COSC 6397 Scientific Visualization

Fall 2012

Instructor: Guoning Chen

Location: PGH 376

Time: Tue/Th. 10am~11:30am

Office hours: Tue/Th. 11:30am~12:30pm at PGH 531 (temporary)

Course summary

Scientific visualization is now a powerful tool in helping domain experts from various scientific and engineering areas understand and present their large scale and complex simulation and experimental data. This course presents introductory topics on visualization, and introduces a number of classical and recently developed visualization techniques for various data forms, such as scalar, vector, tensor fields. By taking this course, students are expected to have the ability to design proper algorithm and system for the visualization of a given data in any standard form.


Syllabus

Prerequisites:

Textbook: (recommended, but not required)

Grading: 5 assignments (60%) + 1 final project and presentation (30%) + course participation (10%) (based on C/C++ and OpenGL)

Late Policy: Late assignments will be marked off 20% for each weekday that it is late.

Academic Dishonesty: You can discuss course materials, algorithms, and programming skills. But, please do you own work! DO NOT copy code from others or internet!


Schedule

Week1 Introduction, Visualization Pipeline and Scientific data,

(Assignment1)

Week2 Colors, Iso-contouring, and Iso-surfacing

Week3 Direct volume rendering

(Assignment2 out)

Week4 Transfer function, Scalar field topology, Applications

Week5 Flow Vis 2D (geometric-based, texture-based)

Week6 Flow Vis 2D (feature-based)

(Assignment3 out)

Week7 Flow Vis (time-varying and 3D data), introduction of the final project topics

(Assignment 4)

Week8 TBA (travel to VisWeek!)

Final project proposal due on 10/22!!!

Week9 10/23 Visualization systems (VisIt, Paraview) 10/25 Tensor Vis (intro, the math)

Week10 Tensor Vis (pseudo-color, texture-based, integration-based)

Week11 11/06 Tensor Vis (glyph design and packing) 11/08 Student presentation (Final project topic)

Week12 Student presentation (Final project topic)

Week13 11/20 Tensor Vis (topology-based) 11/22 no class (Thanksgiving!)

Week14 11/27 Hot topics (Asymmetric tensor analysis and visualization) 11/29 Hot topics

Week15 Info Vis

Week16 12/11 Final week 12/13 Final project presentation


Lectures

1. Introduction, visualization pipeline, data

In this week, we will learn the basic pipeline of visualization, especially scientific data visualization. We will get familiar with the data that we will be facing through the whole course and how to represent them.

Lec1_slides

Lec2_slides

Additional materials:

2. Colors in scientific visualization

How important colors are in visualization? We will try to answer this question in this week and learn some basic rules for using colors in the visualization. In addition, while colors are essential, they are typically one attributes of other geometry primitives that the rendering are concerned with. What are these geometry primitives, how should we use them for various visualization tasks? We will learn these in this lecture.

Lec3_slides

Additional materials:

3. Iso-contouring and Iso-surfacing

One important visualization technique for scalar fields is to visualize the points with the same specific scalar value as one or more geometry. In 2D, this geometry can be represented as a set of curves, while in 3D they are some surfaces. The specific value is typically selected by the user during the data exploration and visualization interaction.

Lec4_slides

Additional materials:

4. Direct volume rendering

Another visualization technique for 3D scalar fields is direct volume rendering which does not need to create intermediate geometry to represent the data, thus the name "direct volume rendering (DVR)". It makes use of the whole volume information and allows the user to observe the 3D structure of the whole field. There are a number of computational strategies for DVR, including image-order (e.g. raycasting), object-order (e.g. splatting), and domain-dependent (e.g. shear-warp). For all these methods, the two most important steps are the specification of transfer functions and the composition of colors and opacity.

Lec5_6_slides

Lec7_slides (for transfer function)

Additional materials:

5. Scalar field topology

Topology provides a mathematically rigorous means to partition the spatial domain based on the characteristics of the scalar field that is defined on it. It consists of critical points and their connectivity. Different from the volume classification in the transfer function specification for DVR, topology computation is parameter-free and application-independent. In addition, the obtained topological structure helps better understand the scalar field in an abstract and efficient way.

Lec_8_slides

Additional materials:

This is a rather advanced topic. The additional readings are provided at the end of the lecture.

6. Vector field visualization - Direct and geometric method

Vector fields are a common form of data that are generated from various sources. They are widely used to study the behaviors of gas and liquids under certain circumstances, which is dominated by certain aero- and hydro- dynamical systems. Visualizing and analyzing vector fields is important to the understanding of these different dynamical systems. In this part of the lecture, we will learn the basic concepts of vector fields and some simple but effective visualization techniques including the direct method and the geometric-based method.

Lec_9_slides

Additional reading:

7. Texture-based flow visualization

Texture-based method is currently a very popular technique for the visualization of 2D and 2.5D (surface) flows with the advantages of full space coverage and hardware acceleration. LIC (line integral convolution) is considered the first successful texture-based method. Many variations have been proposed since then. Most of them adopt the LIC with different implementation improvement.

LIC_slides

Additional reading:

8. Topology-based vector field visualization

Vector field topology provides the qualitative (or structural) information of the flow data. It also provides a partitioning scheme for spatial domain segmentation so that the flow has homogeneous behavior within a region (i.e. flowing from one repeller to one attractor). This topic will specifically focus on the extraction of topology for 2D steady vector fields. 3D topology will be introduced briefly.

Lec11_12_slides

Additional reading:

9. Visualization of unsteady and 3D flows

Time-dependent flows represent the most popular flow data. The additional time dimension greatly increases the difficulty of their analysis because the originally well-defined features in steady flows are not valid any more under time-varying setting. We will review a number of visualization and analysis techniques that can help partially address the visualization of time-dependent flows.

3D flows have much more complex configuration than their counterpart. In addition, the occlusion of 3D visualization makes the task even more challenging. This topic will review a number of geometric based methods for the effective visualization of 3D flows.

Lec_13_14_slides

Additional reading:

10. Tensor field background and its applications

Tensor fields are now a popular subject in the visualization community. It measures the local higher ordered property on a higher dimensional manifold compared to scalar (0D property) and vector (1D property). Examples include stress/strain tensor, curvature tensor, metric tensor, diffusion tensor, and velocity gradient tensor. This lecture will emphasize the importance of tensors with a number of applications, and introduce the basic concepts and computations of this complex data form with the focus on second order tensors.

Lec_15_slides

Additional reading:

11. Tensor field visualization: texture-based and integration based methods

This lecture will cover the texture-based and geometric-based visualization techniques for second order tensor visualization. Two extended texture-based methods will be introduced, including the hyperLIC and extended IBFV. Hyperstreamline computation and placement will be introduced for the geometric-based visualization as well as its application in diffusion tensor imaging.

Lec_16_slides

Additional reading:

12. Tensor field visualization: glyph packing

Glyphs are good at describing the local patterns of tensors. With proper placement technique, the trend of the placed glyphs can reveal certain global patterns of the tensor field. We will look at a few glyph design and packing schemes in this lecture, especially the superquardic glyphs and the particle-system based glyph packing.

Lec_16_slides

Additional reading:

13. Tensor field topology

Similar to scalar field and vector field topology, tensor field topology provides the structural information of the fields which can be used to partition the spatial domain for later visualization and processing. In this lecture, we will specifically focus on the topology of second-order symmetric definite tensor fields which is well -defined.

Lec_17_slides

Additional reading:

14. Advanced topic: asymmetric tensor fiend analysis and visualization

Lec_18_slides

Additional reading:

15. Hot topics in visualization: illustrative visualization, big data, uncertainty, and many more

With the development of visualization, the research topics have expanded to beyond the traditional core areas of visualization. In this session, we will select a number of recently popular research topics to see why they are useful.

Lec_19_slides

Additional reading:

16. Information visualization

Compared to scientific visualization which focuses on geometric data, information data visualization typically handles abstract data forms that cannot be put in physical space. These abstract data forms occur in many applications ranging from business and marketing, financial industries, computer and social networking, to medicine. In this session, we will select a number of important information visualization techniques to look at.

Lec_20_slides:

Additional reading:

16. Evaluating your visualization: user studies

There are typically diverse solutions to address a specific visualization problem. How to evaluate the effectiveness of different visualization techniques is important to help domain experts make decision on which technique is more suitable for their needs. One way to evaluate different techniques is to perform user studies. This has now become a common drill in evaluation. This lecture will try to summarize some principles on how to set up a good user study to produce useful results.

Lec_20_slides

Additional reading

Student presentations

Pranav Mantini: FTLE and LCS

Mario Rincon : Exploring Photic Extremum Lines (PELs) for 3D Surface Visualization

Daniel Biediger: MS Lesion Visualization Assisted Segmentation

Olga Datskova: Parallel Visualization of Large Scale Vector-Fields

Xifeng Gao: Streak Lines as Tangent Curves of a Derived Vector Field


Assignments

Assignment 1: Color mapping, iso-contouring (data)

Assignment 2: 3D scalar field visualization

Assignment 3: 2D vector field visualization (arrow plots and LIC) (data_files)

Assignment 4: 3D vector field visualization (arrows, streamlines, stream ribbons)

Assignment 5: 2D tensor field visualization (Glyph packing) (Canceled)

Final project topics:

1. Advanced texture-based flow visualization

IBFVS: Jarke J. van Wijk, Image Based Flow Visualization for Curved Surfaces, IEEE Visualization 2003. [demo program].

ISA: Robert S. Laramee, Bruno Jobard, and Helwig Hauser, Image Space Based Visualization of Unsteady Flow On Surfaces. in Proceedings of IEEE Visualization (IEEE Vis 2003), pages 131-138, October 19-24, 2003, Seattle, Washington.

Robert S. Laramee, Jarke J. van Wijk, Bruno Jobard, and Helwig Hauser, ISA and IBFVS: Image Space Based Visualization of Flow on Surfaces in IEEE Transactions on Visualization and Computer Graphics (IEEE TVCG), Vol. 10, No. 6, November/December 2004, pages 637-648.

Variations of LIC on surface

Professor Zhanping Liu's webpage on flow visualization.

2. Vector field topology

ECG

Guoning Chen, Konstantin Mischaikow, Robert S. Laramee, Pawel Pilarczyk, and Eugene Zhang. "Vector Field Editing and Periodic Orbit Extraction Using Morse Decomposition". IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 4, 2007, pp. 769-785.

MCG

Guoning Chen, Konstantin Mischaikow, Robert S. Laramee, and Eugene Zhang. "Efficient Morse Decompositions of Vector Fields". IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 4, 2008, pp. 848-862.

Andrzej Szymczak and Eugene Zhang. Robust Morse Decompositions of Piecewise Constant Vector Fields, IEEE Transactions on Visualization and Computer Graphics, 18(6), 938-951, 2012.

3D topology

H. Theisel, T. Weinkauf, H.-C. Hege, H.-P. Seidel. Saddle connectors-an approach to visualizing the topological skeleton of complex 3D vector fields. IEEE Visualization 2003, pp. 225-232.

Other 3D field analysis technique

T Weinkauf, H Theisel. Curvature measures of 3D vector fields and their applications. Journal of WSCG 10 (2), 507-514, 2002.

Out-of-core vector field analysis (new research, no much work on this topic yet)

3. Time-varying vector field analysis

Feature tracking

T. Weinkauf, H. Theisel, A. Van Gelder, and A. Pang. Stable Feature Flow Fields. IEEE Transactions on Visualization and Computer Graphics 17(6), June 2011 .

T. Schafhitzel, K. Baysal, M. Vaaraniemi, U. Rist, D. Weiskopf. Visualizing the Evolution and Interaction of Vortices and Shear Layers in Time-Dependent 3D Flow, IEEE Transactions on Visualization and Computer Graphics, Vol. 17, No. 4, 412-425, 2011.

X. Tricoche, T. Wischgoll, G. Scheuermann, and H. Hagen. Topology Tracking for the Visualization of Time-Dependent Two-Dimensional Flows. Computer & Graphics 26, 2002, pp. 249-257.

C. Garth, X. Tricoche, and G. Scheuermann. Tracking of Vector Field Singularities in Unstructured 3D Time-Dependent Data Sets. Proc. IEEE Visualization '04, 2004, pp. 329-336.

FTLE for unsteady flow

Christoph Garth, Florian Gerhardt, Xavier Tricoche, Hans Hagen, "Efficient Computation and Visualization of Coherent Structures in Fluid Flow Applications", in "IEEE Transactions on Visualization and Computer Graphics (Proceedings IEEE Visualization 2007)", Volume 13, Number 6, pp 1464--1471, 2007.

F. Sadlo and D. Weiskopf. Time-Dependent 2-D Vector Field Topology: An Approach Inspired by Lagrangian Coherent Structures. Computer Graphics Forum, Vol. 29, No. 1, 88-100, 2010.

Markus Uffinger, Filip Sadlo, Member, IEEE, and Thomas Ertl. A Time-Dependent Vector Field Topology Based on Streak Surfaces. IEEE TVCG (accepted, prePrint).

4. 3D (time-varying) vector field visualization

Geometric-based method

Christoph Garth, Hari Krishnan, Xavier Tricoche, T. Bobach, Ken Joy, "Generation of Accurate Integral Surfaces in Time-Dependent Vector Fields", in "Proceedings of IEEE Visualization '08", 2008.

Hari Krishnan, Christoph Garth, Ken Joy, "Time and Streak Surfaces for Flow Visualization in Large Time-Varying Data Sets", in "Proceedings of IEEE Visualization '09", pp 1267--1274, 2009.

Matthew Edumunds, Tony McLoughlin, Robert S. Laramee, Guoning Chen, Eugene Zhang, and Nelson Max, Advanced, Automatic Stream Surface Seeding and Filtering, in Theory and Practice of Computer Graphics (TPCG) 2012, pages 53-60, 13-14 September 2012, Didcot, Oxfordshire, UK.

More geometric techniques can be found in a recent survey paper: Tony McLoughlin, Robert S. Laramee, Ronald Peikert, Frits H. Post, and Min Chen, Over Two Decades of Integration-Based, Geometric Flow Visualization in EUROGRAPHICS 2009, State of the Art Reports, pages 73-92, 30 March - 3 April 2009.

Texture-based method

Victoria Interrante and Chester Grosch, "Strategies for Effectively Visualizing 3D Flow with Volume LIC," Proceedings of IEEE Visualization 97. Oct 19-24, Phoenix, Arizona, pp. 421-424, 1997.

C. Rezk-Salama, P. Hastreiter, C. Teitzel, and T. Ertl, "Interactive Exploration of Volume Line Integral Convolution Based on 3D-Texture Mapping," Proceedings of IEEE Visualization 99, Oct 24-29, San Francisco, California, pp. 233-240, 1999.

Zhanping Liu and Robert J. Moorhead II, "A Texture-Based Hardware-Independent Technique for Time-Varying Volume Flow Visualization," Journal of Visualization, Vol. 8, No. 3, pp. 235~244, 2005.

5. Scalar field analysis

Reeb graph

V. Pascucci, G. Scorzelli, P.-T. Bremer, and A. Mascarenhas, Robust On-line Computation of Reeb Graphs: Simplicity and Speed. ACM Transactions on graphics, pp. 58.1-58.9, 2007, Proceedings of SIGGRAPH 2007.

Morse-Smale Complex

Attila Gyulassy, Peer-Timo Bremer, Valerio Pascucci, Bernd Hamann. A Practical Approach to Morse Smale Complex Computation: Scalability and Generality. IEEE Trans. Vis. Comput. Graph. (IEEE Visualization 2008), 14(6): 1619-1626, 2008.

P.-T. Bremer, G. Weber, J. Tierny, V. Pascucci, M. Day, and J. Bell, Interactive Exploration and Analysis of Large Scale Simulations Using Topology-based Data Segmentation. IEEE Transactions on Visualization and Computer Graphics, Vol. 17(9): pp. 1307-1324, 2011.

6. Asymmtric tensor field visualization

Guoning Chen, Darrel Palke, Zhongzang Lin, Harry Yeh, Paul Vincent, Robert S. Laramee and Eugene Zhang. "Asymmetric Tensor Field Visualization for Surfaces", IEEE TVCG (Proceeding of IEEE Visualization 2011), Vol.17, No. 12, pp 1979-1988, 2011.

Eugene Zhang, Harry Yeh, Zhongzang Lin, and Robert S. Laramee, "Asymmetric Tensor Analysis for Flow Visualization", IEEE Transactions on Visualization and Computer Graphics, Vol. 15(1), 2009, pp. 106-122.

Xiaoqiang Zheng, Alex Pang. 2D asymmetric tensor field analysis, IEEE Visualization 2005.

7. Diffusion tensor imaging

Gordon Kindlmann and Carl-Fredrik Westin. Diffusion tensor visualization with glyph packing, IEEE Visualization 2006.

G. Reina, K. Bidmon, F. Enders, P. Hastreiter, and T. Ertl. GPU-Based Hyperstreamlines for Diffusion Tensor Imaging. EuroVis 2006.

An old survey, Diffusion Tensor Imaging: Concepts and Applications. 2001.

8. GPU-based real-time volume rendering

J. Kruger and R. Westermann, Acceleration Techniques for GPU-based Volume Rendering. IEEE Visualization 2003.

P. Schlegel, M. Makhinya and R. Pajarola. Extinction-Based Shading and Illumination in GPU Volume Ray-Casting. IEEE TVCG Vol. 17(12): pp. 1795 - 1802, 2011.

Daniel Jonsson, Erik Sunden, Anders Ynnerman, and Timo Ropinski. Interactive Volume Rendering with Volumetric Illumination. Eurographics STAR program - 2012.

Open source for your reference: Exposure render.

9. Illustrative visualization

Xuexiang Xie, Ying He, Feng Tian, Hock-Soon Seah, Xianfeng Gu, and Hong Qin. An Effective Illustrative Visualization Framework Based on Photic Extremum Lines (PELs). IEEE Visualization 2007.

Cheng-Kai Chen, Shi Yan, Nelson Max, and Kwan-Liu Ma. An Illustrative Visualization Framework for 3D Vector Fields. Computer Graphics Forum, vol. 30, no. 6, pp. 1941–1951, September 2011.

A. Brambilla, R. Carnecky, R. Peikert, I. Viola and H. Hauser, Illustrative Flow Visualization: State of the Art, Trends and Challenges, Eurographics STAR Reports, pp. 75-94, 2012.

IEEE Visualization Tutorial on Illustrative Visualization

10. Information visualization

Large scale dynamic graph visualization

Michael Burch, Corinna Vehlow, Fabian Beck, Stephan Diehl, and Daniel Weiskopf. Parallel Edge Splatting for Scalable Dynamic Graph Visualization. IEEE Information Visualization 2011.

Danny Holten and Jarke J. van Wijk. Force-Directed Edge Bundling for Graph Visualization. EuroVis2009

Gautam Kumar and Michael Garland. Visual Exploration of Complex Time-Varying Graphs, IEEE Information Visualization 2006.

High-dimensional data visualization

Enrico Bertini, Andrada Tatu, and Daniel Keim, Quality Metrics in High-Dimensional Data Visualization: An Overview and Systematization. IEEE Information visualization 2011.

S. Gerber, P.-T. Bremer, v. Pascucci, and R. Whitaker, Visual Exploration of High Dimensional Scalar Functions. IEEE Transactions on Visualization and Computer Graphics 16(6), pp. 1271-1280, 2010 (this is actually a scientific visualization paper).

11. Others (name a good project then we can discuss)

Final Project Showcase: