CS237 Assignments

David Laidlaw
Brown University
Fall 2000


Assignments for each class. Note that handins are due by noon the day of class to allow for review before class. Handins are to be made online to a directory on the CS department machines. You must have a CS account to do this, so please make sure that you get an account the first day of classes. TA Joe Lee (jcl@cs.brown.edu) will arrange for the accounts. You'll need to see him in person to get your account and password.

When you are logged in to a CS machine (in the Sun lab, for instance, or over the network), you can deliver assignments to:

     /pro/web/web/courses/cs237/asgns/DATE/LOGIN.EXT

where you replace DATE with the due date (e.g., 9-7), LOGIN with your CS login (e.g., dhl), and EXT with the type of file (e.g., txt). If multiple handins are due the same day, please number them (e.g., dhl1.txt, dhl2.txt). For handins the first week, those without CS account can e-mail their handins to jcl@cs.brown.edu and he will put them into the appropriate assignments directory.

Almost all of the readings we will do are online to reduce copying effort and costs and to keep color imagery intact. Printing them for your own use is fine. Please look at the color images in color, though! Some of the files are huge (40-50 Mb). You will not be able to get them over a phone line.

Please respect the grant proposals you will be reading. They are not published documents and should not be circulated outside of class. Please make sure that you destroy any copies of those documents when you are finished with them for class.

Th 9/7/00

If you don't already have one, make sure you are signed up to get a CS computer account! Contact jcl@cs.brown.edu.
Hand in (by noon!): personal background
Read, with an eye toward your essay (see below):
Hand in by noon: an essay, 250-750 words, describing three visualization research topics of interest to you. Base the topics on the readings. For each topic, explain your motivation and how it fits in (or doesn't) with all of the readings.

Tu 9/12/00

These readings will give you a feel for what goes into a research grant proposal and what comes out of it.

The NSF Grant Proposal Guide (1995) describes how to write a grant proposal. While some of the instructions are specific to NSF, much of the document gives good advice on how to write any proposal.

Read a Program Announcement. Typically, NSF accepts both unsolicited grant applications (for whatever a proposer thinks is worth doing) and solicited applications. Applications are solicited via a Program Announcement (PA), sometimes called a Request for Proposals (RFP). The NSF Knowledge and Distributed Intelligence (KDI) Program Announcement gives one example of what they were looking for last year.
Read proposal 3D Free-Form Models for Geometric Recovery and Applications to Archaeology, Cooper, Joukowsky, Kimia, Laidlaw, Mumford. This is a proposal in response to the KDI solicitation. It was successful and was funded last September. You don't need to understand all of the math and shape modeling. Get the big picture as an example of a multi-disciplinary research project.
Hand in by noon: your review.
Read NSF reviews of the proposal (after you write yours) and add any new discussion questions to your review.
Read progress report to NSF as of June. This gives a feel for what NSF wants to see while a project is in process. Keep in mind for your intermediate progress reports during the semester.
Peruse the web site for the project to see what's going on and what's been done. Update your handin based on the reviews and results. Don't forget questions for our visitor on Tuesday!
Hand in a list of four possible collaborators from other disciplines for your class project. Read the RFP for class projects to understand more about the criteria for judging a project idea. Possible collaborators can be from the page of bio info for the class, the list of project ideas suggested by various researchers around campus, and any personal contacts you have. Describe the discipline of each possible collaborator and how it is distinct from your area. At least two must be contributors to the list of project ideas or established researchers.

You will need to meet with at least three of the four possible collaborators and report on those meetings on 9/19. These meetings will help you develop the interdisciplinary part of your project. Get started scheduling these meetings and look at what you'll need to hand in as a report.

Th 9/14/00

Read: Computer Graphics Tools for Understanding Tensor-Valued Volume Data: A Painting Metaphor, Laidlaw. This is a second example of an interdisciplinary visualization proposal. The application areas are quite different and the proposal is more focused on visualization. Skim the whole proposal, then read the Project Summary and Project Description.
Write: your own review. Do the review before reading the NSF reviews, and then answer the subsequent questions after the other readings.
Read: NSF Reviews to get a feel for what reviewers thought of the proposal.
Read: annual status report to NSF. Once again, this gives a feel for what NSF is interested in
Read the following to get an idea of the results from the grant. Look for the main ideas and, possibly, for project inspiration.
Update your handin with answers to the relevant questions about the reviews and results.
Read followon proposal and its reviews
Update your handin with answers to the relevant questions about the follow-on proposal.
Continue interviewing possible collaborators.

Tu 9/19/00

Hand in interview reports.
Hand in at least three possible proposal titles. For each, include a brief description, a list of participants, and your evaluation of the proposal you imagine. Use the RFP to guide your project ideas and to self-evaluate them.
NIH guide to proposals -- read the interesting and relevant parts.
Johnson proposal. This proposal is 10 years old, so the work is not current. It does show an excellent example of a successful non-clinical NIH grant proposal. Non-clinical work is often quite difficult to get funded by NIH. Note the structure of the proposal, with well-formulated hypotheses to test.
Read partial list of resulting papers
R.S. MacLeod, C.R. Johnson, and M.A. Matheson. Visualization of bioelectric fields. IEEE Computer Graphics and Applications, pp. 10-12, July 1993. (paper)
Add discussion questions/topics to grant review, including specific questions for today's guest.

Th 9/21/00

Hand in the results of a literature search for each of your proposal choices still in the running. For each citation you hand in, make sure that you have read at least the abstract of the paper.
Schedule a meeting with the rhetoric fellow to prepare your class presentation on 10/3 or 10/5.
Evaluate the project ideas of everyone in the class: Mike , Scott , Josh , Marty . Reviews should be based on the RFP . Hand in to the assignments directory using filenames of the form (if you are rmk and you are reviewing jmt's proposal ideas) "jmt_by_rmk.txt". You should be handing in three sets of reviews (in addition to your own, if you didn't hand it in on Tuesday).
Read original Brooks toolsmith paper. You'll find the beginning essentially identical, but persevere to the later, different parts.
Hand in your review.

Tu 9/26/00

Hand in by noon: title, short description, and list of participants on your proposal.

You might also want to start reading the materials for Thursday, since they are long.

Thu 9/28/00

Handins for this class should be in a single text file and are listed with each of the readings below.
Read the Human Brain Project program announcement from NIH. Pay particular attention to the Research Objectives, Review Criteria, and Award Criteria; the rest can be skimmed. Hand in a few sentences summarizing the research objectives and list the review criteria.
Read a Human Brain Project grant proposal. This proposal is a renewal of a project funded five years earlier. It is in pieces on the web in a slightly preliminary form. Read the overview, atlas project, both algorithms projects, and the responsive workbench project. Skim the connectivity project and all four "cores." Ignore the forms Review the proposal according to NIH review criteria and the specific review criteria in the program announcement and turn in the review.
Read the grant review . Hand in a list of at least three non-obvious points you would like to make to the class about the reviews. Relate the review you did to the reviews received from NIH.
Read the 1999 annual report, the 2000 annual report, and one of the resulting publications, ( fig 1 , fig 2 , fig 3 , fig 4 , fig 5 ). Explain what you feel is the most compelling advance that the paper describes. Explain how that is in keeping with both the work that was proposed (and cite the relevant sections) and with the program announcement research goals and evaluation criteria.
Russ Jacobs and Scott Fraser will teleport to class Thursday and will be available to answer questions. Together, they run one of the best examples of a multidisciplinary research lab that I've seen. Please list, as the last item in your handin, three questions for them about the proposal, multi-disciplinary research, etc.

Continue to work on your proposals and prepare for class presentations. We'll talk about presentations in class on Tuesday.

Tu 10/3/00

Proposals due by noon. Hand in to the assignments directory in PDF format. Follow instructions in RFP.

Mike and Josh be prepared to present.

No readings for this class. Continue to work on your proposals and prepare for class presentations.

Th 10/5/00

Scott and Marty be prepared to present.

Hand in the one proposal review that you did pre-presentation. Put it in the 10-10 directory.

Reviews of everyone else's proposals are due next Tuesday, but if you can get them done sooner, please hand them so that proposal revisions can be made with as much input and time as possible.

After your presentation, work on revising your proposals based on comments during the presentation, my review, the classmate review that's been turned in, and any other reviews that are available.

Have a scheduled time for meeting with Pavani to go over your written proposal. She'll get them back to you on the 10th or 11th. You'll need to incorporate her suggestions by the 17th, so the meeting should be soon enough before the 17th to have time for revisions.

Tu 10/10/00

Hand in reviews for everyone else's proposals. Use the review criteria in the RFP (reviewee_by_reviewer.txt). Pick up the reviews for your proposal and continue revising your proposal.

Hand in an annotated list of references you would like to propose that the class read and discuss during the remainder of the semester. The list should include at least 6 papers relevant to your project. Your annotations (1-3 sentences is enough) should indicate why you feel the paper is important and relevant for the class. I expect that many of the papers will come from the references of your proposal. In addition to the 6+ papers, list another 6 (or more) topics you'd like to learn about, but for which you can't find a specific paper. We'll work on finding relevant readings.

Th 10/12/00

No class today. Makeup class will be next Wednesday at noon in CIT506.

Continue to revise proposals for 10/17.

Meet with writing fellow this week to discuss comments on your proposal.

Tu 10/17/00

Finish revising draft proposals. Be sure to consider 1) reading fellow input, 2) written critiques from fellow students, 3) comments from professor, and 4) suggestions made during your presentation.

Hand in final proposals to asgns directory.

Th 10/19/00

Review everyone's final proposals. Hand in, by noon, all reviews in the online review form. Name each review reviewee_by_reviewer.txt. Bring 7 hardcopies of your reviews to class.

jsd is primary reviewer for rmk.

rmk is primary reviewer for jmt.

jmt is primary reviewer for marty.

marty is primary reviewer for jsd.

For the proposal you are primary on, tabulate (sum) the average overall score for the proposal and be prepared to provide it. Also be prepared to summarize the reviews.

FRIDAY! 10/18/00! 4PM (MAKEUP CLASS!)

Don't forget to come to class at 4pm in 506!

Tu 10/24/00

Th 10/26/00 Get going on those projects!

Tu 10/31/00

Check out the papers to be presented over the next few weeks. Gear up to read them and be prepared to present the one(s) assigned to you.
Costumes optional :-)
Meet at the cave for class.

Th 11/02/00

Marty will present "Imaging the Universe at Radio Wavelengths," Crutcher, IEEE Computationa Science and Engineering 1(2), 1994, 39-49.
Others, read the paper and hand in a list of three discussion questions regarding the paper.
Scott will present "Static and Moving Patterns," Chapter 6 from Information Visualization: Perception for Design by Colin Ware Morgan Kaufmann Publishers, 2000.
Others, read the paper and hand in a list of your favorite three lessons and a new example of how you would apply each of the lessons to a visualization problem.

Tu 11/07/00

Each PI should be prepared to describe progress on their project relative to the plan in the proposal. Focus on accomplishments -- bring pictures, describe preliminary or partial results. Mention problems and proposed solutions. We'll have 15-20 minutes for each proposal, including feedback from the class.
Mike will present "Perception of Three-Dimensional Shape from Texture is Based on Patterns of Oriented Energy;"," by Li and Zaidi.
Others, bring in three textured things to class and explain how the texture and the perception of their shape works or doesn't work. Turn in the explanations by noon to the assignments directory. In addition, describe the texture that you would use to best show the shape of 3D objects in the cave. Your description can include pictures/diagrams.

Th 11/09/00

Wear clothes that you can get paint on :-)

Tu 11/14/00

Josh will present "Large Datasets at a Glance: Combining Textures and Colors in Scientific Visualization" by Healey/Enns, IEEE Transactions on Visualization and Computer Graphics. (Note: .ps.gz file may be easier to read online -- Acroread 4.0 messes up on the antialiasing.)
Others, read the paper and hand write a one page critical evaluation of the paper. Also, list the result you found the most surprising.

Th 11/16/00

Scott will present ``Evaluating Stereo and Motion Cues for Visualizing Information Nets in Three Dimensions'', Ware, TOG 15(2), 1996.
Others, read the paper and a) summarize the results in 3 sentences; b) explain what features distinguish this paper from others (in a positive sense); and c) what were the weaknesses of the paper.
Mike will present Vicki Interrante's Visualization Viewpoints column from the latest IEEE Computer Graphics and Applications.
Others, read the column and list three takehome messages. Explain why you think they are interesting and important.
Remember that your talks after Thanksgiving need to be in conjunction with Pavani, our Rhetoric Fellow. Check out your scheduled time and arrange for at least two and preferably three meetings with Pavani before your talk time. The first meeting should be a week in advance to go over the concept for your presentation. The second meeting should be a day or two later to go over a draft of the slides you plan to use. The third meeting should be a rehearsal at least 36 hours before your presentation so that you have time to incorporate feedback. Note that some of the presentations are the Tuesday after Thanksgiving -- you'll need to start your meetings *before* Thanksgiving to meet the above deadlines!

Tu 11/21/00

Each PI should be prepared to describe progress on their project relative to the plan in the proposal. Focus on accomplishments -- bring pictures, describe preliminary or partial results. Mention problems and proposed solutions. We'll have 15-20 minutes for each proposal, including feedback from the class.
Josh will present ``Visualizing 3D Flow,'' Victoria Interrante and Chester Grosch, CG&A 18(4), 1998. This paper goes into some ideas for texture creation in 3D.
Others, describe three aspects of the images from the paper that work and three aspects that don't work.

Th 11/23/00

Thanksgiving -- no class!

Tu 11/28/00

Marty will present ``Conveying the 3D Shape of Smoothly Curving Transparent Surfaces via Texture,'' Interrante, Fuchs, Pizer.
Others, read the paper and speculate about why the principal curvature textures didn't work best. Compare these results with the Li and Zaidi results -- are they consistent?
Scott will present ``Image-Guided Streamline Placement,'' Greg Turk and David Banks, SIGGRAPH 96. Check out the animation (use xanim).
Others, read the paper. Then, given the three tasks in Mike/Scott's project, predict how effective the methods described will be for those tasks. The tasks are: count critical points, identify the types of critical points, and trace flow lines from an arbitrary starting point. Explain your predictions.

Th 11/30/00

Don't forget the radio-telescope field trip today! We'll leave from Lubrano at class-meeting time.
Drafts of your final abstract are due tomorrow (Friday) at noon. They should fit on a single page, two columns, 9pt font. Including pictures! Look at examples from last year. asgns/onepage/example.tex gives an example of a tex file that produces a reasonable one-page abstract . Please put your draft abstract in this same directory in pdf format. Everyone should write their own abstract. You may consult orally with your partner, but must write on your own. Your results won't be complete, so leave blanks for what isn't ready (most likely, just numbers that you'll fill in later). Do as much of the writing as you can. The abstract should be very nearly complete.
Arrange to meet with Pavani about her comments during the week between the 8th and the 14th.

Tu 12/05/00

Mike will present a chapter from Delmarcell's thesis: "Review of Vector Icons" . (Also available here.)
Others, read the paper and pick your favorite three icons and explain for what application and why you prefer them.
Josh will present `` Visualizing second-order tensor fields with hyperstream lines,'' Thierry Delmarcelle and Lambertus Hesselink, CG\&A 13(4), 1993. (Also available here.)
Others, read the paper and hand in three points of discussion.

FRIDAY 12/08/00, 12-1:30, CIT 506

Look back at the syllabus and any other course materials to prepare for filling out course evaluations. I'll step back and review where we've gone over the semester and where I hope you are more prepared to go in the future.

Th 12/14/00

Final demos/presentations. Hand in the final version of your abstracts.

"Using Visual Texture for Information Display", ACM Transactions on Graphics, 14(1): 3-20.

11/16/99

``Ray Tracing Volume Densities,'' James T. Kajiya and Brian P. Von Herzen, SIGGRAPH '84, 165-174.

``Volume Rendering,'' Robert A. Drebin and Loren Carpenter and Pat Hanrahan, SIGGRAPH '88, 65-74.

``Display of Surfaces From Volume Data,'' Marc Levoy, CG\&A 8(3), 1988, 29-37.

11/18/99

``Vestibular Cues and Virtual Environments'', Harris et al, Proc. of IEEE VRAIS '98.

``Marching Cubes: A High Resolution 3D Surface Construction Algorithm,'' William E. Lorensen and Harvey E. Cline, SIGGRAPH '87, 163-169.

Attend Vicki Interrante's talk right after class.

11/23/99

Once again, each PI should be prepared to describe progress on their project relative to the plan in the proposal. Focus on accomplishments -- bring pictures, describe preliminary or partial results. Mention problems and proposed solutions. We'll have 10-15 minutes for each proposal this time.

``Cone Trees: Animated 3D Visualization of Hierarchical Information,'' CHI '91, 189-194.

11/25/99

Don't eat for two days so that you have plenty of room for Thanksgiving dinner :-).

11/30/99

``Imaging Vector Fields Using Line Integral Convolution,'' Brian Cabral and Leith (Casey) Leedom, SIGGRAPH '93.

``Image-Guided Streamline Placement,'' Greg Turk and David Banks, SIGGRAPH 96

12/02/99

``Visualizing vector field topology in fluid flows,'' James L. Helman and Lambertus Hesselink, CG\&A, 11(3), 1991.

``Visualizing 3D Flow,'' Victoria Interrante and Chester Grosch, CG\&A 18(4), 1998.

12/07/99

``Visualizing second-order tensor fields with hyperstream lines,'' Thierry Delmarcelle and Lambertus Hesselink, CG\&A 13(4), 1993.

``Eigenimage Filtering in MR Imaging,'' Joe P. Windham and Mahmoud A. Abd-Allah and David A. Reimann and Jerry W. Froelich and Allan M. Haggar, Journal of Computer Assisted Tomography 12(1), 1988, 1-9.

``Partial-Volume Bayesian Classification of Material Mixtures in MR Volume Data using Voxel Histograms,'' David H. Laidlaw and Kurt W. Fleischer and Alan H. Barr, IEEE Transactions on Medical Imaging 17(1), 1998, 74-86.

12/09/99

We'll build some taxonomies of visualization in class. Look back over the course and think about what you would like taxonomies of -- methods, data, problems, venues, etc. -- and what you would put under each category.

Hand in by noon your draft taxonomies.

Hand in by classtime your 1-page double-column abstract for inclusion in the class proceedings. asgns/onepage/example.tex gives an example of a tex file that produces a reasonable one-page abstract . Please put your abstract in this same directory in pdf format. -->

12/13/99

Prepare final presentations and demos. Each presentation will be 10 minutes, with a few additional minutes for questions.

Copyright 2000 David H. Laidlaw