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Fast combinative volume rendering by indexed data structure

Progress in Natural Science:Materials International 2001年第12期11卷 40-45页

作者：孙文武王文成吴恩华 Beijing 100080 China China Faculty of Science and Technology Chinese Academy of Sciences Institute of Software Laboratory of Computer Science University of Macao

It is beneficial to study the interesting contents in a data set by combining and rendering various contents of the data. In this regard, an indexed data structure is proposed to facilitate the reorganization of data so that the contents of the data can be combined conveniently and only the selected contents in the data are processed for rendering. Based on the structure, the cells of different contents can be queued up easily so that the volume rendering can be conducted more accurately and quickly. Experimental results show that the indexed data structure is very efficient in improving combinative volume rendering.

关键词： data structure combinative volume rendering data visualization.

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G-TREE - A NEW data structure FOR ORGANIZING MULTIDIMENSIONAL data

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IEEE TRANSACTIONS ON KNOWLEDGE AND data ENGINEERING 1994年第2期6卷 341-347页

作者： KUMAR, A Graduate School of Management Comell University Medical College Ithaca NY USA

This paper describes an efficient data structure called the (G-tree (or grid tree) for organizing multidimensional data. The data structure combines the features of grids and B-trees in a novel manner. It also exploits an ordering property that numbers the partitions in such a way that partitions that are spatially close to one another in a multidimensional space are also close in terms of their partition numbers. This structure adapts well to dynamic data spaces with a high frequency of insertions and deletions, and to nonuniform distributions of data. We demonstrate that it is possible to perform insertion, retrieval, and deletion operations, and to run various range queries efficiently using this structure. A comparision with the BD tree, zkdb tree and the KDB tree is carried out, and the advantages of the G-tree over the other structures are discussed. The simulated bucket utilization rates for the G-tree are also reported.

关键词： data structure MULTIDIMENSIONAL data B-TREE KDB TREE BD TREE GRID FILES G-TREE BUCKET UTILIZATION RANGE QUERIES

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Shell: A Spatial Decomposition data structure for Ray Traversal on GPU

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IEEE TRANSACTIONS ON COMPUTERS 2016年第1期65卷 230-243页

作者： Xiao, Kai Hu, Xiaobo Sharon Zhou, Bo Chen, Danny Ziyi Univ Notre Dame Dept Comp Sci & Engn Notre Dame IN 46556 USA Altera Corp San Jose CA 95134 USA

Shared memory many-core processors such as GPUs have been extensively used in accelerating computation-intensive algorithms and applications. When porting existing algorithms from sequential or other parallel architecture models to shared memory many-core architectures, non-trivial modifications are often needed to match the execution patterns of the target algorithms with the characteristics of many-core architectures. Ray traversal is a fundamental process in many applications, and is commonly accelerated by spatial decomposition schemes captured in hierarchical data structures (e.g., kd-trees). However, ray traversal using hierarchical data structures needs to conduct repeated hierarchical searches. Such search process is time-consuming on shared memory many-core architectures since it incurs considerable amounts of expensive memory accesses and execution divergence. In this paper, we propose a novel spatial decomposition based data structure, called Shell, which completely avoids hierarchical search for ray traversal. In Shell, a structure is built on the boundary of each region in the decomposed space, which allows any ray traversing in a region to find the next neighboring region to traverse using table lookup schemes, without any hierarchical search. While our ray traversal approach works for other spatial decomposition paradigms and many-core processors in higher dimensional scenes, we illustrate it using kd-tree on GPU for 3D scenario and compare with the fastest known kd-tree searching algorithms for ray traversal. Experimental results in graphics ray tracing and radiation dose calculation show that our approach improves the performance by 3.5-5.5x over the fastest known kd-tree based approaches.

关键词： GPU ray traversal data structure spatial decomposition kd-tree

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AHF: array-based half-facet data structure for mixed-dimensional and non-manifold meshes

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ENGINEERING WITH COMPUTERS 2015年第3期31卷 389-404页

作者： Dyedov, Vladimir Ray, Navamita Einstein, Daniel Jiao, Xiangmin Tautges, Timothy J. SUNY Stony Brook Dept Appl Math & Stat Stony Brook NY 11794 USA Argonne Natl Lab Math & Comp Sci Argonne IL 60439 USA Pacific NW Natl Lab Div Biol Sci Richland WA 99352 USA

We present an Array-based Half-Facet mesh data structure, or AHF, for efficient mesh query and modification operations. The AHF extends the compact array-based half-edge and half-face data structures (T. J. Alumbaugh and X. Jiao, Compact array-based mesh data structures, IMR, 2005) to support mixed-dimensional and non-manifold meshes. The design goals of our data structure include generality to support such meshes, efficiency of neighborhood queries and mesh modification, compactness of memory footprint, and facilitation of interoperability of mesh-based application codes. To accomplish these goals, our data structure uses sibling half-facets as a core abstraction, coupled with other explicit and implicit representations of entities. A unique feature of our data structure is a comprehensive implementation in MATLAB, which allows rapid prototyping, debugging, testing, and deployment of meshing algorithms and other mesh-based numerical methods. We have also developed a C++ implementation built on top of MOAB (T.J. Tautges, R. Meyers, and K. Merkley, MOAB: A Mesh-Oriented database, Sandia National Laboratories, 2004). We present some comparisons of the memory requirements and computational costs, and also demonstrate its effectiveness with a few sample applications.

关键词： Mesh generation data structure Non-manifold Mixed-dimensional meshes Sibling half-facets MATLAB

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Harnessing data structure for recovery of randomly missing structural vibration responses time history: Sparse representation versus low-rank structure

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MECHANICAL SYSTEMS AND SIGNAL PROCESSING 2016年 74卷 165-182页

作者： Yang, Yongchao Nagarajaiah, Satish Rice Univ Dept Civil & Environm Engn Houston TX 77005 USA Rice Univ Dept Mech Engn Houston TX 77005 USA

Randomly missing data of structural vibration responses time history often occurs in structural dynamics and health monitoring. For example, structural vibration responses are often corrupted by outliers or erroneous measurements due to sensor malfunction;in wireless sensing platforms, data loss during wireless communication is a common issue. Besides, to alleviate the wireless data sampling or communication burden, certain accounts of data are often discarded during sampling or before transmission. In these and other applications, recovery of the randomly missing structural vibration responses from the available, incomplete data, is essential for system identification and structural health monitoring;it is an ill-posed inverse problem, however. This paper explicitly harnesses the data structure itself-of the structural vibration responses-to address this (inverse) problem. What is relevant is an empirical, but often practically true, observation, that is, typically there are only few modes active in the structural vibration responses;hence a sparse representation (in frequency domain) of the single-channel data vector, or, a low-rank structure (by singular value decomposition) of the multi-channel data matrix. Exploiting such prior knowledge of data structure (intra-channel sparse or inter-channel low-rank), the new theories of l(1)-minimization sparse recovery and nuclear-norm-minimization low-rank matrix completion enable recovery of the randomly missing or corrupted structural vibration response data. The performance of these two alternatives, in terms of recovery accuracy and computational time under different data missing rates, is investigated on a few structural vibration response data sets-the seismic responses of the super high-rise Canton Tower and the structural health monitoring accelerations of a real large-scale cable-stayed bridge. Encouraging results are obtained and the applicability and limitation of the presented methods are discussed. (C) 2015 E

关键词： Structural Health Monitoring Structural Dynamics Incomplete data data structure Sparse Representation Low-rank structure

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Configurable Open-source data structure for Distributed Conforming Unstructured Homogeneous Meshes with GPU Support

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ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE 2022年第3期48卷 1–30页

作者： Klinkovsky, Jakub Oberhuber, Tomas Fucik, Radek Zabka, Vitezslav Czech Tech Univ Fac Nucl Sci & Phys Engn Dept Math Trojanova 13 Prague 12000 2 Czech Republic

A general multi-purpose data structure for an efficient representation of conforming unstructured homogeneous meshes for scientific computations on CPU and GPU-based systems is presented. The data structure is provided as open-source software as part of the TNL library (https://***/). The abstract representation supports almost any cell shape and common 2D quadrilateral, 3D hexahedron and arbitrarily dimensional simplex shapes are currently built into the library. The implementation is highly configurable via templates of the C++ language, which allows avoiding the storage of unnecessary dynamic data. The internal memory layout is based on state-of-the-art sparse matrix storage formats, which are optimized for different hardware architectures in order to provide high-performance computations. The proposed data structure is also suitable for meshes decomposed into several subdomains and distributed computing using the Message Passing Interface (MPI). The efficiency of the implemented data structure on CPU and GPU hardware architectures is demonstrated on several benchmark problems and a comparison with another library. Its applicability to advanced numerical methods is demonstrated with an example problem of two-phase flow in porous media using a numerical scheme based on the mixed-hybrid finite element method (MHFEM). We show GPU speedups that rise above 20 in 2D and 50 in 3D when compared to sequential CPU computations, and above 2 in 2D and 9 in 3D when compared to 12-threaded CPU computations.

关键词： Unstructured mesh data structure GPGPU MPI performance evaluation

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Design and Development of a data structure Visualisation System Using the Ant Colony Algorithm

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RECENT ADVANCES IN ELECTRICAL & ELECTRONIC ENGINEERING 2023年第2期16卷 103-109页

作者： Li, Xiaojuan Khan, Mudassir Ansari, Mohd Dilshad Shijiazhuang Vocat Coll Ind & Commerce Shijiazhuang 050000 Hebei Peoples R China King Khalid Univ Dept Comp Sci Coll Sci & Arts Tanumah Abha Saudi Arabia CMR Coll Engn & Technol Hyderabad India

Aim: A data structure visualisation system uses object-oriented thinking and COM technology to dynamically and interactively simulate and track data structure algorithms and realize the dynamic synchronisation and visualisation of abstract data structures and algorithms using the data modelling function and self-test function. Background: Teaching data structures and algorithms is difficult because of their abstraction and dynamics;the use of icons in classroom teaching can be partially abstracted into intuition, but analysing the instantaneous dynamic characteristics of the object and the dynamic execution process of the algorithm is difficult. Objective: A data structure visualisation system employs a data modelling function, visual data structures, a user-friendly and flexible interface, and multipath features for multilevel users. Such systems can be designed more effectively by using the ant colony algorithm. Methods: The more the ants pass by a certain path, the higher the concentration of residual pheromone, and the higher the probability of the subsequent ant selecting that path. Therefore, the individuals in an ant colony communicate messages and cooperate with each other for foraging. Results: The resulting speedup ratio indicates that the speedup is smaller when the number of nodes is 100 or more;the acceleration is higher when the node reaches a certain scale, and the speedup ratio does not change considerably. In this study, the traffic simulation software VISSIM was used to generate road network data;the generated traffic data were analysed and used to design a traffic network data structure. Conclusion: The traffic network data model oriented to the ant colony algorithm was established through abstraction. Accordingly, a parallel ant colony algorithm based on cloud computing was implemented. Finally, a Hadoop cloud computing platform was established and used to run and test the parallel ant colony algorithm program;several experiments were conducted,

关键词： data structure object-oriented ant colony algorithm dynamic commentary structure

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A GENERAL data structure FOR IMAGE-ANALYSIS BASED ON A DESCRIPTION OF CONNECTED COMPONENTS

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COMPUTING 1989年第1期42卷 17-34页

作者： BARTNECK, N AEG Research Center Ulm Federal Republic of Germany

Transition from the iconic representation of a scene to be analyzed to a symbolic description of relevant primitives is an important step in many concepts for image analysis. A data structure is described consisting of connected regions and lines as most obvious kinds of primitive elements for representing images in a general symbolic form. Methods for creating such kind of description and possibilities for managing these data in an appropriate form are described exemplarily.

关键词： AMS Subject Classification: 68G10 connectivity analysis data structure Image analysis line approximation

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The importance of data structure in statistical analysis of dendritic spine morphology

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JOURNAL OF NEUROSCIENCE METHODS 2018年 296卷 93-98页

作者： Paternoster, Veerle Rajkumar, Anto P. Nyengaard, Jens Randel Borglum, Anders Dupont Grove, Jakob Christensen, Jane Hvarregaard Lundbeck Fdn Initiat Integrat Psychiat Res IPSYCH Copenhagen Denmark Aarhus Univ Ctr Integrat Sequencing ISEQ Aarhus Denmark Aarhus Univ Dept Clin Med Translat Neuropsychiat Unit Aarhus Denmark Aarhus Univ Dept Biomed Bartholins Alle 6 Aarhus Denmark Kings Coll London Inst Psychiat Psychol & Neurosci Dept Old Age Psychiat London England South London & Maudsley NHS Fdn Trust Mental Hlth Older Adults & Dementia Clin Acad Grp London England Aarhus Univ Hosp Ctr Stochast Geometry & Adv Bioimaging Dept Clin Med Stereol & Elect Microscopy Lab Aarhus Denmark Aarhus Univ Bioinformat Res Ctr BiRC Aarhus Denmark

Background: Dendritic spine morphology is heterogeneous and highly dynamic. To study the changing or aberrant morphology in test setups, often spines from several neurons from a few experimental units e.g. mice or primary neuronal cultures are measured. This strategy results in a multilevel data structure, which, when not properly addressed, has a high risk of producing false positive and false negative findings. Methods: We used mixed-effects models to deal with data with a multilevel data structure and compared this method to analyses at each level. We apply these statistical tests to a dataset of dendritic spine morphology parameters to illustrate advantages of multilevel mixed-effects model, and disadvantages of other models. Results: We present an application of mixed-effects models for analyzing dendritic spine morphology datasets while correcting for the data structure. Comparison with existing methods: We further show that analyses at spine level and aggregated levels do not adequately account for the data structure, and that they may lead to erroneous results. Conclusion: We highlight the importance of data structure in dendritic spine morphology analyses and highly recommend the use of mixed-effects models or other appropriate statistical methods to deal with multilevel datasets. Mixed-effects models are easy to use and superior to commonly used methods by including the data structure and the addition of other explanatory variables, for example sex, and age, etc., as well as interactions between variables or between variables and level identifiers. (C) 2018 Elsevier B.V. All rights reserved.

关键词： Dendritic spines Mixed-effects models Statistics and numerical data data structure

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Exploratory data structure comparisons: three new visual tools based on principal component analysis

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JOURNAL OF APPLIED STATISTICS 2021年第9期48卷 1675-1695页

作者： Petersen, Anne Helby Markussen, Bo Christensen, Karl Bang Univ Copenhagen Dept Publ Hlth Oster Farimagsgade 5 Copenhagen Denmark Univ Copenhagen Dept Math Sci Copenhagen Denmark

datasets are sometimes divided into distinct subsets, e.g. due to multi-center sampling, or to variations in instruments, questionnaire item ordering or mode of administration, and the data analyst then needs to assess whether a joint analysis is meaningful. The Principal Component Analysis-based data structure Comparisons (PCADSC) tools are three new non-parametric, visual diagnostic tools for investigating differences in structure for two subsets of a dataset through covariance matrix comparisons by use of principal component analysis. The PCADCS tools are demonstrated in a data example using European Social Survey data on psychological well-being in three countries, Denmark, Sweden, and Bulgaria. The data structures are found to be different in Denmark and Bulgaria, and thus a comparison of for example mean psychological well-being scores is not meaningful. However, when comparing Denmark and Sweden, very similar data structures, and thus comparable concepts of well-being, are found. Therefore, inter-country comparisons are warranted for these countries.

关键词： Principal component analysis exploratory data analysis covariance matrix data structure

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