def iir_noise_filter(name, df, current_col):
#extracting sampling rate from parameter file
parafile = name + '-parameters.txt'
try:
params = read_csv(parafile, delim_whitespace=True, engine='python', names=['0','1','2','3'], index_col=0)
except:
print('Cannot find parameter file')
samplerate = params['2']['Samplerate']
Samplingrates = {"2.5Hz":2.5, "5Hz":5.0, "10Hz":10.0, "15Hz":15.0,
"25Hz":25.0, "30Hz":30.0, "50Hz":50.0, "60Hz":60.0,
"100Hz":100.0, "500Hz":500.0, "1KHz":1000.0, "2KHz":2000.0,
"3.75KHz":3750.0, "7.5KHz":7500.0, "15KHz":1500.0, "30KHz":30000.0}
samplerate = Samplingrates[samplerate]
#constructing IIR notch filters
fs = samplerate # Sample frequency (Hz)
f0 = 60.0 # Frequency to be removed from signal (Hz)
Q = 2.0 # Quality factor
# Design notch filter
b, a = signal.iirnotch(f0, Q, fs)
c, d = signal.iirnotch(f0*2, Q, fs)
e, f = signal.iirnotch(f0*4, Q, fs)
g, h = signal.iirnotch(f0*5, Q, fs)
i, j = signal.iirnotch(f0*6, Q, fs)
#apply filters
yf1 = signal.filtfilt(b,a,df[current_col]) #60Hz filter
yf2 = signal.filtfilt(c,d,yf1) #120Hz filter
yf3 = signal.filtfilt(e,f,yf2) #240Hz filter
yf4 = signal.filtfilt(g,h,yf3) #300Hz filter
yf5 = signal.filtfilt(i,j,yf4) #360Hz filter
return yf5
def notch(x, Q):
fs = 10000
f0 = 50
w0 = f0 / (fs / 2)
b, a = scisig.iirnotch(w0, Q)
y = scisig.filtfilt(b, a, x)
return y
def notch_filter(data,f0,Q,Fs):
# f0 = Frequency to be removed from signal (Hz)
# Q = Quality factor
w0 = f0/(Fs/2) # Normalized Frequency
# Design notch filter
b, a = signal.iirnotch(w0, Q)
zi = signal.lfilter_zi(b, a)
y = signal.filtfilt(b, a, data)
return y
def refresh_notch_filter(self, f=50, enable=True):
if enable:
w0 = f / (self.fs / 2)
self.bNotch, self.aNotch = signal.iirnotch(w0, 1)
else:
self.bNotch = np.array([1])
self.aNotch = np.array([1])
self.xbufNotch = [0 for i in range(len(self.bNotch) - 1)]
self.ybufNotch = [0 for i in range(len(self.aNotch) - 1)]
def read_data(data,
dataset_path,
M=25,
each_lead_time=2.5,
num_samples=10000,
num_leads=12,
images_per_record=10,
power_line_freq=50,
bandwidth=10):
'''
num_samples = 10000 # no of samples to read from each record
num_leads = 12 # 12 leads out of given 15 to be choosen
sampling_freq = 1000 # 1000 Hz
each_lead_time = 2.5 # 2.5 seconds
M = 25 # mov avg filter
images_per_record = 10
power_line_freq = 50
'''
fields = []
signals = []
Q = power_line_freq / bandwidth
for i in data:
sig, f = wfdb.rdsamp(dataset_path + i[:-1],
channels=[x for x in range(num_leads)],
sampfrom=0,
sampto=num_samples)
sampling_freq = f['fs']
b, a = iirnotch(power_line_freq, Q, sampling_freq)
s = np.zeros((num_samples - M + 1, num_leads))
for leads in range(num_leads):
sig[:, leads] = lfilter(b, a, sig[:, leads])
s[:, leads] = np.convolve(sig[:, leads],
np.ones((M, )) / M,
mode='valid')
if (f['comments'][4] == 'Reason for admission: Myocardial infarction'
or f['comments'][4]
== 'Reason for admission: Healthy control'):
for copies in range(images_per_record):
if (each_lead_time * sampling_freq * (copies + 1)) < len(s):
s_temp = s[int(each_lead_time * sampling_freq * copies):
int(each_lead_time * sampling_freq *
(copies +
1))] # 2.5 sec interval is selected
s_temp = s_temp - s_temp.mean(
axis=0) # remove baseline drift
signals += [s_temp]
fields += [f]
print("Dataset Read!!!")
return signals, fields
def notch_pass_filter(
data,
center,
interval=2,
fs=1000
): # interval = 대역폭 (좌우로 얼마나 지울지) sharp 하게 적용하자, 차라리 for 문으로 49,50,51을 모두 sharp하게 지우자
b, a = signal.iirnotch(center, center / interval, fs)
filtered_data = signal.lfilter(b, a, data)
return filtered_data
def notch(data, notch_Hz, bandwidth):
nyquist_Hz = data.samplerate_Hz / 2
w0 = notch_Hz / nyquist_Hz
quality = w0 / bandwidth
b, a = signal.iirnotch(w0, quality)
filtereddata = signal.lfilter(b, a, data.values)
return Timeseries(filtereddata,
timestamps=data.times,
samplerate_Hz=data.samplerate_Hz,
units=data.units)
def notch_filter(y, fs):
f0 = random.uniform(30.0, 2000)
print(f0)
w0 = f0 / (fs / 2)
Q = 0.01
b, a = signal.iirnotch(w0, Q)
# y = signal.filtfilt(b, a, y)
y = signal.lfilter(b, a, y)
return y
def notch_filter(data, cutoff, fs):
'''
陷波滤波器，cutoff为被限制频率，值为0 < cutoff < (fs/2)
'''
w0 = cutoff / (fs / 2)
Q = min(3 / w0, 3) # 质量系数
assert w0 > 0 and w0 <= 1
b, a = iirnotch(w0, Q)
y = lfilter(b, a, data)
return y
def check_bpmd(data, sfreq):
"""
The standard bandpass median difference check as described in 18.8.2 in the manual.
:param data: the data matrix
:return: a boolean array indicating good(True) and bad(False) signal quality for each channel
"""
# Apply Notch filters
fif_num, fif_dem = signal.iirnotch(50,
50 / Filtering.BANDWITH,
fs=sfreq)
six_num, six_dem = signal.iirnotch(60,
60 / Filtering.BANDWITH,
fs=sfreq)
notch_data = [
signal.lfilter(six_num, six_dem,
signal.lfilter(fif_num, fif_dem, row))
for row in data
]
notch_freqs = [fftpack.rfft(row) for row in notch_data]
notch_mean = [
sum(row[51 - 2:51 + 2]) / len(row[51 - 2:51 + 2]) +
sum(row[61 - 2:61 + 2]) / len(row[61 - 2:61 + 2])
for row in notch_freqs
]
notch_mean = [val / 2 for val in notch_mean]
# Apply Band Pass
band_num, band_dem = signal.butter(
2, [0.1 / (sfreq / 2), 30 / (sfreq / 2)],
output='ba',
btype="bandpass")
band_data = [
signal.lfilter(band_num, band_dem,
signal.lfilter(band_num, band_dem, row))
for row in data
]
band_freqs = [fftpack.rfft(row) for row in band_data]
band_mean = [sum(row[1:30]) / len(row[1:30]) for row in band_freqs]
return [
band_mean[i] - notch_mean[i] > 0.1 for i in range(len(band_mean))
]
def notchFilter(waveform, f_notch, Q):
"""
apply notch filter of some frequency f_notch (Hz) with some quality factor Q
"""
wf = waveform
clk = 100e6 # 100 MHz sampling frequency of SIS 3302
b_notch, a_notch = signal.iirnotch(f_notch, Q, clk)
wf_notch = signal.filtfilt(b_notch, a_notch, wf)
return wf_notch
def get_filter(Fs, power_line_fr):
fs = Fs # Sample frequency (Hz)
f0 = power_line_fr # Frequency to be removed from signal (Hz)
Q = 20.0 # Quality factor
w0 = f0 / (fs / 2) # Normalized Frequency
# Design notch filter
b, a = signal.iirnotch(w0, Q)
return b, a
def notch_iir(fs,f0,data):
'''
fs: Sample frequency (Hz)
f0: Frequency to be removed from signal (Hz)
'''
Q = 10.# 30.0 # Quality factor
w0 = float(f0)/(fs/2) # Normalized Frequency
b, a = signal.iirnotch(w0, Q)
return lfilter(b, a, data)
def iir_band_filter(ite_data,
fs,
btype,
ftype,
order=None,
Quality=None,
window=None,
lowcut=None,
highcut=None,
zerophase=None,
rps=None):
fe = fs / 2.0
if not lowcut == '' and not highcut == '':
wn = [lowcut / fe, highcut / fe]
elif not lowcut == '':
wn = lowcut / fe
elif not highcut == '':
wn = highcut / fe
if rps[0] == '':
rps[0] = 10
if rps[1] == '':
rps[1] = 10
if btype in ["butter", "bessel", "cheby1", "cheby2", "ellip"]:
z, p, k = signal.iirfilter(order,
wn,
btype=ftype,
ftype=btype,
output="zpk",
rp=rps[0],
rs=rps[1])
try:
sos = signal.zpk2sos(z, p, k)
ite_data = signal.sosfilt(sos, ite_data)
if zerophase:
ite_data = signal.sosfilt(sos, ite_data[::-1])[::-1]
except:
print('A filter had an issue: ', 'btype', btype, 'ftype', ftype,
'order', order, 'Quality', Quality, 'window', window,
'lowcut', lowcut, 'highcut', highcut, 'rps', rps)
elif btype == "iirnotch":
b, a = signal.iirnotch(lowcut, Quality, fs)
y = signal.filtfilt(b, a, ite_data)
elif btype == "Moving average":
z2 = np.cumsum(np.pad(ite_data, ((window, 0)),
'constant',
constant_values=0),
axis=0)
z1 = np.cumsum(np.pad(ite_data, ((0, window)),
'constant',
constant_values=ite_data[-1]),
axis=0)
ite_data = (z1 - z2)[(window - 1):-1] / window
return ite_data
def __init__(self, recording, freq=3000, q=30, chunk_size=30000, cache_chunks=False):
assert HAVE_NFR, "To use the NotchFilterRecording, install scipy: \n\n pip install scipy\n\n"
self._freq = freq
self._q = q
fn = 0.5 * float(recording.get_sampling_frequency())
self._b, self._a = ss.iirnotch(self._freq / fn, self._q)
if not np.all(np.abs(np.roots(self._a)) < 1):
raise ValueError('Filter is not stable')
FilterRecording.__init__(self, recording=recording, chunk_size=chunk_size, cache_chunks=cache_chunks)
self.copy_channel_properties(recording)
def __init__(self, recording, freq=3000, q=30, chunk_size=30000, cache_chunks=False):
self._freq = freq
self._q = q
fn = 0.5 * float(recording.get_sampling_frequency())
self._b, self._a = ss.iirnotch(self._freq / fn, self._q)
if not np.all(np.abs(np.roots(self._a)) < 1):
raise ValueError('Filter is not stable')
FilterRecording.__init__(self, recording=recording, chunk_size=chunk_size, cache_chunks=cache_chunks)
self._kwargs = {'recording': recording.make_serialized_dict(), 'freq': freq,
'q': q, 'chunk_size': chunk_size, 'cache_chunks': cache_chunks}
def all(order=1, ts=0.001, Q=10):
x = range(0, 20000)
y = range(0, 20000)
yy = range(0, 20000)
y_sqrt = range(0, 20000)
i = 0
while i < 4000:
y[i] = 220.0 * m.sqrt(2) * m.sin(i / 100.0)
y_sqrt[i] = m.sqrt(y[i] * y[i])
yy[i] = calc_rms(y[i])
i += 1
while i < 8000:
y[i] = 180.0 * m.sqrt(2) * m.sin(i / 100.0)
y_sqrt[i] = m.sqrt(y[i] * y[i])
yy[i] = calc_rms(y[i])
i += 1
while i < 14000:
y[i] = 260.0 * m.sqrt(2) * m.sin(i / 100.0)
y_sqrt[i] = m.sqrt(y[i] * y[i])
yy[i] = calc_rms(y[i])
i += 1
while i < len(x):
y[i] = 230.0 * m.sqrt(2) * m.sin(i / 100.0)
y_sqrt[i] = m.sqrt(y[i] * y[i])
yy[i] = calc_rms(y[i])
i += 1
#LPF filter
b, a = butter(order, ts, 'low', False)
yy_lpf100 = lfilter(b, a, yy)
#resample and second lpf
yy_lpf100_1KHz = yy_lpf100[0::20] # 20KHz->1kHz
b2, a2 = butter(1, 7.0 / 1000, 'low', False) # Fc=7Hz at Fs=1Khz
yy_lpf7_1KHz = lfilter(b2, a2, yy_lpf100_1KHz)
yy_lpf7 = signal.resample(yy_lpf7_1KHz, 20000) #1KHz->20kHz
#notch filter
w0 = 2 / 314.15926
b_notch, a_notch = signal.iirnotch(w0, Q)
yy_notch = lfilter(b_notch, a_notch, yy)
#plt.plot (yy_lpf,yy_notch)
print "size is "
print len(yy_lpf7)
# plt.plot (range(0,1000),yy_lpf100_1KHz,yy_lpf7_1KHz)
plt.plot(x, yy_lpf7, yy_notch)
# plt.plot (x,yy_lpf100,yy_lpf7)
plt.legend(('Old', 'New'), loc='upper-right')
plt.title('Exisiting implementation vs New /notch filter 50Hz q=5/')
plt.show()
def iir_notch(y, f0, fs, Q=30):
w0 = f0 / (fs / 2)
Q = 30
b, a = iirnotch(w0, Q)
# filter response
w, h = freqz(b, a)
filt_freq = w * fs / (2 * np.pi)
y_filt = filtfilt(b, a, y)
return y_filt
def __init__(self):
# microphone setup
self.chunk = 1024 * 2
self.format = pyaudio.paInt16
self.channels = 1
self.rate = 44100
# set up graph
pg.setConfigOptions(antialias=True)
self.win = pg.GraphicsWindow()
self.win.setWindowTitle("Spectrum Analyzer")
self.waveform = self.win.addPlot(title="Waveform", )
self.spectrum = self.win.addPlot(title="Spectrum", )
# make window for spectrogram plot
self.win.nextRow()
self.spectrogram = self.win.addPlot()
self.img = pg.ImageItem()
self.spectrogram.addItem(self.img)
self.data = np.zeros((500, int(self.chunk / 10)))
# self.data = np.random.rand(500 ,int(self.chunk/4))
self.img.setImage(self.data)
self.spectrogram.hideAxis('bottom')
self.spectrogram.hideAxis('left')
self.traces = dict() # to hold the data we will plot
# set up audio stream
self.p = pyaudio.PyAudio()
self.stream = self.p.open(format=self.format,
channels=self.channels,
rate=self.rate,
input=True,
output=True,
frames_per_buffer=self.chunk)
self.t = np.linspace(0, self.chunk / self.rate,
self.chunk) # dt is just 1/(sample rate)
self.f = np.linspace(
0, self.rate, self.chunk
) # We can only go up to half of the sample frequency to satisfy NYQUIST sampling condition
# set up notch filter for middle c (261.63 hz)
self.b_notch, self.a_notch = signal.iirnotch(261.63, 1.0, self.rate)
nyq = self.rate / 2
self.max_freq = 1000 / nyq
self.min_freq = 100 / nyq
# use fifth order butterworth band-pass filter
self.b_band, self.a_band = signal.butter(
5, [self.min_freq, self.max_freq], btype='band')
self.filteredWaveform = self.win.addPlot(title="Filtered Waveform")
def _line_notch(self):
"""notch filter at specified frequency hz (standard = 50)"""
fs = self.sampl_rate
f0 = self.notch_freq / globals.FREQ_CORRECTION # correct the frequency against scipy failure
Q = self.quality
w0 = f0 / (fs / 2)
b, a = iirnotch(w0, Q)
for j, data in enumerate(self.channels):
for i in range(data.shape[1]):
data[:, i] = filtfilt(b, a, data[:, i])
self.channels[j] = data
def notch_filter(freq=60.0, fs=250, Q=60):
"""
Design notch filter. Outputs numerator and denominator polynomials of iir filter.
inputs:
freq (float)
order (int)
fs (int)
outputs:
(ndarray), (ndarray)
"""
return signal.iirnotch(freq, freq / Q, fs=fs)
def notch_filter(self,data,f0,Q,fs):
n, m = data.shape
b, a = signal.iirnotch(f0*2/fs, Q)
for i in range(m):
filtedData = signal.lfilter(b, a, (data[:, i]))
if i == 0:
alldata = filtedData
else:
alldata = np.vstack((alldata, filtedData))
alldata = alldata.T
return alldata
def initialize_filters(self):
#Set up the filters
self.notch_b, self.notch_a = signal.iirnotch(self.notch_freq, self.notch_freq / 6, fs=self.sampling_freq)
self.butter_b, self.butter_a = signal.butter(self.order,
[self.low_pass / (self.sampling_freq / 2), self.high_pass / (self.sampling_freq / 2)],
'bandpass')
nz = signal.lfilter_zi(self.notch_b, self.notch_a)
bz = signal.lfilter_zi(self.butter_b, self.butter_a)
self.notch_z = [nz for i in range(self.num_channels)]
self.butter_z = [bz for i in range(self.num_channels)]
return
def filtering(channel):
from scipy import signal
import numpy as np
import matplotlib.pyplot as plt
fs = 128.0 # Sample frequency (Hz)
f0 = 50 # Frequency to be removed from signal (Hz)
w0 = f0 / (fs / 2) # Normalized Frequency
Q = 30
b, a = signal.iirnotch(w0, Q)
channel = signal.filtfilt(b, a, channel)
return (channel)
def NotchFilter(self, data, fc=60, fs=1024, order=5, Q=1):
# Frequência normalizada:
notch = []
for i in data:
wn = fc / (fs / 2) # Para o filtro NOTCH 60 Hz
b11, a11 = signal.iirnotch(wn,
Q) # Design notch filter - Fc = 60Hz
filtradoRede = signal.filtfilt(
b11, a11,
i) # Passa um filtro NOTCH no SINAL para remover 60Hz
notch.append(filtradoRede)
return np.array(notch)
def NotchFilter(signal, notchf=[60.], Q=90., QScale=True, samplefreq=None):
assert samplefreq is not None
w0 = np.array(notchf)/(float(samplefreq)/2.0) # all W0 for the notch frequency
if QScale:
bw = w0[0]/Q
Qf = (w0/bw)**np.sqrt(2) # Bandwidth is constant, Qf varies
else:
Qf = Q * np.ones(len(notchf)) # all Qf are the same (so bandwidth varies)
for i, f0 in enumerate(notchf):
b, a = spSignal.iirnotch(w0[i], Qf[i])
signal = spSignal.lfilter(b, a, signal, axis=-1, zi=None)
return signal
def bandstop_filter(data, w0, Q):
"""
data: (n_samples, n_channels)
"""
b, a = iirnotch(w0, Q)
try:
raw_filt = np.zeros(data.shape)
for i in range(data.shape[1]): # iterate over number of channels
raw_filt[:, i] = lfilter(b, a, data[:, i])
return raw_filt
except: # if 1D array
return lfilter(b, a, data)
def filter(ephys,freq_range,filt_order = 2,ripple = 0.2,attenuation = 40,filt_type='bandpass',fs=30e3):
## notch filter first:
[b,a] = signal.iirnotch(60/(fs/2),Q=30)
ephys = signal.filtfilt(b,a,ephys,axis=0)
# design Elliptic filter:
[b,a] = signal.ellip(filt_order,ripple,attenuation,[x/(fs/2) for x in freq_range],btype=filt_type)
filtered_trace = signal.filtfilt(b,a,ephys,axis=0)
return filtered_trace
def notch_filter(waveform, notch_freq, qual_factor=10, f_dig=1E8):
"""
apply notch filter with some quality factor Q
"""
nyquist = 0.5 * f_dig
w0 = notch_freq / nyquist
# "quality factor" which determines width of notch
Q = qual_factor
num, den = signal.iirnotch(w0, Q)
return signal.lfilter(num, den, waveform)
def applyFilterNotch50Hz(self, input_sensor_array, design_filter=False):
if design_filter == True:
# From: AlterEgo Paper
#
# A notch filter is applied at 60 Hz to
# nullify line interference in hardware. The notch filter is
# applied, despite the butterworth filter, because of the gentle
# roll-off attenuation of the latter.
fs = self._sampleRate # Sample frequency (Hz)
f0 = 50.0 # Frequency to be removed from signal (Hz)
Q = 30.0 # Quality factor
w0 = f0 / (fs / 2) # Normalized Frequency
# Design notch filter
b, a = signal.iirnotch(w0, Q)
# Frequency response
w, h = signal.freqz(b, a)
# Generate frequency axis
freq = w * fs / (2 * np.pi)
# Plot
fig, ax = plt.subplots(2, 1, figsize=(8, 6))
ax[0].plot(freq, 20 * np.log10(abs(h)), color='blue')
ax[0].set_title("Frequency Response")
ax[0].set_ylabel("Amplitude (dB)", color='blue')
ax[0].set_xlim([0, 100])
ax[0].set_ylim([-25, 10])
ax[0].grid()
ax[1].plot(freq,
np.unwrap(np.angle(h)) * 180 / np.pi,
color='green')
ax[1].set_ylabel("Angle (degrees)", color='green')
ax[1].set_xlabel("Frequency (Hz)")
ax[1].set_xlim([0, 100])
ax[1].set_yticks([-90, -60, -30, 0, 30, 60, 90])
ax[1].set_ylim([-90, 90])
ax[1].grid()
plt.show()
self._iirNotch50Hz__a = a
self._iirNotch50Hz__b = b
# Applies the filter to the buffer, goind forward and backwords,
# this will remove phase changes and makes the filter more linear in phase.
#
# filtered_buter_array_0 = signal.filtfilt(b, a, input_sensor_array)
filtered_buter_array = signal.filtfilt(self._iirNotch50Hz__b,
self._iirNotch50Hz__a,
input_sensor_array)
return filtered_buter_array
def update_filter(self, init=False):
# Ensure that the lower frequency is first
f_crit = np.sort(
self.f_crit) if np.ndim(self.f_crit) > 0 else self.f_crit
# Constructing the filter
if self.filter == 'notch':
b, a = signal.iirnotch(w0=f_crit, Q=30, fs=self.SF)
else:
if self.filter_method == 'ellip':
# Elliptic
b, a = signal.ellip(N=5,
rp=0.01,
rs=100,
Wn=f_crit,
btype=self.filter,
fs=self.SF)
elif self.filter_method == 'cheby':
# Chebychev
b, a = signal.cheby1(N=5,
rp=0.01,
Wn=f_crit,
btype=self.filter,
fs=self.SF)
else:
# Butterworth
b, a = signal.butter(N=5,
Wn=f_crit,
btype=self.filter,
fs=self.SF)
# Frequency response
w, h = signal.freqz(b, a, whole=True, fs=self.SF)
self.h = np.abs(np.fft.fftshift(h))
self.w = w - self.SF // 2
# Filtering
self.s_filtered = signal.lfilter(b, a, self.s)
if not init:
self.axs[0].lines[1].set_data(self.w, self.h)
x_lim = self.axs[0].get_xlim()
y_lim = self.axs[0].get_ylim()
# Clear the fill by over-filling with white
self.axs[0].fill([-self.SF, -self.SF + 1, self.SF - 1, self.SF],
[-1, 2, 2, -1],
facecolor='white')
# Create new fill
if self.filter_idx % 2 == 1 or self.filter_idx == 4:
self.axs[0].fill(self.w,
np.concatenate([[0], self.h[1:-1], [0]]),
facecolor=self.fill_color)
else:
self.axs[0].fill(self.w, self.h, facecolor=self.fill_color)
self.axs[0].set_xlim(x_lim)
self.axs[0].set_ylim(y_lim)
def notch_filtering(wav, fs, w0, Q):#陷波滤波器
""" Apply a notch (band-stop) filter to the audio signal.
Args:
wav: Waveform.
fs: Sampling frequency of the waveform.
w0: See scipy.signal.iirnotch.
Q: See scipy.signal.iirnotch.
Returns:
wav: Filtered waveform.
"""
b, a = iirnotch(2 * w0/fs, Q)
wav = lfilter(b, a, wav)
return wav
for ch in range(channels):
data = Samples[:, ch]
t = np.arange(0, len(data))
p = np.polynomial.polynomial.polyfit(t, data, 3)
data = data - np.polynomial.polynomial.polyval(t, p)
Samples[:, ch] = data
sig = Samples.T
b, a = signal.butter(4, 45 / fsample, 'low', analog=True)
sig = signal.filtfilt(b, a, sig, axis=1)
b, a = signal.butter(4, 2 / fsample, 'high', analog=True)
sig = signal.filtfilt(b, a, sig, axis=1)
Q = 30.0 # Quality factor
w0 = 50/(fsample/2) # Normalized Frequency
b, a = signal.iirnotch(w0, Q)
sig = signal.filtfilt(b, a, sig)
Samples = sig.T
# plt.figure()
# # plt.plot(Samples)
# plt.plot(Samples[int(time_point*fsample):int((time_point+22)*fsample), :])
# plt.legend(layout.label.tolist())
# plt.show()
f_min = 1
f_max = 45
chan_tmp = []
scaling = 0.1
#extracting sampling rate from parameter file
parafile = name + '-parameters.txt'
params = pd.read_csv(parafile, delim_whitespace=True, engine='python', names=['0','1','2','3'], index_col=0)
samplerate = params['2']['Samplerate']
Samplingrates = {"2.5Hz":2.5, "5Hz":5.0, "10Hz":10.0, "15Hz":15.0,
"25Hz":25.0, "30Hz":30.0, "50Hz":50.0, "60Hz":60.0,
"100Hz":100.0, "500Hz":500.0, "1KHz":1000.0, "2KHz":2000.0,
"3.75KHz":3750.0, "7.5KHz":7500.0, "15KHz":1500.0, "30KHz":30000.0}
samplerate = Samplingrates[samplerate]
#constructing IIR notch filters
fs = samplerate # Sample frequency (Hz)
f0 = 60.0 # Frequency to be removed from signal (Hz)
Q = 2.0 # Quality factor
# Design notch filter
b, a = signal.iirnotch(f0, Q, fs)
c, d = signal.iirnotch(f0*2, Q, fs)
e, f = signal.iirnotch(f0*4, Q, fs)
g, h = signal.iirnotch(f0*5, Q, fs)
i, j = signal.iirnotch(f0*6, Q, fs)
#apply filters
yf1 = signal.filtfilt(b,a,dat.current) #60Hz filter
yf2 = signal.filtfilt(c,d,yf1) #120Hz filter
yf3 = signal.filtfilt(e,f,yf2) #240Hz filter
yf4 = signal.filtfilt(g,h,yf3) #300Hz filter
yf5 = signal.filtfilt(i,j,yf4) #360Hz filter
#generate output plots
fig = plt.figure(figsize=(6,4))
plt.plot(dat.potential, yf5*-1000000000,'b')
