[vtkusers] How to store a binary image skeleton as a tree or graph?

[Jeff Baumes]

I don't know of anything that does this type of traversal and tracking of
branches out of the box, at least in VTK. It sounds like you want vtkGraph
(which you create with vtkMutableUndirectedGraph/vtkMutableDirectedGraph)
instead of vtkTree since you may have back edges. You can give the vertices
positions with graph->SetPoint(i, x, y, z), and add other properties by
calling graph->Get[Vertex|Edge]Data()->AddArray(arr). As for traversal, the
most flexible way would be to use boost's dfs/bfs traversal algorithms,
which is possible if you build VTK with vtkInfovisBoost and
vtkInfovisBoostGraphAlgorithms modules enabled. A vtkGraph instance can be
used directly with boost's algorithms if you include
vtkBoostGraphAdapter.h. See
Infovis/BoostGraphAlgorithms/vtkBoostBreadthFirstSearch.cxx for an example
of how to implement a bfs_visitor.

BTW, you can view the graph with vtkGraphLayoutView. Make sure to set the
layout strategy to PassThrough and turn on 3D interaction if you set your
own 3D coordinates.

Jeff

On Thu, Jul 26, 2012 at 9:56 AM, Roman Grothausmann <
roman.grothausmann at helmholtz-berlin.de> wrote:

> Dear mailing list members,
>
>
> My aim is to store the result of AnalyzeSkeleton imagej plug-in (
> http://fiji.sc/wiki/index.**php/AnalyzeSkeleton#Loop_**
> detection_and_pruning<http://fiji.sc/wiki/index.php/AnalyzeSkeleton#Loop_detection_and_pruning>)
> as an itk or vtk tree. Or if easier, the result of Skeletonize3D, i.e. a
> not analysed skeleton, into a vtkGraph (there seems to be no itkGraph
> strucutre).
> Each tree or graph node should also store its voxel position it originated
> from. Therefore, the vtk structures might be better, since they already
> offer to store extra data, which itkTree does not (if I'm not mistaken).
>
> What would be the best way to do this?
>
> At the moment my plan is to use a ConstNeighborhoodIterator starting at
> the root of the tree, which is supplied by the user. I'd add each
> CenterPixel as a node to the tree and check its 26 neighbors for other
> foreground pixels. If there is at least one, take that as the next center
> pixel and so iterate on. However, I'd need to keep track of branching
> points (i.e. nodes with more than one child). Therefore, it might be best
> to recursively traverse through the tree up to its leafs, adding branches
> from the leafs. This would need, I think, separate
> ConstNeighborhoodIterators for each branch.
>
> Before I start implementing this, I wonder, is there perhaps already a
> filter/tree-generator that does this? Can the KdTreeGenerator be used for
> my purpose some how?
>
> Any help or hints are very much appreciated
> Roman
>
>
>
> --
> Roman Grothausmann
>
> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
> Bereich Funktionale Materialien
> Institut für angewandte Materialforschung
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>
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