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Fast morphological reconstruction of large logical masks.

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Fast morphological reconstruction of large logical masks.


Sven (view profile)


MATLAB's imreconstruct is slow for large 3D logical masks. bwreconstruct is a faster replacement.

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MATLAB's imreconstruct() is optimised for 2D images (logical or numeric), but it suffers when working with large logical 3D (or higher dimension) matrices. bwreconstruct uses bwconncomp() to speed up this reconstruction considerably. It is around 10 times faster for one-off reconstructions, and faster still for multiple reconstructions (i.e., reconstructing a mask from a series of different markers).

  IM = BWRECONSTRUCT(MARKER,MASK) performs morphological reconstruction
  of the logical MARKER under the logical MASK. MARKER and MASK are two
  two binary images with the same size, resulting in a binary image IM of
  equivalent size.

  IM = BWRECONSTRUCT(MARKER,MASKCC) performs similarly, but uses the
  connected component structure MASKCC. MASKCC is the output from
  BWCONNCOMP(MASK), and when it is already available, using MASKCC is
  faster than providing a MASK binary image.

  IM = IMRECONSTRUCT(MARKER,MASK,CONN) performs morphological
  reconstruction with the specified connectivity. CONN may have the
  following scalar values:

      4 two-dimensional four-connected neighborhood
      8 two-dimensional eight-connected neighborhood
      6 three-dimensional six-connected neighborhood
      18 three-dimensional 18-connected neighborhood
      26 three-dimensional 26-connected neighborhood

  Connectivity may be defined in a more general way (see IMRECONSTRUCT
  for details).

  Class support
  MARKER and MASK must be logical arrays with the same dimension. If
  MASKCC is used instead of MASK, it must relate to this same dimension.

  Performance Note
  This function performs faster than IMRECONSTRUCT for large binary
  images of 3 or higher dimensions. For 2D or small images (sizes below
  50-by-50-by-50, for example), IMRECONSTRUCT is still the faster option.

      mask = false(100,100,100);
      mask(:,[3 50 75],:) = true;
      marker = false(size(mask));
      marker(45:55,45:55,50:55) = true;
      tic, im1 = imreconstruct(marker,mask); toc
      tic, im2 = bwreconstruct(marker,mask); toc
      isequal(im1, im2)
      figure, patch(isosurface(im2,0.5),'FaceColor','g','EdgeColor','none'), hold on
      patch(isosurface(mask & ~im2,0.5),'FaceColor','r','EdgeColor','none')
      axis image, view(3), camlight

Note: I fully expect this to become a redundant function within a release or two of the IP toolbox!

Required Products Image Processing Toolbox
MATLAB release MATLAB 8.1 (R2013a)
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