A new technique, called the polymerization algorithm, is described for the hierarchical segmentation of polymerized volume data sets (PVDS) using the Lblock data structure. The Lblock data structure is defined as a 3dimensional isorectangular block of enhanced vertex information. Segmentation of the PVDS is attained by intersecting and merging Lblock coverings of the enhanced volumetric data. The data structure allows for easy compression, storage, segmentation, and reconstruction of volumetric data obtained from scanning a mammalian brain at submicron resolution, using threedimensional light microscopy (knifeedge scanning microscopy (KESM), confocal microscopy (CFM), and multiphoton microscopy (MPM)). A hybrid technique using the polymerization algorithm and an existing vectorbased tracing algorithm is developed. Both the polymerized and the hybrid algorithm have been tested and their analyzed results are presented.

The goals of this research include developing and identifying software technologies, which facilitate the use of buildings described in Building Information Modeling (BIM) tools in both a simulation and visualization. The study focused on the development of a tool to fulfill the visualization needs of a Visual Energy Use System. To accomplish this, the study identified an open BIM file standard, the Industry Foundation Classes (IFC). The study also identified a video game based 3D virtual environment, the Doom 3 Engine. A tool developed during the study, IFCtoMAP, converts IFC data into the .MAP file format understood by the Doom 3 Engine. Finally, the study identified the IFCtoIDF utility, which translates IFC data into a format understood by the building energy simulation program EnergyPlus. Data from the Building Information Modeling tool Revit Building exports to the .IFC file format, which in turn drives the two conversion utilities IFCtoMAP and IFCtoIDF. The output of the IFCtoIDF tool consists of an .IDF file that EnergyPlus uses to perform an energy simulation. The output of the IFCtoMAP tool consists of a .MAP file, which the Doom 3 game engine uses to display three dimensional first person perspective visualization. The result of the study was the successful creation of an automated tool that converts building geometry found in .IFC files into the .MAP file format understood by Doom 3 game engine. This document details the methods employed by the IFCtoMAP software along with a brief discussion of the IFCtoIDF conversion utility.

In visualization problems, surface shape is often a piece of data that must be shown effectively. One factor that strongly affects shape perception is texture. For example, patterns of texture on a surface can show the surface orientation from foreshortening or compression of the texture marks, and surface depth through size variation from perspective projection. However, texture is generally under-used in the scientific visualization community. The benefits of using texture on single surfaces also apply to layered surfaces. Layering of multiple surfaces in a single viewpoint allows direct comparison of surface shape. The studies presented in this dissertation aim to find optimal methods for texturing of both single and layered surfaces. This line of research starts with open, many-parameter experiments using human subjects to find what factors are important for optimal texturing of layered surfaces. These experiments showed that texture shape parameters are very important, and that texture brightness is critical so that shading cues are available. Also, the optimal textures seem to be task dependent; a feature finding task needed relatively little texture information, but more shape-dependent tasks needed stronger texture cues. In visualization problems, surface shape is often a piece of data that must be shown effectively. One factor that strongly affects shape perception is texture. For example, patterns of texture on a surface can show the surface orientation from foreshortening or compression of the texture marks, and surface depth through size variation from perspective projection. However, texture is generally under-used in the scientific visualization community. The benefits of using texture on single surfaces also apply to layered surfaces. Layering of multiple surfaces in a single viewpoint allows direct comparison of surface shape. The studies presented in this dissertation aim to find optimal methods for texturing of both single and layered surfaces. This line of research starts with open, many-parameter experiments using human subjects to find what factors are important for optimal texturing of layered surfaces. These experiments showed that texture shape parameters are very important, and that texture brightness is critical so that shading cues are available. Also, the optimal textures seem to be task dependent; a feature finding task needed relatively little texture information, but more shape-dependent tasks needed stronger texture cues.

Very large sets of multi-source, multi-dimensional and time varying data are generated during the execution of construction projects, especially large-scale infrastructure projects. Emphasized in this thesis is how data visualization can provide important insights during the planning, implementation and post project analysis phases of linear projects in an urban environment, which are attended by a complex working environment and multiple stakeholders. These insights can lead to enhanced communication and better decision making. Thesis objectives are four fold: (i) examine how the representation of a schedule using linear planning charts can assist with assessing the quality of a schedule in terms of the construction strategy, communicate schedule intent to projects participants, and assist with telling the as-built story; (ii) explore images useful for representing multi source, multi-dimensional, time varying as-built construction data in support of management functions specifically with regards to communication and decision making; (iii) demonstrate the ability of visual representations of construction data to assist in telling the as-built story of a project in a manner that provides useful insights to project participants; and, (iv) critique the images presented in light of the data visualization principles and interaction tools identified, and suggest improvements as appropriate and possibly other images, including properties desired. In addressing these objectives, the methodology involved a review of computer science and construction literature as it pertains to data visualization and a case study of a past project which reflected the scale and complexity of planning and executing linear projects in an urban environment. The planned and as-built story were captured from the available data depicting the contractor’s perspective in the project’s product, process, and as-built views which were replicated in a research software system called REPCON software. This system supports selected data visualization capabilities, which were examined and critiqued as part of this thesis. It is demonstrated that data visualization is a powerful paradigm for gaining insights into the quality of a project’s plan and for understanding a project’s as-built performance. Greater benefits could be achieved by exploiting cutting edge visualization tools and by designing and implementing a more comprehensive set of images.

This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\'s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality.

Code duplication, or code cloning, is a common phenomena in the development of large software systems. Developers have a love-hate relationship with cloning. On one hand, cloning speeds up the development process. On the other hand, clone management is a challenging task as software evolves. Cloning has commonly been considered as undesirable for software maintenance and several research efforts have been devoted to automatically detect clones and eliminate clones aggressively. However, there is little empirical work done to analyze the consequences of cloning with respect to the software quality. Recent studies show that cloning is not necessarily undesirable. Cloning can used to minimize risks and there are cases where cloning is used as a design technique. In this thesis, three visualization techniques are proposed to aid researchers in analyzing cloning in studying large software systems. All of the visualizations abstract and display cloning information at the subsystem level but with different emphases. At the subsystem level, clones can be classified as external clones and internal clones. External clones refer to code duplicates that reside in the same subsystem, whereas external clones are clones that are spread across different subsystems. Software architecture quality attributes such as cohesion and coupling are introduced to contribute to the study of cloning at the architecture level. The Clone Cohesion and Coupling (CCC) Graph and the Clone System Hierarchy (CSH) Graph display the cloning information for one single release. In particular, the CCC Graph highlights the amount of internal and external cloning for each subsystems; whereas the CSH Graph focuses more on the details of the spread of cloning. Finally, the Clone System Evolution (CSE) Graph shows the evolution of cloning over a period of time.

This study examined the use of computer visualizations in urban planning and whether they facilitate effective decision-making and communication within community engagement. The objective was to determine the potential for the human element in the visualization process to impact the public’s evaluations of a future landscape. A response equivalence experiment was performed that compared evaluations based on actual urban landscapes to those based on accurately prepared, as well as intentionally persuasive, visualizations of the same landscapes. To ensure the persuasive visualizations assessed were akin to those used in practice an investigation of procedures and professional attitudes regarding visualization use was carried out, including surveys of municipal planning departments and key-informant interviews with visualization preparers. Results from the response equivalence analysis show that a visualization preparer can positively influence preferences for an urban park or mixed use streetscape by using subtle techniques that enhance the aesthetic appearance of the virtual environment. These same techniques also have a considerable impact on aspects of landscape perception such as maintenance, safety, social inclusiveness and place identity. Findings indicate that qualitative instruments are necessary for measuring response equivalence as social aspects of landscape perception are important to the validity of simulations. Finally, it is argued that the current context of visualization use in planning practice is a threat to legitimate public engagement and the health of stakeholder relationships. A two pronged approach to effective visualization use is proposed, suggesting equal emphasis on changing professional attitudes toward the technology and creating a public with a deeper understanding of the visualization process.

Simulation plays a key role in the computer-aided design of systems, primarily because it helps in catching design bugs at an early stage and in quickly ruling out many unreasonable options in the design space. There is a wealth of tools and languages that have been proposed over the years for the design and verification of hybrid systems and most of them provide 3D visualization utility for facilitating design process. However, their visualization systems often rely on some external configuration files written in naive 3D APIs like VRML or Java3D and complicated connections have to be established between the simulation data and the visualization. Numerous efforts have to be invested in visualization related modeling and certain level of understanding of the low level 3D libraries are needed. Thus it is not an easy job for non-professions to build a 3D visualization. In this thesis we explore the idea that in a hybrid system model, almost all the information need for visualization is already in place. This means that very few annotation should be enough to fully specify a useful 3D visualization. Based on this idea, we propose a lightweight 3D visualization framework which allows the user to expresses the three-dimensional object in a high level and abstract way and to take advantage of the data already in the simulation. We evaluate our approaching by building a prototype extension of modeling language called Acumen. The result of this thesis work is included in Acumen's official release version that can be download at www.acumen-language.org. To build a 3D visualization in Acumen, only very few annotations need to be added to the simulation model and are included inside one reserved variable. Non-professions like students who are studying Cyber-physical systems can easily use this tool to visualize their models in Acumen without any prerequisite knowledge regarding 3D visualization technology. We also developed a number of benchmarks to test the correctness and functionality of Acumen3D. Besides, as a lager case study into the expressivity of Acumen and its visualizaiton efficiency, we developed a simplified model of a Ping Pong game. We gained experience about how to model complex hybrid system in Acumen. Moreover by comparing modeling such a hybrid system in Java3D and in Acumen3D, we find concrete evidence that modelling it in Acumen3D is easier in that of less code and less prerequisite knowledge and more supporting built in functions.

Code duplication, or code cloning, is a common phenomena in the development of large software systems. Developers have a love-hate relationship with cloning. On one hand, cloning speeds up the development process. On the other hand, clone management is a challenging task as software evolves. Cloning has commonly been considered as undesirable for software maintenance and several research efforts have been devoted to automatically detect clones and eliminate clones aggressively. However, there is little empirical work done to analyze the consequences of cloning with respect to the software quality. Recent studies show that cloning is not necessarily undesirable. Cloning can used to minimize risks and there are cases where cloning is used as a design technique. In this thesis, three visualization techniques are proposed to aid researchers in analyzing cloning in studying large software systems. All of the visualizations abstract and display cloning information at the subsystem level but with different emphases. At the subsystem level, clones can be classified as external clones and internal clones. External clones refer to code duplicates that reside in the same subsystem, whereas external clones are clones that are spread across different subsystems. Software architecture quality attributes such as cohesion and coupling are introduced to contribute to the study of cloning at the architecture level. The Clone Cohesion and Coupling (CCC) Graph and the Clone System Hierarchy (CSH) Graph display the cloning information for one single release. In particular, the CCC Graph highlights the amount of internal and external cloning for each subsystems; whereas the CSH Graph focuses more on the details of the spread of cloning. Finally, the Clone System Evolution (CSE) Graph shows the evolution of cloning over a period of time.

This study examined the use of computer visualizations in urban planning and whether they facilitate effective decision-making and communication within community engagement. The objective was to determine the potential for the human element in the visualization process to impact the public’s evaluations of a future landscape. A response equivalence experiment was performed that compared evaluations based on actual urban landscapes to those based on accurately prepared, as well as intentionally persuasive, visualizations of the same landscapes. To ensure the persuasive visualizations assessed were akin to those used in practice an investigation of procedures and professional attitudes regarding visualization use was carried out, including surveys of municipal planning departments and key-informant interviews with visualization preparers. Results from the response equivalence analysis show that a visualization preparer can positively influence preferences for an urban park or mixed use streetscape by using subtle techniques that enhance the aesthetic appearance of the virtual environment. These same techniques also have a considerable impact on aspects of landscape perception such as maintenance, safety, social inclusiveness and place identity. Findings indicate that qualitative instruments are necessary for measuring response equivalence as social aspects of landscape perception are important to the validity of simulations. Finally, it is argued that the current context of visualization use in planning practice is a threat to legitimate public engagement and the health of stakeholder relationships. A two pronged approach to effective visualization use is proposed, suggesting equal emphasis on changing professional attitudes toward the technology and creating a public with a deeper understanding of the visualization process.