CS 453 / 553 -- Scientific Visualization

Spring Quarter 2019

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

Classes Projects Handouts Grades VHR

This page was last updated: June 14, 2019

Announcements:

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 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 cover the visualization of such data using techniques such as 2D graphics, 3D graphs, contours, isosurfaces, terrains, flows, and volumes. The class will also cover displaying time-varying data through the use of animations.

Introductory courses in computer graphics emphasize converting geometry into a display. In visualization, we also need to know about converting data into geometry:

The goals of this course are to leave you "career-ready" i.e., 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.

For some of the projects, we will use a free, open source, visualization package called Paraview.
Paraview runs on Windows desktop systems, and can be freely downloaded from. https://www.paraview.org/download/.
There are Linux and MacOS versions of ParaView, but they are the multi-CPU flavor.

For other projects, you will write your own C/C++ OpenGL code, although you will be given a skeleton that does all of the program "boilerplate" for you, leaving you to do the very specific parts of the visualization. The idea is that, at some point, you can't avoid writing your own code. This happens when (1) what you want to do exceeds the capabilities of any of the packages or (2) you want to integrate visualization techniques into some other piece of code.

If you need it, 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, including your own.

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://teach.engr.oregonstate.edu and click on Create a new account (Enable your Engineering resources) at the bottom of the first page (even before you login to teach).

CS 453/553 topics include:

Prerequisites

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/C++ really well to start, but you should come in having programmed in something. CS 453/553 is a tough way to learn to program for the first time ...

Learning Objectives

On completion of the course, students will:

  1. Demonstrate a working knowledge of the ParaView visualization software package, including using for scalar, vector, terrain, and volume visualization.
  2. Demonstrate a proficiency with 3D interactive OpenGL programming, including a user interface.
  3. Articulate how data is characterized in terms of spatial and data dimension.
  4. 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.
  5. Demonstrate how to geometrize vector data using a variety of approaches such as vector clouds, streamlines, multi-streamlines, ribbon traces, and blob traces.
  6. Articulate what makes each method appropriate or not appropriate for what one is trying to accomplish.
  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 conceptualization animation.
  11. Articulate how these and other techniques can be used in real-world applications.
  12. Evaluate the effectiveness of existing visualizations.

In addition, those taking this course as CS 553 will also have demonstrated the ability to:

  1. Find your own data, determine how to read it in, and apply the most appropriate visualization techniques to understand and present it.

Professor

The class is being taught by Professor Mike Bailey.

Office: Kelley 2117 (second floor, south side)
E-mail: mjb@cs.oregonstate.edu
Phone: 541-737-2542

Office Hours:

Mondays 2:00 - 4:00 Kelley 2117
Wednesdays 2:00 - 4:00 Kelley 2117
Thursdays 12:30 - 2:30 Kelley 2117
    or, by appointment -- send email
    or, anytime my office door is open

TA

Our TA for this class is Wenbo Hou, a very experienced computer graphics grad student.

Combined Office Hours

Wenbo Hou Prof. Bailey
houw@oregonstate.edu mjb@cs.oregonstate.edu
Mondays, 10:30 - 2:00 Mondays, 2:00 - 4:00
Tuesdays, 11:00 - 2:00  
Wednesdays, 10:30 - 2:00 Wednesdays, 2:00 - 4:00
  Thursdays, 12:30 - 2:30
Fridays, 2:00 - 5:00  
CGEL (Bat 244) Kelley 2117

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 has 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.

Handouts

These handouts are meant to go along with what we will talk about in class. It is up to you if and how you print them. The one-per-page versions are easy to read, but consume more paper and ink. The six-per-page versions are harder to read, but consume less paper and ink. The two-per-page and four-per-page versions are in the middle. You can decide whether or not it is worth printing them in color.

The Visualization Process 1pp 2pp 4pp 6pp
Getting Started with OpenGL (from CS 450/550) 1pp 2pp 4pp 6pp
Scalar Visualization 1pp 2pp 4pp 6pp
Color In Visualization 1pp 2pp 4pp 6pp
ParaView Web page with notes
OpenGL-GLUT-GLUI PDF
Vector Visualization 1pp 2pp 4pp 6pp
Hyperbolic Geometry 1pp 2pp 4pp 6pp
Terrain Visualization 1pp 2pp 4pp 6pp
Directly Visualizing Volume Data 1pp 2pp 4pp 6pp
Using the Accumulation Buffer for Visualization 1pp 2pp 4pp 6pp
Using the Stencil Buffer for Visualization 1pp 2pp 4pp 6pp
Resampling Scattered Data 1pp 2pp 4pp 6pp
Finding More Information PDF
Using Kaltura to record turn-in videos for class assignments PDF

Labs

The CGEL will be available for your use, but you can also use your own computer systems.

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

Security

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

Textbook

There is no required textbook for this class. Everything will be done with notes and web pages.

If you want to brush up on computer graphics, I recommend the OSU CS 450/550 notes, which can be found here. Especially look at the Getting Started with OpenGL notes.

The OSU ParaView noteset can be found here.

A nice ParaView Getting Started Guide can be found here.

A nice ParaView tutorial can be found here.

The ParaView people have made a free copy of their book available here.

If you are dying to have the physical ParaView book, here is how to get it:

Utkarsh Ayachit, The ParaView Guide, Kitware, 2015.
It's available on Amazon ($77) here.

Class Schedule

To see an academic year calendar, click here.
Class time is: Monday, Wednesday, and Friday, 9:00 - 9:50. Unless otherwise specified, all classes will be held in Kearney 112.

1 April 1 Introductions. General course information.
The Visualization Process.
Intro to ParaView
2 April 3 Introduction to Scalar Visualization: point clouds.
Project #1.
3 April 5 Prof. Bailey out of the office -- no class today
4 April 8 Range sliders.
5 April 10 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.
6 April 12 Scalar visualization: colored planes and contour lines.
7 April 15 Isosurfaces.
ParaView scalar visualization.
8 April 17 ParaView scalar visualization.
9 April 19 ParaView scalar visualization.
ParaView animation
10 April 22 Hyperbolic geometry
11 April 24 Vector visualization: vector clouds, particle traces, streamlines, line traces, ribbon traces, blob traces.
12 April 26 Test #1 review.
https://www.youtube.com/watch?v=iHJUmw5FCsM
https://www.youtube.com/watch?v=EgumU0Ns1YI
http://www.ncsa.illinois.edu/enabling/vis/cadens/making_of
ParaView vector visualization.
13 April 29 Optional help session: test and projects.
14 Wednesday, May 1 Test #1
15 May 3 Prof. Bailey out of the office -- no class today.
16 May 6 Go over test answers.
17 May 8 Terrain visualization.
18 May 10 Terrain visualization using ParaView. Map projections.
19 May 13 Parallel coordinates.
20 May 15 Engineering Expo prep day. Class today is an optional help session in Kelley room 2114.
21 May 17 Engineering Expo -- no class today
22 May 20 Volume Visualization: rendering, transfer functions, parallel texture planes, uses.
23 May 22 Volume visualization: ParaView
24 May 24 The Stencil Buffer in data visualization: magic lenses, outlining polygons, hidden line removal.
The Accumulation Buffer in visualization: motion blur, depth of field.
25 May 27 Memorial Day -- no class today
26 May 29 The Ethics of Visualization. The difference between visualization and conceptualization.
27 May 31 Prof. Bailey out of the office -- no class today
28 June 3 Interpolated scalar values within a triangle. Re-sampling. Delauney Triangulation. Voronoi diagrams.
29 June 5 Test #2 review
Class Evaluations: it is important that you come today!
More information: books, periodicals, professional organizations, conferences.
30 June 7 Optional Help Session -- Kelley 2114
* Thursday, June 13 Test #2 9:30 - 11:00 AM, Thursday, June 13
You can confirm this for yourself by going here.

Projects

Project # Points Title Due Date
1 40 Grayscale Point Clouds April 8
2 100 Point Clouds, Colors, and Range Sliders April 15
3 100 ParaView Scalar Visualization April 23
4 100 Hyperbolic Geometry April 29
5 80 Vector Clouds with Range Sliders May 8
6 100 ParaView Vector Visualization May 15
7 100 ParaView Terrain Visualization May 22
8 80 ParaView Volume Visualization May 29
553-Project 100 Roll-your own scientific visualization project June 9

Using Your Own Data

Where necessary, I will give you data or equations to use to generate data for the projects. What if you have some of your own data that will work for the methods being used in a particular project?

Yes! Very cool. Feel free to use it.

However, talk with me first. I want to be sure that (1) your data really is appropriate, and (2) you can import it easily so you don't spend the bulk of the time until the due date just trying to read it.

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 453/553 will be graded on a fill-the-bucket basis. There will be 11 quizzes, ?? projects, and two tests. You get to keep all the points you earn.
The quizzes will be done via Canvas. They will open each Friday afternoon right after class and close Sunday night at 23:59:00. Canvas is very unforgiving about due times -- don't push it.

... with the exception of ...

Quiz #0 is due to me by 4:00 PM on Friday, April 5. Fortunately, it is not too hard:

  1. Get a 3"x5" index card (I'll give you one the first day of class).
  2. Print your name neatly at the top (holding the card horizontally).
  3. Print the course number you are taking this under (CS 453 or CS 553) neatly next to your name.
  4. Also, printing neatly, tell me why you are taking this class. What do you hope to get out of being here?
  5. Be honest -- no sucking up!
  6. Bring the card to my office (Kelley 2117: second floor, south side) sometime when I am there. (Don't throw it under the door.)

If you are taking both of my classes this quarter, please fill out an index card for each.

Those taking the class as CS 553 will also do a roll-your-own scientific visualization project. (Those taking the class as CS 453 will get a free 100 points for not doing this assignment.)

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
1080 A 
1050 A-
1020 B+
990 B 
960 B-
930 C+
900 C 
870 C-
840 D+
810 D 
780 D-

Project Turn-In Procedures

Bonus Days

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

Each of you has been granted five bonus days, which are no-questions-asked one-day extensions which may be applied to any project, subject to the following rules:

  1. Up to 2 bonus days may be applied to any one project
  2. Bonus Days cannot be applied to tests
  3. Bonus Days cannot be applied such that they extend a project due date past the start of Test #2.

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

Class Rules

Students With Disabilities

Accommodations for students with disabilities are determined and approved by Disability Access Services (DAS). If you, as a student, believe you are elig ible for accommodations but have not obtained approval please contact DAS immediately at 541-737-4098 or at http://ds.oregonstate.edu.DAS notifies students and faculty members of approved academic accommodations and coordinates implementation of those accommodations. While not required, students and faculty members are encouraged to discuss details of the implementation of individual accommodations.

Religious Holidays

Oregon State University strives to respect all religious practices. If you have religious holidays that are in conflict with any of the requirements of this class, please see me immediately so that we can make alternative arrangements.

Life Events

As {John Lennon? Allen Saunders?} has said: "Life is what happens to you while you're busy making other plans". I care about you as a person. When life happens to you, send me an email and come see me. I might be able to help, I might not. But I surely can listen. You are not alone.

Basic Needs

Any student who has difficulty affording groceries or accessing sufficient food to eat every day, or who lacks a safe and stable place to live, is urged to contact the Human Services Resource Center (HSRC) for support: hsrc@oregonstate.edu, 541-737-3747. The HSRC has a food pantry, a textbook lending program, and other resources to help. Furthermore, if you are comfortable doing so, please talk with me. I will do everything I can do to help you.

Other Useful Online Graphics and Visualization Information