Modeling, Inference and Clustering for Equivalence Classes of 3-D Orientations Chuanlong Du Iowa State University
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Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Modeling, inference and clustering for equivalence classes of 3-D orientations Chuanlong Du Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Statistics and Probability Commons Recommended Citation Du, Chuanlong, "Modeling, inference and clustering for equivalence classes of 3-D orientations" (2014). Graduate Theses and Dissertations. 13738. https://lib.dr.iastate.edu/etd/13738 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Modeling, inference and clustering for equivalence classes of 3-D orientations by Chuanlong Du A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Statistics Program of Study Committee: Stephen Vardeman, Co-major Professor Daniel Nordman, Co-major Professor Dan Nettleton Huaiqing Wu Guang Song Iowa State University Ames, Iowa 2014 Copyright c Chuanlong Du, 2014. All rights reserved. ii DEDICATION I would like to dedicate this dissertation to my mother Jinyan Xu. She always encourages me to follow my heart and to seek my dreams. Her words have always inspired me and encouraged me to face difficulties and challenges I came across in my life. I would also like to dedicate this dissertation to my wife Lisha Li without whose support and help I would not have been able to complete this work. iii TABLE OF CONTENTS LIST OF TABLES . vi LIST OF FIGURES . vii ACKNOWLEDGEMENTS . ix ABSTRACT . x CHAPTER 1. GENERAL INTRODUCTION . 1 1.1 Introduction . .1 1.2 Dissertation Organization . .3 CHAPTER 2. BAYESIAN INFERENCE FOR A NEW CLASS OF DIS- TRIBUTIONS ON EQUIVALENCE CLASSES OF 3-D ORIENTATIONS WITH APPLICATIONS TO MATERIALS SCIENCE . 4 Abstract . .4 2.1 Introduction . .5 2.2 Models for Equivalence Classes of Rotation Matrices . .8 2.2.1 UARS([S]; κ) Models for Equivalence Classes of Rotation Matrices . .8 2.2.2 Likelihood-based Confidence Regions for the SMF([S]; κ) Distribution on [Ω]....................................... 10 2.3 One-Sample Bayes Inference for the SMF([S]; κ) Distribution on [Ω] . 12 2.3.1 Cone-Shaped Credible Regions for [S]................... 12 2.3.2 One-Sample Bayes Methods . 13 2.3.3 Simulation Results and Comparison to Likelihood-based Methods . 15 2.4 Comparison to Inferences Based on SMF(S; κ) Models on Ω for Preprocessed Data 16 2.4.1 A First Comparison Based on Repeated Measurements . 17 iv 2.4.2 Another Comparison Based on Real Data . 19 2.4.3 A Comparison Based on a Small Simulation . 20 2.5 Extensions of Models to Other Equivalence Classes of Rotations . 21 2.6 Conclusion . 23 CHAPTER 3. A METHOD FOR MAPPING GRAINS IN EBSD SCANS OF MATERIAL SPECIMENS USING SPATIALLY INFORMED CLUS- TERING OF 3-D ORIENTATIONS . 24 Abstract . 24 3.1 Introduction . 25 3.2 Distance Between Orienlocations . 26 3.2.1 Distance Between Orientations . 26 3.2.2 Distance Between Equivalence Classes of Orientations . 27 3.2.3 Euclidean Distance . 28 3.2.4 A Combined Distance of Orientations and Locations for Orienlocations 28 3.2.5 Penalized Distances for Orientations and Locations . 29 3.3 Clustering Orienlocations . 29 3.4 Application to Real Data with Discussions . 31 3.4.1 Non-smoothed Grain Maps . 31 3.4.2 Smoothed Grain Maps . 35 3.5 A Simulation Study of the Clustering Algorithm . 37 3.6 Conclusion . 38 CHAPTER 4. A CLASS OF STATIONARY AND ERGODIC MARKOV CHAINS DEFINED ON PARTITIONS OF A FINITE SET WITH AP- PLICATIONS IN BAYESIAN CLUSTERING . 40 Abstract . 40 4.1 Introduction . 40 4.2 Definition of Markov Chains on Partitions . 41 4.3 Some Important Properties of the Du(n,G,F ) Process . 42 v 4.4 An Illustration of the Use of the Du(n,G,F ) Process in Bayesian Clustering . 45 4.5 Conclusion . 47 CHAPTER 5. GENERAL CONCLUSIONS . 49 APPENDIX A. UARS(S; κ) MODELS FOR ROTATION MATRICES . 51 APPENDIX B. DETAILED PROOFS OF THEOREMS IN CHAPTER 4.3. 53 BIBLIOGRAPHY . 59 vi LIST OF TABLES 2.1 Values of tuning parameters ρ and σ.................... 16 2.2 Coverage rates (as percentages) for κ and [S] for nominally 95% Bayes regions, inverted likelihood ratio test regions and Wald regions, for some choices of (n; κ)................................ 17 3.1 Artificial data for a toy example of agglomerative hierarchical clustering. 30 4.1 Simulated data from normal distributions. 46 vii LIST OF FIGURES 1.1 On the left, three edges of a (non-rotated) cube are aligned with a 3 standard coordinate reference frame in R ; each individual edge has a direction corresponding to a column of 3 × 3 identity matrix I3. The right figure illustrates a cube after a rotation; the resulting orientation can be represented by a 3 × 3 rotation matrix O = [x0 y0 z0], where the columns of O indicate how columns of I3 (i.e., edges of the cube) move upon rotation. (Further, in the Euler axis-angle representation of a rotation from AppendixA, the rotation can be described by \turning" 3 the cube through an angle r about a fixed axis in the direction of u 2 R , kuk =1.) ..................................2 1.2 An illustration of 6 labelings (coordinate systems) on a cuboid based on selecting the 2 bottom left points as the origin. .3 2.1 Histograms of rotation angles at locations 114, where the angles are expressed as multiples of π=6 showing concentrations at (0; 3; 4; 6) ∗ π=6 =(0; pi=2; pi; 2pi=3) (as expected under cube labeling ambiguities). .6 2.2 Variance of C(rjκ) against κ........................ 10 2.3 Cone-shaped region for [S]. ........................ 13 2.4 Histograms of posterior draws for κ for SMF(S; κ) and SMF([S]; κ) models (repeated real measurements example). 18 2.5 Histograms of posterior draws for κ for SMF(S; κ) and SMF([S]; κ) models (second real data example). 20 viii 2.6 Histograms of posterior draws for κ for SMF(S; κ) and SMF([S]; κ) models (simulated data example). 21 2.7 Right-hand coordinate systems on a symmetric cuboid. 22 3.1 Grain map with w = 1000, co = 4, ao = 0, cl = 4, al = 0 and n = 25. 32 3.2 Smoothed grain map with w = 1000, co = 4, ao = 0, cl = 4, al = 0 and n =25..................................... 32 3.3 Each grain map corresponds to a different factor combination (!, co, ao, cl, al, n) (the first line of parameters above plots), where n = 25 is the maximal number of clusters allowed. The 3 rows of grain maps correspond to ! of 1000, 100 and 10 respectively. The 3 columns of grain maps penalize no distances, the Euclidean distances and the orientation distances respectively. The second line of parameters above each plot contains the number of points smoothed out in each smoothing round. 33 3.4 Each grain map corresponds to a different factor combination (!, co, ao, cl, al, n) (the first line of parameters above plots), where n = 20 is the maximal number of clusters allowed. The 3 rows of grain maps correspond to ! of 5, 1 and 0 respectively. The 3 columns of grain maps penalize no distances, the Euclidean distances and the orientation distances respectively, except the bottom right one. The second line of parameters above each plot contains the number of points smoothed out in each smoothing round. 34 3.5 Best grain maps and corresponding parameters used to produce these grain maps for different combinations of κout and κin. The 3 rows of grain maps correspond to κout of 10, 5 and 3, and the 3 columns of grain maps correspond to κin of 10, 20 and 50. 39 ix ACKNOWLEDGEMENTS I would like to take this opportunity to express my thanks to those who helped me with var- ious aspects of conducting research and the writing of this dissertation. First and foremost, Dr. Steve Vardeman and Dr. Dan Nordman for their guidance, patience and support throughout this research and the writing of this dissertation. Their insights and words of encouragement have often inspired me and renewed my hopes for completing my graduate education. Second, I'd like to thank Dr. Dan Nettleton for supporting me as a research assistant during my last 3 year at Iowa State University. I would also like to thank my committee members for their efforts and contributions to this work. x ABSTRACT Investigating cubic crystalline structures of specimens is an important way to study prop- erties of materials in text analysis. Crystals in metal specimens have internally homogeneous orientations relative to a pre-chosen reference coordinate system. Clusters of crystals in the metal with locally similar orientations constitute so-called \grains." The nature of these grains (shape, size, etc.) affects physical properties (e.g., hardness, conductivity, etc.) of the mate- rial. Electron backscatter diffraction (EBSD) machines are often use to measure orientations of crystals in metal specimens. However, orientations reported by EBSD machines are in truth equivalence classes of crystallographically symmetric orientations. Motivated by the materials science applications, we formulate parametric probability models for \unlabeled orientation data." This amounts to developing models on equivalence classes of 3-D rotations. A Bayesian method is developed for inferencing parameters in the models, which is generally superior to large-sample methods based on likelihood estimation. We also proposed an algorithms for clustering equivalence classes of 3-D orientations.