Amplitude eeg
=============

This script demonstrates how to emulate amplitude-integrated EEG with the nssa package.

Author: Tim Hermans (tim-hermans@hotmail.com).

Link to script: `feature_extraction/amplitude_eeg.py <https://gitlab.com/timhermans/nnsa_public/-/blob/main/examples/feature_extraction/amplitude_eeg.py>`_



.. code-block:: python

    
    import numpy as np
    import matplotlib.pyplot as plt
    
    import os
    
    from nnsa import AmplitudeEeg, TimeSeries, EdfReader
    
    plt.close('all')


First define a filepath to an edf file on you PC that you want to read (include the file extension). 



.. code-block:: python

    
    # Specify path to an EDF(+) file.
    filepath = 'C:/data_temp/test.edf'


Load data or create mock-data is file cannot be found. 



.. code-block:: python

    if os.path.exists(filepath):
        print('Reading EDF...')
        with EdfReader(filepath) as r:
            ds = r.read_eeg_dataset()
        eeg_ts = ds.create_bipolar_channel(channel_1='EEG C3', channel_2='EEG C4')
    
        # Get the eeg data as an array.
        eeg = eeg_ts.signal
        fs = eeg_ts.fs
        t = eeg_ts.time
    else:
        # Create mock-data (not representative for any EEG).
        print('Generating mock data...')
        fs = 200
        n = fs*3600
        t = np.arange(n)/fs
        eeg = 300 * \
              np.sin(t*2*np.pi*3) * \
              np.sin(t*2*np.pi*8) * \
              np.sin(t*2*np.pi*13)


Plot the signal. 



.. code-block:: python

    fig, axes = plt.subplots(4, 1, tight_layout=True, sharex='all')
    ax = axes[0]
    ax.plot(t, eeg)
    ax.set_ylabel('EEG')


Various algorithms exists for emulating aEEG. Several of them are implemented in nnsa. You can choose the algorithm when initializing an AmplitdeEeg object. Choose from 'NEAT', 'TW', 'ZHANG'. See the functions in the nnsa.feature_extraction_aeeg module for each of these methods for more information (e.g. compute_aeeg_tw()). 




Let us compare several methods. 



.. code-block:: python

    
    # Loop over methods, compute aEEG and plot.
    for ax, method in zip(axes[1:], ['NEAT', 'TW', 'ZHANG']):
        # Create instance of AmplitudeEeg object and specify parameters.
        aeeg = AmplitudeEeg(method=method)
        aeeg_result = aeeg.process(eeg, fs, verbose=1)
    
        # Plot the envelope.
        aeeg_result.plot(ax=ax, time_scale='seconds')
        ax.set_title(method)