def compute_normalising_constant_bivariatefisher(self,
specific_neurons=None):
'''
Depending on neuron_sigma, we have different normalising constants per neurons.
The full formula, for kappa3 != 0 is more complex, we do not use it for now:
Z = 4 pi^2 \sum_{m=0}^\infty n_choose_k(2m, m) (\kappa_3^2/(4 kappa_1 kappa_2))^m I_m(kappa_1) I_m(kappa_2)
Here, for \kappa_3=0, only m=0 used
'''
if self.normalisation is None:
self.normalisation = np.zeros(self.M)
self.normalisation_fisher_all = np.zeros((self.M, self.R))
self.normalisation_gauss_all = np.zeros((self.M, self.R))
# The normalising constant
# Overflows have happened, but they have no real consequence, as 1/inf = 0.0, appropriately.
if specific_neurons is None:
# precompute separate ones
self.normalisation_fisher_all = 2. * np.pi * scsp.i0(self.neurons_sigma)
self.normalisation_gauss_all = np.sqrt(self.neurons_sigma) / (
np.sqrt(2 * np.pi))
self.normalisation = np.prod(self.normalisation_fisher_all, axis=-1)
else:
self.normalisation_fisher_all[specific_neurons] = 2. * np.pi * scsp.i0(
self.neurons_sigma[specific_neurons])
self.normalisation_gauss_all[specific_neurons] = np.sqrt(
self.neurons_sigma[specific_neurons]) / (np.sqrt(2 * np.pi))
self.normalisation[specific_neurons] = np.prod(
self.normalisation_fisher_all[specific_neurons], axis=-1)
def compute_fisher_information_theoretical(self, sigma=None):
'''
Compute the theoretical, large N limit estimate of the Fisher Information
This one assumes a diagonal covariance matrix, wrong for the complete model.
'''
assert self.R <= 2, "Not implemented for R>2"
if self.population_code_type == 'conjunctive':
rho = 1. / (4 * np.pi**2 / (self.M))
# rho = 1./(2*np.pi/(self.M))
elif self.population_code_type == 'feature':
# M/2 neuron per 2pi dimension.
print "This looks wrong, doesnt fit at all"
rho = 1. / (np.pi**2. / self.M**2.)
else:
print 'Fisher information not defined for population type ' + self.population_code_type
return 0
kappa1 = self.rc_scale[0]
kappa2 = self.rc_scale[1]
return kappa1**2. * rho * (
scsp.i0(2 * kappa1) - scsp.iv(2, 2 * kappa1)
) * scsp.i0(2 * kappa2) / (
sigma**2. * 8 * np.pi**2. * scsp.i0(kappa1)**2. * scsp.i0(kappa2)**2.)
def kaiser_discrete(alpha):
N = 29
M = N - 1
ns = np.arange(M + 0.1)
z = 2 * ns / M - 1
wn = i0(np.pi * alpha * np.sqrt(1 - (z) ** 2)) / i0(np.pi * alpha)
return wn
def tetmConstants(self, ri, ro, neff, wl, EH, c, idx):
a = numpy.empty((2, 2))
n = self.maxIndex(wl)
u = self.u(ro, neff, wl)
urp = self.u(ri, neff, wl)
if neff < n:
B1 = j0(u)
B2 = y0(u)
F1 = j0(urp) / B1
F2 = y0(urp) / B2
F3 = -j1(urp) / B1
F4 = -y1(urp) / B2
c1 = wl.k0 * ro / u
else:
B1 = i0(u)
B2 = k0(u)
F1 = i0(urp) / B1
F2 = k0(urp) / B2
F3 = i1(urp) / B1
F4 = -k1(urp) / B2
c1 = -wl.k0 * ro / u
c3 = c * c1
a[0, 0] = F1
a[0, 1] = F2
a[1, 0] = F3 * c3
a[1, 1] = F4 * c3
return numpy.linalg.solve(a, EH.take(idx))
def test_bessel_i0(self):
x_single = np.arange(-3, 3).reshape(1, 3, 2).astype(np.float32)
x_double = np.arange(-3, 3).reshape(1, 3, 2).astype(np.float64)
try:
from scipy import special # pylint: disable=g-import-not-at-top
self.assertAllClose(special.i0(x_single),
self.evaluate(special_math_ops.bessel_i0(x_single)))
self.assertAllClose(special.i0(x_double),
self.evaluate(special_math_ops.bessel_i0(x_double)))
except ImportError as e:
tf_logging.warn('Cannot test special functions: %s' % str(e))
def window(x, name, a=2, alpha=5):
if np.abs(x) <= a:
if name == 'lanczos':
return np.sinc(x / a)
if name == 'hann':
return 0.5 * (1 + np.cos(np.pi * x / a))
if name == 'kaiser':
return i0(np.pi * alpha * np.sqrt(1 - (x / a) ** 2)) / i0(np.pi * alpha)
if name == None or window == 'boxcar':
return 1.
else:
return 0.
def _tecoeq(self, v0, nu):
u1r1, u2r1, u2r2, s1, s2, n1sq, n2sq, n3sq = self.__params(v0)
(f11a, f11b) = ((j0(u1r1), jn(2, u1r1)) if s1 > 0 else
(i0(u1r1), -iv(2, u1r1)))
if s2 > 0:
f22a, f22b = j0(u2r2), y0(u2r2)
f2a = jn(2, u2r1) * f22b - yn(2, u2r1) * f22a
f2b = j0(u2r1) * f22b - y0(u2r1) * f22a
else: # a
f22a, f22b = i0(u2r2), k0(u2r2)
f2a = kn(2, u2r1) * f22a - iv(2, u2r1) * f22b
f2b = i0(u2r1) * f22b - k0(u2r1) * f22a
return f11a * f2a - f11b * f2b
def kaiser_window(xs, halfwidth, alpha):
"""
Return the kaiser window function for the values 'xs' when the
the half-width of the window should be 'haldwidth' with
the folloff parameter 'alpha'. The following values are
particularly interesting:
alpha
-----
0 Rectangular Window
5 Similar to Hamming window
6 Similar to Hanning window
8.6 Almost identical to the Blackman window
"""
win = i0(alpha*Num.sqrt(1.0-(xs/halfwidth)**2.0))/i0(alpha)
return Num.where(Num.fabs(xs)<=halfwidth, win, 0.0)
def _evaluate(self,R,z,phi=0.,t=0.):
"""
NAME:
_evaluate
PURPOSE:
evaluate the potential at (R,z)
INPUT:
R - Cylindrical Galactocentric radius
z - vertical height
phi - azimuth
t - time
OUTPUT:
potential at (R,z)
HISTORY:
2012-12-26 - Written - Bovy (IAS)
"""
if self._new:
#if R > 6.: return self._kp(R,z)
if nu.fabs(z) < 10.**-6.:
y= 0.5*self._alpha*R
return -nu.pi*R*(special.i0(y)*special.k1(y)-special.i1(y)*special.k0(y))
kalphamax= 10.
ks= kalphamax*0.5*(self._glx+1.)
weights= kalphamax*self._glw
sqrtp= nu.sqrt(z**2.+(ks+R)**2.)
sqrtm= nu.sqrt(z**2.+(ks-R)**2.)
evalInt= nu.arcsin(2.*ks/(sqrtp+sqrtm))*ks*special.k0(self._alpha*ks)
return -2.*self._alpha*nu.sum(weights*evalInt)
raise NotImplementedError("Not new=True not implemented for RazorThinExponentialDiskPotential")
def testValuePR0(self):
"Test vonMisesKappaConjugate probability by changing R0"
try:
from scipy.special import i0, i1
except ImportError:
self.skipTest("this test requires the scipy Python module")
c = 10.0
no = 1.0
self.kappa.set_scale(no)
for i in range(100):
R0 = uniform(0.0, 10.0)
self.J = IMP.isd.vonMisesKappaConjugateRestraint(self.m, self.kappa, c, R0)
ratio = i1(no) / i0(no)
py = exp(no * R0) / i0(no) ** c
cpp = self.J.get_probability()
self.assertAlmostEqual(cpp, py, delta=0.001)
def estimate_distribution(hours):
"""
Estimate the parameters of the von Mises distribution for the data.
Arguments:
hours: A NumPy array holding incident times as floats between 0 and 24.
Returns:
mu: The distribution's center as a float between -pi and pi.
kappa: The distribution's measure of concentration as a float.
More information about the von Mises distribution:
https://en.wikipedia.org/wiki/Von_Mises_distribution
"""
theta = hours_to_radians(hours)
z = np.vectorize(complex)(np.cos(theta), np.sin(theta))
n = len(z)
z_mean = np.mean(z)
mu = np.arctan2(z_mean.imag, z_mean.real)
r2 = np.mean(z.real)**2 + np.mean(z.imag)**2
re = np.sqrt(n/(n - 1)*(r2 - 1/n))
x = np.arange(0, 10, 1e-4)
y = np.abs(i1(x)/i0(x) - re)
kappa = x[np.argmin(y)]
return mu, kappa
def mmse_stsa(infile, outfile, noise_sum):
signal, params = read_signal(infile, WINSIZE)
nf = len(signal)/(WINSIZE/2) - 1
sig_out=sp.zeros(len(signal),sp.float32)
G = sp.ones(WINSIZE)
prevGamma = G
alpha = 0.98
window = sp.hanning(WINSIZE)
gamma15=spc.gamma(1.5)
lambdaD = noise_sum / 5.0
percentage = 0
for no in xrange(nf):
p = int(math.floor(1. * no / nf * 100))
if (p > percentage):
percentage = p
print "{}%".format(p),
y = get_frame(signal, WINSIZE, no)
Y = sp.fft(y*window)
Yr = sp.absolute(Y)
Yp = sp.angle(Y)
gamma = Yr**2/lambdaD
xi = alpha * G**2 * prevGamma + (1-alpha)*sp.maximum(gamma-1, 0)
prevGamma = gamma
nu = gamma * xi / (1+xi)
G = (gamma15 * sp.sqrt(nu) / gamma ) * sp.exp(-nu/2) * ((1+nu)*spc.i0(nu/2)+nu*spc.i1(nu/2))
idx = sp.isnan(G) + sp.isinf(G)
G[idx] = xi[idx] / (xi[idx] + 1)
Yr = G * Yr
Y = Yr * sp.exp(Yp*1j)
y_o = sp.real(sp.ifft(Y))
add_signal(sig_out, y_o, WINSIZE, no)
write_signal(outfile, params, sig_out)
def pdf_vn(x, b, loc):
"""pdf of von mises distribution
has fixed scale=1, otherwise same as scipy.stats.vonmises
"""
return np.exp(b * np.cos(x - loc)) / (2.0 * np.pi * special.i0(b))
def vonMises_fn(phi, k, mu):
"""
The vonMises function generates a weighting for different
cyclic quantities phi from a vonMises distribution centered
around mu with a kernel width k.
"""
return (1/(2*np.pi*ss.i0(k))) * np.e**(k*np.cos(2*(phi-mu)))
def testValueEc(self):
"Test vonMisesKappaConjugate energy by changing c"
try:
from scipy.special import i0, i1
except ImportError:
self.skipTest("this test requires the scipy Python module")
R0 = 1
no = 1.0
self.kappa.set_scale(no)
for i in range(100):
c = uniform(1.0, 100)
self.J = IMP.isd.vonMisesKappaConjugateRestraint(self.m, self.kappa, c, R0)
ratio = i1(no) / i0(no)
py = -no * R0 + c * log(i0(no))
cpp = self.J.evaluate(False)
self.assertAlmostEqual(cpp, py, delta=0.001)
def circularKDE(parameters, kdeStep=np.pi/16.):
"""
Create a probability distribution function for radial-type data,
e.g. bearings. Returns the grid on which the PDF is defined, the
PDF itself and the corresponding CDF.
By default, the grid is specified on [0,2\*pi)
:param parameters: :class:`numpy.ndarray` of parameter values.
:param float kdeStep: Increment of the ordinate at which the
distribution will be estimated.
:returns: :class:`numpy.ndarray` of the grid, the PDF and the CDF.
"""
bw = KPDF.UPDFOptimumBandwidth(parameters)
grid = np.arange(0, 2 * np.pi +kdeStep, kdeStep)
pdf = np.empty(len(grid), 'float')
chi = 1./(2 * np.pi * i0(bw))
for k in parameters:
kH = chi * np.exp(bw * np.cos(grid-k))
pdf += kH/kH.sum()
pdf = pdf/len(pdf)
cy = stats.cdf(grid, pdf)
return grid, pdf, cy
def momentum(self,k1,t1,k2,t2):
#qq = lambda phi: k1**2 + k2**2 - 2*k1*k2*(cos(t2-t1) - 2*sin(t2)*sin(t1)*sin(phi)**2)
#poten = lambda phi: exp( -1*self.a**2*qq(phi/2.)/4. )
#return self.A*self.a**3/(8*pi**1.5)*quad(poten,0,2*pi)[0]
arg1 = -1*(k1**2 + k2**2 - 2*k1*k2*cos(t2)*cos(t1))*self.a/4.0
arg2 = self.a**2*k1*k2*sin(t1)*sin(t2)
return self.A*self.a**3/4*pi**0.5*exp( arg1 )*i0( arg2 )
def _tmcoeq(self, v0, nu):
u1r1, u2r1, u2r2, s1, s2, n1sq, n2sq, n3sq = self.__params(v0)
if s1 == 0: # e
f11a, f11b = 2, 1
elif s1 > 0: # a, b, d
f11a, f11b = j0(u1r1) * u1r1, j1(u1r1)
else: # c
f11a, f11b = i0(u1r1) * u1r1, i1(u1r1)
if s2 > 0:
f22a, f22b = j0(u2r2), y0(u2r2)
f2a = j1(u2r1) * f22b - y1(u2r1) * f22a
f2b = j0(u2r1) * f22b - y0(u2r1) * f22a
else: # a
f22a, f22b = i0(u2r2), k0(u2r2)
f2a = i1(u2r1) * f22b + k1(u2r1) * f22a
f2b = i0(u2r1) * f22b - k0(u2r1) * f22a
return f11a * n2sq * f2a - f11b * n1sq * f2b * u2r1
def kappa_to_stddev(kappa):
'''
Convert kappa to wrapped gaussian std dev
std = 1 - I_1(kappa)/I_0(kappa)
'''
# return 1.0 - scsp.i1(kappa)/scsp.i0(kappa)
return np.sqrt(-2.*np.log(scsp.i1(kappa)/scsp.i0(kappa)))
def rotation_velocity(pos):
rho = (pos[0]**2 + pos[1]**2)**0.5
phi = np.arctan2(pos[1], pos[0])
y = rho/(2*Rd)
sigma0 = M_dm / (2*pi*Rd**2)
speed = (4*pi*G*sigma0*y**2*(i0(y)*k0(y) - i1(y)*k1(y)) +
(G*M_dm*rho)/(rho+a_dm)**2 + (G*M_bulge*rho)/(rho+a_bulge)**2)**0.5
return (-speed*sin(phi), speed*cos(phi), 0)
def vonmisespdf(x, mu, K):
'''
Von Mises PDF (switch to Normal if high kappa)
'''
if K > 700.:
return np.sqrt(K)/(np.sqrt(2*np.pi))*np.exp(-0.5*(x - mu)**2.*K)
else:
return np.exp(K*np.cos(x-mu)) / (2.*np.pi * spsp.i0(K))
def testValueEKappa(self):
"Test vonMisesKappaConjugate energy by changing kappa"
try:
from scipy.special import i0,i1
except ImportError:
self.skipTest("this test requires the scipy Python module")
c=10
R0=1
self.J = IMP.isd.vonMisesKappaConjugateRestraint(self.kappa,c,R0)
self.m.add_restraint(self.J)
for i in xrange(100):
no=uniform(0.1,100)
self.kappa.set_scale(no)
ratio=i1(no)/i0(no)
py=-no*R0 + c*log(i0(no))
cpp=self.J.evaluate(None)
self.assertAlmostEqual(cpp,py,delta=0.001)
def testDerivativeKappa(self):
"Test vonMisesKappaConjugate derivative by changing kappa"
try:
from scipy.special import i0,i1
except ImportError:
self.skipTest("this test requires the scipy Python module")
c=10
R0=1
self.J = IMP.isd.vonMisesKappaConjugateRestraint(self.kappa,c,R0)
self.m.add_restraint(self.J)
for i in xrange(100):
no=uniform(0.1,100)
self.kappa.set_scale(no)
self.m.evaluate(self.DA)
ratio=i1(no)/i0(no)
self.assertAlmostEqual(self.kappa.get_scale_derivative(),
-R0 + c*i1(no)/i0(no), delta=0.001)
def kaiser(M,beta,sym=1):
"""Return a Kaiser window of length M with shape parameter beta.
"""
if M < 1:
return array([])
if M == 1:
return ones(1,'d')
odd = M % 2
if not sym and not odd:
M = M+1
n = arange(0,M)
alpha = (M-1)/2.0
w = special.i0(beta * sqrt(1-((n-alpha)/alpha)**2.0))/special.i0(beta)
if not sym and not odd:
w = w[:-1]
return w
def testValuePc(self):
"test probability by changing c"
try:
from scipy.special import i0,i1
except ImportError:
self.skipTest("this test requires the scipy Python module")
R0=1.0
no=1.0
self.kappa.set_scale(no)
for i in xrange(100):
c=uniform(2.0,75)
self.J = IMP.isd.vonMisesKappaConjugateRestraint(self.kappa,c,R0)
self.m.add_restraint(self.J)
ratio=i1(no)/i0(no)
py=exp(no*R0)/i0(no)**c
cpp=self.J.get_probability()
self.assertAlmostEqual(cpp,py,delta=0.001)
self.m.remove_restraint(self.J)
def gradient(self,phases,log10_ens=3,free=False):
e,width,loc = self._make_p(log10_ens)
my_i0 = i0(1./width)
my_i1 = i1(1./width)
z = TWOPI*(phases-loc)
cz = np.cos(z)
sz = np.sin(z)
f = (np.exp(cz)/width)/my_i0
return np.asarray([-cz/width**2*f,TWOPI*(sz/width+my_i1/my_i0)*f])
def _margdistphase_loglr(self, mf_snr, opt_snr):
"""Returns the log likelihood ratio marginalized over distance and
phase.
"""
logl = numpy.log(special.i0(mf_snr))
logl_marg = logl/self._dist_array
opt_snr_marg = opt_snr/self._dist_array**2
return special.logsumexp(logl_marg - 0.5*opt_snr_marg,
b=self._deltad*self.dist_prior)
def population_code_response_2D(theta1,
theta2,
pref_angles,
N=10,
kappa=0.1,
amplitude=1.0):
return amplitude * np.exp(kappa * np.cos(theta1 - pref_angles[:, 0]) +
kappa * np.cos(theta2 - pref_angles[:, 1])
) / (4. * np.pi**2. * scsp.i0(kappa)**2.)
def _run(self, rzlist, t):
r = rzlist[0]
z = rzlist[1]
temperature = self.T0 + (self.TL - self.T0) * z / self.L + \
(self.g0 / (2 * self.k)) * z * (self.L - z)
sum = 0
for n in xrange(0, self.Nsum):
nodd = float(2 * n + 1)
lam = nodd * np.pi / self.L
iratio = (2. / np.pi) * i0(lam * r) / i0(lam * self.b)
sum += (2 * self.Tb - self.T0) * iratio * np.sin(lam * z) / nodd
sum += self.TL * iratio * (-1)**nodd * np.sin(lam * z) / nodd
sum += -(2 * self.g0 * self.L**2 / (np.pi**2 * self.k)) * np.sin(lam * z) / nodd**2
temperature += sum
return ExactSolution([r, z, temperature],
names=['position_r', 'position_z', 'temperature'],
jumps=[]
)
def Gamma(nw_rad, lay_ox, L_d, L_tf, eps_1, eps_2, eps_3):
fact1 = (nw_rad + lay_ox)/L_d
fact2 = nw_rad/L_tf
fact3 = fact1**(-1)
fact4 = (nw_rad + lay_ox)/nw_rad
num = eps_1*k0(fact1)*(L_d/L_tf)*i1(fact2)
denom1 = k0(fact1)*fact3
denom2 = log(fact4)*k1(fact1)*(eps_3/eps_2)
denom3 = (denom1 + denom2)*eps_1*fact2*i1(fact2)
denom = denom3 + eps_3*k1(fact1)*i0(fact2)
gamma = num/denom
return gamma
# parameter to define the user-defined von Mises on the SEMI-CIRCLE
ll = 2.0
# parameter to define the stats von Mises on the SEMI-CIRCLE
scal = 0.5
#%% plot some modified Bessel functions:
kappp = np.array(np.arange(1e-3,12,4))
mu1 = np.pi/4
l_lim = -np.pi/2 - mu1
u_lim = np.pi/2 - mu1
t_ = np.linspace( l_lim, u_lim, N )
fig, ax = plt.subplots(1, 1, figsize=(9,3))
for kap in kappp:
# check the I0 for shifting:
I0a = integrate.quad(lambda x: (np.exp(kap*np.cos(2*x))), l_lim, u_lim) - np.pi*special.i0(kap)
I0c = integrate.quad(lambda x: (np.exp(kap*np.cos(2*x))), -np.pi/2, np.pi/2) - np.pi*special.i0(kap)
I0b = integrate.quad(lambda x: (np.exp(kap*np.cos(2*(x-mu1)))), -np.pi/2, np.pi/2) - np.pi*special.i0(kap)
print('I0a, I0b, I0c: ',I0a[0], I0b[0], I0c[0])
# check the I1 for shifting:
I1a = integrate.quad(lambda x: (np.exp(kap*np.cos(2*x)))*(np.cos(2*x)), l_lim, u_lim) - np.pi*special.i1(kap)
I1c = integrate.quad(lambda x: (np.exp(kap*np.cos(2*x)))*(np.cos(2*x)), -np.pi/2, np.pi/2) - np.pi*special.i1(kap)
I1b = integrate.quad(lambda x: (np.exp(kap*np.cos(2*(x-mu1))))*(np.cos(2*(x-mu1))), -np.pi/2, np.pi/2) - np.pi*special.i1(kap)
I1d = integrate.quad(lambda x: (np.exp(kap*np.cos(2*(x-mu1))))*(np.cos(2*(x-mu1))), l_lim, u_lim) - np.pi*special.i1(kap)
print('I1a, I1c, I1b, I1d: ',I1a[0], I1c[0], I1b[0], I1d[0])
# check the integral of the VM:
VM = np.exp(kap*np.cos(2*(t_-mu1)))/(np.pi*i0(kap))
Ivm1a = integrate.quad(lambda x: (np.exp(kap*np.cos(2*(x-mu1))))/(np.pi*i0(kap)), l_lim, u_lim)
Ivm2a = integrate.quad(lambda x: (np.exp(kap*np.cos(2*x)))/(np.pi*i0(kap)), l_lim, u_lim)
Ivm1b = integrate.quad(lambda x: (np.exp(kap*np.cos(2*(x-mu1))))/(np.pi*i0(kap)), -np.pi/2, np.pi/2)
Ivm2b = integrate.quad(lambda x: (np.exp(kap*np.cos(2*x)))/(np.pi*i0(kap)), -np.pi/2, np.pi/2)
print(zm)
## p1, Dp1, p2, Dp2, p2star, Dp2star
p1_iterable = ((par['alpha_m'] * k1(par['alpha_m'] * locs['rad'][i]) /
k0(par['alpha_m'] * locs['rad'][i])) for i in range(n))
p1 = numpy.fromiter(p1_iterable, float)
Dp1 = p1 * numpy.identity(n)
## in p2: should check if delta means delta_h or delta_m
## in confirm.nb it is delta_h = k_h * a_h * alpha_h (patch dependent)
p2_iterable = ((locs['delta'])[i] * i1(locs['alpha'][i] * locs['rad'][i]) /
(par['am'] * par['km'] * i0(locs['alpha'][i] * locs['rad'][i]))
for i in range(n))
p2 = numpy.fromiter(p2_iterable, float)
Dp2 = p2 * numpy.identity(n)
p2star_iterable = (
par['km'] * par['alpha_m'] * par['am'] *
i1(par['alpha_m'] * locs['rad'][i]) /
(par['am'] * par['km'] * i0(par['alpha_m'] * locs['rad'][i]))
for i in range(n))
p2star = numpy.fromiter(p2star_iterable, float)
Dp2star = p2star * numpy.identity(n)
## S matrix
def __call__(self,phases,log10_ens=3):
e,width,loc = self._make_p(log10_ens)
z = TWOPI*(phases-loc)
return np.exp(np.cos(z)/width)/i0(1./width)
def fun_mle(x):
#FIX: square or square-root(z2) was missing
#val = z2 - ((i1(x) / i0(x)))**2 #
val = z - i1(x) / i0(x)
#print val
return val
def plot(Phi, myinit, prob, ana):
# Parse myinit
gdata, Sdata, Kdata = myinit
# Parse gdata
x1f, x1c, x2f, x2c = gdata
nx2, nx1 = len(x2c), len(x1c)
# Plot Phi
fig = plt.figure(facecolor='white')
ax1 = fig.add_subplot(111)
X, Y = np.meshgrid(x1f, x2f, indexing='xy')
if ana:
XC, YC = np.meshgrid(x1c, x2c, indexing='xy')
X1C, X2C = np.sqrt(XC**2. + YC**2.), np.arctan2(YC, XC)
X2C[X2C < 0] += 2. * np.pi
if prob == 'exp':
Rd = 0.5
sig0 = 1.
y = X1C / (2. * Rd)
Phiana = -np.pi * G * sig0 * X1C * (i0(y) * kn(1, y) -
i1(y) * kn(0, y))
elif prob == 'constant':
sig0 = 2.e-3
v_max = x1c / np.max(x1c)
u_min = np.min(x1c) / x1c
grana = 4 * G * sig0 * ((ellipe(v_max) - ellipk(v_max)) / v_max +
ellipk(u_min) - ellipe(u_min))
elif prob == 'mestel':
v0 = 1.
eps = np.max(x1f)
Phiana = v0**2. * (np.log(X1C / eps) + np.log(0.5))
elif prob == 'kuzmin':
a = 1.
M = 1.
Phiana = -G * M / np.sqrt(X1C**2. + a**2.)
elif prob == 'cylinders':
sig = 0.1
Rk = lambda rk, pk: np.sqrt(X1C**2. + rk**2. - 2. * X1C * rk * np.
cos(X2C - pk))
yk = lambda rk, pk: Rk(rk, pk) / (2. * sig)
Phik = lambda rk, pk: -0.5 * (G / sig**2.) * Rk(rk, pk) * (i0(
yk(rk, pk)) * kn(1, yk(rk, pk)) - i1(yk(rk, pk)) * kn(
0, yk(rk, pk)))
Phiana = 2. * Phik(3., 1e-3) + 0.5 * Phik(3., np.pi + 1e-3) + Phik(
2.0, 0.75 * np.pi)
else:
print(
'[plot]: Analytic solution not provided for prob: %s, exiting...'
% (prob))
quit()
print('[plot]: Plotting analytical solution for %s prob' % (prob))
# Compute RMS error
rms = np.sqrt(np.sum((Phiana - Phi)**2.) / (float(Phiana.size)))
# Plot analytic result
plt.figure(facecolor='white')
plt.plot(x1c, Phi[nx2 / 2, :], 'b.', label='$\Phi_G$ (numerical)')
plt.plot(x1c, Phiana[nx2 / 2, :], 'r--', label='$\Phi_G$ (analytical)')
plt.xlabel('R [code units]')
plt.ylabel('$\Phi_G$')
plt.title('RMS error: %3.2e' % (rms))
plt.legend(loc=4)
im = ax1.pcolorfast(X, Y, Phi, cmap='magma')
ax1.set_aspect('equal')
ax1.set_xlabel('x [code units]')
ax1.set_ylabel('y [code units]')
cbar = fig.colorbar(im, label='$\Phi_G$')
# Plot data
data = Sdata
'''
fig1 = plt.figure(facecolor='white')
ax2 = fig1.add_subplot(111)
im = ax2.pcolorfast(X, Y, data,cmap='magma')
ax2.set_aspect('equal')
ax2.set_xlabel('x [code units]')
ax2.set_ylabel('y [code units]')
cbar = fig1.colorbar(im,label='$\Sigma$')
'''
plt.show()
return
def EqF6(self,x):
"""
Relation between rotation and Gaussian broadening kernels by least-squares fitting
"""
result = 1./sqrt(2.)-(12.*(self["linLimb"]+2.*self["quadLimb"])*exp(-x**2))/(x**2*(-6.+2.*self["linLimb"]+self["quadLimb"])) \
+ (6.*exp(-x**2/2.))/(x**3*(-6.+2.*self["linLimb"]+self["quadLimb"])) * ( -2.*x**3*(-1.+self["linLimb"]+self["quadLimb"])*i0(x**2/2.) \
+ 2.*x*(-2.*self["quadLimb"]+x**2*(-1.+self["linLimb"]+self["quadLimb"])) * i1(x**2/2.)
+ sqrt(pi)*exp(x**2/2.)*(self["linLimb"]+2.*self["quadLimb"])*erf(x) )
return result
def _margtimephase_loglr(self, mf_snr, opt_snr):
"""Returns the log likelihood ratio marginalized over time and phase.
"""
return special.logsumexp(numpy.log(special.i0(mf_snr)),
b=self._deltat) - 0.5 * opt_snr
def fun_mle(x):
val = z - i1(x) / i0(x)
return val
def kirchhoff_roughness(dat, picknum, freq, filt_n=101, eps=3.15):
"""
Roughness by Kirchhoff Theory
Christianson et al. (2016), equation C2
Paramaters
----------
freq: float
antenna frequency
filt_n: int; optional
number of traces included in the median filter
eps: float; optional
relative permittivity of ice
"""
if 'interp' not in vars(dat.flags):
raise KeyError('Do interpolation before roughness calculation.')
# calculate the speed and wavelength
eps0 = 8.8541878128e-12 # vacuum permittivity
mu0 = 1.25663706212e-6 # vacuum permeability
u = 1. / np.sqrt(eps * eps0 * mu0) # speed of light in ice
lam = u / freq # wavelength m
# get a pick depth
if 'z' in vars(dat.picks):
Z = dat.picks.z
else:
print('Warning: setting pick depth for constant velocity in ice.')
Z = dat.picks.time * u / 2 / 1e6
# Find window size based on the width of the first Fresnel zone
D1 = np.sqrt(2. * lam *
(np.nanmean(Z) / np.sqrt(eps))) # Width of Fresnel zone
dx = dat.trace_int[0] # m spacing between traces
N = int(round(D1 / (2. * dx))) # number of traces in the Fresnel window
# -----------------------------------------------------------------------------
# Define the bed geometry
bed_raw = dat.elev - Z[picknum]
bed_filt = medfilt(bed_raw, filt_n)
# RMS bed roughness; Christianson et al. (2016) equation C2
ED1 = np.nan * np.empty((len(bed_filt), ))
for n in range(N, len(bed_filt) - N + 1):
b = bed_filt[n - N:n + N].copy()
b = b[np.where(~np.isnan(b))]
if len(b) <= 1:
ED1[n] = np.nan
else:
b_ = detrend(b)
b_sum = 0.
for i in range(len(b)):
b_sum += (b_[i])**2.
ED1[n] = np.sqrt((1 / (len(b) - 1.)) * b_sum)
# Find the power reduction by Kirchoff theory
# Christianson et al. (2016), equation C1
g = 4. * np.pi * ED1 / lam
b = (i0((g**2.) / 2.))**2.
pn = np.exp(-(g**2.)) * b
return ED1, pn
def w(r, z, dp):
#return i0(k * r) + k0(k * r) - ((1 + pow(m, 2)) * dp / M) - 1
return c1(z, dp) * i0(k * r) + c2(z, dp) * k0(k * r) - (
(1 + pow(m, 2)) * dp / M) - 1
def c1(z, dp):
term_1 = c - (k0(k * r1) - k0(k * r2(z))) * c2(z, dp)
term_2 = i0(k * r1) - i0(k * r2(z))
return term_1 / term_2
def von_mises_cdf_normalapprox(k, x):
b = np.sqrt(2/np.pi)*np.exp(k)/i0(k)
z = b*np.sin(x/2.)
return scipy.stats.norm.cdf(z)
def kaiser(N, beta, flag='asymmetric', length='full'):
r'''
The Kaiser window function
.. math::
w[n] = I_0\left( \beta \sqrt{1-\frac{4n^2}{(M-1)^2}} \right)/I_0(\beta)
with
.. math::
\quad -\frac{M-1}{2} \leq n \leq \frac{M-1}{2},
where :math:`I_0` is the modified zeroth-order Bessel function.
Parameters
----------
N: int
the window length
beta: float
Shape parameter, determines trade-off between main-lobe width and
side lobe level. As beta gets large, the window narrows.
flag: string, optional
Possible values
- *asymmetric*: asymmetric windows are used
for overlapping transforms (:math:`M=N`)
- *symmetric*: the window is symmetric (:math:`M=N-1`)
- *mdct*: impose MDCT condition on the window (:math:`M=N-1` and
:math:`w[n]^2 + w[n+N/2]^2=1`)
length: string, optional
Possible values
- *full*: the full length window is computed
- *right*: the right half of the window is computed
- *left*: the left half of the window is computed
'''
# first choose the indexes of points to compute
if length == 'left': # left side of window
t = np.arange(0, N / 2)
elif length == 'right': # right side of window
t = np.arange(N / 2, N)
else: # full window by default
t = np.arange(0, N)
# if asymmetric window, denominator is N, if symmetric it is N-1
if flag in ['symmetric', 'mdct']:
t = t / float(N - 1)
else:
t = t / float(N)
n = np.arange(0, N)
alpha = (N - 1) / 2.0
w = (special.i0(beta * np.sqrt(1 - ((n - alpha) / alpha)**2.0)) /
special.i0(beta))
# make the window respect MDCT condition
if flag == 'mdct':
d = w[:N / 2] + w[N / 2:]
w[:N / 2] *= 1. / d
w[N / 2:] *= 1. / d
# compute window
return w
def _margphase_loglr(self, mf_snr, opt_snr):
"""Returns the log likelihood ratio marginalized over phase.
"""
return numpy.log(special.i0(mf_snr)) - 0.5 * opt_snr
def kaiser(M, beta, sym=True):
r"""Return a Kaiser window.
The Kaiser window is a taper formed by using a Bessel function.
Parameters
----------
M : int
Number of points in the output window. If zero or less, an empty
array is returned.
beta : float
Shape parameter, determines trade-off between main-lobe width and
side lobe level. As beta gets large, the window narrows.
sym : bool, optional
When True (default), generates a symmetric window, for use in filter
design.
When False, generates a periodic window, for use in spectral analysis.
Returns
-------
w : ndarray
The window, with the maximum value normalized to 1 (though the value 1
does not appear if `M` is even and `sym` is True).
Notes
-----
The Kaiser window is defined as
.. math:: w(n) = I_0\left( \beta \sqrt{1-\frac{4n^2}{(M-1)^2}}
\right)/I_0(\beta)
with
.. math:: \quad -\frac{M-1}{2} \leq n \leq \frac{M-1}{2},
where :math:`I_0` is the modified zeroth-order Bessel function.
The Kaiser was named for Jim Kaiser, who discovered a simple approximation
to the DPSS window based on Bessel functions.
The Kaiser window is a very good approximation to the Digital Prolate
Spheroidal Sequence, or Slepian window, which is the transform which
maximizes the energy in the main lobe of the window relative to total
energy.
The Kaiser can approximate many other windows by varying the beta
parameter.
==== =======================
beta Window shape
==== =======================
0 Rectangular
5 Similar to a Hamming
6 Similar to a Hann
8.6 Similar to a Blackman
==== =======================
A beta value of 14 is probably a good starting point. Note that as beta
gets large, the window narrows, and so the number of samples needs to be
large enough to sample the increasingly narrow spike, otherwise NaNs will
get returned.
Most references to the Kaiser window come from the signal processing
literature, where it is used as one of many windowing functions for
smoothing values. It is also known as an apodization (which means
"removing the foot", i.e. smoothing discontinuities at the beginning
and end of the sampled signal) or tapering function.
References
----------
.. [1] J. F. Kaiser, "Digital Filters" - Ch 7 in "Systems analysis by
digital computer", Editors: F.F. Kuo and J.F. Kaiser, p 218-285.
John Wiley and Sons, New York, (1966).
.. [2] E.R. Kanasewich, "Time Sequence Analysis in Geophysics", The
University of Alberta Press, 1975, pp. 177-178.
.. [3] Wikipedia, "Window function",
http://en.wikipedia.org/wiki/Window_function
Examples
--------
Plot the window and its frequency response:
>>> from scipy import signal
>>> from scipy.fftpack import fft, fftshift
>>> import matplotlib.pyplot as plt
>>> window = signal.kaiser(51, beta=14)
>>> plt.plot(window)
>>> plt.title(r"Kaiser window ($\beta$=14)")
>>> plt.ylabel("Amplitude")
>>> plt.xlabel("Sample")
>>> plt.figure()
>>> A = fft(window, 2048) / (len(window)/2.0)
>>> freq = np.linspace(-0.5, 0.5, len(A))
>>> response = 20 * np.log10(np.abs(fftshift(A / abs(A).max())))
>>> plt.plot(freq, response)
>>> plt.axis([-0.5, 0.5, -120, 0])
>>> plt.title(r"Frequency response of the Kaiser window ($\beta$=14)")
>>> plt.ylabel("Normalized magnitude [dB]")
>>> plt.xlabel("Normalized frequency [cycles per sample]")
"""
# Docstring adapted from NumPy's kaiser function
if M < 1:
return np.array([])
if M == 1:
return np.ones(1, 'd')
odd = M % 2
if not sym and not odd:
M = M + 1
n = np.arange(0, M)
alpha = (M - 1) / 2.0
w = (special.i0(beta * np.sqrt(1 - ((n - alpha) / alpha)**2.0)) /
special.i0(beta))
if not sym and not odd:
w = w[:-1]
return w
def get_vonMises_pdf(mu, kappa):
return lambda x: np.exp(kappa * np.cos(x - mu)) / (2 * np.pi * i0(kappa))
def von_mises_cdf_normalapprox(k,x,C1):
b = np.sqrt(2/np.pi)*np.exp(k)/i0(k)
z = b*np.sin(x/2.)
C = 24*k
chi = z - z**3/((C-2*z**2-16)/3.-(z**4+7/4.*z**2+167./2)/(C+C1-z**2+3))**2
return scipy.stats.norm.cdf(z)
# Draw samples from the distribution: mu, kappa = 0.0, 4.0 # mean and dispersion s = np.random.vonmises(mu, kappa, 1000) # Display the histogram of the samples, along with # the probability density function: import matplotlib.pyplot as plt from scipy.special import i0 plt.hist(s, 50, normed=True) x = np.linspace(-np.pi, np.pi, num=51) y = np.exp(kappa * np.cos(x - mu)) / (2 * np.pi * i0(kappa)) plt.plot(x, y, linewidth=2, color='r') plt.show()
def zeroeth_order_bessel(x):
return i0(x)
def write2dShape(file_name, H, L, sample_file, h, hill_name, AR):
if (hill_name == "RUSHIL"):
H = 0.117 #float(sys.argv[2]) # [m]
# ground shape equation
n = AR #1.0/3 n = H/a
m = n + sqrt(n**2 + 1)
a = H / n # [m] hill half length
zeta = linspace(-a, a, 101)
X = 0.5 * zeta * (1 + a**2 / (zeta**2 + m**2 * (a**2 - zeta**2)))
Y = 0.5 * m * sqrt(a**2 - zeta**2) * (1 - a**2 / (zeta**2 + m**2 *
(a**2 - zeta**2)))
X = insert(X, 0, -L)
X = append(X, L)
Y = insert(Y, 0, 0)
Y = append(Y, 0)
elif (hill_name == "MartinezBump2D"):
A = 3.1926
H = 200 # [m]
a = H * AR # [m]
X0 = X = linspace(-a, a, 101) # [m]
Y0 = Y = -H * 1 / 6.04844 * (sp.j0(A) * sp.i0(A * X / a) -
sp.i0(A) * sp.j0(A * X / a))
X = insert(X, 0, -L)
X = append(X, L)
Y = insert(Y, 0, 0)
Y = append(Y, 0)
h = 10
# opening file
infile = open(file_name, "r")
outfile = open(file_name + "_t", "w")
N = i = 0
polyLineStart = polyLineEnd = []
value = 0.0
# reading first line
line, N = infile.readline(), N + 1
while line:
# finding the "polyLine" lines (expecting 2)
if line.find("polyLine") > 0:
outfile.write(line)
# saving start of polyLine
polyLineStart.append(N + 1)
i += 1
# writing new ground shape
for x, y in zip(X, Y):
groundLine = " ( %12.10f %12.10f %12.10f )\n" % (
x, y, value)
outfile.write(groundLine)
value = 0.1
# finding end of polyline
farFromTheEnd = 1
while farFromTheEnd:
if line.find("(") < 0 and line.find(")") > 0:
polyLineEnd.append(N - 1)
farFromTheEnd = 0
outfile.write(line)
line, N = infile.readline(), N + 1
else:
outfile.write(line)
# reading new line
line, N = infile.readline(), N + 1
# close files
infile.close()
outfile.close()
# copying original to new and viceversa
subprocess.call("cp -r " + file_name + " " + file_name + "_temp",
shell=True)
subprocess.call("cp -r " + file_name + "_t " + file_name, shell=True)
# Write sample file
# changing line so that it ends at +/- 1000 m
X0 = insert(X0, 0, -1000)
X0 = append(X0, 1000)
Y0 = Y
# interpolating for a refined line
xSample = linspace(-1000, 1000, 2000)
ySample = interp(xSample, X0, Y0)
# opening file
infile = open(sample_file, "r")
outfile = open(sample_file + "_t", "w")
N = i = 0
value = 0.0
# reading first line
line = infile.readline()
while line:
# finding the "nonuniform" line
if line.find("points") > 0 and line.find("//") < 0:
outfile.write(line)
# writing new sample line shape
for x, y in zip(xSample, ySample):
sampleLine = " ( %12.10f %12.10f %12.10f )\n" % (x, y + h,
value)
outfile.write(sampleLine)
line = infile.readline()
else:
outfile.write(line)
# reading new line
line = infile.readline()
# close files
infile.close()
outfile.close()
# copying original to new and viceversa
subprocess.call("cp -r " + sample_file + " " + sample_file + "_temp",
shell=True)
subprocess.call("cp -r " + sample_file + "_t " + sample_file, shell=True)
def limit(temp, freq, tc, d=0, bcs=BCS):
"""
Calculate the approximate complex conductivity to normal conductivity
ratio in the limit hf << ∆ and kB T << ∆ given some temperature, frequency
and transition temperature.
Parameters
----------
temp : float, iterable of size N
Temperature in units of Kelvin.
freq : float, iterable of size N
Frequency in units of Hz.
tc: float
The transition temperature in units of Kelvin.
d: float (optional)
Ratio of the imaginary gap to the real gap energy at zero temperature.
bcs: float (optional)
BCS constant that relates the gap to the transition temperature.
∆ = bcs * kB * Tc. The default is superconductivity.utils.BCS.
Returns
-------
sigma : numpy.ndarray, dtype=numpy.complex128
The complex conductivity at temp and freq.
Notes
-----
Extension of Mattis-Bardeen theory to a complex gap parameter covered in
Noguchi T. et al. Physics Proc., 36, 2012.
Noguchi T. et al. IEEE Trans. Appl. SuperCon., 28, 4, 2018.
The real part of the gap is assumed to follow the BCS temperature
dependence expanded at low temperatures. See equation 2.53 in
Gao J. 2008. CalTech. PhD dissertation.
No temperature dependence is assumed for the complex portion of the gap
parameter.
"""
# coerce inputs into numpy array
temp, freq = coerce_arrays(temp, freq)
assert (temp >= 0).all(), "Temperature must be >= 0."
# break up gap into real and imaginary parts
delta1 = delta_bcs(0, tc, bcs=bcs)
delta2 = d * delta1
# allocate memory for complex conductivity
sigma1 = np.zeros(freq.size)
sigma2 = np.zeros(freq.size)
# separate out zero temperature
zero = (temp == 0)
not_zero = (temp != 0)
freq0 = freq[zero]
freq1 = freq[not_zero]
temp1 = temp[not_zero]
# define some parameters
xi = sc.h * freq1 / (2 * sc.k * temp1)
eta = delta1 / (sc.k * temp1)
# calculate complex conductivity
sigma1[zero] = np.pi * delta2 / (sc.h * freq0)
sigma2[zero] = np.pi * delta1 / (sc.h * freq0)
sigma1[not_zero] = (4 * delta1 / (sc.h * freq1) * np.exp(-eta) * np.sinh(xi) * sp.k0(xi) +
np.pi * delta2 / (sc.h * freq1) *
(1 + 2 * delta1 / (sc.k * temp1) * np.exp(-eta) * np.exp(-xi) * sp.i0(xi)))
sigma2[not_zero] = np.pi * delta1 / (sc.h * freq1) * (1 - np.sqrt(2 * np.pi / eta) * np.exp(-eta) -
2 * np.exp(-eta) * np.exp(-xi) * sp.i0(xi))
return combine_sigma(sigma1, sigma2)
def f(x):
# Modified Bessel function of order 0
return i0(x)
def fun_correction(x):
val = nobs_ratio * (z - nobs_inv) - i1(x) / i0(x)
#print val
return val
def minfunc(kbT, s2s1, hw, D0):
xi = hw / (2 * kbT)
return np.abs(np.pi / 4 *
((np.exp(D0 / kbT) - 2 * np.exp(-xi) * i0(xi)) /
(np.sinh(xi) * k0(xi))) - s2s1)
def gendataNeg(X):
l = '%6s%23s%23s%23s%23s\n' % ('x', 'I0', 'I1', 'I2', 'I3')
for i, x in enumerate(X):
l += '%6.2f%23.15e%23.15e%23.15e%23.15e\n' % (x, sp.i0(x), sp.i1(x),
sp.iv(2, x), sp.iv(3, x))
return l
def _i0(x, xp):
"""Wrapper for i0 that calls either the CPU or GPU implementation."""
if xp is np:
return i0(x)
else:
return i0_cupy(x)
def _L(P0, P):
"""
The likelihood of P0 given P, L(P0|P), from Vaillancourt (2006).
"""
L = _PDF(P, P0) / P / np.sqrt(np.pi / 2.0)
return L / np.exp(-P**2 / 4.0) / i0(P**2 / 4.0)
def lap_transgwflow_cyl(s,
rad=None,
rpart=None,
Spart=None,
Tpart=None,
Qw=None,
Twell=None):
'''
The solution of the diskmodel for transient flow under a pumping condition
in a confined aquifer in Laplace-space.
The solutions assumes concentric disks around the pumpingwell,
where each disk has its own transmissivity and storativity value.
Parameters
----------
s : :class:`numpy.ndarray`
Array with all Laplace-space-points
where the function should be evaluated
rad : :class:`numpy.ndarray`
Array with all radii where the function should be evaluated
rpart : :class:`numpy.ndarray`
Given radii separating the disks as well as starting- and endpoints
Tpart : :class:`numpy.ndarray`
Given transmissivity values for each disk
Spart : :class:`numpy.ndarray`
Given storativity values for each disk
Qw : :class:`float`
Pumpingrate at the well
Twell : :class:`float`, optional
Transmissivity at the well. Default: ``Tpart[0]``
Returns
-------
lap_transgwflow_cyl : :class:`numpy.ndarray`
Array with all values in laplace-space
Example
-------
>>> lap_transgwflow_cyl([5,10],[1,2,3],[0,2,10],[1e-3,1e-3],[1e-3,2e-3],-1)
array([[ -2.71359196e+00, -1.66671965e-01, -2.82986917e-02],
[ -4.58447458e-01, -1.12056319e-02, -9.85673855e-04]])
'''
# ensure that input is treated as arrays
s = np.squeeze(s).reshape(-1)
rad = np.squeeze(rad).reshape(-1)
rpart = np.squeeze(rpart).reshape(-1)
Spart = np.squeeze(Spart).reshape(-1)
Tpart = np.squeeze(Tpart).reshape(-1)
# get the number of partitions
parts = len(Tpart)
# initialize the result
res = np.zeros(s.shape + rad.shape)
# set the general pumping-condtion
if Twell is None:
Twell = Tpart[0]
Q = Qw / (2.0 * np.pi * Twell)
# if there is a homgeneouse aquifer, compute the result by hand
if parts == 1:
# calculate the square-root of the diffusivities
difsr = np.sqrt(Spart[0] / Tpart[0])
for si, se in np.ndenumerate(s):
Cs = np.sqrt(se) * difsr
# set the pumping-condition at the well
Qs = Q / se
# incorporate the boundary-conditions
if rpart[0] == 0.0:
Bs = Qs
if rpart[-1] == np.inf:
As = 0.0
else:
As = -Qs * k0(Cs * rpart[-1]) / i0(Cs * rpart[-1])
else:
if rpart[-1] == np.inf:
As = 0.0
Bs = Qs / (Cs * rpart[0] * k1(Cs * rpart[0]))
else:
det = i1(Cs*rpart[0])*k0(Cs*rpart[-1]) \
+ k1(Cs*rpart[0])*i0(Cs*rpart[-1])
As = -Qs / (Cs * rpart[0]) * k0(Cs * rpart[-1]) / det
Bs = Qs / (Cs * rpart[0]) * i0(Cs * rpart[-1]) / det
# calculate the head
for ri, re in np.ndenumerate(rad):
if re < rpart[-1]:
res[si + ri] = As * i0(Cs * re) + Bs * k0(Cs * re)
# if there is more than one partition, create an equation system
else:
# initialize LHS and RHS for the linear equation system
# Mb is the banded matrix for the Eq-System
V = np.zeros(2 * (parts))
Mb = np.zeros((5, 2 * (parts)))
# the positions of the diagonals of the matrix set in Mb
diagpos = [2, 1, 0, -1, -2]
# set the standard boundary conditions for rwell=0.0 and rinf=np.inf
Mb[1, 1] = 1.0
Mb[-2, -2] = 1.0
# calculate the consecutive fractions of the transmissivities
Tfrac = Tpart[:-1] / Tpart[1:]
# calculate the square-root of the diffusivities
difsr = np.sqrt(Spart / Tpart)
# calculate a temporal substitution
tmp = Tfrac * difsr[:-1] / difsr[1:]
# match the radii to the different disks
pos = np.searchsorted(rpart, rad) - 1
# iterate over the laplace-variable
for si, se in enumerate(s):
Cs = np.sqrt(se) * difsr
# set the pumping-condition at the well
# TODO: implement other pumping conditions
V[0] = Q / se
# set the boundary-conditions if needed
if rpart[0] > 0.0:
Mb[1, 1] = Cs[0] * rpart[0] * k1(Cs[0] * rpart[0])
Mb[0, 2] = -Cs[0] * rpart[0] * i1(Cs[0] * rpart[0])
if rpart[-1] < np.inf:
Mb[-3, -1] = k0(Cs[-1] * rpart[-1])
Mb[-2, -2] = i0(Cs[-1] * rpart[-1])
# generate the equation system as banded matrix
for i in range(parts - 1):
Mb[0, 2 * i + 3] = -k0(Cs[i + 1] * rpart[i + 1])
Mb[1, 2 * i + 2:2 * i + 4] = [
-i0(Cs[i + 1] * rpart[i + 1]),
k1(Cs[i + 1] * rpart[i + 1])
]
Mb[2, 2 * i + 1:2 * i + 3] = [
k0(Cs[i] * rpart[i + 1]), -i1(Cs[i + 1] * rpart[i + 1])
]
Mb[3, 2 * i:2 * i + 2] = [
i0(Cs[i] * rpart[i + 1]),
-tmp[i] * k1(Cs[i] * rpart[i + 1])
]
Mb[4, 2 * i] = tmp[i] * i1(Cs[i] * rpart[i + 1])
# genearate the cooeficient matrix as a spare matrix
M = sps.spdiags(Mb, diagpos, 2 * parts, 2 * parts, format="csc")
# solve the Eq-Sys and ignore errors from the umf-pack
with warnings.catch_warnings():
# warnings.simplefilter("ignore")
warnings.simplefilter("ignore", SLV_WARN)
X = sps.linalg.spsolve(M, V, use_umfpack=True)
# to suppress numerical errors, set NAN values to 0
X[np.logical_not(np.isfinite(X))] = 0.0
# calculate the head
res[si, :] = X[2 * pos] * i0(Cs[pos] * rad) + X[2 * pos + 1] * k0(
Cs[pos] * rad)
# set problematic values to 0
# --> the algorithm tends to violate small values,
# therefore this approachu is suitable
res[np.logical_not(np.isfinite(res))] = 0.0
return res
def MMSESTSA(signal, fs, IS=0.25, W=1024, NoiseMargin=3, saved_params=None):
'''
MMSE-STSA method
Args:
signal : 一次元の入力信号
fs : サンプリング周波数
IS : 初期化用の無音 [sec] (default: 0.25)
'''
# window length is 25 msec
#W = np.fix( 0.25 * fs )
# Shift percentage is 40% (=10msec)
# Overlap-Add method works good with this value(.4)
SP = 0.4
wnd = np.hamming(W)
# pre-emphasis
pre_emph = 0
signal = scipy.signal.lfilter([1 - pre_emph], 1, signal)
# number of initial silence segments
NIS = int(np.fix((IS * fs - W) / (SP * W) + 1))
# This function chops the signal into frames
y = segment(signal, W, SP, wnd)
Y = np.fft.fft(y, axis=0)
# Noisy Speech Phase
YPhase = np.angle(Y[0:int(np.fix(len(Y) / 2)) + 1, :])
# Spectrogram
Y = np.abs(Y[0:int(np.fix(len(Y) / 2)) + 1, :])
numberOfFrames = Y.shape[1]
# initial Noise Power Spectrum mean
N = np.mean(Y[:, 0:NIS].T).T
# initial Noise Power Spectrum variance
LambdaD = np.mean((Y[:, 0:NIS].T)**2).T
# used in smoothing xi (For Deciesion Directed method for estimation of A Priori SNR)
alpha = 0.99
# This is a smoothing factor for the noise updating
NoiseLength = 9
NoiseCounter = 0
if saved_params != None:
NIS = 0
N = saved_params['N']
LambdaD = saved_params['LambdaD']
NoiseCounter = saved_params['NoiseCounter']
# Initial Gain used in calculation of the new xi
G = np.ones(N.shape)
Gamma = G
# Gamma function at 1.5
Gamma1p5 = spc.gamma(1.5)
X = np.zeros(Y.shape)
for i in range(numberOfFrames):
Y_i = Y[:, i]
# If initial silence ignore VAD
if i < NIS:
SpeechFlag = 0
NoiseCounter = 100
else:
# %Magnitude Spectrum Distance VAD
NoiseFlag, SpeechFlag, NoiseCounter = vad(Y_i, N, NoiseCounter,
NoiseMargin)
# If not Speech Update Noise Parameters
if SpeechFlag == 0:
N = (NoiseLength * N + Y_i) / (NoiseLength + 1)
LambdaD = (NoiseLength * LambdaD + (Y_i**2)) / (1 + NoiseLength)
# A postiriori SNR
gammaNew = (Y_i**2) / LambdaD
# Decision Directed Method for A Priori SNR
xi = alpha * (G**2) * Gamma + (1 - alpha) * np.maximum(gammaNew - 1, 0)
Gamma = gammaNew
# A Function used in Calculation of Gain
nu = Gamma * xi / (1 + xi)
# MMSE STSA algo
G = (Gamma1p5 * np.sqrt(nu) / Gamma) * np.exp(-nu / 2.0) *\
((1.0 + nu) * spc.i0(nu / 2.0) + nu * spc.i1(nu / 2.0))
Indx = np.isnan(G) | np.isinf(G)
G[Indx] = xi[Indx] / (1 + xi[Indx])
X[:, i] = G * Y_i
output = OverlapAdd2(X, YPhase, W, SP * W)
return output, {'N': N, 'LambdaD': LambdaD, 'NoiseCounter': NoiseCounter}
def activations(self, sig, n_noise_frames=20):
"""
Returns continuous activations of the voice activity detector.
Parameters
----------
sig : ndarray
audio signal
n_noise_frames : int
number of frames at start of file to use for initial noise model
"""
frames = self.stft(sig)
n_frames = frames.shape[0]
noise_var_tmp = zeros(self.NFFT // 2 + 1)
for n in xrange(n_noise_frames):
frame = frames[n]
noise_var_tmp = noise_var_tmp + (conj(frame) * frame).real
noise_var_orig = noise_var_tmp / n_noise_frames
noise_var_old = noise_var_orig
G_old = 1
A_MMSE = zeros((self.NFFT // 2 + 1, n_frames))
G_MMSE = zeros((self.NFFT // 2 + 1, n_frames))
cum_Lambda = zeros(n_frames)
for n in xrange(n_frames):
frame = frames[n]
frame_var = (conj(frame) * frame).real
noise_var = noise_var_orig
if self.max_est_iter == -1 or n < self.max_est_iter:
noise_var_prev = noise_var_orig
for iter_idx in xrange(self.n_iters):
gamma = frame_var / noise_var
Y_mag = np.abs(frame)
if n:
xi = (self.alpha *
((A_MMSE[:, n - 1]**2 / noise_var_old) +
(1 - self.alpha) * maximum(gamma - 1, 0)))
else:
xi = (self.alpha +
(1 - self.alpha) * maximum(gamma - 1, 0))
v = xi * gamma / (1 + xi)
bessel_1 = i1(v / 2)
bessel_0 = i0(v / 2)
g_upd = (sqrt(pi) / 2) * (sqrt(v) / gamma) * np.exp(v/-2) * \
((1 + v) * bessel_0 + v * bessel_1)
np.putmask(g_upd, np.logical_not(np.isfinite(g_upd)), 1.)
G_MMSE[:, n] = g_upd
A_MMSE[:, n] = G_MMSE[:, n] * Y_mag
gamma_term = gamma * xi / (1 + xi)
gamma_term = minimum(gamma_term, 1e-2)
Lambda_mean = (1 / (1 + xi) + exp(gamma_term)).mean()
weight = Lambda_mean / (1 + Lambda_mean)
if isnan(weight):
weight = 1
noise_var = \
weight * noise_var_orig + (1 - weight) * frame_var
diff = np.abs(np.sum(noise_var - noise_var_prev))
if diff < self.epsilon:
break
noise_var_prev = noise_var
gamma = frame_var / noise_var
Y_mag = np.abs(frame)
if n:
xi = self.alpha * ((A_MMSE[:, n - 1]**2 / noise_var_old) +
(1 - self.alpha) * maximum(gamma - 1, 0))
else:
xi = self.alpha + (1 - self.alpha) * maximum(gamma - 1, 0)
v = (xi * gamma) / (1 + xi)
bessel_0 = i0(v / 2)
bessel_1 = i1(v / 2)
g_upd = (sqrt(pi) / 2) * (sqrt(v) / gamma) * \
exp(v/-2) * ((1 + v) * bessel_0 + v * bessel_1)
np.putmask(g_upd, np.logical_not(np.isfinite(g_upd)), 1.)
G_MMSE[:, n] = g_upd
A_MMSE[:, n] = G_MMSE[:, n] * Y_mag
Lambda_mean = (log(1 / (1 + xi)) + gamma * xi / (1 + xi)).mean()
G = ((self.a01 + self.a11 * G_old) /
(self.a00 + self.a10 * G_old) * Lambda_mean)
cum_Lambda[n] = G
G_old = G
noise_var_old = noise_var
return cum_Lambda
