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+{"version": "0.9.5", "fields": ["qualname", "fullname", "doc"], "ref": "fullname", "documentStore": {"docs": {"skeletor": {"fullname": "skeletor", "modulename": "skeletor", "qualname": "", "type": "module", "doc": "
What is skeletor?
\n\n
Unlike its namesake, this skeletor\ndoes not (yet) seek to conquer Eternia but to turn meshes into skeletons.
\n\n
Before we get started some terminology:
\n\n
\n- a mesh is something that consists of vertices and faces
\n- a skeleton is a (hierarchical) tree-like structure consisting of vertices\n(also called nodes) and edges that connect them
\n
\n\n
Skeletons are useful for a range of reasons. For example:
\n\n
\n- Typically smaller (less vertices) than the mesh
\n- Have an implicit sense of topology (e.g. \"this node is distal to that node\")
\n
\n\n
Extracting skeletons from meshes (or other types of data such as voxels) is\nnon-trivial and there are a great many research papers exploring various\ndifferent approaches (see Google scholar).
\n\n
skeletor implements some algorithms that I found useful in my work with\nneurons. In my experience there is unfortuntely no magic bullet when it\ncomes to skeletonization and chances are you will have to fiddle around a bit\nto get decent results.
\n\n
Installation
\n\n
From PyPI:
\n\n
\n\n
For the bleeding-edge version from Github:
\n\n
pip3 install git+git://github.com/schlegelp/skeletor@master\n
\n\n
Getting started
\n\n
A skeletonization pipeline typically consists of:
\n\n
\n- Some pre-processing of the mesh (e.g. fixing some potential errors like\ndegenerate faces, unreferenced vertices, etc.)
\n- The skeletonization itself
\n- Some post-processing of the skeleton (e.g. adding radius information)
\n
\n\n
\n\n
Here is a complete list of available functions:
\n\n
\n\n\n | function | \n description | \n
\n\n\n\n | example data | \n | \n
\n\n skeletor.example_mesh() | \n load an example mesh | \n
\n\n | pre-processing | \n | \n
\n\n skeletor.pre.fix_mesh() | \n fix some common errors found in meshes | \n
\n\n skeletor.pre.remesh() | \n re-generate mesh (uses Blender 3D) | \n
\n\n skeletor.pre.simplify() | \n reduce mesh complexity (uses Blender 3D) | \n
\n\n skeletor.pre.contract() | \n contract mesh to facilitate skeletonization [1] | \n
\n\n | skeletonization | \n | \n
\n\n skeletor.skeletonize.by_wavefront() | \n very fast, works well for tubular meshes (like neurons) | \n
\n\n skeletor.skeletonize.by_vertex_clusters() | \n very fast but needs mesh to be contracted (see above) | \n
\n\n skeletor.skeletonize.by_edge_collapse() | \n presented in [1] but never got this to work well | \n
\n\n skeletor.skeletonize.by_teasar() | \n very fast and robust, works on mesh surface | \n
\n\n skeletor.skeletonize.by_tangent_ball() | \n very fast, best on smooth meshes | \n
\n\n | postprocessing | \n | \n
\n\n skeletor.post.clean_up() | \n fix some potential errors in the skeleton | \n
\n\n skeletor.post.radii() | \n add radius information using various method | \n
\n\n
\n\n
\n\n
See docstrings of the respective functions for details.
\n\n
A pipeline might look like this:
\n\n
\nskeletor.pre.fix_mesh() to fix the meshskeletor.pre.simplify() to simplify the meshskeletor.pre.contract() to contract the mesh [1]skeletor.skeletonize.vertex_clusters() to generate a skeletonskeletor.post.clean_up() to clean up some potential issues with the skeletonskeletor.post.radii() to extract radii either by k-nearest neighbours or ray-casting
\n\n
In my experience there is no one-size-fits-all. You will have to play around to\nfind the right approach and parameters to get nice skeletons for your meshes.\nIf you need help just open an issue.
\n\n
Also check out the Gotchas below!
\n\n
Examples
\n\n
First load the example mesh (a fruit fly neuron):
\n\n
>>> import skeletor as sk\n>>> mesh = sk.example_mesh()\n>>> mesh\n<trimesh.Trimesh(vertices.shape=(6582, 3), faces.shape=(13772, 3))>\n
\n\n
Next see if there is stuff to fix in the mesh (degenerate faces, duplicate\nvertices, etc.):
\n\n
>>> fixed = sk.pre.fix_mesh(mesh, remove_disconnected=5, inplace=False)\n>>> fixed\n<trimesh.Trimesh(vertices.shape=(6213, 3), faces.shape=(12805, 3))>\n
\n\n
Now for tubular meshes like this neuron, the \"wave front\" skeletonization method\nperforms really well: it works by casting waves across the mesh and collapsing\nthe resulting rings into a skeleton (kinda like when you throw a stone in a\npond and track the expanding ripples).
\n\n
>>> skel = sk.skeletonize.by_wavefront(fixed, waves=1, step_size=1)\n>>> skel\n<Skeleton(vertices=(1258, 3), edges=(1194, 2), method=wavefront)>\n
\n\n
All skeletonization methods return a Skeleton object. These are just\nconvenient objects to bundle the various outputs of the skeletonization.
\n\n
>>> # x/y/z location of skeleton vertices (nodes)\n>>> skel.vertices\narray([[16744, 36720, 26407],\n ...,\n [22076, 23217, 24472]])\n>>> # child -> parent edges\n>>> skel.edges\narray([[ 64, 31],\n ...,\n [1257, 1252]])\n>>> # Mapping for mesh to skeleton vertex indices\n>>> skel.mesh_map\narray([ 157, 158, 1062, ..., 525, 474, 547])\n>>> # SWC table\n>>> skel.swc.head()\n node_id parent_id x y z radius\n0 0 -1 16744.005859 36720.058594 26407.902344 0.000000\n1 1 -1 5602.751953 22266.756510 15799.991211 7.542587\n2 2 -1 16442.666667 14999.978516 10887.916016 5.333333\n
\n\n
SWC is a commonly used format for saving skeletons. Skeleton objects\nhave a method for quickly saving a correctly formatted SWC file:
\n\n
>>> skel.save_swc('~/Documents/my_skeleton.swc')\n
\n\n
If you installed pyglet (see above) you can also use trimesh's plotting\ncapabilities to inspect the results:
\n\n
>>> skel.show(mesh=True)\n
\n\n
![\"skeletor_example\"](\"https://github.com/schlegelp/skeletor/raw/master/_static/example1.png\")
\n\n
That looks pretty good already but let's run some pro-forma postprocessing.
\n\n
>>> sk.post.clean_up(skel, inplace=True)\n<Skeleton(vertices=(1071, 3), edges=(1070, 2))>\n
\n\n
So that would be a full pipeline mesh to skeleton. Don't expect your own meshes\nto produce such nice results off the bat though. Chances are you will need to\nplay around to find the right recipe. If you don't know where to start, I suggest\nyou try out mesh contraction + vertex clustering first:
\n\n
>>> import skeletor as sk\n>>> mesh = sk.example_mesh()\n>>> fixed = sk.pre.fix_mesh(mesh, remove_disconnected=5, inplace=False)\n>>> # Contract mesh to 10% (0.1) of original volume\n>>> cont = sk.pre.contract(fixed, epsilon=0.1)\n>>> # Skeletonize\n>>> skel = sk.skeletonize.by_vertex_clusters(cont, sampling_dist=100)\n>>> # Replace contracted mesh with original for postprocessing and plotting\n>>> skel.mesh = fixed\n>>> # Add radii (vertex cluster method does not do that automatically)\n>>> sk.post.radii(skel, method='knn')\n>>> skel.show(mesh=True)\n
\n\n
Gotchas
\n\n
\n- while this is a general purpose library, my personal focus is on neurons and\nthis has certainly influenced things like default parameter values and certain\npost-processing steps
\n- meshes need to be triangular (we are using
trimesh) \n- use
sk.pre.simplify if your mesh is very complex (half a million vertices is\nwhere things start getting sluggish) \n- a good mesh contraction is often half the battle
\n- if the mesh consists of multiple disconnected pieces the skeleton will\nlikewise be fragmented (i.e. will have multiple roots)
\n
\n\n
Benchmarks
\n\n
![\"skeletor_benchmark\"](\"https://github.com/schlegelp/skeletor/raw/master/benchmarks/benchmark_2.png\")
\n\n
Benchmarks\nwere run on a 2018 MacBook Pro (2.2 GHz Core i7, 32Gb memory) with optional\nfastremap dependency installed. Note some of these functions (e.g.\ncontraction and TEASAR/vertex cluster skeletonization) vary a lot in\nspeed based on parameterization.
\n\n
What about algorithm X?
\n\n
skeletor contains some algorithms that I found easy enough to implement\nand useful for my work with neurons. If you have some interesting paper/approach\nthat could make a nice addition to skeletor, please get in touch on Github.\nPull requests are always welcome!
\n\n
References
\n\n
[1] Au OK, Tai CL, Chu HK, Cohen-Or D, Lee TY. Skeleton extraction by mesh contraction. ACM Transactions on Graphics (TOG). 2008 Aug 1;27(3):44.
\n\n
The abstract and the paper can be found here.\nAlso see this YouTube video.
\n\n
Some of the code in skeletor was modified from the\nPy_BL_MeshSkeletonization\naddon created by #0K Srinivasan Ramachandran and published under GPL3.
\n\n
Top-level functions and classes
\n\n
At top-level we only expose example_mesh() and the Skeleton class (which\nyou probably won't ever need to touch manually). Everything else is neatly\ntucked away into submodules (see side-bar or above table).
\n"}, "skeletor.Skeleton": {"fullname": "skeletor.Skeleton", "modulename": "skeletor", "qualname": "Skeleton", "type": "class", "doc": "
Class representing a skeleton.
\n\n
Typically returned as results from a skeletonization.
\n\n
Attributes
\n\n
\n- swc (pd.DataFrame, optional):\nSWC table.
\n- vertices ((N, 3) array):\nVertex (node) positions.
\n- edges ((M, 2) array):\nIndices of connected vertex pairs.
\n- radii ((N, ) array, optional):\nRadii for each vertex (node) in the skeleton.
\n- mesh (trimesh, optional):\nThe original mesh.
\n- mesh_map (array, optional):\nSame length as
mesh. Maps mesh vertices to vertices (nodes)\nin the skeleton. \n- skel_map (array of arrays, optional):\nInverse of
mesh_map: maps skeleton vertices (nodes) to mesh\nvertices. \n- method (str, optional):\nWhich method was used to generate the skeleton.
\n
\n"}, "skeletor.Skeleton.__init__": {"fullname": "skeletor.Skeleton.__init__", "modulename": "skeletor", "qualname": "Skeleton.__init__", "type": "function", "doc": "
\n", "parameters": ["self", "swc", "mesh", "mesh_map", "method"], "funcdef": "def"}, "skeletor.Skeleton.edges": {"fullname": "skeletor.Skeleton.edges", "modulename": "skeletor", "qualname": "Skeleton.edges", "type": "variable", "doc": "
Return skeleton edges.
\n"}, "skeletor.Skeleton.vertices": {"fullname": "skeletor.Skeleton.vertices", "modulename": "skeletor", "qualname": "Skeleton.vertices", "type": "variable", "doc": "
Return skeleton vertices (nodes).
\n"}, "skeletor.Skeleton.radius": {"fullname": "skeletor.Skeleton.radius", "modulename": "skeletor", "qualname": "Skeleton.radius", "type": "variable", "doc": "
Return radii.
\n"}, "skeletor.Skeleton.skeleton": {"fullname": "skeletor.Skeleton.skeleton", "modulename": "skeletor", "qualname": "Skeleton.skeleton", "type": "variable", "doc": "
Skeleton as trimesh Path3D.
\n"}, "skeletor.Skeleton.skel_map": {"fullname": "skeletor.Skeleton.skel_map", "modulename": "skeletor", "qualname": "Skeleton.skel_map", "type": "variable", "doc": "
Skeleton vertex (nodes) to mesh vertices. Based on mesh_map.
\n"}, "skeletor.Skeleton.reindex": {"fullname": "skeletor.Skeleton.reindex", "modulename": "skeletor", "qualname": "Skeleton.reindex", "type": "function", "doc": "
Clean up skeleton.
\n", "parameters": ["self", "inplace"], "funcdef": "def"}, "skeletor.Skeleton.copy": {"fullname": "skeletor.Skeleton.copy", "modulename": "skeletor", "qualname": "Skeleton.copy", "type": "function", "doc": "
Return copy of the skeleton.
\n", "parameters": ["self"], "funcdef": "def"}, "skeletor.Skeleton.save_swc": {"fullname": "skeletor.Skeleton.save_swc", "modulename": "skeletor", "qualname": "Skeleton.save_swc", "type": "function", "doc": "
Save skeleton in SWC format.
\n\n
Parameters
\n\n
\n- filepath (path-like):\nFilepath to save SWC to.
\n
\n", "parameters": ["self", "filepath"], "funcdef": "def"}, "skeletor.Skeleton.scene": {"fullname": "skeletor.Skeleton.scene", "modulename": "skeletor", "qualname": "Skeleton.scene", "type": "function", "doc": "
Return a Scene object containing the skeleton.
\n\n
Returns
\n\n
\n- scene (trimesh.scene.scene.Scene):\nContains the skeleton and optionally the mesh.
\n
\n", "parameters": ["self", "mesh", "kwargs"], "funcdef": "def"}, "skeletor.Skeleton.show": {"fullname": "skeletor.Skeleton.show", "modulename": "skeletor", "qualname": "Skeleton.show", "type": "function", "doc": "
Render the skeleton in an opengl window. Requires pyglet.
\n\n
Parameters
\n\n
\n- mesh (bool):\nIf True, will render transparent mesh on top of the\nskeleton.
\n
\n\n
Returns
\n\n
\n- scene (trimesh.scene.Scene):\nScene with skeleton in it.
\n
\n", "parameters": ["self", "mesh", "kwargs"], "funcdef": "def"}, "skeletor.example_mesh": {"fullname": "skeletor.example_mesh", "modulename": "skeletor", "qualname": "example_mesh", "type": "function", "doc": "
Load and return example mesh.
\n\n
The example mesh is a fruit fly neuron (an olfactory projection neuron of\nthe DA1 glomerulus) segmented from an EM image data set. It is part of the\nJanelia hemibrain data set (see here) [1].
\n\n
References
\n\n
[1] Louis K. Scheffer et al., eLife. 2020. doi: 10.7554/eLife.57443\nA connectome and analysis of the adult Drosophila central brain
\n\n
Returns
\n\n
\n\n
Examples
\n\n
>>> import skeletor as sk\n>>> # Load this example mesh\n>>> mesh = sk.example_mesh()\n
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skeletor API documentation
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