CS 419H -- Visualizing 3D Scientific Data

Fall 2006

http://eecs.oregonstate.edu/~mjb/cs419h

IM	Lectures	Projects	Handouts	Grades	VHR

This page was last updated: November 29, 2006

Announcements:

• For Wednesday, November 29, please print the More Information handout.

• Click here to get the starting animation network.

What We Will Be Doing This Quarter

The worlds of science and engineering are being smothered with data. In both simulation and sensing, datasets are becoming larger and faster and easier to obtain. This creates a fundamental crisis in that scientists and engineers are under pressure to be able to understand larger amounts of data in less time, and be able to show and explain it to others.

This course will cover the fundamentals of 3D scientific and engineering multidimensional data: how to create datasets and how to formulate them so that good visualization is possible. It will then cover the visualization of such data using techniques such as 2D graphics, 3D graphs, contours, isosurfaces, terrains, and flows. The class will also cover displaying time-varying data through the use of animations, including how to edit the animations through Adobe Premiere.

The class will use real datasets whenever possible. Students will also be encouraged to obtain their own domain-specific data for the assignments. Project assignments will not only consist of generating compelling visualizations, but will also consist of writing reports and making class presentations.

The hope is that students will leave the course well-equipped to contribute more to their respective fields by being "Renaissance Scientists", capable of not only gathering and manipulating data, but also able to picture it and present it for the benefit of others.

We will cover a variety of topics in advanced computer graphics and scientific/engineering visualization. Introductory courses in computer graphics emphasize converting geometry into a display. In visualization, we also need to know about converting data into geometry:

You will have access to the graphics systems in Oregon State's brand new Computer Graphics Education Lab (CGEL) in BAT 244. You are also free to develop the projects on other systems.

CS 419H topics include:

• Color
• Visualization data models
• Intro to OpenDX
• Terrain visualization
• Indirect Volume Visualization - point clouds, contour planes
• Indirect Volume Visualization - shaded surfaces, isosurfaces
• Vector Visualization - arrow clouds, streamlines, streaklines, tufts
• Direct Volume Visualization - cropping, transfer functions, rendering
• Writing your own modules
• Exporting from OpenDX - images, animations
• Editing animations

Prerequisites

Professor

The Virtual Hand Raise

I recognize that it sometimes takes a certain amount of courage to ask a question in class. But, the worst thing of all is to not ask! So, this class also offers a feature called the Virtual Hand Raise. Click here to get into it. It will allow you to send me a question or comment, completely anonymously. I will answer all questions submitted this way at the start of the next class.

Labs

OpenDX is a free package. It might exist elsewhere on campus, or you can get it yourself and install it. You can also buy a handy CD from Visualization and Imagery Solutions, Inc. (the same small company that sells the book). This is the easiest solution, although it costs a little bit of money ($35). The only trick is that OpenDX expects an X Window server to be running. How you do this is left as an exercise to the reader.

What If I Don't Have a Computer Account for the CGEL?

If you don't have an account that already works in the CGEL, you can get one by virtue of being enrolled in this course. Go to: http://engr.oregonstate.edu/teach to set it up.

Security

Textbook

Other Good References

Lecture Schedule

To see an academic year calendar, click here.

Class lecture time is: Monday and Wednesday, 10:00 - 10:50. Unless otherwise specified, all lectures will be held in Batcheller Hall room 244.

Projects

Grading

Click here to see the current grade posting.

CS 419H will be graded on a fill-the-bucket basis. There will be several projects, two tests, and maybe some quizzes. You get to keep all the points you earn.

Your final grade will be based on your overall class point total. Based on an available point total of 880, grade cutoffs will be no higher than:

OpenDX Documents

OpenDX Quick Guide -- as if 150 pages is "quick"??

OpenDX User Guide -- Appendix A, Appendix F, and the Glossary are really good

OpenDX User Reference Manual -- the modules are described in alphabetical chapters

OpenDX Program Guide -- writing your own OpenDX modules

Handouts

Datasets

Click here to go to the directory of sample OpenDX networks.

To run one, copy both the xxx.net file and the xxx.cfg file into the same directory. Then read the .net file by clicking on Edit Visual Programs in the main OpenDX menu.

You can also load these programs by clicking on Samples in the main OpenDX menu.

Project Turn-In Procedures

• To turn in your binary, go to: http://engr.oregonstate.edu/teach
  Then login and select Submit Assignment. Follow the instructions to upload your executable.

• Your project will be graded and the score posted to the class web page.

• If you disagree with the score, or want to know why you did not receive full credit, then turn in a note to me along with a listing of your program.
  You have one week after the grades are posted to do this!

Class Rules

• Lab Rules: No propping any lab doors open, no food or drink in the lab.

• Computer Security: We take computer security very seriously. Anyone caught abusing the system or causing deliberate damage will be asked to drop the class and the matter will be turned over to the Dean's Office.

• Cheating: You are expected to do your own work. Sharing code is considered cheating. Anyone caught cheating will fail this class, and the matter will be turned over to the Dean's Office.

  Students With Disabilities

  Accommodations are collaborative efforts between students, faculty and Disability Access Services (DAS). Students with accommodations approved through DAS are responsible for contacting the faculty member in charge of the course prior to or during the first week of the term to discuss accommodations. Students who believe they are eligible for accommodations but who have not yet obtained approval through DAS should contact DAS immediately at 737-4098.

• You are expected to read and understand Oregon State's Academic Dishonesty Policy. You can find it here. If you do not understand some part of it, ask me!

• Working Together: It is OK to work together by sharing information, but each person's projects must be original work with no sharing of code.

  The only address I will ever use to email you will be mjb at some Oregon State domain. If you get an email from a different address claiming to be me, do not respond to it, and let me know right away.

Other Useful Online Graphics and Visualization Information

• SIGGRAPH (The Special Interest Group on Computer Graphics): http://www.siggraph.org

• SIGGRAPH Online Computer Graphics Bibliography Database: http://www.siggraph.org/publications/bibliography

• Color:
  • Colour Lovers (interesting colors and color scales) http://www.colourlovers.com
  • Color photography in 1909-1915 http://www.loc.gov/exhibits/empire

• Open DX:
  • Open Data Explorer (OpenDX): http://www.opendx.org
  • Viz Solutions, Inc. http://www.vizsolutions.com
  • Cornell's OpenDX Extensions ftp://ftp.tc.cornell.edu/pub/Data.Explorer/extensions

• Visualization Toolkit (vtk)
  • vtk Home Page: http://public.kitware.com/VTK
  • vtk Documentation: http://public.kitware.com/VTK/doc/nightly/html
  • vtk Example Code: http://public.kitware.com/VTK/example-code.php

• Google's new search service aimed at scientists and academic researchers: http://scholar.google.com

Student Registration

Click here to record yourself on the CS 419H student roster. This is Project #1, and is worth 20 points.

Do you like Computer Graphics? Do you want to do more?

We are currently teaching or planning to teach:

In addition, we are planning a series of Advanced Topics courses, collectively grouped under the reserved CS 559 course name. These courses include: