Class Description

Scientific visualization combines computer graphics, numerical methods, and mathematical models of the physical world to create a visual framework for understanding and solving scientific problems. The mathematical and algorithmic foundations of scientific visualization (for example, scalar, vector, and tensor fields) will be explained in the context of real-world data from scientific and biomedical domains. The course is also intended for students outside computer science who are experienced with programming and computing with scientific data. Programming projects will be in C99.
Prerequisites: CSMC 15400 is a prerequisite, because of the programming work in C, and the need to be aware of how things are actually working at the level of the CPU and its interaction with the memory hierarchy. Also, your math background should include linear algebra.

People

Instructor	Gordon Kindlmann Office hours: Wednesdays 12:30-1:45pm JCL 249 (and via Zoom, link in EdStem)
TA	Zhuokai Zhao Office hours: Mondays 4-5pm (via Zoom, link in EdStem)

Assignments and Grading

This week-by-week diagram illustrates the schedule of assignments; the syllabus will detail everything as the quarter goes. Assignments are weighted in your grade according to these percentages:

• 6% each: 5 homeworks. These are completed individually. Homeworks involve math, and some small self-contained programming exercises.
• 11% each: 5 projects. Projects require C (C99) coding. These may be done individually or in pairs, but the same pair may work on at most three projects together (more precisely: a pair may submit work in at most three subdirectories of their shared repository).
• 5% in-lab coding midterm, to ensure that you can write C code on your own.
• 10% written final exam (during finals week, date TBD).
• The lowest 10% of your graded work will be dropped when determining your final numeric grade.

Homeworks and projects are due at 10:00pm, Chicago time, to encourage you to get some sleep. It is also important that you actively participate in the class, via in-person and online class discussion, and by doing the quizes in the Panopto videos (which are there more to assess attention than to stump you). Class participation will help decide borderline cases of letter grade assignment. Students in 33710 will have to do an additional short project (to be defined in a flexible way, such as a written report or self-directed programming project) but all students (23710 and 33710) will do the work listed above.

On the programming projects, you may do better by working as a pair with another student, but you must do so responsibly:

• Prior to the original (non-extended) project deadline, students form a pair through work-groups.cs.uchicago.edu. Then, only the code in the new shared repository (in its per-project subdirectory) will be graded. The code in the individual student repositories will be ignored for grading that project.
• Both students have to mutually agree to work as a pair.
• By forming a pair, students agree to communicate early and often about their shared work. Neither student should ever be in the dark about what their partner is doing, or when they'll finish it.

Late Policy

Throughout the quarter, you can take up to six 24-hour extensions (“late-chips”) on any assignment except hw1. Only one extension may be used per assignment. You request late-chips at work-groups.cs.uchicago.edu, but must do so before the original (non-extended) project deadline. In the case of two students working in a pair for a project, both students use their extension at the same time. Let the instructor know as early as possible about circumstances that make it hard for you to finish the work by the deadline.

Communication and Resources

• This class web page has all the needed information about videos, readings, and assignments. The Canvas page for the class is only used for hosting Panopto videos and EdStem discussion.
• Videos: Pre-recorded videos will be hosted via Panopto and linked from the syllabus. PDFs of the slides will also be available, so that you can download and take notes on the slide PDF, as well as access the hyperlinks within it. The intent is to record videos a week prior to when you should watch them. The videos will be the primary source of information content in the class.
• In-person class meetings: We will use class "lecture" times to discuss the videos and readings, to work through examples, and to debug code together. There may be Zoom access (depending on need), but it will not be recorded.
• In-person lab meetings: Lab meeting times will be for working through coding issues, and will be the primary form of "office hours" for the instructor. One lab session (1 Feb, week 4) will be for an in-lab coding midterm exam.
• The class EdStem page (called variously "Ed Discussion" or just "ED") will be how assignments are discussed, and all announcements are mode. Everyone registered just prior to the first class will be enrolled there, and the instructor will periodically sync EdStem enrollment with class registration. To ask questions directly to the professor or TA, post a private question on EdStem. If the answer to your question is something that will benefit others, we may ask you to re-post the question as non-private.
• There is no single textbook. There will be assigned readings from papers in the visualization literature, and from the instructor's "Foundations of Scientific Visualization" (FSV) notes.
• Email to students will be addressed to their CNetID@uchicago.edu address.
• The SVN for SciVis page describes how svn will be used for getting files related to the projects (such as datasets), and for handing in homework and projects.
• There are two reference platforms for this class: the CSIL (Intel-based) Macs, and the CS department Linux machines (e.g. linux.cs.uchicago.edu). Reference executables will be distributed for both platforms, and both platforms will be used for grading (Macs for correctness, Linux for cleanliness including using valgrind). We also hope to support you working on your own Mac or Linux laptops, but patience and collaborative effort will be required. Windows (even with Cygwin) will not be supported.

If you are having trouble understanding or completing the work for this class, ask questions, and ask questions early. Office hours and EdStem are the best resources for asking questions, rather than email. If your question goes unanswered, please post a private EdStem note with a title starting with "Unanswered Question".

Academic Honesty

In this course, as in all your courses, you must adhere to the University-wide Academic Honesty policies of the Student Manual. These are also described by the College under Academic Integrity & Student Conduct; expand the "Academic Integrity" section at the page bottom. To paraphrase:

1. Never copy work from any other source and submit it as your own.
2. Never allow your work to be copied.
3. Never submit work identical to another student's.
4. Document all collaboration
5. Cite your sources.

There are harsh consequences for breaking these rules. Any student who is determined to have participated in academic dishonesty will not be allowed to withdraw and will receive a course grade no higher than a C. You will also be reported to your adviser and may face further discipline as a result.

Please note that sharing your work publicly (such as posting it to the web) definitely breaks the second rule. With respect to the third rule, you may discuss the general idea of how to solve a particular problem with another student (in which case, you must document it per the fourth rule), but you may not share your work directly. When it comes time to sit down and start writing or typing, you must do the work by yourself (or with your partner for that project). Discussion of class work must be entirely voluntary and never transactional. If you have any questions or concerns about this policy, or about the behavior of another student with respect to it, please ask your instructor (via email or private note on EdStem) as soon as possible. This statement of Academic Honesty is based on that of Adam Shaw.

Sexual Misconduct

Our school is committed to fostering a safe, productive learning environment. Title IX and our school policy prohibits discrimination on the basis of sex. Sexual misconduct – including assult, harassment, stalking, and domestic and dating violence — is also prohibited. Harassment can take the form of, for example, any repeated unwelcome comments of a sexual nature, or any sexual advance associated with seeking help on class work. Review the Policy on Harassment, Discrimination, and Sexual Misconduct, in particular the Sexual Misconduct and Definitions, so you understand what this covers.

Our school encourages anyone experiencing sexual misconduct to talk to someone about what happened, so they can get the support they need and our school can respond appropriately.

If you wish to speak confidentially about an incident of sexual misconduct, want more information about filing a report, or have questions about policies, procedures, or support services, please contact our Title IX Coordinator; see the Reporting Options section of the policy. Our school is legally obligated to investigate reports of sexual misconduct after a formal complaint is filed or signed by the Title IX Coordinator, but a request for confidentiality will be respected to the extent possible. As a faculty member, I am required to report any harassment that I learn about to the Title IX Coordinator.