Hi. When I import gmatch4py there is a warning: for optimal results, the Cython 'munkr

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Importing Cython 'munkres' module about gmatch4py HOT 1 CLOSED

jacquesfize commented on July 28, 2024

Importing Cython 'munkres' module

from gmatch4py.

Comments (1)

jacquesfize commented on July 28, 2024

Hi @emmanuelasso

For my part, the installation of the munkres module worked smoothly. Here, my installation script:

virtualenv -p python3 test_munkres
cd test_munkres
source bin/activate
pip install numpy cython scipy
pip install git+https://github.com/jfrelinger/cython-munkres-wrapper.git

If the munkres algorithm is not installed, the scipy.optimize.linear_sum_assignment is used. However, in terms of performance, the munkres package is much faster. As an example:

import numpy as np
from munkres import munkres
from scipy.optimize import linear_sum_assignment

a = np.random.randint(0,10,81).reshape(9,9).astype(float)

%time linear_sum_assignment(a)
CPU times: user 759 µs, sys: 208 µs, total: 967 µs
Wall time: 800 µs
Out[18]: (array([0, 1, 2, 3, 4, 5, 6, 7, 8]), array([5, 2, 0, 3, 8, 7, 1, 4, 6]))

%time munkres(a)
CPU times: user 46 µs, sys: 4 µs, total: 50 µs
Wall time: 54.1 µs
Out[19]:
array([[False, False, False, False, False,  True, False, False, False],
       [False, False,  True, False, False, False, False, False, False],
       [ True, False, False, False, False, False, False, False, False],
       [False, False, False,  True, False, False, False, False, False],
       [False, False, False, False, False, False, False, False,  True],
       [False, False, False, False, False, False, False,  True, False],
       [False,  True, False, False, False, False, False, False, False],
       [False, False, False, False,  True, False, False, False, False],
       [False, False, False, False, False, False,  True, False, False]])