Engineering:TCON 2011

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2011-03-03

Attendees: Steve, Nicole, Jim, Andrey, Suarez, Ron, Stephen A., Daniel H, Dominique B., Xioadong, Greg Sharp, Mark S, Dominik, Hans

Agenda:

• C++/C wrapping of modules
  • Hans and Greg figured out what was going wrong. In BRAINS tools they did a trick to get around Bill's trick. It takes 8 minutes to build BRAINSfit, to break it down into smaller compilation units and test it using ITK testing framework. It has a thin wrapper around program to add comparator functions. BRAINSfit is a small 3 line wrapper around BRAINS fit primary that takes argc and argv and includes generated header file. You can't include CLP header file in both compilation units since functions are defined in header file. See error at link time. If you put the right ifdef compiling for slicer and module description is defined you can make it work. Hans would like to see the CLP broken apart into a compile until and a header unit. Jim: harder to build and link - but is done through macros. Could have a test before include CLP.h. Hans: wants to be able to include the .h file in every file. Change: now would have to write a programCLP.h and programCLP.cxx.
  • definitely needs to be done in Slicer4, tbd in Slicer3 (Hans using Slicer3 in his class).
    • the add executable, add library lines macros would need to be touched, need to link new object file
    • before when build both a shared and a command line module it would have to rebuild all the itk stuff twice, Casey made the change to not require it
    • Steve: came up wrt diffusion modules because they're using vtk nrrd readers that don't know about shared memory pointers
    • Hans: was building itk files three times for exec, lib, testing
  • Jim will take a look at what breaks when try to split it out, code generation is easy, the add_executable will be a bit tricky
  • Hans: suggests adding the .cxx to the GenerateCLP macro that defines the .h, to use in the CMakeLists. Hans will do the changes to all the execution modules that need to be changed once the infrastructure is changed (or not).
  • One BRAINSfit test failing: any multi threaded mutual information code is suspect to the bug that they found. Quick fix: restrict to one thread, huge slow down (2-4x). Bug is in the Mattes mutual information optimize metric (?) in the registration framework for certain number of threads (4,7, etc). Stephen A will look at it after March 9.
• Annotation module widget priority for ROI nodes
  • Ron, Daniel agrees to put it as higher than the bidimensional widget
  • Crop volume is in the critical path for the volume rendering module, as well as others
  • Reformat widget to priority list? will require taking something out. Will is working on a new widget, wait on that. Andrey says the reformat widget will be useful in volume rendering as well. General Slicer4 widget (was integrated in the 3d viewer in Slicer3). Nicole is taking on the integration of the vtk widgets.
• Contributing modules to Slicer4 (policy review)
  • by default new modules should got to an external repository (NITRC, external module) and remain there for a while until whole module goes into Slicer4 if it's determined to be core functionality
  • Slicer4 core to remail lean, but external modules to be first class citizens.
  • Documentation requirements, building and testing on the factory machine every night.
  • If a new module fails it shouldn't break Slicer4 building or running
  • Timeline on extension mechanism in Slicer4?
    • Steve wanted to get the base nightly builds working first, but need to get the extensions built nightly asap
    • new feature in next release of cdash and cmake, ctest upload command to upload binaries, can get a list of uploads from dashboard
    • harvest the information from the cdash dashboard and make it available to the extension manager rather than have the extension manager communicate directly with the (sometimes slow) dashboards. Only let uploads come from factory machines.

2011-02-10

Attendees: Jim, Mark, Tina, Nicole, Dan

Agenda:

• Updates from ITK meeting
• http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
  • Heads up given to everyone that progress report is due on wiki by mid April

2011-02-03

Attendees: Suares, Dominik, Kilian, Dominique, Nicole, Daniel, Stephen, Tina, Xiaodong

Agenda:

• ITK meeting in progress in Boston. Steve and Jim attending it.
• http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0
  • Automatic documentation generation options are being explored at Kitware. Stephen will report as progress is made.
• http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
  • Heads up given to everyone that progress report is due on wiki by mid April

2011-01-27

No tcon today.

2011-01-20

Attendees: Xiaodong, Wendy, Tina, Mark, Nicole, Dominik, Daniel,

Agenda

• Slicer 3.6.3
• http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week
• http://wiki.na-mic.org/Wiki/index.php/Resources#Active_Job_Openings

2011-01-06

Attendees: Steve, Stephen, Jim, Ron, Tina, Dan Marcus, Xiaodong

Agenda:

• News: DCMTK 3.6 was released today
• http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week#Projects
• Command line module logic, supporting multiple argument for images in Slicer3/4
• Discussion of ITK support for large (greater than 4Gig) image volumes on win64. This will be further investigated at project week. It is only one of several issues to be researched as part of porting slicer3 and slicer4 to win64. Dave Partyka has a project to work on this at project week.