Spring 07: Geol 558X, Comp Sci 558X, HCI 558X - Syllabus

Introduction to the 3D visualization of scientific data

Ref. #: HCI 558X: 8518005, Geol 558X: 8516005, CS 558X: 8517005
3 credits, Tuesday/Thursdays 9-11 (lecture and/or practical exercises)
For graduate students in science and engineering. Prior experience in computer programming is helpful but is not required
2268 Hoover Hall (Linux Lab), limited to 10 students
Instructor: Chris Harding (charding@iastate.edu, www.vrac.iastate.edu/~charding/hci558)


3D visualization is used in many scientific and engineering disciplines to investigate and comprehend complex three-dimensional data sets. This course will introduce the major concepts used in visualizing scientific information with 3D computer graphics and will show how these 3D visualization techniques relate to the relevant concepts in human visual perception. The course is a mixture of lecture and practical exercise, it will use the Open Data Explorer software (Open DX, formerly IBM Data Explorer) to demonstrate 3D visualization techniques. The textbook used is written specifically for Open DX (OpenDX - Paths to Visualization).

Course Objectives:
Basic understanding of the major principles and workflows of 3D scientific visualization and how they relate to human visual perception.
Application of this understanding to analyze, comprehend and criticize existing 3D visualizations.
Gather practical experience in creating small interactive scientific 3D visualizations using the higher level 3D visualization software Open DX(or optionally, for Comp Sci, using an API such as VTK).

Course topics:
Scientific foundations of 3D data visualization and relevant principles of human visual perception: light, color, display, space perception, visual data objects, thinking and interacting with visualizations.
Visualization techniques: 2D (color, height field, isovalue contours, glyphs, clustering, patterns) and 3D (isosurface contours, direct volume rendering, slicing, glyphs).
Advanced visualization techniques (discrete data, glyphs, textures, dimensional reduction, animation, non-visual presentation of data).
Examples of Overview of 3D visualizations in different scientific domains

Grading:
Several 10 min. quizzes 25%
Midterm: 3-5 page research paper 25%
Final: theoretical and practical 10%+25%
Optional class project
Class participation %15

Required Text:
We will use Open DX as visualization software. “OpenDX Paths to Visualization” is a 207 page textbook (or pdf-file) that provides a hands-on introduction to Open DX. Available via VIS, Inc. (http://www.vizsolutions.com/paths.html), printed book: $55.00 + shipping/handling, single user eBook $40.00. If there is enough demand we might order all the books together save on shipping.

Supplemental Texts:

I will use some material from Colin Ware’s excellent book: “Information Visualization – Perception for Design” (2. Ed.) 486 pages, ISBN: 1-55860-819-2,  $65 ($54 at Amazon)

For those also interested in the Visualization Toolkit VTK , Kitware, Inc. offers two books: “The Visualization Toolkit An Object-Oriented Approach To 3D Graphics”, 3rd Edition, 520 pages, ISBN 1-930934-12-2 and “The Visualization Toolkit User's Guide”, 344 pages,ISBN 1-930934-13-0, http://public.kitware.com/VTK/buy-books.php, $85

Course Structure:

The will be a lecture in the first hour followed by a 10 minute pause and a 1-2 hour practical (lab) exercises on the computers that may lead into longer assignments. I will hand out part of the lecture material (slides) beforehand to supplement your notes – the slides will be available on the server.

Both parts (lecture and practical exercises) will take place in 2268 Hoover Hall (Linux Lab), you may also need to return to the linux lab to work on assignments or on your class project.

Practical exercises:

We will work through the various exercise described in the Open DX textbook. These exercises will take approximately 2 hrs per week to complete. Once we are through the textbook exercises we will apply visualization techniques to new data sets – this we help with your final project and the practical part of the final exam.

Reading and class presentation of visualization papers:

In the early parts of the course we will together identify a set of broader topics in visualization (visualization techniques, case studies, etc.) and assign each student a topic. Instead of a midterm, each student will conduct individual (literature) research on this topic (the instructor will of course be available for advice!) – the results should be a 3 – 5 page write-up of your findings and a 10 minute powerpoint presentation. We will spread these talks around midterm time (1-2 per week).

List of potential topics:

Quizzes:
There will be severl written quizzes. You will be given 10 min. to answer 3 out of 4 questions on paper. These will be non multiple-choice questions that test your knowledge about the proceeding lectures, you may use your textbook and your notes; For example I may ask you to write down the 3 major steps in scientific visualization or I may show you a graphic and ask you to explain what is going on.

Class project (optional):
The idea is to build on the skills and knowledge you have acquired in the first 2/3 of the course to work through a full visualization with data from your domain.

Final exam :
The final exam will consists of a multiple-choice part and a practical part. The MC questions will be about material covered in the lecture-part during the entire semester, you can use your notes and books (open books exam). The practical part will consist of several small visualization tasks similar to the exercises in the text book for which you have 90 min.

General expectations:
As this is a graduate course I assume you are able to take responsibility for your education i.e., you should not expect me to fill your head with knowledge. This means that everybody is expected to contribute to the learning process and part of your grade will come from these contributions.
Attendance:  I do ASSUME attendance in class, which provides you with the very important opportunity to ask questions! No “make-ups” will be provided for in-class quizzes, discussions, or activities missed due to absence from class.

Course files on the server:
In the linux lab: /lockers/hci558

Non-discrimination Statement:
“Iowa State University does not discriminate on the basis of race, color, age, religion, national origin, sexual orientation, gender identity, sex, marital status, disability, or status as a U.S. veteran. Inquiries can be directed to the Director of Equal Opportunity and Diversity, 3680 Beardshear Hall, (515) 294-7612.”

Disability Accommodation:
Any student who feels s/he may need an accommodation based on the impact of a disability should contact me privately to discuss your specific needs.  Please contact the Disability Resources Office at 515-294-6624 in room 1070 Student Services Building to coordinate reasonable accommodations for students with documented disabilities.

Academic Dishonesty:
I expect students to follow the ISU rules regarding Academic Dishonesty (see http://www.public.iastate.edu/~catalog/2003-05/geninfo/regulate.htm#dishonest)