Slicer3 Q&A 2008-11-18

Logistics

Note changed time: 2:30-4:00 at the 2nd floor demo room at 1249 Boylston.

Attendees

Anyone is welcome, please sign up if you plan to attend:

Steve Pieper, Haytham Elhawary, Jan Gumprecht, Andriy Fedorov, Jayender Jagadeesan, Daniel Haehn, Madeleine Seeland

Questions

The name in parentheses defines the person who asks the question, and therefore is responsible for documenting the response.

Debugging

• Best debugging practices in Slicer (hints for debugging on Linux/Windows, debugging GUI event handling) (Fedorov)

In Linux, you can attach the debugger to Slicer as it is running. To do this, first find the process id (pid) of Slicer3-real, then start gdb and attach to pid. Tell gdb to continue, and once you have a crash, you can identify the faulting code line with gdb command 'where'. Here's an example:

[andrey@beat ~] ps -ef |grep Slicer3-real
andrey     486   443  0 13:21 pts/6    00:00:00 grep Slicer3-real
andrey   31341 31340 88 13:20 pts/2    00:00:59 /home/andrey/local/src/Slicer/Sl
icer3-build/bin/Slicer3-real
[andrey@beat ~] gdb
GNU gdb 6.8
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
(gdb) attach 31341
Attaching to process 31341
Reading symbols from /home/andrey/local/src/Slicer/Slicer3-build/bin/Slicer3-real...done.
...
(gdb) c
Continuing.
[New Thread 0x437cb950 (LWP 493)]
[Thread 0x437cb950 (LWP 493) exited]
...
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7f77be4de790 (LWP 31341)]
0x00007f77a93cd396 in __dynamic_cast () from /usr/lib64/libstdc++.so.6
(gdb) where
#0  0x00007f77a93cd396 in __dynamic_cast () from /usr/lib64/libstdc++.so.6
#1  0x000000000042e320 in Slicer3_main (argc=1, argv=0x7fffc6637d08)
    at /home/andrey/local/src/Slicer/Slicer3/Applications/GUI/Slicer3.cxx:1986
#2  0x000000000042f5c5 in main (argc=1, argv=0x7fffc6637d08)
    at /home/andrey/local/src/Slicer/Slicer3/Applications/GUI/Slicer3.cxx:2135
(gdb) q
The program is running.  Quit anyway (and detach it)? (y or n) y
Detaching from program: /home/andrey/local/src/Slicer/Slicer3-build/bin/Slicer3-real, process 31341

The key for debugging is to set up the correct shared library paths before launching the debugger. You can attach to an existing process, as shown above, or create a new shell with the right paths. One simple thing for unix is:

./Slicer3 --launch xterm

This approach also works for windows; for example, see these examples for visual studio. Once you have a debugger in the right shell, you can single step through the startup procedure or debug command line modules.

On Windows, it is useful to install rxvt package in Cygwin.

Example Code

• What existing modules in Slicer can serve as a good examples to follow (examples of good programming style, GUI, architecture, etc.)? (GradientAnisotropicDiffusion is one?) (Fedorov)

Yes, the "GAD" example is our prototype module that shows the basics of an interactive module. There is a C++ and a Python version. There is also ScriptedModuleExample showing how to write an interactive module in Tcl.

TractographyFiducialSeeding is a good example of more complex module.

• What are the prerequisites of what a novice Slicer developer should know/learn to program in Slicer? (C/C++, CMake, ITK, VTK, Tcl/Tk, KWWidgets (?)) (Fedorov/Haytham)

It depends on how deep you want to go (need to go) to accomplish your research goals. For algorithm developers we focus primarily on ITK && C++ going through the execution model since that is the lowest barrier -- but it limits you to 'batch mode' interactions. For something interactive, like an IGT application, perhaps the minimum is (Tcl || Python || C++) && VTK && KWWidgets. For the developer who wants to be able to 'do it all' you need to be familiar with all the components of the NA-MIC Kit.

Tcl Coding

• Advantages and disadvantages of writing parts of the modules in Tcl (example advantage: no recompilation is needed to make changes) (Fedorov)

Advantages of Tcl:

• Tcl is Mature, Stable, Well-Engineered, Widely Used, Actively Developed... (see [1])
• Interactive programming
  • no need to recompile source code (can source in directly with tkcon)
  • programmatic debugging - can access all classes and methods to confirm correct values and behavior, even create new renderers on-the-fly)
• expressive syntax (code is much shorter than equivalent C++)
• powerful standard library (elegant cross platform abstractions)
• already widely used in slicer (KWWidgets, testing, launcher, build process...)

Disadvantages of Tcl:

• Inefficient for numerics, image processing, or rendering (write an ITK or VTK class for these or use numpy for numerics)
• Some people prefer to use only one language for consistency everywhere (for this, use C++)
• Unfamiliar syntax
• Cannot use C++ debugger
• Cannot define new VTK or ITK classes
• Some VTK class methods are not available from wrapped code

Tcl Interactor (tkcon)

• Howto for Slicer Tcl interactor (Fedorov -- I would appreciate if someone help me documenting replies to this and other questions)

This is one of the most powerful tools in slicer. See the tkcon documentation for general capabilities. The tkcon has been enhanced in slicer to support method name completion for vtk classes (shift-tab) and wrapping statements in square brackets (control-]). See this (partly out-of-date) slicer2 documentation of what you can do with tkcon.

Volume Visualization

• High-level architecture/diagram of Slicer volume visualization: relationship between vtkMRMLScalarVolumeNode/vtkMRMLScalarVolumeDisplayNode/vtkMRMLScene, howto for volume rendering, ... (Fedorov)

Alex Yarmarkovich will discuss

ITK Filters

• Guidelines on the use of ITK filters from Slicer and what to expect. In case analogous functionality is available both in ITK and VTK, what should be used? (Fedorov)

In general, ITK code has been designed for correctness, while VTK code was designed as examples for a textbook (paraphrasing Bill Lorensen).

The current 'best practice' for simple filters, per Steve Pieper and Jim Miller, is to encapsulate the ITK code inside a VTK class as done in Libs/vtkITK/vtkITKWandImageFilter.h and Libs/vtkITK/vtkITKWandImageFilter.cxx

• Is there a framework for creating a workflow of command line modules programmatically? (Fedorov)

Memory Management and Leaks

• Memory management: how to avoid memory leaks, differences in memory management between different components. Deallocation of image volumes created in a module. (Fedorov)

• How to track down memory leaks of a particular loadable module -- is it possible to get per-module leak report? (Fedorov)

This can be very tricky so it's best to watch for leaks as the code is being developed. First you should try to start with a non-leaking version to start with.

You can check with:

./Slicer3 --exec exit

which will bring up the interface and then exit.

You can also use the --ignore-module <module name> command line argument to suppress a particular module to see if it is the source of the leak. See this leak test script for an example of how this can be used systematically to find a leaking module (note this script is still in development).

Event Management

• Overview of different classes of events in Slicer, and what action should be done in what observer (GUI events, MRML events, Logic events, Scene events, anything else?...) (Fedorov/Haytham)

• How do the Logic Methods keep track of the MRML node events? Which Logic Methods are involved? Are Macros used, and if so, where are they defined? (Haytham)

Debugging VTK Pipelines

• What is the best way to debug vtkPipelines? (e.g. a Pipeline viewer etc.) (Jan)

The best approach here is to write a small test program that confirms how you think the pipeline *should* work. I write these in tcl, but C++ or python work too. Ideally if you can factor out the parts which depend on slicer-specific data structures you can quickly narrow down how to use the VTK classes in a pipeline. Sometimes there are bugs in VTK that need to get fixed. Having the standalone test case is crucial for demonstrating these bugs and getting them fixed.