https://github.com/Image-Py/sknw
build net work from skeleton image (2D-3D)
https://github.com/Image-Py/sknw
Last synced: 8 months ago
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build net work from skeleton image (2D-3D)
- Host: GitHub
- URL: https://github.com/Image-Py/sknw
- Owner: Image-Py
- License: bsd-3-clause
- Created: 2017-06-18T21:41:54.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2022-03-23T12:18:01.000Z (over 3 years ago)
- Last Synced: 2025-03-17T10:06:00.750Z (8 months ago)
- Language: Python
- Size: 16.6 KB
- Stars: 230
- Watchers: 9
- Forks: 48
- Open Issues: 22
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Skeleton Network
======================
build net work from nd skeleton image
### graph = sknw.build_sknw(ske， multi=False, iso=True, ring=True, full=True)
> **ske:** should be a nd skeleton image
>
> **multi:** if True，a multigraph is retured, which allows more than one edge between two nodes and self-self edge.
>
> **iso:** if True, return one-pixel node
>
> **ring:** if True, return ring without any branch (and insert a self-connected node in the ring)
>
> **full:** if True, every edge start from the node's centroid. else touch the node block but not from the centroid.
>
> **return:** is a networkx Graph object
### graph detail:
> **graph.nodes[id]['pts'] :** Numpy(x, n), coordinates of nodes points
>
> **graph.nodes[id]['o']:** Numpy(n), centroid of the node
>
> **graph.edge(id1, id2)['pts']:** Numpy(x, n), sequence of the edge point
>
> **graph.edge(id1, id2)['weight']:** float, length of this edge
>
> *if it's a multigraph, you must add a index after two node id to get the edge, like: graph.edge(id1, id2)[0].*
### Build Graph:
build Graph by Skeleton, then plot as a vector Graph in matplotlib.
```python
from skimage.morphology import skeletonize
from skimage import data
import sknw
# open and skeletonize
img = data.horse()
ske = skeletonize(~img).astype(np.uint16)
# build graph from skeleton
graph = sknw.build_sknw(ske)
# draw image
plt.imshow(img, cmap='gray')
# draw edges by pts
for (s,e) in graph.edges():
ps = graph[s][e]['pts']
plt.plot(ps[:,1], ps[:,0], 'green')
# draw node by o
nodes = graph.nodes()
ps = np.array([nodes[i]['o'] for i in nodes])
plt.plot(ps[:,1], ps[:,0], 'r.')
# title and show
plt.title('Build Graph')
plt.show()
```
### Find Path
then you can use networkx do what you want
### 3D Skeleton
sknw can works on nd image, this is a 3d demo by mayavi
### About ImagePy
[https://github.com/Image-Py/imagepy](https://github.com/Image-Py/imagepy)
ImagePy is my opensource image processihng framework. It is the ImageJ of Python, you can wrap any numpy based function esaily. And sknw is a sub module of ImagePy. You can use sknw without any code.
