add setup file, and tests infrasturcture

.coveragerc

@@ -0,0 +1,8 @@
+[report]
+include = */covmatTest/*
+omit =
+    */python?.?/*
+    */site-packages/pytest/*
+    */setup.py
+    */tests/*
+    */examples/*

.gitignore

@@ -0,0 +1,7 @@
+*.pyc
+.DS_Store
+.coverage
+.coveralls.yml
+/dist
+/*.egg-info/*
+

MANIFEST.in

@@ -0,0 +1 @@
+include README.md

covmatTest/__init__.py

@@ -0,0 +1 @@
+from .get_covmat import get_covmat

covmatTest/get_covmat.py

@@ -0,0 +1,59 @@
+from pyriemann.estimation import Covariances
+from alphawaves.dataset import AlphaWaves
+import numpy as np
+import mne
+import random
+
+"""
+=============================
+Get a covariance matrice sample from alphawaves dataset
+=============================
+
+TODO
+
+"""
+# Authors: Gregoire Cattan <[email protected]>
+#
+# License: Apache 2.0
+
+import warnings
+warnings.filterwarnings("ignore")
+
+trials = []
+
+
+def _get_trials(raw):
+    events = mne.find_events(raw=raw, shortest_event=1, verbose=False)
+    event_id = {'closed': 1, 'open': 2}
+    epochs = mne.Epochs(raw, events, event_id, tmin=2.0, tmax=8.0, baseline=None,
+                        verbose=False, preload=True)
+    epochs.pick_types(eeg=True)
+    return epochs.get_data()
+
+def _init():
+    dataset = AlphaWaves(useMontagePosition = False) 
+
+    subjects = dataset.subject_list
+    n_subjects = len(subjects)
+    subject = random.randint(0, n_subjects - 1)
+
+    raw = dataset._get_single_subject_data(subject)
+
+    global trials
+    trials = _get_trials(raw)
+    return len(trials)
+
+def _get_covmat(n_channels):
+    global trials
+    n_trials = len(trials)
+    if n_trials == 0:
+        n_trials = _init()
+    index = random.randint(0, n_trials - 1)
+    trial = np.array([trials[index][:n_channels,:]])
+    return Covariances(estimator='lwf').fit_transform(trial)
+
+def get_covmat(n_matrices, n_channels):
+    covset = np.zeros((n_matrices, n_channels, n_channels))
+    for i in range(0, n_matrices):
+        covset[i] = _get_covmat(n_channels)
+    return covset

setup.py

@@ -0,0 +1,122 @@
+"""A setuptools based setup module.
+See:
+https://packaging.python.org/en/latest/distributing.html
+https://github.com/pypa/sampleproject
+"""
+
+from setuptools import setup, find_packages
+from os import path
+from io import open
+
+here = path.abspath(path.dirname(__file__))
+
+with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+    long_description = f.read()
+
+setup(
+
+    name='covmatTest',
+
+    version='0.1',
+
+    license='Apache 2.0',
+
+    description='Alpha Waves Dataset',
+
+    long_description=long_description,
+
+    long_description_content_type='text/markdown',
+
+    url='https://github.com/gcattan/covmatTest',
+
+    author='Gregoire Cattan',
+
+    author_email='[email protected]',  # Optional
+
+    # For a list of valid classifiers, see https://pypi.org/classifiers/
+    classifiers=[
+        # How mature is this project? Common values are
+        #   3 - Alpha
+        #   4 - Beta
+        #   5 - Production/Stable
+        'Development Status :: 3 - Alpha',
+
+        # Indicate who your project is intended for
+        'Intended Audience :: Science/Research',
+                'Topic :: Scientific/Engineering',
+
+        # Pick your license as you wish
+        'License :: OSI Approved',
+
+        # Specify the Python versions you support here. In particular, ensure
+        # that you indicate whether you support Python 2, Python 3 or both.
+        'Programming Language :: Python :: 3.7',
+    ],
+
+    # Note that this is a string of words separated by whitespace, not a list.
+    keywords='EEG neuroscience test covariance matrices',  # Optional
+
+    packages=find_packages(exclude=['contrib', 'docs', 'tests']),  # Required
+
+    # For an analysis of "install_requires" vs pip's requirements files see:
+    # https://packaging.python.org/en/latest/requirements.html
+    install_requires=["alphawaves"],
+
+    # List additional groups of dependencies here (e.g. development
+    # dependencies). Users will be able to install these using the "extras"
+    # syntax, for example:
+    #
+    #   $ pip install sampleproject[dev]
+    #
+    # Similar to `install_requires` above, these must be valid existing
+    # projects.
+    # extras_require={  # Optional
+    #     'dev': ['check-manifest'],
+    #     'test': ['coverage'],
+    # },
+
+    # If there are data files included in your packages that need to be
+    # installed, specify them here.
+    #
+    # If using Python 2.6 or earlier, then these have to be included in
+    # MANIFEST.in as well.
+    # package_data={  # Optional
+    #     'sample': ['package_data.dat'],
+    # },
+
+    # Although 'package_data' is the preferred approach, in some case you may
+    # need to place data files outside of your packages. See:
+    # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files
+    #
+    # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
+    # data_files=[('my_data', ['data/data_file'])],  # Optional
+
+    # To provide executable scripts, use entry points in preference to the
+    # "scripts" keyword. Entry points provide cross-platform support and allow
+    # `pip` to create the appropriate form of executable for the target
+    # platform.
+    #
+    # For example, the following would provide a command called `sample` which
+    # executes the function `main` from this package when invoked:
+    # entry_points={  # Optional
+    #     'console_scripts': [
+    #         'sample=sample:main',
+    #     ],
+    # },
+
+    # List additional URLs that are relevant to your project as a dict.
+    #
+    # This field corresponds to the "Project-URL" metadata fields:
+    # https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
+    #
+    # Examples listed include a pattern for specifying where the package tracks
+    # issues, where the source is hosted, where to say thanks to the package
+    # maintainers, and where to support the project financially. The key is
+    # what's used to render the link text on PyPI.
+    # project_urls={  # Optional
+    #     'Bug Reports': 'https://github.com/pypa/sampleproject/issues',
+    #     'Funding': 'https://donate.pypi.org',
+    #     'Say Thanks!': 'http://saythanks.io/to/example',
+    #     'Source': 'https://github.com/pypa/sampleproject/',
+    # },
+)

tests/conftest.py

@@ -0,0 +1,33 @@
+import pytest
+from pytest import approx
+import numpy as np
+
+
+def is_positive_semi_definite(X):
+    cs = X.shape[-1]
+    return np.all(np.linalg.eigvals(X.reshape((-1, cs, cs))) >= 0.0)
+
+
+def is_positive_definite(X):
+    cs = X.shape[-1]
+    return np.all(np.linalg.eigvals(X.reshape((-1, cs, cs))) > 0.0)
+
+
+def is_symmetric(X):
+    return X == approx(np.swapaxes(X, -2, -1))
+
+
+@pytest.fixture
+def is_spd():
+    def _is_spd(X):
+        return is_symmetric(X) and is_positive_definite(X)
+
+    return _is_spd
+
+
+@pytest.fixture
+def is_spsd():
+    def _is_spsd(X):
+        return is_symmetric(X) and is_positive_semi_definite(X)
+
+    return _is_spsd

tests/test_get_covmat.py

@@ -0,0 +1,5 @@
+from covmatTest import get_covmat
+
+
+def test_canary(is_spd, is_spds):
+    get_covmat(1, 1)