def shaper(shape,
order,
peaktime,
dt=1E-9,
pz=0.0,
normalize=True,
return_zpk=False,
bipolar=False):
if shape == 'gaussian':
f = gaussian_shaper
elif shape == 'crrc':
f = crrc_shaper
else:
raise ValueError('specified shaper shape not supported')
dzpk, azpk = f(order, peaktime, dt=dt, pz=pz)
zeros, poles, gain = dzpk
if bipolar:
zeros = np.append(zeros, [1])
if normalize:
sos = signal.zpk2sos(zeros, poles, 1)
t = np.arange(-1 * peaktime, 2 * peaktime, dt)
tail = np.zeros_like(t)
tail[t > 0] = np.exp(-t[t > 0] * pz)
ytail = signal.sosfilt(sos, tail)
gain = 1. / np.max(ytail)
sos = signal.zpk2sos(zeros, poles, gain)
dzpk = zeros, poles, gain
else:
sos = signal.zpk2sos(*dzpk)
if return_zpk:
return sos, dzpk, azpk
else:
return sos
def bandpass(self, data):
# raise for some bad scenarios
if self.high - 1.0 > -1e-6:
msg = ("Selected high corner frequency ({}) of bandpass is at or "
"above Nyquist ({}). Applying a high-pass instead.").format(
self.freqmax, self.fe)
logger.warning(msg)
#warnings.warn(msg)
return highpass(data,
freq=self.freqmin,
df=self.sampling_rate,
corners=self.corners,
zerophase=self.zerophase)
if self.low > 1:
msg = "Selected low corner frequency is above Nyquist."
raise ValueError(msg)
if self.zi is None:
z, p, k = iirfilter(self.corners, [self.low, self.high],
btype='bandpass',
ftype='butter',
output='zpk')
self.sos = zpk2sos(z, p, k)
self.zi = sosfilt_zi(self.sos)
data, self.zi = sosfilt(self.sos, data, zi=self.zi)
return data
def _butter_bandpass(self, lowcut, highcut, fs, order):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
z, p, k = butter(order, [low, high], btype='bandpass', output='zpk')
sos = zpk2sos(z, p, k)
return sos
def cheby_bandpass(data, cutoff, fs, Rs = 100):
"""
cheby_bandpass(data, flow, fhigh, fs, , Rs = 100)
Parameters
----------
data : 1d ndarray, signal
cutoff : List [lowcut = Float, low bound frequency limit, highcut = Float, upper bound frequency limit]
fs : Int, sampling rate
Rs: Int, stopband attenuation in Db, Optional, Default value = 100.
Returns
-------
y : 1d ndarray, filtered signal
"""
flow = cutoff[0]; fhigh = cutoff[1]
Fn = fs/2 # Nyquist Frequency (Hz)
Wp = [flow/Fn, fhigh/Fn] # Passband Frequency (Normalised)
Ws = [(flow-1)/Fn, (fhigh+1)/Fn] # Stopband Frequency (Normalised)
Rp = 1 # Passband Ripple (dB)
Rs = 100
# Get Filter Order
n, Ws = cheb2ord(Wp,Ws,Rp,Rs);
# Design Filter
z,p,k = cheby2(n,Rs,Ws,btype = 'bandpass', analog=False, output='zpk')
# Convert to second order sections
sos = zpk2sos(z,p,k);
# filter data
y = sosfiltfilt(sos,data)
return y
def generate_noise(fs=1024, f1=15, f2=100, amplify=1):
bg_raw = np.random.randn(1000)
# f1 and f2 is a bandpass
sosBP1 = sig.butter(8, [f1 / (fs / 2), f2 / (fs / 2)],
btype='bandpass',
output='sos')
# invertable band pass
fz = [4, 400]
fp = [15, 20, 150]
_, z0, _ = sig.butter(10, fz[0] / (fs / 2), btype='lowpass', output='zpk')
_, p0, _ = sig.butter(8, fp[0] / (fs / 2), btype='lowpass', output='zpk')
_, p1, _ = sig.butter(1, fp[1] / (fs / 2), btype='lowpass', output='zpk')
_, p2, _ = sig.butter(3, fp[1] / (fs / 2), btype='lowpass', output='zpk')
_, z1, _ = sig.butter(2, fz[1] / (fs / 2), btype='lowpass', output='zpk')
zs = np.concatenate((z0, z1))
ps = np.concatenate((p0, p1))
BP = sig.zpk2sos(zs, ps, 1, pairing='keep_odd')
sosBP = np.concatenate([sosBP1, BP], axis=0)
# filter the data using many second-order-sections
bg = sig.sosfilt(sosBP, bg_raw) * amplify
return bg
def butter_highpass(data, cutoff, fs, order = 5):
"""
butter_highpass(data, cutoff, fs, order = 5)
Parameters
----------
data : 1d ndarray, signal
cutoff : Float, cutoff frequency
fs : Int, sampling rate
order : Int, filter order. The default is 5.
Returns
-------
y : 1d ndarray, filtered signal
"""
nyq = 0.5 * fs # Nyquist Frequency (Hz)
normal_cutoff = cutoff[0] / nyq # Low-bound Frequency (Normalised)
# Design filter
z,p,k = butter(order, normal_cutoff, btype='high', analog=False, output ='zpk')
sos = zpk2sos(z,p,k) # Convert to second order sections
y = sosfiltfilt(sos, data) # Filter data
return y
def add_antialias(self,Fs,freq,maxorder=8):
# From obspy
nyquist = Fs * 0.5
# rp - maximum ripple of passband, rs - attenuation of stopband
rp, rs, order = 1, 96, 1e99
ws = freq / nyquist # stop band frequency
wp = ws # pass band frequency
# raise for some bad scenarios
if ws > 1:
ws = 1.0
msg = "** Selected corner frequency is above Nyquist. " + \
"** Setting Nyquist as high corner."
warnings.warn(msg)
while True:
if order <= maxorder:
break
wp = wp * 0.99
order, wn = cheb2ord(wp, ws, rp, rs, analog=0)
z, p, k = cheby2(order, rs, wn,
btype='low', analog=0, output='zpk')
self.anti_alias = zpk2sos(z,p,k)
return()
def lowpass(freq, df, corners=4):
"""
Butterworth-Lowpass Filter.
Filter data removing data over certain frequency ``freq`` using ``corners``
corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freq: Filter corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:param zerophase: If True, apply filter once forwards and once backwards.
This results in twice the number of corners but zero phase shift in
the resulting filtered trace.
:return: Filtered data.
"""
fe = 0.5 * df
f = freq / fe
# raise for some bad scenarios
if f > 1:
f = 1.0
msg = "Selected corner frequency is above Nyquist. " + \
"Setting Nyquist as high corner."
warnings.warn(msg)
z, p, k = iirfilter(corners, f, btype='lowpass', ftype='butter',
output='zpk')
sos = zpk2sos(z, p, k)
return sos
def bandpass_in_time_domain_sos(data,
freqmin=0.01,
freqmax=1.0,
sample_rate=0.5,
order=2,
axis=-1,
taper=None,
zerophase=True,
**kwargs):
fe = 0.5 * sample_rate
low = freqmin / fe
high = freqmax / fe
# raise for some bad scenarios
if high - 1.0 > -1e-6:
print("freqmax ({}) of bandpass is at or above Nyquist ({}). Ignoring."
).format(freqmax, fe)
return data
if low > 1:
print(
"Selected freqmin ({}) is above Nyquist. Ignoring".format(freqmin))
return data
z, p, k = iirfilter(order, [low, high],
btype='band',
ftype='butter',
output='zpk') #,fs=sample_rate)
sos = zpk2sos(z, p, k)
if zerophase:
result = sosfilt(sos, data)
return np.flip(sosfilt(sos, np.flip(result, axis=axis)), axis=axis)
else:
return sosfilt(sos, data, axis=axis)
def lowpass(freq, df, corners=4):
"""
Butterworth-Lowpass Filter.
Filter data removing data over certain frequency ``freq`` using ``corners``
corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freq: Filter corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:param zerophase: If True, apply filter once forwards and once backwards.
This results in twice the number of corners but zero phase shift in
the resulting filtered trace.
:return: Filtered data.
"""
fe = 0.5 * df
f = freq / fe
# raise for some bad scenarios
if f > 1:
f = 1.0
msg = "Selected corner frequency is above Nyquist. " + \
"Setting Nyquist as high corner."
warnings.warn(msg)
z, p, k = iirfilter(corners,
f,
btype='lowpass',
ftype='butter',
output='zpk')
sos = zpk2sos(z, p, k)
return sos
def low_pass_filter(source, sr, cutoff_freq, order):
"""Function that takes an 1D array as an argument and returns the filtered
signal following the application of a low pass filter with a cutoff frequency = cutoff_freq and
order = order
Args : source (np.array) = The signal to be filtered
sr (int) = The sampling rate of the signal
cutoff_freq (int) = the cutoff frequency of the lowpass filter
order (int) = the order of the lowpass filter
Returns : sink (np.array) = The centered moving average of the input signal
"""
for name, arg in zip(("sr", "cutoff_freq", "order"), (sr, cutoff_freq, order)):
if not isinstance(arg, int):
raise RuntimeError("The argument {0} is of incorrect type. Input : {1}, Requiered : int"
.format(name, type(arg)))
source = np.array(source)
if len(source.shape) == 1:
nyq = sr / 2 # The nyquist frequency
normalized_cutoff = cutoff_freq / nyq
z, p, k = signal.butter(order, normalized_cutoff, output="zpk")
lesos = signal.zpk2sos(z, p, k)
filtered = signal.sosfilt(lesos, source)
sink = np.array(filtered)
return sink
else:
raise RuntimeError("The input array has too many dimensions. Input : {0}D, Requiered : 1D"
.format(len(source.shape)))
def bandstop(data, freqmin, freqmax, df, corners=4, zerophase=False):
"""
Butterworth-Bandstop Filter.
Filter data removing data between frequencies ``freqmin`` and ``freqmax``
using ``corners`` corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
Parameters
----------
data : array
Data to filter.
freqmin : float
Stop band low corner frequency.
freqmax : float
Stop band high corner frequency.
df : float
Sampling rate in Hz.
corners : int
Filter corners / order.
**Default:** ``4``
zerophase : bool
If True, apply filter once forwards and once backwards. This results in twice the filter order but zero phase shift in the resulting filtered trace.
**Default:** ``False``
Returns
-------
data : array
Filtered data.
"""
fe = 0.5 * df
low = freqmin / fe
high = freqmax / fe
# raise for some bad scenarios
if high > 1:
high = 1.0
msg = "Selected high corner frequency is above Nyquist. " + \
"Setting Nyquist as high corner."
warnings.warn(msg)
if low > 1:
msg = "Selected low corner frequency is above Nyquist."
raise ValueError(msg)
z, p, k = iirfilter(corners, [low, high],
btype='bandstop',
ftype='butter',
output='zpk')
sos = zpk2sos(z, p, k)
if zerophase:
firstpass = sosfilt(sos, data)
return sosfilt(sos, firstpass[::-1])[::-1]
else:
return sosfilt(sos, data)
def butter_bandpass(data, cutoff, fs, order = 10):
"""
butter_bandpass(data, cutoff, fs, order = 10)
Parameters
----------
data : 1d ndarray, signal
cutoff : List [lowcut = Float, low bound frequency limit, highcut = Float, upper bound frequency limit]
fs : Int, sampling rate
order : Int, filter order. The default is 5.
Returns
-------
y : 1d ndarray, filtered signal
"""
nyq = 0.5 * fs # Nyquist Frequency (Hz)
low = cutoff[0] / nyq # Low-bound Frequency (Normalised)
high = cutoff[1] / nyq # Upper-bound Frequency (Normalised)
# Design filter
z,p,k = butter(order, [low, high], btype='band', analog=False, output ='zpk')
# Convert to second order sections
sos = zpk2sos(z,p,k)
# Filter data
y = sosfiltfilt(sos, data)
return y
def highpass(data, freq, df, corners=4, zerophase=False):
"""
Butterworth-Highpass Filter.
Filter data removing data below certain frequency ``freq`` using
``corners`` corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freq: Filter corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:param zerophase: If True, apply filter once forwards and once backwards.
This results in twice the number of corners but zero phase shift in
the resulting filtered trace.
:return: Filtered data.
"""
fe = 0.5 * df
f = freq / fe
# raise for some bad scenarios
if f > 1:
msg = "Selected corner frequency is above Nyquist."
raise ValueError(msg)
z, p, k = iirfilter(corners, f, btype='highpass', ftype='butter',
output='zpk')
sos = zpk2sos(z, p, k)
if zerophase:
firstpass = sosfilt(sos, data)
return sosfilt(sos, firstpass[::-1])[::-1]
else:
return sosfilt(sos, data)
def _design_iir(wp,
ws,
sample_rate,
gpass,
gstop,
analog=False,
ftype='cheby1',
output='zpk'):
nyq = sample_rate / 2.
wp = atleast_1d(wp)
ws = atleast_1d(ws)
if analog:
wp *= TWO_PI
ws *= TWO_PI
else:
wp /= nyq
ws /= nyq
z, p, k = signal.iirdesign(wp,
ws,
gpass,
gstop,
analog=analog,
ftype=ftype,
output='zpk')
if analog:
z /= -TWO_PI
p /= -TWO_PI
if output == 'zpk':
return z, p, k
elif output == 'ba':
return signal.zpk2tf(z, p, k)
elif output == 'sos':
return signal.zpk2sos(z, p, k)
else:
raise ValueError("'%s' is not a valid output form." % output)
def bandpass(data, freq_min, freq_max, sample_frequency, corners=4):
"""
Zero-Phase Butterworth-Bandpass Filter.
Filter data from ``freqmin`` to ``freqmax`` using ``corners``
corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freqmin: Pass band low corner frequency.
:param freqmax: Pass band high corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:return: Filtered data.
"""
nyquist = 0.5 * sample_frequency
low = freq_min / nyquist
high = freq_max / nyquist
zeroes, poles, gain = iirfilter(corners, [low, high],
btype='band',
ftype='butter',
output='zpk')
sos = zpk2sos(zeroes, poles, gain)
firstpass = sosfilt(sos, data)
return sosfilt(sos, firstpass[::-1])[::-1]
def band_stop(ite_data,
freqmin,
freqmax,
samp_freq,
corners=4,
zerophase=True):
fe = samp_freq / 2.0
low = freqmin / fe
high = freqmax / fe
# raise error for illegal input
if high - 1.0 > -1e-6:
msg = (
"Selected high corner frequency ({}) of bandpass is at or above Nyquist ({}). Applying a high-pass instead."
).format(freqmax, fe)
return False
if low > 1:
msg = "selected low corner requency is above Nyquist"
return False
z, p, k = signal.iirfilter(corners, [low, high],
btype='bandstop',
ftype='butter',
output='zpk')
sos = zpk2sos(z, p, k)
ite_data = sosfilt(sos, ite_data)
if zerophase:
ite_data = sosfilt(sos, ite_data[::-1])[::-1]
return ite_data
def highpass(data, freq, df, corners=4, zerophase=False):
"""
Butterworth-Highpass Filter.
Filter data removing data below certain frequency ``freq`` using
``corners`` corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freq: Filter corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:param zerophase: If True, apply filter once forwards and once backwards.
This results in twice the number of corners but zero phase shift in
the resulting filtered trace.
:return: Filtered data.
"""
fe = 0.5 * df
f = freq / fe
# raise for some bad scenarios
if f > 1:
msg = "Selected corner frequency is above Nyquist."
raise ValueError(msg)
z, p, k = iirfilter(corners, f, btype='highpass', ftype='butter',
output='zpk')
sos = zpk2sos(z, p, k)
if zerophase:
firstpass = sosfilt(sos, data)
return sosfilt(sos, firstpass[::-1])[::-1]
else:
return sosfilt(sos, data)
def stream_filter_bessel(stream,
center_freq,
gamma=0.5,
corners=4,
zerophase=False):
filtered_stream = obspy.Stream()
for tr in stream.copy():
fe = 0.5 * tr.stats.sampling_rate
freqmin = center_freq - (gamma * center_freq)
freqmax = center_freq + (gamma * center_freq)
low = freqmin / fe
high = freqmax / fe
z, p, k = signal.iirfilter(corners, [low, high],
btype='bandpass',
ftype='bessel',
output='zpk')
sos = signal.zpk2sos(z, p, k)
if zerophase:
first_pass = signal.sosfilt(sos, tr.data)
second_pass = signal.sosfilt(sos, first_pass[::-1])[::-1]
tr.data = second_pass
filtered_stream += tr
else:
filtered_data = signal.sosfilt(sos, tr.data)
tr.data = filtered_data
filtered_stream += tr
return filtered_stream
def _design_iir(wp, ws, sample_rate, gpass, gstop,
analog=False, ftype='cheby1', output='zpk'):
# pylint: disable=invalid-name
nyq = sample_rate / 2.
wp = numpy.atleast_1d(wp)
ws = numpy.atleast_1d(ws)
if analog: # convert Hz to rad/s
wp *= TWO_PI
ws *= TWO_PI
else: # convert Hz to half-cycles / sample
wp /= nyq
ws /= nyq
z, p, k = signal.iirdesign(wp, ws, gpass, gstop, analog=analog,
ftype=ftype, output='zpk')
if analog: # convert back to Hz
z /= -TWO_PI
p /= -TWO_PI
k *= TWO_PI ** z.size / -TWO_PI ** p.size
if output == 'zpk':
return z, p, k
elif output == 'ba':
return signal.zpk2tf(z, p, k)
elif output == 'sos':
return signal.zpk2sos(z, p, k)
else:
raise ValueError("'%s' is not a valid output form." % output)
def bandpass(data, fs, fl, fh, order=None, axis=-1):
""" Apply Butterworth bandpass filter using scipy.signal.sosfiltfilt method
Parameters
----------
data: array
fs: sampling frequency
fl, fh: low and high frequency for bandpass
axis: axis to apply the filter on
Returns:
--------
data_filt: filtered array
"""
if order is None:
order = 8
# Make filter
nyq = fs/2.
low, high = fl/nyq, fh/nyq # normalize frequency
z, p, k = sig.butter(order, [low, high], btype='bandpass', output='zpk')
sos = sig.zpk2sos(z, p, k)
# Apply filter and return output
data_filt = sig.sosfiltfilt(sos, data, axis=axis)
return data_filt
def highpass(rawData, samplFreq, highpassCutOff):
#This function high passes the data with sampling frequency samplFreq with a highpass
# cut off of highpassCutOff
#
# Usage: [highPassedData] = highpass(rawData, samplFreq, highpassCutOff)
#
# rawData : raw time series Data
# samplFreq: sampling Frequency of Data
# highpassCutOff: The high pass frequency cut off.
#
numberOfChannels = len(rawData)
dataLength = len(rawData[0])
duration = dataLength / samplFreq
halfDataLength = dataLength / 2 + 1
for channelNumber in xrange(numberOfChannels):
if (len(rawData[channelNumber]) != dataLength):
sys.exit('Data length not consistent\n')
nyquistFrequency = samplFreq / 2.0
lpefOrder = 0
if (highpassCutOff > 0):
hpfOrder = 12
hpfZeros, hpfPoles, hpfGain = sig.butter(hpfOrder,
highpassCutOff /
nyquistFrequency,
btype='highpass',
output='zpk')
hpfSOS = sig.zpk2sos(hpfZeros, hpfPoles, hpfGain)
#magnitude response of high pass filter
minimumFrequencyStep = 1.0 / duration
frequencies = np.arange(0, nyquistFrequency, minimumFrequencyStep)
hpfArgument = np.power((frequencies / highpassCutOff), 2 * hpfOrder)
hpfResponse = hpfArgument / (1 + hpfArgument)
highPassCutOffIndex = np.ceil(highpassCutOff / minimumFrequencyStep)
highPassedData = []
for channelNumber in xrange(numberOfChannels):
if (highpassCutOff > 0):
x = sig.sosfilt(hpfSOS, rawData[channelNumber])
x = np.flipud(x)
x = sig.sosfilt(hpfSOS, x)
x = np.flipud(x)
else:
x = rawData[channelNumber]
x[0:lpefOrder] = np.zeros(lpefOrder)
x[dataLength - lpefOrder:dataLength - 1] = np.zeros(lpefOrder)
highPassedData.append(x)
highPassedData = np.asarray(highPassedData)
return highPassedData
def chebyBandpassFilter(data, cutoff, gstop=40, gpass=1, fs=2048.):
"""
Design a filter with scipy functions avoiding unstable results (when using
ab output and filtfilt(), lfilter()...).
Cf. ()[]
Parameters
----------
data : instance of numpy.array | instance of pandas.core.DataFrame
Data to be filtered. Each column will be filtered if data is a
dataframe.
cutoff : array-like of float
Pass and stop frequencies in order:
- the first element is the stop limit in the lower bound
- the second element is the lower bound of the pass-band
- the third element is the upper bound of the pass-band
- the fourth element is the stop limit in the upper bound
For instance, [0.9, 1, 45, 48] will create a band-pass filter between
1 Hz and 45 Hz.
gstop : int
The minimum attenuation in the stopband (dB).
gpass : int
The maximum loss in the passband (dB).
Returns:
zpk :
filteredData : instance of numpy.array | instance of pandas.core.DataFrame
The filtered data.
"""
wp = [cutoff[1] / (fs / 2), cutoff[2] / (fs / 2)]
ws = [cutoff[0] / (fs / 2), cutoff[3] / (fs / 2)]
z, p, k = iirdesign(wp=wp,
ws=ws,
gstop=gstop,
gpass=gpass,
ftype='cheby2',
output='zpk')
zpk = [z, p, k]
sos = zpk2sos(z, p, k)
order, Wn = cheb2ord(wp=wp, ws=ws, gstop=gstop, gpass=gpass, analog=False)
print 'Creating cheby filter of order %d...' % order
if (data.ndim == 2):
print 'Data contain multiple columns. Apply filter on each columns.'
filteredData = np.zeros(data.shape)
for electrode in range(data.shape[1]):
# print 'Filtering electrode %s...' % electrode
filteredData[:, electrode] = sosfiltfilt(sos, data[:, electrode])
else:
# Use sosfiltfilt instead of filtfilt fixed the artifacts at the beggining
# of the signal
filteredData = sosfiltfilt(sos, data)
return zpk, filteredData
def test_filter(self, losc):
zpk = [], [], 1
fts = losc.filter(zpk, analog=True)
utils.assert_quantity_sub_equal(losc, fts)
# check SOS filters can be used directly
zpk = filter_design.highpass(50, sample_rate=losc.sample_rate)
sos = signal.zpk2sos(*zpk)
utils.assert_quantity_almost_equal(losc.filter(zpk), losc.filter(sos))
def highpass(rawData, samplFreq, highpassCutOff):
#This function high passes the data with sampling frequency samplFreq with a highpass
# cut off of highpassCutOff
#
# Usage: [highPassedData] = highpass(rawData, samplFreq, highpassCutOff)
#
# rawData : raw time series Data
# samplFreq: sampling Frequency of Data
# highpassCutOff: The high pass frequency cut off.
#
numberOfChannels = len(rawData)
dataLength = len(rawData[0])
duration = dataLength/samplFreq
halfDataLength = dataLength/2 + 1
for channelNumber in xrange(numberOfChannels):
if(len(rawData[channelNumber]) != dataLength):
sys.exit('Data length not consistent\n')
nyquistFrequency = samplFreq/2.0
lpefOrder = 0
if(highpassCutOff>0):
hpfOrder = 12
hpfZeros, hpfPoles, hpfGain = sig.butter(hpfOrder, highpassCutOff/nyquistFrequency, btype = 'highpass', output = 'zpk' )
hpfSOS = sig.zpk2sos(hpfZeros, hpfPoles, hpfGain)
#magnitude response of high pass filter
minimumFrequencyStep = 1.0/duration
frequencies = np.arange(0, nyquistFrequency, minimumFrequencyStep)
hpfArgument = np.power((frequencies / highpassCutOff), 2*hpfOrder)
hpfResponse = hpfArgument/(1 + hpfArgument)
highPassCutOffIndex = np.ceil(highpassCutOff/minimumFrequencyStep)
highPassedData = []
for channelNumber in xrange(numberOfChannels):
if(highpassCutOff>0):
x = sig.sosfilt(hpfSOS, rawData[channelNumber])
x = np.flipud(x)
x = sig.sosfilt(hpfSOS, x)
x = np.flipud(x)
else:
x = rawData[channelNumber]
x[0:lpefOrder] = np.zeros(lpefOrder)
x[dataLength - lpefOrder:dataLength-1] = np.zeros(lpefOrder)
highPassedData.append(x)
highPassedData = np.asarray(highPassedData)
return highPassedData
def butter_bandstop_filter(lowcut, highcut, fs, order):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
z, p, k = butter(order, [low, high], btype='bandstop', output='zpk')
assert np.all(np.abs(p) < 1), 'unstable filter'
sos = zpk2sos(z, p, k)
# sos = iirdesign([low-0.01, high+0.01], [low+0.01, high-0.01], 3, 40, output='sos')
return sos
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 preprocessEEG(eeg,
fs,
eogChannels=None,
badChannels=None,
hpCutoff=0.5,
stdThresh=4):
"""
Preprocess EEG data and return data that has been filtered with bad channels removed.
Input:
eeg - ndarray of samples x channels (TxD)
fs - sampling rate in Hz
eogChannels - list/tuple of which channels in EEG are EOG (Default = None)
badChannels - list/tuple of channels in EEG to remove (Default = None)
hpCutoff - cutoff of the high-pass filter in Hz (Default = 0.5 Hz)
stdThresh - # of standard deviations to tolerate before marking sample outlier (Default = 4)
"""
z, p, k = sig.butter(5, hpCutoff / fs * 2, 'highpass', output='zpk')
sos = sig.zpk2sos(z, p, k)
T, D = eeg.shape
eeg = eeg - np.concatenate([eeg[[0], :]
for i in range(T)]) # remove starting offset
eeg = sig.sosfilt(sos, eeg) # apply high-pass filtering
if eogChannels is not None:
eeg = eeg - np.dot(eeg[:, eogChannels],
lin.lstsq(eeg[:, eogChannels],
eeg)[0]) # regress out EOG data
eeg = np.delete(eeg, eogChannels, axis=1)
# detect outliers > stdThresh
stdThresh = stdThresh * np.std(eeg, 0)
stdThresh = np.stack([stdThresh for _ in range(T)], axis=0)
eeg[np.nonzero(np.abs(eeg) > stdThresh)] = 0 # remove outliers
h = np.zeros(int(np.around(fs * 0.04)))
h[0] = 1
eeg = sig.lfilter(h, 1, np.flipud(sig.lfilter(h, 1, np.flipud(eeg))))
eeg[np.isnan(eeg)] = 0.0
if badChannels is not None:
eeg[:, badChannels] = 0 # zero out bad channels
return eeg
def filter_from_npz(filename, fs):
with np.load(filename) as data:
z = data['z']
p = data['p']
k = data['k']
#sos conversion
zd, pd, kd = zpk_bilinear(z, p, k, fs)
sys_disc = sig.ZerosPolesGain(zd, pd, kd, dt=1 / fs)
sos = sig.zpk2sos(sys_disc.zeros, sys_disc.poles, sys_disc.gain)
return sos
def lowpass(data, freq, df, corners=4, zerophase=False):
"""
Butterworth-Lowpass Filter.
Filter data removing data over certain frequency ``freq`` using ``corners``
corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
Parameters
----------
data : array
Data to filter.
freq : float
Filter corner frequency.
df : float
Sampling rate in Hz.
corners : int
Filter corners / order.
**Default:** ``4``
zerophase : bool
If True, apply filter once forwards and once backwards. This results in twice the filter order but zero phase shift in the resulting filtered trace.
**Default:** ``False``
Returns
-------
data : array
Filtered data.
"""
fe = 0.5 * df
f = freq / fe
# raise for some bad scenarios
if f > 1:
f = 1.0
msg = "Selected corner frequency is above Nyquist. " + \
"Setting Nyquist as high corner."
warnings.warn(msg)
z, p, k = iirfilter(corners,
f,
btype='lowpass',
ftype='butter',
output='zpk')
sos = zpk2sos(z, p, k)
if zerophase:
firstpass = sosfilt(sos, data)
return sosfilt(sos, firstpass[::-1])[::-1]
else:
return sosfilt(sos, data)
def lowpass_filter(data, SRD, freq, order):
sampling_rate = SRD
nyq = sampling_rate / 2
cutoff = freq
normalized_cutoff = cutoff / nyq
z, p, k = signal.butter(order, normalized_cutoff, output="zpk")
lesos = signal.zpk2sos(z, p, k)
filtered = signal.sosfilt(lesos, data)
filtered = np.array(filtered)
return filtered
def band_pass_filter(data, minfreq = 0.5, maxfreq = 0.8, df = 4, corners = 4):
fe = 0.5 * df
low = minfreq / fe
high = maxfreq / fe
z, p, k = sig.iirfilter(corners, [low, high], btype='band',
ftype='butter', output='zpk')
sos = sig.zpk2sos(z, p, k)
return sig.sosfilt(sos, data)
def cost_filter(fs, zeros, poles, zero_order, pole_order):
s_zeros = []
s_poles = []
if sum(zero_order) != sum(pole_order):
raise ValueError('Bandpass not invertible!')
for ii, fz in enumerate(zeros):
_, sz, _ = sig.butter(zero_order[ii], fz / (fs / 2), output='zpk')
s_zeros.append(sz)
for ii, fp in enumerate(poles):
_, sp, _ = sig.butter(pole_order[ii], fp / (fs / 2), output='zpk')
s_poles.append(sp)
s_zeros = np.concatenate(s_zeros)
s_poles = np.concatenate(s_poles)
BP = sig.zpk2sos(s_zeros, s_poles, 1, pairing='keep_odd')
invBP = sig.zpk2sos(s_poles, s_zeros, 1, pairing='keep_odd')
return BP, invBP
def test_equivalence(self):
x = np.random.RandomState(0).randn(1000)
for order in range(1, 6):
zpk = signal.butter(order, 0.35, output="zpk")
b, a = signal.zpk2tf(*zpk)
sos = signal.zpk2sos(*zpk)
y = signal.filtfilt(b, a, x)
y_sos = sosfiltfilt(sos, x)
np.testing.assert_allclose(y,
y_sos,
atol=1e-12,
err_msg=f"order={order}")
def zpk2sos_quant(discrete_system, Qformat):
sos = signal.zpk2sos(*discrete_system, pairing='nearest')
# Trick for higher accuracy on small numerator coefficients
non_zeros = sos[0,:3] > 0
b_factor = np.prod(sos[0,:3][non_zeros]) ** (1/non_zeros.sum())
sos[0,:3] /= b_factor
sos[:,:3] *= b_factor ** (1/sos.shape[0])
sos_quant = quantizer_real(sos, Qformat)
return sos, sos_quant
def test_filter(self, losc):
zpk = [], [], 1
fts = losc.filter(zpk, analog=True)
utils.assert_quantity_sub_equal(losc, fts)
# check SOS filters can be used directly
zpk = filter_design.highpass(50, sample_rate=losc.sample_rate)
try:
sos = signal.zpk2sos(*zpk)
except AttributeError: # scipy < 0.16
pass
else:
utils.assert_quantity_almost_equal(losc.filter(zpk),
losc.filter(sos))
def A_weighting(fs, output='ba'):
"""
Design of a digital A-weighting filter.
Designs a digital A-weighting filter for
sampling frequency `fs`.
Warning: fs should normally be higher than 20 kHz. For example,
fs = 48000 yields a class 1-compliant filter.
Parameters
----------
fs : float
Sampling frequency
output : {'ba', 'zpk', 'sos'}, optional
Type of output: numerator/denominator ('ba'), pole-zero ('zpk'), or
second-order sections ('sos'). Default is 'ba'.
Examples
--------
Plot frequency response
>>> from scipy.signal import freqz
>>> import matplotlib.pyplot as plt
>>> fs = 200000
>>> b, a = A_weighting(fs)
>>> f = np.logspace(np.log10(10), np.log10(fs/2), 1000)
>>> w = 2*pi * f / fs
>>> w, h = freqz(b, a, w)
>>> plt.semilogx(w*fs/(2*pi), 20*np.log10(abs(h)))
>>> plt.grid(True, color='0.7', linestyle='-', which='both', axis='both')
>>> plt.axis([10, 100e3, -50, 20])
Since this uses the bilinear transform, frequency response around fs/2 will
be inaccurate at lower sampling rates.
"""
z, p, k = ABC_weighting('A')
# Use the bilinear transformation to get the digital filter.
z_d, p_d, k_d = _zpkbilinear(z, p, k, fs)
if output == 'zpk':
return z_d, p_d, k_d
elif output in {'ba', 'tf'}:
return zpk2tf(z_d, p_d, k_d)
elif output == 'sos':
return zpk2sos(z_d, p_d, k_d)
else:
raise ValueError("'%s' is not a valid output form." % output)
def lowpass_cheby_2(data, freq, df, maxorder=12, ba=False,
freq_passband=False):
"""
Cheby2-Lowpass Filter
Filter data by passing data only below a certain frequency.
The main purpose of this cheby2 filter is downsampling.
#318 shows some plots of this filter design itself.
This method will iteratively design a filter, whose pass
band frequency is determined dynamically, such that the
values above the stop band frequency are lower than -96dB.
:type data: numpy.ndarray
:param data: Data to filter.
:param freq: The frequency above which signals are attenuated
with 95 dB
:param df: Sampling rate in Hz.
:param maxorder: Maximal order of the designed cheby2 filter
:param ba: If True return only the filter coefficients (b, a) instead
of filtering
:param freq_passband: If True return additionally to the filtered data,
the iteratively determined pass band frequency
:return: Filtered data.
"""
nyquist = df * 0.5
# rp - maximum ripple of passband, rs - attenuation of stopband
rp, rs, order = 1, 96, 1e99
ws = freq / nyquist # stop band frequency
wp = ws # pass band frequency
# raise for some bad scenarios
if ws > 1:
ws = 1.0
msg = "Selected corner frequency is above Nyquist. " + \
"Setting Nyquist as high corner."
warnings.warn(msg)
while True:
if order <= maxorder:
break
wp = wp * 0.99
order, wn = cheb2ord(wp, ws, rp, rs, analog=0)
if ba:
return cheby2(order, rs, wn, btype='low', analog=0, output='ba')
z, p, k = cheby2(order, rs, wn, btype='low', analog=0, output='zpk')
sos = zpk2sos(z, p, k)
if freq_passband:
return sosfilt(sos, data), wp * nyquist
return sosfilt(sos, data)
def bandpass(data, freqmin, freqmax, df, corners=4, zerophase=False):
"""
Butterworth-Bandpass Filter.
Filter data from ``freqmin`` to ``freqmax`` using ``corners``
corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freqmin: Pass band low corner frequency.
:param freqmax: Pass band high corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:param zerophase: If True, apply filter once forwards and once backwards.
This results in twice the filter order but zero phase shift in
the resulting filtered trace.
:return: Filtered data.
"""
fe = 0.5 * df
low = freqmin / fe
high = freqmax / fe
# raise for some bad scenarios
if high - 1.0 > -1e-6:
msg = ("Selected high corner frequency ({}) of bandpass is at or "
"above Nyquist ({}). Applying a high-pass instead.").format(
freqmax, fe)
warnings.warn(msg)
return highpass(data, freq=freqmin, df=df, corners=corners,
zerophase=zerophase)
if low > 1:
msg = "Selected low corner frequency is above Nyquist."
raise ValueError(msg)
z, p, k = iirfilter(corners, [low, high], btype='band',
ftype='butter', output='zpk')
sos = zpk2sos(z, p, k)
if zerophase:
firstpass = sosfilt(sos, data)
return sosfilt(sos, firstpass[::-1])[::-1]
else:
return sosfilt(sos, data)
def bandstop(data, freqmin, freqmax, df, corners=4, zerophase=False):
"""
Butterworth-Bandstop Filter.
Filter data removing data between frequencies ``freqmin`` and ``freqmax``
using ``corners`` corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freqmin: Stop band low corner frequency.
:param freqmax: Stop band high corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:param zerophase: If True, apply filter once forwards and once backwards.
This results in twice the number of corners but zero phase shift in
the resulting filtered trace.
:return: Filtered data.
"""
fe = 0.5 * df
low = freqmin / fe
high = freqmax / fe
# raise for some bad scenarios
if high > 1:
high = 1.0
msg = "Selected high corner frequency is above Nyquist. " + \
"Setting Nyquist as high corner."
warnings.warn(msg)
if low > 1:
msg = "Selected low corner frequency is above Nyquist."
raise ValueError(msg)
z, p, k = iirfilter(corners, [low, high],
btype='bandstop', ftype='butter', output='zpk')
sos = zpk2sos(z, p, k)
if zerophase:
firstpass = sosfilt(sos, data)
return sosfilt(sos, firstpass[::-1])[::-1]
else:
return sosfilt(sos, data)
def bandpass(freqmin, freqmax, df, corners=4):
"""
From obspy with modification.
Butterworth-Bandpass Filter.
Filter data from ``freqmin`` to ``freqmax`` using ``corners``
corners.
The filter uses :func:`scipy.signal.iirfilter` (for design)
and :func:`scipy.signal.sosfilt` (for applying the filter).
:type data: numpy.ndarray
:param data: Data to filter.
:param freqmin: Pass band low corner frequency.
:param freqmax: Pass band high corner frequency.
:param df: Sampling rate in Hz.
:param corners: Filter corners / order.
:param zerophase: If True, apply filter once forwards and once backwards.
This results in twice the filter order but zero phase shift in
the resulting filtered trace.
:return: Filtered data.
"""
fe = 0.5 * df
low = freqmin / fe
high = freqmax / fe
# raise for some bad scenarios
if high > 1:
high = 1.0
msg = "Selected high corner frequency is above Nyquist. " + \
"Setting Nyquist as high corner."
warnings.warn(msg)
if low > 1:
msg = "Selected low corner frequency is above Nyquist."
raise ValueError(msg)
z, p, k = iirfilter(corners, [low, high], btype='band',
ftype='butter', output='zpk')
sos = zpk2sos(z, p, k)
return sos
def ITU_R_468_weighting(fs, output='ba'):
"""
Return ITU-R 468 digital weighting filter transfer function
Parameters
----------
fs : float
Sampling frequency
Examples
--------
>>> from scipy.signal import freqz
>>> import matplotlib.pyplot as plt
>>> fs = 200000
>>> b, a = ITU_R_468_weighting(fs)
>>> f = np.logspace(np.log10(10), np.log10(fs/2), 1000)
>>> w = 2*pi * f / fs
>>> w, h = freqz(b, a, w)
>>> plt.semilogx(w*fs/(2*pi), 20*np.log10(abs(h)))
>>> plt.grid(True, color='0.7', linestyle='-', which='both', axis='both')
>>> plt.axis([10, 100e3, -50, 20])
"""
z, p, k = ITU_R_468_weighting_analog()
# Use the bilinear transformation to get the digital filter.
zz, pz, kz = _zpkbilinear(z, p, k, fs)
if output == 'zpk':
return zz, pz, kz
elif output in {'ba', 'tf'}:
return zpk2tf(zz, pz, kz)
elif output == 'sos':
return zpk2sos(zz, pz, kz)
else:
raise ValueError("'%s' is not a valid output form." % output)
def _design_iir(wp, ws, sample_rate, gpass, gstop,
analog=False, ftype='cheby1', output='zpk'):
nyq = sample_rate / 2.
wp = atleast_1d(wp)
ws = atleast_1d(ws)
if analog:
wp *= TWO_PI
ws *= TWO_PI
else:
wp /= nyq
ws /= nyq
z, p, k = signal.iirdesign(wp, ws, gpass, gstop, analog=analog,
ftype=ftype, output='zpk')
if analog:
z /= -TWO_PI
p /= -TWO_PI
if output == 'zpk':
return z, p, k
elif output == 'ba':
return signal.zpk2tf(z, p, k)
elif output == 'sos':
return signal.zpk2sos(z, p, k)
else:
raise ValueError("'%s' is not a valid output form." % output)
# Frequence de coupure dans la bande attenuee fa = 4000 ws = fa/(fe/2) # Taux d'ondulation dans la bande passante (dB) delta1 = 3 # Taux d'ondulation dans la bande attenuee (dB) delta2 = 30 # Determination de l'ordre et de la frequence de coupure N, Wn = signal.buttord(wp, ws, delta1, delta2) # Determination des coefficients a, b = signal.butter(N, Wn) # Determination de la reponse frequentielle w, h = signal.freqz(b, a, whole=True) # Plot f, (ax1, ax2) = plt.subplots(2) ax1.plot(w, 20 * np.log10(abs(h))) ax2.plot(w, np.unwrap(np.angle(h))) plt.show() # Decomposition en cellules du 1er et du 2eme ordre Z = signal.zpk2sos(np.roots(a), np.roots(b), a[0]) print(Z)
def plane_25d(x0, r0, npw, fs, max_order=None, c=None, s2z=matchedz_zpk):
r"""Virtual plane wave by 2.5-dimensional NFC-HOA.
.. math::
D(\phi_0, s) =
2\e{\frac{s}{c}r_0}
\sum_{m=-M}^{M}
(-1)^m
\Big(\frac{s}{s-\frac{c}{r_0}\sigma_0}\Big)^\mu
\prod_{l=1}^{\nu}
\frac{s^2}{(s-\frac{c}{r_0}\sigma_l)^2+(\frac{c}{r_0}\omega_l)^2}
\e{\i m(\phi_0 - \phi_\text{pw})}
The driving function is represented in the Laplace domain,
from which the recursive filters are designed.
:math:`\sigma_l + \i\omega_l` denotes the complex roots of
the reverse Bessel polynomial.
The number of second-order sections is
:math:`\nu = \big\lfloor\tfrac{|m|}{2}\big\rfloor`,
whereas the number of first-order section :math:`\mu` is either 0 or 1
for even and odd :math:`|m|`, respectively.
Parameters
----------
x0 : (N, 3) array_like
Sequence of secondary source positions.
r0 : float
Radius of the circular secondary source distribution.
npw : (3,) array_like
Unit vector (propagation direction) of plane wave.
fs : int
Sampling frequency in Hertz.
max_order : int, optional
Ambisonics order.
c : float, optional
Speed of sound in m/s.
s2z : callable, optional
Function transforming s-domain poles and zeros into z-domain,
e.g. :func:`matchedz_zpk`, :func:`scipy.signal.bilinear_zpk`.
Returns
-------
delay : float
Overall delay in seconds.
weight : float
Overall weight.
sos : list of numpy.ndarray
Second-order section filters :func:`scipy.signal.sosfilt`.
phaseshift : (N,) numpy.ndarray
Phase shift in radians.
selection : (N,) numpy.ndarray
Boolean array containing only ``True`` indicating that
all secondary source are "active" for NFC-HOA.
secondary_source_function : callable
A function that can be used to create the sound field of a
single secondary source. See `sfs.td.synthesize()`.
Examples
--------
.. plot::
:context: close-figs
delay, weight, sos, phaseshift, selection, secondary_source = \
sfs.td.nfchoa.plane_25d(array.x, R, npw, fs)
d = sfs.td.nfchoa.driving_signals_25d(
delay, weight, sos, phaseshift, signal)
plot(d, selection, secondary_source)
"""
if max_order is None:
max_order = _util.max_order_circular_harmonics(len(x0))
if c is None:
c = _default.c
x0 = _util.asarray_of_rows(x0)
npw = _util.asarray_1d(npw)
phi0, _, _ = _util.cart2sph(*x0.T)
phipw, _, _ = _util.cart2sph(*npw)
phaseshift = phi0 - phipw + _np.pi
delay = -r0 / c
weight = 2
sos = []
for m in range(max_order + 1):
_, p, _ = _sig.besselap(m, norm='delay')
s_zeros = _np.zeros(m)
s_poles = c / r0 * p
s_gain = 1
z_zeros, z_poles, z_gain = s2z(s_zeros, s_poles, s_gain, fs)
sos.append(_sig.zpk2sos(z_zeros, z_poles, z_gain, pairing='nearest'))
selection = _util.source_selection_all(len(x0))
return (delay, weight, sos, phaseshift, selection,
_secondary_source_point(c))
def point_3d(x0, r0, xs, fs, max_order=None, c=None, s2z=matchedz_zpk):
r"""Virtual point source by 3-dimensional NFC-HOA.
.. math::
D(\phi_0, s) =
\frac{\e{\frac{s}{c}(r_0-r_\text{s})}}{4 \pi r_0 r_\text{s}}
\sum_{n=0}^{N}
(2n+1) P_{n}(\cos\Theta)
\Big(\frac{s-\frac{c}{r_\text{s}}\sigma_0}{s-\frac{c}{r_0}\sigma_0}\Big)^\mu
\prod_{l=1}^{\nu}
\frac{(s-\frac{c}{r_\text{s}}\sigma_l)^2-(\frac{c}{r_\text{s}}\omega_l)^2}
{(s-\frac{c}{r_0}\sigma_l)^2+(\frac{c}{r_0}\omega_l)^2}
The driving function is represented in the Laplace domain,
from which the recursive filters are designed.
:math:`\sigma_l + \i\omega_l` denotes the complex roots of
the reverse Bessel polynomial.
The number of second-order sections is
:math:`\nu = \big\lfloor\tfrac{|m|}{2}\big\rfloor`,
whereas the number of first-order section :math:`\mu` is either 0 or 1
for even and odd :math:`|m|`, respectively.
:math:`P_{n}(\cdot)` denotes the Legendre polynomial of degree :math:`n`,
and :math:`\Theta` the angle between :math:`(\theta, \phi)`
and :math:`(\theta_\text{s}, \phi_\text{s})`.
Parameters
----------
x0 : (N, 3) array_like
Sequence of secondary source positions.
r0 : float
Radius of the spherial secondary source distribution.
xs : (3,) array_like
Virtual source position.
fs : int
Sampling frequency in Hertz.
max_order : int, optional
Ambisonics order.
c : float, optional
Speed of sound in m/s.
s2z : callable, optional
Function transforming s-domain poles and zeros into z-domain,
e.g. :func:`matchedz_zpk`, :func:`scipy.signal.bilinear_zpk`.
Returns
-------
delay : float
Overall delay in seconds.
weight : float
Overall weight.
sos : list of numpy.ndarray
Second-order section filters :func:`scipy.signal.sosfilt`.
phaseshift : (N,) numpy.ndarray
Phase shift in radians.
selection : (N,) numpy.ndarray
Boolean array containing only ``True`` indicating that
all secondary source are "active" for NFC-HOA.
secondary_source_function : callable
A function that can be used to create the sound field of a
single secondary source. See `sfs.td.synthesize()`.
"""
if max_order is None:
max_order = _util.max_order_spherical_harmonics(len(x0))
if c is None:
c = _default.c
x0 = _util.asarray_of_rows(x0)
xs = _util.asarray_1d(xs)
phi0, theta0, _ = _util.cart2sph(*x0.T)
phis, thetas, rs = _util.cart2sph(*xs)
phaseshift = _np.arccos(_np.dot(x0 / r0, xs / rs))
delay = (rs - r0) / c
weight = 1 / r0 / rs
sos = []
for m in range(max_order + 1):
_, p, _ = _sig.besselap(m, norm='delay')
s_zeros = c / rs * p
s_poles = c / r0 * p
s_gain = 1
z_zeros, z_poles, z_gain = s2z(s_zeros, s_poles, s_gain, fs)
sos.append(_sig.zpk2sos(z_zeros, z_poles, z_gain, pairing='nearest'))
selection = _util.source_selection_all(len(x0))
return (delay, weight, sos, phaseshift, selection,
_secondary_source_point(c))
def filter(self, *filt):
"""Apply the given filter to this `TimeSeries`.
All recognised filter arguments are converted either into cascading
second-order sections (if scipy >= 0.16 is installed), or into the
``(numerator, denominator)`` representation before being applied
to this `TimeSeries`.
.. note::
All filters are presumed to be digital (Z-domain), if you have
an analog ZPK (in Hertz or in rad/s) you should be using
`TimeSeries.zpk` instead.
.. note::
When using `scipy` < 0.16 some higher-order filters may be
unstable. With `scipy` >= 0.16 higher-order filters are
decomposed into second-order-sections, and so are much more stable.
Parameters
----------
*filt
one of:
- :class:`scipy.signal.lti`
- `MxN` `numpy.ndarray` of second-order-sections
(`scipy` >= 0.16 only)
- ``(numerator, denominator)`` polynomials
- ``(zeros, poles, gain)``
- ``(A, B, C, D)`` 'state-space' representation
Returns
-------
result : `TimeSeries`
the filtered version of the input `TimeSeries`
See also
--------
TimeSeries.zpk
for instructions on how to filter using a ZPK with frequencies
in Hertz
scipy.signal.sosfilter
for details on the second-order section filtering method
(`scipy` >= 0.16 only)
scipy.signal.lfilter
for details on the filtering method
Raises
------
ValueError
If ``filt`` arguments cannot be interpreted properly
"""
sos = None
# single argument given
if len(filt) == 1:
filt = filt[0]
# detect LTI
if isinstance(filt, signal.lti):
filt = filt
a = filt.den
b = filt.num
# detect SOS
elif isinstance(filt, numpy.ndarray) and filt.ndim == 2:
sos = filt
# detect taps
else:
b = filt
a = [1]
# detect TF
elif len(filt) == 2:
b, a = filt
elif len(filt) == 3:
try:
sos = signal.zpk2sos(*filt)
except AttributeError:
b, a = signal.zpk2tf(*filt)
elif len(filt) == 4:
try:
zpk = signal.ss2zpk(*filt)
sos = signal.zpk2sos(zpk)
except AttributeError:
b, a = signal.ss2tf(*filt)
else:
raise ValueError("Cannot interpret filter arguments. Please "
"give either a signal.lti object, or a "
"tuple in zpk or ba format. See "
"scipy.signal docs for details.")
if sos is not None:
new = signal.sosfilt(sos, self, axis=0).view(self.__class__)
else:
new = signal.lfilter(b, a, self, axis=0).view(self.__class__)
new.__dict__ = self.copy_metadata()
return new
#dt = np.sum(np.abs(examp_time[:-1])) / (ntimesteps-1)
dt = duration / ntimesteps
dt_test = abs(examp_time[-1]-examp_time[0]) / ntimesteps
if dt_test != dt and rank == 0:
msg = 'Small discrepancy between inferred and prescribed sampling rate:'
warn(msg)
print(dt)
print(dt_test)
# Determine the sampling rate
fs_old = 1./dt
# Get filter coeff
z, p, k = cheby2_lowpass(fs_old,freq)
sos = zpk2sos(z, p, k)
# Determine which channels to save...
if channel is not 'all':
cha_incr = 3
if channel == 'MXN':
cha_offset = 0
elif channel == 'MXE':
cha_offset = 1
elif channel == 'MXZ':
cha_offset = 2
else:
cha_incr = 1
cha_offset = 0
counter = 0
def filter_zpk(timeseries, z, p, k):
"""Return a new timeseries that was filtered with a zero-pole-gain filter.
The transfer function in the s-domain looks like:
.. math::
\\frac{H(s) = (s - s_1) * (s - s_3) * ... * (s - s_n)}{(s - s_2) * (s - s_4) * ... * (s - s_m)}, m >= n
The zeroes, and poles entered in Hz are converted to angular frequency,
along the imaginary axis in the s-domain s=i*omega. Then the zeroes, and
poles are bilinearly transformed via:
.. math::
z(s) = \\frac{(1 + s*T/2)}{(1 - s*T/2)}
Where z is the z-domain value, s is the s-domain value, and T is the
sampling period. After the poles and zeroes have been bilinearly
transformed, then the second-order sections are found and filter the data
using scipy.
Parameters
----------
timeseries: TimeSeries
The TimeSeries instance to be filtered.
z: array
Array of zeros to include in zero-pole-gain filter design.
In units of Hz.
p: array
Array of poles to include in zero-pole-gain filter design.
In units of Hz.
k: float
Gain to include in zero-pole-gain filter design. This gain is a
constant multiplied to the transfer function.
Returns
-------
Time Series: TimeSeries
A new TimeSeries that has been filtered.
Examples
--------
To apply a 5 zeroes at 100Hz, 5 poles at 1Hz, and a gain of 1e-10 filter
to a TimeSeries instance, do:
>>> filtered_data = zpk_filter(timeseries, [100]*5, [1]*5, 1e-10)
"""
# sanity check type
if not isinstance(timeseries, TimeSeries):
raise TypeError("Can only filter TimeSeries instances.")
# sanity check casual filter
degree = len(p) - len(z)
if degree < 0:
raise TypeError("May not have more zeroes than poles. \
Filter is not casual.")
# cast zeroes and poles as arrays and gain as a float
z = np.array(z)
p = np.array(p)
k = float(k)
# put zeroes and poles in the s-domain
# convert from frequency to angular frequency
z *= -2 * np.pi
p *= -2 * np.pi
# get denominator of bilinear transform
fs = 2.0 * timeseries.sample_rate
# zeroes in the z-domain
z_zd = (1 + z/fs) / (1 - z/fs)
# any zeros that were at infinity are moved to the Nyquist frequency
z_zd = z_zd[np.isfinite(z_zd)]
z_zd = np.append(z_zd, -np.ones(degree))
# poles in the z-domain
p_zd = (1 + p/fs) / (1 - p/fs)
# gain change in z-domain
k_zd = k * np.prod(fs - z) / np.prod(fs - p)
# get second-order sections
sos = zpk2sos(z_zd, p_zd, k_zd)
# filter
filtered_data = sosfilt(sos, timeseries.numpy())
return TimeSeries(filtered_data, delta_t = timeseries.delta_t,
dtype=timeseries.dtype,
epoch=timeseries._epoch)
