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build net work from skeleton image (2D-3D)

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- __init__.py
- sknw.py
.gitignore
LICENSE
README.md
setup.py

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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

![image](https://user-images.githubusercontent.com/24822467/144245690-8def3215-344f-464c-a825-bc33568758f7.png)

### 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()
```
![](http://home.imagepy.org/sknw/buildgraph.png "解压")
### Find Path
then you can use networkx do what you want
![](http://home.imagepy.org/sknw/findpath.png "解压")
### 3D Skeleton
sknw can works on nd image, this is a 3d demo by mayavi
![](http://home.imagepy.org/sknw/3dgraph.png "解压")

### 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.

![](http://myvi.imagepy.org/imgs/imagepy.jpg "vessel")

sknw

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