SciVisFall2008/Schedule

2008-10-28T04:35:25Z

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

== 8/26: Introduction to visualization ==

Lecturer: Claudio

Topics: Scientific Visualization

Notes: [http://www.cs.utah.edu/~csilva/courses/cs5630/lec01-notes.pdf lec01-notes.pdf]

Slides: [http://www.cs.utah.edu/~csilva/courses/cs5630/fall2008/lec01.pdf intro]

Animations: [http://www.cs.utah.edu/~csilva/courses/cs5630/fall2007/SevereTstorm.mov NCSA storm animation]

Further reading:

(Optional reading) [http://www.sci.utah.edu/~csilva/papers/cise2008a.pdf 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: [http://www.cs.utah.edu/~csilva/courses/cs5630/lec02-notes.pdf lec02-notes.pdf]

Slides: [http://www.cs.utah.edu/~csilva/courses/cs5630/lec02.pdf lec02.pdf]

Further reading:

(Optional reading) [http://www.cs.utah.edu/~csilva/courses/cs5630/reproducible_vis.pdf 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: [http://www.vistrails.org/download/download.php?type=PUB&id=week2.pdf modeling data]

Slides: [http://www.vistrails.org/download/download.php?type=PUB&id=processing.ppt processing.ppt]

Further reading:

[http://www.cs.wisc.edu/graphics/Courses/559-s2001/notes/hanrahan.pdf Basic Signal Processing]

[http://graphics.cs.uiuc.edu/~garland/papers/quadrics.pdf Surface Simplification Using Quadric Error Metrics]

(Optional Reading) [http://www.sci.utah.edu/~csilva/papers/vis2001b.pdf A Memory Insensitive Technique for Large Model Simplification]

(Optional Reading) [http://graphics.cs.uiuc.edu/~garland/papers/TR-2004-2450.pdf 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: [http://www.vistrails.org/download/download.php?type=PUB&id=week2.pdf modeling data]

Slides: [http://www.vistrails.org/download/download.php?type=PUB&id=processing.ppt processing.ppt]

Further reading:

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

(Optional Reading) [http://www.sci.utah.edu/~csilva/papers/sig2005.pdf Robust Moving Least-squares Fitting with Sharp Features]

(Optional Reading) [http://www.sci.utah.edu/~cscheid/pubs/band_mls.pdf Optimal Bandwidth Selection for MLS Surfaces]

== 9/9: Elementary Plotting Techniques ==

Lecturer: Claudio

Topics: Principles of Graph Construction

Notes: [http://www.sci.utah.edu/~stevec/classes/cs5630/PlottingNotes.pdf PlottingNotes.pdf]

Slides: [http://www.sci.utah.edu/~stevec/slides/SciVis/Plotting1.pdf 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: [http://www.sci.utah.edu/~stevec/classes/cs5630/PlottingNotes.pdf PlottingNotes.pdf]

Slides: [http://www.vistrails.org/download/download.php?type=PUB&id=Plotting2.pdf Plotting2.pdf]

Vistrails: [http://www.sci.utah.edu/~stevec/classes/cs5630/PlottingVistrails.zip 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:

* [http://www.fmrib.ox.ac.uk/analysis/techrep/tr00mj2/tr00mj2/node24.html Histogram Bin Size]
* [http://en.wikipedia.org/wiki/Correlation Correlation]
* [http://en.wikipedia.org/wiki/Linear_regression Linear Regression]
* [http://en.wikipedia.org/wiki/Box_plot Box Plots]

== 9/16: Color and Human Perception ==

Lecturer: Claudio

Topics: Human vision system; Optical illusions

Slides: [http://www.cs.utah.edu/~csilva/courses/cs5630/human-vision.pdf human-vision.pdf]

Links:

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

http://www.grand-illusions.com/gregory2.htm (also, see the related book: [http://www.amazon.com/Eye-Brain-Richard-L-Gregory/dp/0691048371])

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: [http://www.cs.utah.edu/~csilva/courses/cs5630/colorvision-jens.pdf colorvision-jens.pdf]

Links:

Further reading:

[http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm 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:

[http://www.falstad.com/vector Vector Field Applet]

Further Reading:

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

Appendix A of these notes might be useful: [http://www.cs.ubc.ca/~rbridson/fluidsimulation/fluids_notes.pdf]

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

[http://www.amazon.com/Div-Grad-Curl-All-That/dp/0393969975 Div, Grad, Curl, and All That: An Informal Text on Vector Calculus]

[http://www.cambridge.org/uk/catalogue/catalogue.asp?isbn=9780521877619 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: [http://www.vistrails.org/download/download.php?type=PUB&id=2d_scalar_vis.pdf pdf file]

Notes: [http://www.vistrails.org/download/download.php?type=PUB&id=2d_scalar_vis_notes.pdf pdf file]

Vistrails: [http://www.vistrails.org/download/download.php?type=DATA&id=ozone_and_data.zip zip file with ozone.vt and data] [http://www.vistrails.org/download/download.php?type=DATA&id=asymptotic_decider.vt asymptotic decider in 2d] [http://www.vistrails.org/download/download.php?type=DATA&id=elevation.zip 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

[http://www.inf.ufrgs.br/%7Eoliveira/pubs_files/Kuhn_Oliveira_Fernandes_Vis2008.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: [http://www.vistrails.org/download/download.php?type=PUB&id=2d_vector_vis.pdf 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: [http://www.vistrails.org/download/download.php?type=DATA&id=vector_vis_1.zip vistrail with steady vector field vis and data] [http://www.vistrails.org/download/download.php?type=DATA&id=unsteady.zip 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).

[http://wwwcg.in.tum.de/Download/PE "The Dx9 Particle Engine" as well as a few datasets]

== 10/2: Volume Vis ==

Lecturer: Carlos

Topics: Slicing; Contours; Marching algorithms

Slides: [http://www.cs.utah.edu/~csilva/courses/cs5630/iso-basic.pdf iso-basic.pdf]

References:

[http://portal.acm.org/citation.cfm?id=37401.37422 Marching cubes: A high resolution 3D surface construction algorithm]

[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=175782 The asymptotic decider: resolving the ambiguity in marching cubes]

== 10/2: Volume Vis ==

Lecturer: Carlos

Topics: Accelerating structures; High-quality contours

Slides:

[http://www.cs.utah.edu/~csilva/courses/cs5630/iso-speed.pdf iso-speed.pdf]

[http://www.cs.utah.edu/~csilva/courses/cs5630/iso-speed-2.pdf iso-speed-2.pdf]

References:

[http://doi.ieeecomputersociety.org/10.1109/2945.489388 A Near Optimal Isosurface Extraction Algorithm Using the Span Space]

[http://doi.ieeecomputersociety.org/10.1109/2945.485619 Automatic Isosurface Propagation Using an Extrema Graph and Sorted Boundary Cell Lists]

[http://doi.ieeecomputersociety.org/10.1109/2945.597798 Speeding Up Isosurface Extraction Using Interval Trees]

[http://doi.ieeecomputersociety.org/10.1109/SVVG.2004.5 Implicit Occluders]

== 10/9: Volume Vis ==

Lecturer: Carlos Scheidegger

Topics: High quality isosurfaces

Slides: [http://www.cs.utah.edu/~csilva/courses/cs5630/iso-quality.pdf iso-quality.pdf]

References:

[http://www.cs.utah.edu/~csilva/2007-sub/macet.pdf Edge Transformations for Improving Mesh Quality of Marching Cubes]

[http://www.sci.utah.edu/~csilva/papers/tvcg2006acr.pdf High-Quality Extraction of Isosurfaces from Regular and Irregular Grids]

[http://portal.acm.org/citation.cfm?id=566570.566586 Dual contouring of hermite data]

[http://www.sci.utah.edu/%7Emiriah/research/meshing/vis07meyer.pdf Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles]

[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1260744 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: [http://www.sci.utah.edu/~stevec/classes/cs5630/VolumeRendering1.pdf VolumeRendering1.pdf]

Notes: [http://www.sci.utah.edu/~stevec/classes/cs5630/dvr.pdf dvr.pdf]

vistrails: [http://www.sci.utah.edu/~stevec/classes/cs5630/VolumeRenderingVistrails.zip VolumeRenderingVistrails.zip]

References:
[http://www.llnl.gov/graphics/docs/OpticalModelsLong.pdf 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: [http://www.sci.utah.edu/~stevec/classes/cs5630/VolumeRendering2.pdf VolumeRendering2.pdf]

Notes: same as previous class

vistrails: same as previous class

References:

[http://graphics.stanford.edu/papers/volume-cga88/ Display of Surfaces from Volume Data] - Ray casting paper

[http://portal.acm.org/citation.cfm?id=329138 Interactive Volume Rendering] - Splatting paper, paper requires ACM digital library access

[http://portal.acm.org/citation.cfm?id=197972&dl=ACM&coll=GUIDE Accelerated volume rendering and tomographic reconstruction using texture mapping hardware] - Texture slicing paper, requires ACM digital library access

[http://graphics.stanford.edu/papers/shear/ 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.

== 11/4: Simplification Techniques ==

Lecturer: Claudio

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

== 11/6: Direct Volume Rendering ==

Lecturer: Claudio

Topics: Unstructured grid techniques

== 11/11: Direct Volume Rendering ==

Lecturer: Claudio

Topics: Transfer function specification

== 11/13: Tensor Visualization ==

Lecturer: Claudio

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

== 11/15: 3D Vector Vis and Topology ==

Lecturer: Claudio

Topics: 3D techniques, critical points

== 11/18: Information Visualization ==

Lecturer: Claudio

Topics: Parallel coordinates; Graph visualization

== 11/20: Information Visualization ==

Lecturer: Claudio

Topics: Trees and Graphs; InfoVis Examples

== 11/25: TBD ==

== 11/27: Thanksgiving ==

== 12/2: Aesthetic Issues in Vis ==

Lecturer: Claudio

Topics: Tufte principles

== 12/4: Aesthetic Issues in Vis ==

Lecturer: Claudio

Topics: NPR and Illustrative techniques for Vis

== 12/9: TBD ==

== 12/11: TBD ==

VistrailsWiki - User contributions [en]

SciVisFall2008/Schedule