CS 453 / 553 -- Scientific Visualization

Spring Quarter 2019

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


Classes Projects Handouts Grades VHR



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This page was last updated: February 12, 2019


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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, and flows. 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.

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.

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://engr.oregonstate.edu/teach to set it up.

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. Read a scientific-visualization-related research paper and write a 5-page analysis paper of it. (I will make some of these available for you, or you can propose your own. It has to be a real research paper, though.)

Professor

The class is being taught by Professor Mike Bailey.

Office: Kelley 2117
E-mail: mjb@cs.oregonstate.edu
Phone: 541-737-2542

Office Hours:

TBD.    
    or, by appointment -- send email
    or, anytime my office door is open

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

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

Paraview runs on Windows systems (sorry, no Linux or Mac), and can be freely downloaded.

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.

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 real 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 PDF
Color In Visualization 1pp 2pp 6pp
ParaView Web page with notes
Scalar Visualization 1pp 2pp 6pp
OpenGL-GLUT-GLUI PDF
Vector Visualization 1pp 2pp 6pp
Hyperbolic Geometry 1pp 2pp 6pp
Terrain Visualization 1pp 2pp 6pp
Directly Visualizing Volume Data 1pp 2pp 6pp
Resampling Scattered Data 1pp 2pp 6pp
Finding More Information PDF

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 it is:

Utkarsh Ayachit, The ParaView Guide, Kitware, 2015.
It's available on Amazon ($79) 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 Weniger 149.

1 April 1 Introductions. General course information.
The Visualization Process.
Intro to ParaView
2 April 3 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.
3 April 5 Prof. Bailey out of the office -- no class today
4 April 8 Visualization data definitions.
Introduction to Scalar Visualization: point clouds.
Project #1.
5 April 10 Scalar visualization: colored planes.
6 April 12 Contouring (isolines).
7 April 15 Project #4.
Isosurfaces. Project #5.
8 April 17 TBD.
9 April 19 TBD.
10 April 22 TBD.
11 April 24 TBD.
12 April 26 Vector visualization: vector clouds, particle traces, streamlines, line traces, ribbon traces, blob traces. Project #6.
13 April 29 More vector visualization.
Test #1 review.
14 May 1 Hyperbolic geometry. Project #7.
15 May 3 Test #1
16 May 6 Go over test answers.
17 May 8 Project #8
18 May 10 3D terrain mapping.
19 May 13
20 May 15 3D terrain mapping. Map projections for terrain visualization.
21 May 17 Engineering Expo -- no class today
22 May 20 3D terrain mapping.
Project #8.
23 May 22 3D terrain mapping.
24 May 24 3D terrain mapping.
25 May 27 Memorial Day -- no class today
26 May 29 Volume Visualization: rendering, transfer functions, parallel texture planes, uses.
Project #8
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 The Ethics of Visualization. The difference between visualization and conceptualization.
Test #2 review
30 June 7 Test #2 review.
Class Evaluations: it is important that you come today!
Books, periodicals, professional organizations, conferences.
* June ?? Test #2 ??:?? - ??:?? AM, ?????, June ?? ????? ???.
You can confirm this for yourself by going here.

Projects

Project # Points Title Due Date
1 100 Point Clouds and Colors April 14
2 100 Range Sliders April 14
3 100 Volume Slicing: Colored Planes April 29
4 100 Volume Slicing: Contour Planes April 29
5 80 Isosurfaces April 29
6 100 Vector field visualization May 8
7 80 Hyperbolic Geometry May 17
8 120 Oregon Terrain Visualization May 27
9 100 Volume Rendering June 8
553-Paper 100 Paper Analysis 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.

Your final grade will be based on your overall class point total. Based on an available point total of 1130, grade cutoffs will be no higher than:

Points Grade
995
935 B+
885
835 C+
785
735 D+
685

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 450 or CS 550) 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 an essay summarizing a research paper. (Those taking the class as CS 453 will get a free 100 points for this assignment.)

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