python做空间聚类,在python中将500,000个地理空间点聚类

I'm currently faced with the problem of finding a way to cluster around 500,000 latitude/longitude pairs in python. So far I've tried computing a distance matrix with numpy (to pass into the scikit-learn DBSCAN) but with such a large input it quickly spits out a Memory Error.

The points are stored in tuples containing the latitude, longitude, and the data value at that point.

In short, what is the most efficient way to spatially cluster a large number of latitude/longitude pairs in python? For this application, I'm willing to sacrifice some accuracy in the name of speed.

Edit:

The number of clusters for the algorithm to find is unknown ahead of time.

解决方案

I don't have your data so I just generated 500k random numbers into three columns.

import numpy as np

import matplotlib.pyplot as plt

from scipy.cluster.vq import kmeans2, whiten

arr = np.random.randn(500000*3).reshape((500000, 3))

x, y = kmeans2(whiten(arr), 7, iter = 20) #

plt.scatter(arr[:,0], arr[:,1], c=y, alpha=0.33333);

out[1]:

I timed this and it took 1.96 seconds to run this Kmeans2 so I don't think it has to do with the size of your data. Put your data in a 500000 x 3 numpy array and try kmeans2.