How to apply euclidean distance function to a groupby object in pandas dataframe?

Question

I have a set of objects and their positions over time. I would like to get the average distance between objects for each time point. An example dataframe is as follows:

Answer 1

You could pass an array of the points to scipy.spatial.distaince.pdist and it will calculate all pair-wise distances between Xi and Xj for i>j. Then take the mean.

import numpy as np
from scipy import spatial

df.groupby('time').apply(lambda x: spatial.distance.pdist(np.array(list(zip(x.x, x.y)))).mean())

Outputs:

time
0     1.550094
1    10.049876
2    53.037722
dtype: float64