KOLAM : human computer interfaces fro visual analytics in big data imagery

In the present day, we are faced with a deluge of disparate and dynamic information from multiple heterogeneous sources. Among these are the big data imagery datasets that are rapidly being generated via mature acquisition methods in the geospatial, surveillance (specifically, Wide Area Motion Imagery or WAMI) and biomedical domains. The need to interactively visualize these imagery datasets by using multiple types of views (as needed) into the data is common to these domains. Furthermore, researchers in each domain have additional needs: users of WAMI datasets also need to interactively track objects of interest using algorithms of their choice, visualize the resulting object trajectories and interactively edit these results as needed. While software tools that fulfill each of these requirements individually are available and well-used at present, there is still a need for tools that can combine the desired aspects of visualization, human computer interaction (HCI), data analysis, data management, and (geo-)spatial and temporal data processing into a single flexible and extensible system. KOLAM is an open, cross-platform, interoperable, scalable and extensible framework for visualization and analysis that we have developed to fulfil the above needs. The novel contributions in this thesis are the following: 1) Spatio-temporal caching for animating both giga-pixel and Full Motion Video (FMV) imagery, 2) Human computer interfaces purposefully designed to accommodate big data visualization, 3) Human-in-the-loop interactive video object tracking - ground-truthing of moving objects in wide area imagery using algorithm assisted human-in-the-loop coupled tracking, 4) Coordinated visualization using stacked layers, side-by-side layers/video sub-windows and embedded imagery, 5) Efficient one-click manual tracking, editing and data management of trajectories, 6) Efficient labeling of image segmentation regions and passing these results to desired modules, 7) Visualization of image processing results generated by non-interactive operators using layers, 8) Extension of interactive imagery and trajectory visualization to multi-monitor wall display environments, 9) Geospatial applications: Providing rapid roam, zoom and hyper-jump spatial operations, interactive blending, colormap and histogram enhancement, spherical projection and terrain maps, 10) Biomedical applications: Visualization and target tracking of cell motility in time-lapse cell imagery, collecting ground-truth from experts on whole-slide imagery (WSI) for developing histopathology analytic algorithms and computer-aided diagnosis for cancer grading, and easy-to-use tissue annotation features.Includes bibliographical reference

VR Jugglerを用いたPCクラスタによる没入型ディスプレイの構築

　PCクラスタを構成することにより、没入型VR環境を構築した。システムは、低価格、アプリケーション構築の容易性、システムのスケーラビリティといった設計指針に基づいて実装された。GPU搭載のPCを４台つなげて、立体視映像を同期生成する。没入型VR環境を構築するためのフレームワークとして、VR Jugglerを利用した。複数のPCをネットワーク接続し、同期的にグラフィックス・レンダリングを行う機能を提供する。仮想世界のシーンを構築するフレームワークとして、OpenSceneGraphを利用した。教育応用を目的として、ラムサール条約に登録されている干潟を自由に動き回る体験ができる可視化アプリケーションを開発した

Optimization of Display-Wall Aware Applications on Cluster Based Systems

Actualment, els sistemes d'informació i comunicació que treballen amb grans volums de dades requereixen l'ús de plataformes que permetin una representació entenible des del punt de vista de l'usuari. En aquesta tesi s'analitzen les plataformes Cluster Display Wall, usades per a la visualització de dades massives, i es treballa concretament amb la plataforma Liquid Galaxy, desenvolupada per Google. Mitjançant la plataforma Liquid Galaxy, es realitza un estudi de rendiment d'aplicacions de visualització representatives, identificant els aspectes de rendiment més rellevants i els possibles colls d'ampolla. De forma específica, s'estudia amb major profunditat un cas representatiu d'aplicació de visualització, el Google Earth. El comportament del sistema executant Google Earth s'analitza mitjançant diferents tipus de test amb usuaris reals. Per a aquest fi, es defineix una nova mètrica de rendiment, basada en la ratio de visualització, i es valora la usabilitat del sistema mitjançant els atributs tradicionals d'efectivitat, eficiència i satisfacció. Adicionalment, el rendiment del sistema es modela analíticament i es prova la precisió del model comparant-ho amb resultats reals.Nowadays, information and communication systems that work with a high volume of data require infrastructures that allow an understandable representation of it from the user's point of view. This thesis analyzes the Cluster Display Wall platforms, used to visualized massive amounts of data, and specifically studies the Liquid Galaxy platform, developed by Google. Using the Liquid Galaxy platform, a performance study of representative visualization applications was performed, identifying the most relevant aspects of performance and possible bottlenecks. Specifically, we study in greater depth a representative case of visualization application, Google Earth. The system behavior while running Google Earth was analyzed through different kinds of tests with real users. For this, a new performance metric was defined, based on the visualization ratio, and the usability of the system was assessed through the traditional attributes of effectiveness, efficiency and satisfaction. Additionally, the system performance was analytically modeled and the accuracy of the model was tested by comparing it with actual results.Actualmente, los sistemas de información y comunicación que trabajan con grandes volúmenes de datos requieren el uso de plataformas que permitan una representación entendible desde el punto de vista del usuario. En esta tesis se analizan las plataformas Cluster Display Wall, usadas para la visualización de datos masivos, y se trabaja en concreto con la plataforma Liquid Galaxy, desarrollada por Google. Mediante la plataforma Liquid Galaxy, se realiza un estudio de rendimiento de aplicaciones de visualización representativas, identificando los aspectos de rendimiento más relevantes y los posibles cuellos de botella. De forma específica, se estudia en mayor profundidad un caso representativo de aplicación de visualización, el Google Earth. El comportamiento del sistema ejecutando Google Earth se analiza mediante diferentes tipos de test con usuarios reales. Para ello se define una nueva métrica de rendimiento, basada en el ratio de visualización, y se valora la usabilidad del sistema mediante los atributos tradicionales de efectividad, eficiencia y satisfacción. Adicionalmente, el rendimiento del sistema se modela analíticamente y se prueba la precisión del modelo comparándolo con resultados reales

Розробка протоколу сеансового рівня для високошвидкісних регіонально-розподілених мереж

The paper presents the implementation of the protocol based on UDP, with optimized speed. Published the results of protocol testing in practical case. Demonstrated the possibility of implementing effective and practical applications based on the protocols UDPВ работе представлена реализация протокола на базе UDP, оптимизированово за эффективность передачи данных. Приведены результаты практического тестирования протокола, продемонстрирована возможность реализации эффективных и практических приложений на базе протоколов UDPУ роботі представлено реалізацію протоколу на базі UDP, оптимізовану за ефективність передачі даних. Приведено результати практичного тестування протоколу, продемонстровано можливість реалізації ефективних та практичних додатків на базі протоколів UD

Architectures for ubiquitous 3D on heterogeneous computing platforms

Today, a wide scope for 3D graphics applications exists, including domains such as scientific visualization, 3D-enabled web pages, and entertainment. At the same time, the devices and platforms that run and display the applications are more heterogeneous than ever. Display environments range from mobile devices to desktop systems and ultimately to distributed displays that facilitate collaborative interaction. While the capability of the client devices may vary considerably, the visualization experiences running on them should be consistent. The field of application should dictate how and on what devices users access the application, not the technical requirements to realize the 3D output. The goal of this thesis is to examine the diverse challenges involved in providing consistent and scalable visualization experiences to heterogeneous computing platforms and display setups. While we could not address the myriad of possible use cases, we developed a comprehensive set of rendering architectures in the major domains of scientific and medical visualization, web-based 3D applications, and movie virtual production. To provide the required service quality, performance, and scalability for different client devices and displays, our architectures focus on the efficient utilization and combination of the available client, server, and network resources. We present innovative solutions that incorporate methods for hybrid and distributed rendering as well as means to manage data sets and stream rendering results. We establish the browser as a promising platform for accessible and portable visualization services. We collaborated with experts from the medical field and the movie industry to evaluate the usability of our technology in real-world scenarios. The presented architectures achieve a wide coverage of display and rendering setups and at the same time share major components and concepts. Thus, they build a strong foundation for a unified system that supports a variety of use cases.Heutzutage existiert ein großer Anwendungsbereich für 3D-Grafikapplikationen wie wissenschaftliche Visualisierungen, 3D-Inhalte in Webseiten, und Unterhaltungssoftware. Gleichzeitig sind die Geräte und Plattformen, welche die Anwendungen ausführen und anzeigen, heterogener als je zuvor. Anzeigegeräte reichen von mobilen Geräten zu Desktop-Systemen bis hin zu verteilten Bildschirmumgebungen, die eine kollaborative Anwendung begünstigen. Während die Leistungsfähigkeit der Geräte stark schwanken kann, sollten die dort laufenden Visualisierungen konsistent sein. Das Anwendungsfeld sollte bestimmen, wie und auf welchem Gerät Benutzer auf die Anwendung zugreifen, nicht die technischen Voraussetzungen zur Erzeugung der 3D-Grafik. Das Ziel dieser Thesis ist es, die diversen Herausforderungen zu untersuchen, die bei der Bereitstellung von konsistenten und skalierbaren Visualisierungsanwendungen auf heterogenen Plattformen eine Rolle spielen. Während wir nicht die Vielzahl an möglichen Anwendungsfällen abdecken konnten, haben wir eine repräsentative Auswahl an Rendering-Architekturen in den Kernbereichen wissenschaftliche Visualisierung, web-basierte 3D-Anwendungen, und virtuelle Filmproduktion entwickelt. Um die geforderte Qualität, Leistung, und Skalierbarkeit für verschiedene Client-Geräte und -Anzeigen zu gewährleisten, fokussieren sich unsere Architekturen auf die effiziente Nutzung und Kombination der verfügbaren Client-, Server-, und Netzwerkressourcen. Wir präsentieren innovative Lösungen, die hybrides und verteiltes Rendering als auch das Verwalten der Datensätze und Streaming der 3D-Ausgabe umfassen. Wir etablieren den Web-Browser als vielversprechende Plattform für zugängliche und portierbare Visualisierungsdienste. Um die Verwendbarkeit unserer Technologie in realitätsnahen Szenarien zu testen, haben wir mit Experten aus der Medizin und Filmindustrie zusammengearbeitet. Unsere Architekturen erreichen eine umfassende Abdeckung von Anzeige- und Rendering-Szenarien und teilen sich gleichzeitig wesentliche Komponenten und Konzepte. Sie bilden daher eine starke Grundlage für ein einheitliches System, das eine Vielzahl an Anwendungsfällen unterstützt

Development of a Powerwall-based solution for the manual flagging of radio astronomy data from eMerlin

This project was created with the intention of establishing an optimisation method for the manual flagging of interferometric data of the eMerlin radio astronomy array, using a Powerwall as a visualisation tool. The complexity of this process which is due to the amount of variables and parameters demands a deep understanding of the data treatment. Once the data is achieved by the antennas the signals are correlated. This process generates undesired signals which mostly coming from radio frequency interference. Also when the calibration is performed some values can mislead the expected outcome. Although the flagging is supported with algorithms this method is not one hundred percent accurate. That is why visual inspection is still required. The possibility to use a Powerwall as a visualisation system allows different and new dynamics in terms of the interaction of the analyst with the information required to make the flagging

Interactive Visualization on High-Resolution Tiled Display Walls with Network Accessible Compute- and Display-Resources

Papers number 2-7 and appendix B and C of this thesis are not available in Munin: 2. Hagen, T-M.S., Johnsen, E.S., Stødle, D., Bjorndalen, J.M. and Anshus, O.: 'Liberating the Desktop', First International Conference on Advances in Computer-Human Interaction (2008), pp 89-94. Available at http://dx.doi.org/10.1109/ACHI.2008.20 3. Tor-Magne Stien Hagen, Oleg Jakobsen, Phuong Hoai Ha, and Otto J. Anshus: 'Comparing the Performance of Multiple Single-Cores versus a Single Multi-Core' (manuscript)4. Tor-Magne Stien Hagen, Phuong Hoai Ha, and Otto J. Anshus: 'Experimental Fault-Tolerant Synchronization for Reliable Computation on Graphics Processors' (manuscript) 5. Tor-Magne Stien Hagen, Daniel Stødle and Otto J. Anshus: 'On-Demand High-Performance Visualization of Spatial Data on High-Resolution Tiled Display Walls', Proceedings of the International Conference on Imaging Theory and Applications and International Conference on Information Visualization Theory and Applications (2010), pages 112-119. Available at http://dx.doi.org/10.5220/0002849601120119 6. Bård Fjukstad, Tor-Magne Stien Hagen, Daniel Stødle, Phuong Hoai Ha, John Markus Bjørndalen and Otto Anshus: 'Interactive Weather Simulation and Visualization on a Display Wall with Many-Core Compute Nodes', Para 2010 – State of the Art in Scientific and Parallel Computing. Available at http://vefir.hi.is/para10/extab/para10-paper-60 7. Tor-Magne Stien Hagen, Daniel Stødle, John Markus Bjørndalen, and Otto Anshus: 'A Step towards Making Local and Remote Desktop Applications Interoperable with High-Resolution Tiled Display Walls', Lecture Notes in Computer Science (2011), Volume 6723/2011, 194-207. Available at http://dx.doi.org/10.1007/978-3-642-21387-8_15The vast volume of scientific data produced today requires tools that can enable scientists to explore large amounts of data to extract meaningful information. One such tool is interactive visualization. The amount of data that can be simultaneously visualized on a computer display is proportional to the display’s resolution. While computer systems in general have seen a remarkable increase in performance the last decades, display resolution has not evolved at the same rate. Increased resolution can be provided by tiling several displays in a grid. A system comprised of multiple displays tiled in such a grid is referred to as a display wall. Display walls provide orders of magnitude more resolution than typical desktop displays, and can provide insight into problems not possible to visualize on desktop displays. However, their distributed and parallel architecture creates several challenges for designing systems that can support interactive visualization. One challenge is compatibility issues with existing software designed for personal desktop computers. Another set of challenges include identifying characteristics of visualization systems that can: (i) Maintain synchronous state and display-output when executed over multiple display nodes; (ii) scale to multiple display nodes without being limited by shared interconnect bottlenecks; (iii) utilize additional computational resources such as desktop computers, clusters and supercomputers for workload distribution; and (iv) use data from local and remote compute- and data-resources with interactive performance. This dissertation presents Network Accessible Compute (NAC) resources and Network Accessible Display (NAD) resources for interactive visualization of data on displays ranging from laptops to high-resolution tiled display walls. A NAD is a display having functionality that enables usage over a network connection. A NAC is a computational resource that can produce content for network accessible displays. A system consisting of NACs and NADs is either push-based (NACs provide NADs with content) or pull-based (NADs request content from NACs). To attack the compatibility challenge, a push-based system was developed. The system enables several simultaneous users to mirror multiple regions from the desktop of their computers (NACs) onto nearby NADs (among others a 22 megapixel display wall) without requiring usage of separate DVI/VGA cables, permanent installation of third party software or opening firewall ports. The system has lower performance than that of a DVI/VGA cable approach, but increases flexibility such as the possibility to share network accessible displays from multiple computers. At a resolution of 800 by 600 pixels, the system can mirror dynamic content between a NAC and a NAD at 38.6 frames per second (FPS). At 1600x1200 pixels, the refresh rate is 12.85 FPS. The bottleneck of the system is frame buffer capturing and encoding/decoding of pixels. These two functional parts are executed in sequence, limiting the usage of additional CPU cores. By pipelining and executing these parts on separate CPU cores, higher frame rates can be expected and by a factor of two in the best case. To attack all presented challenges, a pull-based system, WallScope, was developed. WallScope enables interactive visualization of local and remote data sets on high-resolution tiled display walls. The WallScope architecture comprises a compute-side and a display-side. The compute-side comprises a set of static and dynamic NACs. Static NACs are considered permanent to the system once added. This type of NAC typically has strict underlying security and access policies. Examples of such NACs are clusters, grids and supercomputers. Dynamic NACs are compute resources that can register on-the-fly to become compute nodes in the system. Examples of this type of NAC are laptops and desktop computers. The display-side comprises of a set of NADs and a data set containing data customized for the particular application domain of the NADs. NADs are based on a sort-first rendering approach where a visualization client is executed on each display-node. The state of these visualization clients is provided by a separate state server, enabling central control of load and refresh-rate. Based on the state received from the state server, the visualization clients request content from the data set. The data set is live in that it translates these requests into compute messages and forwards them to available NACs. Results of the computations are returned to the NADs for the final rendering. The live data set is close to the NADs, both in terms of bandwidth and latency, to enable interactive visualization. WallScope can visualize the Earth, gigapixel images, and other data available through the live data set. When visualizing the Earth on a 28-node display wall by combining the Blue Marble data set with the Landsat data set using a set of static NACs, the bottleneck of WallScope is the computation involved in combining the data sets. However, the time used to combine data sets on the NACs decreases by a factor of 23 when going from 1 to 26 compute nodes. The display-side can decode 414.2 megapixels of images per second (19 frames per second) when visualizing the Earth. The decoding process is multi-threaded and higher frame rates are expected using multi-core CPUs. WallScope can rasterize a 350-page PDF document into 550 megapixels of image-tiles and display these image-tiles on a 28-node display wall in 74.66 seconds (PNG) and 20.66 seconds (JPG) using a single quad-core desktop computer as a dynamic NAC. This time is reduced to 4.20 seconds (PNG) and 2.40 seconds (JPG) using 28 quad-core NACs. This shows that the application output from personal desktop computers can be decoupled from the resolution of the local desktop and display for usage on high-resolution tiled display walls. It also shows that the performance can be increased by adding computational resources giving a resulting speedup of 17.77 (PNG) and 8.59 (JPG) using 28 compute nodes. Three principles are formulated based on the concepts and systems researched and developed: (i) Establishing the end-to-end principle through customization, is a principle stating that the setup and interaction between a display-side and a compute-side in a visualization context can be performed by customizing one or both sides; (ii) Personal Computer (PC) – Personal Compute Resource (PCR) duality states that a user’s computer is both a PC and a PCR, implying that desktop applications can be utilized locally using attached interaction devices and display(s), or remotely by other visualization systems for domain specific production of data based on a user’s personal desktop install; and (iii) domain specific best-effort synchronization stating that for distributed visualization systems running on tiled display walls, state handling can be performed using a best-effort synchronization approach, where visualization clients eventually will get the correct state after a given period of time. Compared to state-of-the-art systems presented in the literature, the contributions of this dissertation enable utilization of a broader range of compute resources from a display wall, while at the same time providing better control over where to provide functionality and where to distribute workload between compute-nodes and display-nodes in a visualization context

Web-based Stereoscopic Collaboration for Medical Visualization

Medizinische Volumenvisualisierung ist ein wertvolles Werkzeug zur Betrachtung von Volumen- daten in der medizinischen Praxis und Lehre. Eine interaktive, stereoskopische und kollaborative Darstellung in Echtzeit ist notwendig, um die Daten vollständig und im Detail verstehen zu können. Solche Visualisierung von hochauflösenden Daten ist jedoch wegen hoher Hardware- Anforderungen fast nur an speziellen Visualisierungssystemen möglich. Remote-Visualisierung wird verwendet, um solche Visualisierung peripher nutzen zu können. Dies benötigt jedoch fast immer komplexe Software-Deployments, wodurch eine universelle ad-hoc Nutzbarkeit erschwert wird. Aus diesem Sachverhalt ergibt sich folgende Hypothese: Ein hoch performantes Remote- Visualisierungssystem, welches für Stereoskopie und einfache Benutzbarkeit spezialisiert ist, kann für interaktive, stereoskopische und kollaborative medizinische Volumenvisualisierung genutzt werden. Die neueste Literatur über Remote-Visualisierung beschreibt Anwendungen, welche nur reine Webbrowser benötigen. Allerdings wird bei diesen kein besonderer Schwerpunkt auf die perfor- mante Nutzbarkeit von jedem Teilnehmer gesetzt, noch die notwendige Funktion bereitgestellt, um mehrere stereoskopische Präsentationssysteme zu bedienen. Durch die Bekanntheit von Web- browsern, deren einfach Nutzbarkeit und weite Verbreitung hat sich folgende spezifische Frage ergeben: Können wir ein System entwickeln, welches alle Aspekte unterstützt, aber nur einen reinen Webbrowser ohne zusätzliche Software als Client benötigt? Ein Proof of Concept wurde durchgeführt um die Hypothese zu verifizieren. Dazu gehörte eine Prototyp-Entwicklung, deren praktische Anwendung, deren Performanzmessung und -vergleich. Der resultierende Prototyp (CoWebViz) ist eines der ersten Webbrowser basierten Systeme, welches flüssige und interaktive Remote-Visualisierung in Realzeit und ohne zusätzliche Soft- ware ermöglicht. Tests und Vergleiche zeigen, dass der Ansatz eine bessere Performanz hat als andere ähnliche getestete Systeme. Die simultane Nutzung verschiedener stereoskopischer Präsen- tationssysteme mit so einem einfachen Remote-Visualisierungssystem ist zur Zeit einzigartig. Die Nutzung für die normalerweise sehr ressourcen-intensive stereoskopische und kollaborative Anatomieausbildung, gemeinsam mit interkontinentalen Teilnehmern, zeigt die Machbarkeit und den vereinfachenden Charakter des Ansatzes. Die Machbarkeit des Ansatzes wurde auch durch die erfolgreiche Nutzung für andere Anwendungsfälle gezeigt, wie z.B. im Grid-computing und in der Chirurgie

JuxtaView - a Tool for Interactive Visualization of Large Imagery on Scalable Tiled Displays

JuxtaView is a cluster-based application for viewing ultra-high-resolution images on scalable tiled displays. We present in JuxtaView, a new parallel computing and distributed memory approach for out-of-core montage visualization, using LambdaRAM, a software-based networklevel cache system. The ultimate goal of JuxtaView is to enable a user to interactively roam through potentially terabytes of distributed, spatially referenced image data such as those from electron microscopes, satellites and aerial photographs. In working towards this goal, we describe our first prototype implemented over a local area network, where the image is distributed using LambdaRAM, on the memory of all nodes of a PC cluster driving a tiled display wall. Aggressive pre-fetching schemes employed by LambdaRAM help to reduce latency involved in remote memory access. We compare LambdaRAM with a more traditional memorymapped file approach for out-of-core visualization. 1