Links

• GUI
  • XML reference Documentation/Nightly/Developers/SlicerExecutionModel - Slicer Wiki

Debugging

TL;DR Pycharm Professional instructions work

• These instructions: SlicerRt/SlicerDebuggingTools: Extension for 3D Slicer containing various tools for module development and debugging¹
  • No need to change anything in module code
• During debugging everything freezes
• You can use pycharm python CLI to look around etc. — neat!

not TL;DR

• SlicerRt/SlicerDebuggingTools: Extension for 3D Slicer containing various tools for module development and debugging¹
  • needs pycharm Pro
  • SlicerDebuggingTools/PyDevRemoteDebug/PyDevRemoteDebug.py at master · SlicerRt/SlicerDebuggingTools
  • source of the 3dslicer bits
• pdb-attach · PyPI can attach to random programs,
  • os.getpid() is my friend
• Documentation/4.5/Developers/FAQ/Python Scripting - Slicer Wiki at some point it was possible to use python-remote-pdb
• ionelmc/python-remote-pdb: Remote vanilla PDB (over TCP sockets). 2y ago last commit
• I can use these same instructions mostly for pdb-attach, I see no reason it shouldn’t work, python is python
• it Kiiiinda works but breaks after the first button
• Giving up for now
• Update: installed Pycharm Pro, works!
  • Pycharm Pro egg was in /opt/pycharm-professional/debug-eggs/pydevd-pycharm.egg

Basics

Starting Slicer

Loads the module automatically (for some reason doing it manually doesn’t preserve it across restarts?..)

Slicer  --additional-module-path /path/to/my/extension/one/lower/than/what/i/would/pick/in/Slicer/GUI

Logging

• Not directly mentioned in the help because they state it’s always better to use the debugger²
• Slicer/Base/Python/slicer/slicerqt.py at main · Slicer/Slicer has the slicer setup
• I can do logging.warning("test") in the python console and it works
• Slicer settings allow changing the loglevel of its python console!

Module types: CLI modules

Different types of modules exist: Module Overview — 3D Slicer documentation

In the first tests there was a lot of latency.

Solution: CLI modules (not extensions) that can run in the background and whose status can be queried, which can be added to new extension from extension editor.

Now I understad this better:

• CLI modules are simple I/O, non-blocking, that’s where the networkig logic should go to
• scripted are python scripts with GUIs

• This bit about running CLI in the backgroundPython FAQ — 3D Slicer documentation

Looking into the sample code

Module of type scripted

• Created an extension of type cmake, to which I added a module of type scripted. It’s the sample thresholding extension
  • Base class: Slicer/Base/Python/slicer/ScriptedLoadableModule.py at main · Slicer/Slicer
• Sample data
  • It shows how to add sample data to the extension for testing
  • It can then be found in the Sample Data module, named after the extension itself!

Module of type scriptedCLI

• I hope it’s the same as type CLI, but only with python

• I think it’s lassoan/SlicerPythonCLIExample: Example extension for 3D Slicer that demonstrates how to make a Python script available as a CLI module

• Is a CLI script w/ an XML that has module metadata + examples

  • CLI module goes in the same examles menu
  • and a basic UI has been generated for it? Wow
  • Running it from the UI actually shows a progress bar and it doesn’t block the interface! Woohoo!

• Adding it added it to CMakeLists.xml: add_subdirectory(my_scripted_cli)

• python dev tools actually show the CLI used to run a CLI module!

  • the input arguments are filepaths, and slicer automatically generates and then deletes temporary files for this when running

• can’t debug it the usual way, I guess I’ll have to add the pydevd-pycharm things to the code

[VTK] /opt/3dslicer/bin/python-real /home/.../cli_model_service.py /tmp/Slicer-sh/IACHCI_vtkMRMLScalarVolumeNodeD.nrrd 1 /tmp/Slicer-sh/IACHCI_vtkMRMLScalarVolumeNodeF.nrrd 

(Auto-creating) GUI

• Slicer/Docs/developer_guide/parameter_nodes/gui_creation.md at main · Slicer/Slicer seems interesting

• CLI modules have an interface specified by the .xml file, and the interface is generated based on it

  • couldn’t find any documentation on how to write the XML: Documentation/Nightly/Developers/SlicerExecutionModel - Slicer Wiki

• Bits about the XML

  • channel is either input or output, and only for pics.
  • No parameter names, just their index

• If I read the volume as volume, it uses the .nrrd file extension by default — and I want .nii

  • Script repository deals with these settings, but I can’t use them from within a CLI module Script repository — 3D Slicer documentation

Auto-loading the module at startup

Module from console with arguments - Support - 3D Slicer Community

Slicer.exe --python-code "selectModule('SampleData'); getModuleGui('SampleData').setCategoryVisible('BuiltIn', False)"

File operations

Script repository — 3D Slicer documentation:

# Create a new directory where the scene will be saved into
import time
sceneSaveDirectory = slicer.app.temporaryPath + "/saved-scene-" + time.strftime("%Y%m%d-%H%M%S")
if not os.access(sceneSaveDirectory, os.F_OK):
  os.makedirs(sceneSaveDirectory)

Inspiration

• User_Manual.md · develop · OpenDose / SlicerOpenDose3D · GitLab
  • openDose3D is a cool example extension that shows many things
• SlicerTotalSegmentator/TotalSegmentator/TotalSegmentator.py at main · lassoan/SlicerTotalSegmentator

  		outputSegmentation.AddDefaultStorageNode()
  		outputSegmentation.GetStorageNode().SetFileName(output_segmentation_path)
  		outputSegmentation.GetStorageNode().ReadData(outputSegmentation)
  

Useful bits from documentation

• There’s a node type for tables
  • statistics become a table
  • also: many modules exist
    • Documentation/Nightly/Extensions/MeshStatistics - Slicer Wiki / DCBIA-OrthoLab/MeshStatisticsExtension
      • does a lot including creating a table GUI programmatically and CSV export etc.
• Colors: are not just colors, but class/label names as well