v1.2
pyEEG is a library fo processing EEG data build mostly on top of MNE-py and scikit-learn. It is framed to work with data collected with naturalsistic stimuli, therefore with continuous recordings rather than trial-based designs. It allows analysis of continuous m/eeg and generation of temporal response functions with continuous signals as stimuli or real-valued events (e.g. word-level or phoneme-level features).
The documentation is not hosted anywhere, in order to read through it, it has to be build locally either as a PDF stand-alone or as a set of html files that can be browse using any internet browser.
- Use doctest for systematic testing of some functions
- fix imports (for now, cannot do
import pyeeg
to access all modules...)
- Functional connectivity methods:
- Estimate connectivity (in construction)
- Graph theory metrics (path length, clustering coeff.)
- Pipeline
pyRiemann
andpyeeg
this one into some workflows..
pyEEG requires:
- Python (>= 3.5)
- NumPy (>= 1.11.0)
- SciPy (>= 1.0.0)
- mne (>= 0.16)
- pandas (>= 0.23.0)
- scikit-learn (>= 0.20.0)
- matplotlib (>= 2.0)
- h5py (>= 2.8.0)
Install requirements:
pip install -r requirements.txt
To generate the doc, Python package sphinx
(>= 1.1.0), sphinx_rtd_theme
and nbsphinx
are required (sphinx
can be installed from conda
and the others from pip
).
From terminal (or conda
shell in Windows), cd
in root directory of the library (directory containing setup.py
file) and type:
To get the package installed only through symbolic links, namely so that you can modify the source code and use modified versions at will when importing the package in your python scripts do:
python setup.py develop
Otherwise, for a standard installation (but this will require to be installed if you need to install another version of the library):
python setup.py install
See files in examples/
.
See examples/CCA_envelope.ipynb
See examples/TRF_wordonsets.ipynb
See examples/import_WordVectors.ipynb
You can generate an offline HTML version, or a PDF file of all the docs by following the following instructions (HTML pages are easier to navigate in and prettier than the PDF thanks to the nice theme brought by sphinx_rtd_theme
).
To generate the documentation you will need sphinx
to be installed in your Python environment, as well as the extension nbsphinx
(for Jupyter Notebook integration) and the theme package sphinx_rtd_theme
. Install those with:
conda install sphinx
conda install -c conda-forge nbsphinx
pip install sphinx_rtd_theme
You can access the doc as HTML or PDF format. To generate the documentation HTML pages, type in a terminal:
For Unix environment (from root directory):
make doc
For Windows environment (from docs
folder):
cd docs
make.bat html
Then you can open the docs/build/html/index.html
page in your favourite browser.
And for PDF version, simply use docpdf
instead of doc
above.
Then open docs/build/latex/pyEEG.pdf
in a PDF viewer.
Note: The PDF documentation can only be generated if
latex
andlatxmk
are present on the machine
To clean files created during build process (can be necessary to re-build the documentation):
make clean