SimpleITK: Difference between revisions

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* [[ITK_Release_4/SimpleITK/Tcon 2010 08 17|8/17/2010]]
* [[ITK_Release_4/SimpleITK/Tcon 2010 08 17|8/17/2010]]


== Tcon topics 8/17/2010 ==
*Next ITKv4 Meeting - Potentially October 4-6
*Additional Conference Calls held last week
**'''SimpleITK'''
**'''Microscopy'''
***Summary: What changes to the ITK fundamentals required for large image sizes. There may be issues for video processing as well
****How to deal with time as a dimension
****Memory management (Streaming)
***Possible changes to the image structure - Luis will make proposal to handle these issues and present to the group
****Video processing may require a ring buffer structure
****Iterators may need to be updated to avoid access to the buffer pointer
****Possibility of using image adapters
***Multi-resolution Images
****Possibility of support for this at the level of the image reader (JPEG2000: support for 2D images in files)
****Query image reader for different resolution images
***Non-regular image spacing
****Potential different time point for top and bottom of image
****VTK Rectilinear grid handles this
****What filters are required to handle non-uniform spacing. Can convolution be applied and then resample to regular spacing
****Does this cause a data explosion
***File formats
****Desire for more file format support: probably would benefit from just 2-3 formats
****64 bit TIFF reader, Vendor specific private tags
****Update to libTiff is required
****Streaming support exists for Meta, VTK, MRC. ImageSeriesReader will stream slice-by-slice
**'''WrapITK'''
*Sequestered reference applications
*Clean-up Releases
**Currently running behind
**Limited coverage for Windows machines on the Dashboard - Need to turn on BUILD_EXAMPLES for these machines
**Need to updated OpenJPEG (version 2) and libTiff
*DICOM
**Design for QR of PACS without writing to disk
***Currently requires to locally save a copy of the file(s) before reading as an ITK image
***How do you know what you are going to get (e.g. multi-planar scout images)
***Create a database or data structure to present to the programmer and then create an image from the bulk data
***What API is required to support this functionality
***Data structure to hold information (DOM specification - Larry Tarbox from XIP - Stephen Alyward)
***Potential to pass Metadata Dictionary




Revision as of 19:28, 1 September 2010

Simple ITK

Goals

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

Advisory Review Board (ARB)

  • The Advisory Review Board is composed of groups and individual who are potential users of the Simple ITK Layer.
  • They provide advice to ITK developers of the simple layer regarding the design and implementation of the SimpleITK API.

Examples of Other Librarires

Sandbox

Scope

Current open questions

  • Internal execution mechanism
    • switch statement, supported by macros
    • Factory mechanism, new image types could be added at runtime
    • Meta-programming
  • Datatypes
    • What to support "out of the box"?
    • How easy/difficult to add new datatypes to a build?
  • Compile times
    • Templates radically extend CPU and memory requirements
  • Library size / scope
    • Custom SWIG files vs. automatically generated SWIG
    • Automation for SimpleITK facade generation from ITK classes?

Suggested Areas to Cover

  • IO
  • Basic Filters
  • Registration
    • Basic Framework
    • Deformable registration
      • BSplines
      • Demons
  • Segmentation
    • Region Growing
    • Level Sets
    • Classifiers
  • Meshes ? (Not Yet)

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 8/26/2010

  • Gerrit
    • What sort of work flow should we follow?
    • How do we get this set up correctly with git and github?
  • Interoperability with ITK
    • Are we all agreed that this is a top priority?
  • Flexibility w.r.t. dimensions
    • Are we all agreed that no more than 2D and 3D is needed?
  • Flexibility w.r.t. types
    • Fixed set of types? (Just a thought)
    • Everything cast to doubles? (Again, just a thought)
    • Typing system
      • PixelTypeID
      • Instantiation
      • Runtime choosing of methods
      • Macros
        • Not pretty
        • Fairly intuitive
      • Meta-Programming
        • Hard to understand completely
        • Adds ability for each filter to specify what types it works for
  • Dynamic casting
    • Should there be convenience methods to do this?
    • Should the user have to do it themselves?
  • User seeing templates
    • Are we all agreed that the user should never see templates?
    • image creation without templates?
  • Documentation
    • Doxygen
    • Tutorial?
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