SampEn

Partial port of v1.2 C-language code for estimating Sample Entropy using SampEn from PhysioNet to Python.

C-language code last updated 1 November 2004, by George Moody.

Original author Doug Lake. dlake@virginia.edu

Installation

Via PIP

$ pip install sampen

Via Git

Clone the repo:

$ git clone git@github.com:jbergantine/sampen.git

This will create a new directory with the repo in it. Change into that directory and install:

$ cd sampen && python setup.py install

Usage

Unlike the original C code which loads time series data either from standard input or a file, this script expects the time series to be expressed in a list of floats. If the time series exists in a flat text file that can be loaded into Python and saved into a list::

from sampen import sampen2


# initialize a list
series_data = []

# open the file and read each line into the list
with open('relative/path/to/file.txt', 'r') as file:
    for row in file:
        series_data.append(float(row.strip(' \t\n\r')))

# calculate the sample entropy
sampen_of_series = sampen2(series_data)

The default maximum epoch length (m) is 2, the default tolerance (r) is 0.2.

The estimate of the conditional probability that the subseries of the epoch length that matches pointwise within the tolerance (that is, the Sample Entropy) will be the last item in the returned tuple.

The earlier items in the returned tuple will be the sample entropies for lengths 0 up to the maximum epoch.

Therefore, inspecting the returned data:

>>> sampen_of_series

Returns something like::

[
    (0, 2.140629540027156, 0.0028357991885715863)
    (1, 2.162868347337613, 0.004903248034526253),
    (
        # Epoch length for max epoch
        2,
        # SampEn
        2.123328492035711,
        # Standard Deviation
        0.007596323621379352
    ),
]

Contributing

  1. Fork the repository on GitHub
  2. Create a named feature branch (like feature/add_component_x)
  3. Write your change
  4. Write tests for your change (if applicable)
  5. Run the tests, ensuring they all pass
  6. Submit a Pull Request using GitHub

Running Tests

$ python setup.py test

With TOX

First, install Tox, then run the tests.

$ pip install tox
$ tox

Documentation

Documentation is written in ReStructuredText and built with Sphinx.

  1. Install sphinx and sphinx-autobuild as necessary
  2. Edit docs/index.rst
  3. Build the HTML with $ make html from within the docs directory

Tagging Releases

Update version and download_url in setup.py.

Update the version and release in docs/conf.rst

Remake documentation