SimpleITK

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Simple ITK

Goals

  • Provide an easy-access layer to ITK for non-C++ expert developers

Sandbox

Scope

Suggested Areas to Cover

  • IO
  • Basic Filters
  • Registration
    • Basic Framework
    • Deformable registration
      • BSplines
      • Demons
  • Segmentation
    • Region Growing
    • Level Sets
    • Classifiers

Types

  • Image pixel types supported
    • int8_t
    • int16_t
    • int32_t
    • float
  • Image dimensions supported
    • 3D
    • Is 2D managed as a 3D image of 1 slice ?
      • Performance penalty for neighborhood filters... ?
      • Could be "2D" versions of 3D filters, i.e. RecursiveGaussianFilter2D. This would work on a slice-by-slice basis.

Languages

Wrapped languages will be any that SWIG supports, if someone is willing to write tests / any needed glue code.

  • C++ Layer
  • Python
  • Lua
  • Java
  • ?

Implementation Details

  • Coding Style
    • Copyright Headers & License
  • Const correctness (can we avoid using const's completely?)
  • Testing
    • C++ testing (Google Test?)
    • Python tests (PyUnit?)
    • Lua tests (?!?)
    • Java tests (JUnit)
    • ? other languages ?
  • Managing basic types
    • Arrays
    • Regions
    • Transforms
  • Not so basic types (could these be enums passed as ivars?)
    • Interpolators
    • Optimizers
    • Metrics

Plan

  • Image classes
  • IO

TCons

Tcon topics 7/15/2010

Toll-Free #:      1-800-704-9804 
International #:  1-404-920-6604
Participant Code: 61466276

Thursday, July 15th, 3:30-5:00pm EDT
(2:30-4:00pm Central).
  • General architecture
  • Wrapping efficiency
  • Should SimpleITK be mixable with normal ITK ?
    • At C++ level ?
    • At WrapITK (Python, Tcl ) level ?
    • Provide access to the underlying ITK image ?
  • SimpleImage class
    • Include casting to other image types.
    • Introduce in ITK an itk::ImageBase class that is not templated over Dimension.
  • Use Pointer semantics ?
    • image->getDepth() vs image.getDepth()
  • What kind of flexibility to provide for Users to add functionalities to SimpleITK
    • It should be easy to write (even if the class is conceptually complex).
    • User says : "I need this data type X..."
      • Then, how hard is for the developer of SimpleITK classes to satisfy the user's request.
  • Design a Simple calling convention
    • Procedural-like notation...
    • out = Gaussian().setSigma(2).execute(image)
    • out = Gaussian( image, 2 )
    • Gaussian gaussian( 2 ) // sigma as argument to the constructor
    • gaussian( "Sigma",2, "Width", 2 ); // arguments packed as key,value pair
    • Add introspection to ITK proper
      • All filters provide a list of "Key, Type" pairs
      • SetParameter( "parameterName", parameterValue );

Tcon topics 7/16/2010

  • IO class to combine ImageFileReader and ImageSeriesReader into a single class.
  • Namespace to use : "sitk" or "stk".
  • Const-correctness: (yes)
  • Thread-safety:
    • The same instance of the object can't be used from multiple-threads.
    • Multiple-threads can create instances of an object type.
  • Testing
    • Based on the same testing framework as ITK.
    • Higher quality bar than ITK proper.
  • Exposing basic types:
    • Avoid exposing low level types such as Region, Array...
  • Registration
    • Implement pre-fabricated modules that contain a full registration framework
    • Used the Finder (dynamic registration) pattern to reduce compilation time (enable parallel compilation).
      • Finder will locate even internal components (such as interpolators) by name (using a string).
    • Should the output be a
      • Resampled ?
      • Transform ?
      • Transform Parameters ?

Tcon topics 7/22/2010

  • Should SimpleITK be mixable with VTK?
    • SimpleImage class include casting to vtkImage?
    • Concept: interactive programming languages are really cool if they include data visualization. We need to have a way to visualize images as we process them.