def downSampleAnalogSignal(analogSignal, downSampleFactor):
'''
Downsamples the input analogsignal, with the downsampled signal having the same t_start as analogsignal
:param analogSignal: neo.analogsignal
:param downSampleFactor: int, must be at least 1
:return: analogSignalDown, neo.analogsignal with sampling rate = analogsignal.sampling_rate/factor
and analogSignalDown.t_start = analogSignal.t_start
'''
assert type(downSampleFactor) == int, 'downsample factor must be an int'
assert downSampleFactor >= 1, 'downsample factor must be atleast 1'
if downSampleFactor == 1:
return analogSignal.copy()
else:
newSamplingRate = analogSignal.sampling_rate / downSampleFactor
downSamplingIndices = range(0, analogSignal.shape[0], downSampleFactor)
analogSignalMagnitude = analogSignal.magnitude[downSamplingIndices]
analogSignalDown = AnalogSignal(signal=analogSignalMagnitude,
units=analogSignal.units,
sampling_rate=newSamplingRate,
t_start=analogSignal.t_start)
analogSignalDown = analogSignalDown.reshape(
(analogSignalDown.shape[0], ))
return analogSignalDown
def calibrateSignal(inputSignal, calibString, calibUnitStr, forceUnits=None):
if calibString.find(';') > 0:
calibStrings = calibString.split(';')
elif calibString.find(':') > 0:
calibStrings = calibString.split(':')
elif all([x.isdigit() or x == '.' for x in calibString]):
calibStrings = [calibString]
else:
raise (ValueError(
"Improper Calibration string {}".format(calibString)))
ipSignalMag = inputSignal.magnitude.copy()
ipSigUnits = inputSignal.units
for calibString in calibStrings:
calib, startTime, endTime = parseCalibString(calibString, calibUnitStr)
if endTime is None:
endTime = inputSignal.t_stop
if startTime is None:
startTime = inputSignal.t_start
startIndex = int(
(startTime - inputSignal.t_start) * inputSignal.sampling_rate)
endIndex = int(
(endTime - inputSignal.t_start) * inputSignal.sampling_rate)
ipSignalMag[startIndex:endIndex] *= calib.magnitude
if forceUnits is not None:
ipSigUnits = forceUnits
else:
if ipSigUnits == qu.Quantity(1):
ipSigUnits = calib.units
elif ipSigUnits != calib.units:
raise (Exception('CalibStrings given don\'t have the same units'))
outputSignal = AnalogSignal(signal=ipSignalMag,
units=ipSigUnits,
sampling_rate=inputSignal.sampling_rate,
t_start=inputSignal.t_start)
outputSignal = outputSignal.reshape((outputSignal.shape[0], ))
return outputSignal
def downSampleVibSignal(self):
self.downSamplingFactor = int(
round(self.vibrationSignal.sampling_rate / (4 * self.maximumFreq)))
newSamplingRate = self.vibrationSignal.sampling_rate / self.downSamplingFactor
downSamplingIndices = range(0, self.vibrationSignal.shape[0],
self.downSamplingFactor)
vibSigDownMag = self.vibrationSignal.magnitude[downSamplingIndices]
vibSigDownMag -= np.median(vibSigDownMag)
self.vibrationSignalDownStdDev = np.std(
vibSigDownMag) * self.vibrationSignal.units
temp = AnalogSignal(signal=vibSigDownMag,
units=self.vibrationSignal.units,
sampling_rate=newSamplingRate,
t_start=self.vibrationSignal.t_start)
self.vibrationSignalDown = temp.reshape((temp.shape[0], ))
def downSampleVoltageSignal(self, downSamplingFactor=None):
if downSamplingFactor is None:
downSamplingFactor = self.downSamplingFactor
newSamplingRate = self.voltageSignal.sampling_rate / downSamplingFactor
downSamplingIndices = range(0, self.voltageSignal.shape[0],
downSamplingFactor)
voltageSignalDown = AnalogSignal(
signal=self.voltageSignal.magnitude[downSamplingIndices],
units=self.voltageSignal.units,
sampling_rate=newSamplingRate,
t_start=self.voltageSignal.t_start)
voltageSignalDown = voltageSignalDown.reshape(
(voltageSignalDown.shape[0], ))
return voltageSignalDown
def filterButterworth(analogSignal, cutoff=100, transitionWidth=40, rippleDB=20):
cutoff *= qu.Hz
nyqFreq = analogSignal.sampling_rate / 2
# b, a = iirfilter(order, cutoff / nyqFreq, btype='highpass', ftype='butter')
transitionWidth = transitionWidth * qu.Hz
N, beta = kaiserord(rippleDB, transitionWidth / nyqFreq)
tapsLP = firwin(N, cutoff / nyqFreq, window=('kaiser', beta))
temp = np.zeros((N,))
temp[(N - 1) / 2] = 1
tapsHP = temp - tapsLP
delay = (N - 1) * 0.5 * analogSignal.sampling_period
w, h = freqz(tapsHP, 1.0, int(nyqFreq))
f = w * (nyqFreq) / (2 * PI)
sigM = analogSignal.magnitude
sigM = sigM.reshape((sigM.shape[0],))
sigMFiltered = lfilter(tapsHP, 1.0, sigM)
temp = AnalogSignal(
signal=sigMFiltered,
sampling_rate=analogSignal.sampling_rate,
units=analogSignal.units,
t_start=analogSignal.t_start - delay
)
filteredSignal = temp.reshape((temp.shape[0],))
# from scipy.fftpack import fft
# plt.ion()
# fig1 = plt.figure()
#
# plt.plot(f, h, 'b-o')
# plt.xlabel('Frequency(Hz)')
# plt.ylabel('Gain')
# plt.draw()
#
# fig2 = plt.figure()
#
#
# plt.plot(analogSignal.times, analogSignal, 'r')
# plt.plot(filteredSignal.times, filteredSignal, 'b')
# plt.legend(['Original Signal', 'Filtered Signal'])
# plt.xlabel('Time in ' + analogSignal.sampling_period.dimensionality.string)
# plt.draw()
#
# fig3 = plt.figure()
#
#
# freqResolution = 5 * qu.Hz
# NFFT = np.ceil(2 * nyqFreq / freqResolution).simplified
# NFFT = int(np.ceil(NFFT / 2) * 2)
# actualFreqResolution = 2 * nyqFreq / NFFT
# frequencies = np.arange(int(NFFT/2)) * actualFreqResolution
#
#
# outSig = filteredSignal.magnitude
#
#
# origFFT = fft(sigM, NFFT)
# origFFT[0] = 0
# plt.plot(frequencies, np.abs(origFFT)[:int(NFFT/2)])
#
# filtFFT = fft(outSig, NFFT)
# plt.plot(frequencies, np.abs(filtFFT)[:int(NFFT/2)])
#
# plt.legend(['FFT of Original Signal', 'FFT of Filtered Signal'])
# plt.xlabel('Frequency(Hz)')
# plt.draw()
# raw_input()
# plt.close(fig1.number)
# plt.close(fig2.number)
# plt.close(fig3.number)
return filteredSignal
blk = nixFile.blocks["Simulation Traces"]
dlint1MemV = blk.data_arrays["DLInt1 MemV"]
dlint1SpikesMT = blk.multi_tags["DLInt1 Spikes"]
dlint2MemV = blk.data_arrays["DLInt2 MemV"]
dlint2SpikesMT = blk.multi_tags["DLInt2 Spikes"]
sinInput = blk.data_arrays["Input Vibration Signal"]
joSpikesMT = blk.multi_tags["JO Spikes"]
dlint1MemVAS = dataArray2AnalogSignal(dlint1MemV)
dlint2MemVAS = dataArray2AnalogSignal(dlint2MemV)
temp = dataArray2AnalogSignal(sinInput)
sinInputAS = AnalogSignal(signal=15 * temp.magnitude,
units=temp.units,
t_start=temp.t_start,
sampling_period=temp.sampling_period)
sinInputAS = sinInputAS.reshape((sinInputAS.shape[0], ))
dlint1SpikesST = multiTag2SpikeTrain(dlint1SpikesMT, sinInputAS.t_start,
sinInputAS.t_stop)
dlint2SpikesST = multiTag2SpikeTrain(dlint2SpikesMT, sinInputAS.t_start,
sinInputAS.t_stop)
joSpikesST = multiTag2SpikeTrain(joSpikesMT, sinInputAS.t_start,
sinInputAS.t_stop)
# fig0, ax0 = plt.subplots(figsize=(2.5, 1.5))
# fig1, ax1 = plt.subplots(figsize=(2.5, 1.5))
# fig2, ax2 = plt.subplots(figsize=(2.5, 1.75))
#
fig0, ax0 = plt.subplots(figsize=(2.85, 1.5))
fig1, ax1 = plt.subplots(figsize=(2.85, 1.5))
fig2, ax2 = plt.subplots(figsize=(2.85, 1.75))
