Browsing by Subject "Visualization."
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Item Open Access 3D mesh animation system targeted for multi-touch environments(2009) Ceylan, DuyguFast developments in computer technology have given rise to different application areas such as multimedia, computer games, and Virtual Reality. All these application areas are based on animation of 3D models of real world objects. For this purpose, many tools have been developed to enable computer modeling and animation. Yet, most of these tools require a certain amount of experience about geometric modeling and animation principles, which creates a handicap for inexperienced users. This thesis introduces a solution to this problem by presenting a mesh animation system targeted specially for novice users. The main approach is based on one of the fundamental model representation concepts, Laplacian framework, which is successfully used in model editing applications. The solution presented perceives a model as a combination of smaller salient parts and uses the Laplacian framework to allow these parts to be manipulated simultaneously to produce a sense of movement. The interaction techniques developed enable users to carry manipulation and global transformation actions at the same time to create more pleasing results. Furthermore, the approach utilizes the multi-touch screen technology and direct manipulation principles to increase the usability of the system. The methods described are experimented by creating simple animations with several 3D models; which demonstrates the advantages of the proposed solution.Item Open Access Animated mesh simplification based on saliency metrics(2008) Tolgay, AhmetMesh saliency identifies the visually important parts of a mesh. Mesh simplification algorithms using mesh saliency as simplification criterion preserve the salient features of a static 3D model. In this thesis, we propose a saliency measure that will be used to simplify animated 3D models. This saliency measure uses the acceleration and deceleration information about a dynamic 3D mesh in addition to the saliency information for static meshes. This provides the preservation of sharp features and visually important cues during animation. Since oscillating motions are also important in determining saliency, we propose a technique to detect oscillating motions and incorporate it into the saliency based animated model simplification algorithm. The proposed technique is experimented on animated models making oscillating motions and promising visual results are obtained.Item Open Access Chisio : a visual framework for compound graph editing and layout(2007) Küçükkeçeci, CihanGraphs are data models, widely used in many areas from networking to biology to computer science. Visualization, interactive editing ability and layout of graphs are critical issues when analyzing the underlying relational information. There are many commercial and non-commercial graph visualization tools. However, overall support for compound or hierarchically organized graph representations is very limited. We introduce a new open-source editing and layout framework named Chisio for compound graphs. Chisio is developed as a free, easy-to-use and powerful academic graph visualization tool, supporting various automatic layout algorithms. It is written in Java and based on Eclipse’s Graphical Editing Framework (GEF). Chisio can be used as a finished generic compound graph editor with standard graph editing facilities such as zoom, scroll, add or remove graph objects, move, and resize. Object property and layout options dialogs are provided to modify existing graph object properties and layout options, respectively. In addition, printing or saving the current drawing as a static image and persistent storage facilities are supported. Saved graphs or GraphML formatted files created by other tools can be loaded into Chisio. Furthermore, a highlight mechanism is provided to emphasize subgraphs of users interest. The framework has an architecture suitable for easy customization of the tool for end-users’ specific needs as well. Also Chisio offers several layout styles from the basic spring embedder to hierarchical layout to compound spring embedder to circular layout. Furthermore, new algorithms are straightforward to add, making Chisio an ideal test environment for layout algorithm developers.Item Open Access Chisio Web : a web-based framework for customizable visualization of relational information(2012) Sümer, Selçuk OnurGraphs are widely used to represent complex relational information. Graph visualization is crucial for effective analysis of information. In simple graphs, nodes are generally considered as uniform-sized components and they cannot be nested. This is often not sufficient to visualize complex relationships, because relational information is often clustered or hierarchically organized into groups or nested structures. There exist many free, open source software in the field of web-based graph visualization. However, none fully supports compound or clustered graphs. Moreover, customization provided by such software is often limited to the basic visual properties of nodes and edges. It requires a lot of effort to build an advanced customization of visual properties and interactive functionality with these software. In this thesis, we introduce a free, open source, general-purpose, web-based graph visualization framework, named Chisio Web (ChiWeb). ChiWeb supports visualization, interactive editing and layout of both simple and compound graphs. ChiWeb is implemented in ActionScript language and based on Flare, which is an open source ActionScript library designed for data visualization. ChiWeb is specifically designed for easy customization with respect to visualization and functionality. ChiWeb can be used as a library to create a custom graph visualization with an advanced application behavior for particular needs of a specific domain. The elements and functionality that can be easily customized with ChiWeb are: visual styles, controls for interactive events such as node creation, key and mouse functionality, context menus, toolbars, and inspector windows. Furthermore, ChiWeb’s architecture allows easy integration of new graph layout algorithms.Item Open Access A circular layout algorithm for clustered graphs(2009) Belviranlı, Mehmet EsatVisualization of information is essential for comprehension and analysis of the acquired data in any field of study. Graph layout is an important problem in information visualization and plays a crucial role in the drawing of graph-based data. There are many styles and ways to draw a graph depending on the type of the data. Clustered graph visualization is one popular aspect of the graph layout problem and there have been many studies on it. However, only a few of them focus on using circular layout to represent clusters. We present a new, elegant algorithm for layout of clustered graphs using a circular style. The algorithm is based on traditional force-directed layout scheme and uses circles to draw each cluster in the graph. In addition it can handle non-uniform node dimensions. It is the first algorithm to properly address layout of the quotient graph while considering inter-cluster relations as well as intra-cluster edge crossings. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has been successfully implemented as part of Chisio, version 1.1. Chisio is an open source general purpose graph editor developed by i-Vis (information visualization) Research Group of Bilkent University.Item Open Access An improved spring embedder layout algorithm for compound graphs(2012) Karaçelik, AlperInteractive graph editing plays an important role in information visualization systems. For qualified analysis of the given data, an automated layout calculation is needed. There have been numerous results published about automatic layout of simple graphs, where the vertices are depicted as points in a 2D or 3D plane and edges as straight lines connecting those points. But simple graphs are insufficient to cover most real life information. Relational information is often clustered or hierarchically organized into groups or nested structures. Compound spring embedder (CoSE) of Chisio project is a layout algorithm based on a force-directed layout scheme for undirected, non-uniform node sized compound graphs. In order to satisfy the end-user, layout calculation process has to finish fast, and the resulting layout should be eye pleasing. Therefore, several methods were developed for improving both running time and the visual quality of the layout. With the purpose of improving the visual quality of CoSE, we adapted a multi-level scaling strategy. For improving the performance of the CoSE, the grid-variant algorithm proposed by Fruchterman and Reingold and parallel force calculation strategy by using graphics processing unit (GPU) were also adopted. Additionally, tuning of the parameters like spring constant and cooling factor were considered, as they affect the behavior of the physical system dramatically. Our experiments show that after some tuning and adaptation of the methods above, running time decreased and the visual quality of the layout improved significantly.Item Open Access Integrating biological pathways and genomic profiles with ChiBE 2(2013) Çakır, MerveBiological pathways store information about spatial and temporal organization of interactions taking place in an organism. They hold valuable information that can assist scientific community in understanding the details of a particular mechanism or deciphering the reasons of disruption when the system goes wrong. However, extracting knowledge from these pathways is not trivial as they can be huge and complicated. Additionally, simple visualization of pathways will only reveal limited knowledge, whereas their integration with experimental results can identify distinct and intriguing relationships. Therefore, it is critical to have tools that are specialized in analyzing and understanding biological pathways. ChiBE is one such tool that can visualize, manipulate and analyze pathway data stored in BioPAX format. While preparing the second version of the tool, there have been improvements regarding pathway searches, high throughput data integration, and database connections. Visual notation has also been updated in order to follow standards in visualizations defined by the SBGN community. Previously defined pathway query algorithms have been adapted to be compatible with the BioPAX model. New query types have also been designed to offer a wider range of options. With these queries, ChiBE now offers a variety of ways of pathway decomposition and thorough analysis of complex pathway views. There has also been improvements in integration of high throughput experimental results. To offer easy access to expression microarrays, a gateway to the GEO database has been added. The cBio Cancer Genomics Portal is also now reachable within ChiBE in order to obtain information about genomic status of various cancer cells. After simply asking for an identifier of a particular experiment, ChiBE retrieves the results from databases and then integrates them with the available pathway view through color codes. Furthermore, a connection to DAVID database is available, in case users want to annotate a list of genes with respect to biological terms associated with them. With these new features and improvements, ChiBE 2 has become a comprehensive tool that offers a wide range of analysis options with a genomics-oriented workflow to deepen our understanding of biological pathways.Item Open Access Model-based camera tracking for augmented reality(2014) Aman, AytekAugmented reality (AR) is the enhancement of real scenes with virtual entities. It is used to enhance user experience and interaction in various ways. Educational applications, architectural visualizations, military training scenarios and pure entertainment-based applications are often enhanced by augmented reality to provide more immersive and interactive experience for the users. With hand-held devices getting more powerful and cheap, such applications are becoming very popular. To provide natural AR experiences, extrinsic camera parameters (position and rotation) must be calculated in an accurate, robust and efficient way so that virtual entities can be overlaid onto the real environments correctly. Estimating extrinsic camera parameters in real-time is a challenging task. In most camera tracking frameworks, visual tracking serve as the main method for estimating the camera pose. In visual tracking systems, keypoint and edge features are often used for pose estimation. For rich-textured environments, keypoint-based methods work quite well and heavily used. Edge-based tracking, on the other hand, is more preferable when the environment is rich in geometry but has little or no visible texture. Pose estimation for edge based tracking systems generally depends on the control points that are assigned on the model edges. For accurate tracking, visibility of these control points must be determined in a correct manner. Control point visibility determination is computationally expensive process. We propose a method to reduce computational cost of the edge-based tracking by preprocessing the visibility information of the control points. For that purpose, we use persistent control points which are generated in the world space during preprocessing step. Additionally, we use more accurate adaptive projection algorithm for persistent control points to provide more uniform control point distribution in the screen space. We test our camera tracker in different environments to show the effectiveness and performance of the proposed algorithm. The preprocessed visibility information enables constant time calculations of control point visibility while preserving the accuracy of the tracker. We demonstrate a sample AR application with user interaction to present our AR framework, which is developed for a commercially available and widely used game engine.Item Open Access Perceptually driven stereoscopic camera control in 3D virtual environments(2013) Kevinç, Elif BengüDepth notion and how to perceive depth have long been studied in the eld of psychology, physiology, and even art. Human visual perception enables to perceive spatial layout of the outside world by using visual depth cues. Binocular disparity among these depth cues, is based on the separation between two di erent views that are observed by two eyes. Disparity concept constitutes the base of the construction of the stereoscopic vision. Emerging technologies try to replicate binocular disparity principles in order to provide 3D illusion and stereoscopic vision. However, the complexity of applying the underlying principles of 3D perception, confronted researchers the problem of wrongly produced stereoscopic contents. It is still a great challenge to give realistic but also comfortable 3D experience. In this work, we present a camera control mechanism: a novel approach for disparity control and a model for path generation. We try to address the challenges of stereoscopic 3D production by presenting comfortable viewing experience to users. Therefore, our disparity system approaches the accommodation/convergence con- ict problem, which is the most known issue that causes visual fatigue in stereo systems, by taking objects' importance into consideration. Stereo camera parameters are calculated automatically with an optimization process. In the second part of our control mechanism, the camera path is constructed for a given 3D environment and scene elements. Moving around important regions of objects is a desired scene exploration task. In this respect, object saliencies are used for viewpoint selection around scene elements. Path structure is generated by using linked B ezier curves which assures to pass through pre-determined viewpoints. Though there is considerable amount of research found in the eld of stereo creation, we believe that approaching this problem from scene content aspect provides a uniquely promising experience. We validate our assumption with user studies in which our method and existing two other disparity control models are compared. The study results show that our method shows superior results in quality, depth, and comfort.Item Open Access Representation, editing and real-time visualization of complex 3D terrains(2012) Koca, ÇetinTerrain rendering is a crucial part of many real-time computer graphics applications such as video games and visual simulations. It provides the main frame-ofreference for the observer and constitutes the basis of an imaginary or simulated world that encases the observer. Storing and rendering terrain models in real-time applications usually require a specialized approach due to the sheer magnitude of data available and the level of detail demanded. The easiest way to process and visualize such large amounts of data in real-time is to constrain the terrain model in several ways. This process of regularization decreases the amount of data to be processed and also the amount of processing power needed at the cost of expressivity and the ability to create interesting terrains. The most popular terrain representation, by far, used by modern real-time graphics applications is a regular 2D grid where the vertices are displaced in a third dimension by a displacement map, conventionally called a height map. It is the simplest and fastest possible terrain representation, but it is not possible to represent complex terrain models that include interesting terrain features such as caves, overhangs, cliffs and arches using a simple 2D grid and a height map. We propose a novel terrain representation combining the voxel and height map approaches that is expressive enough to allow creating complex terrains with caves, overhangs, cliffs and arches, and efficient enough to allow terrain editing, deformations and rendering in real-time. We also explore how to apply lighting, texturing, shadowing and level-of-detail to the proposed terrain representation.Item Open Access A three-dimensional nonlinear finite element method implementation toward surgery simulation(2011) Gülümser, EmirFinite Element Method (FEM) is a widely used numerical technique for finding approximate solutions to the complex problems of engineering and mathematical physics that cannot be solved with analytical methods. In most of the applications that require simulation to be fast, linear FEM is widely used. Linear FEM works with a high degree of accuracy with small deformations. However, linear FEM fails in accuracy when large deformations are used. Therefore, nonlinear FEM is the suitable method for crucial applications like surgical simulators. In this thesis, we propose a new formulation and finite element solution to the nonlinear 3D elasticity theory. Nonlinear stiffness matrices are constructed by using the Green-Lagrange strains (large deformation), which are derived directly from the infinitesimal strains (small deformation) by adding the nonlinear terms that are discarded in infinitesimal strain theory. The proposed solution is a more comprehensible nonlinear FEM for those who have knowledge about linear FEM since the proposed method directly derived from the infinitesimal strains. We implemented both linear and nonlinear FEM by using same material properties with the same tetrahedral elements to examine the advantages of nonlinear FEM over the linear FEM. In our experiments, it is shown that nonlinear FEM gives more accurate results when compared to linear FEM when rotations and high external forces are involved. Moreover, the proposed nonlinear solution achieved significant speed-ups for the calculation of stiffness matrices and for the solution of a system as a whole.Item Open Access VISIBIOweb : a web-based visualization and layout service for biological pathways(2009) Dilek, AlptuğA biological pathway is a representation of biological reactions between molecules in a living cell. At present, there are hundreds of Internet-accessible databases storing biological pathway data. Exchanging, handling, and storing this data are crucial in terms of both providing understandability and allowing further enhancements on the gathered data. As a result of this necessity, many biological models were developed to cluster the data in a meaningful manner under a semantically reasonable hierarchy. As the amount and complexity of the data increases, visualization of pathways becomes inevitable. Graphs are inherently suitable for modeling pathways. The task of creating a visual representation for pathways dynamically requires methods from the area of graph visualization. As a result, many software systems, which can interpret the pathway data with a graph structure and visualize the constructed graph, emerged. However, many of these software systems are insufficient due to poor complexity handling of the underlying model, lack of visual standardization or long installation steps. In this thesis, we introduce VISIBIOweb, a new open-source and web-based visualization service for biological pathway models stored in BioPAX (Biological Pathways Exchange Language) format. VISIBIOweb runs on Apache Tomcat server and is implemented in Java based on Eclipse GEF (Graphical Editing Framework). Google Maps API is used on the client side as the core component to visualize the representation constructed on the server. VISIBIOweb supports basic graph viewing functionalities such as zooming, scrolling, and selection of graph objects. The inspector window is provided to view the properties of the selected graph object. Once the view for the uploaded biological model is created, it can be stored as a static image. The biological models can also be persisted and embedded within other web sites just like Google Maps. The layout information of the constructed graph is also provided in an XML-based format. The introduction of such a format is a good starting point to develop an official layout extension for BioPAX format.Item Open Access Visualization of urban environments(2007) Yılmaz, TürkerModeling and visualization of large geometric environments is a popular research area in computer graphics. In this dissertation, a framework for modeling and stereoscopic visualization of large and complex urban environments is presented. The occlusion culling and view-frustum culling is performed to eliminate most of the geometry that do not contribute to the user’s final view. For the occlusion culling process, the shrinking method is employed but performed using a novel Minkowski-difference-based approach. In order to represent partial visibility, a novel building representation method, called the slice-wise representation is developed. This method is able to represent the preprocessed partial visibility with huge reductions in the storage requirement. The resultant visibility list is rendered using a graphics-processing-unit-based algorithm, which perfectly fits into the proposed slice-wise representation. The stereoscopic visualization depends on the calculated eye positions during walkthrough and the visibility lists for both eyes are determined using the preprocessed occlusion information. The view-frustum culling operation is performed once instead of two for both eyes. The proposed algorithms were implemented on personal computers. Performance experiments show that, the proposed occlusion culling method and the usage of the slice-wise representation increase the frame rate performance by 81 %; the graphics-processing-unit-based display algorithm increases it by an additional 315 % and decrease the storage requirement by 97 % as compared to occlusion culling using building-level granularity and not using the graphics hardware. We show that, a smooth and real-time visualization of large and complex urban environments can be achieved by using the proposed framework.Item Open Access Volumetric rendering techniques for scientific visualization(2014) Okuyan, ErhanDirect volume rendering is widely used in many applications where the inside of a transparent or a partially transparent material should be visualized. We have explored several aspects of the problem. First, we proposed a view-dependent selective refinement scheme in order to reduce the high computational requirements without affecting the image quality significantly. Then, we explored the parallel implementations of direct volume rendering: both on GPU and on multi-core systems. Finally, we used direct volume rendering approaches to create a tool, MaterialVis, to visualize amorphous and/or crystalline materials. Visualization of large volumetric datasets has always been an important problem. Due to the high computational requirements of volume-rendering techniques, achieving interactive rates is a real challenge. We present a selective refinement scheme that dynamically refines the mesh according to the camera parameters. This scheme automatically determines the impact of different parts of the mesh on the output image and refines the mesh accordingly, without needing any user input. The viewdependent refinement scheme uses a progressive mesh representation that is based on an edge collapse-based tetrahedral mesh simplification algorithm. We tested our view-dependent refinement framework on an existing state-of-the-art volume renderer. Thanks to low overhead dynamic view-dependent refinement, we achieve interactive frame rates for rendering common datasets at decent image resolutions. Achieving interactive rates for direct volume rendering of large unstructured volumetric grids is a challenging problem, but parallelizing direct volume rendering algorithms can help achieve this goal. Using Compute Unified Device Architecture (CUDA), we propose a GPU-based volume rendering algorithm that itself is based on a cell projection-based ray-casting algorithm designed for CPU implementations. We also propose a multi-core parallelized version of the cell-projection algorithm using OpenMP. In both algorithms, we favor image quality over rendering speed. Our algorithm has a low memory footprint, allowing us to render large datasets. Our algorithm support progressive rendering. We compared the GPU implementation with the serial and multi-core implementations. We observed significant speed-ups, that, together with progressive rendering, enabling reaching interactive rates for large datasets. Visualization of materials is an indispensable part of their structural analysis. We developed a visualization tool for amorphous as well as crystalline structures, called MaterialVis. Unlike the existing tools, MaterialVis represents material structures as a volume and a surface manifold, in addition to plain atomic coordinates. Both amorphous and crystalline structures exhibit topological features as well as various defects. MaterialVis provides a wide range of functionality to visualize such topological structures and crystal defects interactively. Direct volume rendering techniques are used to visualize the volumetric features of materials, such as crystal defects, which are responsible for the distinct fingerprints of a specific sample. In addition, the tool provides surface visualization to extract hidden topological features within the material. Together with the rich set of parameters and options to control the visualization, MaterialVis allows users to visualize various aspects of materials very efficiently as generated by modern analytical techniques such as the Atom Probe Tomography.