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Simple ITK

Goals

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

Examples of Other Librarires

CIMG: http://cimg.sourceforge.net

Sandbox

Dan's: http://github.com/dblezek/SimpleITK (This is currently the "unofficial" SimpleITK repository)
Gabe's: http://github.com/gabehart/SimpleITK (Experiments with multi-image filters, e.g. AddImage)
Brad's: http://github.com/blowekamp/SimpleITK (Meta-programming experiment)

Scope

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 7/15/2010

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.
- - 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

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
- Example implemented: http://github.com/blowekamp/SimpleITK/network
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
  - In Java: be able to convert a simpleImage into a Java BufferedImage class, and back.
  - In Python: be able to convert an simpleImage into a Python Image or at least a python array.
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

SimpleITK

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