After rethinking the problem, I have come to the conclusion that there is a simplier straight forward solution that does not need to wait for ITK v5 and maybe new features.

It could be solved the following way:

1. Rework the itk::MultiOutputNaryFunctorImageFilter
   • filter should alllow also mask that are a subgeometry of the input(s)
   • Override generate output to
     • 1 If no mask is set or Mask geometry equals input geometry -> use default implementation
     • 2. If mask is a subgeometry of input, 1) graft the outputs, 2) fill everything with 0., 3) take the region of the mask and pass it to the region splitter, the rest should be like in the default implementation.

2. Rework the Pixelbased generator class.
   • the generator should use the auto crop filter on the mask to reduce it to minimal possible size befor passing it to the itk filter.

This combined will only thread over the minimal region covered by the mask, which should substentially boost the performances for small mask use cases.

@kompan @thomass I added you to let you know, in case performance is still an issue in your supported projects. Let me know.