def centroid(xarr, yarr, kern=default_kernal, mask=None, mode="same"):
"""Find the centroid of a line following a similar algorithm as
the center1d algorithm in IRAF. xarr and yarr should be an area
around the desired feature to be centroided. The default kernal
is used if the user does not specific one.
The algorithm solves for the solution to the equation
..math:: \int (I-I_0) f(x-x_0) dx = 0
returns xc
"""
if len(yarr) < len(kern):
raise SpectrographError("Array has to be larger than kernal")
if mask is not None:
# catch the fact that at the edges it
if mask.sum() < len(default_kernal):
warr = np.convolve(yarr, kern, mode=mode)
xc = np.interp(0, warr[mask], xarr[mask])
return xc
else:
yarr = yarr[mask]
xarr = xarr[mask]
# convle the input array with the default kernal
warr = np.convolve(yarr, kern, mode=mode)
# interpolate the results
xc = np.interp(0, warr, xarr)
return xc
def high_pass_filter(x, y, L):
y_filter = -np.ones(L)/L
y_filter[L/2] += 1
new_y = np.convolve(y, y_filter, 'valid')
x_filter = np.zeros(L)
x_filter[L/2] = 1
return np.convolve(x, x_filter, 'valid'), np.convolve(y, y_filter, 'valid')
def function1D(self, t):
A = self.getParamValue(0)
B = self.getParamValue(1)
R = self.getParamValue(2)
T0 = self.getParamValue(3)
Scale = self.getParamValue(4)
HatWidth = self.getParamValue(5)
KConv = self.getParamValue(6)
# A/2 Scale factor has been removed to make A and Scale independent
f_int = Scale*((1-R)*np.power((A*(t-T0)),2)*
np.exp(-A*(t-T0))+2*R*A**2*B/np.power((A-B),3) *
(np.exp(-B*(t-T0))-np.exp(-A*(t-T0))*(1+(A-B)*(t-T0)+0.5*np.power((A-B),2)*np.power((t-T0),2))))
f_int[t<T0] = 0
mid_point_hat = len(f_int)//2
gc_x = np.array(range(len(f_int))).astype(float)
ppd = 0.0*gc_x
lowIDX = int(np.floor(np.max([mid_point_hat-np.abs(HatWidth),0])))
highIDX = int(np.ceil(np.min([mid_point_hat+np.abs(HatWidth),len(gc_x)])))
ppd[lowIDX:highIDX] = 1.0
ppd = ppd/sum(ppd)
gc_x = np.array(range(len(f_int))).astype(float)
gc_x = 2*(gc_x-np.min(gc_x))/(np.max(gc_x)-np.min(gc_x))-1
gc_f = np.exp(-KConv*np.power(gc_x,2))
gc_f = gc_f/np.sum(gc_f)
npad = len(f_int) - 1
first = npad - npad//2
f_int = np.convolve(f_int,ppd,'full')[first:first+len(f_int)]
f_int = np.convolve(f_int,gc_f,'full')[first:first+len(f_int)]
return f_int
def filter(dat, bin_freq, type='exp', window=300, prm=0.2):
"""
turn psth into firing rate estimate. window size is in ms
"""
if dat is None:
return None, None
window = np.int(window / (1. / bin_freq * 1000))
r = np.arange(-window, window + 1)
kern = np.exp(r * -prm)
kern[: len(kern) / 2] = 0
kern = kern / kern.sum()
if len(dat.shape) > 1:
fr = np.zeros_like(dat, dtype=np.float)
for d in range(len(dat)):
fr[d] = np.convolve(dat[d], kern, 'same')
else:
fr = np.convolve(dat, kern, 'same')
# import pylab as plt
# plt.subplot(311)
# plt.plot(kern)
# plt.subplot(312)
# plt.plot(dat[:5, :50].T)
# plt.subplot(313)
# plt.plot(fr[:5, :50].T)
# plt.show()
return fr, len(kern) / 2
def richardson_lucy_deconvolution(self, psf, iterations=15,
mask=None):
"""1D Richardson-Lucy Poissonian deconvolution of
the spectrum by the given kernel.
Parameters
----------
iterations: int
Number of iterations of the deconvolution. Note that
increasing the value will increase the noise amplification.
psf: EELSSpectrum
It must have the same signal dimension as the current
spectrum and a spatial dimension of 0 or the same as the
current spectrum.
Notes:
-----
For details on the algorithm see Gloter, A., A. Douiri,
M. Tence, and C. Colliex. “Improving Energy Resolution of
EELS Spectra: An Alternative to the Monochromator Solution.”
Ultramicroscopy 96, no. 3–4 (September 2003): 385–400.
"""
self._check_signal_dimension_equals_one()
ds = self.deepcopy()
ds.data = ds.data.copy()
ds.mapped_parameters.title += (
' after Richardson-Lucy deconvolution %i iterations' %
iterations)
if ds.tmp_parameters.has_item('filename'):
ds.tmp_parameters.filename += (
'_after_R-L_deconvolution_%iiter' % iterations)
psf_size = psf.axes_manager.signal_axes[0].size
kernel = psf()
imax = kernel.argmax()
j = 0
maxval = self.axes_manager.navigation_size
if maxval > 0:
pbar = progressbar(maxval=maxval)
for D in self:
D = D.data.copy()
if psf.axes_manager.navigation_dimension != 0:
kernel = psf(axes_manager=self.axes_manager)
imax = kernel.argmax()
s = ds(axes_manager=self.axes_manager)
mimax = psf_size -1 - imax
O = D.copy()
for i in xrange(iterations):
first = np.convolve(kernel, O)[imax: imax + psf_size]
O = O * (np.convolve(kernel[::-1],
D / first)[mimax: mimax + psf_size])
s[:] = O
j += 1
if maxval > 0:
pbar.update(j)
if maxval > 0:
pbar.finish()
return ds
def noiseFilter(data_in): N = int(np.ceil((4 / b))) if not N % 2: N += 1 # Make sure that N is odd. n = np.arange(N) # Compute a low-pass filter with cutoff frequency fH. hlpf = np.sinc(2 * fH * (n - (N - 1) / 2.)) hlpf *= np.blackman(N) hlpf = hlpf / np.sum(hlpf) # Compute a high-pass filter with cutoff frequency fL. hhpf = np.sinc(2 * fL * (n - (N - 1) / 2.)) hhpf *= np.blackman(N) hhpf = hhpf / np.sum(hhpf) hhpf = -hhpf hhpf[(N - 1) / 2] += 1 # Convolve both filters. h = np.convolve(hlpf, hhpf) s = np.convolve(data_in, hlpf) fig, ax = plt.subplots() ax.plot(data_in) plt.show() fig1, ax1 = plt.subplots() ax1.plot(s) plt.show() return s
def auto_guess(f, data):
"""
Use the linewidth and the transmission ratio on and off resonance
to guess the initial Q values. Estimate the linewidth by
smoothing then looking for the extrema of the first
derivative. This may fail if the resonance is very close to the
edge of the data.
"""
p = Parameters()
bw = f.max() - f.min()
# Allow f_0 to vary by +/- the bandwidth over which we have data
p.add('f_0', value = f[np.argmin(abs(data))],
min = f.min() - bw, max = f.max() + bw)
off = np.mean((np.abs(data[0]), np.abs(data[-1])))
p.add('A_mag', value = off,
min = 0, max = 1e6)
p.add('A_phase', value = np.mean(np.angle(data)),
min = -np.pi, max = np.pi)
width = int(f.size / 10)
gaussian = np.exp(-np.linspace(-4, 4, width)**2)
gaussian /= np.sum(gaussian) # not necessary
smoothed = np.convolve(gaussian, abs(data), mode='same')
derivative = np.convolve(np.array([1, -1]), smoothed, mode='same')
# Exclude the edges, which are affected by zero padding.
linewidth = (f[np.argmax(derivative[width:-width])] -
f[np.argmin(derivative[width:-width])])
p.add('Q', value = p['f_0'].value / linewidth,
min = 1, max = 1e7) # This seems to stop an occasional failure mode.
p.add('Q_e_real', value = (p['Q'].value /
(1 - np.min(np.abs(data)) / off)),
min = 1, max = 1e6) # As above.
p.add('Q_e_imag', value = 0, min = -1e6, max = 1e6)
return p
def gauss_filter(dat, bin_freq, window=300, sigma=100):
"""
turn psth into firing rate estimate. window size is in ms
"""
if dat is None:
return None, None
window = np.int(1. / bin_freq * window)
sigma = np.int(1. / bin_freq * sigma)
r = range(-int(window / 2), int(window / 2) + 1)
gaus = [1 / (sigma * np.sqrt(2 * np.pi)) *
np.exp(-float(x) ** 2 / (2 * sigma ** 2)) for x in r]
if len(dat.shape) > 1:
fr = np.zeros_like(dat, dtype=np.float)
for d in range(len(dat)):
fr[d] = np.convolve(dat[d], gaus, 'same')
else:
fr = np.convolve(dat, gaus, 'same')
# import pylab as plt
# print bin_freq
# plt.subplot(311)
# plt.plot(gaus)
# plt.subplot(312)
# plt.plot(dat[:5].T)
# plt.subplot(313)
# plt.plot(fr[:5].T)
# plt.show()
return fr, len(gaus) / 2
def runExperiment3():
"""
Change task at iteration=500, test continuous learning
:return:
"""
Nelements = 20
noiseLevel = 0.0
encoder = initializeEncoder(Nelements, seed=1)
cla, sdrClassifier = initializeClassifiers(Nelements, encoder)
(negLLTrack,
accuracyTrack) = runSimulation(encoder, cla, sdrClassifier,
noiseLevel, changeTaskAfter=500)
plt.figure(5)
negLLTrack = numpy.array(negLLTrack)
v = numpy.ones((5,)) / 5
plt.subplot(2, 2, 1)
plt.plot(numpy.convolve(negLLTrack[:, 1], v, 'valid'))
plt.plot(numpy.convolve(negLLTrack[:, 0], v, 'valid'))
plt.ylim([-4, .1])
plt.ylabel(' Log-Likelihood')
plt.xlabel(' Iteration ')
plt.title(' Noise Level: ' + str(noiseLevel))
plt.legend(['SDR Classifier', 'CLA Classifier'], loc=4)
if not os.path.exists('results'):
os.makedirs('results')
plt.savefig(os.path.join('results', 'LLvsTraining_ChangeAt500.pdf'))
def find_strand_shift(gdb, fwd_track, rev_track):
# use a single chromosome to find shift between strands
# that gives max covariance.
if gdb.assembly == "dm3":
chrom = gdb.get_chromosome("chr2L")
else:
chrom = gdb.get_chromosome("chr21")
sys.stderr.write("retrieving values\n")
fwd_vals = fwd_track.get_nparray(chrom)
rev_vals = rev_track.get_nparray(chrom)
# smooth values using sliding window
sys.stderr.write("smoothing values\n")
win = np.ones(SMOOTH_WIN_SIZE)
fwd_vals = np.convolve(fwd_vals, win, mode="same")
rev_vals = np.convolve(rev_vals, win, mode="same")
# only use regions with high density of sites so all of contribution
# to covariance comes from these
fwd_cutoff = scipy.stats.scoreatpercentile(fwd_vals, 95)
rev_cutoff = scipy.stats.scoreatpercentile(rev_vals, 95)
fwd_vals[fwd_vals < fwd_cutoff] = 0
rev_vals[rev_vals < rev_cutoff] = 0
# find the shift that yields the max covariance
max_cov_shift = find_max_cov(fwd_vals, rev_vals)
return max_cov_shift
def _jacobian(self, param, y, weights=None):
if weights is None:
weights = 1.
if self.convolved is True:
counter = 0
grad = np.zeros(len(self.axis.axis))
for component in self: # Cut the parameters list
if component.active:
component.fetch_values_from_array(
param[
counter:counter +
component._nfree_param],
onlyfree=True)
if component.convolved:
for parameter in component.free_parameters:
par_grad = np.convolve(
parameter.grad(self.convolution_axis),
self.low_loss(self.axes_manager),
mode="valid")
if parameter._twins:
for par in parameter._twins:
np.add(par_grad, np.convolve(
par.grad(
self.convolution_axis),
self.low_loss(self.axes_manager),
mode="valid"), par_grad)
grad = np.vstack((grad, par_grad))
else:
for parameter in component.free_parameters:
par_grad = parameter.grad(self.axis.axis)
if parameter._twins:
for par in parameter._twins:
np.add(par_grad, par.grad(
self.axis.axis), par_grad)
grad = np.vstack((grad, par_grad))
counter += component._nfree_param
to_return = grad[1:, self.channel_switches] * weights
else:
axis = self.axis.axis[self.channel_switches]
counter = 0
grad = axis
for component in self: # Cut the parameters list
if component.active:
component.fetch_values_from_array(
param[
counter:counter +
component._nfree_param],
onlyfree=True)
for parameter in component.free_parameters:
par_grad = parameter.grad(axis)
if parameter._twins:
for par in parameter._twins:
np.add(par_grad, par.grad(
axis), par_grad)
grad = np.vstack((grad, par_grad))
counter += component._nfree_param
to_return = grad[1:, :] * weights
if self.signal.metadata.Signal.binned is True:
to_return *= self.signal.axes_manager[-1].scale
return to_return
def output(self):
"""The natural output for this analyzer is the analytic signal"""
data = self.input.data
sampling_rate = self.input.sampling_rate
a_signal =\
ts.TimeSeries(data=np.zeros(self.freqs.shape+data.shape,
dtype='D'),sampling_rate=sampling_rate)
if self.freqs.ndim == 0:
w = self.wavelet(self.freqs,self.sd,
sampling_rate=sampling_rate,ns=5,
normed='area')
nd = (w.shape[0]-1)/2
a_signal.data[...] = (np.convolve(data,np.real(w),mode='same') +
1j*np.convolve(data,np.imag(w),mode='same'))
else:
for i,(f,sd) in enumerate(zip(self.freqs,self.sd)):
w = self.wavelet(f,sd,sampling_rate=sampling_rate,
ns=5,normed='area')
nd = (w.shape[0]-1)/2
a_signal.data[i,...] = (np.convolve(data,np.real(w),mode='same')+1j*np.convolve(data,np.imag(w),mode='same'))
return a_signal
def smooth(self, signal, pad=True):
"""
Returns smoothed signal (or it's n-th derivative).
Parameters
----------
y : array_like, shape (N,)
the values of the time history of the signal.
pad : bool
pad first and last values to lessen the end effects.
Returns
-------
ys : ndarray, shape (N)
the smoothed signal (or it's n-th derivative).
"""
coeff = self._coeff
n = size(coeff - 1) // 2
y = np.squeeze(signal)
if pad:
first_vals = y[0] - abs(y[n:0:-1] - y[0])
last_vals = y[-1] + abs(y[-2:-n - 2:-1] - y[-1])
y = concatenate((first_vals, y, last_vals))
n *= 2
d = y.ndim
if d > 1:
y1 = y.reshape(y.shape[0], -1)
res = []
for i in range(y1.shape[1]):
res.append(convolve(y1[:, i], coeff)[n:-n])
res = np.asarray(res).T
else:
res = convolve(y, coeff)[n:-n]
return res
def apply_window_function(cls, input_array, window_size, output_array):
sum_filter = np.ones((window_size,), dtype=np.float32)/window_size
squares = np.square(input_array)
sum_of_squares = np.convolve(squares, sum_filter, mode='valid')
sums = np.convolve(input_array, sum_filter, mode='valid')
squares_of_sums = np.square(sums)
output_array[:] = squares_of_sums/sum_of_squares
def find_blinks_using_edge(data, plot = False, **kwargs):
"""Find location of blinks in data"""
global window_size_
records = OrderedDict()
window = np.ones(window_size_)/window_size_
t, y = data[:,0], data[:,1]
# Smooth out the vectors.
yvec = np.convolve(y, window, 'same')
records['smooth'] = (t, y)
newY = 0.5*yvec.mean() - yvec
newY = newY + np.fabs(newY)
window = np.ones(window_size_)/(window_size_)
yy = np.convolve(newY, window, 'same')
blinks = []
while yy.max() > 10:
i = np.argmax(yy)
isBlink, a = get_blink(i, yy)
if isBlink:
blinks.append((i, a))
xvec, yvec = [], []
for i, x in sorted(blinks):
xvec.append(t[i])
yvec.append(x)
return xvec, yvec
def slidingWindowV(P,inner=3,outer=64,maxM=50,minM=7,maxT=59,norm=True): """ Enhance the constrast vertically (along frequency dimension) Cut off extreme values and demean the image Utilize numpy convolve to get the mean at a given pixel Remove local mean with inner exclusion region Args: P: 2-d numpy array image inner: inner exclusion region outer: length of the window maxM: size of the output image in the y-dimension norm: boolean to cut off extreme values Returns: Q: 2-d numpy contrast enhanced vertically """ Q = P.copy() m, n = Q.shape if norm: mval, sval = np.mean(Q[minM:maxM,:maxT]), np.std(Q[minM:maxM,:maxT]) fact_ = 1.5 Q[Q > mval + fact_*sval] = mval + fact_*sval Q[Q < mval - fact_*sval] = mval - fact_*sval Q[:minM,:] = mval wInner = np.ones(inner) wOuter = np.ones(outer) for i in range(maxT): Q[:,i] = Q[:,i] - (np.convolve(Q[:,i],wOuter,'same') - np.convolve(Q[:,i],wInner,'same'))/(outer - inner) Q[Q < 0] = 0. return Q[:maxM,:]
def find_center_by_convolution(IM, **kwargs):
""" Center the image by convolution of two projections along each axis.
Code from the ``linbasex`` juptyer notebook
Parameters
----------
IM: numpy 2D array
image data
Returns
-------
center: tuple
(row-center, col-center)
"""
# projection along axis=0 of image (rows)
QL_raw0 = IM.sum(axis=1)
# projection along axis=1 of image (cols)
QL_raw1 = IM.sum(axis=0)
# autocorrelate projections
conv_0 = np.convolve(QL_raw0, QL_raw0, mode='full')
conv_1 = np.convolve(QL_raw1, QL_raw1, mode='full')
len_conv = len(conv_0)/2
# Take the first max, should there be several equal maxima.
# 10May16 - axes swapped - check this
center = (np.argmax(conv_0)/2, np.argmax(conv_1)/2)
if "projections" in kwargs.keys():
return center, conv_0, conv_1
else:
return center
def plot_data(data, nplots = 4):
global window_size_
window = np.ones(window_size_) / window_size_
tvec, yvec = data[:,0], data[:,1]
pylab.subplot(nplots, 1, 1)
pylab.plot(tvec, yvec, label="raw data")
pylab.legend()
yvec = np.convolve(yvec, window, 'same')
pylab.subplot(nplots, 1, 2)
pylab.plot(tvec, yvec, label='Window size = %s' % window_size_)
pylab.plot([0, tvec[-1]], [0.5*np.mean(yvec)]*2, label = '0.5*Mean pupil size')
pylab.legend()
pylab.subplot(nplots, 1, 4)
# When area reduces to half of eye pupil, it should be considered.
newY = 0.5*yvec.mean() - yvec
newY = newY + np.fabs(newY)
window = np.ones(3*window_size_)/(3*window_size_)
yy = np.convolve(newY, window, 'same')
pylab.plot(tvec, yy, label='Blinks')
pylab.xlabel("Time (seconds)")
outfile = 'output.png'
print("[INFO] Writing to %s" % outfile)
pylab.savefig(outfile)
def get_divergence_diversity_sliding(aft, block_length, VERBOSE=0):
'''Get local divergence and diversity in a sliding window'''
cons_ind = Patient.get_initial_consensus_noinsertions(aft, return_ind=True)
ind_N = cons_ind == 5
cons_ind[ind_N] = 0
aft_nonanc = 1.0 - aft[:, cons_ind, np.arange(aft.shape[2])]
aft_nonanc[:, ind_N] = 0
aft_var = (aft * (1 - aft)).sum(axis=1)
struct = np.ones(block_length)
dg = np.ma.array(np.apply_along_axis(lambda x: np.convolve(x, struct, mode='valid'),
axis=1, arr=aft_nonanc), hard_mask=True)
ds = np.ma.array(np.apply_along_axis(lambda x: np.convolve(x, struct, mode='valid'),
axis=1, arr=aft_var), hard_mask=True)
# NOTE: normalization happens based on actual coverage
norm = np.apply_along_axis(lambda x: np.convolve(x, struct, mode='valid'),
axis=1, arr=(-aft[:, 0].mask))
dg.mask = norm < block_length
dg /= norm
ds.mask = norm < block_length
ds /= norm
x = np.arange(dg.shape[1]) + (block_length - 1) / 2.0
return (x, dg, ds)
def lsf2poly(lsf):
"""Convert line spectral frequencies to prediction filter coefficients
returns a vector a containing the prediction filter coefficients from a vector lsf of line spectral frequencies.
.. doctest::
>>> from spectrum import lsf2poly
>>> lsf = [0.7842 , 1.5605 , 1.8776 , 1.8984, 2.3593]
>>> a = lsf2poly(lsf)
# array([ 1.00000000e+00, 6.14837835e-01, 9.89884967e-01,
# 9.31594056e-05, 3.13713832e-03, -8.12002261e-03 ])
.. seealso:: poly2lsf, rc2poly, ac2poly, rc2is
"""
# Reference: A.M. Kondoz, "Digital Speech: Coding for Low Bit Rate Communications
# Systems" John Wiley & Sons 1994 ,Chapter 4
# Line spectral frequencies must be real.
lsf = numpy.array(lsf)
if max(lsf) > numpy.pi or min(lsf) < 0:
raise ValueError('Line spectral frequencies must be between 0 and pi.')
p = len(lsf) # model order
# Form zeros using the LSFs and unit amplitudes
z = numpy.exp(1.j * lsf)
# Separate the zeros to those belonging to P and Q
rQ = z[0::2]
rP = z[1::2]
# Include the conjugates as well
rQ = numpy.concatenate((rQ, rQ.conjugate()))
rP = numpy.concatenate((rP, rP.conjugate()))
# Form the polynomials P and Q, note that these should be real
Q = numpy.poly(rQ);
P = numpy.poly(rP);
# Form the sum and difference filters by including known roots at z = 1 and
# z = -1
if p%2:
# Odd order: z = +1 and z = -1 are roots of the difference filter, P1(z)
P1 = numpy.convolve(P, [1, 0, -1])
Q1 = Q
else:
# Even order: z = -1 is a root of the sum filter, Q1(z) and z = 1 is a
# root of the difference filter, P1(z)
P1 = numpy.convolve(P, [1, -1])
Q1 = numpy.convolve(Q, [1, 1])
# Prediction polynomial is formed by averaging P1 and Q1
a = .5 * (P1+Q1)
return a[0:-1:1] # do not return last element
def watrous(z,scale,kernel=numpy.array([1.,4.,6.,4.,1.])/16.):
z=numpy.float32(z)
s=z.shape
sk=kernel.shape[0]
if len(s) == 1:
n=s[0]
w=numpy.zeros((s[0]*3,scale),dtype=numpy.float)
temp=z[0:n]
temp=temp[::-1]
w[0:n,0]=temp
w[n:s[0]+n,0]=z
temp=z[s[0]-n:]
temp=temp[::-1]
w[s[0]+n:,0]=temp
for i in range(0,scale-1):
# print i
k1=numpy.zeros((sk-1)*2.**i+1,dtype=numpy.float)
i1=numpy.array((numpy.arange(sk))*2.**i,dtype=numpy.int)
k1[i1]=kernel
tsmooth=numpy.convolve(w[:,i],k1,mode='same')
#tsmooth=scipy.signal.fftconvolve(w[:,i],k1,mode='same')
#print tsmooth[1000]
w[:,i]=w[:,i]-tsmooth
w[:,i+1]=tsmooth
w=w[n:s[0]+n,:]
elif len(s)==2:
w=numpy.zeros((s[0],s[1],scale),dtype=numpy.float)
w[:,:,0]=z
for i in range(0,scale-1):
k1=numpy.zeros((sk-1)*2.**i+1,dtype=numpy.float)
i1=numpy.array((numpy.arange(sk))*2.**i,dtype=numpy.int)
k1[i1]=kernel
k2=numpy.dot(k1,k1)
tsmooth=numpy.convolve(w[:,:,i],k2,mode='same')
#tsmooth=scipy.signal.fftconvolve(w[:,:,i],k2,mode='same')
w[:,:,i]=w[:,:,i]-tsmooth
w[:,:,i+1]=tsmooth
elif len(s)==3:
w=numpy.zeros((s[0],s[1],s[2]),dtype=numpy.float)
for l in range(0,s[2]):
w[:,:,l,0]=z[:,:,l]
for i in range(0,scale-1):
k1=numpy.zeros((sk-1)*2.**i+1,dtype=numpy.float)
i1=numpy.array((numpy.arange(sk))*2.**i,dtype=numpy.int)
k1[i1]=kernel
k2=numpy.dot(k1,k1)
tsmooth=numpy.convolve(w[:,:,l,i],k2,mode='same')
#tsmooth=scipy.signal.fftconvolve(w[:,:,l,i],k2,mode='same')
w[:,:,l,i]=w[:,:,l,i]-tsmooth
w[:,:,l,i+1]=tsmooth
else:
print("Wrong dimensions!")
return -1
return w
def cohere():
"""
Compute the coherence of two signals
mpl_examples/pylab_examples/cohere_demo.py
"""
import numpy as np
from smartplotlib import xyplot, subplot, alias
# make a little extra space between the subplots
dt = 0.01
t = np.arange(0, 30, dt)
nse1 = np.random.randn(len(t)) # white noise 1
nse2 = np.random.randn(len(t)) # white noise 2
r = np.exp(-t/0.05)
cnse1 = np.convolve(nse1, r, mode='same')*dt # colored noise 1
cnse2 = np.convolve(nse2, r, mode='same')*dt # colored noise 2
# two signals with a coherent part and a random part
s1 = 0.01*np.sin(2*np.pi*10*t) + cnse1
s2 = 0.01*np.sin(2*np.pi*10*t) + cnse2
ps1 = xyplot(t, s1, fmt='b-', y2= s2, fmt2="g-",
axes=211, xlabel="time", ylabel="s1 & s2")
ps1.go("fclear", "axes", "plot")
c = xyplot.cohere(s1, s2, 256, 1./dt,
ylabel="coherence", axes=212)
c.go("axes", "plot", "draw", "show")
return c
def score_region(motifs, seq):
# code the sequence
coded_seq = {}
for base in 'ACGT':
coded_seq[base] = np.zeros(len(seq), dtype='float32')
for i, base in enumerate(seq.upper()):
coded_seq[base][i] = 1
coded_RC_seq = {}
for base in 'TGCA':
coded_seq[base] = np.zeros(len(seq), dtype='float32')
motif_scores = []
for motif in motifs:
score_mat = motif.motif_data
scores = np.zeros(len(seq)-len(score_mat)+1, dtype='float32')
for base, base_scores in zip('ACGT', score_mat.T):
scores += np.convolve(coded_seq[base], base_scores, mode='valid')
for i, base in enumerate(seq.upper()):
coded_seq[base][len(seq)-i-1] = 1
RC_scores = np.zeros(len(seq)-len(score_mat)+1, dtype='float32')
for base, base_scores in zip('TCGA', score_mat.T):
scores += np.convolve(coded_seq[base], base_scores, mode='valid')
max_scores = np.vstack((scores, RC_scores)).max(0)
motif_scores.append( max_scores.mean() )
return np.array(motif_scores)
def csd():
import numpy as np
from smartplotlib import xyplot, alias
# make some data
dt = 0.01
t = np.arange(0, 30, dt)
nse1 = np.random.randn(len(t)) # white noise 1
nse2 = np.random.randn(len(t)) # white noise 2
r = np.exp(-t/0.05)
cnse1 = np.convolve(nse1, r, mode='same')*dt # colored noise 1
cnse2 = np.convolve(nse2, r, mode='same')*dt # colored noise 2
# two signals with a coherent part and a random part
s1 = 0.01*np.sin(2*np.pi*10*t) + cnse1
s2 = 0.01*np.sin(2*np.pi*10*t) + cnse2
xy = xyplot.derive(xlabel="time", ylabel="s1 & s2",
xlim=(0,5), axes=211)
csd = xyplot.csd(s1, s2, 256, 1./dt, axes=212)
xy.go("fclear", "axes")
xy.plot(t, s1, 'b-', t, s2, 'g-')
csd.go("plot", "axes", "show", "draw")
def get_spline(data): """ Returns array of cubic spline interpolation polynoms (for every interval [x[i -1]; x[i]] ) """ h = set_h(data) A = set_matrix_A(h) B = set_vector_B(data, h) m = find_vector_m(A, B) spline_array = [] for i in range(1,len(data)): xi_minus_x_cub = [(data[i][0] ** 3), -3 * (data[i][0] ** 2), 3*(data[i][0]), -1] s1 = list(np.convolve( (m[i - 1] / (6 * h[i-1])), xi_minus_x_cub)) x_minus_xi_1_cub = [-(data[i-1][0] ** 3), 3 * (data[i-1][0] ** 2), -3 * data[i-1][0], 1] s2 = list(np.convolve( (m[i] / (6 * h[i-1])), x_minus_xi_1_cub )) ai = data[i-1][1] - ((m[i-1]*h[i-1]**2)/6) s3 = list(np.convolve((ai/h[i-1]), [data[i][0], -1])) bi = data[i][1] - ((m[i]*h[i-1]**2)/6) s4 = list(np.convolve((bi/h[i-1]), [-data[i-1][0], 1])) iter_length = max(len(s1), len(s2), len(s3), len(s4)) for k in range(iter_length - len(s1)): s1.append(0) for k in range(iter_length - len(s2)): s2.append(0) for k in range(iter_length - len(s3)): s3.append(0) for k in range(iter_length - len(s4)): s4.append(0) spline = [0 for t in range(iter_length)] for j in range(iter_length): spline[j] = s1[j] + s2[j] + s3[j] + s4[j] spline_array.append(spline) return spline_array
def running_average_masked(obs, ws, min_valid_fraction=0.95):
'''
calculates a running average via convolution, fixing the edges
obs -- observations (a masked array)
ws -- window size (number of points to average)
'''
#tmp_vals = np.convolve(np.ones(ws, dtype=float), obs*(1-obs.mask), mode='same')
tmp_vals = np.convolve(np.ones(ws, dtype=float), obs.filled(0), mode='same')
# if the array is not masked, edges needs to be explictly fixed due to smaller counts
if len(obs.mask.shape) == 0:
tmp_valid = ws*np.ones_like(tmp_vals)
# fix the edges. using mode='same' assumes zeros outside the range
if ws%2==0:
tmp_vals[:ws//2]*=float(ws)/np.arange(ws//2,ws)
if ws//2>1:
tmp_vals[-ws//2+1:]*=float(ws)/np.arange(ws-1,ws//2,-1.0)
else:
tmp_vals[:ws//2]*=float(ws)/np.arange(ws//2+1,ws)
tmp_vals[-ws//2:]*=float(ws)/np.arange(ws,ws//2,-1.0)
# if the array is masked, then we get the normalizer from counting the unmasked values
else:
tmp_valid = np.convolve(np.ones(ws, dtype=float), (1-obs.mask), mode='same')
run_avg = np.ma.array(tmp_vals / tmp_valid)
run_avg.mask = tmp_valid < ws * min_valid_fraction
return run_avg
def perbaseToWindowAverageMasked(
V,
arMasked,
cooStart,
cooStop,
wndWidth,
kernel='sum', # can be sum, or mean
):
assert arMasked.shape==V.shape, (arMasked.shape,V.shape)
krn = np.ones( (wndWidth,), 'int32' )
Vconv = np.convolve( V*((1-arMasked).astype('uint64')), krn, 'full' )
Vconv = Vconv[ (wndWidth-1):Vconv.shape[0]:wndWidth ]
assert Vconv.shape[0]==(V.shape[0]/wndWidth + min(V.shape[0]%wndWidth,1))
nBpMasked = np.convolve( arMasked, np.ones(wndWidth,'int32'), 'full' )
nBpMasked = nBpMasked[ (wndWidth-1):nBpMasked.shape[0]:wndWidth ]
assert nBpMasked.shape[0]==Vconv.shape[0]
outStarts = cooStart+np.arange(Vconv.shape[0])*wndWidth
nBpUnmasked = wndWidth - nBpMasked
if kernel=='mean':
nBpUnmasked[-1] = cooStop - outStarts[-1] + 1
Vconv = (ma.masked_array( Vconv, nBpUnmasked == 0 ) / nBpUnmasked.astype('float64')).filled(0.)
return outStarts,Vconv,nBpUnmasked
def make_synth(rc,wavelet):
'''
Convolves reflectivities with wavelet.
INPUT
rc: 2D numpy array containing reflectivities
wavelet
OUTPUT
synth: 2D numpy array containing seismic data
Works with 1D arrays now (2015-05-07).
'''
nt=np.size(wavelet)
if rc.ndim>1:
[n_samples, n_traces] = rc.shape
synth = np.zeros((n_samples+nt-1, n_traces))
for i in range(n_traces):
synth[:,i] = np.convolve(rc[:,i], wavelet)
synth = synth[np.ceil(len(wavelet))/2:-np.ceil(len(wavelet))/2, :]
synth=np.concatenate((synth,np.zeros((1,n_traces))))
else:
n_samples = rc.size
synth = np.zeros(n_samples+nt-1)
synth = np.convolve(rc, wavelet)
synth = synth[np.ceil(len(wavelet))/2:-np.ceil(len(wavelet))/2]
synth=np.concatenate((synth,[0]))
return synth
def __init__(self,
simulator,
n = 60 * 60 * 2, # 1 hour
stdev_coef = 1.5,
days = 5,
trading_hours_per_day = 3.75,
tick_size = 1,
smooth_n = 3
):
self.__dict__.update(locals())
del self.self
self.price = self.simulator.history['last_price'].astype('int')
self.vol = self.simulator.history['vol']
self.m = int(days * trading_hours_per_day * 60 * 60 * 2)
self.w = np.ones(self.n + 1) / float(self.n + 1)
self.y = self.price - np.convolve(self.price, self.w, mode='same')
denorm = np.sqrt(np.convolve(self.y**2, self.w, mode='same'))
denorm_mean = denorm.mean()
denorm2 = (denorm > denorm_mean) * denorm + (denorm <= denorm_mean) * denorm_mean
# self.ny = self.y
# self.ny = (denorm > 0) * self.y / denorm
self.ny = (denorm2 > 0) * self.y / denorm2
self.ny_mean_EMA = EMA(self.m * 1. / self.n)
self.ny_stdev_EMA = EMA(self.m * 1. / self.n)
self.start_tick = self.n * 4
self.saliency = np.zeros(self.price.max() + self.simulator.stopprofit + 10)
self.saliency2 = np.zeros(self.price.max() + self.simulator.stopprofit + 10)
self.saliency_EMA = EMA(self.m)
self.saliency2_EMA = EMA(self.m)
self.mean_saliency_EMA = EMA(self.m * 1. / self.n)
assert self.smooth_n % 2 == 1
self.smooth_w = np.ones((self.smooth_n - 1) * self.tick_size + 1) / self.smooth_n
def lowpass( x, dt, cutoff, window='hann', repeat=0 ):
"""
Lowpass filter
Parameters
----------
x : samples
dt : sampling interval
cutoff : cutoff frequency
window : can be either 'hann' for zero-phase Hann window filter
or an integer n for an n-pole Butterworth filter.
"""
if not cutoff:
return x
if window == 'hann':
n = 2 * int( 0.5 / (cutoff * dt) ) + 1
if n > 0:
w = 0.5 - 0.5 * np.cos(
2.0 * np.pi * np.arange( n ) / (n - 1) )
w /= w.sum()
x = np.convolve( x, w, 'same' )
if repeat:
x = np.convolve( x, w, 'same' )
else:
import scipy.signal
wn = cutoff * 2.0 * dt
b, a = scipy.signal.butter( window, wn )
x = scipy.signal.lfilter( b, a, x )
if repeat < 0:
x = scipy.signal.lfilter( b, a, x[...,::-1] )[...,::-1]
elif repeat:
x = scipy.signal.lfilter( b, a, x )
return x
def convolve_spectra_with_COS_LSF(input_x,
input_flux,
rest_wavelength,
redshift,
vel_kms=True,
chan=None,
directory_with_COS_LSF='./'):
if directory_with_COS_LSF[-1] != '/':
directory_with_COS_LSF += '/'
if vel_kms:
input_vel = input_x
else:
input_vel = ang_to_vel(input_x, rest_wavelength, redshift)
input_delta_x = np.abs(input_x[0] - input_x[1])
input_total_x_range = np.max(input_x) - np.min(input_x)
observed_lambda = rest_wavelength * (1. + redshift)
if chan == None:
if observed_lambda > 1450.:
chan = 'G160M'
angstroms_per_pixel = 0.012
else:
chan = 'G130M'
angstroms_per_pixel = 0.0096
elif ((chan != 'G160M') & (chan != 'G130M')):
raise ValueError(
'Improper channel (chan) passed. Acceptable inputs are None, G130M, and G160M, the latter two must be strings!'
)
lsf = np.loadtxt('%sCOS_%s_LSF.dat' % (directory_with_COS_LSF, chan),
delimiter=',',
comments='#')
if chan == 'G130M':
lsf_wavelengths = np.array(
[1150., 1200., 1250., 1300., 1350., 1400., 1450.])
else:
lsf_wavelengths = np.array(
[1450., 1500., 1550., 1600., 1650., 1700., 1750.])
lsf_index = find_nearest_index(
lsf_wavelengths,
observed_lambda) + 1 # +1 because first column is pixel number
lsf_to_use = lsf[:, lsf_index]
if vel_kms:
lsf_delta_x = (np.abs(lsf[0, 0] - lsf[1, 0]) * angstroms_per_pixel *
c_kms) / (observed_lambda)
else:
lsf_delta_x = (np.abs(lsf[0, 0] - lsf[1, 0]) * angstroms_per_pixel)
number_of_input_points = int(input_total_x_range / lsf_delta_x)
resampled_input_flux, resampled_input_vel = signal.resample(
1. - input_flux, number_of_input_points, input_vel)
convolved_line = np.convolve(resampled_input_flux, lsf_to_use, mode='same')
resampled_input_flux = 1. - resampled_input_flux
convolved_line = 1. - convolved_line
if vel_kms:
resampled_input_wavelength = vel_to_ang(resampled_input_vel,
rest_wavelength, redshift)
else:
resampled_input_wavelength = signal.resample(input_x,
number_of_input_points)
return resampled_input_vel, resampled_input_wavelength, convolved_line
Department of Mechanical Engineering
"""
import numpy as np
import matplotlib.pyplot as plt
dt = 0.01
t = np.arange(0, 30, dt)
np.random.seed(1)
nse1 = np.random.randn(len(t)) # white noise 1
nse2 = np.random.randn(len(t)) # white noise 2
r = np.exp(-t / 0.05)
cnse1 = np.convolve(nse1, r, mode="same") * dt
cnse2 = np.convolve(nse2, r, mode="same") * dt
s1 = 0.01 * np.sin(2 * np.pi * 10 * t) + cnse1
s2 = 0.01 * np.sin(2 * np.pi * 10 * t) + cnse2
fig, ax = plt.subplots(2, 1)
ax[0].plot(t, s1, t, s2)
ax[0].set_xlim(0, 5)
ax[0].set_xlabel('time')
ax[0].set_ylabel('s1 and s2')
ax[0].grid(True)
cxy, f = ax[1].csd(s1, s2, 256, 1. / dt)
ax[1].set_ylabel('CSD (db)')
#------------------------------------------------------------ # Generate random x, y with a given covariance length np.random.seed(1) x = np.linspace(0, 1, 500) h = 0.01 C = np.exp(-0.5 * (x - x[:, None]) ** 2 / h ** 2) y = 0.8 + 0.3 * np.random.multivariate_normal(np.zeros(len(x)), C) #------------------------------------------------------------ # Define a normalized top-hat window function w = np.zeros_like(x) w[(x > 0.12) & (x < 0.28)] = 1 #------------------------------------------------------------ # Perform the convolution y_norm = np.convolve(np.ones_like(y), w, mode='full') valid_indices = (y_norm != 0) y_norm = y_norm[valid_indices] y_w = np.convolve(y, w, mode='full')[valid_indices] / y_norm # trick: convolve with x-coordinate to find the center of the window at # each point. x_w = np.convolve(x, w, mode='full')[valid_indices] / y_norm #------------------------------------------------------------ # Compute the Fourier transforms of the signal and window y_fft = np.fft.fft(y) w_fft = np.fft.fft(w) yw_fft = y_fft * w_fft
def smooth(x, window_len=11, window='hanning', periodic=False):
"""smooth the data using a window with requested size.
if periodic = True
This method is based on the convolution of a scaled window with the signal.
The signal is prepared by introducing reflected copies of the signal
(with the window size) in both ends so that transient parts are minimized
in the begining and end part of the output signal.
if periodic = False
do not modify the incoming signal
input:
x: the input signal
window_len: the dimension of the smoothing window; should be an odd integer
window: the type of window from 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'
flat window will produce a moving average smoothing.
output:
the smoothed signal
example:
t=linspace(-2,2,0.1)
x=sin(t)+randn(len(t))*0.1
y=smooth(x)
see also:
numpy.hanning, numpy.hamming, numpy.bartlett, numpy.blackman, numpy.convolve
scipy.signal.lfilter
TODO: the window parameter could be the window itself if an array instead of a string
from: http://www.scipy.org/Cookbook/SignalSmooth
modified by vcvicek
"""
if x.ndim != 1:
raise ValueError, "smooth only accepts 1 dimension arrays."
if x.size < window_len:
raise ValueError, "Input vector needs to be bigger than window size."
if window_len < 3:
return x
if not window in ['flat', 'hanning', 'hamming', 'bartlett', 'blackman']:
raise ValueError, "Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'"
if periodic:
s = numpy.r_[2 * x[0] - x[window_len - 1::-1], x,
2 * x[-1] - x[-1:-window_len:-1]]
else:
s = x
#print(len(s))
if window == 'flat': #moving average
w = numpy.ones(window_len, 'd')
else:
w = eval('numpy.' + window + '(window_len)')
if periodic:
y = numpy.convolve(w / w.sum(), s, mode='same')
return y[window_len:-window_len + 1]
else:
y = numpy.convolve(w / w.sum(), s, mode='valid')
return y
def CalucNeighborExp(feat, rate, exp, conv):
target_movie_len = len(feat)
neighbor = target_movie_len * rate
self_distance = np.zeros((len(feat), len(feat)))
# euclid distance
for i in range(len(feat)):
self_distance[i] = np.linalg.norm(feat - feat[i], axis=1)
# battatyalia distance
# feat_sum = feat.sum(axis=1)
# feat_sum[feat_sum==0] = 1.0
# for i in range(len(feat)):
# tmp1 = np.sqrt(feat*feat[i])
# tmp1 = tmp1.sum(axis=1)
# tmp2 = np.sqrt(feat_sum*feat_sum[i])
# self_distance[i] = np.sqrt(1-tmp1.astype(np.float32)/tmp2)
# self_distance[self_distance!=self_distance] = 0.0
threshold = otsu(self_distance.flatten())
alpha = exp
beta = alpha / float(target_movie_len)
f = lambda x: (math.e)**(beta * x)
neighbor_num = np.zeros(target_movie_len)
idx = [True for i in range(target_movie_len)]
for i in range(target_movie_len):
s = i - int(neighbor / 2.) if i - int(neighbor / 2.) >= 0 else 0
e = i + int(neighbor / 2.) if i + int(
neighbor / 2.) < target_movie_len else target_movie_len - 1
l = np.arange(len(feat))
# first_len = len(l[:s])
# latter_len = len(l[e+1:])
inter_len = len(l[s:e + 1])
# first = np.arange(first_len).astype(np.float32)
# if first_len != 0 and first_len != 1: first /= first.max()
# latter = np.arange(latter_len).astype(np.float32)
# if latter_len != 0 and latter_len != 1: latter /= latter.max()
first = np.array(l[:s])
latter = np.array(l[e + 1:])
first = np.array(list(map(f, first - s + 1)))
latter = np.array(list(map(f, -(latter - e - 1))))
inter = np.array([np.nan for _ in range(inter_len)])
ll = np.concatenate((first, inter, latter))
ll[ll != ll] = 0
# r = np.array(list(map(f,ll)))
# r[r!=r] = 0
tmp = np.copy(idx)
tmp[s:e + 1] = False
# neighbor_num[i] = sum(self_distance[i][tmp]<threshold)
neighbor_num[i] = sum(ll[self_distance[i] < threshold])
num = conv
kernel = np.ones(num) / num
neighbor_num = np.convolve(neighbor_num, kernel, mode='same')
# neighbor_num = neighbor_num/float(target_movie_len)
return neighbor_num
def load_data(ticker='AAPL',
momentum_window=30,
newsTimeToMarket=0,
X_window_average=40,
set_verbosity=True):
X_path = '../tensorflow_model/for_server/SentimentSingleNewsFullNoNorm/' + str(
ticker) + '.csv'
Y_path = '../tensorflow_model/for_server/DataSetIndexes/indexes' + str(
ticker) + '.csv'
x = pd.read_csv(X_path)
x.drop('Unnamed: 0', axis=1, inplace=True)
x = x.rename(index=str, columns={"initTime": "PUBLICATION_DATE"})
x = x.sort_values(by=['PUBLICATION_DATE'])
x = x.reset_index(drop=True)
y = pd.read_csv(Y_path)
for i, row in x.iterrows():
x.at[i, 'PUBLICATION_DATE'] = datetime.strptime(
x['PUBLICATION_DATE'][i],
'%Y-%m-%d %H:%M:%S') + timedelta(hours=newsTimeToMarket)
momentum_window = 30
y = y.rename(index=str, columns={"Unnamed: 0": "DATE"})
for i, row in y.iterrows():
y['DATE'].at[i] = datetime.strptime(y['DATE'][i],
'%Y-%m-%d %H:%M:%S')
z = list()
for i in range(0, y.shape[0] - momentum_window):
z.append((y['close'][i] - y['close'][i - momentum_window]) /
y['close'][i])
y = y.reset_index(drop=True)
y.drop(np.arange(y.shape[0] - momentum_window, y.shape[0]),
inplace=True)
y = y.reset_index(drop=True)
y['labels'] = [sign(entry) for entry in z]
min_max_scaler = preprocessing.MinMaxScaler()
initDate = max(y['DATE'][0], x['PUBLICATION_DATE'][0])
finalDate = min(y['DATE'][len(y) - 1],
x['PUBLICATION_DATE'][len(x) - 1])
i = 0
j = 0
close = []
labels = []
pos = []
neg = []
dates = []
# ALLINEAMENTO INIZIO
while (y['DATE'][j] < initDate):
j += 1
while (x['PUBLICATION_DATE'][i] < initDate):
i += 1
while (x['PUBLICATION_DATE'][i] < finalDate
and y['DATE'][j] < finalDate):
timeSlotPos = list()
timeSlotNeg = list()
while (i < len(x) - 1 and y['DATE'][j] > x['PUBLICATION_DATE'][i]):
timeSlotPos.append(x['POSITIVE'][i])
timeSlotNeg.append(x['NEGATIVE'][i])
i += 1
if (len(timeSlotPos) == 0):
timeSlotPos.append(0)
timeSlotNeg.append(0)
pos.append(np.mean(np.asarray(timeSlotPos), axis=0))
neg.append(np.mean(np.asarray(timeSlotNeg), axis=0))
close.append(y['close'][j])
labels.append(y['labels'][j])
dates.append(
str(y['DATE'][j].year) + '/' + str(y['DATE'][j].month))
j += 1
pos = np.convolve(np.asarray(pos),
np.repeat(1.0, X_window_average) / X_window_average,
'same')
neg = np.convolve(np.asarray(neg),
np.repeat(1.0, X_window_average) / X_window_average,
'same')
Data.pos = pos
Data.neg = neg
Data.Y = labels
matplotlib.rc('xtick', labelsize=35)
matplotlib.rc('ytick', labelsize=35)
import matplotlib as mpl
mpl.rcParams['text.usetex']=True
mpl.rcParams['text.latex.unicode']=True
# %%
# %% Stimuli
T = 5000
D = 3
smooth = 100
noise = np.random.randn(T,D)
X = noise.copy()
for ii in range(D):
X[:,ii] = np.convolve(noise[:,ii],np.ones(smooth),'same')/smooth *1
# %% Network settings
N = 20
Phi = np.random.randn(D,N)
J = np.random.randn(N,N)/N**0.5
J = 0.5*(J + J.T) #make symmetric
J = J-np.diag(J)
#vv = np.random.randn(N)
#J = np.outer(vv,vv)*0.1 + np.random.randn(N,N)*0.05
#J = J_nMF.copy()
def Current(h,J,s):
theta = h + J @ s
return theta
# Comparison with impedances: FREQUENCY DOMAIN (TWCs from impedance sources, params: R_S, frequency_R, a_factor)
TWC200_4 = TravelingWaveCavity(0.876e6, 200.222e6, 3.899e-6)
TWC200_5 = TravelingWaveCavity(1.38e6, 200.222e6, 4.897e-6)
# indVoltageTWC = InducedVoltageTime(beam, profile, [TWC200_4, TWC200_4, TWC200_5, TWC200_5])
indVoltageTWC = InducedVoltageTime(beam, profile, [TWC200_4])
indVoltage = TotalInducedVoltage(beam, profile, [indVoltageTWC])
indVoltage.induced_voltage_sum()
plt.plot(indVoltage.time_array, indVoltage.induced_voltage*1e-6, color='limegreen', label='Time domain w FFT (imp)')
# Comparison with impedances: TIME DOMAIN
TWC200_4.wake_calc(profile.bin_centers - profile.bin_centers[0])
TWC200_5.wake_calc(profile.bin_centers - profile.bin_centers[0])
# wake1 = 2*(TWC200_4.wake + TWC200_5.wake)
wake1 = TWC200_4.wake
Vind = -profile.Beam.ratio*profile.Beam.Particle.charge*e*\
np.convolve(wake1, profile.n_macroparticles, mode='full')[:140]
plt.plot(convtime[:140], Vind*1e-6, ':k', label='Time domain w conv (imp)')
# Wake from impulse response
OTFB_4.TWC.impulse_response_gen(omega_c, profile.bin_centers)
OTFB_5.TWC.impulse_response_gen(omega_c, profile.bin_centers)
OTFB_4.TWC.compute_wakes(profile.bin_centers)
OTFB_5.TWC.compute_wakes(profile.bin_centers)
# wake2 = 2*(OTFB_4.TWC.W_beam + OTFB_5.TWC.W_beam)
wake2 = OTFB_4.TWC.W_beam
Vind = -profile.Beam.ratio*profile.Beam.Particle.charge*e*\
np.convolve(wake2, profile.n_macroparticles, mode='full')[:140]
plt.plot(convtime[:140], Vind*1e-6, '--', color='turquoise', label='From wake, OTFB')
plt.xlabel("Time [s]")
plt.ylabel("Induced voltage [MV]")
plt.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
def plot_boxcar():
"""Makes a plot showing the effect of convolution with a boxcar window.
"""
# start with a square signal
signal = thinkdsp.SquareSignal(freq=440)
wave = signal.make_wave(duration=1, framerate=44100)
# and a boxcar window
window = np.ones(11)
window /= sum(window)
# select a short segment of the wave
segment = wave.segment(duration=0.01)
# and pad with window out to the length of the array
N = len(segment)
padded = thinkdsp.zero_pad(window, N)
# compute the first element of the smoothed signal
prod = padded * segment.ys
print(sum(prod))
# compute the rest of the smoothed signal
smoothed = np.zeros(N)
rolled = padded
for i in range(N):
smoothed[i] = sum(rolled * segment.ys)
rolled = np.roll(rolled, 1)
# plot the results
segment.plot(color=GRAY)
smooth = thinkdsp.Wave(smoothed, framerate=wave.framerate)
smooth.plot()
thinkplot.config(xlabel='Time(s)', ylim=[-1.05, 1.05])
thinkplot.save(root='convolution2')
# compute the same thing using np.convolve
segment.plot(color=GRAY)
ys = np.convolve(segment.ys, window, mode='valid')
smooth2 = thinkdsp.Wave(ys, framerate=wave.framerate)
smooth2.plot()
thinkplot.config(xlabel='Time(s)', ylim=[-1.05, 1.05])
thinkplot.save(root='convolution3')
# plot the spectrum before and after smoothing
spectrum = wave.make_spectrum()
spectrum.plot(color=GRAY)
ys = np.convolve(wave.ys, window, mode='same')
smooth = thinkdsp.Wave(ys, framerate=wave.framerate)
spectrum2 = smooth.make_spectrum()
spectrum2.plot()
thinkplot.config(xlabel='Frequency (Hz)',
ylabel='Amplitude',
xlim=[0, 22050])
thinkplot.save(root='convolution4')
# plot the ratio of the original and smoothed spectrum
amps = spectrum.amps
amps2 = spectrum2.amps
ratio = amps2 / amps
ratio[amps<560] = 0
thinkplot.plot(ratio)
thinkplot.config(xlabel='Frequency (Hz)',
ylabel='Amplitude ratio',
xlim=[0, 22050])
thinkplot.save(root='convolution5')
# plot the same ratio along with the FFT of the window
padded = thinkdsp.zero_pad(window, len(wave))
dft_window = np.fft.rfft(padded)
thinkplot.plot(abs(dft_window), color=GRAY, label='boxcar filter')
thinkplot.plot(ratio, label='amplitude ratio')
thinkplot.config(xlabel='Frequency (Hz)',
ylabel='Amplitude ratio',
xlim=[0, 22050])
thinkplot.save(root='convolution6')
reveal_type(np.count_nonzero(
A, axis=0)) # E: Union[numpy.signedinteger[Any], numpy.ndarray]
reveal_type(np.isfortran(i8)) # E: bool
reveal_type(np.isfortran(A)) # E: bool
reveal_type(np.argwhere(i8)) # E: numpy.ndarray
reveal_type(np.argwhere(A)) # E: numpy.ndarray
reveal_type(np.flatnonzero(i8)) # E: numpy.ndarray
reveal_type(np.flatnonzero(A)) # E: numpy.ndarray
reveal_type(np.correlate(B, A, mode="valid")) # E: numpy.ndarray
reveal_type(np.correlate(A, A, mode="same")) # E: numpy.ndarray
reveal_type(np.convolve(B, A, mode="valid")) # E: numpy.ndarray
reveal_type(np.convolve(A, A, mode="same")) # E: numpy.ndarray
reveal_type(np.outer(i8, A)) # E: numpy.ndarray
reveal_type(np.outer(B, A)) # E: numpy.ndarray
reveal_type(np.outer(A, A)) # E: numpy.ndarray
reveal_type(np.outer(A, A, out=C)) # E: SubClass
reveal_type(np.tensordot(B, A)) # E: numpy.ndarray
reveal_type(np.tensordot(A, A)) # E: numpy.ndarray
reveal_type(np.tensordot(A, A, axes=0)) # E: numpy.ndarray
reveal_type(np.tensordot(A, A, axes=(0, 1))) # E: numpy.ndarray
reveal_type(np.isscalar(i8)) # E: bool
reveal_type(np.isscalar(A)) # E: bool
reveal_type(np.isscalar(B)) # E: bool
def plot(paths,
strategies,
limits=(0, 1),
convolve=False,
mylabels=None,
myloc='lower right'):
font = {'family': 'normal', 'size': 21}
matplotlib.rc('font', **font)
current_palette = sns.color_palette()
sns.set_style('whitegrid')
figure(num=None, figsize=(12, 8), dpi=80, facecolor='w', edgecolor='k')
plt.ylim(limits[0], limits[1])
plt.xlim(0, 1000)
linewidth = 3
markersize = 7
results = read_results(results_file=paths[0])
for i in range(1, len(paths)):
results.update(read_results(results_file=paths[i]))
if len(strategies) == 0:
strategies = list(results.keys())
if mylabels == None:
mylabels = strategies
plot_policy_by_episode = False
if plot_policy_by_episode:
strategies = []
labels = []
keys = []
for i in range(0, prop.NUM_EPISODES):
strategies.append("policy_{}".format(str(i)))
labels.append("policy_{}".format(str(i)))
keys.append(i)
else:
labels = mylabels
keys = range(len(strategies))
with_stddev = True
if convolve:
with_stddev = False
width = 10
for i in keys:
means = np.array(results[strategies[i]][0])
# Convolve output (moving average)
if convolve:
means = np.convolve(means, np.ones(width), 'valid') / width
std = np.array(results[strategies[i]][1])
x = [x * ACQ_SIZE + INIT_SIZE for x in range(len(means))]
if labels[i].endswith('ALIL'):
color = 'cyan'
plt.plot(x,
means,
marker='.',
label=labels[i],
linewidth=linewidth,
markersize=markersize,
color=color)
if with_stddev:
plt.fill_between(x, means + std, means - std, alpha=0.1)
elif labels[i].endswith('andom'):
color = 'black'
plt.plot(x,
means,
marker='.',
label=labels[i],
linestyle='--',
linewidth=5,
markersize=markersize,
color=color)
if with_stddev:
plt.fill_between(x,
means + std,
means - std,
alpha=0.1,
color=color)
else:
plt.plot(x,
means,
marker='.',
label=labels[i],
linewidth=linewidth,
markersize=markersize)
if with_stddev:
plt.fill_between(x, means + std, means - std, alpha=0.1)
plt.legend(loc='lower right', ncol=3, prop={'size': 20})
plt.ylabel("Test data accuracy score")
plt.xlabel("Labeling effort")
#plt.savefig(path + '.pdf', format="pdf", dpi=None, facecolor='w', edgecolor='w', orientation='portrait', papertype=None, transparent=False, bbox_inches='tight', pad_inches=0.0, frameon=None, metadata=None)
plt.show()
def smooth(y, box_pts):
box = np.ones(box_pts) / box_pts
y_smooth = np.convolve(y, box, mode='same')
return [i for i in y_smooth]
def window_rms(a):
window_length = len(a)
square = np.power(a, 2)
window = np.ones(window_length) / float(window_length)
return np.sqrt(np.convolve(square, window, 'valid'))
def smooth_curve(x):
window_len = 11
s = np.r_[x[window_len - 1:0:-1], x, x[-1:-window_len:-1]]
w = np.kaiser(window_len, 2)
y = np.convolve(w / w.sum(), s, mode='valid')
return y[5:len(y) - 5]
def movingaverage(values, window):
weigths = np.repeat(1.0, window) / window
smas = np.convolve(values, weigths, 'valid')
return smas # as a numpy array
def _ema(self, data, window):
weights = np.exp(np.linspace(-1., 1., window))
weights /= weights.sum()
ema = np.convolve(data[:, [0]][:, 0],
np.flip(weights, 0))
return ema[len(data)-1:-len(data)+1]
def get_total(incidence=True, smooth=True):
def countData(dicti, date, value, count):
date = str(date)
value = str(value)
def add2dict_dict(dicti, value):
if value not in dicti:
dicti[value] = dict()
# return dicti
def add2dict(dicti, value, count):
if value not in dicti:
dicti[value] = count
else:
dicti[value] += count
# return dicti
add2dict_dict(dicti, date)
add2dict(dicti[date], value, count)
# return dicti
def get_cases(dicti, date):
plus = minus = null = 0
try:
minus = -dicti[date]['-1']
except:
None
try:
plus = dicti[date]['1']
except:
None
try:
null = dicti[date]['0']
except:
None
return null, plus, minus
def download_raw_data():
time_case_dict = dict()
time_death_dict = dict()
notFinished = True
offset = 0 # 0
while notFinished:
with urllib.request.urlopen(
"https://services7.arcgis.com/mOBPykOjAyBO2ZKk/arcgis/rest/services/RKI_COVID19/"
"FeatureServer/0/query?where=1%3D1&outFields=Meldedatum,Refdatum,AnzahlFall,AnzahlTodesfall,NeuerFall,NeuerTodesfall&"
"outSR=4326&" + "resultOffset={:}".format(offset) +
"&f=json") as url:
data = json.loads(url.read().decode())
if 'exceededTransferLimit' not in data:
notFinished = False
offset = offset + len(data['features'])
print(offset)
# if offset > 10000:
# notFinished = False
for it in data[
'features']: # alternativ statt Meldedatum: Refdatum
countData(time_case_dict,
int(it['attributes']['Meldedatum'] / 1000),
it['attributes']['NeuerFall'],
it['attributes']['AnzahlFall'])
countData(time_death_dict,
int(it['attributes']['Meldedatum'] / 1000),
it['attributes']['NeuerTodesfall'],
it['attributes']['AnzahlTodesfall'])
save_obj(time_case_dict, 'case')
save_obj(time_death_dict, 'death')
if not os.path.exists('obj'):
os.mkdir('obj')
if not os.path.isfile('obj/case.pkl'):
download_raw_data()
if time.time() - os.path.getmtime('obj/case.pkl') > 3600:
download_raw_data()
time_case_dict = load_obj('case')
time_death_dict = load_obj('death')
time_array = np.array(list(time_case_dict.keys()), dtype=int)
time_array.sort()
case_list = np.zeros((3, len(time_array)))
death_list = np.zeros((3, len(time_array)))
time_list = []
for i, item in enumerate(time_array):
case_list[0, i], case_list[1, i], case_list[-1, i] = get_cases(
time_case_dict, str(item))
time_list.append(datetime.datetime.fromtimestamp(item))
time_list = to_datetime(time_list)
if not smooth:
return time_list, case_list[0] + case_list[1] #+case_list[-1])
if incidence:
factor = 1 / count_age('Gesamt') * 100000
else:
factor = 1
return time_list, np.convolve(case_list[0] + case_list[1],
[1, 1, 1, 1, 1, 1, 1], 'full')[:-6] * factor
def ExpMovingAverage(values, window):
weights = np.exp(np.linspace(-1., 0., window))
weights /= weights.sum()
a = np.convolve(values, weights, mode='full')[:len(values)]
a[:window] = a[window]
return a
K = len(longer)-len(shorter)+1
convolution = np.zeros(K, longer.dtype)
for i in range(K):
convolution[i] = np.dot(longer[i:len(shorter)+i], shorter[::-1])
return convolution
# def convolvetest(a, w, b = 0, stride = 1, pad = 0):
# """
# compute 1d convolutional (with bias)
# """
# w_old = a.shape[0]
# f = w.shape[0]
# a_pad = np.pad(a, pad_width=pad, mode = 'constant', constant_values = 0)
# w_new = int((w_old - f + 2*pad)/stride) + 1
# a_res = np.zeros((w_new))
# for i in range(w_new):
# start = i*stride
# end = start + f
# a_res[i] = np.sum(a_pad[start:end]*w) + b
# return a_res
# a = np.random.normal(0.0, 1.0, 100)
# b = np.random.normal(0.0, 1.0, 11)
a = np.array([1,2,3])
b = np.array([3,4,5])
#Hàm có sẵn convolve của python tính linear convolution
# print(np.allclose(np.convolve(a, b, mode='same'),
# convolvetest(np.pad(a, ((len(b)-1)/2, (len(b)-1)/2), mode='constant', constant_values=0.0), b)))
print(np.allclose(np.convolve(a, b, mode='same'), convolvetest(a, b)))
print(a)
print(b)
print(convolvetest(a,b))
def process_yeast(dir_path,
excels_path,
template1,
template2,
debug=False,
extensions=['[jJ][pP][gG]', '[pP][nN][gG]']):
global activityThreshold
# if len(sys.argv) == 1:
# print("Usage test.py <path_to_images>")
# exit(-1)
path = []
output_path = os.path.join(dir_path, 'output')
for ext in extensions:
path.extend(glob.glob(os.path.join(
dir_path,
"*.{}".format(ext)))) # glob.glob(sys.argv[1] + "/*.JPG")
path.sort()
df = pd.read_excel(excels_path, engine='openpyxl')
# clusterPaths=[]
baits = {}
for file in path:
name = Path(file).stem.split('.')[0]
properties = name.split('_')
baitNo = properties[1].split('-')[-1]
if baitNo not in baits:
baits[baitNo] = []
baits[baitNo].append(file)
for bait in baits.keys():
headers = '<thead><tr>' + '<th colspan="3">Bait Number {}</th>'.format(
bait
) + '<th colspan="2">TF</th>' + ''.join(
[
'<th colspan="3">Day {}</th>'.format(name.split('_')[-1][0])
for name in baits[bait]
]
) + '</tr>' + '<tr><th>Index</th><th>Activated</th><th>Coordinate</th><th>TF1</th><th>TF2</th>' + (
header * len(baits[bait])) + '</tr></thead>'
dataframes = []
outputPaths = []
fileNames = []
for imagePath in baits[bait]:
name = Path(imagePath).stem
name = name.split('.')
fileNames.append(name)
outputPath = os.path.join(output_path,
name[0]) # "./output/{}".format(name[0])
Path(outputPath).mkdir(parents=True, exist_ok=True)
outputPaths.append(outputPath)
# clusterPath = os.path.join(output_path, "cluster/") # "./output/cluster/"
# clusterPaths.append(clusterPath)
# rmtree(clusterPath, ignore_errors=True)
# for i in range(10, 110, 10):
# Path(clusterPath + str(i)).mkdir(parents=True, exist_ok=True)
# dataframe = pd.read_excel(os.path.join(output_path, name[
# 0] + ".xlsx"), engine = 'openpyxl') # pd.read_excel(name[0] + ".xlsx", engine='openpyxl')
dataframe = df.copy(deep=True)
# print(list(dataframe.columns))
image = cv2.imread(imagePath)
if image is None:
return -1, "Can't access image at " + dir_path
img = cv2.Canny(image, 20, 30)
# cv2.imwrite(os.path.join(output_path, 'edge-detect.jpg'), img)#'edge-detect.jpg', img)
# template1 = cv2.imread(os.path.join(output_path,'upperLeft.png'), 0)
# template2 = cv2.imread(os.path.join(output_path,'bottomRight.png'), 0)
res = cv2.matchTemplate(img, template1, cv2.TM_CCORR_NORMED)
res1 = cv2.matchTemplate(img, template2, cv2.TM_CCORR_NORMED)
min_val, max_val, min_loc, max_loc = cv2.minMaxLoc(res)
top_left = np.add(max_loc, [140, 40])
min_val, max_val, min_loc, max_loc = cv2.minMaxLoc(res1)
bottom_right = np.add(max_loc, [0, 140])
img = image[top_left[1]:bottom_right[1],
top_left[0]:bottom_right[0]]
# cv2.imwrite(os.path.join(output_path, 'first crop.png'), img)
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
levelRange = getLevelRange(gray)
gray = rescaleIntensity(gray, [0, levelRange[1]])
gray = cv2.Sobel(gray, cv2.CV_8UC1, 1, 0, ksize=5)
gray = cv2.medianBlur(gray, 5)
gray = cv2.GaussianBlur(gray, (5, 5), 3)
levelRange = getLevelRange(gray)
gray = rescaleIntensity(gray, [sum(levelRange) / 2, levelRange[1]])
gray = ((gray > 90) * 255).astype(np.uint8)
# cv2.imwrite(os.path.join(output_path, 'gray.jpg'), gray)
xProj, yProj = getHistogramProjection(gray)
smooth = 5
xProj = np.convolve(xProj,
[1 / smooth
for i in range(smooth)])[:-(smooth - 1)]
yProj = np.convolve(yProj,
[1 / smooth
for i in range(smooth)])[:-(smooth - 1)]
xProj = (xProj > 20) * xProj
yProj = (yProj > 20) * yProj
xNonZero = [i for i, elem in enumerate(xProj) if elem > 30]
yNonZero = [i for i, elem in enumerate(yProj) if elem > 30]
crop = img
xpeaks, xGrad = getPeaks(xProj, 0, 0)
ypeaks, yGrad = getPeaks(yProj, 0, 0)
outputPercent = []
outputIntensity = []
outputArea = []
hsvCrop = cv2.cvtColor(crop, cv2.COLOR_BGR2HSV)
outputImage = []
# reference, refCols = getIndex("3-B7", xpeaks, ypeaks)
for c in df["Coordinate"]:
if (len(c.split("-")[1]) > 1):
index, colonies = getIndex(c, xpeaks, ypeaks)
roi = (hsvCrop[index[1][0]:index[1][1],
index[0][0]:index[0][1]])[:, :, 2]
hsvImage = np.zeros_like(roi, dtype=np.uint8)
for ix, colony in enumerate(colonies):
subRoi = roi[colony[1][0]:colony[1][1],
colony[0][0]:colony[0][1]]
levelRange = getLevelRange(subRoi)
if True:
colonyProcessed = rescaleIntensity(
subRoi, [0, levelRange[1]])
colonyProcessed = cv2.GaussianBlur(
colonyProcessed, (3, 3), 2.5)
colonyProcessed = cv2.medianBlur(colonyProcessed,
ksize=9)
test = getLevelRange(colonyProcessed, 0.05)
# if test[1] - test[0] <= 127:
# test[0] = 127
colonyProcessed = cv2.threshold(
colonyProcessed, test[0], 255,
cv2.THRESH_BINARY_INV)[1]
contours, hierarchy = cv2.findContours(
colonyProcessed, cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
center = np.divide(colonyProcessed.shape, 2)
centerContour = None
minDistance = colonyProcessed.size
for contour in contours:
moments = cv2.moments(contour)
if moments["m00"] != 0:
centroid = [
int(moments["m10"] / moments["m00"]),
int(moments["m01"] / moments["m00"])
]
distance = math.sqrt(
np.sum(np.square(centroid - center)))
if distance < minDistance:
centerContour = contour
minDistance = distance
colonyProcessed = np.zeros_like(colonyProcessed,
dtype=np.uint8)
colonyProcessed = cv2.drawContours(
colonyProcessed, [centerContour], 0,
(255, 255, 255), cv2.FILLED)
hsvImage[
colony[1][0]:colony[1][1],
colony[0][0]:colony[0][1]] = colonyProcessed
inv = (hsvCrop[index[1][0]:index[1][1],
index[0][0]:index[0][1]])[:, :, 0]
inv = rescaleIntensity(inv, [getLevelRange(inv)[0], 255])
invRange = getLevelRange(inv, 0)
if invRange[1] - invRange[0] < 3:
inv = np.zeros_like(inv, dtype=np.uint8)
roi = cv2.bitwise_and(inv, inv, mask=hsvImage)
if c == '1-B5':
print('')
roi[roi <= getLevelRange(
roi, skipZero=True, percentile=.10)[0]] = 0
areaImage = roi.copy()
areaImage[areaImage > 0] = 1
area = np.sum(areaImage)
intensity = roi.copy()
intensity = np.divide(intensity,
np.subtract(256, intensity))
outputIntensity.append(np.sum(intensity))
outputArea.append(area)
cv2.imwrite(
os.path.join(outputPath, c +
".png"), # outputPath + "/" + c + ".png",
crop[index[1][0]:index[1][1], index[0][0]:index[0][1]])
if debug:
cv2.imwrite(
os.path.join(outputPath, c) + "_final.png", roi)
cv2.imwrite(
os.path.join(outputPath, c) + "_preMask.png", inv)
cv2.imwrite(
os.path.join(outputPath, c) + "_mask.png",
hsvImage)
outputImage.append(os.path.join(name[0], c + ".png"))
else:
outputArea.append(math.nan)
outputIntensity.append(math.nan)
outputPercent.append(0)
outputImage.append(None)
outputIntensity = np.nan_to_num(outputIntensity,
nan=np.nanmin(outputIntensity))
outputArea = np.nan_to_num(outputArea, nan=-1)
dataframe["Intensity"] = outputIntensity
dataframe["Area"] = outputArea
dataframe["Image"] = outputImage
for i, p in enumerate(xpeaks):
if i % 4 == 0:
cv2.line(crop, (p, 0), (p, crop.shape[1] - 1), (0, 0, 255),
thickness=3)
else:
cv2.line(crop, (p, 0), (p, crop.shape[1] - 1), (0, 0, 0),
thickness=1)
for i, p in enumerate(ypeaks):
if i % 4 == 0:
cv2.line(crop, (0, p), (crop.shape[1] - 1, p), (0, 0, 255),
thickness=3)
else:
cv2.line(crop, (0, p), (crop.shape[1] - 1, p), (0, 0, 0),
thickness=1)
cv2.imwrite(os.path.join(output_path, name[0] + '_crop.png'), crop)
dataframes.append(dataframe)
intensities = []
area = []
plateMedianArea = []
plateMedian = []
for dataframe in dataframes:
intensities.extend(list(dataframe['Intensity']))
area.extend(list(dataframe['Area']))
plateMedianArea.append(np.median(dataframe['Area']))
plateMedian.append(np.median(dataframe['Intensity']))
median = np.median(plateMedian)
aMedian = np.median(plateMedianArea)
for dataframe in dataframes:
normalized = np.array(list(dataframe['Intensity'])) / median
# normalized = stats.zscore(normalized)
dataframe['Intensity'] = normalized.round(3)
normalized = np.array(list(dataframe['Area'])) / aMedian
# normalized = stats.zscore(normalized)
dataframe['Area'] = normalized.round(3)
# detected = genOutputIntensity > activityThreshold
for dataframe, name in zip(dataframes, fileNames):
excelColumns = list(dataframe.columns)
excelColumns.remove('Image')
dataframe[excelColumns].to_excel(
os.path.join(output_path, name[0]) + ".xlsx", index=False)
customDF = [
dataframes[0][[
'Coordinate', 'TF1', 'TF2', 'Intensity', 'Area', 'Image'
]]
]
if len(dataframe) > 1:
customDF.extend(dataframe[['Intensity', 'Area', 'Image']]
for dataframe in dataframes[1:])
dataframe = pd.concat(customDF, axis=1)
#Insert Additional rows
dataframe = addRows(dataframe)
#end
dataframe.insert(0, 'Activated',
[False for i in range(len(dataframe.index))])
# ################################################################
# dataframe = main_add_cols(dataframe) # COSMIN
# ################################################################
# activityThreshold = dataframe['EMP_EMP_Intensity'][0]
# dataframe.insert(0, 'Activated', [False for i in range(len(dataframe.index))])
opHtml = html.format(
name[0], css,
dataframe.to_html(header=False,
escape=False,
formatters=dict(
Activated=checkBoxGenerator,
Image=imageTageGenerator)).replace(
"<tbody>", headers + '\n<tbody>'),
javascript, downloadHTML)
file = open(
os.path.join(output_path,
'{}.html'.format(name[0][:name[0].rfind('_')])), "w")
file.write(opHtml)
file.close()
return 0, 'ok'
def pan_tompkin(self, ecg, fs):
''' Initialize '''
delay = 0
skip = 0 # Becomes one when a T wave is detected
m_selected_RR = 0
mean_RR = 0
ser_back = 0
''' Noise Cancelation (Filtering) (5-15 Hz) '''
if fs == 200:
''' Remove the mean of Signal '''
ecg = ecg - np.mean(ecg)
''' Low Pass Filter H(z) = (( 1 - z^(-6))^2) / (1-z^(-1))^2 '''
''' It has come to my attention the original filter does not achieve 12 Hz
b = [1, 0, 0, 0, 0, 0, -2, 0, 0, 0, 0, 0, 1]
a = [1, -2, 1]
ecg_l = filter(b, a, ecg)
delay = 6
'''
Wn = 12 * 2 / fs
N = 3
a, b = signal.butter(N, Wn, btype='lowpass')
ecg_l = signal.filtfilt(a, b, ecg)
ecg_l = ecg_l / np.max(np.abs(ecg_l))
''' High Pass Filter H(z) = (-1 + 32z^(-16) + z^(-32)) / (1+z^(-1))'''
''' It has come to my attention the original filter does not achieve 5 Hz
b = np.zeros((1,33))
b(1) = -1
b(17) = 32
b(33) = 1
a = [1, 1]
ecg_h = filter(b, a, ecg_l) -> Without delay
delay = delay + 16'''
Wn = 5 * 2 / fs
N = 3 # Order of 3 less processing
a, b = signal.butter(N, Wn, btype='highpass') # Bandpass filtering
ecg_h = signal.filtfilt(a,
b,
ecg_l,
padlen=3 * (max(len(a), len(b)) - 1))
ecg_h = ecg_h / np.max(np.abs(ecg_h))
else:
''' Band Pass Filter for noise cancelation of other sampling frequencies (Filtering)'''
f1 = 5 # cutoff low frequency to get rid of baseline wander
f2 = 15 # cutoff frequency to discard high frequency noise
Wn = [f1 * 2 / fs, f2 * 2 / fs] # cutoff based on fs
N = 3 # order of 3 less processing
a, b = signal.butter(N=N, Wn=Wn,
btype='bandpass') # Bandpass filtering
ecg_h = signal.filtfilt(a,
b,
ecg,
padlen=3 * (max(len(a), len(b)) - 1))
ecg_h = ecg_h / np.max(np.abs(ecg_h))
''' Derivative Filter '''
''' H(z) = (1/8T)(-z^(-2) - 2z^(-1) + 2z + z^(2)) '''
vector = [1, 2, 0, -2, -1]
if fs != 200:
int_c = 160 / fs
b = interp1d(range(1, 6),
[i * fs / 8
for i in vector])(np.arange(1, 5.1, int_c))
else:
b = [i * fs / 8 for i in vector]
ecg_d = signal.filtfilt(b,
1,
ecg_h,
padlen=3 * (max(len(a), len(b)) - 1))
ecg_d = ecg_d / np.max(ecg_d)
''' Squaring nonlinearly enhance the dominant peaks '''
ecg_s = ecg_d**2
''' Moving Average '''
''' Y(nT) = (1/N)[x(nT-(N-1)T) + x(nT - (N-2) T) + ... + x(nT)] '''
temp_vector = np.ones((1, round(0.150 * fs))) / round(0.150 * fs)
temp_vector = temp_vector.flatten()
ecg_m = np.convolve(ecg_s, temp_vector)
delay = delay + round(0.150 * fs) / 2
''' Fiducial Marks '''
''' Note : a minimum distance of 40 samples is considered between each R wave since in physiological
point of view, no RR wave can occur in less than 200ms distance'''
pks = []
locs = peakutils.indexes(y=ecg_m, thres=0, min_dist=round(0.2 * fs))
for val in locs:
pks.append(ecg_m[val])
''' Initialize Some Other Parameters '''
LLp = len(pks)
''' Stores QRS with respect to Signal and Filtered Signal '''
qrs_c = np.zeros(LLp) # Amplitude of R
qrs_i = np.zeros(LLp) # index
qrs_i_raw = np.zeros(LLp) # Amplitude of R
qrs_amp_raw = np.zeros(LLp) # index
''' Noise Buffers '''
nois_c = np.zeros(LLp)
nois_i = np.zeros(LLp)
''' Buffers for signal and noise '''
SIGL_buf = np.zeros(LLp)
NOISL_buf = np.zeros(LLp)
THRS_buf = np.zeros(LLp)
SIGL_buf1 = np.zeros(LLp)
NOISL_buf1 = np.zeros(LLp)
THRS_buf1 = np.zeros(LLp)
''' Initialize the training phase (2 seconds of the signal) to determine the THR_SIG and THR_NOISE '''
THR_SIG = np.max(
ecg_m[:2 * fs + 1]) * 1 / 3 # 0.33 of the max amplitude
THR_NOISE = np.mean(
ecg_m[:2 * fs + 1]
) * 1 / 2 # 0.5 of the mean signal is considered to be noise
SIG_LEV = THR_SIG
NOISE_LEV = THR_NOISE
''' Initialize bandpath filter threshold (2 seconds of the bandpass signal) '''
THR_SIG1 = np.max(ecg_h[:2 * fs + 1]) * 1 / 3
THR_NOISE1 = np.mean(ecg_h[:2 * fs + 1]) * 1 / 2
SIG_LEV1 = THR_SIG1 # Signal level in Bandpassed filter
NOISE_LEV1 = THR_NOISE1 # Noise level in Bandpassed filter
''' Thresholding and decision rule '''
Beat_C = 0
Beat_C1 = 0
Noise_Count = 0
for i in range(LLp):
''' Locate the corresponding peak in the filtered signal '''
if locs[i] - round(0.150 * fs) >= 1 and locs[i] <= len(ecg_h):
temp_vec = ecg_h[
locs[i] - round(0.150 * fs):locs[i] +
1] # -1 since matlab works differently with indexes
y_i = np.max(temp_vec)
x_i = list(temp_vec).index(y_i)
else:
if i == 0:
temp_vec = ecg_h[:locs[i] + 1]
y_i = np.max(temp_vec)
x_i = list(temp_vec).index(y_i)
ser_back = 1
elif locs[i] >= len(ecg_h):
temp_vec = ecg_h[int(locs[i] - round(0.150 * fs)):]
y_i = np.max(temp_vec)
x_i = list(temp_vec).index(y_i)
''' Update the Hearth Rate '''
if Beat_C >= 9:
diffRR = np.diff(qrs_i[Beat_C -
9:Beat_C]) # Calculate RR interval
mean_RR = np.mean(
diffRR
) # Calculate the mean of 8 previous R waves interval
comp = qrs_i[Beat_C - 1] - qrs_i[Beat_C - 2] # Latest RR
if comp <= 0.92 * mean_RR or comp >= 1.16 * mean_RR:
''' lower down thresholds to detect better in MVI '''
THR_SIG = 0.5 * THR_SIG
THR_SIG1 = 0.5 * THR_SIG1
else:
m_selected_RR = mean_RR #The latest regular beats mean
''' Calculate the mean last 8 R waves to ensure that QRS is not '''
if bool(m_selected_RR):
test_m = m_selected_RR #if the regular RR available use it
elif bool(mean_RR) and m_selected_RR == 0:
test_m = mean_RR
else:
test_m = 0
if bool(test_m):
if locs[i] - qrs_i[Beat_C - 1] >= round(
1.66 * test_m): # it shows a QRS is missed
temp_vec = ecg_m[int(qrs_i[Beat_C - 1] + round(0.2 * fs)
):int(locs[i] - round(0.2 * fs)) + 1]
pks_temp = np.max(
temp_vec
) #search back and locate the max in the interval
locs_temp = list(temp_vec).index(pks_temp)
locs_temp = qrs_i[Beat_C - 1] + round(
0.200 * fs) + locs_temp
if pks_temp > THR_NOISE:
Beat_C = Beat_C + 1
qrs_c[Beat_C - 1] = pks_temp
qrs_i[Beat_C - 1] = locs_temp
''' Locate in Filtered Signal '''
if locs_temp <= len(ecg_h):
#temp_vec = ecg_h[int(locs_temp-round(0.150*fs)):int(locs_temp)+1]
temp_vec = ecg_h[int(locs_temp -
round(0.150 * fs)) +
1:int(locs_temp) + 2]
y_i_t = np.max(temp_vec)
x_i_t = list(temp_vec).index(y_i_t)
else:
temp_vec = ecg_h[int(locs_temp -
round(0.150 * fs)):]
y_i_t = np.max(temp_vec)
x_i_t = list(temp_vec).index(y_i_t)
''' Band Pass Signal Threshold '''
if y_i_t > THR_NOISE1:
Beat_C1 = Beat_C1 + 1
temp_value = locs_temp - round(0.150 * fs) + x_i_t
qrs_i_raw[Beat_C1 -
1] = temp_value # save index of bandpass
qrs_amp_raw[
Beat_C1 -
1] = y_i_t # save amplitude of bandpass
SIG_LEV1 = 0.25 * y_i_t + 0.75 * SIG_LEV1 #when found with the second threshold
not_nois = 1
SIG_LEV = 0.25 * pks_temp + 0.75 * SIG_LEV
else:
not_nois = 0
''' Find noise and QRS Peaks '''
if pks[i] >= THR_SIG:
''' if NO QRS in 360 ms of the previous QRS See if T wave '''
if Beat_C >= 3:
if locs[i] - qrs_i[Beat_C - 1] <= round(0.36 * fs):
temp_vec = ecg_m[locs[i] - round(0.075 * fs):locs[i] +
1]
Slope1 = np.mean(
np.diff(temp_vec)
) # mean slope of the waveform at that position
temp_vec = ecg_m[int(qrs_i[Beat_C - 1] -
int(round(0.075 * fs))) -
1:int(qrs_i[Beat_C - 1]) + 1]
Slope2 = np.mean(
np.diff(temp_vec)) # mean slope of previous R wave
if np.abs(Slope1) <= np.abs(
0.5 *
Slope2): # slope less then 0.5 of previous R
Noise_Count = Noise_Count + 1
nois_c[Noise_Count] = pks[i]
nois_i[Noise_Count] = locs[i]
skip = 1 # T wave identification
else:
skip = 0
''' Skip is 1 when a T wave is detected '''
if skip == 0:
Beat_C = Beat_C + 1
qrs_c[Beat_C - 1] = pks[i]
qrs_i[Beat_C - 1] = locs[i]
''' Band pass Filter check threshold '''
if y_i >= THR_SIG1:
Beat_C1 = Beat_C1 + 1
if bool(ser_back):
# +1 to agree with Matlab implementation
temp_value = x_i + 1
qrs_i_raw[Beat_C1 - 1] = temp_value
else:
temp_value = locs[i] - round(0.150 * fs) + x_i
qrs_i_raw[Beat_C1 - 1] = temp_value
qrs_amp_raw[Beat_C1 - 1] = y_i
SIG_LEV1 = 0.125 * y_i + 0.875 * SIG_LEV1
SIG_LEV = 0.125 * pks[i] + 0.875 * SIG_LEV
elif THR_NOISE <= pks[i] and pks[i] < THR_SIG:
NOISE_LEV1 = 0.125 * y_i + 0.875 * NOISE_LEV1
NOISE_LEV = 0.125 * pks[i] + 0.875 * NOISE_LEV
elif pks[i] < THR_NOISE:
nois_c[Noise_Count] = pks[i]
nois_i[Noise_Count] = locs[i]
Noise_Count = Noise_Count + 1
NOISE_LEV1 = 0.125 * y_i + 0.875 * NOISE_LEV1
NOISE_LEV = 0.125 * pks[i] + 0.875 * NOISE_LEV
''' Adjust the threshold with SNR '''
if NOISE_LEV != 0 or SIG_LEV != 0:
THR_SIG = NOISE_LEV + 0.25 * (np.abs(SIG_LEV - NOISE_LEV))
THR_NOISE = 0.5 * THR_SIG
''' Adjust the threshold with SNR for bandpassed signal '''
if NOISE_LEV1 != 0 or SIG_LEV1 != 0:
THR_SIG1 = NOISE_LEV1 + 0.25 * (np.abs(SIG_LEV1 - NOISE_LEV1))
THR_NOISE1 = 0.5 * THR_SIG1
''' take a track of thresholds of smoothed signal '''
SIGL_buf[i] = SIG_LEV
NOISL_buf[i] = NOISE_LEV
THRS_buf[i] = THR_SIG
''' take a track of thresholds of filtered signal '''
SIGL_buf1[i] = SIG_LEV1
NOISL_buf1[i] = NOISE_LEV1
THRS_buf1[i] = THR_SIG1
''' reset parameters '''
skip = 0
not_nois = 0
ser_back = 0
''' Adjust lengths '''
qrs_i_raw = qrs_i_raw[:Beat_C1]
qrs_amp_raw = qrs_amp_raw[:Beat_C1]
qrs_c = qrs_c[:Beat_C + 1]
qrs_i = qrs_i[:Beat_C + 1]
return qrs_amp_raw, qrs_i_raw, delay
"""
Compute the coherence of two signals
"""
import matplotlib.pyplot as plt
import numpy as np
# make a little extra space between the subplots
plt.subplots_adjust(wspace=0.5)
dt = 0.01
t = np.arange(0, 30, dt)
nse1 = np.random.randn(len(t)) # white noise 1
nse2 = np.random.randn(len(t)) # white noise 2
r = np.exp(-t / 0.05)
cnse1 = np.convolve(nse1, r, mode='same') * dt # colored noise 1
cnse2 = np.convolve(nse2, r, mode='same') * dt # colored noise 2
# two signals with a coherent part and a random part
s1 = 0.01 * np.sin(2 * np.pi * 10 * t) + cnse1
s2 = 0.01 * np.sin(2 * np.pi * 10 * t) + cnse2
plt.subplot(211)
plt.plot(t, s1, t, s2)
plt.xlim(0, 5)
plt.xlabel('time')
plt.ylabel('s1 and s2')
plt.grid(True)
plt.subplot(212)
cxy, f = plt.cohere(s1, s2, 256, 1. / dt)
def grpdelay(b, a=1, nfft=512, whole='none', analog=False, Fs=2. * pi):
#==================================================================
"""
Calculate group delay of a discrete time filter, specified by
numerator coefficients `b` and denominator coefficients `a` of the system
function `H` ( `z`).
When only `b` is given, the group delay of the transversal (FIR)
filter specified by `b` is calculated.
Parameters
----------
b : array_like
Numerator coefficients (transversal part of filter)
a : array_like (optional, default = 1 for FIR-filter)
Denominator coefficients (recursive part of filter)
whole : string (optional, default : 'none')
Only when whole = 'whole' calculate group delay around
the complete unit circle (0 ... 2 pi)
N : integer (optional, default: 512)
Number of FFT-points
FS : float (optional, default: FS = 2*pi)
Sampling frequency.
Returns
-------
tau_g : ndarray
The group delay
w : ndarray
The angular frequency points where the group delay was computed
Notes
-----
The group delay :math:`\\tau_g(\\omega)` of discrete and continuous time
systems is defined by
.. math::
\\tau_g(\\omega) = - \\phi'(\\omega)
= -\\frac{\\partial \\phi(\\omega)}{\\partial \\omega}
= -\\frac{\\partial }{\\partial \\omega}\\angle H( \\omega)
A useful form for calculating the group delay is obtained by deriving the
*logarithmic* frequency response in polar form as described in [JOS]_ for
discrete time systems:
.. math::
\\ln ( H( \\omega))
= \\ln \\left({H_A( \\omega)} e^{j \\phi(\\omega)} \\right)
= \\ln \\left({H_A( \\omega)} \\right) + j \\phi(\\omega)
\\Rightarrow \\; \\frac{\\partial }{\\partial \\omega} \\ln ( H( \\omega))
= \\frac{H_A'( \\omega)}{H_A( \\omega)} + j \\phi'(\\omega)
where :math:`H_A(\\omega)` is the amplitude response. :math:`H_A(\\omega)` and
its derivative :math:`H_A'(\\omega)` are real-valued, therefore, the group
delay can be calculated from
.. math::
\\tau_g(\\omega) = -\\phi'(\\omega) =
-\\Im \\left\\{ \\frac{\\partial }{\\partial \\omega}
\\ln ( H( \\omega)) \\right\\}
=-\\Im \\left\\{ \\frac{H'(\\omega)}{H(\\omega)} \\right\\}
The derivative of a polynome :math:`P(s)` (continuous-time system) or :math:`P(z)`
(discrete-time system) w.r.t. :math:`\\omega` is calculated by:
.. math::
\\frac{\\partial }{\\partial \\omega} P(s = j \\omega)
= \\frac{\\partial }{\\partial \\omega} \\sum_{k = 0}^N c_k (j \\omega)^k
= j \\sum_{k = 0}^{N-1} (k+1) c_{k+1} (j \\omega)^{k}
= j P_R(s = j \\omega)
\\frac{\\partial }{\\partial \\omega} P(z = e^{j \\omega T})
= \\frac{\\partial }{\\partial \\omega} \\sum_{k = 0}^N c_k e^{-j k \\omega T}
= -jT \\sum_{k = 0}^{N} k c_{k} e^{-j k \\omega T}
= -jT P_R(z = e^{j \\omega T})
where :math:`P_R` is the "ramped" polynome, i.e. its `k` th coefficient is
multiplied by `k` resp. `k` + 1.
yielding:
.. math::
\\tau_g(\\omega) = -\\Im \\left\\{ \\frac{H'(\\omega)}{H(\\omega)} \\right\\}
\\quad \\text{ resp. } \\quad
\\tau_g(\\omega) = -\\Im \\left\\{ \\frac{H'(e^{j \\omega T})}
{H(e^{j \\omega T})} \\right\\}
where::
(H'(e^jwT)) ( H_R(e^jwT)) (H_R(e^jwT))
tau_g(w) = -im |---------| = -im |-jT ----------| = T re |----------|
( H(e^jwT)) ( H(e^jwT) ) ( H(e^jwT) )
where :math:`H(e^{j\\omega T})` is calculated via the DFT at NFFT points and
the derivative
of the polynomial terms :math:`b_k z^-k` using :math:`\\partial / \\partial w b_k e^-jkwT` = -b_k jkT e^-jkwT.
This is equivalent to muliplying the polynome with a ramp `k`,
yielding the "ramped" function H_R(e^jwT).
For analog functions with b_k s^k the procedure is analogous, but there is no
sampling time and the exponent is positive.
.. [JOS] Julius O. Smith III, "Numerical Computation of Group Delay" in
"Introduction to Digital Filters with Audio Applications",
Center for Computer Research in Music and Acoustics (CCRMA),
Stanford University, http://ccrma.stanford.edu/~jos/filters/Numerical_Computation_Group_Delay.html, referenced 2014-04-02,
.. [Lyons] Richard Lyons, "Understanding Digital Signal Processing", 3rd Ed.,
Prentice Hall, 2010.
Examples
--------
>>> b = [1,2,3] # Coefficients of H(z) = 1 + 2 z^2 + 3 z^3
>>> tau_g, td = dsp_lib.grpdelay(b)
"""
## If the denominator of the computation becomes too small, the group delay
## is set to zero. (The group delay approaches infinity when
## there are poles or zeros very close to the unit circle in the z plane.)
##
## Theory: group delay, g(w) = -d/dw [arg{H(e^jw)}], is the rate of change of
## phase with respect to frequency. It can be computed as:
##
## d/dw H(e^-jw)
## g(w) = -------------
## H(e^-jw)
##
## where
## H(z) = B(z)/A(z) = sum(b_k z^k)/sum(a_k z^k).
##
## By the quotient rule,
## A(z) d/dw B(z) - B(z) d/dw A(z)
## d/dw H(z) = -------------------------------
## A(z) A(z)
## Substituting into the expression above yields:
## A dB - B dA
## g(w) = ----------- = dB/B - dA/A
## A B
##
## Note that,
## d/dw B(e^-jw) = sum(k b_k e^-jwk)
## d/dw A(e^-jw) = sum(k a_k e^-jwk)
## which is just the FFT of the coefficients multiplied by a ramp.
##
## As a further optimization when nfft>>length(a), the IIR filter (b,a)
## is converted to the FIR filter conv(b,fliplr(conj(a))).
if whole != 'whole':
nfft = 2 * nfft
nfft = int(nfft)
#
w = Fs * np.arange(0, nfft) / nfft # create frequency vector
try:
len(a)
except TypeError:
a = 1
oa = 0 # a is a scalar or empty -> order of a = 0
c = b
try:
len(b)
except TypeError:
print('No proper filter coefficients: len(a) = len(b) = 1 !')
else:
oa = len(a) - 1 # order of denom. a(z) resp. a(s)
c = np.convolve(b, a[::-1]) # a[::-1] reverses denominator coeffs a
# c(z) = b(z) * a(1/z)*z^(-oa)
try:
len(b)
except TypeError:
b = 1
ob = 0 # b is a scalar or empty -> order of b = 0
else:
ob = len(b) - 1 # order of b(z)
if analog:
a_b = np.convolve(a, b)
if ob > 1:
br_a = np.convolve(b[1:] * np.arange(1, ob), a)
else:
br_a = 0
ar_b = np.convolve(a[1:] * np.arange(1, oa), b)
num = np.fft.fft(ar_b - br_a, nfft)
den = np.fft.fft(a_b, nfft)
else:
oc = oa + ob # order of c(z)
cr = c * np.arange(
0, oc + 1) # multiply with ramp -> derivative of c wrt 1/z
num = np.fft.fft(cr, nfft) #
den = np.fft.fft(c, nfft) #
#
minmag = 10. * np.spacing(1) # equivalent to matlab "eps"
polebins = np.where(abs(den) < minmag)[0] # find zeros of denominator
# polebins = np.where(abs(num) < minmag)[0] # find zeros of numerator
if np.size(polebins) > 0: # check whether polebins array is empty
print('*** grpdelay warning: group delay singular -> setting to 0 at:')
for i in polebins:
print('f = {0} '.format((Fs * i / nfft)))
num[i] = 0
den[i] = 1
if analog:
tau_g = np.real(num / den)
else:
tau_g = np.real(num / den) - oa
#
if whole != 'whole':
nfft = nfft // 2
tau_g = tau_g[0:nfft]
w = w[0:nfft]
return tau_g, w
def __init__(self,
samples_per_symbol=_def_samples_per_symbol,
bits_per_symbol=_def_bits_per_symbol,
h_numerator=_def_h_numerator,
h_denominator=_def_h_denominator,
cpm_type=_def_cpm_type,
bt=_def_bt,
symbols_per_pulse=_def_symbols_per_pulse,
generic_taps=_def_generic_taps,
verbose=_def_verbose,
log=_def_log):
gr.hier_block2.__init__(
self,
"cpm_mod",
gr.io_signature(1, 1, gr.sizeof_char), # Input signature
gr.io_signature(1, 1, gr.sizeof_gr_complex)) # Output signature
self._samples_per_symbol = samples_per_symbol
self._bits_per_symbol = bits_per_symbol
self._h_numerator = h_numerator
self._h_denominator = h_denominator
self._cpm_type = cpm_type
self._bt = bt
if cpm_type == 0 or cpm_type == 2 or cpm_type == 3: # CPFSK, RC, Generic
self._symbols_per_pulse = symbols_per_pulse
elif cpm_type == 1: # GMSK
self._symbols_per_pulse = 4
else:
raise TypeError, (
"cpm_type must be an integer in {0,1,2,3}, is %r" %
(cpm_type, ))
self._generic_taps = numpy.array(generic_taps)
if samples_per_symbol < 2:
raise TypeError, ("samples_per_symbol must be >= 2, is %r" %
(samples_per_symbol, ))
self.nsymbols = 2**bits_per_symbol
self.sym_alphabet = numpy.arange(-(self.nsymbols - 1), self.nsymbols,
2).tolist()
self.ntaps = int(self._symbols_per_pulse * samples_per_symbol)
sensitivity = 2 * pi * h_numerator / h_denominator / samples_per_symbol
# Unpack Bytes into bits_per_symbol groups
self.B2s = blocks.packed_to_unpacked_bb(bits_per_symbol,
gr.GR_MSB_FIRST)
# Turn it into symmetric PAM data.
self.pam = digital_swig.chunks_to_symbols_bf(self.sym_alphabet, 1)
# Generate pulse (sum of taps = samples_per_symbol/2)
if cpm_type == 0: # CPFSK
self.taps = (1.0 / self._symbols_per_pulse / 2, ) * self.ntaps
elif cpm_type == 1: # GMSK
gaussian_taps = filter.firdes.gaussian(
1.0 / 2, # gain
samples_per_symbol, # symbol_rate
bt, # bandwidth * symbol time
self.ntaps # number of taps
)
sqwave = (1, ) * samples_per_symbol # rectangular window
self.taps = numpy.convolve(numpy.array(gaussian_taps),
numpy.array(sqwave))
elif cpm_type == 2: # Raised Cosine
# generalize it for arbitrary roll-off factor
self.taps = (1 - numpy.cos(
2 * pi * numpy.arange(0, self.ntaps) / samples_per_symbol /
self._symbols_per_pulse)) / (2 * self._symbols_per_pulse)
elif cpm_type == 3: # Generic CPM
self.taps = generic_taps
else:
raise TypeError, (
"cpm_type must be an integer in {0,1,2,3}, is %r" %
(cpm_type, ))
self.filter = filter.pfb.arb_resampler_fff(samples_per_symbol,
self.taps)
# FM modulation
self.fmmod = analog.frequency_modulator_fc(sensitivity)
if verbose:
self._print_verbage()
if log:
self._setup_logging()
# Connect
self.connect(self, self.B2s, self.pam, self.filter, self.fmmod, self)