This course introduces principles, methods and techniques for visual analysis of scientific data. Students will learn how to make effective visualization of scalar, vector and tensor field data using state of the art techniques including those for surface and volume geometry representation. Throughout the course, students will acquire hands-on experience using visualization software on real science and engineering use cases. This course is complementary to CS 5820 Data Visualization, which focuses on visualization related to tabular data (e.g., graphs, text, and maps).

Lecturer: Dr. Steve Petruzza TA: Yiming Zhao

Topics include: algorithms and techniques in scientific visualization, in situ analytics, perception.

Prerequisites: 2.0 GPA; grade of C- or better in CS 2420.

Resources

• [DV] Data Visualization: Principles and Practice, 2nd Edition by Alexandru C. Telea

Gradings

• Homework (65%)
• Project (30%). The 30% are split between the two milestones and the proposal. 5% are assigned to your proposal, 5% to your first milestone, and 20% to your final submission.
• Participation (5%), assessed via quiz and in class participation.

Class schedule

Day	Topic	References	Homework
Jan 9	Introduction	DV Ch. 1
Jan 11	Visualization pipeline	DV 4
Jan 16	MLK Day
Jan 18	Scientific data model	DV Ch. 3	HW1
Jan 23	Plotting data
Jan 25	Introduction to ParaView
Jan 30	ParaView
Feb 1	Visualization Tool Kit (VTK)
Feb 6	Visualization of 2D scalar field	DV Ch. 5	HW2
Feb 8	Visualization of 2D scalar field (2)
Feb 13	Paraview Lab	DV Ch. 10
Feb 15	Visualization of 3D scalar fields		HW3
Feb 20	President’s day
Feb 22	Large scale interactive data visualization (OpenVisus)
Feb 27	Volume rendering
Mar 1	Vector fields visualization	DV Ch. 6	HW4
Mar 6	Spring break
Mar 8	Spring break
Mar 13	Vector fields visualization (2)	DV Ch. 6
Mar 15	Vector fields visualization (3)
Mar 20	Topological analysis
Mar 22	Tensor visualization	DV Ch. 7	HW5
Mar 27	Perception
Mar 29	Project preparation
Apr 3	Perception (2)		HW6
Apr 5	Uncertainty visualization
Apr 10	In situ and parallel visualization
Apr 12	No class.
Apr 17	Project preparation
Apr 19	Project presentations
Apr 24	Project presentations 2
Apr 26	No class.

The schedule above is subject to change. “HW*” are indicative of when a homework will be assigned. Homework are generally due after one or two weeks.

Homework

• You will submit your assignment using the Canvas System.
• You are required to do your own work. You will be responsible to ensure that your assignment is submitted correctly. If you have multiple files to submit, you need to zip multiple files into one file before submission. Please verify the information in the confirmation email. If the assignment is submitted incorrectly, you can resubmit it. The system keeps track of the last file submitted for each assignment. If you do not get the confirmation information within a few minutes, you can assume the assignment has not been submitted.
• At the top of each assignment, please include comments that consist of your name, your contact email, and assignment name or number. For programming assignments please clearly add comments for each important variable and section.

Late Policy

You can turn in your homework assignments up to two days late, however, for each day that an assignment is turned in late we will deduct 10% off the total possible points. That is, one-day late is 10% off, two-days is 20% off. Submission after two days will be graded 0. We suggest to submit partial solutions to get partial credit.

Regrading Policy

It is very important to us that all assignments are properly graded. If you believe there is an error in your assignment grading, please submit an explanation via email to us (via Canvas) within 7 days of receiving the grade. No regrade requests will be accepted orally, and no regrade requests will be accepted more than 7 days after you receive the grade for the assignment.

Projects

The goal of the scientific visualization project is to design a software solution to achieve a compelling and insightful visualization using scientific simulations and/or experimental data. This can be achieved also developing and/or extending existing visualization software tools. For your project, you will work in a team of 2-3 persons which can be formed autonomously. Students without a partner will be assigned randomly to a team. The project is composed of three assignment: (i) a proposal, where you will describe goals, schedule, data and metrics of success; (ii) a progress report and (iii) a final report and presentation.

Grading Scheme

Name	Range
A	>= 93%
A-	< 93% to 90%
B+	< 90% to 87%
B	< 87% to 83%
B-	< 83% to 80%
C+	< 80% to 77%
C	< 77% to 73%
C-	< 73% to 70%
D+	< 70% to 67%
D	< 67% to 60%
F	< 60% to 0%

Grading Policy and Grades

• Each programming assignment is graded based on the following factors: code efficiency, code structure, technique difficulty, code readability, etc.
• Your scores for each assignment and exam will be available through the Canvas System. You will be shown each individual score, your percent to date, and any comments. You will be notified via email whenever you receive a score or when a change is made to a score.
• If you want to dispute a score, contact the professor within two days of having received the original score. I will review your submission and respond to you. I will not consider changes in scores if you do not contact me within one week of when the score is sent to you.

Academic Freedom and Professional Responsibilities

Academic freedom is the right to teach, study, discuss, investigate, discover, create, and publish freely. Academic freedom protects the rights of faculty members in teaching and of students in learning. Freedom in research is fundamental to the advancement of truth. Faculty members are entitled to full freedom in teaching, research, and creative activities, subject to the limitations imposed by professional responsibility. USU Policy 403 further defines academic freedom and professional responsibilities.

Academic Integrity - “The Honor System”

The University expects that students and faculty alike maintain the highest standards of academic honesty. The Code of Policies and Procedures for Students at Utah State University (Student Conduct) addresses academic integrity and honesty and notes the following:

Academic Integrity: Students have a responsibility to promote academic integrity at the University by not participating in or facilitating others’ participation in any act of academic dishonesty and by reporting all violations or suspected violations of the Academic Integrity Standard to their instructors.

The Honor Pledge: To enhance the learning environment at Utah State University and to develop student academic integrity, each student agrees to the following Honor Pledge: “I pledge, on my honor, to conduct myself with the foremost level of academic integrity”. Violations of the Academic Integrity Standard (academic violations) include, but are not limited to cheating, falsification, and plagiarism

Plagiarism

Plagiarism includes knowingly “representing by paraphrase or direct quotation, the published or unpublished work of another person as one’s own in any academic exercise or activity without full and clear acknowledgment. It also includes the unacknowledged use of materials prepared by another person or agency engaged in the selling of term papers or other academic materials.” The penalties for plagiarism are severe. They include warning or reprimand, grade adjustment, probation, suspension, expulsion, withholding of transcripts, and denial or revocation of degrees.

Course Fees

Instructors that utilize course fees should identify the amount and explain the purpose of the course fee on the top half of the first page of the syllabus. Course fees are listed in the catalog.

Grievance Process

Students who feel they have been unfairly treated [in matters other than discipline, admission, residency, employment, traffic, and parking - which are addressed by procedures separate and independent from the Student Code] may file a grievance through the channels and procedures described in the Student Code: Article VII Grievances

Discrimination and Sexual Misconduct

USU strives to provide an environment for students and employees that is free from discrimination and sexual misconduct. If you experience sexual misconduct or discrimination at any point during the semester inside or outside of class, you are encouraged to contact the USU Title IX Coordinator via Old Main room 161 in Logan, 435-797-1266, titleix@usu.edu, or at equity.usu.edu/report. You can learn more about the USU resources available for individuals who have experienced sexual misconduct at sexualrespect.usu.edu. Resources for individuals who have experienced discrimination are listed at equity.usu.edu.

Required Reporting of Sexual Misconduct

The instructor is designated by USU as a “reporting employee.” This means that if you share information about sexual misconduct (sexual harassment, sexual assault, relationship violence, or sex-based stalking) with the instructor, they will report that information to the USU Title IX Coordinator. The instructor is also required to tell you about designated confidential resources, supportive measures, and how you can file a report with the USU Title IX Coordinator.

Students with Disabilities

USU welcomes students with disabilities. If you have, or suspect you may have, a physical, mental health, or learning disability that may require accommodations in this course, please contact the Disability Resource Center (DRC) as early in the semester as possible (University Inn # 101, 435‐797‐2444, drc@usu.edu). All disability related accommodations must be approved by the DRC. Once approved, the DRC will coordinate with faculty to provide accommodations. Students who are at a higher risk for complications from COVID-19 or who contract COVID-19 may also be eligible for accommodations.

Withdrawal Policy, “I” Grade Policy and Dropping Courses

If a student does not attend a class during the first week of the term or by the second class meeting, whichever comes first, the instructor may submit a request to have the student dropped from the course. (This does not remove responsibility from the student to drop courses which they do not plan to attend.) Students who are dropped from courses will be notified by the Registrar’s Office through their preferred e-mail account.

Students may drop courses without notation on the permanent record through the first 20 percent of the class. If a student drops a course following the first 20 percent of the class, a W will be permanently affixed to the student’s record (check General Catalog for exact dates).

Students with extenuating circumstances should refer to the policy regarding Complete Withdrawal from the University and the Incomplete (I) Grade policy in the General Catalog.

No-Test Days Policy

For classes that meet for a full semester, a five-day period designated as “no-test” days precedes final examinations. During this time, no major examinations, including final examinations will be given in order that students may concentrate on classwork, the completion of special assignments, writing projects, and other preparation for duly scheduled final examinations. Approved exceptions include final papers, weekly chapter quizzes, quizzes, projects, and examinations associated with a lab that does not meet during final examinations. This policy does not apply to classes that meet only during the second 7-week session of the semester or to classes offered during the summer term. Complete information related to Final Examination Policies can be reviewed in the General Catalog.

Assumption of Risk

All classes, programs, and extracurricular activities within the University involve some risk, and some involve travel. The University provides opportunities to participate in these programs on a voluntary basis. Therefore, students should not participate in them if they do not care to assume the risks. Students can ask the respective program leaders/sponsors about the possible risks a program may generate, and if students are not willing to assume the risks, they should not select that program. By voluntarily participating in classes, programs, and extracurricular activities, students do so at their own risk. General information about University Risk Management policies, insurance coverage, vehicle use policies, and risk management forms can be found at http://www.usu.edu/riskmgt/.

Mental Health

Mental health is critically important for the success of USU students. As a student, you may experience a range of issues that can cause barriers to learning, such as strained relationships, increased anxiety, alcohol/drug problems, feeling down, difficulty concentrating and/or lack of motivation. These mental health concerns or stressful events may lead to diminished academic performance or reduce your ability to participate in daily activities. Utah State University provides free services for students to assist them with addressing these and other concerns. You can learn more about the broad range of confidential mental health services available on campus at Counseling and Psychological Services (CAPS).

Students are also encouraged to download the “SafeUT App” to their smartphones. The SafeUT application is a 24/7 statewide crisis text and tip service that provides real-time crisis intervention to students through texting and a confidential tip program that can help anyone with emotional crises, bullying, relationship problems, mental health, or suicide related issues.