface meshes, which are
composed of collections of planar polygons. Such meshes nowadays are the
most common discrete representation of the surface of a virtual shape. These
meshes are automatically, or sometimes interactively, examined, in order to
understand, evaluate or match their overall structure or some details. This
process is called 3D shape analysis and can be done by extracting relevant
geometric or topological features. Such shape characteristics can simplify the
way the object is looked at, can help recognition and can describe and
categorize it according to specific criteria. In this book, we will review
various mathematical definitions of mesh features and some algorithms to
compute them. We will then give a few application examples where these
features are used to globally or locally analyze a 3D shape.

It is important to note that this book is not about 3D shape analysis, but
only about feature definition and computation. 3D shape analysis has a wider
spectrum than feature detection. Among concepts that will not be tackled in
this book are global shape descriptor/signature definition and spectral shape
analysis. The interested reader can refer to [BIA 14] or [LÉV 10] to learn more
about these notions.

Before going into details about surface features from a mathematical and
computational point of view, and detailing some applications in Chapters 1–3,
xii Geometric and Topological Mesh Feature Extraction for 3D Shape Analysis

we start by giving some general definitions about meshes, which will be useful
in the following chapters. For the interested reader, we also quickly go over
how features are defined and calculated in other fields.

I.2. Background on meshes

In many (but not all) contexts where a sampling of a surface is available,

this surface is approximated by a mesh. A surface mesh is formally defined
as a triplet of sets M = (V, E, F ), where V is the set of vertices, which are
points in the 3D Euclidean space R3 sampling the surface at stake; E is the
set of edges, which are segments whose endpoints are vertices of V : E ⊂
V × V ; and F is the set of faces, which are polygons whose vertices and edges
are vertices and edges of V and E respectively. A volume mesh is defined as
a quadruplet of sets (V, E, F, T ). The additional set T is a set of polyhedra
whose vertices, edges and faces are part of V , E and F respectively. Since in
this book we will focus on the surface of a shape, we will not consider such
volume meshes and we will restrict ourselves to surface meshes. In practice,
several properties are often required. The polygonal faces must be planar. It
is often convenient to limit oneself to triangular faces since such faces are
necessarily planar, but sometimes it is useful to allow quadrangular faces, i.e.
faces with four edges. For most applications, faces must be convex. Here again,
restricting the work to triangles is a way to ensure convexity.

A mesh approximates the surface of an object with a finite number of

geometric primitives (points, segments and polygons). The geometry of the
mesh is thus a simplification of the geometry of the underlying shape and is
given by the 3D coordinates of its vertices and by the geometric information
carried by the edges and the faces. For example, the normal vectors to the
faces are local estimates of the normal vector to the surface. This geometry is
decorrelated to the topology of the mesh, which encodes the neighboring
information between primitives. Two meshes can share the same topology but
not the same geometry or vice versa (see Figure I.1). Note that what we call
here topology is not closely related to the topology of the surface, as will be
studied in Chapter 2.

The topology of a mesh is defined with the following notions, which come
from the terminology used for graphs in computer science. Incidence: two
primitives (vertices, edges, faces) are incident to each other if one is a border
 Introduction xiii

of the other. A vertex and an edge are incident to each other if the vertex
is an endpoint of this edge. A vertex and a face are incident to each other
if the vertex is a vertex of the face. Finally, an edge and a face are incident
to each other if the edge is an edge of the face. Adjacency: two primitives
(vertices, edges, faces) of dimension n are adjacent to each other if they share
the same dimension and are incident to the same primitive of dimension n − 1
or n + 1. Two vertices are adjacent if they are endpoints of the same edge.
Two edges are adjacent if they share a common endpoint or a common face.
Two faces are adjacent if they share a common edge. Note that in graph theory,
two edges that share a common endpoint are said to be incident. We use the
term adjacent here for the sake of simplicity. Neighborhood: the topological k-
neighborhood of a vertex v on a mesh is given by the set of vertices which can
be reached from v using at most k adjacency relationships. For example, the
1-neighborhood of v is the set of vertices which share an edge with v, and the
2-neighborhood of v also includes the set of vertices which share an edge with
a vertex of the 1-neighborhood of v. Finally, we call the degree or valency of
a vertex v the number of 1-neighbors of v. Equivalently, this is the number of
edges incident to v.

Figure I.1. Three meshes that share either the same topology
but not the same geometry (left and middle) or the same
geometry but not the same topology (middle and right)

Since the mesh represents the boundary of a volumetric object, it is usually

required that the surface “looks like” a disk locally, and that there is no
pinch point for example, or three faces sharing an edge. This is formalized
through the notion of manifoldness, which we will study in Chapter 2. Roughly
speaking, a surface is said to be a manifold if the neighborhood of each point
can be smoothly deformed to a disk, without shearing or gluing. Alternatively,
a surface is a manifold with boundary if the neighborhood of each point can be
smoothly deformed to a disk or a half-disk. For example, an egg is a manifold
(it is equivalent to a sphere from a topological point of view, although it is
not geometrically a sphere), and an egg on which the top has been removed
xiv Geometric and Topological Mesh Feature Extraction for 3D Shape Analysis

is a manifold with boundary. More general than a manifold is the notion of

simplicial complex. A simplicial complex is a mesh M with the following two
properties:
1) every edge of a face of F is in E, and every vertex of an edge of E is
in V ;
2) the intersection of any two primitives of M is either empty or a primitive
of M . For example, the intersection of two different faces is either empty or a
vertex or an edge of the mesh. It cannot be a segment or a point inside these
faces.

Note that, for example, isolated vertices or faces only connected by a vertex
and not an edge are allowed in a simplicial complex while they are not in a
manifold mesh.

Meshes are widely used because of several good properties. First, they are
relatively easy and fast to create from a set of points. Second, their storage
cost is low, since only the 3D coordinates of the vertices and some topological
information (e.g. the vertices defining each face) need to be stored. Third,
they are adaptable, can handle even complicated geometries and can be used
in various scenarios. Finally, they are often easy to process since the
neighborhood information is explicitly given by the primitives. However, they
face a few drawbacks: the resulting surface is not smooth and they may be
difficult to edit since this usually requires the computation of an extended
neighborhood for each vertex.

I.3. Definition of a feature

According to the English Oxford Dictionaries [OXF 17], a feature is

“a distinctive attribute or aspect of something”. This raises two main questions
related to the object under study:
– distinctive: what is involved in the process of distinguishing?
– attribute: how is an attribute defined?

Different definitions of features have been proposed for 3D shapes, which

differ on their answers to these two questions. For the sake of completeness,
 Introduction xv

we review here a few of them before introducing the core of our topic, which
will be developed in the following chapters.

I.3.1. Surface feature from a topographic point of view

In topography, experts have defined a limited number of Earth (or another

planet) surface features. These features are of two kinds: points or lines. The
main ones are:
– a hill corresponds to a point where the ground slopes down in all
directions. In other words, it is a local height maximum;
– a depression is a local height minimum;
– a saddle is a low point between two hills. The ground slopes up in two
opposite directions, but slopes down in the two other, orthogonal directions;
– a ridge is a line where at each point the ground slopes up in one direction
and down in the three other ones;
– a valley is a line where at each point the ground slopes up in three
directions and down in the last direction.

These terms can actually be mathematically defined and are not restricted
to planets, as we will see in Chapter 1. Other features include draws, spurs,
cliffs, cuts and fills [DEP 11]. The main advantage of these definitions is that
any non-expert is able to distinguish a feature on a terrain, as soon as he or
she is able to check in which directions the ground slopes up or down. The
main drawback is that they somehow depend on the choice of the scale: the
ground can be slightly sloping down for a few meters in a direction but overall
sloping up in the same direction for a longer distance. Hence, more robust and
general-purpose definitions have been proposed in other fields.

I.3.2. Surface feature from a perceptual point of view

In visual perception, a feature is usually defined as a salient point or region

on a 3D shape, i.e. a point or region that can easily be distinguished from
its surroundings by the human eye. Multiple mathematical definitions have
been proposed, which usually relate features to surface geometric properties at
multiple scales.
xvi Geometric and Topological Mesh Feature Extraction for 3D Shape Analysis

In computer graphics, seminal work includes the introduction of the

concept of mesh saliency by Lee, Varshney and Jacobs [LEE 05], which
extends to 3D meshes the definition proposed by [ITT 98] for 2D images.
Earlier works mostly projected a 3D surface into a 2D image to determine its
visual features. Lee et al. define mesh saliency for a given vertex as a
combination of saliencies at different scales. These saliencies are themselves
computed as differences between Gaussian-weighted averages of the mean
curvature of neighboring vertices computed at a fine and a coarse scale. A
feature is then defined as a region on the mesh with high, or locally
maximum, saliency values. Note that this original mesh saliency definition is
purely geometry-based, but other information such as color can be
incorporated.

Almost at the same time, Gal and Cohen-Or proposed another purely
geometric approach, in which the surface is first approximated by quadric
patches [GAL 06]. A descriptor is then defined for each patch, as the center of
mass of the patch together with the highest Gaussian curvature across the
patch. A salient geometric feature is finally defined as a cluster of descriptors
with locally high curvature and a high variance of curvatures. Leifman et al.
defined regions of interest on a 3D mesh according to three properties: vertex
distinctness, shape extremities and patch association [LEI 16]. A distinct
vertex is defined as a vertex whose spin image descriptor [JOH 99] is far from
others, using diffusion distance at three different scales. Contrary to these
purely local approaches, Song et al. considered global geometric properties of
the shape [SON 14]. Specifically, the spectrum of the Laplacian matrix of the
mesh is used through a multiscale approach to find the most obvious
saliencies.

Following Lee et al., some authors have taken inspiration from visual
perception theories to define salient features on a 3D surface. Based on the
concept of visual masking, Lavoué defined a perceptual measure of noise on a
mesh called roughness, which is computed at every vertex as an asymmetric
difference between the maximum curvature on the mesh and on a smoothed
version of it [LAV 09]. Detected rough vertices are distinct from sharp edge
features. Wu et al. linearly combine a local property, the visual contrast and a
global one, rarity, to define saliency [WU 13]. The local contrast is computed
by segmenting the mesh into almost planar patches and computing distances
between the means of multiscale descriptors of all vertices in neighboring
patches. The global rarity value of a vertex is simply the sum of the distances
 Introduction xvii

between the descriptor of this vertex and the descriptors of all other vertices
in the mesh. Nader et al. proposed a bottom-up approach based on user
experiments to estimate the visual contrast on a flat-shaded [NAD 16a] or
smooth-shaded [NAD 16b] 3D mesh. Similarly to [LAV 09], their work is
based on the concept of visual masking, as well as others such as contrast
sensitivity and visual regularity.

Since a feature should, by definition, be distinctive, Shilane and

Funkhouser introduced the idea of defining a feature on an object with respect
to similar objects [SHI 07]. In their approach, a region is said to be distinctive
if its shape is consistent with regions on objects of the same class but different
from objects in other classes. The shape of a region is described through a
multiscale Harmonic Shape Descriptor [KAZ 03], which decomposes a
spherical region into concentric shells of varying radii. Going further, Chen
et al. studied the points selected on 3D surfaces by more than 1,000
non-trained users [CHE 12]. The question asked to the users was to select
points that the other people were likely to select. They found out that the most
obvious feature points can be retrieved at minimum curvature local extrema.
Locations for less obvious feature points include symmetry axes and centers
of large convex parts. Lau et al. extended the concept of mesh saliency to
detect the regions on the surface of a 3D object which are the most likely to
be grasped, pressed or touched by a human user [LAU 16]. These regions are
learned from manually labeled salient regions using deep neural networks.

I.3.3. Surface feature from a machine vision point of view

Automatically computing distinctive features in an image is one of the

main goals of computer vision. In this context, features, also called keypoints,
are usually defined as pixels, or connected sets of pixels, with specific
appearance or geometric properties (motion can also be taken into account in
the case of videos). For example, a feature can be located at a place of a sharp
change in color or texture, or at the edge or the endpoint of an object. Features
should represent in a compact manner the relevant information with respect to
a specific goal, such as describing the objects in the image. They should also
be stable in the image under some geometric transformations, such as rotation
or scaling. Feature definition usually comprises two stages: detection and
description. Feature detection aims to compute the relevant keypoints for a
given application, while feature description expresses the specific properties
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