SimpleITK: Difference between revisions

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* [[ITK_Release_4/SimpleITK/Tcon 2010 07 16|7/16/2010]]
* [[ITK_Release_4/SimpleITK/Tcon 2010 07 16|7/16/2010]]
== Tcon topics 7/16/2010 ==
* IO class to combine ImageFileReader and ImageSeriesReader into a single class.
*** Make this class in ITK proper first, then expose it in simple ITK.
* 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 Image ?
*** Transform ? ( <----This one )
*** Transform Parameters ?
** There will be a simpleResample that takes a simpleTransform as argument
** There will be simpleTransformReader & simpleTransformWriter
* Segmentation
** Output should be a LabelMap (plus a naming convention)
*** Make this class in ITK proper first, then expose it in simple ITK.
*** Along with Readers and Writers.
** "Feature" associated with every label.
** The Registration resampler should be able to map label images as well (to map a segmentation from an atlas to a subject, for example).
** Level Sets will be packaged at a modular level (with their preprocessing filters included).


== Tcon topics 7/22/2010 ==
== Tcon topics 7/22/2010 ==

Revision as of 19:16, 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 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.

Tcon topics 8/12/2010

Notes from discussions held during the tcon:

  • Gabe Hart reported on experiments with wrapping SimpleITK for Java
    • How to manage classpath ?
    • How to organize ITK classes into jar file.
      • Should they follow the distribution of "modular ITK" ?
  • Synergy between WrapITK and SimpleITK
    • Could we use WrapITK infrastructure to generate the instantiations of SimpleITK ?
  • Brad L. reported on experiments using template metaprogramming for selecting pixel types
  • Discussion about what pixel types to provide
    • Should they be extendable by a user ?
    • How about "unsigned long" ? (or is it Label Maps what we really want ?)
  • Label Maps
    • We agree in that they should be a first class citizen object, at the pair of the image
    • How to map LabelObjects from one image grid coordinates to another ?
      • Do we need a "resample label map" filter ?
  • Procedural look and feel
    • Should SimpleITK has a procedural look ? (ala Matlab ?)
    • Or the sequence of "create object, set parameter, set parameter.... execute"
    • Can we have both ?
      • Without one diminishing the other ?
  • What to do with basic Arrat types ?
    • Point, Vector, CovariantVector
      • How to hide their dimension ?
    • Introduce a generic "Array" class at SimpleITK level ?
      • maybe with an internal enum indicating that it is a Point, Vector or CovariantVector ?
      • Manage Dimension dynamically (or hide it internally), just like the simple Image class.
  • SimpleITK making it look natural in Wrapped languages
    • Provide functionalities for converting ITK classes into classes of the target language
  • SimpleITK & Visualization
    • Should we provide some simple visualization capabilities ?
    • Easy conversion from ITK simpleImage to vtkImageData
    • Basic Viewer example (maybe based on Qt+VTK: or CTK for that matter) that takes origin, spacing and orientation into account.
  • What pixel types to include ?
    • Suggested for Microscopy
      • unsigned char (int8)
      • signed short (int16)
      • unsigned short (uint16)
      • signed int (int32)
      • unsigned int (uint32)
      • float (float32)
      • double

Tcon topics 8/13/2010

  • How many classes to expose ?
    • Start with the classes exposed in v3d plugins (~80)
    • Grow to about ~200 ~300 classes
    • From there, listen to community feedback regarding new classes to add.
  • Support for Large Data
    • SimpleITK must be usable for building real applications.
    • It must support image larger than the available RAM.
  • Identify Target Customers for SimpleITK
    • Groups that are not using ITK at this point, because this consider it too complicated
    • Invite them to be early evaluators of the SimpleITK prototypes.
  • Reviewing the MetaProgramming layer used by Brad L. to instantiate types
  • How to manage multiple component images ?
    • Have an array of simpleITK images ?
  • How to manage time ?
    • ND+t ?


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


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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