Automatic Mapping and Characterisation of Linear Depositional Bedforms: Theory and Application Using Bathymetry from the North West Shelf of Australia

publishedVersio

Distributed texture-based terrain synthesis

Terrain synthesis is an important field of Computer Graphics that deals with the generation of 3D landscape models for use in virtual environments. The field has evolved to a stage where large and even infinite landscapes can be generated in realtime. However, user control of the generation process is still minimal, as well as the creation of virtual landscapes that mimic real terrain. This thesis investigates the use of texture synthesis techniques on real landscapes to improve realism and the use of sketch-based interfaces to enable intuitive user control

Fast, Realistic Terrain Synthesis

The authoring of realistic terrain models is necessary to generate immersive virtual environments for computer games and film visual effects. However, creating these landscapes is difficult – it usually involves an artist spending many hours sculpting a model in a 3D design program. Specialised terrain generation programs exist to rapidly create artificial terrains, such as Bryce (2013) and Terragen (2013). These make use of complex algorithms to pseudo-randomly generate the terrains, which can then be exported into a 3D editing program for fine tuning. Height-maps are a 2D data-structure, which stores elevation values, and can be used to represent terrain data. They are also a common format used with terrain generation and editing systems. Height-maps share the same storage design as image files, as such they can be viewed like any picture and image transformation algorithms can be applied to them. Early techniques for generating terrains include fractal generation and physical simulation. These methods proved difficult to use as the algorithms were manipulated with a set of parameters. However, the outcome from changing the values is not known, which results in the user changing values over several iterations to produce their desired terrain. An improved technique brings in a higher degree of user control as well as improved realism, known as texture-based terrain synthesis. This borrows techniques from texture synthesis, which is the process of algorithmically generating a larger image from a smaller sample image. Texture-based terrain synthesis makes use or real-world terrain data to produce highly realistic landscapes, which improves upon previous techniques. Recent work in texture-based synthesis has focused on improving both the realism and user control, through the use of sketching interfaces. We present a patch-based terrain synthesis system that utilises a user sketch to control the location of desired terrain features, such as ridges and valleys. Digital Elevation Models (DEMs) of real landscapes are used as exemplars, from which candidate patches of data are extracted and matched against the user’s sketch. The best candidates are merged seamlessly into the final terrain. Because real landscapes are used the resulting terrain appears highly realistic. Our research contributes a new version of this approach that employs multiple input terrains and acceleration using a modern Graphics Processing Unit (GPU). The use of multiple inputs increases the candidate pool of patches and thus the system is capable of producing more varied terrains. This addresses the limitation where supplying the wrong type of input terrain would fail to synthesise anything useful, for example supplying the system with a mountainous DEM and expecting deep valleys in the output. We developed a hybrid multithreaded CPU and GPU implementation that achieves a 45 times speedup

Spatializing the Soil-Ecological Factorial: Data Driven Integrated Land Management Tools

Soils form the dynamic interface of many processes key to the function of terrestrial ecosystems. Many soil properties both influence and are influenced by activity of flora and fauna. Interactions between soils, biota, and climate determine the potential ecosystem services that a given unique ecological site (ES) can support, and how resilient a site is to various pressures and disturbances. Soil data are needed to fully understand how these factors interact, but because this data is difficult to obtain, existing soil maps are sometimes not detailed enough to fully explore relationships. Environmental raster GIS data layers were used to increase the detail of maps by representing soil forming factors and associated ecological pedomemory legacies important to understanding ecological potential. This dissertation presents methods and tools to help create these new soil maps at appropriate resolution and theme for field scale assessment of ecological sites that enable land managers to plan and implement appropriate management decisions.;USDA-NRCS soil surveys were disaggregated to higher resolution maps using a semi-automated expert training routine to implement a random forest classification model. This transformed soil map polygons of variable thematic and spatial resolution (soil map unit concepts) to a consistent 30-meter raster grid of unified theme (soil taxa). Disaggregated maps (DM) showed highly variable accuracy (25--75% overall validation accuracy) that mirrored that of the original soil surveys evaluated in Arizona (AZ) and West Virginia (WV). However, disaggregated maps expressed the soil data at a much more detailed spatial scale with a more interpretable legend. The WV surveys exhibited much lower accuracy than the AZ survey evaluated. This lower accuracy in WV is likely due to the forested setting and highly dissected landscape, two factors that create more intrinsic soil variability that is harder to explain with spatial covariates.;Ecological site descriptions (ESD) document soil-ecosystem groups that produce unique amounts and types of biological constituents and respond similarly to disturbance and environmental variation. ESD are linked to soil map unit components in USDA-NRCS soil surveys and are used as the basis for land management planning on rangelands and forestlands. The component level connection makes DM a good way to spatialize ESD because both are spatially represented at the same thematic level, whereas conventional soil maps have polygons that often have multiple components linked to a delineation.;However, in the evaluation of mapping ESD via DM, the DM turned out not to document the key difference in spodic soil properties that distinguished the important ecotone between northern hardwood and alpine red spruce conifer ESDs in Pocahontas and Randolph counties, WV. So, to adjust, spodic soil properties were mapped directly using digital soil mapping approaches. A strong spatial model of spodic soil morphology presence was developed from a random forest probability model and showed correspondence to red spruce and hemlock occurrences in local historic land deed witness trees from records between 1752 and 1899. From this result, areas with spodic soil properties were assumed to be associated with historic red spruce communities, although 68% of those areas in the WV study area are currently under hardwood cover. This would seem to indicate that hardwoods have encroached on the historic extent of spruce, which is consistent with other recent studies. O-horizon thickness was also observed to be one cm thicker for every 10% greater importance value of red spruce or hemlock versus that of hardwood species at field sites. From these observations, it was calculated conservatively that at least 3.74-6.62 Tg of C have likely been lost from red spruce influenced ecological sites in WV due to historic disturbance related conversions of forest to hardwood composition. These results highlight the value of working within a soil-ecological factorial framework (e.g. an ESD) to contextualize land management options and potential derived services or negative consequences of each available action

Feature-rich distance-based terrain synthesis

This thesis describes a novel terrain synthesis method based on distances in a weighted graph. The method begins with a regular lattice with arbitrary edge weights; heights are determined by path cost from a set of generator nodes. The shapes of individual terrain features, such as mountains, hills, and craters, are specified by a monotonically decreasing profile describing the cross-sectional shape of a feature, while the locations of features in the terrain are specified by placing the generators. Pathing places ridges whose initial location have a dendritic shape. The method is robust and easy to control, making it possible to create pareidolia effects. It can produce a wide range of realistic synthetic terrains such as mountain ranges, craters, faults, cinder cones, and hills. The algorithm incorporates random graph edge weights, permits the inclusion of multiple topography profiles, and allows precise control over placement of terrain features and their heights. These properties all allow the artist to create highly heterogeneous terrains that compare quite favorably to existing methods

Hydrogen bonding and the stability of the polypeptide backbone

The tertiary structures of globular proteins are crucial in determining reactivity and specificity as biological catalysts and signalling systems. The rules determining the final fold of a protein are still unknown, but some progress has been made in defining tertiary structure in terms of the secondary structure, the conformation of the polypeptide chain. Perhaps surprisingly, not all of the conformational properties of this backbone are known, and several new approaches to studying these are described. Most studies of peptide structure have focused on hydrogen bonding, and this is used as a starting point for this study. Different descriptions of the hydrogen bond, from geometric rules to ab initio calculations, are considered, and an approach based on analysing contributions of individual polar groups to the potential energy using semi empirical Lennard-Jones calculations is chosen on grounds of accuracy, flexibility, and ease of calculation. Using this approach, it is shown that electrostatic interactions between main chain atoms stabilise the right handed twist found in Beta-strands and similar interactions between main-chain atoms not hydrogen bonded to each other influence the geometries of hydrogen bonds in Alpha-helices and Beta-sheets. A role for water and tertiary hydrogen bonds in determining backbone conformation is suggested. The same technique makes it possible to investigate interatomic repulsions as well as attractions. A detailed analysis of the attractions and repulsions in an idealised polypeptide explains many of the features of helical structures in proteins, and suggests a hitherto unexpected directional helix forming pathway, which is supported by a range of kinetic and structural data. Software for automated searching of a hydrogen bond database is developed, and used to identify hydrogen bonded rings formed by amide side chains and main chain peptides. Integrating the database with novel visualisation techniques allows a previously unidentified property of beta sheets, the hydrophobic ridge, to be detected. A range of different computational approaches was used surging this research, from molecular modelling to database searching. Several pieces of software were developed, and these are described together with some observations about the types of software and working environments which were found to be useful in structural biochemistry, and what types of software technology could be developed to make this task easier