📐 Closely

Find the closest pairs in an array.

Closely compares distances of arrays/embeddings and sorts them.

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.

Distance Metric

The distance metric can be changed from the default euclidean to any supported by scipy.spatial.distance.cdist, eg, cosine, hamming, etc:

closely.solve(X, metric='cosine`)

Example

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

# Create dataset
X = np.random.random((100,2))
pairs, distances = 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]))

plt.show() 

Check pairs:

In [10]: pairs                                                                                                                                
Out[10]: 
array([[ 7, 16],
       [96, 50]])

Output:

Credit and Explanation

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