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DebuggingTools extension for 3D Slicer

Extension for 3D Slicer containing various tools for module development and debugging.

Included modules:

  • Python Debugger (in category: Developer Tools): Visual debugging (setting breakpoints, execute code step-by-step, view variables, stack, etc.) of Python scripts in Slicer using PyCharm, Visual Studio Code, Eclipse, etc.
  • 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.
  • Node info: Browse nodes in the Slicer scene, find referenced and referencing nodes, create dockable widgets to display content of selected nodes.

Authors: Andras Lasso (PerkLab, Queen's University), Mikael Brudfors (Laboratorio de Imagen Medica, Hospital Gregorio Maranon).

Python Debugger

Debugging Slicer in PyDev

Python debuggers:

  • PyCharm: Easiest to set up and most convenient. Requires professional version, which is only free for academic users.
  • Visual Studio: A bit less capable than PyCharm (the debugger cannot automatically reconnect after Slicer is restarted, there is no auto-complete in the Python console).
  • Visual Studio Code: Same capabilities as in Visual Studio Code, but it is a bit more complicated to set up (need to open a workspace/folder, which unloads all edited files; need to edit a json file to configure the debugger configuration)
  • Eclipse: Has less features than other editors and not as convenient, but has the unique feature of being able to jump to any line within the current function.

Instructions for PyCharm

One-time setup

  • Install Professional Edition of [PyCharm]](https://www.jetbrains.com/pycharm/download/). Professional version is avaialable for anybody with an academic email address for free. Free Community edition will not work, as it does not include remote debug server.
  • In PyCharm:
    • In the menu select: Run / Edit configurations
    • Click the small + icon in the top-left (Add new configuration)
    • Select Python remote debug configuration or Python debug server as template
    • Set Name: Slicer remote debugger
    • Set Port: 5678
    • Click OK
  • In Slicer:
    • Install the DebuggingTools extension
    • Open the Python debugger module (in Developer Tools category)
    • In the Settings section select debugger: PyCharm
    • If pycharm-debug.egg path is not detected automatically then set the path with the selector (it is usually in the debug-eggs subfolder of the PyCharm installation)

Start debugging

  • In PyCharm:
    • In the menu select: Run / Debug, click Slicer remote debugger
  • In Slicer:
    • Open the Python debugger module (in Developer Tools category)
    • Click on Connect button. Slicer will become unresponsive until the debugger is attached.
  • In PyCharm:
    • Load your .py file and add breakpoints (menu: Run / Toggle Line Breakpoint) where you want your execution to stop for debugging.
    • Important: once Slicer is paused at a breakpoint, you can open a terminal, where you can enter Python commands. In that terminal you have access to all Slicer variables, it has auto-complete, etc. Click the small terminal icon Show Python Prompt to open the Python terminal.

Python debugging console in PyCharm

Troubleshooting
Connection refused

If attaching the debugger with "Connection refused" error message then:

  • Make sure the debug server is started. It is indicated by PyCharm should displaying this message Starting debug server at port 5678 ... Waiting for process connection
  • On Linux, make sure the 5678 port is enabled on the firewall by this command: sudo ufw allow 5678

Instructions for Visual Studio Code

One-time setup

  • Install Visual Studio Code (free, available on Windows, Linux, and Mac)
  • Install Python extension by Microsoft
  • Start Visual Studio Code and set up remote debugger connection to Slicer:
    • Open a folder that contains your Python files by selecting in menu: File / Open folder
    • Open a Python file
    • Select in menu: Run / Add configuration
    • Choose "Remote attach", use localhost for host name, and 5678 for port number
    • Visual Studio should show launch.json file that contains a Python: Remote Attach entry in configurations element. Remove pathMappings section (otherwise the debugger with fail to add breakpoints with the message pydev debugger: warning: try to add breakpoint to file that does not exist). The resulting launch.json file should look something like this:
{
    // Use IntelliSense to learn about possible attributes.
    // Hover to view descriptions of existing attributes.
    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
    "version": "0.2.0",
    "configurations": [
        {
            "name": "Python: Remote Attach",
            "type": "python",
            "request": "attach",
            "port": 5678,
            "host": "localhost"
        }
    ]
}
  • Click the "Run and debug" icon in the left side of the screen (see 1 in the screenshot below)
  • Choose Python: Remote Attach configuration at the top of the debug panel (see 2 in the screenshot below). Do not click the green button yet (3 in the screenshot below): connection will fail because the connection has not been initiated in Slicer yet.

Adding Python debug configuration in Visual Studio Code

Example of Python debugging using Visual Studio Code

Start debugging

  • In Slicer:
    • Open the Python debugger module (in Developer Tools category)
    • Click on Connect button. Slicer will become unresponsive until the debugger is attached.
  • In Visual Studio Code:
    • Click debugger icon on the left side of the screen (see 1 in the screenshot above)
    • Click Start debugging button (green triangle, see 3 in the screenshot above)
    • Add a breakpoint to the Python file where you want to start debugging by clicking slightly to the left from the line number (a red dot will appear there, see 4 in the screenshot above)

Instructions for Eclipse

One-time setup

  • Install Eclipse with PyDev: the simplest is to use the standalone preconfigured 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 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. Slicer will become unresponsive until the debugger is attached.
    • 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).

Instructions for Visual Studio

One-time setup

  • Enable Python development component for Visual Studio (if has not been enabled already):
    • Start Visual Studio Installer application
    • Click Modify button of your Visual Studio configuration
    • Check the Python development checkbox
  • In Slicer:

Start debugging

  • In Slicer:
    • Open the Python debugger module (in Developer Tools category)
    • Click on Connect button. Slicer will become unresponsive until the debugger is attached.
  • In Visual Studio:
    • In menu, select Debug > Attach to Process (Ctrl+Alt+P) to display the Attach to Process window
    • Attach to -> Python code
    • Process -> SlicerApp-real.exe
    • Press Enter (or click Attach button). The popup window in Slicer should disappear.
    • For connecting again, Debug > Reattach to Process (Shift+Alt+P) function can be used