Projects/Slicer3/2007 Project Week Python support in Slicer3

Return to Project Week Main Page

Key Investigators

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

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

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