Neighbors in a 2D array python

Question

I have a 2D numpy array as follows:

start = np.array([
    [1,1,0,1],
    [1,0,0,1],
    [0,1,0,0]
                ])

I need to get the same matrix, but replace each value with the number of neighbors to which I could get by moving by one step in any direction, but walking only along 1

As a result, I should get the follow:

finish = np.array([
    [4,4,0,2],
    [4,0,0,2],
    [0,4,0,0]
                 ])

It seems to me that this is a well-known problem, but I have not even figured out how to formulate it in search, since everything that I was looking for is a bit different. What's the best way to do this?

Mr. T · Accepted Answer · 2021-02-20 16:55:14Z

2

You can use the scipy.ndimage labeling function with a customized structure array s:

import numpy as np
from scipy.ndimage import label    

start = np.asarray([ [1,1,0,1],
                   [1,0,0,1],
                   [0,1,0,0] ])

#structure array what to consider as "neighbors"
s = [[1,1,1],
     [1,1,1],
     [1,1,1]]

#label blobs in array
labeledarr,_ = label(start, structure=s)

#retrieve blobs and the number of elements within each blobs
blobnr, blobval = np.unique(labeledarr.ravel(), return_counts=True)

#substitute blob label with the number of elements
finish = np.zeros_like(labeledarr)
for k, v in zip(blobnr[1:], blobval[1:]):
    finish[labeledarr==k] = v

print(finish)

Output:

[[4 4 0 2]
 [4 0 0 2]
 [0 4 0 0]]

I am sure the final step of substituting the label number with the value of its occurrence can be optimized in terms of speed.
And @mad-physicist rightly mentioned that the initially used labeledarr.flat should be substituted by labeledarr.ravel(). The reasons for this are explained here.

edited Feb 20, 2021 at 16:55

answered Feb 20, 2021 at 13:56

Mr. T

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1 Comment

Mad Physicist Over a year ago

Ravel is probably preferable to flat

Ricoter · Accepted Answer · 2021-02-21 00:38:30Z

You can use scipy.ndimage.label to label connected regions and return the number of regions as @Mr.T points out. This can than be used to create a boolean mask for indexing and counting.

Credits should go to @Mr.T as he came up with a similar solution first. This answer is still posted as the second part is different, I find it more readable and its 40% faster on my machine.

import numpy as np
from scipy.ndimage import label

a = [[1,1,0,1],
     [1,0,0,1],
     [0,1,0,0]]) 

# Label connected regions, the second arg defines the connection structure
labeled, n_labels = label(a, np.ones((3,3)))

# Replace label value with the size of the connected region
b = np.zeros_like(labeled)
for i in range(1, n_labels+1):
    target = (labeled==i)
    b[target] = np.count_nonzero(target)

print(b)

output:

[[4 4 0 2]
 [4 0 0 2]
 [0 4 0 0]]

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