Note
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EEG Artifact: ATAR and ICA¶
In this example we compare ICA with ATAR
import numpy as np
import matplotlib.pyplot as plt
import warnings
warnings.filterwarnings("ignore")
import spkit as sp
print('spkit version :', sp.__version__)
spkit version : 0.0.9.7
Load and filter EEG Signal¶
# Load sample EEG Data ( 16 sec, 128 smapling rate, 14 channel)
# Filter signal (with IIR highpass 0.5Hz)
X, fs, ch_names = sp.data.eeg_sample_14ch()
Xf = sp.filter_X(X.copy(),fs=128.0, band=[0.5], btype='highpass',ftype='SOS')
print(Xf.shape)
(2048, 14)
ATAR - three modes¶
XR1 = sp.eeg.ATAR(Xf.copy(),verbose=1,OptMode='soft',winsize=128)
XR2 = sp.eeg.ATAR(Xf.copy(),verbose=1,OptMode='elim',winsize=128)
XR3 = sp.eeg.ATAR(Xf.copy(),verbose=1,OptMode='linAtten',winsize=128)
Artifact removal using ICA¶
XR4 = sp.eeg.ICA_filtering(Xf.copy(),winsize=128, ICA_method='extended-infomax',kur_thr=2,corr_thr=0.8,
AF_ch_index = [0,13] ,F_ch_index=[1,2,11,12])
XR5 = sp.eeg.ICA_filtering(Xf.copy(),winsize=128, ICA_method='infomax',kur_thr=2,corr_thr=0.8,
AF_ch_index = [0,13] ,F_ch_index=[1,2,11,12])
XR6 = sp.eeg.ICA_filtering(Xf.copy(),winsize=128, ICA_method='picard',kur_thr=2,corr_thr=0.8,
AF_ch_index = [0,13] ,F_ch_index=[1,2,11,12])
ICA Artifact Removal : extended-infomax
3%|▓ |2112\65|
6%|▓▓▓ |2112\129|
9%|▓▓▓▓ |2112\193|
12%|▓▓▓▓▓▓ |2112\257|
15%|▓▓▓▓▓▓▓ |2112\321|
18%|▓▓▓▓▓▓▓▓▓ |2112\385|
21%|▓▓▓▓▓▓▓▓▓▓ |2112\449|
24%|▓▓▓▓▓▓▓▓▓▓▓▓ |2112\513|
27%|▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\577|
30%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\641|
33%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\705|
36%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\769|
39%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\833|
42%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\897|
45%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\961|
48%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1025|
51%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1089|
54%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1153|
57%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1217|
60%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1281|
63%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1345|
66%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1409|
69%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1473|
72%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1537|
75%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1601|
78%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1665|
81%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1729|
84%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1793|
87%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1857|
90%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1921|
93%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1985|
97%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\2049|
100%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓|2112\2113|
Done!
ICA Artifact Removal : infomax
3%|▓ |2112\65|
6%|▓▓▓ |2112\129|
9%|▓▓▓▓ |2112\193|
12%|▓▓▓▓▓▓ |2112\257|
15%|▓▓▓▓▓▓▓ |2112\321|
18%|▓▓▓▓▓▓▓▓▓ |2112\385|
21%|▓▓▓▓▓▓▓▓▓▓ |2112\449|
24%|▓▓▓▓▓▓▓▓▓▓▓▓ |2112\513|
27%|▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\577|
30%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\641|
33%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\705|
36%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\769|
39%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\833|
42%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\897|
45%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\961|
48%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1025|
51%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1089|
54%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1153|
57%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1217|
60%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1281|
63%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1345|
66%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1409|
69%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1473|
72%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1537|
75%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1601|
78%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1665|
81%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1729|
84%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1793|
87%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1857|
90%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1921|
93%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1985|
97%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\2049|
100%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓|2112\2113|
Done!
ICA Artifact Removal : picard
3%|▓ |2112\65|
6%|▓▓▓ |2112\129|
9%|▓▓▓▓ |2112\193|
12%|▓▓▓▓▓▓ |2112\257|
15%|▓▓▓▓▓▓▓ |2112\321|
18%|▓▓▓▓▓▓▓▓▓ |2112\385|
21%|▓▓▓▓▓▓▓▓▓▓ |2112\449|
24%|▓▓▓▓▓▓▓▓▓▓▓▓ |2112\513|
27%|▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\577|
30%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\641|
33%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\705|
36%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\769|
39%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\833|
42%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\897|
45%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\961|
48%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1025|
51%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1089|
54%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1153|
57%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1217|
60%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1281|
63%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1345|
66%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1409|
69%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1473|
72%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1537|
75%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1601|
78%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1665|
81%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1729|
84%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1793|
87%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1857|
90%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1921|
93%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\1985|
97%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ |2112\2049|
100%|▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓|2112\2113|
Done!
Plots of Corrections¶
sep=150
t = np.arange(Xf.shape[0])/fs
plt.figure(figsize=(12,8))
plt.subplot(321)
plt.plot(t,XR1+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ATAR: Soft-thresholding')
plt.title('ATAR')
plt.subplot(322)
plt.plot(t,XR4+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ICA: extended-infomax')
plt.title('ICA Based')
plt.subplot(323)
plt.plot(t,XR2+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ATAR: Elimination')
plt.subplot(324)
plt.plot(t,XR5+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ICA: infomax')
plt.subplot(325)
plt.plot(t,XR3+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ATAR: Linear Atten.')
plt.subplot(326)
plt.plot(t,XR6+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ICA: picard')
plt.subplots_adjust(wspace=0.1,hspace=0.15)
plt.suptitle('Correction using : ATAR and ICA')
plt.show()
Plots of Residuals¶
sep=150
t = np.arange(Xf.shape[0])/fs
plt.figure(figsize=(12,8))
plt.subplot(321)
plt.plot(t,Xf-XR1+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ATAR: Soft-thresholding')
plt.title('ATAR')
plt.subplot(322)
plt.plot(t,Xf-XR4+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ICA: extended-infomax')
plt.title('ICA Based')
plt.subplot(323)
plt.plot(t,Xf-XR2+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ATAR: Elimination')
plt.subplot(324)
plt.plot(t,Xf-XR5+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ICA: infomax')
plt.subplot(325)
plt.plot(t,Xf-XR3+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ATAR: Linear Atten.')
plt.subplot(326)
plt.plot(t,Xf-XR6+np.arange(14)*sep)
plt.xlim([t[0],t[-1]])
plt.yticks([])
plt.ylabel('ICA: picard')
plt.subplots_adjust(wspace=0.1,hspace=0.15)
plt.suptitle('Residual: Xf-XR (removed)')
plt.show()
Total running time of the script: (0 minutes 9.201 seconds)
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