[ITK] ITK NeighborhoodIterator alternative

[Matt McCormick]

Hi Michael and David,

The way that memory is accessed with a NeighborhoodIterator can make
it relatively slow.  There are many memory accesses that need to take
place, and since all pixels from a neighborhood are not in the same
location in memory, this interferes with cache lines, etc. [1].

For computing the response of large kernel sizes, FFT-based
convolution will be much faster [2].

Since many more checks are at the boundary of an image, working with
the NeighborhoodIterator can be sped up by using  an
ImageBoundaryFacesCalculator [3].  This is covered in more detail in
The Software Guide.

HTH,
Matt

PS. David, your conda recipe for ITK looks great! Would you be
interested in submitting it to upstream [4]?

[1] http://arstechnica.com/gadgets/2002/07/caching/

[2] http://www.itk.org/Doxygen/html/classitk_1_1FFTConvolutionImageFilter.html

[3] http://www.itk.org/Doxygen/html/structitk_1_1NeighborhoodAlgorithm_1_1ImageBoundaryFacesCalculator.html

[4] https://github.com/conda/conda-recipes


On Mon, Feb 9, 2015 at 5:00 PM, David Froger <david.froger.ml at mailoo.org> wrote:
> Hi,
>
> I have the same question, this benchmark shows that NeighborhoodIterator
> are very slow for large 2D images:
> https://github.com/dfroger/quickstart/tree/master/itk/iterators
>
> Did I made something wrong in using NeighborhoodIterator? Is there an efficent
> alternative?
>
> ITK was built in release mode.
>
> Thanks,
> David
>
> Quoting Brehler, Michael (2015-01-29 10:15:49)
>> Hi,
>>
>>
>>
>> I am using the ITK NeighborhoodIterator to calculate response images of 3D box
>> filters with varying size on volumetric images. The iterator is very convenient
>> but especially for large filter sizes (27x27x27 and above) this method is very
>> slow. Is there an efficient alterative?
>>
>>
>>
>> Regards,
>>
>> Michael
>>
>>
>>
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