CODEWITHSUNDEEP
pythonpython-3.xpython-2.7scipy
nostres
nostres

Reputation: 89

Find shortest distance between points of two arrays with scipy

I have two arrays centroids and nodes

I need to find the shortest distance of each point in centroids to any point in nodes

The output for centroids is following

array([[12.52512263, 55.78940022],
       [12.52027731, 55.7893347 ],
       [12.51987146, 55.78855611]])

The output for nodes is following

array([[12.5217378, 55.7799275],
       [12.5122589, 55.7811443],
       [12.5241664, 55.7843297],
       [12.5189395, 55.7802709]])

I use the following code to get the shortest distance

shortdist_from_centroid_to_node = np.min(cdist(centroids,nodes))

However, this is the output I get (I should get 3 lines of output)

Out[131]: 3.0575613850140956e-05

Can anyone specify what the problem is here? Thanks.

Upvotes: 0

Views: 375

Answers (3)

RomainL.
RomainL.

Reputation: 1014

When you doing np.min it return the minimal value of the 2d-array. You want the minimum value for each centroids.

shortest_distance_to_centroid = [min(x) for x in cdist(centroids,nodes)]

To have the associate index one way would be to get the index of the corresponding value. Another is to write a custom min() function that also return the index (so you parse the list only once)

[(list(x).index(min(x)), min(x)) for x in cdist(centroids,nodes)]  # the cast list() is needed because numpy array don't have index methods

solution with a custom function:

def my_min(x):
       current_min = x[0]
       current_index = [1]

       for i, v in enumerate(x[1:]):
              if v < current_min:
                     current_min = v
                     current_index = i + 1
       return (current_index, current_min)

[my_min(x) for x in cdist(centroids,nodes)]

Upvotes: 1

ZhaoYi
ZhaoYi

Reputation: 251

I guess what you need is just add an arg called axis, just like this:

shortdist_from_centroid_to_node = np.min(cdist(centroids,nodes), axis=1)

As for the meaning of the axis arg, you could refer to numpy.min. All in all you need minimum on each row rather than on the whole matrix.

Upvotes: 1

Tasnuva Leeya
Tasnuva Leeya

Reputation: 2795

If I am not wrong your code says you are trying to access the min value hence you are getting a single value. remove np.min() try:

shortdist_from_centroid_to_node = cdist(centroids,nodes)

Upvotes: 0

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