CS 553 -- Scientific Visualization

Winter Quarter 2009

http://cs.oregonstate.edu/~mjb/cs553

IM Lectures Projects Handouts Grades VHR

This page was last updated: March 10, 2009

Announcements:

What We Will Be Doing This Quarter

The goals of this course are to leave you both work-ready and research-ready for tasks that require 3D graphics to understand and gain insight into complex scientific and engineering data.

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 OSU's Computer Graphics Education Lab (CGEL in Batcheller Hall 244. You are also free to develop the projects on other systems. All projects will be done in C/C++ using OpenGL, GLUT (the GL Utility Toolkit), and GLUI (the GL User Interface package).

CS 553 topics include:



Prerequisites

This is a C programming-intensive class. Prior experience with Linux or Windows and programming is a good idea!

You can take this course with little or no graphics experience, but please do not take it for credit if you are not a moderately experienced programmer. You don't have to know C really well to start, but you should come in having programmed in something. CS 553 is a tough way to learn to program for the first time ...

Learning Objectives

On completion of the course, students will:

  1. Demonstrate a proficiency with 3D interactive OpenGL programming, including a user interface.
  2. Articulate how data is characterized in terms of spatial and data dimension.
  3. Demonstrate how to geometrize scalar data using a variety of approaches such as range sliders, point clouds, colored cutting planes, contoured cutting planes, and isosurfaces.
  4. Demonstrate how to geometrize vector data using a variety of approaches such as vector clouds, streamlines, multi-streamlines, ribbon traces, and blob traces.
  5. Artciulate what makes each method appropriate or not appropriate for what one is trying to accomplish.
  6. Demonstrate how to perform interactive direct volume rendering, including rendering, interaction, and transfer functions.
  7. Demonstrate how to perform interactive terrain visualization, including height exaggeration, lighting, texture mapping, and displaying a moving, transparent data object on top of it.
  8. Evaluate ethical situations in the use of visualization.
  9. Articulate the theory and practice of resampling scattered data.
  10. Demonstrate how to create a simple keyframe proof-of-concept animation.
  11. Articulate how these and other techniques can be used in state-of-the-art real-world applications.
  12. Evaluate existing visualizations.



Professor

The class is being taught by Professor Mike Bailey.

Office: Kelley 2117
Phone: 541-737-2542
E-mail: mjb@cs.oregonstate.edu
Web site: http://cs.oregonstate.edu/~mjb

Office Hours:

Sundays 7:00 - 8:00 PM Instant Messaging
Mondays 12:00 - 2:00 My office
Wednesdays 12:00 - 2:00 My office
Thursdays 11:00 - 1:00 My office
    or, by appointment -- send email

There are several options to reach me during IM office hours. Click here to find out what they are.

The Virtual Hand Raise

I recognize that it takes a certain amount of courage to ask a question in class. But, the worst decision of all is to not ask! So, this class 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

You can use any GLUI-GLUT-OpenGL environment you can find (eg, Linux, UNIX, Visual C++) for program development.

You will have access to the College of Engineering Computer Graphics Education Lab in Batcheller Hall 244.

No matter where you work, all projects must be turned in as either Linux or PC executable files.


Security

We take computer security very seriously. Please use intelligently-chosen passwords and protect them.



Textbook

You are expected to have the following book handy:

Dave Shreiner, Mason Woo, Jackie Neider, and Tom Davis OpenGL Programming Guide, Sixth Edition, Addison-Wesley, 2007.

You need access to this book, but don't need to own it yourself. Sharing works well. (Although all serious graphics people do own this book...)

This book is available from the OSU bookstore. (If you have the third, fourth, or fifth edition, this will be fine.) Other course material will consist of web pages, handouts, and notes taken in class.

Also, the following book is very good:

Ed Angel, OpenGL: A Primer, Third Edition, Addison-Wesley, 2007.

It doesn't explain much from scratch, but it is really good at reminding you how to do certain things in OpenGL. Its examples use GLUT.



Other Good References

Lecture Schedule

To see an academic year calendar, click here.

Class lecture time is: Monday, Wednesday, and Friday, 9:00 - 9:50. Unless otherwise specified, all lectures will be held in Strand Agriculture Hall (STAG) room 310.

1 Jan 5 Introductions. General course information.
The Visualization Process.

OpenGL-GLUT-GLUI. Geometry vs. Topology. glBegin()-glEnd().
Project #1, which is due at 23:59:59 Tuesday night.

2 Jan 7 Class today will be in the Computer Graphics Education Lab, Batcheller Hall room 244.

Be sure to print the handouts for today. (See the Announcements section above.)
sample.cpp, the GLUI user interface library, Visual C++, perspective vs. orthographic projections.
Project #2.

3 Jan 9 Class today will be in the Computer Graphics Education Lab, Batcheller Hall room 244.

More sample.cpp, intensity depth cueing.

4 Jan 12 Color! RGB, HSV, CMYK, La*b* color spaces. Different color scales. Mapping scalar values to colors. General rules of thumb when using color in scientific and engineering visualization. Color gamuts.
5 Jan 14 Color, continued.
Data visualization using color and range sliders. Project #3.
6 Jan 16 Visualization data definitions. 2D scalar visualization: 2D scatter plots, colored surface plots, contouring (isolines).
7 Jan 19 OSU Holiday -- No class today
8 Jan 21 3D scalar visualization. 3D scatter plots, volume slices, Project #4.
9 Jan 23 Wireframe isosurfaces. Project #5.
Polygon isosurfaces.
10 Jan 26 Hyperbolic geometry. Project 6.

Vector visualization: vector clouds, particle traces, streamlines, streaklines, line traces, ribbon traces, blob traces. First order versus second order accuracy.

11 Jan 28 Vector visualization, continued. Project #7.
12 Jan 30 Stereographics: binocular views, separating the images, ChromaDepth, ColorCode, lenticular displays.
13 Feb 2 Graphics program benchmarking. Performance tips. Project #8.
Test #1 review.
14 Feb 4 Transparency for visualization.
Texture-mapping for visualization.
15 Feb 6 Test #1
16 Feb 9 Go over test answers.
Terrain mapping. Project #9. Map projections for terrain visualization.
17 Feb 11 Volume Rendering: rendering, transfer functions.
18 Feb 13 Volume visualization, continued.
Volume analysis.
19 Feb 16 Volume Rendering: parallel texture planes. Project #10.
20 Feb 18 OpenGL Lighting and what you can do with it
21 Feb 20 Stencil Buffer: magic lenses, outlining polygons, hidden line removal.
Accumulation Buffer: motion blur, depth of field.
22 Feb 23 GPU programming for visualization
23 Feb 25 Spline curves.
Keyframe Animation.
24 Feb 27 Keyframe Animation, continued.
Project #11.
25 Mar 2 Interpolated scalar values within a triangle. Re-sampling. Delauney Triangulation. Voronoi diagrams.
26 Mar 4 Prof. Bailey out of town -- no class today.
27 Mar 6 The Ethics of Visualization. The difference between visualization and conceptualization (DVD).
28 Mar 9 OpenDX. Class today will be in the Computer Graphics Education Lab, Batcheller Hall room 244.
29 Mar 11 OpenDX. Class today will be in the Computer Graphics Education Lab, Batcheller Hall room 244.
30 Mar 13 Class Evaluations: it is important that you come today!
Test #2 review.
Books, periodicals, professional organizations, conferences, vendors. Job interviewing tips. Future trends to look for.
* Mar 19 Test #2 Thursday, March 19, 9:30 - 11:00 AM, STAG 310.



Attendance

As with most college courses, attendance at the lectures is optional. However, anything discussed in class is eligible to be on a test, and might be needed to complete a project. If you have to miss a class, be sure to get the notes from someone else who was able to attend. Also, be aware that cool videos tend to be shown at the start of class. You snooze, you lose!



Projects

Project # Points Title Due Date
1 20 Register your Grade-Posting Alias Jan 6
2 40 Simple Grayscale Point Cloud Jan 12
3 80 Point Clouds, Colors, and Range Sliders Jan 22
4 100 Volume Slicing Jan 30
5 80 Wireframe Isosurfaces Jan 30
6 80 Hyperbolic Geometry Feb 6
7 100 Vector field visualization Feb 13
8 60 Performance Characterization Feb 18
9 120 Terrain Visualization Feb 25
10 130 Volume Interaction Mar 8
11 100 Keyframe Animation Mar 16

Projects 2-11 are programming projects requiring you to use OpenGL, GLUT, and GLUI. All user interface options must be visible in a GLUI window. (You can also use GLUT pop-up menus and keyboard strikes if you want, but I am only going to grade using your GLUI window.)

The last three GLUI items in your user interface must be a Debug checkbox, a Reset button, and a Quit button.

Forgiveness Days

Projects are due at 23:59:59 on the listed due date, with the following exception:

Each student is granted five Forgiveness Days, which are no-questions-asked one-day extensions which may be applied to any project, subject to the following rules:

  1. No more than 2 Forgiveness Days may be applied to any one project
  2. Forgiveness Days cannot be applied to tests
  3. Forgiveness Days cannot be applied such that they extend a project due date past the end of Finals Week

Click here to get a copy of the Forgiveness Day Submission Form. Fill this out and turn it in the next class period after turning in your project.



Grading

Grades will be posted through this web page. To protect your privacy, they will be posted by your alias that you give me in Project #1.

Click here to see the current grade posting.

CS 553 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 1110, grade cutoffs will be no higher than:

Points Grade
1075 A 
1025 B+
975 B 
925 C+
875 C 
825 D+
775 D 



Handouts

The Visualization Process PDF
OpenGL-GLUT-GLUI PDF
glutMainLoop PDF
sample.cpp Text
GLUI Documentation PDF
Color In Visualization (1 slide per page) PDF
Color In Visualization (2 slides per page) PDF
Color In Visualization (6 slides per page) PDF
Marching Cubes PDF.
StereoGraphics PDF.
OpenGL Performance Notes PDF.
Vertex Arrays PDF.
OpenGL Transparency PDF.
OpenGL Texture Mapping PDF.
Volume Visualization (2 slides per page) PDF
Volume Visualization (4 slides per page) PDF
Volume Visualization (6 slides per page) PDF
OpenGL Lighting PDF
Stencil Buffer PDF
Accumulation Buffer PDF
Introduction to Shaders for Visualization PDF
More Information notes PDF



Project Turn-In Procedures



Class Rules


Expectations of Student Conduct

The goal of Oregon State University is to provide students with a general education so that they will acquire knowledge, skills, and wisdom to deal with and contribute to contemporary society in constructive ways.

The State Board of Higher Education and the University, through the Student Conduct Committee, have established regulations and policies deemed necessary to achieve the University's objective as an educational institution. All members of the University community have a strong responsibility to protect and maintain an academic climate in which the freedom to learn can be enjoyed by all.

If an individual's conduct does not meet University standards, the possibility of disciplinary action arises. The Student Conduct Program attempts to emphasize those kinds of experiences that assist the individual involved to think out, evaluate, and become accountable for personal behavior; to establish a personal code of conduct; and if need be, to redirect behavior in order to meet University expectations.

In enforcing student conduct regulations, the University follows due process procedures. Great emphasis is placed on the consideration of each individual case rather than attempting to have matching "penalties" or actions for specific incidents. The ultimate objective of the Student Conduct Program is treatment in their relationships with the institution. Through a fair consideration of all factors in each case, an attempt is made to prevent arbitrary and authoritarian action by an administrator or by student groups. Members of the staff of the Student Conduct Program are available to consult with and counsel students who believe that their individual rights have been violated or who are experiencing behavioral difficulties.

For more information, see the Office of Student Conduct web page at: http://oregonstate.edu/admin/stucon/achon.htm


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.



FAQs

In many on-line newsgroups or web topics, there is an entity known as a Frequently Asked Questions list, or a FAQ. Here we have several FAQs, arranged by topic. Click below to see individual FAQs:

OpenGL
Linux C Compiler FAQ
Visual C++



Other Useful Online Graphics and Visualization Information



Student Registration

Click here to record yourself on the CS 553 student roster. This is Project #1, and is worth 20 points.