# SciVisFall2008/Schedule

### From VisTrailsWiki

## 8/26: Introduction to visualization

Lecturer: Claudio

Topics: Scientific Visualization

Notes: lec01-notes.pdf

Slides: intro

Animations: NCSA storm animation

Further reading:

(Optional reading) Provenance for Computational Tasks: A Survey

## 8/28: The visualization pipeline

Lecturer: Claudio

Topics: Procedural vs. Dataflow programming; Using Dataflow for the Vis Pipeline; Dataflow programming with VTK; Dataflow programming with VisTrails; python.

Notes: lec02-notes.pdf

Slides: lec02.pdf

Further reading:

(Optional reading) Provenance for Visualizations: Reproducibility and Beyond, C. Silva, J. Freire, and S. Callahan, IEEE Computing in Science and Engineering, 2008.

## 9/2: Modeling Data for Visualization

Lecturer: Claudio

Topics: Discrete vs continous data; Sampling and interpolation; Point vs triangulated data; Meshing data types; Regular vs irregular data; Tabular data; Vector and tensor fields

Notes: modeling data

Slides: processing.ppt

Further reading:

Surface Simplification Using Quadric Error Metrics

(Optional Reading) A Memory Insensitive Technique for Large Model Simplification

(Optional Reading) Quadric-based Simplification in any Dimension

## 9/4: Modeling Data for Visualization

Lecturer: Claudio

Topics: Geometry Processing: Reconstruction and meshing; Simplification; Smoothing; Other Filtering algorithms

Notes: modeling data

Slides: processing.ppt

Further reading:

http://en.wikipedia.org/wiki/Least_squares

(Optional Reading) Robust Moving Least-squares Fitting with Sharp Features

(Optional Reading) Optimal Bandwidth Selection for MLS Surfaces

## 9/9: Elementary Plotting Techniques

Lecturer: Claudio

Topics: Principles of Graph Construction

Notes: PlottingNotes.pdf

Slides: Plotting1.pdf

Further Reading: There is no required reading for this lecture. For those interested in more depth, the following books are very useful:

- The Elements of Graphing Data. William S. Cleveland, Hobart Press, 2nd Edition, 1994.

- Visualizing Data. William S. Cleveland, Hobart Press, 1993.

- The Visual Display of Quantitative Information. Edward R. Tufte, Graphics Press, 2001.

- Visual Explanations: Images and Quantities, Evidence and Narrative. Edward R. Tufte, Graphics Press, 2997.

## 9/11: Elementary Plotting Techniques

Lecturer: Claudio

Topics: Simple Plotting Methods: Dot Plots, Connected Symbol Plots, Scatter Plots, Histograms, Others. Advanced Plotting Methods: Multimodal, Higher Dimensional, Correlation, Uncertainty and Variation.

Notes: PlottingNotes.pdf

Slides: Plotting2.pdf

Vistrails: PlottingVistrails.zip - Unzip this file in the examples directory of your VisTrails installation and it will add the vistrails along with their data sets (in the data directory). If you don't have permission to write to this directory (CADE users), then unzip the file where you want. Just be aware that in this case the paths for the data files may not be correct for most vistrails and will need to be fixed before they will execute properly.

Further Reading: There is no required reading for this lecture. Some articles of interest:

## 9/16: Color and Human Perception

Lecturer: Claudio

Topics: Human vision system; Optical illusions

Slides: human-vision.pdf

Links:

http://en.wikipedia.org/wiki/Eye

http://www.grand-illusions.com/gregory2.htm (also, see the related book: [1])

http://en.wikipedia.org/wiki/Purkinje_effect

http://www.handprint.com/HP/WCL/color2.html

## 9/18: Color and Human Perception

Lecturer: Jens Krueger

Topics: Color Science; Color spaces; Color Blindness; Color maps; Tone mapping;

Slides: colorvision-jens.pdf

Links:

Further reading:

How Not to Lie with Visualization

http://en.wikipedia.org/wiki/Opponent_process

http://en.wikipedia.org/wiki/Color_models

http://en.wikipedia.org/wiki/Absolute_color_space

http://en.wikipedia.org/wiki/Additive_color

http://en.wikipedia.org/wiki/Subtractive_color

http://en.wikipedia.org/wiki/RGB_color_model

http://en.wikipedia.org/wiki/SRGB_color_space

http://en.wikipedia.org/wiki/CIE_XYZ_color_space

## 9/23: Math refresher

Lecturer: Carlos Scheidegger

Topics: Basic linear algebra; vectors; basic differential geometry (space curves, tangents, normals, surfaces); basic vector calculus (gradient, divergence, curl, gauss' theorem, green's theorem)

Links:

Further Reading:

http://en.wikipedia.org/wiki/Vector_calculus

Appendix A of these notes might be useful: [2]

Two books that take a very accessible approach at vector calculus:

Div, Grad, Curl, and All That: An Informal Text on Vector Calculus

A Student's Guide to Maxwell's Equations

## 9/25 2D Visualization Techniques

Lecturer: Claudio

Topics: 2-D contours, marching quads, marching tris; Color mapping; height fields; NPR

Slides: pdf file

Notes: pdf file

Vistrails: zip file with ozone.vt and data asymptotic decider in 2d heightfields

Note: These vistrails use relative file paths so you don't need to change each of them individually to match your directory structure. Simply unzip the file to whichever location is more convenient. Then, inside VisTrails, open the VisTrails shell, type:

import os os.chdir("c:/directory/where/you/unzipped/it")

This will change the directory so you should be able to just run the pipelines.

Further reading:

http://ieeexplore.ieee.org/iel5/4271943/4271944/04272091.pdf

http://www.jstor.org/stable/pdfplus/2683294.pdf

An Efﬁcient Naturalness-Preserving Image-Recoloring Method for Dichromats

## 9/30: 2D Visualization Techniques

Lecturer: Jens Krueger and Claudio

Topics: 2-D vector fields, div, grad, curl in 2D; Steady vs Unsteady flows; Glyphs; 2-D streamlines, streaklines, pathlines

Slides: pdf file

Further reading:

http://en.wikipedia.org/wiki/Streamlines,_streaklines_and_pathlines

http://en.wikipedia.org/wiki/Euler's_method

http://en.wikipedia.org/wiki/Runge-Kutta

Demos:

http://www.win.tue.nl/~vanwijk/ibfv/

http://www.javaview.de/demo/PaLIC.html

Vistrails: vistrail with steady vector field vis and data vistrail with unsteady vector field vis and data **Note:** Because VTK does not support time-varying datasets directly, we had to create a reasonably ugly hack to simulate unsteady fields. This means the datasets are quite big (80MB in total).

"The Dx9 Particle Engine" as well as a few datasets

## 10/2: Volume Vis

Lecturer: Carlos

Topics: Slicing; Contours; Marching algorithms

Slides: iso-basic.pdf

References:

Marching cubes: A high resolution 3D surface construction algorithm

The asymptotic decider: resolving the ambiguity in marching cubes

## 10/2: Volume Vis

Lecturer: Carlos

Topics: Accelerating structures; High-quality contours

Slides:

References:

A Near Optimal Isosurface Extraction Algorithm Using the Span Space

Automatic Isosurface Propagation Using an Extrema Graph and Sorted Boundary Cell Lists

Speeding Up Isosurface Extraction Using Interval Trees

## 10/9: Volume Vis

Lecturer: Carlos Scheidegger

Topics: High quality isosurfaces

Slides: iso-quality.pdf

References:

Edge Transformations for Improving Mesh Quality of Marching Cubes

High-Quality Extraction of Isosurfaces from Regular and Irregular Grids

Dual contouring of hermite data

Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles

Material interface reconstruction

## 10/14: Fall break

## 10/16: Fall break

## 10/21: Direct Volume Rendering

Lecturer: Huy Vo

Topics: Introduction to volume rendering

Slides: VolumeRendering1.pdf

Notes: dvr.pdf

vistrails: VolumeRenderingVistrails.zip

References: Optical Models for Direct Volume Rendering

## 10/23: Midterm 1

## 10/28: Direct Volume Rendering

Lecturer: Claudio

Topics: Structured grid techniques: ray-casting, splatting, texture slicing, shear-warp

Slides: VolumeRendering2.pdf

Notes: same as previous class

vistrails: same as previous class

References:

Display of Surfaces from Volume Data - Ray casting paper

Interactive Volume Rendering - Splatting paper, paper requires ACM digital library access

Accelerated volume rendering and tomographic reconstruction using texture mapping hardware - Texture slicing paper, requires ACM digital library access

Fast Volume Rendering Using a Shear-Warp Factorization of the Viewing Transformation - Shear-warp paper

## 10/30: Invited Lecture by Professor Joao Comba

Title: Edge Groups: An Approach to Understanding the Mesh Quality of Marching Methods

Abstract: Marching Cubes is the most popular isosurface extraction algorithm due to its simplicity, efficiency and robustness. It has been widely studied, improved, and extended. While much early work was concerned with efficiency and correctness issues, lately there has been a push to improve the quality of Marching Cubes meshes so that they can be used in computational codes. In this work we present a new classification of MC cases that we call Edge Groups, which helps elucidate the issues that impact the triangle quality of the meshes that the method generates. This formulation allows a more systematic way to bound the triangle quality, and is general enough to extend to other polyhedral cell shapes used in other polygonization algorithms. Using this analysis, we also discuss ways to improve the quality of the resulting triangle mesh, including some that require only minor modifications of the original algorithm.

This is joint work with Carlos A. Dietrich, Carlos E. Scheidegger, Luciana P. Nedel and Claudio T. Silva, and was presented last week at IEEE Visualization 2008.

Slides: pdf file

## 11/4: Direct Volume Rendering

Lecturer: Jens Kruger

Topics: Unstructured grid techniques

Slides: unstructured_grid_rendering.pdf

References:

A Survey of GPU-Based Volume Rendering of Unstructured Grid

Hardware-Assisted Visibility Sorting for Unstructured Volume Rendering (This technique is implemented in VTK: http://www.vtk.org/doc/nightly/html/classvtkHAVSVolumeMapper.html)

ZSWEEP: An Efficient and Exact Projection Algorithm for Unstructured Volume Rendering (This technique is implemented in VTK: http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGridVolumeZSweepMapper.html)

## 11/6: Direct Volume Rendering

Lecturer: Claudio

Topics: Unstructured grid techniques (continuation from last class)

## 11/11: Direct Volume Rendering

Lecturer: Claudio

Topics: Transfer function specification

Slides: transfer_functions.pdf

References:

The transfer function bake-off

Multidimensional transfer functions for interactive volume rendering

Semi-automatic generation of transfer functions for direct volume rendering

Additional Question:

The above image is the sphere data and joint histogram discussed in class. Which material boundary is highlighted by the small arc on the right-side of the histogram? The colors in the original dataset can be interpreted as:

0 = Blue

1 = Green

2 = Red

## 11/13: Direct Volume Rendering

Lecturer: Claudio

Topics: Transfer function specification

References:

Generation of transfer functions with stochastic search techniques

Design galleries: a general approach to setting parameters for computer graphics and animation

Transfer-Function Specification for Rendering Disparate Volumes (and corresponding video)

## 11/18: Intro to Geometry Processing

Lecturer: Claudio

## 11/20: Information Visualization

Lecturer: Steve Callahan

Topics: Intro to InfoVis, clustering, parallel coordinates, graph vis, tree vis, cartograms

Slides: InfoVis.pdf

References:

Map of the Market: Tree Map of Stock Market

Interactive Tree of Life: Radial Phylogenetic Tree

Disk Inventory X: Tree Map Disk Utility for Mac

Sequoia View: Tree Map Disk Utility for Windows

World of Music: Music Clustering

Graphviz: Graph layout project

## 11/25: Information Visualization

Lecturer: Steve Callahan

Topics: InfoVis examples; recent developments

References:

## 11/27: Thanksgiving

## 12/2: Aesthetic Issues in Vis

Lecturer: Claudio

Topics: Tufte principles (Part I)

Slides: Tufte.pdf

References:

- Envisioning Information, Edward R. Tufte, Academic Press, 1990
- Visual Explanations: Images and Quantities, Evidence and Narrative, Edward R. Tufte, Academic Press, 1997

## 12/4: Introduction to Computational Topology

Lecturer: Valerio Pascucci

## 12/9: Aesthetic Issues in Vis

Lecturer: Claudio

Topics: Tufte principles (Part II)

Slides: Tufte.pdf

References:

- Envisioning Information, Edward R. Tufte, Academic Press, 1990
- Visual Explanations: Images and Quantities, Evidence and Narrative, Edward R. Tufte, Academic Press, 1997

(This class ended early; but we finished on Thursday.)

## 12/11: Continuation from last class

We finished Tufte.

Then, we discussed the major themes that we covered in class.

Thank you all for participating!

Happy holidays!