Browsing by Subject "Visualization"
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Item Open Access Augmenting bus factor analysis with visualization(2024-01) Ahmed, Muhammad Umair‘Bus factor’, also known as ‘truck factor’, is a measure of how vulnerable a software project is based on the minimum number of people who would have to leave the project (be ‘hit by a bus’) for it to stall. There is existing research on how to calculate bus factor for software projects but limited work on visualizing the bus factor. We believe providing visualization along with conventionally provided numerical bus factor results will help decision-makers manage the workload and knowledge distribution across the project and also help in planning and hiring decisions. This thesis proposes, implements, and evaluates a tool named BFViz to visualize bus factor and contributions for software projects from pre-processed Git history. It is a web application that provides a file-browser-like interface with an interactively navigable treemap. Additionally, it has filename-based filtering, individual contribution data for files and folders, and simulation of contributor departure. The tool is validated with a round of four user evaluations where users, ranging from project owners and engineering managers to developers, complete tasks using the tool on an open-source project that they are involved in and provide feedback with a semi-structured interview and a feature ranking activity. The overall task completion rate for the tasks was 79.55%. All case study participants preferred BFViz over text reports to understand bus factor data. The top three features, by mean ranking, were the contributors’ list, the files and folders’ visualization, and the simulation mode.Item Open Access BilKristal 4.0: A tool for crystal parameters extraction and defect quantification(Elsevier, 2015) Okuyan, E.; Okuyan, C.In this paper, we present a revised version of BilKristal 3.0 tool. Raycast screenshot functionality is added to provide improved visual analysis. We added atomic distance analysis functionality to assess crystalline defects. We improved visualization capabilities by adding high level cut function definitions. Discovered bugs are fixed and small performance optimizations are made. © 2015 Elsevier B.V. All rights reserved.Item Open Access Bina tahsis planlarından 3-boyutlu şehir modellerinin üretilmesi ve görüntülenmesi(IEEE, 2006-04) Oǧuz, Oğuzcan; Aran, Medeni Erol; Yilmaz, Türker; Güdükbay, UğurThis paper presents a method for the automatic generation of different building models to be used to populate virtual cities and a system of visualization of generated city models. The proposed method incorporates randomness but the derivation process could be steered by the help of derivation rules and assigned attributes. The derivation method is inspired by the shape grammars. During the derivation process, the floor plans of the actual cities are used to generate 3D city models. Given the city plans, the derivation rules and definitions of some basic nesnects, the system generates 3D building models and the generated city model could be visualized. © 2006 IEEE.Item Open Access The BioPAX community standard for pathway data sharing(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.Item Open Access Combined filtering and key-frame reduction of motion capture data with application to 3DTV(WSCG, 2006-01-02) Önder, Onur; Erdem, Ç.; Erdem, T.; Güdükbay, Uğur; Özgüç, BülentA new method for combined filtering and key-frame reduction of motion capture data is proposed. Filtering of motion capture data is necessary to eliminate any jitter introduced by a motion capture system. Key-frame reduction, on the other hand, allows animators to easily edit motion data by representing animation curves with a significantly smaller number of key frames. The proposed technique achieves key frame reduction and jitter removal simultaneously by fitting a Hermite curve to motion capture data using dynamic programming. Copyright © UNION Agency - Science Press.Item Open Access Effect of sample locations on computation of the exact scalar diffraction field (in English)(IEEE, 2012) Esmer, G. B.; Özaktaş, Haldun M.; Onural, LeventComputer generated holography is one of common methods to obtain three-dimensional visualization. It can be explained by behavior of propagating waves and interference. To calculate the scalar diffraction pattern on a hologram, there are myriad of algorithms in the literature. Some of them employ several approximations, so the calculated fields may not be the exact scalar diffraction field. However, there are algorithms to compute the exact scalar diffraction field with some limitations on the distribution of the given samples over the space. These algorithms are based on "field model" approach. The performance of an algorithm, based on field model, is investigated according to the distribution of given samples over the space. From the simulations, it was observed that the cumulative information provided by the given samples has to be enough to solve the inverse scalar diffraction field. The cumulative information can be increased by having more samples, but there are some scenarios that differential information obtained from the given samples can be infinitesimal, thus the exact diffraction field may not be computed. © 2012 IEEE.Item Open Access Extraction of 3D navigation space in virtual urban environments(IEEE, 2005-09) Yılmaz, Türker; Güdükbay, UğurUrban scenes are one class of complex geometrical environments in computer graphics. In order to develop navigation systems for urban sceneries, extraction and cellulization of navigation space is one of the most commonly used technique providing a suitable structure for visibility computations. Surprisingly, there is not much work done for the extraction of the navigable area automatically. Urban models, except for the ones where the building footprints are used to generate the model, generally lack navigation space information. Because of this, it is hard to extract and discretize the navigable area for complex urban scenery. In this paper, we propose an algorithm for the extraction of navigation space for urban scenes in threedimensions (3D). Our navigation space extraction algorithm works for scenes, where the buildings are in high complexity. The building models may have pillars or holes where seeing through them is also possible. Besides, for the urban data acquired from different sources which may contain errors, our approach provides a simple and efficient way of discretizing both navigable space and the model itself. The extracted space can instantly be used for visibility calculations such as occlusion culling in 3D space. Furthermore, terrain height field information can be extracted from the resultant structure, hence providing a way to implement urban navigation systems including terrains.Item Open Access Fast and accurate algorithms for quadratic phase integrals in optics and signal processing(SPIE, 2011) Koç, A.; Özaktaş, Haldun M.; Hesselink L.The class of two-dimensional non-separable linear canonical transforms is the most general family of linear canonical transforms, which are important in both signal/image processing and optics. Application areas include noise filtering, image encryption, design and analysis of ABCD systems, etc. To facilitate these applications, one need to obtain a digital computation method and a fast algorithm to calculate the input-output relationships of these transforms. We derive an algorithm of NlogN time, N being the space-bandwidth product. The algorithm controls the space-bandwidth products, to achieve information theoretically sufficient, but not redundant, sampling required for the reconstruction of the underlying continuous functions. © 2011 SPIE.Item Open Access Fire detection and 3D fire propagation estimation for the protection of cultural heritage areas(Copernicus GmbH, 2010) Dimitropoulos, K.; Köse, Kıvanç; Grammalidis, N.; Çetin, A. EnisBeyond taking precautionary measures to avoid a forest fire, early warning and immediate response to a fire breakout are the only ways to avoid great losses and environmental and cultural heritage damages. To this end, this paper aims to present a computer vision based algorithm for wildfire detection and a 3D fire propagation estimation system. The main detection algorithm is composed of four sub-algorithms detecting (i) slow moving objects, (ii) smoke-coloured regions, (iii) rising regions, and (iv) shadow regions. After detecting a wildfire, the main focus should be the estimation of its propagation direction and speed. If the model of the vegetation and other important parameters like wind speed, slope, aspect of the ground surface, etc. are known; the propagation of fire can be estimated. This propagation can then be visualized in any 3D-GIS environment that supports KML files.Item Open Access A framework for applying the principles of depth perception to information visualization(Association for Computing Machinery, 2013) Zeynep, C. Y.; Bulbul, A.; Capin, T.During the visualization of 3D content, using the depth cues selectively to support the design goals and enabling a user to perceive the spatial relationships between the objects are important concerns. In this novel solution, we automate this process by proposing a framework that determines important depth cues for the input scene and the rendering methods to provide these cues. While determining the importance of the cues, we consider the user's tasks and the scene's spatial layout. The importance of each depth cue is calculated using a fuzzy logic-based decision system. Then, suitable rendering methods that provide the important cues are selected by performing a cost-profit analysis on the rendering costs of the methods and their contribution to depth perception. Possible cue conflicts are considered and handled in the system. We also provide formal experimental studies designed for several visualization tasks. A statistical analysis of the experiments verifies the success of our framework. © 2013 ACM.Item Open Access A framework for enhancing depth perception in computer graphics(ACM, 2010-07) Çipiloğlu, Zeynep; Bülbül, Abdullah; Çapin, TolgaThis paper introduces a solution for enhancing depth perception in a given 3D computer-generated scene. For this purpose, we propose a framework that decides on the suitable depth cues for a given scene and the rendering methods which provide these cues. First, the system calculates the importance of each depth cue using a fuzzy logic based algorithm which considers the target tasks in the application and the spatial layout of the scene. Then, a knapsack model is constructed to keep the balance between the rendering costs of the graphical methods that provide these cues and their contibution to depth perception. This cost-profit analysis step selects the proper rendering methods. In this work, we also present several objective and subjective experiments which show that our automated depth enhancement system is statistically (p < 0.05) better than the other method selection techniques that are tested. © 2010 ACM.Item Open Access Graph visualization toolkits(IEEE, 2002) Dogrusoz, U.; Feng, Q.; Madden, B.; Doorley, M.; Frick, A.The Graph Layout Toolkit and Graph Editor Toolkit, which provide a framework for graph visualization useful in a broad array of application areas are introduced. As such, an architectural overview of these tools is presented and discusses the challenges encountered during implementation and integration of theory and research results into such tools. In particular, the automatic graph layout and labeling algorithms and complexity management techniques are discussed. In addition, some examples of applications using these tools are presented.Item Open Access A layout algorithm for undirected compound graphs(Elsevier, 2009-03-15) Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Civril, Ali; Demir, EmekWe present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout scheme with extensions to handle multi-level nesting, edges between nodes of arbitrary nesting levels, varying node sizes, and other possible application-specific constraints. 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 also been successfully implemented as part of a pathway integration and analysis toolkit named PATIKA, for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions. © 2008 Elsevier Inc. All rights reserved.Item Open Access A layout algorithm for undirected compount graphs(2005) Giral, ErhanGraph layout is an important problem in information visualization. All datadriven graph-based information visualization systems require some sort of an automatic geometry generation mechanism, as it is generally not directly available from the data being modeled. This is why graph layout problem has been studied extensively. However, for the case of compound graphs, there are still important gaps in this area. We present a new, elegant algorithm for undirected compound graph layout. The algorithm is based on the traditional force-directed layout scheme with extensions to handle nesting, varying node sizes, and possibly other application-specific constraints. 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 also been successfully implemented as part of a pathway integration and analysis toolkit named Patika for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions.Item Open Access MaterialVis: material visualization tool using direct volume and surface rendering techniques(Elsevier Inc., 2014) Okuyan, E.; Güdükbay, Uğur; Bulutay, C.; Heinig, Karl-HeinzVisualization of the 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.Item Open Access Multiresolution block coding method for visualization of compressed images in multimedia applications(Society of Photo-Optical Instrumentation Engineers, 1994) Gerek, O. N.; Cetin, E. A.Multimedia and Picture Archiving and Communication System (PACS) applications require efficient ways of handling images for communication and visualization. In many Visual Information and Management Systems (VIMS), it may be required to get quick responses to queries. Usually, a VIMS database has a huge number of images and may provide lots of images for each query. For example, in a PACS, the VIMS provides 10 to 100 images for a typical query. Only a few of these images may actually be needed. In order to find the useful ones, the user has to preview each image by fully decompressing it. This is neither computationally efficient, nor user friendly. In this paper, we propose a scheme which provides a magnifying glass type previewing feature. With this method, a multiresolution previewing without decompressing the whole image is possible. Our scheme is based on block transform coding which is the most widely used technique in image and video coding. In the first step of our scheme, all of the queried images are displayed in the lowest possible resolution (constructed from the DC coefficients of the coded blocks). If the user requests more information for a region of a particular image by specifying its size and place, then that region is hierarchically decompressed and displayed. In this way, large amounts of computations and bandwidth usage are avoided and a good user interface is accomplished. This method changes the ordering strategy of transform coefficients, thus reduces the compression ratio, however this effect is small.Item Open Access Nitelik tabanlı sınıflandırıcılar ve koşullu rastgele alan ile dikkat çeken görsel bölge tespiti(IEEE, 2016-05) Demirel, B.; Cinbiş, Ramazan Gökberk; İkizler-Cinbiş, N.Dikkat çeken görsel bölge tahmini, resimlerde ya da sahnelerde insan gözünün öncelikli olarak odaklandıgı bölgeleri bulmayı amaçlayan bir bilgisayarlı görü problemidir. Pekçok bilgisayarlı görü problemi bir sahnedeki arkaplan ögelerini yoksaymayı gerektirdigi için, bu tür problemlerde dikkat çeken görsel bölge tahmini bir önişlem adımı olarak kullanılabilir. Bu çalışmada yukarıdan aşagıya dikkat çeken bölge tahmini probleminin çözümüne yönelik olarak nitelik tabanlı sınıflandırıçılar ve Koşullu Rastgele Alan (KRA) yöntemlerinin bir arada kullanıldıgı bir yöntem sunulmaktadır. Deneysel sonuçlar nitelik tabanlı sınıflandırıcı sonuçlarının görsel bilgiyi alt seviye özelliklere göre daha iyi kodlayabildigini göstermiştir ve geliştirilen yöntemin, Graz-02 veri kümesi üzerinde en iyi yöntemlerle karşılaştırıldıgında umut verici sonuçlar ürettiği gözlenmiştir.Item Open Access Physically-based simulation of hair strips in real-time(UNION Agency - Science Press, 2005) Taşkıran, Hasan Dogu; Güdükbay, UğurIn this paper, we present our implementation of physically-based simulation of hair strips. We used a mass-spring model followed by a hybrid approach where particle systems and the method of clustering of hair strands are employed. All the forces related to springs are implemented: gravity, repulsions from collisions (head and ground), absorption (ground only), frictions (ground and air), internal spring frictions. Real-time performance is achieved for physically-based simulation of hair strips and promising results in terms of the realistic hair behavior and hair rendering are obtained. Copyright UNION Agency - Science Press.Item Open Access Processing of optically-captured digital holograms for three-dimensional display(2009-04) Naughton, T.J.; Kreis, T.; Onural, Levent; Ferraro, P.; Depeursinge, C.; Emery, Y.; Hennelly, B. M.; Kujawiñska, M.In digital holography, holograms are usually optically captured and then two-dimensional slices of the reconstruction volume are reconstructed by computer and displayed on a two-dimensional display. When the recording is of a three-dimensional scene then such two-dimensional display becomes restrictive. We outline our progress on capturing larger ranges of perspectives of three-dimensional scenes, and our progress on four approaches to better visualise this three-dimensional information encoded in the digital holograms. The research has been performed within a European Commission funded research project dedicated the capture, processing, transmission, and display of real-world 3D and 4D scenes using digital holography. © 2009 SPIE.Item Open Access Realistic rendering and animation of a multi-layered human body model(IEEE, 2006) Yeşil, Mehmet Şahin; Güdükbay, UğurA framework for realistic rendering of a multi-layered human body model is proposed in this paper. The human model is composed of three layers: skeleton, muscle, and skin. The skeleton layer, represented by a set of joints and bones, controls the animation of the human body using inverse kinematics. Muscles are represented with action lines that are defined by a set of control points. An action line applies the force produced by a muscle on the bones and on the skin mesh. The skin layer is modeled as a 3D mesh and deformed during animation by binding the skin layer to both the skeleton and muscle layers. The skin is deformed by a two-step algorithm according to the current state of the skeleton and muscle layers. Performance experiments show that it is possible to obtain real-time frame rates for a moderately complex human model containing approximately 33,000 triangles on the skin layer. © 2006 IEEE.