def test_notch_filters(method, filter_length, line_freq, tol):
"""Test notch filters."""
# let's use an ugly, prime sfreq for fun
rng = np.random.RandomState(0)
sfreq = 487
sig_len_secs = 21
t = np.arange(0, int(round(sig_len_secs * sfreq))) / sfreq
# make a "signal"
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a**2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in line_freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
for kind in ('fir', 'iir'):
with pytest.raises(ValueError, match='freqs=None can only be used wi'):
notch_filter(a, sfreq, None, kind)
with catch_logging() as log_file:
b = notch_filter(a,
sfreq,
line_freq,
filter_length,
method=method,
verbose=True)
if line_freq is None:
out = [
line.strip().split(':')[0]
for line in log_file.getvalue().split('\n') if line.startswith(' ')
]
assert len(out) == 4, 'Detected frequencies not logged properly'
out = np.array(out, float)
assert_array_almost_equal(out, line_freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def file_to_nparray(fname,
device,
sfreq=100.0,
verbose=False,
scaling_factor=None,
notch=None):
"""
Create a mne raw instance from csv file.
"""
# get channel names
# in MNE, this means you must config ith two arrays:
# 1) an array of channel names as strings
# 2) corresponding array of channel types. in our case, all channels are type 'eeg'
ch_names = getChannelNames(device)
ch_type = ['eeg'] * len(ch_names)
# add one more channel called 'class_label' as type 'stim'
# this type tells MNE to treat this channel of data as a class label
ch_names.extend(['class_label'])
ch_type.extend(['stim'])
# Read EEG file
data = pd.read_table(fname, header=None, names=ch_names)
# sometimes, rarely, might need to scale the data because your device recorded with an
# incorrect order of magnitude
if scaling_factor is not None:
data.loc[:, :] *= scaling_factor
data.loc[:, 'class_label'] /= scaling_factor
#print data
raw_data = np.array(data[ch_names], dtype=np.float64).T
if notch is not None:
if notch == 60:
print "Applying notch filter at 60Hz"
# notch filter params
notch_filter(raw_data,
Fs=sfreq,
freqs=[60],
filter_length=raw_data.shape[1] - 1,
phase='zero',
fir_window='hamming') # 60Hzin us, 50Hz in Europe
filtered_data = raw_data.astype(int)
# create and populate MNE info structure
info = create_info(ch_names, sfreq=sfreq, ch_types=ch_type)
info['filename'] = fname
# create raw object
return [filtered_data, info]
def fig_gamma_to_hfo(po, pos, sig1, sig2, sig3):
global freq, time_spec, spec_mtrx
ax1 = py.subplot(gs[pos[2]:pos[3], pos[0]:pos[1]])
set_axis(ax1, -0.05, 1.05, letter= po)
tps = [[2, 5], [2, 5],[0.4, 4]]
sigs = [sig1,sig2,sig3]
i=0
dur=10
minute = int(60/dur)
for sig,tp in zip(sigs,tps):
sig = notch_filter(sig, Fs, np.arange(50, 450, 50))
freq_g, time_spec, spec_mtrx1 = spectrogram(sig, Fs, nperseg=Fs*dur, noverlap=0)
cp = np.max(spec_mtrx1[30*dur:65*dur], axis = 0)
cp2 = np.max(spec_mtrx1[80*dur:180*dur], axis = 0)
if i==0:
ax1.plot([0,1], [cp[int(tp[0]*minute)], cp[tp[1]*minute]], '-o', color = 'navy', label='Gamma 30-65 Hz')
ax1.plot([0,1], [cp2[int(tp[0]*minute)], cp2[tp[1]*minute]],'-o', color='indianred', label= 'KX HFO')
else:
ax1.plot([0,1], [cp[int(tp[0]*minute)], cp[tp[1]*minute]],'-o', color = 'navy')
ax1.plot([0,1], [cp2[int(tp[0]*minute)], cp2[tp[1]*minute]],'-o', color='indianred')
i+=1
# ax1.plot([hfo_power[0], hfo_power[30], hfo_power[-1]])
ax1.legend(loc='lower right', bbox_to_anchor=(1.4, 1), ncol=1, frameon = True, fontsize = 12)
py.xticks([0,1], ['bef. KX', 'after KX'])
py.xlim(-0.5, 1.5)
py.yscale('log')
py.ylabel('power $mV^2$')
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
def test_notch_filters():
"""Test notch filters."""
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = ['auto', 'auto', 'auto', 8192, 'auto']
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
with catch_logging() as log_file:
with warnings.catch_warnings(record=True):
b = notch_filter(a, sfreq, lf, fl, method=meth, verbose=True)
if lf is None:
out = log_file.getvalue().split('\n')[:-1]
if len(out) != 2 and len(out) != 3: # force_serial: len(out) == 3
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[-1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_notch_filters():
"""Test notch filters
"""
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, "fft")
assert_raises(ValueError, notch_filter, a, sfreq, None, "iir")
methods = ["spectrum_fit", "spectrum_fit", "fft", "fft", "iir"]
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
with catch_logging() as log_file:
b = notch_filter(a, sfreq, lf, filter_length=fl, method=meth, verbose="INFO")
if lf is None:
out = log_file.getvalue().split("\n")[:-1]
if len(out) != 2:
raise ValueError("Detected frequencies not logged properly")
out = np.fromstring(out[1], sep=", ")
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_notch_filters():
"""Test notch filters."""
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = ['auto', 'auto', 'auto', 8192, 'auto']
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
with catch_logging() as log_file:
with warnings.catch_warnings(record=True):
b = notch_filter(a, sfreq, lf, fl, method=meth, verbose=True)
if lf is None:
out = log_file.getvalue().split('\n')[:-1]
if len(out) != 2 and len(out) != 3: # force_serial: len(out) == 3
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[-1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def notch_filtfilt(data, fs, fs_cut, fs_band, verbose=False):
# Fp1 = fs_cut - fs_band / 2 and Fs2 = fs_cut + fs_band / 2
return notch_filter(x=data,
Fs=fs,
freqs=fs_cut,
trans_bandwidth=fs_band,
verbose=verbose)
def test_filter_auto():
"""Test filter auto parameters."""
# test that our overlap-add filtering doesn't introduce strange
# artifacts (from mne_analyze mailing list 2015/06/25)
N = 300
sfreq = 100.
lp = 10.
sine_freq = 1.
x = np.ones(N)
t = np.arange(N) / sfreq
x += np.sin(2 * np.pi * sine_freq * t)
x_orig = x.copy()
for pad in ('reflect_limited', 'reflect', 'edge'):
for fir_design in ('firwin2', 'firwin'):
kwargs = dict(fir_design=fir_design, pad=pad)
x = x_orig.copy()
x_filt = filter_data(x, sfreq, None, lp, **kwargs)
assert_array_equal(x, x_orig)
n_edge = 10
assert_allclose(x[n_edge:-n_edge],
x_filt[n_edge:-n_edge],
atol=1e-2)
assert_array_equal(x_filt,
filter_data(x, sfreq, None, lp, None, **kwargs))
assert_array_equal(x, x_orig)
assert_array_equal(x_filt, filter_data(x, sfreq, None, lp,
**kwargs))
assert_array_equal(x, x_orig)
assert_array_equal(
x_filt, filter_data(x, sfreq, None, lp, copy=False, **kwargs))
assert_array_equal(x, x_filt)
# degenerate conditions
pytest.raises(ValueError, filter_data, x, -sfreq, 1, 10)
pytest.raises(ValueError, filter_data, x, sfreq, 1, sfreq * 0.75)
with pytest.raises(ValueError, match='Data to be filtered must be real'):
filter_data(x.astype(np.float32), sfreq, None, 10)
with pytest.raises(ValueError, match='Data to be filtered must be real'):
filter_data([1j], 1000., None, 40.)
with pytest.raises(TypeError, match='instance of ndarray'):
filter_data('foo', 1000., None, 40.)
# gh-10258
raw = RawArray([[0.]], create_info(1, 1000., 'eeg'))
with pytest.raises(TypeError, match=r'.*copy\(\)\.filter\(\.\.\.\)` in.*'):
filter_data(raw, 1000., None, 40.)
with pytest.raises(TypeError, match=r'.*copy\(\)\.notch_filter\(\.\.\..*'):
notch_filter(raw, 1000., [60.])
def fig_power(po,
pos,
sig_loc,
start=400,
stop=405,
Title='',
asteriks=[90, 200]):
global freq
from mpl_toolkits.axes_grid.inset_locator import inset_axes
ax1 = py.subplot(gs[pos[2]:pos[3], pos[0]:pos[1]])
set_axis(ax1, -0.1, 1.05, letter=po)
labels = ['Olf. bulb', 'Thalamus', 'Visual ctrx']
for i in range(2, -1, -1):
sig_loc[i] = notch_filter(sig_loc[i], Fs, np.arange(50, 450, 50))
freq, sp = welch(sig_loc[i], Fs, nperseg=1 * Fs)
ax1.plot(freq, sp, lw=2, label=labels[i])
py.legend(loc=2, fontsize=15)
ax1.text(asteriks[0], asteriks[1], '*', fontsize=20)
ax1.text(160, 440, '?', fontsize=20)
py.xlim(0, 260)
py.ylim(0, 500)
py.ylabel('power ($mv^2$)')
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
py.xlabel('Frequency (Hz)')
if po != 'B3':
inset_axes = inset_axes(ax1, width="23%", height=1.0, loc=1)
for n in range(3, sig_loc.shape[0]):
sig_loc[n] = notch_filter(sig_loc[n], Fs, np.arange(50, 450, 50))
freq, sp = welch(sig_loc[n], Fs, nperseg=10 * Fs)
py.plot(freq, sp, lw=0.7, color='green')
py.ylim(0, 220)
py.xlim(0, 260)
py.xticks(fontsize=11)
py.yticks(fontsize=11)
# py.ylim(.1, 10e4)
# py.yscale('log')
# py.text(200,100, 'Olf. bulb propofol')
py.xlabel('Frequency (Hz)')
if po == 'B1':
ax1.legend(loc='lower right',
bbox_to_anchor=(1.2, 1.1),
ncol=3,
frameon=True,
fontsize=15)
def pilot_plot():
py.figure()
import seaborn as sns
clrs = sns.color_palette('husl', n_colors=50)
for i in range(0,32,1):
cat3_order[i] = notch_filter(cat3_order[i], Fs, np.arange(50, 350, 50))
freq, sp = welch(cat3_order[i], Fs, nperseg=10*Fs)
py.plot(freq[50:3000], sp[50:3000], label = str(i), color = clrs[i])
py.legend()
def notch_filter(dat, Fs=250, freqs=60):
# apply notch filter only on 60 Hz, default setting of OpenBCI
# sampling rate is 250 Hz
# `dat` is an array
# https://www.martinos.org/mne/stable/generated/mne.filter.notch_filter.html
# `notch_filter` can be a class method in data
# https://www.martinos.org/mne/stable/generated/mne.io.RawArray.html?highlight=notch_filter#mne.io.RawArray.notch_filter
# e.g.: dat.notch_filter(60)
return mf.notch_filter(dat, Fs, freqs)
def run(x, fs, n_jobs):
plt.figure()
plt.plot(x.T)
plt.figure()
plt.psd(x, Fs=fs)
x2 = notch_filter(x, fs, np.arange(60, 241, 60), notch_widths=5, filter_length='auto', copy=True, n_jobs=n_jobs)
plt.figure()
plt.plot(x2.T)
plt.figure()
plt.psd(x2, Fs=fs)
plt.show()
def bandstop_filter(X, y, sfreq, bandwidth, freqs_to_notch):
"""Apply a band-stop filter with desired bandwidth at the desired frequency
position.
Suggested e.g. in [1]_ and [2]_
Parameters
----------
X : torch.Tensor
EEG input example or batch.
y : torch.Tensor
EEG labels for the example or batch.
sfreq : float
Sampling frequency of the signals to be filtered.
bandwidth : float
Bandwidth of the filter, i.e. distance between the low and high cut
frequencies.
freqs_to_notch : array-like | None
Array of floats of size ``(batch_size,)`` containing the center of the
frequency band to filter out for each sample in the batch. Frequencies
should be greater than ``bandwidth/2 + transition`` and lower than
``sfreq/2 - bandwidth/2 - transition`` (where ``transition = 1 Hz``).
Returns
-------
torch.Tensor
Transformed inputs.
torch.Tensor
Transformed labels.
References
----------
.. [1] Cheng, J. Y., Goh, H., Dogrusoz, K., Tuzel, O., & Azemi, E. (2020).
Subject-aware contrastive learning for biosignals. arXiv preprint
arXiv:2007.04871.
.. [2] Mohsenvand, M. N., Izadi, M. R., & Maes, P. (2020). Contrastive
Representation Learning for Electroencephalogram Classification. In
Machine Learning for Health (pp. 238-253). PMLR.
"""
if bandwidth == 0:
return X, y
transformed_X = X.clone()
for c, (sample, notched_freq) in enumerate(
zip(transformed_X, freqs_to_notch)):
sample = sample.cpu().numpy().astype(np.float64)
transformed_X[c] = torch.as_tensor(notch_filter(
sample,
Fs=sfreq,
freqs=notched_freq,
method='fir',
notch_widths=bandwidth,
verbose=False
))
return transformed_X, y
def fig_power(po, pos, sig_loc, start=400, stop = 405, Title = '', asteriks=[0,0]):
global freq
from mpl_toolkits.axes_grid.inset_locator import inset_axes
ax1 = py.subplot(gs[pos[2]:pos[3], pos[0]:pos[1]])
py.title(Title, fontsize=15)
set_axis(ax1, -0.1, 1.05, letter= po)
labels= ['Olf. bulb', 'Thalamus', 'Visual ctrx']
for i in range(2,-1,-1):
sig_loc[i] = notch_filter(sig_loc[i], Fs, np.arange(50, 450, 50))
freq, sp = welch(sig_loc[i], Fs, nperseg = 1*Fs)
ax1.plot(freq, sp, lw=4, label=labels[i])
# ax1.text(asteriks[0], asteriks[1] , '*', fontsize=20)
py.arrow(asteriks[0], asteriks[1], 0, -12, length_includes_head=True, clip_on = False,
head_width=2, head_length=4)
# py.ylim(.1, 10e4)
py.ylim(0,220)
py.xlim(0, 155)
py.ylabel('power $mV^2$')
ax1.spines['right'].set_visible(False)
ax1.spines['top'].set_visible(False)
py.xlabel('Frequency (Hz)')
if po!='B1':
inset_axes = inset_axes(ax1, width="23%", height=1.0, loc=1)
for n in range(3,sig_loc.shape[0]):
sig_loc[n] = notch_filter(sig_loc[n], Fs, np.arange(50, 450, 50))
freq, sp = welch(sig_loc[n], Fs, nperseg = 1*Fs)
py.plot(freq, sp, lw=2, color='green')
py.ylim(0,220)
py.xlim(0,155)
py.xticks(fontsize=11)
py.yticks(fontsize=11)
# py.ylim(.1, 10e4)
# py.yscale('log')
# py.text(200,100, 'Olf. bulb propofol')
py.xlabel('Frequency (Hz)')
if po=='B1':
ket = mpatches.Patch(color='green', label='Olf. bulb')
kx = mpatches.Patch(color='orange', label='Thalamus LGN')
gam = mpatches.Patch(color='blue', label='Visual cortex')
ax1.legend(loc='lower right', bbox_to_anchor=(1.2, .7), handles=[ket,kx,gam],
ncol=1, frameon = True, fontsize = 15)
def process(self, data):
if self.type == 'low-pass':
return low_pass_filter(data, **self.params)
elif self.type == 'high-pass':
return high_pass_filter(data, **self.params)
elif self.type == 'band-pass':
return band_pass_filter(data, **self.params)
elif self.type == 'band-stop':
return band_stop_filter(data, **self.params)
elif self.type == 'notch':
return notch_filter(data, **self.params)
else:
raise ValueError('Unsupported filter type: {}'.format(self.type))
def test_notch_filters():
"""Test notch filters
"""
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a**2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
if lf is None:
set_log_file(log_file, overwrite=True)
b = notch_filter(a,
sfreq,
lf,
filter_length=fl,
method=meth,
verbose='INFO')
if lf is None:
set_log_file()
with open(log_file) as fid:
out = fid.readlines()
if len(out) != 2:
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def process(self, data):
# fix for new MNE requirements
import numpy as np
data = np.asarray(data, dtype=np.float64)
if self.type == 'low-pass':
return low_pass_filter(data, **self.params)
elif self.type == 'high-pass':
return high_pass_filter(data, **self.params)
elif self.type == 'band-pass':
return band_pass_filter(data, **self.params)
elif self.type == 'band-stop':
return band_stop_filter(data, **self.params)
elif self.type == 'notch':
return notch_filter(data, **self.params)
else:
raise ValueError('Unsupported filter type: {}'.format(self.type))
def process(self, data):
# fix for new MNE requirements
import numpy as np
data = np.asarray(data, dtype=np.float64)
if self.type == 'low-pass':
return low_pass_filter(data, **self.params)
elif self.type == 'high-pass':
return high_pass_filter(data, **self.params)
elif self.type == 'band-pass':
return band_pass_filter(data, **self.params)
elif self.type == 'band-stop':
return band_stop_filter(data, **self.params)
elif self.type == 'notch':
return notch_filter(data, **self.params)
else:
raise ValueError('Unsupported filter type: {}'.format(self.type))
def test_notch_filters():
"""Test notch filters
"""
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
# let's use an ugly, prime sfreq for fun
sfreq = 487.0
sig_len_secs = 20
t = np.arange(0, int(sig_len_secs * sfreq)) / sfreq
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(int(sig_len_secs * sfreq))
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, sfreq, None, 'fft')
assert_raises(ValueError, notch_filter, a, sfreq, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
if lf is None:
set_log_file(log_file, overwrite=True)
b = notch_filter(a, sfreq, lf, filter_length=fl, method=meth,
verbose='INFO')
if lf is None:
set_log_file()
with open(log_file) as fid:
out = fid.readlines()
if len(out) != 2:
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(sum_squared(b) / b.size)
assert_almost_equal(new_power, orig_power, tol)
def test_notch_filters():
"""Test notch filters
"""
# let's use an ugly, prime Fs for fun
Fs = 487.0
sig_len_secs = 20
t = np.arange(0, sig_len_secs * Fs) / Fs
freqs = np.arange(60, 241, 60)
# make a "signal"
rng = np.random.RandomState(0)
a = rng.randn(sig_len_secs * Fs)
orig_power = np.sqrt(np.mean(a ** 2))
# make line noise
a += np.sum([np.sin(2 * np.pi * f * t) for f in freqs], axis=0)
# only allow None line_freqs with 'spectrum_fit' mode
assert_raises(ValueError, notch_filter, a, Fs, None, 'fft')
assert_raises(ValueError, notch_filter, a, Fs, None, 'iir')
methods = ['spectrum_fit', 'spectrum_fit', 'fft', 'fft', 'iir']
filter_lengths = [None, None, None, 8192, None]
line_freqs = [None, freqs, freqs, freqs, freqs]
tols = [2, 1, 1, 1]
for meth, lf, fl, tol in zip(methods, line_freqs, filter_lengths, tols):
if lf is None:
set_log_file(log_file)
b = notch_filter(a, Fs, lf, filter_length=fl, method=meth,
verbose='INFO')
if lf is None:
set_log_file()
out = open(log_file).readlines()
if len(out) != 2:
raise ValueError('Detected frequencies not logged properly')
out = np.fromstring(out[1], sep=', ')
assert_array_almost_equal(out, freqs)
new_power = np.sqrt(np.mean(b ** 2))
assert_almost_equal(new_power, orig_power, tol)
def segment_EEG(EEG,
epoch_time,
Fs,
newFs,
NW,
amplitude_thres=500,
notch_freq=None,
bandpass_freq=None,
start_end_remove_window_num=0,
to_remove_mean=False,
n_jobs=1,
subject_file_name=''): #
"""Segment EEG signals.
"""
std_thres1 = 0.02
std_thres2 = 0.1
flat_seconds = 2
if to_remove_mean:
EEG = EEG - np.mean(EEG, axis=1, keepdims=True)
epoch_size = int(round(epoch_time * Fs))
flat_length = int(round(flat_seconds * Fs))
## filtering
EEG = notch_filter(EEG, Fs, notch_freq, n_jobs=-1,
verbose='error') # (#window, #ch, epoch_size+2padding)
EEG = filter_data(detrend(EEG, axis=1),
Fs,
bandpass_freq[0],
bandpass_freq[1],
n_jobs=-1,
verbose='error')
## segment
start_ids = np.arange(0, EEG.shape[1] - epoch_size + 1, epoch_size)
if start_end_remove_window_num > 0:
start_ids = start_ids[
start_end_remove_window_num:-start_end_remove_window_num]
seg_masks = [seg_mask_explanation[0]] * len(start_ids)
EEG_segs = EEG[:,
list(map(lambda x: np.arange(x, x + epoch_size), start_ids)
)].transpose(1, 0,
2) # (#window, #ch, epoch_size+2padding)
## resampling
mne_epochs = mne.EpochsArray(detrend(EEG_segs, axis=2),
mne.create_info(ch_names=list(
map(str, range(EEG_segs.shape[1]))),
sfreq=Fs,
ch_types='eeg'),
verbose=False)
if newFs != Fs:
Fs = newFs
mne_epochs.resample(Fs, n_jobs=n_jobs)
EEG_segs = mne_epochs.get_data()
epoch_size = int(round(epoch_time * Fs))
flat_length = int(round(flat_seconds * Fs))
## calculate spectrogram
BW = NW * 2. / epoch_time
specs, freq = mne.time_frequency.psd_multitaper(mne_epochs,
fmin=bandpass_freq[0],
fmax=bandpass_freq[1],
adaptive=False,
low_bias=False,
n_jobs=n_jobs,
verbose='ERROR',
bandwidth=BW,
normalization='full')
## mark artifacts
# nan in signal
nan2d = np.any(np.isnan(EEG_segs), axis=2)
nan1d = np.where(np.any(nan2d, axis=1))[0]
for i in nan1d:
seg_masks[i] = seg_mask_explanation[4]
# flat signal
short_segs = EEG_segs.reshape(EEG_segs.shape[0], EEG_segs.shape[1],
EEG_segs.shape[2] // flat_length,
flat_length)
flat2d = np.any(detrend(short_segs, axis=3).std(axis=3) <= std_thres1,
axis=2)
flat2d = np.logical_or(flat2d, np.std(EEG_segs, axis=2) <= std_thres2)
flat1d = np.where(np.any(flat2d, axis=1))[0]
for i in flat1d:
seg_masks[i] = seg_mask_explanation[6]
# big amplitude
amplitude_large2d = np.any(np.abs(EEG_segs) > amplitude_thres, axis=2)
amplitude_large1d = np.where(np.any(amplitude_large2d, axis=1))[0]
for i in amplitude_large1d:
seg_masks[i] = seg_mask_explanation[5]
return EEG_segs, start_ids, seg_masks, specs, freq
# The averages for each conditions are computed.
evoked_std = epochs_standard.average()
evoked_dev = epochs_deviant.average()
del epochs_standard, epochs_deviant
###############################################################################
# Typical preprocessing step is the removal of power line artifact (50 Hz or
# 60 Hz). Here we notch filter the data at 60, 120 and 180 to remove the
# original 60 Hz artifact and the harmonics. Normally this would be done to
# raw data (with :func:`mne.io.Raw.filter`), but to reduce memory consumption
# of this tutorial, we do it at evoked stage.
if use_precomputed:
sfreq = evoked_std.info['sfreq']
notches = [60, 120, 180]
for evoked in (evoked_std, evoked_dev):
evoked.data[:] = notch_filter(evoked.data, sfreq, notches)
evoked.data[:] = filter_data(evoked_std.data, sfreq, None, 100)
###############################################################################
# Here we plot the ERF of standard and deviant conditions. In both conditions
# we can see the P50 and N100 responses. The mismatch negativity is visible
# only in the deviant condition around 100-200 ms. P200 is also visible around
# 170 ms in both conditions but much stronger in the standard condition. P300
# is visible in deviant condition only (decision making in preparation of the
# button press). You can view the topographies from a certain time span by
# painting an area with clicking and holding the left mouse button.
evoked_std.plot(window_title='Standard', gfp=True)
evoked_dev.plot(window_title='Deviant', gfp=True)
###############################################################################
# Show activations as topography figures.
evoked_std = epochs_standard.average()
evoked_dev = epochs_deviant.average()
del epochs_standard, epochs_deviant
###############################################################################
# Typical preprocessing step is the removal of power line artifact (50 Hz or
# 60 Hz). Here we notch filter the data at 60, 120 and 180 to remove the
# original 60 Hz artifact and the harmonics. Normally this would be done to
# raw data (with :func:`mne.io.Raw.filter`), but to reduce memory consumption
# of this tutorial, we do it at evoked stage.
if use_precomputed:
sfreq = evoked_std.info['sfreq']
nchan = evoked_std.info['nchan']
notches = [60, 120, 180]
for ch_idx in range(nchan):
evoked_std.data[ch_idx] = notch_filter(evoked_std.data[ch_idx], sfreq,
notches, verbose='ERROR')
evoked_dev.data[ch_idx] = notch_filter(evoked_dev.data[ch_idx], sfreq,
notches, verbose='ERROR')
evoked_std.data[ch_idx] = low_pass_filter(evoked_std.data[ch_idx],
sfreq, 100, verbose='ERROR')
evoked_dev.data[ch_idx] = low_pass_filter(evoked_dev.data[ch_idx],
sfreq, 100, verbose='ERROR')
###############################################################################
# Here we plot the ERF of standard and deviant conditions. In both conditions
# we can see the P50 and N100 responses. The mismatch negativity is visible
# only in the deviant condition around 100-200 ms. P200 is also visible around
# 170 ms in both conditions but much stronger in the standard condition. P300
# is visible in deviant condition only (decision making in preparation of the
# button press). You can view the topographies from a certain time span by
# painting an area with clicking and holding the left mouse button.
evoked_std = epochs_standard.average()
evoked_dev = epochs_deviant.average()
del epochs_standard, epochs_deviant
###############################################################################
# Typical preprocessing step is the removal of power line artifact (50 Hz or
# 60 Hz). Here we notch filter the data at 60, 120 and 180 to remove the
# original 60 Hz artifact and the harmonics. Normally this would be done to
# raw data (with :func:`mne.io.Raw.filter`), but to reduce memory consumption
# of this tutorial, we do it at evoked stage.
if use_precomputed:
sfreq = evoked_std.info['sfreq']
nchan = evoked_std.info['nchan']
notches = [60, 120, 180]
for ch_idx in range(nchan):
evoked_std.data[ch_idx] = notch_filter(evoked_std.data[ch_idx], sfreq,
notches, verbose='ERROR')
evoked_dev.data[ch_idx] = notch_filter(evoked_dev.data[ch_idx], sfreq,
notches, verbose='ERROR')
evoked_std.data[ch_idx] = low_pass_filter(evoked_std.data[ch_idx],
sfreq, 100, verbose='ERROR')
evoked_dev.data[ch_idx] = low_pass_filter(evoked_dev.data[ch_idx],
sfreq, 100, verbose='ERROR')
###############################################################################
# Here we plot the ERF of standard and deviant conditions. In both conditions
# we can see the P50 and N100 responses. The mismatch negativity is visible
# only in the deviant condition around 100-200 ms. P200 is also visible around
# 170 ms in both conditions but much stronger in the standard condition. P300
# is visible in deviant condition only (decision making in preparation of the
# button press). You can view the topographies from a certain time span by
# painting an area with clicking and holding the left mouse button.
# The averages for each conditions are computed.
evoked_std = epochs_standard.average()
evoked_dev = epochs_deviant.average()
del epochs_standard, epochs_deviant
###############################################################################
# Typical preprocessing step is the removal of power line artifact (50 Hz or
# 60 Hz). Here we notch filter the data at 60, 120 and 180 to remove the
# original 60 Hz artifact and the harmonics. Normally this would be done to
# raw data (with :func:`mne.io.Raw.filter`), but to reduce memory consumption
# of this tutorial, we do it at evoked stage.
if use_precomputed:
sfreq = evoked_std.info['sfreq']
notches = [60, 120, 180]
for evoked in (evoked_std, evoked_dev):
evoked.data[:] = notch_filter(evoked.data, sfreq, notches)
evoked.data[:] = filter_data(evoked_std.data, sfreq, None, 100)
###############################################################################
# Here we plot the ERF of standard and deviant conditions. In both conditions
# we can see the P50 and N100 responses. The mismatch negativity is visible
# only in the deviant condition around 100-200 ms. P200 is also visible around
# 170 ms in both conditions but much stronger in the standard condition. P300
# is visible in deviant condition only (decision making in preparation of the
# button press). You can view the topographies from a certain time span by
# painting an area with clicking and holding the left mouse button.
evoked_std.plot(window_title='Standard', gfp=True)
evoked_dev.plot(window_title='Deviant', gfp=True)
###############################################################################
# Show activations as topography figures.