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NEWS.md

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News

1.3.0 (2023-03-31)

New post-processing methods:

  • skeletor.post.smooth to smooth the skeleton
  • skeletor.post.despike remove spikes from skeleton
  • skeletor.post.remove_bristles to remove single-node bristles from the skeleton

1.2.0 (2022-04-03)

This release mainly improves skeletor.skeletonize.by_wavefront but it also adds a new method to get a graph representation of skeletons: Skeleton.get_graph.

1.1.0 (2021-07-26)

This is a small release that adds a single method to the Skeleton class to quickly save results as SWC file:

>>> skel.to_swc('skeleton.swc')

1.0.0 (2021-04-09)

This release represents a major rework of skeletor. Notably, functions that were previously exposed at top level (e.g. skeletor.contract) have been moved to submodules sorting them by their purpose:

< 1.0.0 >= 1.0.0
skeletor.fix_mesh skeletor.pre.fix_mesh
skeletor.simplify skeletor.pre.simplify
skeletor.remesh skeletor.pre.remesh
skeletor.contract skeletor.pre.contract
skeletor.cleanup skeletor.post.clean_up
skeletor.radii skeletor.post.radii

Similarly skeletor.skeletonize(method='some method') has been broken out into separate functions:

< 1.0.0 >= 1.0.0
skeletor.skeletonize(mesh, method='vertex_clusters') skeletor.skeletonize.by_vertex_clusters(mesh)
skeletor.skeletonize(mesh, method='edge_collapse') skeletor.skeletonize.by_edge_collapse(mesh)

New Features

  • new skeletonization methods skeletor.skeletonize.by_tangent_ball, skeletor.skeletonize.by_wavefront and skeletor.skeletonize.by_teasar
  • all skeletonization functions return a Skeleton object that bundles the results (SWC, nodes/vertices, edges, etc.) and allows for quick visualization
  • SWC tables are now strictly conforming to the format (continuous node IDs, parents always listed before their childs, etc)
  • Skeleton results contain a mesh to skeleton mapping as .mesh_map property
  • added an example mesh: to load it use skeletor.example_mesh()
  • skeletor now has proper tests and a simple documentation

Removals

  • removed drop_disconnected parameter from all skeletonization functions - pleases either use fix_mesh to remove small disconnected pieces from the mesh or drop those in postprocessing
  • output parameter has been removed from all skeletonization functions as the output is now always a Skeleton

Bugfixes

  • plenty