Visualization, Exploration and Data Analysis of Complex Astrophysical Data

In this paper we show how advanced visualization tools can help the researcher in investigating and extracting information from data. The focus is on VisIVO, a novel open source graphics application, which blends high performance multidimensional visualization techniques and up-to-date technologies to cooperate with other applications and to access remote, distributed data archives. VisIVO supports the standards defined by the International Virtual Observatory Alliance in order to make it interoperable with VO data repositories. The paper describes the basic technical details and features of the software and it dedicates a large section to show how VisIVO can be used in several scientific cases.Comment: 32 pages, 15 figures, accepted by PAS

Isosurface extraction and haptic rendering of volumetric data.

Kwong-Wai, Chen.Thesis (M.Phil.)--Chinese University of Hong Kong, 2000.Includes bibliographical references (leaves 114-118).Abstracts in English and Chinese.Abstract --- p.iAcknowledgments --- p.iiiChapter 1 --- Introduction --- p.1Chapter 1.1 --- Volumetric Data --- p.1Chapter 1.2 --- Volume Visualization --- p.4Chapter 1.3 --- Thesis Contributions --- p.5Chapter 1.4 --- Thesis Outline --- p.6Chapter I --- Multi-body Surface Extraction --- p.8Chapter 2 --- Isosurface Extraction --- p.9Chapter 2.1 --- Previous Works --- p.10Chapter 2.1.1 --- Marching Cubes --- p.10Chapter 2.1.2 --- Skeleton Climbing --- p.12Chapter 2.1.3 --- Adaptive Skeleton Climbing --- p.14Chapter 2.2 --- Motivation --- p.17Chapter 3 --- Multi-body Surface Extraction --- p.19Chapter 3.1 --- Multi-body Surface --- p.19Chapter 3.2 --- Building 0-skeleton --- p.21Chapter 3.3 --- Building 1-skeleton --- p.23Chapter 3.3.1 --- Non-binary Faces --- p.24Chapter 3.3.2 --- Non-binary Cubes --- p.30Chapter 3.4 --- General Scheme for Messy Cubes --- p.33Chapter 3.4.1 --- Graph Reduction --- p.34Chapter 3.4.2 --- Position of the Tetrapoints --- p.36Chapter 3.5 --- Triangular Mesh Generation --- p.37Chapter 3.5.1 --- Generating the Edge Loops --- p.38Chapter 3.5.2 --- Triangulating the Edge Loops --- p.41Chapter 3.5.3 --- Incorporating with Adaptive Skeleton Climbing --- p.43Chapter 3.6 --- Implementation and Results --- p.45Chapter II --- Haptic Rendering of Volumetric Data --- p.60Chapter 4 --- Introduction to Haptics --- p.61Chapter 4.1 --- Terminology --- p.62Chapter 4.2 --- Haptic Rendering Process --- p.63Chapter 4.2.1 --- The Overall Process --- p.64Chapter 4.2.2 --- Force Profile --- p.65Chapter 4.2.3 --- Decoupling Processes --- p.66Chapter 4.3 --- The PHANToM´ёØ Haptic Interface --- p.67Chapter 4.4 --- Research Goals --- p.69Chapter 5 --- Haptic Rendering of Geometric Models --- p.70Chapter 5.1 --- Penalty Based Methods --- p.71Chapter 5.1.1 --- Vector Fields for Solid Objects --- p.71Chapter 5.1.2 --- Drawbacks of Penalty Based Methods --- p.72Chapter 5.2 --- Constraint Based Methods --- p.73Chapter 5.2.1 --- Virtual Haptic Interface Point --- p.73Chapter 5.2.2 --- The Constraints --- p.74Chapter 5.2.3 --- Location Computation --- p.78Chapter 5.2.4 --- Force Shading --- p.79Chapter 5.2.5 --- Adding Surface Properties --- p.80Chapter 6 --- Haptic Rendering of Volumetric Data --- p.83Chapter 6.1 --- Volume Haptization --- p.84Chapter 6.2 --- Isosurface Haptic Rendering --- p.86Chapter 6.3 --- Intermediate Representation Approach --- p.89Chapter 6.3.1 --- Introduction --- p.89Chapter 6.3.2 --- Intermediate Virtual Plane --- p.90Chapter 6.3.3 --- Updating Virtual Plane --- p.92Chapter 6.3.4 --- Preventing Force Discontinuity Artifacts --- p.93Chapter 6.3.5 --- Experiments and Results --- p.94Chapter 7 --- Conclusions and Future Research Directions --- p.98Chapter 7.1 --- Conclusions --- p.98Chapter 7.2 --- Future Research Directions --- p.99Chapter A --- Two Proofs of Multi-body Surface Extraction Algorithm --- p.101Chapter A.1 --- Graph Terminology and Theorems --- p.101Chapter A.2 --- Occurrence of Tripoints in Negative-Positive Pairs --- p.103Chapter A.3 --- Validity of the General Scheme --- p.103Chapter B --- An Example of Multi-body Surface Extraction Algorithm --- p.105Chapter B.1 --- Step 1: Building 0-Skeleton --- p.105Chapter B.2 --- Step 2: Building 1-Skeleton --- p.106Chapter B.2.1 --- Step 2a: Building 1-Skeleton and Tripoints on Cube Faces --- p.106Chapter B.2.2 --- Step 2b: Adding Tetrapoints and Tri-edges inside Cube --- p.106Chapter B.3 --- Step 3: Constructing Edge Loops and Triangulating --- p.109Bibliography --- p.11

Artifact-Based Rendering: Harnessing Natural and Traditional Visual Media for More Expressive and Engaging 3D Visualizations

We introduce Artifact-Based Rendering (ABR), a framework of tools, algorithms, and processes that makes it possible to produce real, data-driven 3D scientific visualizations with a visual language derived entirely from colors, lines, textures, and forms created using traditional physical media or found in nature. A theory and process for ABR is presented to address three current needs: (i) designing better visualizations by making it possible for non-programmers to rapidly design and critique many alternative data-to-visual mappings; (ii) expanding the visual vocabulary used in scientific visualizations to depict increasingly complex multivariate data; (iii) bringing a more engaging, natural, and human-relatable handcrafted aesthetic to data visualization. New tools and algorithms to support ABR include front-end applets for constructing artifact-based colormaps, optimizing 3D scanned meshes for use in data visualization, and synthesizing textures from artifacts. These are complemented by an interactive rendering engine with custom algorithms and interfaces that demonstrate multiple new visual styles for depicting point, line, surface, and volume data. A within-the-research-team design study provides early evidence of the shift in visualization design processes that ABR is believed to enable when compared to traditional scientific visualization systems. Qualitative user feedback on applications to climate science and brain imaging support the utility of ABR for scientific discovery and public communication.Comment: Published in IEEE VIS 2019, 9 pages of content with 2 pages of references, 12 figure

Dynamic Multivariate Simplex Splines For Volume Representation And Modeling

Volume representation and modeling of heterogeneous objects acquired from real world are very challenging research tasks and playing fundamental roles in many potential applications, e.g., volume reconstruction, volume simulation and volume registration. In order to accurately and efficiently represent and model the real-world objects, this dissertation proposes an integrated computational framework based on dynamic multivariate simplex splines (DMSS) that can greatly improve the accuracy and efficacy of modeling and simulation of heterogenous objects. The framework can not only reconstruct with high accuracy geometric, material, and other quantities associated with heterogeneous real-world models, but also simulate the complicated dynamics precisely by tightly coupling these physical properties into simulation. The integration of geometric modeling and material modeling is the key to the success of representation and modeling of real-world objects. The proposed framework has been successfully applied to multiple research areas, such as volume reconstruction and visualization, nonrigid volume registration, and physically based modeling and simulation

The Shape of Damping: Optimizing Damping Coefficients to Improve Transparency on Bilateral Telemanipulation

This thesis presents a novel optimization-based passivity control algorithm for hapticenabled bilateral teleoperation systems involving multiple degrees of freedom. In particular, in the context of energy-bounding control, the contribution focuses on the implementation of a passivity layer for an existing time-domain scheme, ensuring optimal transparency of the interaction along subsets of the environment space which are preponderant for the given task, while preserving the energy bounds required for passivity. The involved optimization problem is convex and amenable to real-time implementation. The effectiveness of the proposed design is validated via an experiment performed on a virtual teleoperated environment. The interplay between transparency and stability is a critical aspect in haptic-enabled bilateral teleoperation control. While it is important to present the user with the true impedance of the environment, destabilizing factors such as time delays, stiff environments, and a relaxed grasp on the master device may compromise the stability and safety of the system. Passivity has been exploited as one of the the main tools for providing sufficient conditions for stable teleoperation in several controller design approaches, such as the scattering algorithm, timedomain passivity control, energy bounding algorithm, and passive set position modulation. In this work it is presented an innovative energy-based approach, which builds upon existing time-domain passivity controllers, improving and extending their effectiveness and functionality. The set of damping coefficients are prioritized in each degree of freedom, the resulting transparency presents a realistic force feedback in comparison to the other directions. Thus, the prioritization takes effect using a quadratic programming algorithm to find the optimal values for the damping. Finally, the energy tanks approach on passivity control is a solution used to ensure stability in a system for robotics bilateral manipulation. The bilateral telemanipulation must maintain the principle of passivity in all moments to preserve the system\u2019s stability. This work presents a brief introduction to haptic devices as a master component on the telemanipulation chain; the end effector in the slave side is a representation of an interactive object within an environment having a force sensor as feedback signal. The whole interface is designed into a cross-platform framework named ROS, where the user interacts with the system. Experimental results are presented

Performance Factors in Neurosurgical Simulation and Augmented Reality Image Guidance

Virtual reality surgical simulators have seen widespread adoption in an effort to provide safe, cost-effective and realistic practice of surgical skills. However, the majority of these simulators focus on training low-level technical skills, providing only prototypical surgical cases. For many complex procedures, this approach is deficient in representing anatomical variations that present clinically, failing to challenge users’ higher-level cognitive skills important for navigation and targeting. Surgical simulators offer the means to not only simulate any case conceivable, but to test novel approaches and examine factors that influence performance. Unfortunately, there is a void in the literature surrounding these questions. This thesis was motivated by the need to expand the role of surgical simulators to provide users with clinically relevant scenarios and evaluate human performance in relation to image guidance technologies, patient-specific anatomy, and cognitive abilities. To this end, various tools and methodologies were developed to examine cognitive abilities and knowledge, simulate procedures, and guide complex interventions all within a neurosurgical context. The first chapter provides an introduction to the material. The second chapter describes the development and evaluation of a virtual anatomical training and examination tool. The results suggest that learning occurs and that spatial reasoning ability is an important performance predictor, but subordinate to anatomical knowledge. The third chapter outlines development of automation tools to enable efficient simulation studies and data management. In the fourth chapter, subjects perform abstract targeting tasks on ellipsoid targets with and without augmented reality guidance. While the guidance tool improved accuracy, performance with the tool was strongly tied to target depth estimation – an important consideration for implementation and training with similar guidance tools. In the fifth chapter, neurosurgically experienced subjects were recruited to perform simulated ventriculostomies. Results showed anatomical variations influence performance and could impact outcome. Augmented reality guidance showed no marked improvement in performance, but exhibited a mild learning curve, indicating that additional training may be warranted. The final chapter summarizes the work presented. Our results and novel evaluative methodologies lay the groundwork for further investigation into simulators as versatile research tools to explore performance factors in simulated surgical procedures

Meshless Mechanics and Point-Based Visualization Methods for Surgical Simulations

Computer-based modeling and simulation practices have become an integral part of the medical education field. For surgical simulation applications, realistic constitutive modeling of soft tissue is considered to be one of the most challenging aspects of the problem, because biomechanical soft-tissue models need to reflect the correct elastic response, have to be efficient in order to run at interactive simulation rates, and be able to support operations such as cuts and sutures. Mesh-based solutions, where the connections between the individual degrees of freedom (DoF) are defined explicitly, have been the traditional choice to approach these problems. However, when the problem under investigation contains a discontinuity that disrupts the connectivity between the DoFs, the underlying mesh structure has to be reconfigured in order to handle the newly introduced discontinuity correctly. This reconfiguration for mesh-based techniques is typically called dynamic remeshing, and most of the time it causes the performance bottleneck in the simulation. In this dissertation, the efficiency of point-based meshless methods is investigated for both constitutive modeling of elastic soft tissues and visualization of simulation objects, where arbitrary discontinuities/cuts are applied to the objects in the context of surgical simulation. The point-based deformable object modeling problem is examined in three functional aspects: modeling continuous elastic deformations with, handling discontinuities in, and visualizing a point-based object. Algorithmic and implementation details of the presented techniques are discussed in the dissertation. The presented point-based techniques are implemented as separate components and integrated into the open-source software framework SOFA. The presented meshless continuum mechanics model of elastic tissue were verified by comparing it to the Hertzian non-adhesive frictionless contact theory. Virtual experiments were setup with a point-based deformable block and a rigid indenter, and force-displacement curves obtained from the virtual experiments were compared to the theoretical solutions. The meshless mechanics model of soft tissue and the integrated novel discontinuity treatment technique discussed in this dissertation allows handling cuts of arbitrary shape. The implemented enrichment technique not only modifies the internal mechanics of the soft tissue model, but also updates the point-based visual representation in an efficient way preventing the use of costly dynamic remeshing operations

Visual-auditory visualisation of dynamic multi-scale heterogeneous objects.

The multi-scale phenomena analysis is an area of active research that is connecting simulations with experiments to get a correct insight into the compound dynamic structure. Visualisation is a challenging task due to a large amount of data and a wide range of complex data representations. The analysis of dynamic multi-scale phenomena requires a combination of geometric modelling and rendering techniques for the analysis of the changes in the internal structure in the case of data coming from different sources of various nature. Moreover, the area often addresses the limitations of solely visual data representation and considers the introduction of other sensory stimuli as a well-known tool to enhance visual analysis. However, there is a lack of software tools allowing perform an advanced real-time analysis of heterogeneous phenomena properties. The hardware-accelerated volume rendering allows getting insight into the internal structure of complex multi-scale phenomena. The technique is convenient for detailed visual analysis and highlights the features of interest in complex structures and is an area of active research. However, the conventional volume visualisation is limited to the use of transfer functions that operate on homogeneous material and, as a result, does not provide flexibility in geometry and material distribution modelling that is crucial for the analysis of heterogeneous objects. Moreover, the extension to visual-auditory analysis emphasises the necessity to review the entire conventional volume visualisation pipeline. The multi-sensory feedback highly depends on the use of modern hardware and software advances for real-time modelling and evaluation. In this work, we explore the aspects of the design of visual-auditory pipelines for the analysis of dynamic multi-scale properties of heterogeneous objects that can allow overcoming well-known problems of complex representations solely visual analysis. We consider the similarities between light and sound propagation as a solution to the problem. The approach benefits from a combination of GPU accelerated ray-casting, geometry, optical and auditory properties modelling. We discuss how the modern GPU techniques application in those areas allows introducing a unified approach to the visual-auditory analysis of dynamic multi-scale heterogeneous objects. Similarly to the conventional volume rendering technique based on light propagation, we model auditory feedback as a result of initial impulse propagation through 3D space and its digital representation as a sampled sound wave obtained with the ray-casting procedure. The auditory stimuli can complement visual ones in the analysis of the dynamic multi-scale heterogeneous object. We propose a framework that facilitates the design of dynamic multi-scale heterogeneous objects visual-auditory pipeline and discuss the framework application for two case studies. The first is a molecular phenomena study that is a result of molecular dynamics simulation and quantum simulation. The second explores microstructures in digital fabrication with an arbitrary irregular lattice structure. For considered case studies, the visual-auditory techniques facilitate the interactive analysis of both spatial structure and internal multi-scale properties of volume nature in complex heterogeneous objects. A GPU-accelerated framework for visual-auditory analysis of heterogeneous objects can be applied and extend beyond this research. Thus, to specify the main direction of such extension from the point of view of the potential users, strengthen the value of this research as well as to evaluate the vision of the application of the techniques described above, we carry out a preliminary evaluation. The user study aims to compare our expectations on the visual-auditory approach with the views of the potential users of this system if it is implemented as a software product. A preliminary evaluation study was carried out with limitations imposed by 2020/2021 restrictions. However, it confirms that the main direction for the visual-auditory analysis of heterogeneous objects has been identified correctly and visual and auditory stimuli can complement each other in the analysis of both volume and spatial distribution properties of heterogeneous phenomena. The user reviews also highlight the necessary enhancements that should be introduced to the approach in terms of the design of more complex user interfaces and consideration of additional application cases. To provide a more detailed picture on evaluation results and recommendations introduced, we also identify the key factors that define the user vision of the approach further enhancement and its possible application areas, such as users experience in the area of complex physical phenomena analysis or multi-sensory area. The discussed in this work aspects of heterogeneous objects analysis task, theoretical and practical solutions allow considering the application, further development and enhancement of the results in multidisciplinary areas of GPU accelerated High-performance visualisation pipelines design and multi-sensory analysis