pyRiemann
pyRiemann is a python package for covariance matrices manipulation and classification through Riemannian geometry.
The primary target is classification of multivariate biosignals, like EEG, MEG or EMG.
This is work in progress ... stay tuned.
This code is BSD-licenced (3 clause).
Documentation
The documentation is available on http://pyriemann.readthedocs.io/en/latest/
Install
Using PyPI
pip install pyriemann
or using pip+git for the latest version of the code :
pip install git+https://github.com/pyRiemann/pyRiemann
Anaconda is not currently supported, if you want to use anaconda, you need to create a virtual environment in anaconda, activate it and use the above command to install it.
From sources
For the latest version, you can install the package from the sources using the setup.py script
python setup.py install
or in developer mode to be able to modify the sources.
python setup.py develop
How to use it
Most of the functions mimic the scikit-learn API, and therefore can be directly used with sklearn. For example, for cross-validation classification of EEG signal using the MDM algorithm described in [4] , it is easy as :
import pyriemann
from sklearn.model_selection import cross_val_score
# load your data
X = ... # your EEG data, in format Ntrials x Nchannels X Nsamples
y = ... # the labels
# estimate covariances matrices
cov = pyriemann.estimation.Covariances().fit_transform(X)
# cross validation
mdm = pyriemann.classification.MDM()
accuracy = cross_val_score(mdm, cov, y)
print(accuracy.mean())
You can also pipeline methods using sklearn Pipeline framework. For example, to classify EEG signal using a SVM classifier in the tangent space, described in [5] :
from pyriemann.estimation import Covariances
from pyriemann.tangentspace import TangentSpace
from sklearn.pipeline import make_pipeline
from sklearn.svm import SVC
from sklearn.model_selection import cross_val_score
# load your data
X = ... # your EEG data, in format Ntrials x Nchannels X Nsamples
y = ... # the labels
# build your pipeline
covest = Covariances()
ts = TangentSpace()
svc = SVC(kernel='linear')
clf = make_pipeline(covest,ts,svc)
# cross validation
accuracy = cross_val_score(clf, X, y)
print(accuracy.mean())
Check out the example folder for more examples !
Testing
If you make a modification, run the test suite before submitting a pull request
pytest
