dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Mon, Jan 26, 2009 at 03:33:09PM +0000, A Navaei wrote:
> Anders,
> 
> Kent and I have discussed connecting itk and dolfin and, following
> your advice, one viable way of itk->dolfin data flow can be summarised
> in the following c++ snippet:
> 
> -------------------------------------
> typedef double PixelType
> const unsigned int Dim = 3;
> typedef itk::Image< PixelType, Dim > ImageType;
> 
> class F : public Function
> {
> public:
>  SetImageData(ImageType id) {this->ImageData = id;};
> 
>  void eval(double* values, const double* x) const
>  {
>    values[0] = ImageData.GetPixel(x);
>  }
> 
> protected:
>  ImageType ImageData;
> };
> --------------------------------------
> 
> The problem with the above approach is that direct access of pixel
> data with GetPixel() in itk, and generally in a generic image data
> structure, is not efficient. Typically, in a 2D or 3D image, this
> method is, correspondingly, called 10e4 to 10e6 times leading to slow
> data structure conversion. This is even more pronounces when the
> conversion has to happen many times.
> 
> There are at least 2 alternatives for this:
> 
> (1) Passing the image data pointer to a Function class.
> 
> (2) Looping in the itk API rather than the dolfin API. The c++
> iterator implemented in itk provides a much more efficient interface
> for data assignment, however, we need to have access to dolfin
> Function data.
> 
> In both of the above approaches, we assume that the image data has a
> complete rectangular shape with known sizes which provides a simple
> look-up rule. Is it currently possible to implement either of the
> above methods? If not, how can dolfin be extended to support this?

I suggest just copying all image data to an array in the constructor
so you just access it once.

Then in your eval function you just lookup the values in the array.
Depending on how you represent your function, you might want to
overload the following eval function:

  void eval(double* values, const Data& data) const
  {

  }

You can access the current cell by data.cell(). If you have a DG(0)
representation of your image field, you may then simply map the cell
indices to the pixel values.

-- 
Anders

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