Course Timeline and homework
Course schedule, in and out of class. Subject to change, particularly further in the future. If you have any ideas for a future class, please add them here!
Week 1 : intro
Weeks 2-3 project 1 planning and some tutorials to support that.
Weeks 4-8 project 1, including proposal presentations; journal reviews; project status presentations; project tutorials; unreal; software porting; project 2 planning; paraview yurt surface rendering
Weeks 9-15 project 2; project status presentations; journal review, project tutorials and activities
Class motivation, goals, structure, syllabus, wiki
Give a breakdown of the wiki
What was done last year
What is expected this year
Where to find everything
Project-oriented structure for class
Brief introduction to the YURT
Introduce class projects, software, and collaborators
Start planning projects
HW for 1/28:
Review course home page and subpages
Set up your journal page and link it into top-level journal page
Log 4-5 hours of homework time in your journal
Read some background papers
Read some of last year's wiki
Research data types, data examples, and software tools
Add or refine at least one thing in wiki (aside from journal, e.g. software or data type)
Install Paraview on your computer and bring to class
Do things from Course Activities page
Log time and any issues in your journal
Ponder project ideas (always!)
Go around room and have each person say what they found and added to the wiki
Paraview tutorial (volume rendering) with Ross
If you finish the tutorial early:
Introduce project guidelines (i.e. explain milestones, in class activities, and deliverables)
Introduce Yurt software architecture, David
HW for 1/30:
Continue with activities from previous homework
Review YURT Software, YURT Software Evaluation, and Data, Examples, and Collaborators pages
Pick 2-4 pieces of software to explore and select 1-3 datasets under Data, Examples, and Collaborators page
Using this software and data, create 3-5 potential project ideas in your journal
Do things from Course Activities page
Set up CCV accounts
Yurt software porting strategies by Ben from CCV
PDF on Integration with YURT released (below)
Project ideas discussion
Yurt demo! Yay!
HW for 2/04:
Review wiki / web to solidify your 3-5 project ideas
For each project idea:
list three things you will do during the project
list one class activity we might do for the project
list potential deliverables:
Deliverables are what future readers of the wiki will look at and learn from. Examples might be comparative prose about different software packages, a Consumer-Reports style table of evaluations of features and quality of different software, tutorials showing how to use software for data visualization purposes, measurements of how long it takes and how difficult it is for a group to do a tutorial, etc. A good way to make sure you have a deliverable is to say explicitly where it will go in the wiki.
If you are confused or have any questions, feel free to post on the slack or email the TAs
Brainstorm software evaluation metrics
Continue adding potential software / data to the wiki
Download Unreal Engine 4.2 and install on the machine you will bring to class.
First half of class:
pair up and review project titles, and activities. Working together, add deliverables to each potential project. Ask questions if you are not sure what to do. Pick your first-choice project.
identify what you need to learn and do before this first project begins so that you can design it to be successful. The projects will start next week, so you have only one more week for this pre-project work. Check out what we will do on 2/6 to help guide this.
go around room and explain the project that you most want to do, including what we might do in class for it and what you need to do before the project.
document your potential pre-project activities in the wiki before leaving class
Second half of class:
HW for 2/06:
Select one project from your list of potential projects and create a plan for your project. This project plan should have milestones to be delivered on 2/11, 2/13, 2/20 (2/18 is a holiday), 2/25, 2/27, and 3/03. The project plan should include activities that span from February to the middle of March
Continue reading, doing, and logging with any extra time
Pair up with someone you haven’t paired up with before and jointly evaluate your pre-project plans. Evaluations should consider:
Will the project deliverables be useful and significant?
Will the project activities improve the potential quality of the project?
Will the project activities help identify and reduce project risks? Risks often involve external dependencies that end up not being met or over-optimistic estimates of time required.
Will the project activities themselves add deliverables to the wiki?
Go over any questions from above, beginning with project concepts, deliverables, and activities described very briefly.
HW for 2/11:
Write your final project plan in your journal
Evaluate your project plan using the following rubric:
o Note that these first project should have milestones for 2/13, 2/20, 2/25, 3/03, 3/05, 3/10. Second-half projects will begin on 3/17 and go through the end of the semester. Here is an evaluation rubric for projects:
Below are a set of questions that should help in evaluating project ideas. Answer each with one of:
neither agree nor disagree
The questions are:
o The proposed project clearly identifies deliverable additions to our VR Software Wiki
o The proposed project involves previously unavailable Yurt data visualization functionality
o The proposed project involves large data visualization along the lines of the "Data Types" wiki page and identifies the specific data and software that it will use
o The proposed project has a realistic schedule with explicit and measurable milestones at least each week and mostly every class
o The proposed project includes an in-class activity
o The proposed project has resources available with sufficient documentation
Prepare 3 minute project descriptions with powerpoint (must be a .pptx or .ppt file) slides sent to David AT LEAST 24 hours ahead title, brief motivation, contributions/deliverables, schedule/milestones progress on first milestone
Project presentations -- three minutes each (plus likely substantial discussion and questions). Include results from your first milestone!
These may fill entire class
We will schedule future class activities as identified in the proposals
If time and need, finish Giuse's Unreal Engine Tutorial
If time begin Gigapixel tutorial
HW for 2/13:
Meet first milestone of project
Work on project and log hours in journal
Add to the wiki
Modifying software for the YURT presentation by Ben
Urgent project shares
Gigapixel tutorial completed
HW for 2/20:
Continue work on project and contributions to the wiki
Send pptx with at least one image/video (not of text...) showing progress on your project. Also include your list of milestones and where you are with each one.
Prepare journal for in-class review. Journals will be evaluated according to the following rubric:
Activities logging rubric -- fill in in your journal
Activities logging rubric
key for each criterion:
5 == exceeds expectations
4 == meets expectations
3 == mostly solid with some gaps
2 == shows some progress
1 == some attempt
0 == not found
Journal activities are explicitly and clearly related to course deliverables
deliverables are described and attributed in wiki
report states total amount of time
total time is appropriate
Using the above rubric, evaluate your journal and include your self-evaluation in your journal
Class 2/18 (University Recess - No Class)
Project Progress Reviews
Discuss potential in-class activities
Peer journal review
HW for 2/25:
Class 2/25 at the Yurt
Do gigapixel in-class viewer part
Check out gigapixel viewer results in Yurt
HW for 2/27:
Work on projects
Ross's Paraview surface rendering tutorial
HW for 3/03:
Prep for Shreya's 3D Slicer Activity
Download 3D Slicer here (stable release 4.10.2, takes up 940MB of space): https://download.slicer.org/
Download one of the folders from BraTS Dataset > HGG > Any of the CBICA folders
(Optional) Learn more about gliomas: https://www.mayoclinic.org/diseases-conditions/glioma/symptoms-causes/syc-20350251
(Optional) Learn more about MRIs: https://www.brainline.org/slideshow/brain-imaging-what-are-different-types
Shreya's Slicer activity (40 minutes-1 hour)
HW for 3/05
Prep for Anessa's Google Cardboard Activity
For iOS devices, run iOS 11 or higher
iOS software requirement: Xcode 10.3 or higher
For Android devices, run Android 5.0 "Lollipop" (API level 21) or higher
Android software requirement: Android Studio version 3.4.1 or higher
End of first project presentations
Continue project presentations
HW for 3/17 (now officially due 3/30, but sooner will help everyone get and give feedback)
Draft of project 2 plan in journal for others to review
Class 3/17 (cancelled, but David will be in zoom at https://brown.zoom.us/j/8372629163)
discuss projects and get feedback on them
maybe group edit a page for new science users with different data types to get going in the yurt
HW for 3/19 (now officially due 3/31
Review project 2 plan for the three people following you in the journal pages
Use same project rubric as for first project
Put your feedback just below the plan
Fill in class activity in the wiki timeline for the class time you would like
Class 3/19 (cancelled, but David will be in zoom at https://brown.zoom.us/j/8372629163)
discuss projects further and get feedback on them
HW for 3/19
review project 2 plan for the three people following you in the journal pages
HW for 3/31 (AFTER BREAK!)
be prepared to present your project 2 plan to class
Class 3/24 (Spring Recess - No Class)
Class 3/26 (Spring Recess - No Class)
Homework for 3/30
see HW for 3/17
Homework for 3/31
see HW for 3/19
in-class project discussions
Project 2 plan presentations
Zach's Python activity in Google Colaboratory. Links can be found in his project 1 documentation. It should take 30-40 minutes to complete.
More Colaboratory work, quick project checkins, connect to yurt.
Howdy, folks. We will be mostly brainstorming on upcoming in-class activities. In working with Spencer, we realized that crafting an engaging, relevant, and topical in-class activity involving paraview was going to be challenging. This seems likely to be the case for Loudon with Unity, Ethan with Unreal, and Brandon with OpenSpace as well.
To help with that crafting process, I'd like the four of you to give think about some options for your activity that will help the rest of us provide feedback and input. Everyone else should think about what activities involving those software packages might be useful for the data you are working with (or maybe just of interest to you personally).
Project progress reports
Loudon's Unity Activity (creating a simple Unity app and guide to port to the Yurt) Time to complete: 1.5 hours
Make sure to have Unity installed with the Linux Build module
Brandon's Openspace data exploration activity (Explained in project 2 plan here ) Time to complete: 1.5 hours
Two Line Element File Example
Class 4/28 (reading period)
Ethan's Unreal In-class activity (probably 1.5 hours)
Spencer's Python Paraview activity (as time permits)
If so, make sure you have downloaded paraview and that there is an executable called pvpython.exe inside the bin folder inside your Paraview build. Run this executable and make sure that a python interpreter starts.
Download this file:
Class 4/30 (reading period)
Continuation of Spencer's Python Paraview scripting and yurting activity
Have paraview running with the python script going when class starts
Class 5/05 (reading period)
last project progress presentations. pptx to David before class. Presentation should include:
The story of your semester
List of wiki pages you will leave for posterity (some that are incomplete are fine). Include items for both of your projects, but focus on the second. Explain how these fit into your semester story.
Examples of the points you are considering including for your poster presentation on 5/15 (see below)
5/15 10:30am ET -- Remote Demos/Posters -- may run past noon
Prepare a 4'x3' "poster" for a session that would have been in the CCV lobby. You'll present to the class as if we were all standing around your poster as you talk, asking questions. Be prepared to share your screen with this poster displayed. If you use powerpoint, you can embed running videos, I believe, which could be particularly visually compelling. Pictures and limited text are usually best for posters -- few poster viewers want to read a paper printed out on a poster.
Capture the main points you would want to convey about your findings and wiki contributions from the semester. You can focus on both projects or pick one, if you wish. We will have ~10 minutes for each presenter, including questions and answers. Leave time for some questions, but also be prepared to present more unprompted material if questions do not arise.
Your presentation can also include an interactive portion either on your computer or in the Yurt, shared via the webcam. Time will be very limited, so interactive pieces need to be carefully scripted and practiced to be concise and clear. You might want to video-capture what you'd like to show so that you avoid the risks of real-time demoing.