Closely :triangular_ruler:

Find the closest pairs in an array.

Getting Started

pip install closely

or install from source:

git clone https://github.com/justinshenk/closely
cd closely
pip install .

How to use

import closely

# X is an n x m numpy array
pairs, distances = closely.solve(X, n=1)

You can specify how many pairs you want to identify with n.

Example

import closely
import numpy as np
import matplotlib.pyplot as plt

# Create dataset
X = np.random.random((100,2))
pairs, distance = closely.solve(X, n=1)

# Plot points
z, y = np.split(X, 2, axis=1)
fig, ax = plt.subplots()
ax.scatter(z, y) 

for i, txt in enumerate(X): 
    if i in pairs: 
        ax.annotate(i, (z[i], y[i]), color='red') 
    else: 
        ax.annotate(i, (z[i], y[i])) 

Check pairs:

In [10]: pairs                                                                                                                                
Out[10]: 
array([[[ 7],
        [16]],

       [[96],
        [50]]])

Output:

Caveats

closely will reduce the dimensionality with PCA of your data to two-dimensions for faster processing.

It also removes the first point in a pair if n>1. In rare cases this leads to false negatives if the data is highly overlapping.

Credit and Explanation

Python code modified from Andriy Lazorenko, packaged and made useful for >2 features by Justin Shenk.