Graphics research at the SCI Institute is closely tied to our work in scientific visualization and information visualization. This research area focuses on algorithm development where graphics meets large scientific datasets. This area of research also involves the use of new platforms such as the iPad, iPhone, large storage systems such as isilon or the latest generation of graphics processing unit and the creation of tailored algorithms to those platforms. Current projects include the development and refinement of ray-tracing algorithms, light scatter algorithms, and efficient volume rendering packages such as Tuvok. Graphics research at SCI impacts nearly all of our other research areas.

Lattice cleaving: a multimaterial tetrahedral meshing algorithm with guaranteesJ. Bronson, J.A. Levine, R.T. Whitaker. In IEEE Transactions on Visualization and Computer Graphics (TVCG), pp. 223--237. 2014. DOI: 10.1109/TVCG.2013.115 PubMed ID: 24356365 We introduce a new algorithm for generating tetrahedral meshes that conform to physical boundaries in volumetric domains consisting of multiple materials. The proposed method allows for an arbitrary number of materials, produces high-quality tetrahedral meshes with upper and lower bounds on dihedral angles, and guarantees geometric fidelity. Moreover, the method is combinatoric so its implementation enables rapid mesh construction. These meshes are structured in a way that also allows grading, to reduce element counts in regions of homogeneity. Additionally, we provide proofs showing that both element quality and geometric fidelity are bounded using this approach. |

A Flexible Framework for Fusing Image Collections into PanoramasW. Widanagamaachchi, P. Rosen, V. Pascucci. In Proceedings of the 2013 SIBGRAPI Conference on Graphics, Patterns, and Images, Note: Awarded Best Paper., pp. 195-202. 2013. DOI: 10.1109/SIBGRAPI.2013.35 Panoramas create summary views of multiple images, which make them a valuable means of analyzing huge quantities of image and video data. This paper introduces the Ray Graph - a general framework for panorama construction. With rays as its vertices, the Ray Graph uses its edges to specify a set of coherency relationships among all input rays. Consequently, by using a set of simple graph traversal rules, a diverse set of panorama structures can be enumerated, which can be used to efficiently and robustly generate panoramic images from image collections. To demonstrate this framework, we first use it to recreate both 360° and street panoramas. We further introduce two new panorama models, the centipede panorama - a hybrid of the 360° and street panoramas, and the storytelling panorama - a time encoding panorama. Finally, we demonstrate the flexibility of this framework by enabling interactive brushing of panoramic regions for removal of undesired features such as occlusions and moving objects. |

Scalable Seams for Gigapixel PanoramasS. Philip, B. Summa, J. Tierny, P.-T. Bremer, V. Pascucci. In Proceedings of the 2013 Eurographics Symposium on Parallel Graphics and Visualization, Note: Awarded Best Paper!, pp. 25--32. 2013. DOI: 10.2312/EGPGV/EGPGV13/025-032 Gigapixel panoramas are an increasingly popular digital image application. They are often created as a mosaic of smaller images composited into a larger single image. The mosaic acquisition can occur over many hours causing the individual images to differ in exposure and lighting conditions. Therefore, to give the appearance of a single seamless image a blending operation is necessary. The quality of this blending depends on the magnitude of discontinuity along the boundaries between the images. Often image boundaries, or seams, are first computed to minimize this transition. Current techniques based on the multi-labeling Graph Cuts method are too slow and memory intensive for panoramas many gigapixels in size. In this paper we present a multithreaded out-of-core seam computing technique that is fast, has a small memory footprint, and gives near perfect scaling up to the number of physical cores of our test system. With this method the time required to compute image boundaries for gigapixel imagery improves from many hours (or even days) to just a few minutes on commodity hardware while still producing boundaries with energy that is on-par, if not better, than Graph Cuts. |

Ambient Occlusion Effects for Combined Volumes and Tubular GeometryM. Schott, T. Martin, A.V.P. Grosset, S.T. Smith, C.D. Hansen. In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 19, No. 6, Note: Selected as Spotlight paper for June 2013 issue, pp. 913--926. 2013. DOI: 10.1109/TVCG.2012.306 This paper details a method for interactive direct volume rendering that computes ambient occlusion effects for visualizations that combine both volumetric and geometric primitives, specifically tube shaped geometric objects representing streamlines, magnetic field lines or DTI fiber tracts. The algorithm extends the recently presented Directional Occlusion Shading model to allow the rendering of those geometric shapes in combination with a context providing 3D volume, considering mutual occlusion between structures represented by a volume or geometry. Stream tube geometries are computed using an effective spline based interpolation and approximation scheme that avoids self intersection and maintains coherent orientation of the stream tube segments to avoid surface deforming twists. Furthermore, strategies to reduce the geometric and specular aliasing of the stream tubes are discussed. |

Transfer Function Design based on User Selected Samples for Intuitive Multivariate Volume ExplorationL. Zhou, C.D. Hansen. In Proceedings of the 2013 IEEE Pacific Visualization Symposium (PacificVis), pp. 73--80. 2013. ISSN: 2165-8765 DOI: 10.1109/PacificVis.2013.6596130 Multivariate volumetric datasets are important to both science and medicine. We propose a transfer function (TF) design approach based on user selected samples in the spatial domain to make multivariate volumetric data visualization more accessible for domain users. Specifically, the user starts the visualization by probing features of interest on slices and the data values are instantly queried by user selection. The queried sample values are then used to automatically and robustly generate high dimensional transfer functions (HDTFs) via kernel density estimation (KDE). Alternatively, 2D Gaussian TFs can be automatically generated in the dimensionality reduced space using these samples. With the extracted features rendered in the volume rendering view, the user can further refine these features using segmentation brushes. Interactivity is achieved in our system and different views are tightly linked. Use cases show that our system has been successfully applied for simulation and complicated seismic data sets. |

Particle Systems for Adaptive, Isotropic Meshing of CAD ModelsJ.R. Bronson, J.A. Levine, R.T. Whitaker. In Engineering with Computers, Vol. 28, No. 4, pp. 331--344. 2012. PubMed ID: 23162181 We present a particle-based approach for generating adaptive triangular surface and tetrahedral volume meshes from computer-aided design models. Input shapes are treated as a collection of smooth, parametric surface patches that can meet non-smoothly on boundaries. Our approach uses a hierarchical sampling scheme that places particles on features in order of increasing dimensionality. These particles reach a good distribution by minimizing an energy computed in 3D world space, with movements occurring in the parametric space of each surface patch. Rather than using a pre-computed measure of feature size, our system automatically adapts to both curvature as well as a notion of topological separation. It also enforces a measure of smoothness on these constraints to construct a sizing field that acts as a proxy to piecewise-smooth feature size. We evaluate our technique with comparisons against other popular triangular meshing techniques for this domain. |

Combined SPHARM-PDM and entropy-based particle systems shape analysis frameworkB. Paniagua, L. Bompard, J. Cates, R.T. Whitaker, M. Datar, C. Vachet, M. Styner. In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 8317, No. 83170L, 2012. DOI: 10.1117/12.911228 PubMed ID: 24027625 Description of purpose: The NA-MIC SPHARM-PDM Toolbox represents an automated set of tools for the computation of 3D structural statistical shape analysis. SPHARM-PDM solves the correspondence problem by defining a first order ellipsoid aligned, uniform spherical parameterization for each object with correspondence established at equivalently parameterized points. However, SPHARM correspondence has shown to be inadequate for some biological shapes that are not well described by a uniform spherical parameterization. Entropy-based particle systems compute correspondence by representing surfaces as discrete point sets that does not rely on any inherent parameterization. However, they are sensitive to initialization and have little ability to recover from initial errors. By combining both methodologies we compute reliable correspondences in topologically challenging biological shapes. Data: Diverse subcortical structures cohorts were used, obtained from MR brain images. Method(s): The SPHARM-PDM shape analysis toolbox was used to compute point based correspondent models that were then used as initializing particles for the entropy-based particle systems. The combined framework was implemented as a stand-alone Slicer3 module, which works as an end-to-end shape analysis module. Results: The combined SPHARM-PDM-Particle framework has demonstrated to improve correspondence in the example dataset over the conventional SPHARM-PDM toolbox. Conclusions: The work presented in this paper demonstrates a two-sided improvement for the scientific community, being able to 1) find good correspondences among spherically topological shapes, that can be used in many morphometry studies 2) offer an end-to-end solution that will facilitate the access to shape analysis framework to users without computer expertise. |

Panorama weaving: fast and flexible seam processingB. Summa, J. Tierny, V. Pascucci. In ACM Trans. Graph., Vol. 31, No. 4, Note: ACM ID:2335434, ACM, New York, NY, USA pp. 83:1--83:11. July, 2012. ISSN: 0730-0301 DOI: 10.1145/2185520.2185579 A fundamental step in stitching several pictures to form a larger mosaic is the computation of boundary seams that minimize the visual artifacts in the transition between images. Current seam computation algorithms use optimization methods that may be slow, sequential, memory intensive, and prone to finding suboptimal solutions related to local minima of the chosen energy function. Moreover, even when these techniques perform well, their solution may not be perceptually ideal (or even good). Such an inflexible approach does not allow the possibility of user-based improvement. This paper introduces the |

GLuRay: Ray Tracing in Scientific Visualization Applications using OpenGL InterceptionC. Brownlee, T. Fogal, C.D. Hansen. In Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization (2012), Edited by H. Childs and T. Kuhlen and F. Marton, pp. 41--50. 2012. DOI: 10.2312/EGPGV/EGPGV12/041-050 Ray tracing in scientific visualization allows for substantial gains in performance and rendering quality with large scale polygonal datasets compared to brute-force rasterization, however implementing new rendering architectures into existing tools is often costly and time consuming. This paper presents a library, GLuRay, which intercepts OpenGL calls from many common visualization applications and renders them with the CPU ray tracer Manta without modification to the underlying visualization tool. Rendering polygonal models such as isosurfaces can be done identically to an OpenGL implementation using provided material and camera properties or superior rendering can be achieved using enhanced settings such as dielectric materials or pinhole cameras with depth of field effects. Comparative benchmarks were conducted on the Texas Advanced Computing Center’s Longhorn cluster using the popular visualization packages ParaView, VisIt, Ensight, and VAPOR. Through the parallel ren- dering package ParaView, scaling up to 64 nodes is demonstrated. With our tests we show that using OpenGL interception to accelerate and enhance visualization programs provides a viable enhancement to existing tools with little overhead and no code modification while allowing for the creation of publication quality renderings using advanced effects and greatly improved large-scale software rendering performance within tools that scientists are currently using. |

Generalized Swept Mid-structure for Polygonal ModelsT. Martin, G. Chen, S. Musuvathy, E. Cohen, C.D. Hansen. In Proceedings of Eurographics 2012, Vol. 31, No. 2 part 4, pp. 805--814. 2012. DOI: 10.1111/j.1467-8659.2012.03061.x We introduce a novel mid-structure called the generalized swept mid-structure (GSM) of a closed polygonal shape, and a framework to compute it. The GSM contains both curve and surface elements and has consistent sheet-by-sheet topology, versus triangle-by-triangle topology produced by other mid-structure methods. To obtain this structure, a harmonic function, defined on the volume that is enclosed by the surface, is used to decompose the volume into a set of slices. A technique for computing the 1D mid-structures of these slices is introduced. The mid-structures of adjacent slices are then iteratively matched through a boundary similarity computation and triangulated to form the GSM. This structure respects the topology of the input surface model is a hybrid mid-structure representation. The construction and topology of the GSM allows for local and global simplification, used in further applications such as parameterization, volumetric mesh generation and medical applications. |

Transfer Function CombinationsL. Zhou, M. Schott, C.D. Hansen. In Computers and Graphics, Vol. 36, No. 6, pp. 596--606. October, 2012. DOI: 10.1016/j.cag.2012.02.007 Direct volume rendering has been an active area of research for over two decades. Transfer function design remains a difficult task since current methods, such as traditional 1D and 2D transfer functions are not always effective for all datasets. Various 1D or 2D transfer function spaces have been proposed to improve classification exploiting different aspects, such as using the gradient magnitude for boundary location and statistical, occlusion, or size metrics. In this paper, we present a novel transfer function method which can provide more specificity for data classification by combining different transfer function spaces. In this work, a 2D transfer function can be combined with 1D transfer functions which improve the classification. Specifically, we use the traditional 2D scalar/gradient magnitude, 2D statistical, and 2D occlusion spectrum transfer functions and combine these with occlusion and/or size-based transfer functions to provide better specificity. We demonstrate the usefulness of the new method by comparing to the following previous techniques: 2D gradient magnitude, 2D occlusion spectrum, 2D statistical transfer functions and 2D size based transfer functions. |

Combined Surface and Volumetric Occlusion ShadingM. Schott, T. Martin, A.V.P. Grosset, C. Brownlee, Thomas Hollt, B.P. Brown, S.T. Smith, C.D. Hansen. In Proceedings of Pacific Vis 2012, pp. 169--176. 2012. DOI: 10.1109/PacificVis.2012.6183588 In this paper, a method for interactive direct volume rendering is proposed that computes ambient occlusion effects for visualizations that combine both volumetric and geometric primitives, specifically tube shaped geometric objects representing streamlines, magnetic field lines or DTI fiber tracts. The proposed algorithm extends the recently proposed Directional Occlusion Shading model to allow the rendering of those geometric shapes in combination with a context providing 3D volume, considering mutual occlusion between structures represented by a volume or geometry. |