# raphaelvallat/entropy

EntroPy: complexity of (EEG) time-series in Python
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docs Dec 8, 2018
entropy
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.gitignore
.travis.yml Oct 17, 2018
MANIFEST.in Oct 16, 2018
appveyor.yml Oct 17, 2018
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requirements.txt Oct 17, 2018
setup.cfg Oct 16, 2018
setup.py

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

## Installation

Develop mode

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

Dependencies

• numpy
• scipy
• scikit-learn
• numba

## Functions

### Entropy

```from entropy import *
import numpy as np
np.random.seed(1234567)
x = np.random.rand(3000)
print(perm_entropy(x, order=3, normalize=True))                 # Permutation entropy
print(spectral_entropy(x, 100, method='welch', normalize=True)) # Spectral entropy
print(svd_entropy(x, order=3, delay=1, normalize=True))         # Singular value decomposition entropy
print(app_entropy(x, order=2, metric='chebyshev'))              # Approximate entropy
print(sample_entropy(x, order=2, metric='chebyshev'))           # Sample entropy```
```0.9995858289645746
0.9945519071575192
0.8482185855709181
2.0754913760787277
2.192416747827227
```

### Fractal dimension

```print(petrosian_fd(x))        # Petrosian fractal dimension
print(katz_fd(x))             # Katz fractal dimension
print(higuchi_fd(x, kmax=10)) # Higuchi fractal dimension```
```1.0303256054255618
9.496389529050981
1.9914197968462963
```

### Other measures

`print(detrended_fluctuation(x)) # Detrended fluctuation analysis`
```0.5082304865081877
```

## Execution time

Here are some benchmarks computed on an average PC (i7-7700HQ CPU @ 2.80 Ghz - 8 Go of RAM).

```from entropy import *
import numpy as np
np.random.seed(1234567)
x = np.random.rand(1000)
# Entropy
%timeit perm_entropy(x, order=3, delay=1)
%timeit spectral_entropy(x, 100, method='fft')
%timeit svd_entropy(x, order=3, delay=1)
%timeit app_entropy(x, order=2) # Slow
%timeit sample_entropy(x, order=2) # Numba
# Fractal dimension
%timeit petrosian_fd(x)
%timeit katz_fd(x)
%timeit higuchi_fd(x) # Numba
# Other
%timeit detrended_fluctuation(x) # Numba```
```127 µs ± 3.86 µs per loop (mean ± std. dev. of 7 runs, 10000 loops each)
150 µs ± 859 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)
42.4 µs ± 306 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)
4.59 ms ± 62.2 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
2.03 ms ± 39.5 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)
16.4 µs ± 251 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)
32.4 µs ± 578 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)
17.4 µs ± 274 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)
755 µs ± 17.1 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. If you can, always double check the results.

## Acknowledgement

Several functions of EntroPy were borrowed from:

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