Processing and rendering of Fourier domain optical coherence tomography images at a line rate over 524 kHz using a graphics processing unit

In Fourier domain optical coherence tomography (FD-OCT), a large amount of interference data needs to be resampled from the wavelength domain to the wavenumber domain prior to Fourier transformation. We present an approach to optimize this data processing, using a graphics processing unit (GPU) and parallel processing algorithms. We demonstrate an increased processing and rendering rate over that previously reported by using GPU paged memory to render data in the GPU rather than copying back to the CPU. This avoids unnecessary and slow data transfer, enabling a processing and display rate of well over 524,000 A-scan/s for a single frame. To the best of our knowledge this is the fastest processing demonstrated to date and the first time that FD-OCT processing and rendering has been demonstrated entirely on a GPU.

Advances in characterisation, calibration and data processing speed of optical coherence tomography systems

This thesis describes advances in the characterisation, calibration and data processing of optical coherence tomography (OCT) systems. Femtosecond (fs) laser inscription was used for producing OCT-phantoms. Transparent materials are generally inert to infra-red radiations, but with fs lasers material modification occurs via non-linear processes when the highly focused light source interacts with the materials. This modification is confined to the focal volume and is highly reproducible. In order to select the best inscription parameters, combination of different inscription parameters were tested, using three fs laser systems, with different operating properties, on a variety of materials. This facilitated the understanding of the key characteristics of the produced structures with the aim of producing viable OCT-phantoms. Finally, OCT-phantoms were successfully designed and fabricated in fused silica. The use of these phantoms to characterise many properties (resolution, distortion, sensitivity decay, scan linearity) of an OCT system was demonstrated. Quantitative methods were developed to support the characterisation of an OCT system collecting images from phantoms and also to improve the quality of the OCT images. Characterisation methods include the measurement of the spatially variant resolution (point spread function (PSF) and modulation transfer function (MTF)), sensitivity and distortion. Processing of OCT data is a computer intensive process. Standard central processing unit (CPU) based processing might take several minutes to a few hours to process acquired data, thus data processing is a significant bottleneck. An alternative choice is to use expensive hardware-based processing such as field programmable gate arrays (FPGAs). However, recently graphics processing unit (GPU) based data processing methods have been developed to minimize this data processing and rendering time. These processing techniques include standard-processing methods which includes a set of algorithms to process the raw data (interference) obtained by the detector and generate A-scans. The work presented here describes accelerated data processing and post processing techniques for OCT systems. The GPU based processing developed, during the PhD, was later implemented into a custom built Fourier domain optical coherence tomography (FD-OCT) system. This system currently processes and renders data in real time. Processing throughput of this system is currently limited by the camera capture rate. OCTphantoms have been heavily used for the qualitative characterization and adjustment/ fine tuning of the operating conditions of OCT system. Currently, investigations are under way to characterize OCT systems using our phantoms. The work presented in this thesis demonstrate several novel techniques of fabricating OCT-phantoms and accelerating OCT data processing using GPUs. In the process of developing phantoms and quantitative methods, a thorough understanding and practical knowledge of OCT and fs laser processing systems was developed. This understanding leads to several novel pieces of research that are not only relevant to OCT but have broader importance. For example, extensive understanding of the properties of fs inscribed structures will be useful in other photonic application such as making of phase mask, wave guides and microfluidic channels. Acceleration of data processing with GPUs is also useful in other fields.

Multi-threaded parallel numerical modelling of femtosecond pulse propagation in laser machining

Femtosecond laser microfabrication has emerged over the last decade as a 3D flexible technology in photonics. Numerical simulations provide an important insight into spatial and temporal beam and pulse shaping during the course of extremely intricate nonlinear propagation (see e.g. [1,2]). Electromagnetics of such propagation is typically described in the form of the generalized Non-Linear Schrdinger Equation (NLSE) coupled with Drude model for plasma [3]. In this paper we consider a multi-threaded parallel numerical solution for a specific model which describes femtosecond laser pulse propagation in transparent media [4, 5]. However our approach can be extended to similar models. The numerical code is implemented in NVIDIA Graphics Processing Unit (GPU) which provides an effitient hardware platform for multi-threded computing. We compare the performance of the described below parallel code implementated for GPU using CUDA programming interface [3] with a serial CPU version used in our previous papers [4,5]. © 2011 IEEE.

High performance numerical modeling of ultra-short laser pulse propagation based on multithreaded parallel hardware

The focus of this study is development of parallelised version of severely sequential and iterative numerical algorithms based on multi-threaded parallel platform such as a graphics processing unit. This requires design and development of a platform-specific numerical solution that can benefit from the parallel capabilities of the chosen platform. Graphics processing unit was chosen as a parallel platform for design and development of a numerical solution for a specific physical model in non-linear optics. This problem appears in describing ultra-short pulse propagation in bulk transparent media that has recently been subject to several theoretical and numerical studies. The mathematical model describing this phenomenon is a challenging and complex problem and its numerical modeling limited on current modern workstations. Numerical modeling of this problem requires a parallelisation of an essentially serial algorithms and elimination of numerical bottlenecks. The main challenge to overcome is parallelisation of the globally non-local mathematical model. This thesis presents a numerical solution for elimination of numerical bottleneck associated with the non-local nature of the mathematical model. The accuracy and performance of the parallel code is identified by back-to-back testing with a similar serial version.

Accuracy and optimal sampling in Monte Carlo solution of population balance equations

Implementation of a Monte Carlo simulation for the solution of population balance equations (PBEs) requires choice of initial sample number (N0), number of replicates (M), and number of bins for probability distribution reconstruction (n). It is found that Squared Hellinger Distance, H2, is a useful measurement of the accuracy of Monte Carlo (MC) simulation, and can be related directly to N0, M, and n. Asymptotic approximations of H2 are deduced and tested for both one-dimensional (1-D) and 2-D PBEs with coalescence. The central processing unit (CPU) cost, C, is found in a power-law relationship, C= aMNb0, with the CPU cost index, b, indicating the weighting of N0 in the total CPU cost. n must be chosen to balance accuracy and resolution. For fixed n, M × N0 determines the accuracy of MC prediction; if b > 1, then the optimal solution strategy uses multiple replications and small sample size. Conversely, if 0 < b < 1, one replicate and a large initial sample size is preferred. © 2015 American Institute of Chemical Engineers AIChE J, 61: 2394–2402, 2015

Distributed processing, reconfigurable processes and active network

The fast spread of the Internet and the increasing demands of the service are leading to radical changes in the structure and management of underlying telecommunications systems. Active networks (ANs) offer the ability to program the network on a per-router, per-user, or even per-packet basis, thus promise greater flexibility than current networks. To make this new network paradigm of active network being widely accepted, a lot of issues need to be solved. Management of the active network is one of the challenges. This thesis investigates an adaptive management solution based on genetic algorithm (GA). The solution uses a distributed GA inspired by bacterium on the active nodes within an active network, to provide adaptive management for the network, especially the service provision problems associated with future network. The thesis also reviews the concepts, theories and technologies associated with the management solution. By exploring the implementation of these active nodes in hardware, this thesis demonstrates the possibility of implementing a GA based adaptive management in the real network that being used today. The concurrent programming language, Handel-C, is used for the description of the design system and a re-configurable computer platform based on a FPGA process element is used for the hardware implementation. The experiment results demonstrate both the availability of the hardware implementation and the efficiency of the proposed management solution.

Digital control system programming from process control diagrams

A graphical process control language has been developed as a means of defining process control software. The user configures a block diagram describing the required control system, from a menu of functional blocks, using a graphics software system with graphics terminal. Additions may be made to the menu of functional blocks, to extend the system capability, and a group of blocks may be defined as a composite block. This latter feature provides for segmentation of the overall system diagram and the repeated use of the same group of blocks within the system. The completed diagram is analyzed by a graphics compiler which generates the programs and data structure to realise the run-time software. The run-time software has been designed as a data-driven system which allows for modifications at the run-time level in both parameters and system configuration. Data structures have been specified to ensure efficient execution and minimal storage requirements in the final control software. Machine independence has been accomodated as far as possible using CORAL 66 as the high level language throughout the entire system; the final run-time code being generated by a CORAL 66 compiler appropriate to the target processor.

The effective use of implicit parallelism through the use of an object-oriented programming language

This thesis explores translating well-written sequential programs in a subset of the Eiffel programming language - without syntactic or semantic extensions - into parallelised programs for execution on a distributed architecture. The main focus is on constructing two object-oriented models: a theoretical self-contained model of concurrency which enables a simplified second model for implementing the compiling process. There is a further presentation of principles that, if followed, maximise the potential levels of parallelism. Model of Concurrency. The concurrency model is designed to be a straightforward target for mapping sequential programs onto, thus making them parallel. It aids the compilation process by providing a high level of abstraction, including a useful model of parallel behaviour which enables easy incorporation of message interchange, locking, and synchronization of objects. Further, the model is sufficient such that a compiler can and has been practically built. Model of Compilation. The compilation-model's structure is based upon an object-oriented view of grammar descriptions and capitalises on both a recursive-descent style of processing and abstract syntax trees to perform the parsing. A composite-object view with an attribute grammar style of processing is used to extract sufficient semantic information for the parallelisation (i.e. code-generation) phase. Programming Principles. The set of principles presented are based upon information hiding, sharing and containment of objects and the dividing up of methods on the basis of a command/query division. When followed, the level of potential parallelism within the presented concurrency model is maximised. Further, these principles naturally arise from good programming practice. Summary. In summary this thesis shows that it is possible to compile well-written programs, written in a subset of Eiffel, into parallel programs without any syntactic additions or semantic alterations to Eiffel: i.e. no parallel primitives are added, and the parallel program is modelled to execute with equivalent semantics to the sequential version. If the programming principles are followed, a parallelised program achieves the maximum level of potential parallelisation within the concurrency model.

Phonological simplifications, apraxia of speech and the interaction between phonological and phonetic processing

Research on aphasia has struggled to identify apraxia of speech (AoS) as an independent deficit affecting a processing level separate from phonological assembly and motor implementation. This is because AoS is characterized by both phonological and phonetic errors and, therefore, can be interpreted as a combination of deficits at the phonological and the motoric level rather than as an independent impairment. We apply novel psycholinguistic analyses to the perceptually phonological errors made by 24 Italian aphasic patients. We show that only patients with relative high rate (>10%) of phonetic errors make sound errors which simplify the phonology of the target. Moreover, simplifications are strongly associated with other variables indicative of articulatory difficulties - such as a predominance of errors on consonants rather than vowels -but not with other measures - such as rate of words reproduced correctly or rates of lexical errors. These results indicate that sound errors cannot arise at a single phonological level because they are different in different patients. Instead, different patterns: (1) provide evidence for separate impairments and the existence of a level of articulatory planning/programming intermediate between phonological selection and motor implementation; (2) validate AoS as an independent impairment at this level, characterized by phonetic errors and phonological simplifications; (3) support the claim that linguistic principles of complexity have an articulatory basis since they only apply in patients with associated articulatory difficulties.