Projects/Slicer3/2007 Project Week Python support in Slicer3

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Key Investigators

• GE: Dan Blezek
• Isomics: Steve Pieper
• Mario Negri Institute: Luca Antiga

Python as a CommandLine Module

Output example

Objective

To extend Python support in Slicer3.

Approach, Plan

• Python scripting language inside Slicer3 to write short, useful scripts for processing

• Python execution model. A Python class required to have
  • a method that spits out the description of the instance variables to be exposed on the GUI, the CLI module way (in this case, instance variables could be wrapped vtk objects or wrapped MRML nodes)
  • a standard method (e.g. Execute()) that runs the class main functionality
  • Slicer would take care of building the GUI and setting the state of the object on the basis of the XML description before calling Execute.

Progress

• Implemented Python Modules
  • Add search for Python in ModuleFactory
    • Can put .py files in the CommandLine Module path
  • Execute Python within Slicer
    • Full access to VTK, vtkTEEM, vtkITK, etc.
  • If the Python module provides an XML description, and an Execute function, will be added as a CommandLine Module
• ToDo
  • Check-in (needs USE_PYTHON guards)
  • Progress reporting
  • Simplify the API
  • Automate command line parsing using XML description

def Execute ( inputVolume, outputVolume, conductance=1.0, timeStep=0.0625, iterations=1 ):
   print "Executing Python Demo Application!"
   # For the moment, be sure to cast...
   conductance = float ( conductance )
   timeStep = float ( timeStep )
   iterations = int ( iterations )
   Slicer = __import__ ( "Slicer" );
   slicer = Slicer.Slicer()
   scene = slicer.MRMLScene
   print "Input: ", inputVolume
   print "Output: ", outputVolume
   inputVolume = scene.GetNodeByID ( inputVolume );
   outputVolume = scene.GetNodeByID ( outputVolume );
   
   filter = slicer.vtkITKGradientAnisotropicDiffusionImageFilter.New()
   filter.SetInput ( inputVolume.GetImageData() )
   filter.Update()
   outputVolume.SetAndObserveImageData(filter.GetOutput())
   matrix = slicer.vtkMatrix4x4.New()
   inputVolume.GetIJKToRASMatrix ( matrix )
   outputVolume.SetIJKToRASMatrix ( matrix )
   return