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8/21: Introduction to visualization

Lecturer: Claudio

Topics: Scientific Visualization

Notes: lec01-notes.pdf

Slides: lec01.pdf


Further reading:

Visualizing Spatial and Temporal Variability in Coastal Observatories, W. Herrera-Jimenez, W. Correa, C. Silva, and A. Baptista, IEEE Visualization 2003.

8/23: 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

VisTrails: During this class, we built a pipeline equivalent to the cone.tcl (see class slides). Here is the vistrails file: cone.vt

Further reading:

Provenance for Visualizations: Reproducibility and Beyond, C. Silva, J. Freire, and S. Callahan, IEEE Computing in Science and Engineering, to appear.

8/28: Modeling Data for Visualization

Lecturer: Carlos

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: TBA

Slides: .ppt file

Further reading:

There is no required reading for this lecture. The notes will be available shortly. The following papers are there for people that are looking to get more advanced material that will not be covered in class.


Geodesic-loxodromes... This is the fancy interpolation for diffusion tensors I mentioned in class.

Bernstein polynomials These are the polynomials used for cubic Bezier curves that I mentioned in class.


Extensions of the Zwart-Powell Box spline... This is a recent paper that shows a class of trivariate reconstruction techniques that are not separable.


Visualization and Analysis of Diffusion Tensor Fields Gordon Kindlmann's PhD. thesis, with everything you ever wanted to know about DTI. Section 2.1 has a good primer in tensor algebra.

8/30: Modeling Data for Visualization

Lecturer: Carlos

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

Notes: .pdf file. If you want to print these, you might want to wait for a week or two, until I finish polishing them.

Slides: .ppt file These slides include simplificatin algorithms, which I'll talk about next week.

9/4: Elementary Plotting Techniques

Lecturer: Steve

Topics: Principles of Graph Construction

Notes: PlottingNotes.pdf

Slides: Plotting1.pdf

Vistrails: See next lecture.

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.

9/6: Elementary Plotting Techniques

Lecturer: Steve

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: - 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:

9/11: Color and Human Perception

Lecturer: Claudio

Topics: Human vision system; Optical illusions

Notes: TBA

Slides: human-vision.pdf

Links: (also, see the related book: [1])

9/13: Color and Human Perception

Lecturer: Claudio

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

Notes: TBA

Slides: colorvision.pdf


Further reading:

How Not to Lie with Visualization

9/18 (a): Color and Human Perception

Lecturer: Claudio

Same material as previous lecture.

9/18 (b): 2D Visualization Techniques

Lecturer: Carlos

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

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

9/20: Math refresher

Lecturer: Carlos

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

9/25: 2D Visualization Techniques

Lecturer: Carlos

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

Slides: pdf file

Notes: coming soon

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).

9/27 (a): 2D Visualization Techniques

Lecturer Carlos

Same material as last lecture.

9/27 (b): Volume Vis

Lecturer: Claudio

Topics: Slicing; Contours; Marching algorithms

Slides: iso-basic.pdf


Marching cubes: A high resolution 3D surface construction algorithm

The asymptotic decider: resolving the ambiguity in marching cubes

10/2: Volume Vis

Lecturer: Claudio

Topics: Accelerating structures; High-quality contours





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

Implicit Occluders

10/4: Volume Vis

Lecturer: Claudio

Topics: High quality isosurfaces

Slides: iso-quality.pdf


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

10/9: Fall break

10/11: Fall break

10/16: Volume Vis

Lecturer: Claudio

Topics: continued from last class

10/18: Direct Volume Rendering

Lecturer: Steve

Topics: Introduction to volume rendering

Slides: VolumeRendering1.pdf

Notes: dvr.pdf


References: Optical Models for Direct Volume Rendering

10/23: Midterm 1

10/25: Direct Volume Rendering

Lecturer: Steve

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

Slides: VolumeRendering2.pdf

Notes: same as previous class

vistrails: same as previous class


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: Cosmology and EEG analysis

Guest lecture: Erik Anderson

Topics: Applications of Visualization Techniques, Multi-modal Visualization

Slides: VisualizationApplications ppt | odp

VisTrail: Contact me here


Working Memory in Schizophrenia - Overview of rTMS in EEG Analysis

Cosmology Code Comparison Project - Cosmological Simulation Project

11/1: Simplification Techniques

Guest lecture: Yuan Zhou

Topics: Simplification techniques: vertex clustering, vertex decimation, iterative contraction, quadric error based surface and tetrahedral simplification

Slides: Simplification


Surface Simplification Using Quadric Error Metrics

Multiresolution Modeling : Survey & Future Opportunities

Quadric-Based Simplication in Any Dimension

Streaming Simplification of Tetrahedral Meshes

11/6: Direct Volume Rendering

Lecturer: Claudio

Topics: Unstructured grid techniques

Slides: TBA

References: TBA

11/8: Direct Volume Rendering

Lecturer: Claudio

Topics: Transfer function specification

Slides: TBA

References: TBA

11/13: Tensor Visualization

Lecturer: Carlos

Topics: DT/MRI intro, glyphs, colormapping, volume rendering

Slides: TBA

References: TBA

11/15: 3D Vector Vis and Toplogy

Lecturer: Carlos

Topics: 3D techniques, critical points

11/20: Information Visualization

Lecturer: Carlos

Topics: Parallel coordinates; Graph visualization

11/22: Thanksgiving

11/27: Information Visualization

Lecturer: Steve

Topics: Hierarchical data vis; brushing; sizing text

11/29: Aesthetic Issues in Vis

Lecturer: Steve

Topics: Tufte principles

12/4: Aesthetic Issues in Vis

Lecturer: Steve

Topics: NPR and Illustrative techniques for Vis

12/6: Misc

Lecturer: Claudio

Topics: Data Management for Vis, Vis for presentation/discovery

12/11: Misc

Lecturer: Claudio

Topics: Recap, Open research questions