Visualisation of complex flows using texture-based techniques

Detailed representations of complex flow datasets are often difficult to generate using traditional vector visualisation techniques such as arrow plots and streamlines. This is particularly true when the flow regime changes in time. Texture-based techniques, which are based on the advection of dense textures, are novel techniques for visualising such flows. We review two popular texture based techniques and their application to flow datasets sourced from active research projects. The techniques investigated were Line integral convolution (LIC) [1], and Image based flow visualisation (IBFV) [18]. We evaluated these and report on their effectiveness from a visualisation perspective. We also report on their ease of implementation and computational overheads.

Calculation of volume from crank angle using reconfigurable hardware

Fast calculation of quantities such as in-cylinder volume and indicated power is important in internal combustion engine research. Multiple channels of data including crank angle and pressure were collected for this purpose using a fully instrumented diesel engine research facility. Currently, existing methods use software to post-process the data, first calculating volume from crank angle, then calculating the indicated work and indicated power from the area enclosed by the pressure-volume indicator diagram. Instead, this work investigates the feasibility of achieving real-time calculation of volume and power via hardware implementation on Field Programmable Gate Arrays (FPGAs). Alternative hardware implementations were investigated using lookup tables, Taylor series methods or the CORDIC (CoOrdinate Rotation DIgital Computer) algorithm to compute the trigonometric operations in the crank angle to volume calculation, and the CORDIC algorithm was found to use the least amount of resources. Simulation of the hardware based implementation showed that the error in the volume and indicated power is less than 0.1%.

Image based flow visualisation of experimental flow fields inside a gross pollutant trap

Typical flow fields in a stormwater gross pollutant trap (GPT) with blocked retaining screens were experimentally captured and visualised. Particle image velocimetry (PIV) software was used to capture the flow field data by tracking neutrally buoyant particles with a high speed camera. A technique was developed to apply the Image Based Flow Visualization (IBFV) algorithm to the experimental raw dataset generated by the PIV software. The dataset consisted of scattered 2D point velocity vectors and the IBFV visualisation facilitates flow feature characterisation within the GPT. The flow features played a pivotal role in understanding gross pollutant capture and retention within the GPT. It was found that the IBFV animations revealed otherwise unnoticed flow features and experimental artefacts. For example, a circular tracer marker in the IBFV program visually highlighted streamlines to investigate specific areas and identify the flow features within the GPT.

Solving tri-diagonal linear systems using field programmable gate arrays

In this paper, we present the outcomes of a project on the exploration of the use of Field Programmable Gate Arrays (FPGAs) as co-processors for scientific computation. We designed a custom circuit for the pipelined solving of multiple tri-diagonal linear systems. The design is well suited for applications that require many independent tri-diagonal system solves, such as finite difference methods for solving PDEs or applications utilising cubic spline interpolation. The selected solver algorithm was the Tri-Diagonal Matrix Algorithm (TDMA or Thomas Algorithm). Our solver supports user specified precision thought the use of a custom floating point VHDL library supporting addition, subtraction, multiplication and division. The variable precision TDMA solver was tested for correctness in simulation mode. The TDMA pipeline was tested successfully in hardware using a simplified solver model. The details of implementation, the limitations, and future work are also discussed.

Computational experiments involving population size for FPGA-based implementation of a GA for the TSP

The feasibility of using an in-hardware implementation of a genetic algorithm (GA) to solve the computationally expensive travelling salesman problem (TSP) is explored, especially in regard to hardware resource requirements for problem and population sizes. We investigate via numerical experiments whether a small population size might prove sufficient to obtain reasonable quality solutions for the TSP, thereby permitting relatively resource efficient hardware implementation on field programmable gate arrays (FPGAs). Software experiments on two TSP benchmarks involving 48 and 532 cities were used to explore the extent to which population size can be reduced without compromising solution quality, and results show that a GA allowed to run for a large number of generations with a smaller population size can yield solutions of comparable quality to those obtained using a larger population. This finding is then used to investigate feasible problem sizes on a targeted Virtex-7 vx485T-2 FPGA platform via exploration of hardware resource requirements for memory and data flow operations.

Simulation of phosphine flow in vertical grain storage : a preliminary numerical study

To fumigate grain stored in a silo, phosphine gas is distributed by a combination of diffusion and fan-forced advection. This initial study of the problem mainly focuses on the advection, numerically modelled as fluid flow in a porous medium. We find satisfactory agreement between the flow predictions of two Computational Fluid Dynamics packages, Comsol and Fluent. The flow predictions demonstrate that the highest velocity (>0.1 m/s) occurs less than 0.2m from the inlet and reduces drastically over one metre of silo height, with the flow elsewhere less than 0.002 m/s or 1% of the velocity injection. The flow predictions are examined to identify silo regions where phosphine dosage levels are likely to be too low for effective grain fumigation.

Calculation of engine parameters using reconfigurable hardware

The feasibility of real-time calculation of parameters for an internal combustion engine via reconfigurable hardware implementation is investigated as an alternative to software computation. A detailed in-hardware field programmable gate array (FPGA)-based design is developed and evaluated using input crank angle and in-cylinder pressure data from fully instrumented diesel engines in the QUT Biofuel Engine Research Facility (BERF). Results indicate the feasibility of employing a hardware-based implementation for real-time processing for speeds comparable to the data sampling rate currently used in the facility, with acceptably low level of discrepancies between hardware and software-based calculation of key engine parameters.

Pilot evaluation of an adolescent risk and injury prevention programme incorporating curriculum and school connectedness components

School connectedness is an important protective factor for adolescent risk-taking behaviour. This study examined a pilot version of the Skills for Preventing Injury in Youth (SPIY) programme, combining teacher professional development for increasing school connectedness (connectedness component) with a risk and injury prevention curriculum for early adolescents (curriculum component). A process evaluation was conducted on the connectedness component, involving assessments of programme reach, participant receptiveness and initial use, and a preliminary impact evaluation was conducted on the combined connectedness and curriculum programme. The connectedness component was well received by teacher participants, who saw benefits for both themselves and their students. Classroom observation also showed that teachers who received professional development made use of the programme strategies. Grade 8 students who participated in the SPIY programme were less likely to report violent behaviour at six-month follow-up than were control students, and trends also suggested reduced transport injuries. The results of this research support the use of the combined SPIY connectedness and curriculum components in a large-scale effectiveness trial to assess the impact of the programme on students’ connectedness, risk-taking and associated injuries.

Feasibility of using telecommunications technology in a Cardiac-Diabetes Self-Management Program

Background: Evidence demonstrates self-management programs are an effective approach to assist patients with chronic diseases such as type 2 diabetes or cardiac conditions to modify their lifestyle for better managing their conditions. Using information technology (IT) has great potential to support self-management programs and assist patients to fulfill their goals in managing their conditions more efficiently and effectively. Examples of different types of technology used in self-management programs that have limited research support include: text messages, telephone followup, web-based programs, and other internet-assisted education. But little is known about the applicability and feasiability of different forms of technology for patients with chronic diseases such as those with type 2 diabetes and critical cardiac conditions. Furthermore, although there is some evidence of the benefits of using IT in supporting self-management programs, further research on the use of IT in such programs is recommended. Objective: To develop and pilot test an integrated Cardiac- Diabetes Self-Management Program (CDSMP) incorporating telephone and text-message follow-up. Methods: A pilot study using randomised controlled trial is conducted in the coronary care unit (CCU) in a Brisbane metropolitan hospital in Australia to collect data on patients with type 2 diabetes admitted to CCU. The main outcomes included self-efficacy levels, knowledge, and quality of life. Results: Initial results reveal that patients with diabetes admitted to the CCU in the experimental group did improve their self-efficacy, and knowledge levels. Acknowledgements: This Project is funded by QUT Early Career Researcher Research Grant

Leveraging R&D Investment for the Australian Built Environment : Industry Report

The overarching goal of this project is to better match funding strategies to industry needs to maximise the benefits of R&D to Australia’s infrastructure and building industry. Project partners are: Queensland Department of Public Works; Queensland Transport and Main Roads; Western Australian Department of Treasury and Finance; John Holland; Queensland University of Technology; Swinburne University of Technology; and VTT Technical Research Centre of Finland (Prof Göran Roos). This project has been endorsed by the Australian Built Environment Industry Innovation Council (BEIIC) with Council member Prof Catherin Bull serving on this project’s Steering Committee. This project seeks to: (i) maximise the value of R&D investment in this sector through improved understanding of future industry research needs; and (ii) address the perceived problem of a disproportionately low R&D investment in this sector, relative to the size and national importance of the sector. This research will develop new theory built on open innovation, dynamic capabilities and absorptive capacity theories in the context of strategic foresighting and roadmapping activities. Four project phases have been designed to address this research: 1: Audit and analysis of R&D investment in the Australian built environment since 1990 - access publically available data relating to R&D investments across Australia from public and private organisations to understand past trends. 2: Examine diffusion mechanisms of research and innovation and its impact on public and private organisations – investigate specific R&D investments to determine the process of realising research support, direction-setting, project engagement, impacts and pathways to adoption. 3: Develop a strategic roadmap for the future of this critical Australian industry - assess the likely future landscapes that R&D investment will both respond to and anticipate. 4: Develop policy to maximise the value of R&D investments to public and private organisations – through translating project learnings into policy guidelines.

Image-based flow visualisation (IBFV) to enhance interpretation of complex flow patterns within a shallow tidal barrier estuary

We applied a texture-based flow visualisation technique to a numerical hydrodynamic model of the Pumicestone Passage in southeast Queensland, Australia. The quality of the visualisations using our flow visualisation tool, are compared with animations generated using more traditional drogue release plot and velocity contour and vector techniques. The texture-based method is found to be far more effective in visualising advective flow within the model domain. In some instances, it also makes it easier for the researcher to identify specific hydrodynamic features within the complex flow regimes of this shallow tidal barrier estuary as compared with the direct and geometric based methods.

Effect of CT electron density identification on Monte Carlo simulations of radiotherapeutic treatments

Introduction: The accurate identification of tissue electron densities is of great importance for Monte Carlo (MC) dose calculations. When converting patient CT data into a voxelised format suitable for MC simulations, however, it is common to simplify the assignment of electron densities so that the complex tissues existing in the human body are categorized into a few basic types. This study examines the effects that the assignment of tissue types and the calculation of densities can have on the results of MC simulations, for the particular case of a Siemen’s Sensation 4 CT scanner located in a radiotherapy centre where QA measurements are routinely made using 11 tissue types (plus air). Methods: DOSXYZnrc phantoms are generated from CT data, using the CTCREATE user code, with the relationship between Hounsfield units (HU) and density determined via linear interpolation between a series of specified points on the ‘CT-density ramp’ (see Figure 1(a)). Tissue types are assigned according to HU ranges. Each voxel in the DOSXYZnrc phantom therefore has an electron density (electrons/cm3) defined by the product of the mass density (from the HU conversion) and the intrinsic electron density (electrons /gram) (from the material assignment), in that voxel. In this study, we consider the problems of density conversion and material identification separately: the CT-density ramp is simplified by decreasing the number of points which define it from 12 down to 8, 3 and 2; and the material-type-assignment is varied by defining the materials which comprise our test phantom (a Supertech head) as two tissues and bone, two plastics and bone, water only and (as an extreme case) lead only. The effect of these parameters on radiological thickness maps derived from simulated portal images is investigated. Results & Discussion: Increasing the degree of simplification of the CT-density ramp results in an increasing effect on the resulting radiological thickness calculated for the Supertech head phantom. For instance, defining the CT-density ramp using 8 points, instead of 12, results in a maximum radiological thickness change of 0.2 cm, whereas defining the CT-density ramp using only 2 points results in a maximum radiological thickness change of 11.2 cm. Changing the definition of the materials comprising the phantom between water and plastic and tissue results in millimetre-scale changes to the resulting radiological thickness. When the entire phantom is defined as lead, this alteration changes the calculated radiological thickness by a maximum of 9.7 cm. Evidently, the simplification of the CT-density ramp has a greater effect on the resulting radiological thickness map than does the alteration of the assignment of tissue types. Conclusions: It is possible to alter the definitions of the tissue types comprising the phantom (or patient) without substantially altering the results of simulated portal images. However, these images are very sensitive to the accurate identification of the HU-density relationship. When converting data from a patient’s CT into a MC simulation phantom, therefore, all possible care should be taken to accurately reproduce the conversion between HU and mass density, for the specific CT scanner used. Acknowledgements: This work is funded by the NHMRC, through a project grant, and supported by the Queensland University of Technology (QUT) and the Royal Brisbane and Women's Hospital (RBWH), Brisbane, Australia. The authors are grateful to the staff of the RBWH, especially Darren Cassidy, for assistance in obtaining the phantom CT data used in this study. The authors also wish to thank Cathy Hargrave, of QUT, for assistance in formatting the CT data, using the Pinnacle TPS. Computational resources and services used in this work were provided by the HPC and Research Support Group, QUT, Brisbane, Australia.

Phantom Scatter and the A-SI EPID

Introduction: The use of amorphous-silicon electronic portal imaging devices (a-Si EPIDs) for dosimetry is complicated by the effects of scattered radiation. In photon radiotherapy, primary signal at the detector can be accompanied by photons scattered from linear accelerator components, detector materials, intervening air, treatment room surfaces (floor, walls, etc) and from the patient/phantom being irradiated. Consequently, EPID measurements which presume to take scatter into account are highly sensitive to the identification of these contributions. One example of this susceptibility is the process of calibrating an EPID for use as a gauge of (radiological) thickness, where specific allowance must be made for the effect of phantom-scatter on the intensity of radiation measured through different thicknesses of phantom. This is usually done via a theoretical calculation which assumes that phantom scatter is linearly related to thickness and field-size. We have, however, undertaken a more detailed study of the scattering effects of fields of different dimensions when applied to phantoms of various thicknesses in order to derive scattered-primary ratios (SPRs) directly from simulation results. This allows us to make a more-accurate calibration of the EPID, and to qualify the appositeness of the theoretical SPR calculations. Methods: This study uses a full MC model of the entire linac-phantom-detector system simulated using EGSnrc/BEAMnrc codes. The Elekta linac and EPID are modelled according to specifications from the manufacturer and the intervening phantoms are modelled as rectilinear blocks of water or plastic, with their densities set to a range of physically realistic and unrealistic values. Transmissions through these various phantoms are calculated using the dose detected in the model EPID and used in an evaluation of the field-size-dependence of SPR, in different media, applying a method suggested for experimental systems by Swindell and Evans [1]. These results are compared firstly with SPRs calculated using the theoretical, linear relationship between SPR and irradiated volume, and secondly with SPRs evaluated from our own experimental data. An alternate evaluation of the SPR in each simulated system is also made by modifying the BEAMnrc user code READPHSP, to identify and count those particles in a given plane of the system that have undergone a scattering event. In addition to these simulations, which are designed to closely replicate the experimental setup, we also used MC models to examine the effects of varying the setup in experimentally challenging ways (changing the size of the air gap between the phantom and the EPID, changing the longitudinal position of the EPID itself). Experimental measurements used in this study were made using an Elekta Precise linear accelerator, operating at 6MV, with an Elekta iView GT a-Si EPID. Results and Discussion: 1. Comparison with theory: With the Elekta iView EPID fixed at 160 cm from the photon source, the phantoms, when positioned isocentrically, are located 41 to 55 cm from the surface of the panel. At this geometry, a close but imperfect agreement (differing by up to 5%) can be identified between the results of the simulations and the theoretical calculations. However, this agreement can be totally disrupted by shifting the phantom out of the isocentric position. Evidently, the allowance made for source-phantom-detector geometry by the theoretical expression for SPR is inadequate to describe the effect that phantom proximity can have on measurements made using an (infamously low-energy sensitive) a-Si EPID. 2. Comparison with experiment: For various square field sizes and across the range of phantom thicknesses, there is good agreement between simulation data and experimental measurements of the transmissions and the derived values of the primary intensities. However, the values of SPR obtained through these simulations and measurements seem to be much more sensitive to slight differences between the simulated and real systems, leading to difficulties in producing a simulated system which adequately replicates the experimental data. (For instance, small changes to simulated phantom density make large differences to resulting SPR.) 3. Comparison with direct calculation: By developing a method for directly counting the number scattered particles reaching the detector after passing through the various isocentric phantom thicknesses, we show that the experimental method discussed above is providing a good measure of the actual degree of scattering produced by the phantom. This calculation also permits the analysis of the scattering sources/sinks within the linac and EPID, as well as the phantom and intervening air. Conclusions: This work challenges the assumption that scatter to and within an EPID can be accounted for using a simple, linear model. Simulations discussed here are intended to contribute to a fuller understanding of the contribution of scattered radiation to the EPID images that are used in dosimetry calculations. Acknowledgements: This work is funded by the NHMRC, through a project grant, and supported by the Queensland University of Technology (QUT) and the Royal Brisbane and Women's Hospital, Brisbane, Australia. The authors are also grateful to Elekta for the provision of manufacturing specifications which permitted the detailed simulation of their linear accelerators and amorphous-silicon electronic portal imaging devices. Computational resources and services used in this work were provided by the HPC and Research Support Group, QUT, Brisbane, Australia.

The development of Monte Carlo techniques for the verification of radiotherapy treatments

Introduction: Recent advances in the planning and delivery of radiotherapy treatments have resulted in improvements in the accuracy and precision with which therapeutic radiation can be administered. As the complexity of the treatments increases it becomes more difficult to predict the dose distribution in the patient accurately. Monte Carlo (MC) methods have the potential to improve the accuracy of the dose calculations and are increasingly being recognised as the ‘gold standard’ for predicting dose deposition in the patient [1]. This project has three main aims: 1. To develop tools that enable the transfer of treatment plan information from the treatment planning system (TPS) to a MC dose calculation engine. 2. To develop tools for comparing the 3D dose distributions calculated by the TPS and the MC dose engine. 3. To investigate the radiobiological significance of any errors between the TPS patient dose distribution and the MC dose distribution in terms of Tumour Control Probability (TCP) and Normal Tissue Complication Probabilities (NTCP). The work presented here addresses the first two aims. Methods: (1a) Plan Importing: A database of commissioned accelerator models (Elekta Precise and Varian 2100CD) has been developed for treatment simulations in the MC system (EGSnrc/BEAMnrc). Beam descriptions can be exported from the TPS using the widespread DICOM framework, and the resultant files are parsed with the assistance of a software library (PixelMed Java DICOM Toolkit). The information in these files (such as the monitor units, the jaw positions and gantry orientation) is used to construct a plan-specific accelerator model which allows an accurate simulation of the patient treatment field. (1b) Dose Simulation: The calculation of a dose distribution requires patient CT images which are prepared for the MC simulation using a tool (CTCREATE) packaged with the system. Beam simulation results are converted to absolute dose per- MU using calibration factors recorded during the commissioning process and treatment simulation. These distributions are combined according to the MU meter settings stored in the exported plan to produce an accurate description of the prescribed dose to the patient. (2) Dose Comparison: TPS dose calculations can be obtained using either a DICOM export or by direct retrieval of binary dose files from the file system. Dose difference, gamma evaluation and normalised dose difference algorithms [2] were employed for the comparison of the TPS dose distribution and the MC dose distribution. These implementations are spatial resolution independent and able to interpolate for comparisons. Results and Discussion: The tools successfully produced Monte Carlo input files for a variety of plans exported from the Eclipse (Varian Medical Systems) and Pinnacle (Philips Medical Systems) planning systems: ranging in complexity from a single uniform square field to a five-field step and shoot IMRT treatment. The simulation of collimated beams has been verified geometrically, and validation of dose distributions in a simple body phantom (QUASAR) will follow. The developed dose comparison algorithms have also been tested with controlled dose distribution changes. Conclusion: The capability of the developed code to independently process treatment plans has been demonstrated. A number of limitations exist: only static fields are currently supported (dynamic wedges and dynamic IMRT will require further development), and the process has not been tested for planning systems other than Eclipse and Pinnacle. The tools will be used to independently assess the accuracy of the current treatment planning system dose calculation algorithms for complex treatment deliveries such as IMRT in treatment sites where patient inhomogeneities are expected to be significant. Acknowledgements: Computational resources and services used in this work were provided by the HPC and Research Support Group, Queensland University of Technology, Brisbane, Australia. Pinnacle dose parsing made possible with the help of Paul Reich, North Coast Cancer Institute, North Coast, New South Wales.