Doktorgradsavhandlinger (NT-fak)
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Doktorgradsavhandlinger (NT-fak)
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Klemetsen, Øystein (Doctoral thesis; Doktorgradsavhandling, 01-Feb-2012)[+][-]
Abstract: The topic covered in this thesis is medical temperature measurement of subcutaneous parts of human tissue with use of microwave radiometry. Radiometry is a completely non-invasive, non-toxic and relatively inexpensive sensing modality. The radiometric technique is based on the measurement of electromagnetic noise power emitted by lossy materials. The method has explicit low investment costs and low technological complexity, but relatively low spatial resolution. Still the method can be useful for some dedicated medical applications. Fundamental radiometric theory and dielectrical properties of biological tissues are derived. The process to realize a miniaturized radiometer is going from active antenna configuration to a complete miniaturized radiometer and finally to a modular radiometer, that is used \textsl{in-vivo} on humans. Different radiometers were designed, simulated, built and tested on realistic human phantoms. \textit{In vivo} experiments were also conducted to verify the prototype radiometer and to test the ability to be used in tailored medical diagnostics. The primary application covered is temperature gradient measurement during microwave hyperthermia and in pediatric vesicouretaral reflux (VUR) detection. Hyperthermia is a therapeutic technique in which cancerous tissue is heated to 40-45$^\circ$C, inducing vascular and cellular changes that improve the therapeutic effectiveness when used in conjunction with chemotherapy or radiation therapy. VUR is abnormal flow of urine from the bladder back to the upper urinary tract. Another application where this radiometer can be of great interest is in breast cancer diagnostic. Breast cancer is a type of cancer that forms in tissues of the breast; usually in the ducts and lobules and can occur in both men and woman. We present results from radiometric measurement on human phantoms during a hyperthermia heating sequence. Experimental evidence shows that radiometry can be used for temperature quality assurance of the heated volume in depth. In VUR detection, the first step is to heat the bladder prior to detection of the reflux. We present results from measurements \textsl{in-vivo} with a water filled balloon in the human mouth, that mimics pediatric bladder heating. Results show that the radiometer can be used as the first step in the novel VUR detection. Radiometry antennas are one of the most critical components in a radiometer system. An elliptical printed circuit board antenna is designed and matched to the human body. Further, an antenna with suction, with use of negative pressure to mount the antenna onto the human body for improved radiometric performance, was also proposed and built. The simple and elegant solution for the coupling of the antenna with use of negative pressure, documents improved performance in estimating the true temperature as well as exhibiting smaller fluctuation in the radiometric signal. Description: The papers of this thesis are not available in Munin:
1. Ø. Klemetsen, Y. Birkelund, and S. K. Jacobsen: 'Design of medical radiometer front-end for improved performance', Progress In Electromagnetics Research B (2011) Vol. 27, 289–306. Available at http://www.jpier.org/PIERB/pier.php?paper=10101204
2. Øystein Klemetsen, Svein Jacobsen and Yngve Birkelund: 'Radiometric temperature reading of a hot ellipsoidal object inside the oral cavity by a shielded microwave antenna put flush to the cheek' (paper in review)
3. Øystein Klemetsen and Svein Jacobsen: 'Improved Radiometric Performance Attained by an Elliptical Microwave Antenna With Suction', IEEE transactions on biomedical engineering (2012)59(1):263-271. Available at http://dx.doi.org/10.1109/TBME.2011.2172441
4. Yngve Birkelund, Øystein Klemetsen, Svein K. Jacobsen, Kavitha Arunachalam, Paolo Maccarini, and Paul R. Stauffer: 'Vesicoureteral Reflux in children : a phantom study of microwave heating and radiometric thermometry of pediatric bladder', IEEE transactions on biomedical engineering (2011)58(11):3269-3278. Available at http://dx.doi.org/10.1109/TBME.2011.2167148
5. Svein Jacobsen and Øystein Klemetsen: 'Improved detectability in medical microwave radio-thermometers as obtained by active antennas', IEEE transactions on biomedical engineering (2008)55(12):2778-2785. Available at http://dx.doi.org/10.1109/TBME.2008.2002156URI: http://hdl.handle.net/10037/3818 File(s) in this item: 1
thesis.pdf (6.930Mb) -
Viken Valvåg, Steffen (Doctoral thesis; Doktorgradsavhandling, 30-Jan-2012)[+][-]
Abstract: MapReduce has become a widely employed programming model for large-scale data-intensive computations. Traditional MapReduce engines employ dynamic routing of data as a core mechanism for fault tolerance and load balancing. An alternative mechanism is static routing, which reduces the need to store temporary copies of intermediate data, but requires a tighter coupling between the components for storage and processing. The initial intuition motivating our work is that reading and writing less temporary data could improve performance, while the tight coupling of storage and processing could be leveraged to improve data locality. We therefore conjecture that a high-performance MapReduce engine can be based on static routing, while preserving the non-functional properties associated with traditional engines. To investigate this thesis, we design, implement, and experiment with Cogset, a distributed MapReduce engine that deviates considerably from the traditional design. We evaluate the performance of Cogset by comparing it to a widely used traditional MapReduce engine using a previously established benchmark. The results confirm our thesis that a high-performance MapReduce engine can be based on static routing, although analysis indicates that the reasons for Cogset's performance improvements are more subtle than expected. Through our work we develop a better understanding of static routing, its benefits and limitations, and its ramifications for a MapReduce engine. A secondary goal of our work is to explore how higher-level abstractions that are commonly built on top of MapReduce will interact with an execution engine based on static routing. Cogset is therefore designed with a generic, low-level core interface, upon which MapReduce is implemented as a relatively thin layer, as one of several supported programming interfaces. At its core, Cogset provides a few fundamental mechanisms for reliable and distributed storage of data, and parallel processing of statically partitioned data. While this dissertation mainly focuses on how these capabilities are leveraged to implement a distributed MapReduce engine, we also demonstrate how two other higher-level abstractions were built on top of Cogset. These may serve as alternative access points for data-intensive applications, and illustrate how some of the lessons learned from Cogset can be applicable in a broader context. Description: The papers of this thesis are not available in Munin:
1. Steffen Viken Valvåg and Dag Johansen: 'Oivos : simple and efficient distributed data processing' (2008). In Proceedings of the 2008 Tenth IEEE International Conference on High Performance Computing and Communications (HPCC 2008), pages 113– 122. IEEE Computer Society. Available at http://dx.doi.org/10.1109/HPCC.2008.105
2. Steffen Viken Valvåg and Dag Johansen: 'Update Maps : a new abstraction for High-Throughput Batch processing' (2009). In Proceedings of the 2009 IEEE International Conference on Networking, Architecture, and Storage (NAS 2009), pages 431–438. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NAS.2009.73
3. Steffen Viken Valvåg and Dag Johansen: 'Cogset : a unified engine for reliable storage and parallel processing' (2009). In Proceedings of the 2009 Sixth IFIP International Conference on Network and Parallel Computing (NPC 2009), pages 174– 181. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NPC.2009.23
4. Steffen Viken Valvåg, Dag Johansen, and Åge Kvalnes: 'Cogset vs. Hadoop : measurements and analysis', (2010). In Proceedings of the 2010 Second IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2010), pages 768–775. IEEE Computer Society. Available at http://dx.doi.org/10.1109/CloudCom.2010.103URI: http://hdl.handle.net/10037/3817 File(s) in this item: 1
thesis.pdf (948.7Kb) -
Johnsen, Magnar Gullikstad (Doctoral thesis; Doktorgradsavhandling, 20-Dec-2011)[+][-]
Abstract: The Open/Closed eld line Boundary (OCB) is the most important boundary in the magnetospheric system. On the dayside, the equatorward edge of the 6300 Å[OI] cusp aurora can be used as a proxy for the OCB. This work, which is a dissertation for the degree of philosophiæ Doctor consists of three scienti c papers focusing on the latitude of the optical cusp OCB and one paper focusing on polar cap patch generation mechanisms in the vicinity of the OCB. In Paper I we use modeling to demonstrate the variability of the cusp aurora with respect to vertical volume emission rate pro les and horizontal modulation owing to neutral wind. A meridian scanning photometer (MSP) simulator has been developed in order to study the manifestation of the cusp aurora in the MSP data from Svalbard. A method for obtaining the OCB location and nding the correct mapping altitude in order to transform the OCB location from MSP scan angle to magnetic latitude is found by simulating the horizontal movement of a reference cusp aurora. The reference cusp aurora, which is based on expected ionospheric and atmospheric conditions and electron precipitation characteristics, is de ned from the modeling results. Uncertainties in the scan angle to magnetic latitude transformation are found by simulating a wide range of realistic cusp auroras deviating from the reference cusp aurora. In Paper II the method of Paper I for finding the OCB is tested on real MSP data and compared with the OCB as obtained by satellite energetic particle measurements with very successful results. In Paper III the method of Paper I is used on 15 years of MSP data from Svalbard in order to study the statistical behavior of the cusp OCB. A possible relationship between the OCB latitude in the cusp and the solar cycle is revealed, and a possible expansion is brie y discussed. By comparing the OCB latitude with solar wind parameters, solar wind-magnetosphere coupling functions and geomagnetic indices, good correlations are found, which are in concurrence with previous satellite based, statistical studies. We nd a relationship between the OCB latitude and the ring current density (SYM/H), demonstrating great complexity in the physics behind the OCB location. We argue that the balance between reconnection dynamics on the dayside and nightside as well as the history or integral of previous events in the magnetospheric system are important factors for governing the cusp OCB latitude. Paper IV gives an overview of the solar wind and ionospheric conditions as measured during the Investigation of Cusp Irregularities 2 sounding rocket campaign. The rocket was launched through a newly produced polar cap patch. Based on the measurements performed in-situ by the rocket instrumentation and with groundbased optics and radars, a new creation mechanism, which partly involves ionization by both particle precipitation and solar irradiation and upwelling from sub F-layer altitudes, is suggested. Description: The papers of this thesis are not available in Munin:
1. M. G. Johnsen, D. A. Lorentzen, J, M. Holmes and U. P. Løvhaug: 'A model based method for obtaining the open/closed field line boundary from the cusp auroral 6300 Å[OI] red line' Journal of Geophysical research (forthcomming paper).
2. M. G. Johnsen and D. A. Lorentzen: 'The dayside open/closed eld line boundary as seen from space- and ground-based instrumentation' Journal of Geophysical research (forthcomming paper).
3. M. G. Johnsen and D. A. Lorentzen: 'A statistical analysis of the optical dayside open/closed field line boundary' Journal of Geophysical research (in press). Availavle at http://dx.doi.org/10.1029/2011JA016984
4. D. A. Lorentzen, J. Moen, K. Oksavik, F. Sigernes, Y. Saito and M. G. Johnsen: 'In situ measurement of a newly created polar cap patch', Journal of Geophysical research (2010), vol. 115, A12323. Available at http://dx.doi.org/10.1029/2010JA015710URI: http://hdl.handle.net/10037/3811 File(s) in this item: 1
thesis.pdf (2.521Mb) -
Sivertsen, Agnar Holten (Doctoral thesis; Doktorgradsavhandling, 11-Nov-2011)[+][-]
Abstract: The manual trimming and inspection of cod fillets by candling, is considered the bottleneck of cod fillet processing. The operation is both labour intensive and expensive, reported to account for as much as 50 % of the cost with cod fillet production. Due to the high labour costs in Norway, it is of great interest for the industry to optimize this process. In this work a hyperspectral imaging system has been developed, capable of inspecting cod fillets, with or without skin, at a conveyor belt speed of 400 mm/seconds, corresponding to the industrial processing speed of one fish per second. The system is designed as proof of concept, and the algorithms are not implemented to be run in real time. A method for segmenting a cod fillet image into the respective parts: loin, belly and tail, using the centerline as a reference system, has been developed. The method is useful for selecting standardized measurement regions on the fillet, and used for extracting data for automatic freshness assessment. Freshness, as days on ice, can be predicted using spectroscopy in part of the visible region (450-700 nm). This can be done with an accuracy comparable to what is reported for sensory evaluation using a panel of trained evaluators. The same system is used for detecting fillets which have been previously frozen, both as whole fish and as fillets with skin. The results show a complete separation between the fresh and frozen-thawed samples. Similar mechanisms are affecting the spectra from fish stored fresh on ice, and fish that has been through the freeze-thaw cycle. The main variations seen in the spectra from cod fillets stored on ice, or frozen and then thawed, are due to oxidation of heme proteins in the muscle. This is supported by independent measurements using two different instruments, and by previous studies pointing to the visible region as the best region for freshness prediction. Detectingobjectsembeddedintissue, usingvisiblelight, isdifficultduetovariability in the optical properties of the surrounding tissue. A method for calibrating the spectral signature from small objects embedded in translucent material has been developed. This method uses the estimated local background spectrum to calibrate the hyperspectral image, and the method is evaluated for automatic nematode detection, using the hyperspectral imaging system, at a commercial cod fillet processing plant. The local calibration method is superior to using traditional spectroscopic pre-treatment methods, and reduces both spatial and spectral variations across the image. The results from the industrial test show that the system can detect nematodes in cod fillets with a performance which is comparable or better, to what is reported by manual inspection. Description: The papers of this thesis are not available in Munin:
1. A. H. Sivertsen, C. Chu, L. Wang, F. Godtliebsen, K. Heia and H. Nilsen: 'Ridge detection with application to automatic fish fillet inspection', Journal of Food Engineering (2009), vol. 90, pp. 317–324. Available at http://dx.doi.org/10.1016/j.jfoodeng.2008.06.035
2. A. H. Sivertsen, K. Heia, S. K. Stormo, E. Elvevoll and H. Nilsen: 'Automatic nematode detection in cod fillets (Gadus Morhua) by transillumination hyperspectral imaging', Journal of Food Science (2011), vol. 76, pp. 77-83. Available at http://dx.doi.org/10.1111/j.1750-3841.2010.01928.x
3. A. H. Sivertsen, K. Heia, K. Hindberg and F. Godtliebsen: 'Automatic nematode detection in cod fillets (Gadus Morhua L.) by hyperspectral imaging' Journal of Food Science (2011), Volume 76, Issue 1, pages S77–S8. Available at http://dx.doi.org/10.1111/j.1750-3841.2010.01928.x
4. A. H. Sivertsen, T. Kimiya and K. Heia: 'Automatic freshness assessment of cod (Gadus morhua) fillets by VIS/NIR spectroscopy', Journal of Food Engineering (2011), vol 103, pp. 317-323. Available at http://dx.doi.org/10.1016/j.jfoodeng.2010.10.030URI: http://hdl.handle.net/10037/3681 File(s) in this item: 1
thesis.pdf (8.438Mb) -
Hagen, Tor-Magne Stien (Doctoral thesis; Doktorgradsavhandling, 26-Sep-2011)[+][-]
Abstract: The 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. Description: 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_15URI: http://hdl.handle.net/10037/3672 File(s) in this item: 2
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