Browsing by Subject "Computer graphics"

Now showing 1 - 20 of 49

Open Access
Algorithms for effective querying of compound graph-based pathway databases
(BioMed Central Ltd., 2009-11-16) Doğrusöz, Uğur; Çetintaş, Ahmet; Demir, Emek; Babur, Özgün
Background: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate them using the well-understood concepts of graph theory in order to predict their structural and dynamic properties. An extension of this graph representation, namely hierarchically structured or compound graphs, in which a member of a biological network may recursively contain a sub-network of a somehow logically similar group of biological objects, provides many additional benefits for analysis of biological pathways, including reduction of complexity by decomposition into distinct components or modules. In this regard, it is essential to effectively query such integrated large compound networks to extract the sub-networks of interest with the help of efficient algorithms and software tools. Results: Towards this goal, we developed a querying framework, along with a number of graph-theoretic algorithms from simple neighborhood queries to shortest paths to feedback loops, that is applicable to all sorts of graph-based pathway databases, from PPIs (protein-protein interactions) to metabolic and signaling pathways. The framework is unique in that it can account for compound or nested structures and ubiquitous entities present in the pathway data. In addition, the queries may be related to each other through "AND" and "OR" operators, and can be recursively organized into a tree, in which the result of one query might be a source and/or target for another, to form more complex queries. The algorithms were implemented within the querying component of a new version of the software tool PATIKAweb (Pathway Analysis Tool for Integration and Knowledge Acquisition) and have proven useful for answering a number of biologically significant questions for large graph-based pathway databases. Conclusion: The PATIKA Project Web site is http://www.patika.org. PATIKAweb version 2.1 is available at http://web.patika.org. © 2009 Dogrusoz et al; licensee BioMed Central Ltd.
Open Access
Animation of boiling phenomena
(IEEE, 2008-05) Bülbül, Abdullah; Küçüktunç, Onur; Özgüç, Bülent
Phenomenon of boiling is a challenging topic for computer graphics due to its complex hydrodynamics and formulation. Realistic fluid animations require very heavy three-dimensional fluid flow calculations, and surface estimations as well. However, realism and performance are the two important objectives of the boiling animation for a real-time application. We present an efficient method for the simulation of boiling water in this paper. The method is based on modeling the bubbles and waves as particles. Grid-based approach is used both for the heating and the fluid surface. Our technique makes it possible to produce the animation of boiling phenomena nearly in real-time. ©2008 IEEE.
Open Access
Attention-aware disparity control in interactive environments
(Springer, 2013) Celikcan, U.; Cimen, G.; Kevinc, E. B.; Capin, T.
Our paper introduces a novel approach for controlling stereo camera parameters in interactive 3D environments in a way that specifically addresses the interplay of binocular depth perception and saliency of scene contents. Our proposed Dynamic Attention-Aware Disparity Control (DADC) method produces depth-rich stereo rendering that improves viewer comfort through joint optimization of stereo parameters. While constructing the optimization model, we consider the importance of scene elements, as well as their distance to the camera and the locus of attention on the display. Our method also optimizes the depth effect of a given scene by considering the individual user's stereoscopic disparity range and comfortable viewing experience by controlling accommodation/convergence conflict. We validate our method in a formal user study that also reveals the advantages, such as superior quality and practical relevance, of considering our method. © 2013 Springer-Verlag Berlin Heidelberg.
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.
Open Access
ChiBE: interactive visualization and manipulation of BioPAX pathway models
(Oxford University Press, 2010-02-01) Babur, Özgün; Doğrusöz, Uğur; Demir, Emek; Sander, C.
SUMMARY: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large pathway datasets requires software that can combine data mapping, querying and visualization as well as providing access to diverse data resources on the Internet. ChiBE is an open source software application that features user-friendly multi-view display, navigation and manipulation of pathway models in BioPAX format. Pathway views are rendered in a feature-rich format, and may be laid out and edited with state-of-the-art visualization methods, including compound or nested structures for visualizing cellular compartments and molecular complexes. Users can easily query and visualize pathways through an integrated Pathway Commons query tool and analyze molecular profiles in pathway context. AVAILABILITY: http://www.bilkent.edu.tr/%7Ebcbi/chibe.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Open Access
A clustering-based method to estimate saliency in 3D animated meshes
(Elsevier Ltd, 2014) Bulbul, A.; Arpa, S.; Capin, T.
We present a model to determine the perceptually significant elements in animated 3D scenes using a motion-saliency method. Our model clusters vertices with similar motion-related behaviors. To find these similarities, for each frame of an animated mesh sequence, vertices' motion properties are analyzed and clustered using a Gestalt approach. Each cluster is analyzed as a single unit and representative vertices of each cluster are used to extract the motion-saliency values of each group. We evaluate our method by performing an eye-tracker-based user study in which we analyze observers' reactions to vertices with high and low saliencies. The experiment results verify that our proposed model correctly detects the regions of interest in each frame of an animated mesh. © 2014 Elsevier Ltd.
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, Bülent
A 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.
Open Access
Comparison of image space subdivision algorithms for parallel volume rendering
(1995) Tanin, Egemen
In many scientific applications, results are presented as unstructured volumetric data sets. Direct Volume Rendering (DVR) is a powerful way of visualizing these volumetric data sets. However, it involves intensive computations. In addition, most of the volumetric data sets also require huge memories. Hence, DVR is a good candidate for parallelization on distributed memory multicomputers. Also most of the engineering simulations are done on multicomputers. Therefore, visualization of these results on the same architectures where simulations are done avoids the overhead of transporting large amount of data. In order to visualize unstructured volumetric data sets, the underlying algorithms should resolve the point location and the view sort problems of the 3D grid points. In this thesis, these problems are solved by using the well-known Scanline Z-Buffer algorithm. Three image space subdivision algorithms, namely horizontal, rectangular, and recursive subdivisions, are utilized to distribute the computations evenly among the processors in the rendering phase. The main parallel algorithm uses Raycasting approach of DVR to visualize the data sets, which is also an image space method. Therefore, the divisions are made in order to obtain a set of sub-images. Static task decomposition is used where each processor is assigned to a single sub-image. The load balance among the processors is achieved by defining the overall work load with in a sub-image by using the milestone operations done in the Scanline Z-Buffer algorithm. The algorithms are developed in a way that they can handle any kind of polygonal, volumetric, and etc. data set where the underlying architecture is also kept flexible in many aspects for the sake of generality and portability. The experimental performance evaluation of the horizontal, rectangular, and recursive subdivision algorithms on an IBM-SP2 system are presented and discussed in a comparative way.
Open Access
A context aware approach for enhancing gesture recognition accuracy on handheld devices
(2010) Yıldırım, Hacı Mehmet
Input capabilities (e.g. joystick, keypad) of handheld devices allow users to interact with the user interface to access the information and mobile services. However, these input capabilities are very limited because of the mobile convenience. New input devices and interaction techniques are needed for handheld devices. Gestural interaction with accelerometer sensor is one of the newest interaction techniques on mobile computing. In this thesis, we introduce solutions that can be used for automatically enhancing the gesture recognition accuracy of accelerometer sensor, and as a standardized gesture library for gestural interaction on touch screen and accelerometer sensor. In this novel solution, we propose a framework that decides on suitable signal processing techniques for acceleration sensor data for a given context of the user. First system recognizes the context of the user using pattern recognition algorithm. Then, system automatically chooses signal ltering techniques for recognized context, and recognizes gestures. Gestures are also standardized for better usage. In this work, we also present several experiments which show the feasibility and e ectiveness of our automated gesture recognition enhancement system.
Open Access
Continuous processing of images through user sketched functional blocks
(Wiley-Blackwell, 1988) Kaya, A.; Ozguc, B.
Our aim is to implement an image processing system with previously defined algorithms through the use of functional blocks connected together to form a diagram that we call a schematic. A functional block means the representation of a routine or function by a visual object in our intent. The arc connecting two blocks is the path and direction through which an image is transferred. In the development of the system we relied on the usage of new developments in software providing for the construction of better interfaces. Most important of these are the object oriented style of programming, iconic interfacing, multiple window and multi-tasking operating systems.
Restricted
Ctrl+C, Ctrl+V
(2000) Maral, Alper
Open Access
Cubist style rendering of 3D virtual environments
(2012) Arpa, Sami
Cubism, pioneered by Pablo Picasso and Georges Braque, was a breakthrough in art, influencing artists to abandon existing traditions. In this thesis, we present a novel approach for cubist rendering of 3D synthetic environments. Rather than merely imitating cubist paintings, we apply the main principles of Analytical Cubism to 3D graphics rendering. In this respect, we develop a new cubist camera providing an extended view, and a perceptually based spatial imprecision technique that keeps the important regions of the scene within a certain area of the output. Additionally, several methods to provide a painterly style are applied. We demonstrate the effectiveness of our extending view method by comparing the visible face counts in the images rendered by the cubist camera model and the traditional perspective camera. Besides, we give an overall discussion of final results and apply user tests in which users compare our results very well with Analytical Cubist paintings but not Synthetic Cubist paintings.
Open Access
Diffusion equation modeling for sound energy flow analysis in multi domain structures
(Acoustical Society of America, 2019) Gül, Zühre Sü; Odabaş, E.; Xiang, N.; Çalışkan, M.
This study investigates reliable models and methods to be applied in sound field analysis of multi-domain structures. The case structures are two monuments, namely, Süleymaniye Mosque and Hagia Sophia in İstanbul. These are both multi-volume spaces with many smaller sub-volumes coupled to each other by coupling apertures in form of arches. A key concern of the study is to examine energy flow decays and understand the mechanism of multi-slope sound energy decays. The methodology involves diffusion equation model (DEM) application in a finite-element scheme for sound energy flow analysis. Energy flow decays, energy flow dips, and spatial flow vectors are examined for single versus multi-domain DEM solutions. It is concluded that specification of different domains with individual diffusion coefficients is a critical setting such that, if not assigned correctly, may mislead the results. The energy flow vector analysis has enabled us to comprehend the architectural features in relation to such energy flow decay dip occurrence. The computational efficiency of DEM is also discussed. The DEM application in this study has proved to be a powerful and practical method in room acoustics applications, specifically for multi-rate decay investigations.
Open Access
Example-based retargeting of human motion to arbitrary mesh models
(Blackwell Publishing Ltd, 2015) Celikcan, U.; Yaz I.O.; Capin, T.
We present a novel method for retargeting human motion to arbitrary 3D mesh models with as little user interaction as possible. Traditional motion-retargeting systems try to preserve the original motion, while satisfying several motion constraints. Our method uses a few pose-to-pose examples provided by the user to extract the desired semantics behind the retargeting process while not limiting the transfer to being only literal. Thus, mesh models with different structures and/or motion semantics from humanoid skeletons become possible targets. Also considering the fact that most publicly available mesh models lack additional structure (e.g. skeleton), our method dispenses with the need for such a structure by means of a built-in surface-based deformation system. As deformation for animation purposes may require non-rigid behaviour, we augment existing rigid deformation approaches to provide volume-preserving and squash-and-stretch deformations. We demonstrate our approach on well-known mesh models along with several publicly available motion-capture sequences. We present a novel method for retargeting human motion to arbitrary 3D mesh models with as little user interaction as possible. Traditional motion-retargeting systems try to preserve the original motion, while satisfying several motion constraints. Our method uses a few pose-to-pose examples provided by the user to extract the desired semantics behind the retargeting process while not limiting the transfer to being only literal. Thus, mesh models with different structures and/or motion semantics from humanoid skeletons become possible targets. © 2014 The Eurographics Association and John Wiley & Sons Ltd.
Open Access
Fast ray tracing 3D models
(1991) İşler, Veysi; Özgüç, Bülent
In many computer graphics applications such as CAD, realistic displays have very important and positive effects on the users of the system. There are several techniques to generate realistic images with the computer. Ray tracing gives the most effective results by simulating the interaction of light with its environment. However, it may require an excessive amount of time to generate an image. In this article, we present a survey of methods developed to speed up the ray tracing algorithm and introduce a fast ray tracer to process a 3D scene that is defined by interactive 3D modeling software.
Open Access
A framework for enhancing depth perception in computer graphics
(ACM, 2010-07) Çipiloğlu, Zeynep; Bülbül, Abdullah; Çapin, Tolga
This 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.
Open Access
A fuzzy logic based approach for enchanging depth perception in computer graphics
(2010) Çipiloğlu, Zeynep
Rapid progress in 3D rendering and display technologies brings the problem of better visualization of 3D content. Providing correct depth information and enabling the user to perceive the spatial relationship between the objects is one of the main concerns during the visualization of 3D content. In this thesis, we introduce a solution that can either be used for automatically enhancing the depth perception of a given scene, or as a component that suggests suitable rendering methods to application developers. In this novel solution, we propose a framework that decides on the suitable depth cues for a given 3D 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 user's 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 contribution to depth perception. This cost-pro t analysis step selects the proper rendering methods for the given scene. In this work, we also present several objective and subjective experiments which show that our automated depth perception enhancement system is statistically (p < 0.05 ) better than the other method selection techniques that are tested.
Open Access
Generating 3D thumbnails for 3D contents
(2010) Yiğit, Yeliz
Creating effective thumbnails is a challenging task because finding important features and preserving the quality of the content is difficult. Additionally, as the popularity of 3D technologies is increasing, the usage area of 3D contents and the 3D content databases are expanding. However, for these contents, 2D thumbnails are insufficient since the current methods for generating them do not maintain the important and recognizable features of the content and give the idea of the content. In this thesis, we introduce a new thumbnail format, 3D thumbnail that helps users to understand the content of the 3D graphical scene or 3D video + depth by preserving the recognizable features and qualities. For creating 3D thumbnails, we developed a framework that generates 3D thumbnails for different 3D contents in order to create meaningful and qualified thumbnails. Thus, the system selects the best viewpoint in order to capture the scene with a high amount of detail for 3D graphical scenes. On the other hand, this process is different for 3D videos. In this case, by a saliency-depth based approach, we find the important objects on the selected frame of the 3D video and preserve them. Finally, after some steps such as placement, 3D rendering etc., the resulting thumbnails give more glorified information about the content. Finally, several experiments are presented which show that our proposed 3D thumbnail format is statistically (p <0.05 ) better than 2D thumbnails.
Open Access
How the ocean personality model affects the perception of crowds
(Institute of Electrical and Electronics Engineers, 2011) Durupınar, F.; Pelechano, N.; Allbeck, J. M.; Güdükbay, Uğur; Badler, N. I.
A personality model named High-Density Autonomous Crowds (HiDAC) simulation system provides individual differences by assigning each person different psychological and physiological traits. Users normally set these parameters to model a crowd's nonuniformity and diversity. The approach creates plausible variations in the crowd and enables novice users to dictate these variations by combining a standard personality model with a high-density crowd simulation. HiDAC addresses the simulation of local behaviors and the global wayfinding of crowds in a dynamically changing environment. It directs autonomous agents' behavior by combining geometric and psychological rules. HiDAC handles collisions through avoidance and response forces. Over long distances, the system applies collision avoidance so that agents can steer around obstacles. HiDAC assigns people specific behaviors. The number of actions they complete depends on their curiosity.
Open Access
Hypersolver: a graphical tool for commonsense set theory
(Elsevier, 1995) Pakkan, M.; Akman, V.
This paper investigates an alternative set theory (due to Aczel) called the Hyperset Theory. Aczel uses a graphical representation for sets and thereby allows the representation of non-well-founded sets. A program, called hypersolver, which can solve systems of equations defined in terms of sets in the universe of this new theory is presented. This may be a useful tool for commonsense reasoning. © 1995.