Proposals:Integration with R Language

Background

This page hosts discussions on how to integrate functionalities of ITK with R language (http://www.r-project.org/)

A reference for this effort is the integration of R in the Titan package (based on VTK).

https://www.kitware.com/InfovisWiki/index.php/R_Titan_Integration

Use Cases

• Statistical Segmentation of Images
  • Multi-modality segmentation
• Statistical Analysis of features extracted from images
  • Group registration
  • Atlas based segmentation
• Segmentation of Images/Volumes using ITK
  • Multi-dimensional array(s) pre-existing in R
  • Results are passed back into R
  • Visualization of results in ITK (through R?)
• Registration of Images/Volumes using ITK
  • Multi-dimensional array(s) pre-existing in R
  • Results are passed back into R
  • Visualization of results in ITK (through R?)

Suggested Implementations

Data Bridge

Making some ITK data structures visible from R by converting or adapting them to R vectors. And conversely, adapting R vectors into ITK data structures.

Candidate ITK classes

• itk::FixedArray (and derived classes)
  • itk::Point
  • itk::Vector
  • itk::Index
  • itk::Offset
  • itk::CovariantVector
  • itk::RGBPixel
  • itk::RGBAPixel
• itk::VariableLenghtVector
• itk::Matrix
• itk::Containers
  • itk::VectorContainer
  • itk::MapContainer
• itk::Image
  • itk::PixelContainer
• itk::Sample
• itk::KdTree

Candidate STL classes

• STL Containers
  • std::list
  • std::queue
  • std::map
  • std::set

Wrapping (WrapITK)

Adapting the wrapping process of WrapITK in order to expose ITK functionalities from R.

R Interface Examples with other languages

• http://www.omegahat.org/RSPerl/
• http://www.omegahat.org/RSPython/
• http://www.omegahat.org/GccTranslationUnit/
• http://www.omegahat.org/Combinations/
• http://dirk.eddelbuettel.com/code/rcpp.html