[Insight-developers] New TransformParameters type proposed

[Williams, Norman K]

This is a good idea, & I agree with Tom Vercauteren's suggestions.


This would dovetail with the work I've done in the HDF5 Transform I/O
and Image I/O class; to implement storing and recalling these image
transforms
is straightforward.

1. Register the Hi-D transforms with the itkTransformFactory (I.e. add them
in itkTransformFactoryBase.cxx)
2. Add some intelligence in HDFTransformIO to detect Hi-D transforms, and
   store the images in the same group layout as HDF5 ImageIO uses.
3. On reading from disk, read the Image parameter into an appropriate
   itk::Image, and assign the image to the transform.

This will require some good design thinking; the HDF image reader and
transform reader should share code.  There's a lot of code in both these
classes that could/should be pushed to a HDF5 helper class.  I'm not sure
where in the ITK Module hierachy such a beast should live.

On 4/19/11 3:45 PM, "M Stauffer (V)" <mstauff at verizon.net> wrote:

>Hi,
>
>We (Brian Avants and I) propose a new TransformParameters class that
>will facilitate the heterogeneous use of both traditional "low
>dimensionality" (Low-D) transform (everything currently in use except
>for BSpline), and newer "high dimensionality" (Hi-D) transforms
>(BSpline, DeformationField, etc). Skelton code is below, after the
>prose.
>
>Motivation 1:
>A common, simple interface for parameter access of both Low-D and Hi-D
>transforms.
>
>Implementation:
>The class dervies from itkArray which is the type currently used for
>transform parameters. The Array interface remains expose, so all
>accessors used by the registration framework remain the same. One new
>method is added, MoveDataPointer - for use by CompositeTransform,
>described below.
>
>Low-D transforms will use TransformParameters as-is.
>
>Hi-D transforms will use one of two further-derived classes, either
>ImageVectorTransformParameters, or VectorImageTransformParameters, for
>parameters stored in either Image<Vector> or VectorImage types,
>respectively. A new method SetParameterImage is added to set the image
>used for parameters. Each class still exposes the Array interface for
>data access.
>
>Motivation 2:
>A memory-efficient method for passing and accessing Hi-D transform
>parameters, in particular within the registration framework.
>
>Implementation:
>The transform class developer is responsible for choosing the correct
>TransformParameter class. For Image-type parameters, he assigns an Image
>parameter object using SetParameterImage(), upon which
>TransformParameters will modify its Array members to point to the Image
>data buffer. This provides direct access to the image buffer data using
>the Array interface. The end-user will not need to do anything other
>than set the image parameter obj as required by the transform class.
>
>Motivation 3:
>A method for CompositeTransform to efficiently work with multiple
>transforms, in particular of Hi-D type, and use the same parameter
>interface as individual transforms.
>
>The TransformParameter class provides a MoveDataPointer method, which
>redirects the Array data pointer to a new memory block (and, within
>derived classes, the Image-type parameter buffer). This call releases
>the TransformParameter class, and any Image assigned to it, from memory
>management responsibility. CompositeTransform will manage the parameter
>memory during its lifetime.
>
>CompositeTransform will:
>1) create a single memory block sized to fit all of the parameters in
>its sub-transforms
>2) copy each sub-transform's parameters into this block
>3) assign each sub-transform's TransformParameters object to point to
>the proper position within this monolithic block (using MoveDataPointer)
>4) take over memory management responsibility
>5) possibly restore the parameter memory to the sub-transforms in its
>dtor (TBD)
>
>This will give the registration framework direct, fast access to all
>parameters within a contiguous block. As each sub-transform is called to
>transform a given point during the registration, it uses its parameters
>from this block via its redirected parameter data pointer.
>
>/*
> *  TransformParameterTypeMockup.h
> *
> */
>
>//Basic parameter class for low-dimensionality transforms.
>//Wraps itkArray, and provides helper routine for changing the
>// data pointer to be consistent with interface required for
>// derived classes.
>template< typename TValue = double >
>class TransformParameters :
>  public Array< TValue >
>{
>  //Set a new data pointer for the Array.
>  //Must point to block with same size as current data.
>  //Memory must be managed by caller after SetData().
>  //Use by CompositeTransform to aggregate sub-transform paramters
>  // into a single block.
>  virtual MoveDataPointer( TValue * pointer )
>    {
>    this->SetData( pointer, this->Size() ); //itkArray method
>    }
>};
>
>//Derived class for High-Dim transforms with parameters of type
>VectorImage.
>//This should probably also work for type Image<Scalar>, but have to
>make sure.
>template< class TImage, typename TValue >
>class VectorImageTransformParameters :
>  public TransformParameters< TValue >
>{
>  //Set the image that holds the parameters.
>  //Point the Array obj to this image for external access.
>  //For VectorImage, the pixel buffer is of type TValue, so we can point
>to
>  // it with the same type as Array, and it has the same size.
>  SetParameterImage( TImage image )
>    {
>    m_Image = image;
>    unsigned int sz = image->GetPixelContainer()->Size();
>    //Set the Array's pointer to the image data buffer
>    this->SetData( image->GetPixelContainer()->GetBufferPointer(), sz );
>    }
>
>  virtual MoveDataPointer( TValue * pointer )
>    {
>    SuperClass::SetData( pointer );
>    //After this call, PixelContainer will *not* manage its memory.
>    this->m_Image->GetPixelContainer()->SetImportPointer( pointer,
>this->Size() );
>    }
>
>};
>
>//Derived class for High-Dim transforms with parameters of type
>Image<Vector>.
>//This requires special handling for vector pixel-type because the
>// PixelContainer has an ElementType == Vector.
>template< class TImage, typename TValue >
>class ImageVectorTransformParameters :
>  public TransformParameters< TValue >
>{
>  //Set the image that holds the parameters.
>  //Point the Array obj to this image for external access.
>  SetParameterImage( TImage image )
>    {
>    m_Image = image;
>    unsigned int vectorSize = TImage::PixelType::Dimension;
>    unsigned int sz = image->GetPixelContainer()->Size() * vectorSize;
>    //Set the Array's pointer to the image data buffer
>    TValue* valuePointer
>      = reinterpret_cast<TValue *>
>      ( image->GetPixelContainer()->GetBufferPointer() );
>    this->SetData( valuePointer, sz );
>    }
>
>  virtual MoveDataPointer( TValue * pointer )
>    {
>    SuperClass::SetData( pointer );
>    //The buffer for Image<Vector> points to Vector type, not TValue, so
>    // have to cast.
>    TImage::PixelContainer::Element* vectorPointer
>      = reinterpret_cast<TImage::PixelContainer::Element *>(pointer);
>    //After this call, PixelContainer will *not* manage its memory.
>    unsigned int sizeInVectors = m_Image->GetPixelContainer()->Size();
>    this->m_Image->GetPixelContainer()->SetImportPointer( vectorPointer,
>                                                          sizeInVectors
>);
>    }
>};
>
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