def bold_convolution(bold_timeseries, duration, win_func=boxcar):
window=win_func(duration)
n_roi = bold_timeseries.data.shape[0]
convolved_bold = []
for i in range(n_roi):
convolution = convolve(np.abs(bold_timeseries.data[i]), window)
convolved_bold.append(convolution)
ts_convolved = TimeSeries(np.vstack(convolved_bold),
sampling_interval=np.float(bold_timeseries.sampling_interval))
return ts_convolved
def bold_convolution(bold_timeseries, duration, win_func=boxcar):
window=win_func(duration)
n_roi = bold_timeseries.data.shape[0]
convolved_bold = []
for i in range(n_roi):
convolution = convolve(np.abs(bold_timeseries.data[i]), window)
convolved_bold.append(convolution)
ts_convolved = TimeSeries(np.vstack(convolved_bold),
sampling_interval=np.float(bold_timeseries.sampling_interval))
return ts_convolved
def process(self, signals):
InstrumentBase.process(self, signals)
sout = []
for sig in signals:
outSig = Signal()
outSig.name = u'FIR (' + sig.name + u')'
#new = signaltools.lfilter(self.num, self.den, sig.dataY)
new = signaltools.convolve(sig.get_dataY(), self.__den)
outSig.set_data(new, None)
sout.append(outSig)
self['xAxisLabel'] = sig['xAxisLabel']
self['yAxisLabel'] = sig['yAxisLabel']
return sout
signal = ifft(ifftshift(signal))
# Adding noise to the signal
snr = -80
snr = db_to_power(snr)
noise = SignalSource(snr, SignalSource.TYPE_GAUSS).get_signal(signal.shape)
signal += noise
signal = np.complex128(np.real(signal))
# Shift signal to zero frequency
first_signal_position = signal_positions.ravel().nonzero()[0][0] - int(window_length / 2)
n_samples_shift = first_signal_position + int(n_signal_positions / 2)
exponential = np.exp(-2j * np.pi * (n_samples_shift / window_length) * np.arange(0, window_length))
signal *= exponential
antialiasing_filter = np.load('filter_coefficients.npy')
plot_dft_abs_phase(signal, frequency_discretization, is_in_db=True)
# antializsing filter
signal = convolve(signal, antialiasing_filter, mode='same')
# decimation
signal = signal[::3]
plot_dft_abs_phase(signal, frequency_discretization/3, is_in_db=True)
# input("Press Enter to finish...")
def filt1d(array, nmed, nlin, fill = False, circ = False):
"""Nonlinear (median+boxcar) filter with edge reflection."""
nmed = 2 * int(nmed/2) + 1
N = len(array)
if N < (3*nmed):
return array
# Check for NaNs
lnan = numpy.isnan(array)
nnan = sum(lnan)
if (nnan != 0):
lnotnan = numpy.where(lnan==0)
s = numpy.shape(lnotnan)
if (len(s)>1):
s = numpy.size(lnotnan)
lnotnan = numpy.reshape(lnotnan, s)
med = numpy.median(array[lnotnan])
# Fill in any data gaps by interpolating over them ...
work = numpy.zeros(N)
il = numpy.min(lnotnan)
ih = numpy.max(lnotnan)
xnew = numpy.arange(ih-il+1) + il
f = interpolate.interp1d(lnotnan, array[lnotnan])
work[il:ih+1] = f(xnew)
# ... or extending slope of nearest data points if at the edges
if (il!=0):
slope = work[il+1] - work[il]
for i in range(il): work[i] = work[il] - slope*(il-i)
if (ih!=N-1):
slope = work[ih] - work[ih-1]
for i in range(N-ih-1)+ih+1: work[i] = work[ih] + slope*(i-ih)
else:
work = numpy.copy(array)
# Edge reflection
nr = min(20, nlin)
sz = max([nmed, nlin])
if sz >= (N-1):
sz = N-2
if circ != False:
wl = work[N-sz:]
wr = work[:sz]
else:
wl = array[0:sz]
pivot = numpy.median(array[:nr])
wl = 2 * pivot - wl
wl = wl[::-1] # reverse array
wr = array[N-sz:N]
pivot = numpy.median(array[N-nr:N])
wr = 2 * pivot - wr
wr = wr[::-1] # reverse array
work2 = numpy.zeros(N + 2 * sz)
work2[0:sz] = wl
work2[sz:sz+N] = work
work2[sz+N:2*sz+N] = wr
# Filter
if nmed > 1: work = signaltools.medfilt(work2, nmed)
else: work = work2
box = scipy.signal.boxcar(2*nlin+1)
work = signaltools.convolve(work, box) / float(2*nlin+1)
padd = (len(work) - N - 2 * sz) / 2
work = work[padd:padd+N+2*sz]
# return to orginal array bounds
result = work[sz:N+sz]
# replace bad data if present
if (fill==False) * (nnan!=0): result[lnan] = numpy.nan
return result
def process(self, signals):
InstrumentBase.process(self, signals)
from scipy.fftpack import fft
from scipy.signal import signaltools
from Numeric import convolve
dOverlay = self['overlay']
dAverages = self['averages']
dLinenumber = FFT_LINENUMBER[self['linenumber']]
dWindow = self['window']
# get float from overlay string etc. "2/3" = float(2./3.)
overlay = [float(a) for a in split(FFT_OVERLAY[dOverlay], '/')]
if len(overlay)==1: fOverlay = float(overlay[0])
else: fOverlay = overlay[0]/overlay[1]
length = dLinenumber
fft_length = dLinenumber
dIncrement = int(length * (1-fOverlay))
sout = []
for s in signals: # process for every signal
data = s.get_dataY()
datalength = s.get_size()
if datalength < length:
data = resize(data, (length,))
datalength = length
av_from = 0
if dWindow!=0: # rectangular
wfunc = getWindowFunction(dWindow, length)
for i in range(dAverages):
av_to = av_from+length
if av_to>datalength:
break # end of data
dt = data[av_from:av_to]
l = len(dt)
if dWindow!=0: # rectangular
dt = signaltools.convolve(dt, wfunc) # weighting by window function
spectrum = fft(dt)
spectrum_real = abs(spectrum[:fft_length/2].real)
# recursive average
if i>1:
out = 0.5*(out + spectrum_real) # averaging
else:
out = spectrum_real # initial or single
av_from += dIncrement
#sig = abs(fft(data)[1:len(s.dataY)/2+1].real)
outSig = SignalSpectrum()
outSig.name = self.name + ': ' + s.name
df = 1.#TODO: s['fs']/float(dLinenumber)
outSig.set_data(out, None)#, df*arange(df, dLinenumber+df))
outSig['xAxisLabel'] = self['xAxisLabel']
outSig['yAxisLabel'] = self['yAxisLabel']
outSig['xUnit'] = self['xUnit']
sout.append(outSig)
return sout
def filt1d(array, nmed, nlin, fill=False, circ=False):
"""Nonlinear (median+boxcar) filter with edge reflection."""
nmed = 2 * int(nmed / 2) + 1
N = len(array)
if N < (3 * nmed):
return array
# Check for NaNs
lnan = numpy.isnan(array)
nnan = sum(lnan)
if (nnan != 0):
lnotnan = numpy.where(lnan == 0)
s = numpy.shape(lnotnan)
if (len(s) > 1):
s = numpy.size(lnotnan)
lnotnan = numpy.reshape(lnotnan, s)
med = numpy.median(array[lnotnan])
# Fill in any data gaps by interpolating over them ...
work = numpy.zeros(N)
il = numpy.min(lnotnan)
ih = numpy.max(lnotnan)
xnew = numpy.arange(ih - il + 1) + il
f = interpolate.interp1d(lnotnan, array[lnotnan])
work[il:ih + 1] = f(xnew)
# ... or extending slope of nearest data points if at the edges
if (il != 0):
slope = work[il + 1] - work[il]
for i in range(il):
work[i] = work[il] - slope * (il - i)
if (ih != N - 1):
slope = work[ih] - work[ih - 1]
for i in range(N - ih - 1) + ih + 1:
work[i] = work[ih] + slope * (i - ih)
else:
work = numpy.copy(array)
# Edge reflection
nr = min(20, nlin)
sz = max([nmed, nlin])
if sz >= (N - 1):
sz = N - 2
if circ != False:
wl = work[N - sz:]
wr = work[:sz]
else:
wl = array[0:sz]
pivot = numpy.median(array[:nr])
wl = 2 * pivot - wl
wl = wl[::-1] # reverse array
wr = array[N - sz:N]
pivot = numpy.median(array[N - nr:N])
wr = 2 * pivot - wr
wr = wr[::-1] # reverse array
work2 = numpy.zeros(N + 2 * sz)
work2[0:sz] = wl
work2[sz:sz + N] = work
work2[sz + N:2 * sz + N] = wr
# Filter
if nmed > 1: work = signaltools.medfilt(work2, nmed)
else: work = work2
box = scipy.signal.boxcar(2 * nlin + 1)
work = signaltools.convolve(work, box) / float(2 * nlin + 1)
padd = (len(work) - N - 2 * sz) / 2
work = work[padd:padd + N + 2 * sz]
# return to orginal array bounds
result = work[sz:N + sz]
# replace bad data if present
if (fill == False) * (nnan != 0): result[lnan] = numpy.nan
return result