pyecog: A Python repository from mikailweston

PyECoG

This module is for detecting epileptiform activity from single channel intracranial EEG (or ECoG) recordings. Currently under heavy construction!

http://jcornford.github.io/pyecog/

Recommended installation procedure:

Install Anaconda. Choose the Python 3, 64-bit version for your operating system (Linux, Windows, or OS X). You can also download python 2, but just make sure your python version for the environment is 3 (next step).

Make a new conda environment and install dependencies for pyecog. To do this open a terminal windows (on Windows, a cmd prompt) and type or copy:

conda create --name pyecog_env python=3.5 jupyter=1 scipy=0.18.1 numpy=1.11.2 scikit-learn=0.18.1 pandas=0.19.2 matplotlib=2 seaborn=0.7.1 h5py=2.6.0 xlrd=1 pyqt=5.6 numba=0.37.0
source activate pyecog_env  # or just "activate pyecog_env" if you are on windows
pip install pyqtgraph==0.10

Note you do not have to make a virtual environment if you will not be using python for anything else. See below.

Click on the green "clone or download" button on the top right of this page. Download the zip file and extract it somewhere on your computer. Navigate to the extracted folder in terminal/cmd line or open a terminal/cmd window at the extracted folder. To do this quickly on windows shift+right click on the folder and select "open a command window here".
Finally, you are ready to run. First activate your python environment with the required dependencies for the Pyecog gui:

activate pyecog_env  # or  "source activate pyecog_env" if on a mac

And then run the gui with:

python start.py

For running without an environment:

Replace step 2 with

   conda install jupyter=1 scipy=0.18.1 numpy=1.11.2 scikit-learn=0.17.1 pandas=0.19.2 matplotlib=2 seaborn=0.7.1 h5py=2.6.0 xlrd=1 pyqt=5.6
   pip install pyqtgraph==0.10

And then do not activate an enviroment before

python start.py

Installing with pip:

This is for when the software is more developed.

1 . After step 2 above, run:

pip install pyecog

Ignore step 3. Open command window and activate the pyecog_env environment if you are using it. Type "pyecog" into the prompt. The Gui should load.

How to use - this needs to be updated

note, some gui elements not implemented (open in jupyter notebook and low pass filter)
[Loading ndf files] (https://github.com/jcornford/pyecog/blob/master/documentation_notebooks/demo_loading_ndfs_notebook.ipynb)

Repository contents: