Documentation/Nightly/Extensions/DebuggingTools

For the latest Slicer documentation, visit the read-the-docs.

Introduction and Acknowledgements

Author: Andras Lasso (PerkLab, Queen's University), Mikael Brudfors (Laboratorio de Imagen Medica, Hospital Gregorio Maranon - http://image.hggm.es/)
Contact: Andras Lasso, <email>lasso@queensu.ca</email>
Project website: http://www.slicerrt.org
License: Slicer license

SparKit   NA-MIC   OCAIRO

Extension Description

Collection of tools for developing and debugging modules.

Modules

• Python Debugger (in category: Developer Tools): allow debugging of Python scripts in the Eclipse integrated development environment using PyDev. Visual debugging (setting breakpoints, execute code step-by-step, view variables, stack, etc.) of Python scripted module is possible by using PyDev.
• Node modified statistics (in category: Developer Tools): Module for collecting statistics on timing of node Modified events. It is useful for estimating refresh rate when a live data stream or temporal data sequence is visualized.

Use Cases

• 

  Debugging Slicer in PyDev

Tutorials

Setup visual Python debugging

• Install PyDev: the simplest is to use the standalone LiClipse package
• Run PyDev and enable the remote debugger tool (if you have trouble following these steps then you can find detailed instructions here):
  • Enable PyDev server: in the menu Window > Customize perspective > Command groups availability > PyDev debug
  • Open the debug window: in the menu Window > Open Perspective > Other > Debug => Without this step the Resume button will be disabled and debugging cannot be started!
• In Slicer:
• Install the Python debugger extension
  • Open the Python debugger module (in Developer Tools category)
  • In the Settings section set the directory that contains the pydevd.py file. Usually it is in the Eclipse plugins directory /...pydev.../pysrc.

Start visual Python debugging

• In PyDev
  • Start the server: on the toolbar click the button "PyDev: start the pydev server"

• In Slicer:
  • Open the Python debugger module (in Developer Tools category)
  • Click on Connect
  • If the debugger is successfully attached, then it will pause Slicer, so Slicer becomes unresponsive (until its execution is resumed in PyDev)
• In PyDev.
  • Slicer execution is now paused. Resume Slicer execution by pressing the "Resume" button on the toolbar.
  • Load your .py file into PyDev and add breakpoints (Ctrl+Shift+B) where you want your execution to stop for debugging.
  • Important: you can open a terminal, where you can enter Python commands while the execution is paused (you have access to all Slicer variable, it has auto-complete, etc.) by clicking on "Open Console" (small button at the top of the console view) then chose "PyDev Console" and then "PyDev Debug Console" (after this the title of the console should be "PyDev Debug Console" instead of the default "Debug Server").

Information for Developers

• Source code: https://subversion.assembla.com/svn/slicerrt/trunk/PyDevRemoteDebug
• Issue tracker: open issues and enhancement requests