Multiple dataset visualization (MDV) framework for scalar volume data

Many applications require comparative analysis of multiple datasets representing different samples, conditions, time instants, or views in order to develop a better understanding of the scientific problem/system under consideration. One effective approach for such analysis is visualization of the data. In this PhD thesis, we propose an innovative multiple dataset visualization (MDV) approach in which two or more datasets of a given type are rendered concurrently in the same visualization. MDV is an important concept for the cases where it is not possible to make an inference based on one dataset, and comparisons between many datasets are required to reveal cross-correlations among them. The proposed MDV framework, which deals with some fundamental issues that arise when several datasets are visualized together, follows a multithreaded architecture consisting of three core components, data preparation/loading, visualization and rendering. The visualization module - the major focus of this study, currently deals with isosurface extraction and texture-based rendering techniques. For isosurface extraction, our all-in-memory approach keeps datasets under consideration and the corresponding geometric data in the memory. Alternatively, the only-polygons- or points-in-memory only keeps the geometric data in memory. To address the issues related to storage and computation, we develop adaptive data coherency and multiresolution schemes. The inter-dataset coherency scheme exploits the similarities among datasets to approximate the portions of isosurfaces of datasets using the isosurface of one or more reference datasets whereas the intra/inter-dataset multiresolution scheme processes the selected portions of each data volume at varying levels of resolution. The graphics hardware-accelerated approaches adopted for MDV include volume clipping, isosurface extraction and volume rendering, which use 3D textures and advanced per fragment operations. With appropriate user-defined threshold criteria, we find that various MDV techniques maintain a linear time-N relationship, improve the geometry generation and rendering time, and increase the maximum N that can be handled (N: number of datasets). Finally, we justify the effectiveness and usefulness of the proposed MDV by visualizing 3D scalar data (representing electron density distributions in magnesium oxide and magnesium silicate) from parallel quantum mechanical simulation

Visualization based on interactive clipping: application to confocal data

We have explored how clipping can be exploited in an interactive manner to visualize massive three-dimensional datasets. In essence, the proposed interactive clipping approach involves the dynamic adjustment of the clipping plane to expose any cross-section of the volume data and subsequent adjustment of the clipped surface to the best view position using a combination of rotation and translation. The thesis describes the design, implementation and application of our interactive-clipping-based visualization system. The implementation is done with OpenGL and C++, thus resulting in a highly portable and flexible system. For illustration, two types of scientific datasets, confocal data of a plant stem and calculated electronic charge density distributions are successfully visualized. The data are displayed using pixel- and texture-based rendering; the latter is shown to give a better performance

Acknowledgements

I would like to express my sincere gratitude to Dr. Bijaya B. Karki, my advisor, for his invaluable guidance and encouragement extended throughout the study. His tenacious supervision, helpful suggestion, patience and time deserve a special mention. I have learnt the basics of scientific visualization under his guidance and would like to acknowledge his command in this area of research. I would like to express my appreciation to my committee members Dr. S. Sitharama Iyengar and Dr. Rajgopal Kannan for their support and suggestions. Thanks are extended to Dr. Bijaya B. Karki for honing my fundamentals in Scientific Visualization. I would like to express my gratitude towards my family members, friends and relatives whose encouragement and support has been a constant source of inspiration during my stay at Louisiana State University. Last, but not the least, I would like to gratefully acknowledge Department of Computer Science, Louisiana State University for providing the resources and need during the project

A systematic approach to multiple datasets visualization of scalar volume data

Many applications require simultaneous display of multiple datasets, representing multiple samples, or multiple conditions, or multiple simulation times, in the same visualization. Such multiple dataset visualization (MDV) has to handle and render massive amounts of data concurrently. We analyze the performance of two widely used techniques, namely, isosurface extraction and texture-based rendering for visualization of multiple sets of the scalar volume data. Preliminary tests performed using up to 25 sets of moderate-size (256 ) data show that the calculated times for the generation and rendering of polygons representing isosurface, and for the mapping of a series of textured slices increase non-uniformly with increasing the number of individual datasets. Both techniques are found to no longer be interactive with the frame-rates dropping below one for six or more datasets. To improve the MDV frame-rate, we propose a scheme based on the combination of hardware-assisted texture mapping and general clipping. In essence, it exploits the 3D surface texture mapping by rendering only the externally visible surfaces of all volume datasets at a given instant, with dynamic clipping enabled to explore the interior of the data. The calculated frame-rates remain above one and are substantially higher than those with the other two techniques.

Exploiting data coherency in multiple dataset visualization

The paper deals with visualization of multiple datasets by exploiting data coherency among the datasets under consideration to address the issues related to storage and computation. The proposed data coherency approach utilizes the similarities among datasets by using the already generated polygon data for one or more reference datasets to approximate the isosurfaces of similar regions in other datasets. For finding the similarity among the multiple datasets, we use the octree data structure and compare datasets block by block. Blocks of a nonreference dataset, whose difference from the corresponding blocks of the reference dataset is within the user defined tolerance level, we use the already extracted polygon data for the reference data blocks to approximate the isosurfaces. Thus, only those non-reference data blocks, which differ from the reference blocks, are processed. Thereby, we reduce the number of polygons to represent the isosurfaces. To overcome the problem of cracks in thus extracted isosurfaces, we use a simple approach of overlapping at the interface between the directly processed and approximated portions of the isosurfaces. We have explored the effects of various factors including the data coherency condition, tolerance level and block size on the performance. Our results show that the proposed data coherency technique considerably improves the overall performance

Using Graphics Hardware for Multiple Datasets Visualization

We have applied three graphics hardware-based approaches to support concurrent visualization of multiple sets of volumetric scalar data. They include volume rendering, clipping and isosurface extraction methods, which exploit 3D textures and advanced per pixel operations. These methods are expected to give better interactive frame rates for multiple datasets visualization (MDV) compared to the software-based methods. The rendering time in each case increases nonlinearly with the increasing the number (N) of the datasets being visualized. We can identify three regimes, which can be characterized by different time-N slope value. The first regime with small slope value continues up to about 5 datasets, then the second regime with medium slope value continues up to about 25 datasets, and finally the third regime with much larger slope value continues up to 35 datasets. With volume shading enabled, the rendering time increases on average whereas the transition and maximum N values decrease. We propose the dynamic-resolution approach for increasing the maximum N and frame rates for above MDV techniques

Vacancy defects in MgO at high pressure

First-principles calculations within the local density and pseudopotential approximations were performed to investigate the effects of pressure on the energetics and structural behavior of charged vacancy defects in MgO. The simulations were performed for a supercell containing 216 atoms with their positions being fully optimized. In particular, the formation and migration energies of cation and anion vacancies were shown to substantially increase over the pressure regime of the Earth\u27s mantle. Our results thus suggest that pressure should suppress intrinsic diffusion mediated by ionic vacancies in MgO over the mantle pressure regime. The calculated three-dimensional data sets for atomic displacements and electron charge density were explored in detail using an interactive visualization system. Although the atomic and electronic structures are highly distorted in the close vicinity of the defects (i.e., in the region covering up to the nearest and next-nearest atoms), the effects are not negligible at farther distances

A computational study of ionic vacancies and diffusion in MgSiO 3 perovskite and post-perovskite

Abstract We have performed first-principles simulations within density functional theory to investigate the effects of pressure on the formation of defects (ionic vacancies) and ionic diffusion in the perovskite (pv) and post-perovskite (ppv) phases of MgSiO 3 . Our results show that the predicted formation enthalpies of three Schottky (MgO, SiO 2 and MgSiO 3 ) defects are similar between the two phases at high pressures (100 to 150 GPa) with MgO Schottky defect being the most favorable. However, the calculated activation enthalpies and activation volumes of diffusion are shown to differ substantially between them. In particular, the activation enthalpies for Mg and Si diffusion in ppv are smaller than the corresponding values for pv, for example, by factors of 2.2 and 3.4, respectively, at 120 GPa, whereas the O migration enthalpy of ppv is only slightly larger than that of pv. The easy migration paths of the cations in ppv are shown to take place along the 〈100〉 direction in which Si-O octahedra share the edges. Visualization of the simulation data reveals that the vacancy defects and migrating ions induce substantial distortions in the atomic and electronic structures around them. It is suggested that diffusion is equally easy for all three species in ppv and is likely to occur through extrinsic processes near the bottom of the lower mantle. Published by Elsevier B.V

A computational study of ionic vacancies and diffusion in MgSiO\u3csub\u3e3\u3c/sub\u3e perovskite and post-perovskite

We have performed first-principles simulations within density functional theory to investigate the effects of pressure on the formation of defects (ionic vacancies) and ionic diffusion in the perovskite (pv) and post-perovskite (ppv) phases of MgSiO . Our results show that the predicted formation enthalpies of three Schottky (MgO, SiO and MgSiO ) defects are similar between the two phases at high pressures (100 to 150 GPa) with MgO Schottky defect being the most favorable. However, the calculated activation enthalpies and activation volumes of diffusion are shown to differ substantially between them. In particular, the activation enthalpies for Mg and Si diffusion in ppv are smaller than the corresponding values for pv, for example, by factors of 2.2 and 3.4, respectively, at 120 GPa, whereas the O migration enthalpy of ppv is only slightly larger than that of pv. The easy migration paths of the cations in ppv are shown to take place along the 〈100〉 direction in which Si-O octahedra share the edges. Visualization of the simulation data reveals that the vacancy defects and migrating ions induce substantial distortions in the atomic and electronic structures around them. It is suggested that diffusion is equally easy for all three species in ppv and is likely to occur through extrinsic processes near the bottom of the lower mantle. 3 2