EntroPy is a Python 3 package providing several time-efficient algorithms for computing the complexity of time-series. It can be used for example to extract features from EEG signals.

Warning

EntroPy is now DEPRECATED. Please use the AntroPy package instead!

# Installation

EntroPy is now DEPRECATED because it could not be installed using pip (see below). Please use the AntroPy package instead!

Important

EntroPy CANNOT BE INSTALLED WITH PIP OR CONDA. There is already a package called entropy on the PyPi repository, which should NOT be mistaken with the current package.

git clone https://github.com/raphaelvallat/entropy.git entropy/
cd entropy/
pip install -r requirements.txt
python setup.py develop


Dependencies

# Functions

Entropy

import numpy as np
import entropy as ent
np.random.seed(1234567)
x = np.random.normal(size=3000)
# Permutation entropy
print(ent.perm_entropy(x, normalize=True))
# Spectral entropy
print(ent.spectral_entropy(x, sf=100, method='welch', normalize=True))
# Singular value decomposition entropy
print(ent.svd_entropy(x, normalize=True))
# Approximate entropy
print(ent.app_entropy(x))
# Sample entropy
print(ent.sample_entropy(x))
# Hjorth mobility and complexity
print(ent.hjorth_params(x))
# Number of zero-crossings
print(ent.num_zerocross(x))
# Lempel-Ziv complexity
print(ent.lziv_complexity('01111000011001', normalize=True))

0.9995371694290871
0.9940882825422431
0.9999110978316078
2.015221318528564
2.198595813245399
(1.4313385010057378, 1.215335712274099)
1531
1.3597696150205727


Fractal dimension

# Petrosian fractal dimension
print(ent.petrosian_fd(x))
# Katz fractal dimension
print(ent.katz_fd(x))
# Higuchi fractal dimension
print(ent.higuchi_fd(x))
# Detrended fluctuation analysis
print(ent.detrended_fluctuation(x))

1.0310643385753608
5.954272156665926
2.005040632258251
0.47903505674073327


## Execution time

Here are some benchmarks computed on a MacBook Pro (2020).

import numpy as np
import entropy as ent
np.random.seed(1234567)
x = np.random.rand(1000)
# Entropy
%timeit ent.perm_entropy(x)
%timeit ent.spectral_entropy(x, sf=100)
%timeit ent.svd_entropy(x)
%timeit ent.app_entropy(x)  # Slow
%timeit ent.sample_entropy(x)  # Numba
# Fractal dimension
%timeit ent.petrosian_fd(x)
%timeit ent.katz_fd(x)
%timeit ent.higuchi_fd(x) # Numba
%timeit ent.detrended_fluctuation(x) # Numba

106 µs ± 5.49 µs per loop (mean ± std. dev. of 7 runs, 10000 loops each)
138 µs ± 3.53 µs per loop (mean ± std. dev. of 7 runs, 10000 loops each)
40.7 µs ± 303 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)
2.44 ms ± 134 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
2.21 ms ± 35.4 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
23.5 µs ± 695 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)
40.1 µs ± 2.09 µs per loop (mean ± std. dev. of 7 runs, 10000 loops each)
13.7 µs ± 251 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)
315 µs ± 10.7 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)


# Development

EntroPy was created and is maintained by Raphael Vallat. Contributions are more than welcome so feel free to contact me, open an issue or submit a pull request!

To see the code or report a bug, please visit the GitHub repository.

Note that this program is provided with NO WARRANTY OF ANY KIND. Always double check the results.

# Acknowledgement

Several functions of EntroPy were adapted from:

All the credit goes to the author of these excellent packages.