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Time Domain Analysis with Plotly

4 min read

Source

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Preamble

In [1]:
import mne
import numpy as np                 # for multi-dimensional containers
import pandas as pd                # for DataFrames
import plotly.graph_objects as go  # for data visualisation
import plotly.io as pio            # to set shahin plot layout

pio.templates['shahin'] = pio.to_templated(go.Figure().update_layout(yaxis=dict(autorange = "reversed"),margin=dict(t=0,r=0,b=40,l=40))).layout.template
pio.templates.default = 'shahin'
pio.renderers.default = "notebook_connected"

Dataset

Download sample data from Mike Cohen.

In [2]:
import warnings
warnings.filterwarnings("ignore")

def load_data(tmin, tmax):
    epochs = mne.io.read_epochs_eeglab('sampleEEGdata.mat').crop(tmin, tmax)
    return epochs

Butterfly Plot of ERP from all sensors (all channels/all trials in time domain)

With MNE.Epochs.to_data_frame()

In [3]:
epochs = load_data(-0.2,1)
values = epochs.to_data_frame()
values = values.groupby("time").mean()
values.head()
Extracting parameters from sampleEEGdata.mat...
99 matching events found
No baseline correction applied
Not setting metadata
0 projection items activated
Ready.
Converting "time" to "<class 'numpy.int64'>"...
Out[3]:
channel Fp1 AF7 AF3 F1 F3 F5 F7 FT7 FC5 FC3 ... CP4 CP2 P2 P4 P6 P8 P10 PO8 PO4 O2
time
-199 -0.891870 -0.701918 -1.706986 -1.024161 -0.976764 -1.014164 -1.002770 -1.402991 -1.496777 -1.314428 ... -1.511028 -1.477739 -1.723046 -1.574034 -1.598564 -1.779448 -0.940347 -1.883280 -1.808410 -2.185663
-195 0.233510 0.506950 -0.445840 0.333534 0.195593 0.212527 0.163632 -0.052681 -0.010986 0.129063 ... 0.125678 0.130709 0.035723 0.130725 0.134243 0.357075 0.358627 -0.038384 -0.170933 -0.259101
-191 -0.507979 -1.007955 -0.986916 -0.328037 -0.593872 -0.573180 -0.562565 -1.356027 -0.634322 -0.383950 ... 0.207923 0.279907 0.127276 0.382046 0.444502 0.647713 0.310199 0.538165 0.387237 0.784565
-188 -0.371972 -0.792418 0.033578 -0.341501 -0.652673 -0.620372 -0.657750 -1.051308 -0.668186 -0.351760 ... -0.173513 -0.230984 -0.433561 -0.238758 -0.352948 -0.364883 0.579337 -0.249470 -0.402957 -0.453058
-184 -0.152894 -0.505432 1.171427 0.201709 -0.251452 -0.286700 -0.341288 -0.404997 -0.500198 -0.006877 ... 0.178264 0.226898 -0.141822 0.106690 0.067396 -0.146313 -0.080451 0.000498 0.049574 0.088095

5 rows × 64 columns

In [4]:
fig = go.Figure(layout=dict(xaxis=dict(title='time'),yaxis=dict(title='voltage')))

for ch in epochs.info['ch_names']:
    fig.add_scatter(x=epochs.times, y=values[ch], name=ch)

fig.show()

With MNE.Epochs.get_data()

In [5]:
epochs = load_data(-0.2,1)
values = epochs.get_data().mean(axis=0)
values = pd.DataFrame(np.transpose(values), columns=epochs.info['ch_names'])
values.head()
Extracting parameters from sampleEEGdata.mat...
99 matching events found
No baseline correction applied
Not setting metadata
0 projection items activated
Ready.
Out[5]:
Fp1 AF7 AF3 F1 F3 F5 F7 FT7 FC5 FC3 ... CP4 CP2 P2 P4 P6 P8 P10 PO8 PO4 O2
0 -8.918701e-07 -7.019182e-07 -1.706986e-06 -1.024161e-06 -9.767636e-07 -1.014164e-06 -1.002770e-06 -1.402991e-06 -1.496777e-06 -1.314428e-06 ... -1.511028e-06 -1.477739e-06 -1.723046e-06 -1.574034e-06 -1.598564e-06 -1.779448e-06 -9.403469e-07 -1.883280e-06 -1.808410e-06 -2.185663e-06
1 2.335097e-07 5.069503e-07 -4.458401e-07 3.335338e-07 1.955928e-07 2.125266e-07 1.636316e-07 -5.268077e-08 -1.098647e-08 1.290634e-07 ... 1.256775e-07 1.307085e-07 3.572303e-08 1.307252e-07 1.342428e-07 3.570746e-07 3.586267e-07 -3.838408e-08 -1.709330e-07 -2.591015e-07
2 -5.079792e-07 -1.007955e-06 -9.869164e-07 -3.280373e-07 -5.938724e-07 -5.731804e-07 -5.625650e-07 -1.356027e-06 -6.343224e-07 -3.839501e-07 ... 2.079225e-07 2.799072e-07 1.272755e-07 3.820456e-07 4.445024e-07 6.477130e-07 3.101987e-07 5.381648e-07 3.872367e-07 7.845649e-07
3 -3.719716e-07 -7.924181e-07 3.357842e-08 -3.415010e-07 -6.526729e-07 -6.203719e-07 -6.577504e-07 -1.051308e-06 -6.681859e-07 -3.517596e-07 ... -1.735130e-07 -2.309843e-07 -4.335609e-07 -2.387584e-07 -3.529476e-07 -3.648834e-07 5.793374e-07 -2.494695e-07 -4.029571e-07 -4.530581e-07
4 -1.528940e-07 -5.054324e-07 1.171427e-06 2.017091e-07 -2.514524e-07 -2.866996e-07 -3.412884e-07 -4.049969e-07 -5.001981e-07 -6.876538e-09 ... 1.782636e-07 2.268977e-07 -1.418217e-07 1.066895e-07 6.739592e-08 -1.463131e-07 -8.045127e-08 4.981451e-10 4.957422e-08 8.809529e-08

5 rows × 64 columns

In [6]:
fig = go.Figure(layout=dict(xaxis=dict(title='time')))

for ch in epochs.info['ch_names']:
    fig.add_scatter(x=epochs.times, y=values[ch], name=ch)

fig.show()