Creating graph vertices from numpy array

Question

I have a numpy array full of values that I would like to create vertices from for every point in the array. I am using networkx as my graphing support method(documentation here: http://networkx.github.io/documentation/latest/tutorial/ )

I would like to treat each element within the array as a pixel location and create a vertex instance at each location. This is easy using a simple for loop:

new=np.arange(16)
gnew=nx.Graph()
for x in new:
    if new[x]>0:
        gnew.add_node(x)
h=gnew.number_of_nodes()
print h

And as expected, 15 nodes will be printed. However, this becomes more tricky when you have identical values. For example:

new=np.ones(16)
gnew=nx.Graph()
for x in new:
    if new[x]>0:
        gnew.add_node(x)
h=gnew.number_of_nodes()
print h

Now, because all values are identical-(1), only one node will be added to the graph. Is there a way to circumnavigate this?

Just a quick comment - G.order() is the same as G.number_of_nodes(), but shorter... — Joel
– Joel, Commented Jun 18, 2015 at 17:34

jgloves · Accepted Answer · 2015-06-18 18:27:41Z

3

NetworkX requires that each node have a unique name. You could generate unique names and then set the elements of your array to be attributes of the nodes, e.g.

new = np.ones(16);
othernew = np.arange(16)

G = nx.Graph()
for i in range(len(othernew)):
   if new[i]>0:
      G.add_node(othernew[i])
      G.node[othernew[i]]['pos'] = new[i] #This gives the node a position attribute with value new[i]

h = G.order()
print(h)

>>16

answered Jun 18, 2015 at 18:27

jgloves

7194 silver badges14 bronze badges

Sign up to request clarification or add additional context in comments.

3 Comments

Brandon Ginley Over a year ago

Thanks @jgloves, I should've checked back here sooner as I just arrived at the same conclusion you did and have written my code in the same way.

jgloves Over a year ago

You're quite welcome. I'm glad you were able to solve it!

FaCoffee Over a year ago

What if your new array is instead a 2D numpy array? So basically, what if you want to turn a raster image into a graph where the attribute of the node is the value in the array?

Collectives™ on Stack Overflow

Creating graph vertices from numpy array

1 Answer 1

3 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

3 Comments

Your Answer

Sign up or log in

Post as a guest

Related