1. BioPSE/map3d Workshops

2. Workshop Goals Make you useful to SCIRun/BioPSE and map3d
Make SCIRun/BioPSE and map3d useful to you!
Send you home with a useful tool

3. Day #1 Schedule 10:00 Introduction (SCR) 10:10 Background (SCR)
10:30 Example Problem (SCR)
11:00 Elements of BioPSE/SCIRun (SCR)
11:45 Demos (VSC)
12:30 Lunch (SCR)
1:25 Lab Introduction (SCR)
1:30 Lab Session (VSC)
4:00 Free Evening

4. Day #2 (Users) Schedule 9:30 Pickup at University Guest House
9:45 Coffee
10:00 Advanced Elements of SCIRun/BioPSE (SCR)
11:10 map3d (SCR)
11:30 Lab Session (VSC)
12:30 Lunch
1:30 Lab Session (cont’d) (VSC)
3:30 Discussion Session (SCR)
6:00 Depart from University Guest House
6:30 Group Dinner (Millcreek Inn)

5. Day #2 (Developers) Schedule 9:00 Pickup at University Guest House
9:30 Background (SCR)
10:00 Advanced Elements of SCIRun/BioPSE (SCR)
11:10 map3d (SCR)
11:30 Installation and Future of SCIRun (SCR)
12:30 Lunch
1:30 Developing Modules in SCIRun/BioPSE (SCR)
3:30 Discussion Session (SCR)
6:00 Depart from University Guest House
6:30 Group Dinner (Millcreek Inn)

6. Day #3 Schedule 9:30 Pickup at University Guest House 9:45 Coffee
10:00 Module Project Discussion (SCR)
11:00 Making a Module (SCR)
12:30 Lunch
1:15 Lab Session (VSC)
4:00 End of Workshop

7. Background PSE background BioPSE/ SCIRun history map3d history
Role of the NCRR Center

8. Overview of the SCIRun/BioPSE Software Systems
Hold on to your hats…

9. Designing and Implementing A Tikhonov Regularization Network
BioPSE Example:
Designing and Implementing
A Tikhonov Regularization Network
There’s just nothing quite like a live demo…

10. “Looking at my data has never been so much fun!”
Using map3d
“Looking at my data has never been so much fun!”

11. Joint Session #1: Advanced
BioPSE/SCIRun

12. Who Are We? Faculty Support Staff Instructors/Developers
Rob MacLeod
Chris Johnson
Steve Parker
Support Staff
Allyne Betancourt
Robert Cummins
Richard Coffey
Nathan Galli
Erik Jorgenson
Blythe Nobleman
Instructors/Developers
Dave Weinstein
Marty Cole
Michael Callahan
McKay Davis
Darby Brown
Chris Butson
Bryan Worthen
Brandon Mansfield
Systems Support
Robert Cummins
Simon Gao

13. Feedback from the Workshops
Modules:
“Modules aren't intuitive--relied upon DMW for module descriptions; need more documentation organized by function with cross reference lists.
Managing fields required knowledge of things that aren't intuitive at all but are very necessary, e.g., interpolants. FieldReader so general that you need to go what's going downstream, but you need to know where it’s going.”
Input/output capabilities:
“There is a need to read more data file types directly, i.e., without the need for converter programs.”
Macro-modules
“There is a need for tools to create and optimize networks, and to combine functionality of existing modules into a macro-module with customizable UI. “

14. Feedback from the Workshops
Interaction problems
“It is often difficult to know what SCIRun is doing--when is it stuck or when is it just busy? When you touch a UI button, what is it doing while it's firing. You think its done, but it is not always there and ready for output. There is a need for more robust global indicators of state…”
Meshing and segmentation tools
“This is a large problem in SCIRun and there needs to be better support for both steps.”
Quantitative visualization in SCIRun
“Having more quantitative information in visualization would be useful. Would be good to be able to look at numbers more easily. No contour plotting in current version, though we do have banded shading to show the contour between the bands.”
Linear algebra support
“There needs to be more flexibility in the kinds of equations that SCIRun can address and solve. In a related question, how much more performance can one gain using SCIRun over Matlab solvers?”

15. Feedback from the Workshops
Documentation of data types
“It would be good to have more information about which kind of data one can use, what are the data types and how can one use them? Also essential is more documentation about algorithms and the functional options for each module.”
Documentation of develop information
“There is a lack of documentation on developer side--module level and dataclass, something in between viewing code and complex module description.”
Documentation of modules
“More explanation on the algorithms used (ie the kind of interpolation). Make more references to papers regarding purpose, concepts and implementations. I know we have papers on our main site, but they should be mentioned in our documentation more.”
Documentation of datasets
“People wanted to know more about the contents of the data files, where they came from, what they were.”

16. Feedback from the Workshops
More workshops
“You should do more workshops in the future.”

17. Documentation: Tutorial

18. Dataflow Dataflow Vocabulary Send and Get GuiVars Scheduler Module
Dataport
Datapipe UI
Send and Get
GuiVars
Scheduler
Dependencies
loops: send_intermediate

19. Network Design

20. Module: Algorithm + UI Algorithm User Interface Module: wrapper
Function
Reusability
User Interface
Buttons, tabs, slides, text entry, …
Hidden state
Module: wrapper
Infrastructure: setup, shutdown
Execute
1) Why am I being told to execute
2) Get data from ports
3) Update UI variables
4) Invoke algorithm
5) Send data out ports

21. Net Files and State Net File
Create modules
Create datapipes
Set UI values
Environment variables to create general purpose nets
SCIRUN_DATA
SCIRUN_DATASET
Human editable… but be careful!
Datasets can also be written out and read in… more on that tomorrow

22. I/O, Bridging, and Thirdparty
Read/Write modules for SCIRun format
“convert” programs for importing / exporting external data formats
Packages = projects
Internal
External: bridging
Store external libraries in Thirdparty
Independent of SCIRun standards
Externally maintained

23. Viewer Module OpenGL Scene graph Widgets See the User’s Guide
for details…

24. Tomorrow’s Lab…

25. Hands-on Demo Session

26. Some things you’ll need to know…
Stiffness Matrix
Leadfield Matrix
Simplex Search
Overview of SCIRun Net

27. Stiffness Matrix
voltage current density
A * F = J

28. Lead Fields
“Look-up Table”
sources
L :
meas. L =

29. Multi-start Simplex Search
- Find the global minimum

30. SCIRun