[Insight-users] creating custom iterators

[Rémi Blanc]

Hi all,

I am seeking some help on iterators.

I am working on a project involving drawing shapes in an image. The 
application works in such a way that first, for each shape, a stencil 
image is generated (smallest box containing the shape), and then 
inserted within an image.
Depending on the user choice, I want to be able to manage different 
types of boundary conditions, including periodic boundary conditions 
(taking the part of the shape that would normally be outside the image, 
and drawing it at the other side of the image).

I started looking at the ShapedNeighborhood iterators, but have troubles 
with them, and am not 100% sure if they are the way to go:
- my attempts to use periodic boundary conditions lead to a crash any 
time I go outside the bounds, while keeping the default ZeroFluxBC works 
(see explanations at the end of the mail).
- it seems the ShapedNeighborhood needs to be instanciated together with 
the region where it should be applied, while in my view, I would first 
need to learn the patterns of background pixels before caring about 
where to apply the stencil.
   -> I don't understand in the manual, section "Shaped neighborhoods: 
morphological operations" why the structuring element is (needs to be?) 
re-defined for each 'face'
- I am actually not interested in iterating over the whole image with 
the neighborhood iterator as in a mathematical morphology filter, but 
only to 'apply' the stencil at a handful locations at most.


I would like to do the following thing:
Typically, even in the smallest rectangular box, some pixels/voxels 
correspond to background.
Since I may draw the same shape at different places in the image (using 
translations of integer grid spacing), I would like to code that some 
voxels of the stencil are just background and avoid iterating through them.
As I mentionned, I would also be able to manage different types of 
boundary conditions efficiently.
=> I need a way to circulate efficiently and simultaneously in the 
stencil and the image in the image (avoiding the background pixels from 
the stencil) while additionnally managing the boundary conditions in the 
image if necessary.


While I am here... I would also like to generate a second iterator, this 
time over the image. The goal here would be to remember which pixels of 
the image have been modified when applying stencils (possibly several of 
them, overlapping, etc...) , so that I don't need to scan the whole 
image to update the next steps of my programs (=> actually, the 
application of stencils is subject to an optimization procedure ; 
re-scanning the whole image while only a small part of it has changed is 
a serious bottelneck, which is actually not necessary in my case to 
update the metric).


Did I miss existing functionalities that could help doing this?
Any hints would be much appreciated,

Thanks a lot,

Rémi


Concerning the crash using periodic boundary conditions and ShapedNeighborhood, I started from  the wiki example ShapedNeighborhoodIterator_Manual.cxx
Replacing :

   typedef  itk::ShapedNeighborhoodIterator<ImageType>  IteratorType;

by

   typedef itk::ZeroFluxNeumannBoundaryCondition<ImageType>  ZFBCType;
   typedef itk::ShapedNeighborhoodIterator<ImageType, ZFBCType>  IteratorType;

the example executes
However, when using

   typedef itk::PeriodicBoundaryCondition<ImageType>  PBCType;
   typedef itk::ShapedNeighborhoodIterator<ImageType,PBCType>  IteratorType;

instead, the program crashes at the first call to ci.GetNeighborhoodIndex()