How to get centroids from SciPy's hierarchical agglomerative clustering?

Question

I am using SciPy\'s hierarchical agglomerative clustering methods to cluster a m x n matrix of features, but after the clustering is complete, I can\'t seem to figure out how to

Answer 1

You can do something like this (D=number of dimensions):

# Sum the vectors in each cluster
lens = {}      # will contain the lengths for each cluster
centroids = {} # will contain the centroids of each cluster
for idx,clno in enumerate(T):
    centroids.setdefault(clno,np.zeros(D)) 
    centroids[clno] += features[idx,:]
    lens.setdefault(clno,0)
    lens[clno] += 1
# Divide by number of observations in each cluster to get the centroid
for clno in centroids:
    centroids[clno] /= float(lens[clno])

This will give you a dictionary with cluster number as the key and the centroid of the specific cluster as the value.