def GetHeadForRadiusTime(self, radius, time):
'''Compute head using the Theis solution
radius distance to injection well [L]
time time since injection started [T]'''
#check if inputs are scalars or lists
RadiusList, RadIsList = self.ListOrSingle(radius)
TimeList, TimIsList = self.ListOrSingle(time)
if not RadIsList and not TimIsList:
ListOut = False
else:
ListOut = True
#initialize output list
Heads = []
for tim in TimeList:
for rad in RadiusList:
u = self.uFactor * rad**2 / tim
head = self.HeadFactor * sci.expn(1, u)
if self.InjectionEnd != -1 and tim > self.InjectionEnd:
u_new = self.uFactor * rad**2 \
/ (tim - self.InjectionEnd)
head = head - self.HeadFactor * sci.expn(1, u_new)
if head < 0.0:
head = 0.0
Heads.append([tim, rad, head])
if ListOut:
return Heads
else:
return Heads[0][2]
def GetHeadForRadiusTime(self, radius, time):
'''Compute head using the Theis solution
radius distance to injection well [L]
time time since injection started [T]'''
#check if inputs are scalars or lists
RadiusList, RadIsList = self.ListOrSingle(radius)
TimeList, TimIsList = self.ListOrSingle(time)
if not RadIsList and not TimIsList:
ListOut = False
else:
ListOut = True
#initialize output list
Heads = []
for tim in TimeList:
for rad in RadiusList:
u = self.uFactor * rad**2 / tim
head = self.HeadFactor * sci.expn(1, u)
if self.InjectionEnd != -1 and tim > self.InjectionEnd:
u_new = self.uFactor * rad**2 \
/ (tim - self.InjectionEnd)
head = head - self.HeadFactor * sci.expn(1, u_new)
if head < 0.0:
head = 0.0
Heads.append([tim, rad, head])
if ListOut:
return Heads
else:
return Heads[0][2]
def posterior(x, n, p1, p2):
"""
calculates the posterior probability that the probability
of developing severe side effects falls within a specific
range given the data:
:param x: num of patients with sever side effects
:param n: tot num patients observed
:param p1: lower bound range
:param p2: upper bound range
:return: posterior probability that p is within the range
[p1, p2] given x and n
"""
if not isinstance(n, int) or n < 1:
raise ValueError("n must be a positive integer")
if not isinstance(x, int) or x < 0:
m = "x must be an integer that is greater than or equal to 0"
raise ValueError(m)
if x > n:
raise ValueError("x cannot be greater than n")
if not isinstance(p1, float) or p1 < 0 or p1 > 1:
raise ValueError("p1 must be a float in the range [0, 1]")
if not isinstance(p2, float) or p2 < 0 or p2 > 1:
raise ValueError("p2 must be a float in the range [0, 1]")
if p2 <= p1:
raise ValueError("p2 must be greater than p1")
inter = intersection(x, n, p1, p2)
return ((special.expn(inter, p2)) / (special.expn(inter, p1)))
def dtint(gamma, xs, cthfun, beta=None):
'''
calculates the (normalized) time for a sound wave to travel from the surface to the shock front (or back)
input: BS gamma, BS beta, position of the shock in rstar units
'''
nxs = size(xs)
if nxs <= 1:
nx = 10000
x = (xs - 1.) * arange(nx) / double(nx - 1) + 1.
if beta is None:
beta = 1. - gamma * exp(gamma) * (expn(1, gamma) -
expn(1, gamma * xs))
csq = 1. / 3. * exp(gamma * x) * (
expn(2, gamma * x) / x + beta * exp(-gamma) - expn(2, gamma)
) # / x**3
cth = cthfun(x)
# print("mean cos = "+str(cth.mean()))
w = where(csq > 0.)
dt = simps((sqrt((3. * cth**2 + 1.) / csq) / cth)[w], x=x[w]) / 2.
else:
dt = zeros(nxs)
for k in arange(nxs):
dt[k] = dtint(gamma, xs[k], cthfun, beta=beta)
return dt
def rhs( theta ):
src = np.zeros(N_g - 2)
for i in range( 0, len(src) ):
for j in range(1, N_g):
src[i] += (delta_tau/(2.*N))*(theta[j]**4 - theta[j-1]**4) \
*(expn(3, abs(i+1-j)*delta_tau) - expn(3, abs(i+2-j)*delta_tau))
return src
def integrated_flux(self, phi0, gamma, e_cutoff, emin, emax):
r'''
'''
rmax = -emax * (emax/self._E0)**(-gamma) * expn(gamma,\
emax/e_cutoff)
rmin = -emin * (emin/self._E0)**(-gamma) * expn(gamma, \
emin/e_cutoff)
return phi0 * (rmax - rmin)
def J_over_JUV_outside_slab(tau, tau_SF):
"""
Compute the mean intensity at height |z| > Lz/2
with tau(z) = tau > tau_SF/2
"""
# if not np.all(np.abs(tau) >= 0.5*tau_SF):
# raise ValueError("optical depth must be larger than or equal to tau_SF/2")
return 0.5/tau_SF*(expn(2,tau - 0.5*tau_SF) - expn(2,tau + 0.5*tau_SF))
def TP(Teq, Teeff, g00, kv1, kv2, kth, alpha):
"""
This function takes stellar, planetary, and atmospheric parameters and
returns the temperature-pressure profile.
Parameters
----------
Teq
Teeff
g00
kv1
kv2
kth
alpha
Returns
-------
T: np.ndarray
The Temperature in Kelvin
P: np.ndarray
The Pressure in bar
"""
Teff = Teeff
f = 1.0 # solar re-radiation factor
A = 0.0 # planetary albedo
g0 = g00
# Compute equilibrium temperature and set up gamma's
T0 = Teq
gamma1 = kv1 / kth
gamma2 = kv2 / kth
# Initialize arrays
logtau = np.arange(-10, 20, .1)
tau = 10**logtau
#computing temperature
T4ir = 0.75 * (Teff**(4.)) * (tau + (2.0 / 3.0))
f1 = 2.0 / 3.0 + 2.0 / (3.0 * gamma1) * (
1. + (gamma1 * tau / 2.0 - 1.0) * sp.exp(-gamma1 * tau)
) + 2.0 * gamma1 / 3.0 * (1.0 - tau**2.0 / 2.0) * special.expn(
2.0, gamma1 * tau)
f2 = 2.0 / 3.0 + 2.0 / (3.0 * gamma2) * (
1. + (gamma2 * tau / 2.0 - 1.0) * sp.exp(-gamma2 * tau)
) + 2.0 * gamma2 / 3.0 * (1.0 - tau**2.0 / 2.0) * special.expn(
2.0, gamma2 * tau)
T4v1 = f * 0.75 * T0**4.0 * (1.0 - alpha) * f1
T4v2 = f * 0.75 * T0**4.0 * alpha * f2
T = (T4ir + T4v1 + T4v2)**(0.25)
P = tau * g0 / (kth * 0.1) / 1.E5
# Return TP profile
return T, P
def J_over_JUV_inside_slab(tau, tau_SF):
"""
Compute the mean intensity at tau(z) assuming that source
distribtuion in a layer of optical depth tau_SF
Compute the mean intensity at tau(z) (optical depth from the midplane)
0 < zz := tau(z)/(tau_SF/2) < 1.0
"""
# if not np.all(np.abs(tau) <= 0.5*tau_SF):
# raise ValueError("tau must be smaller than or equal to tau_SF/2")
return 0.5/tau_SF*(2.0 - expn(2,0.5*tau_SF - tau) - expn(2,0.5*tau_SF + tau))
def F(self,rho,tau):
#tau = tau(:);
#tau(find(tau > 100)) = 100;
if tau>100:
tau=100
#h_inf = besselk(0,rho);
h_inf = kn(0,rho)
expintrho = expn(1,rho)
w = (expintrho-h_inf)/(expintrho-expn(1,rho/2))
I = h_inf - w*expn(1,rho/2*np.exp(abs(tau))) + (w-1)*expn(1,rho*np.cosh(tau))
h=h_inf+self.sign(tau)*I
return h
def F(self, rho, tau):
#tau = tau(:);
#tau(find(tau > 100)) = 100;
if tau > 100:
tau = 100
#h_inf = besselk(0,rho);
h_inf = kn(0, rho)
expintrho = expn(1, rho)
w = (expintrho - h_inf) / (expintrho - expn(1, rho / 2))
I = h_inf - w * expn(1, rho / 2 * np.exp(abs(tau))) + (w - 1) * expn(
1, rho * np.cosh(tau))
h = h_inf + self.sign(tau) * I
return h
def curly_F_tau(Teff, tau):
"""
Function for problem 10
calculates the eddington flux at a given tau
NOTE this is not a F_\nu, assumes a planckian source function
"""
return 2 * np.pi * (trapezoidal(
lambda t: integrated_planck(Teff * (0.5 + 3 / 4 * t)**
(1 / 4)) * sc.expn(2, t - tau), tau, 20,
5000) - trapezoidal(
lambda t: integrated_planck(Teff * (0.5 + 3 / 4 * t)**
(1 / 4)) * sc.expn(2, tau - t), 0, tau,
5000))
def BSsolution(gamma, eta):
nx = 1000
xs, beta = xis(gamma, eta, n=3, x0=20., ifbeta=True)
x = xs**(arange(nx) / double(nx - 1))
u = (1. - exp(gamma) / beta *
(expn(2, gamma) - expn(2, gamma * x) / x))**4 # u/u[0]
v = exp(gamma * x) / x**3 * (expn(1, gamma * x) + beta * exp(-gamma) -
expn(2, gamma)) / u
v = v / v[-1] * 1. / sqrt(xs) / 7. # normalisation
return x, v, u
def exp_int(s, x):
r"""Calculate the exponential integral :math:`E_s(x)`.
Given by: :math:`E_s(x) = \int_1^\infty \frac{e^{-xt}}{t^s}\,\mathrm dt`
Parameters
----------
s : :class:`float`
exponent in the integral (should be > -100)
x : :class:`numpy.ndarray`
input values
"""
if np.isclose(s, 1):
return sps.exp1(x)
if np.isclose(s, np.around(s)) and s > -0.5:
return sps.expn(int(np.around(s)), x)
x = np.array(x, dtype=np.double)
x_neg = x < 0
x = np.abs(x)
x_compare = x**min((10, max(((1 - s), 1))))
res = np.empty_like(x)
# use asymptotic behavior for zeros
x_zero = np.isclose(x_compare, 0, atol=1e-20)
x_inf = x > max(30, -s / 2) # function is like exp(-x)*(1/x + s/x^2)
x_fin = np.logical_not(np.logical_or(x_zero, x_inf))
x_fin_pos = np.logical_and(x_fin, np.logical_not(x_neg))
if s > 1.0: # limit at x=+0
res[x_zero] = 1.0 / (s - 1.0)
else:
res[x_zero] = np.inf
res[x_inf] = np.exp(-x[x_inf]) * (x[x_inf]**-1 - s * x[x_inf]**-2)
res[x_fin_pos] = inc_gamma(1 - s, x[x_fin_pos]) * x[x_fin_pos]**(s - 1)
res[x_neg] = np.nan # nan for x < 0
return res
def scale_bt_rate(inDict, ip, f=1.7):
"""
Apply ionization descaling of [7]_, a Burgess-Tully type scaling to ionization rates and
temperatures. The result of the scaling is to return a scaled temperature between 0 and 1 and a
slowly varying scaled rate as a function of scaled temperature. In addition, the scaled rates
vary slowly along an iso-electronic sequence.
Parameters
----------
inDict : `dict`
the input dictionary should have the following key pairs: `temperature`, array-like and
`rate`, array-like
ip : `float`
the ionization potential in eV.
f : `float` (optional)
the scaling parameter, 1.7 generally works well
Notes
-----
`btTemperature` and `btRate` keys are added to `inDict`
"""
if ('temperature' and 'rate') in inDict.keys():
rT = inDict['temperature'] * const.boltzmannEv / ip
btTemperature = 1. - np.log(f) / np.log(rT + f)
btRate = np.sqrt(rT) * inDict['rate'] * ip**1.5 / (expn(1, 1. / rT))
inDict['btTemperature'] = btTemperature
inDict['btRate'] = btRate
inDict['ip'] = ip
else:
print(' input dict does not have the correct keys')
return
def star_f(z, rho_mean, m_x, r_x, k_x, r_t0): m_x = np.float64(m_x) r_x = np.float64(r_x) k_x = np.float64(k_x) if len(m_x.shape) == 0: m_x = np.array([m_x]) r_x = np.array([r_x]) alpha = 1.0 nu_alpha = 1.0 - (2.0/alpha) G_alpha = sp.gamma(1.0 - nu_alpha) u_k = np.zeros((len(k_x), len(m_x))) for i in range(len(m_x)): r_t = r_t0[i] * r_x[i] x = r_x[i]/r_t x_delta = r_x[i]/r_t K = r_t * k_x E_alpha = sp.expn(np.absolute(nu_alpha), (x_delta ** alpha)) rho_t = (m_x[i]*f_stars(m_x, np.array([m_x[i]]), 1.0)*alpha)/(4.0*np.pi*(r_t**3.0)*(G_alpha - (x_delta**2.0)*E_alpha)) u_k[:,i] = (4.0 * np.pi * (r_t**3.0) * rho_t) / (m_x[i] * (1.0 + (K**2.0))) return u_k
def scale_bt_rate(inDict, ip, f=1.7):
"""
Apply ionization descaling of [1]_, a Burgess-Tully type scaling to ionization rates and
temperatures. The result of the scaling is to return a scaled temperature between 0 and 1 and a
slowly varying scaled rate as a function of scaled temperature. In addition, the scaled rates
vary slowly along an iso-electronic sequence.
Parameters
----------
inDict : `dict`
the input dictionary should have the following key pairs: `temperature`, array-like and
`rate`, array-like
ip : `float`
the ionization potential in eV.
f : `float` (optional)
the scaling parameter, 1.7 generally works well
Notes
-----
`btTemperature` and `btRate` keys are added to `inDict`
References
----------
.. [1] Dere, K. P., 2007, A&A, `466, 771 <http://adsabs.harvard.edu/abs/2007A%26A...466..771D>`_
"""
if ('temperature' and 'rate') in inDict.keys():
rT = inDict['temperature']*const.boltzmannEv/ip
btTemperature = 1. - np.log(f)/np.log(rT + f)
btRate = np.sqrt(rT)*inDict['rate']*ip**1.5/(expn(1,1./rT))
inDict['btTemperature'] = btTemperature
inDict['btRate'] = btRate
inDict['ip'] = ip
else:
print(' input dict does not have the correct keys')
return
def exp_integral(x):
"""Returns truncated iterated logarithm
y = log( -log(x) )
where if x<delta, x = delta and if 1-delta < x,
x = 1-delta.
"""
gamma = 0.577215665
return -gamma - expn(x, 1) - np.log(x)
def in_plane_thin_film(kn):
"""
The mfp shrinkage calculation for in-plane thin film.
.. math:
B(Kn) = 1 - (3/8) Kn(1-4E_3 Kn^{-1}+4E_5 Kn^{-1})
, where E_3 and E_5 are exponential integral polynomials.
Args:
kn (float): The knudsen number.
:param kn:
:return:
"""
e3 = sc.expn(3, 1 / kn) # exponential integral E_3(1/kn)
e5 = sc.expn(5, 1 / kn) # exponential integral E_5{1/kn}
return 1 - 3. / 8. * kn * (1 - 4 * e3 + 4 * e5)
def matchlogtoexpn(p0 = [30, 2e2, -20]):
import scipy.optimize as opt
p = opt.fmin(matchlogtoexpn_score, p0, xtol=1e-9, ftol=1e-9)
m, r0, off = p
plot(funcs.expn(2,rr/20.))
plot(m*log(r0/rr) - off)
return p
def J_over_JUV_avg_slab(tau_SF):
"""
Compute the mean intensity averaged over the entrie volume of the slab
from -Lz/2 < z < Lz/2
or
from -tau_SF/2 < tau < tau_SF/2
"""
return 1.0 / tau_SF * (1.0 - (0.5 - expn(3, tau_SF)) / tau_SF)
def logmmse_gain(parameters=None):
""" calculate suppression gain by MMSE log spectral amplitude method
"""
gamma = parameters['gamma']
ksi = parameters['ksi']
A = ksi / (1 + ksi)
vk = A * gamma
ei_vk = 0.5 * sp.expn(1, vk)
gain = A * np.exp(ei_vk)
return gain
def xis(gamma, eta, n=3, x0=20., ifbeta=False):
'''
solves equation (34) from Basko&Sunyaev (1976)
arguments:
gamma = c R_{NS}^3/(kappa dot{M} A_\perp * afac**2) \simeq (RNS/Rsph) * (RNS**2/across)
eta = (8/21 * u_0 d_0 kappa / \sqrt{2GMR} c )**0.25, u_0 = B^2/8/pi
(gamma = rstar**2/mdot/across[0]/afac**2)
(eta = (8/21/sqrt(2)))**0.25 (umag*sqrt(rstar)*d0**2)**0.25, where d0 = (across/4./pi/rstar/sin(theta))[0]
'''
if ((eta * gamma**0.25) < 1.) | (gamma > 1000.):
return nan
x = fsolve(fxis, x0, args=(gamma, eta, n), maxfev=1000, xtol=1e-10)
# print(fxis(x, gamma, eta, n))
if ifbeta:
print("beta")
beta = 1. - gamma * exp(gamma) * (expn(1, gamma) - expn(1, gamma * x))
return x, beta
else:
return x
def eta(gamma, tau):
import scipy.special as spe
part1 = 2.0 / 3.0 + 2.0 / (3.0 * gamma) * (
1.0 + (gamma * tau / 2.0 - 1.0) * np.exp(-1.0 * gamma * tau))
part2 = 2.0 * gamma / 3.0 * (1.0 - tau**2/2.0) * \
spe.expn(2, (gamma * tau))
return part1 + part2
def calc_Jrad(z, S4pi, zstar, fp, fm, dz_pc):
J = 0.0
for S4pi_, zstar_ in zip(S4pi, zstar):
Dz = 0.2*dz_pc
tau_SF = fp(zstar_ + Dz) - fp(zstar_ - Dz)
#print(tau_SF)
if z >= zstar_ + Dz:
tau = fp(z) - fp(zstar_)
J += S4pi_*0.5*expn(1, tau)
#J += SFUV4pi_*J_over_JUV_outside_slab(tau, tau_SF)
elif z <= zstar_ - Dz:
tau = fm(z) - fm(zstar_)
J += S4pi_*0.5*expn(1, tau)
#J += SFUV4pi_*J_over_JUV_outside_slab(tau, tau_SF)
else:
J += S4pi_*J_over_JUV_avg_slab(tau_SF)
#J += SFUV4pi_*J_over_JUV_inside_slab(0.0, tau_SF)
pass
return J
def denoise(wav, noise_profile: NoiseProfile, eta=0.15):
wav, dtype = to_float(wav)
wav += np.finfo(np.float64).eps
p = noise_profile
nframes = int(
math.floor(len(wav) / p.len2) - math.floor(p.window_size / p.len2))
x_final = np.zeros(nframes * p.len2)
aa = 0.98
mu = 0.98
ksi_min = 10**(-25 / 10)
x_old = np.zeros(p.len1)
xk_prev = np.zeros(p.len1)
noise_mu2 = p.noise_mu2
for k in range(0, nframes * p.len2, p.len2):
insign = p.win * wav[k:k + p.window_size]
spec = np.fft.fft(insign, p.n_fft, axis=0)
sig = np.absolute(spec)
sig2 = sig**2
gammak = np.minimum(sig2 / noise_mu2, 40)
if xk_prev.all() == 0:
ksi = aa + (1 - aa) * np.maximum(gammak - 1, 0)
else:
ksi = aa * xk_prev / noise_mu2 + (1 - aa) * np.maximum(
gammak - 1, 0)
ksi = np.maximum(ksi_min, ksi)
log_sigma_k = gammak * ksi / (1 + ksi) - np.log(1 + ksi)
vad_decision = np.sum(log_sigma_k) / p.window_size
if vad_decision < eta:
noise_mu2 = mu * noise_mu2 + (1 - mu) * sig2
a = ksi / (1 + ksi)
vk = a * gammak
ei_vk = 0.5 * expn(1, np.maximum(vk, 1e-8))
hw = a * np.exp(ei_vk)
sig = sig * hw
xk_prev = sig**2
xi_w = np.fft.ifft(hw * spec, p.n_fft, axis=0)
xi_w = np.real(xi_w)
x_final[k:k + p.len2] = x_old + xi_w[0:p.len1]
x_old = xi_w[p.len1:p.window_size]
output = from_float(x_final, dtype)
output = np.pad(output, (0, len(wav) - len(output)), mode="constant")
return output
def cross_plane_thin_film(kn):
"""The mfp shrinkage calculation for cross-plane thin film.
.. math::
B(Kn)=1 + 3. * Kn(E_5 Kn^{-1} - 1. / 4.)
where E_5 are exponential integral polynomials.
Args:
kn (float): The knudsen number.
"""
e5 = sc.expn(5, 1 / kn)
return 1 + 3. * kn * (e5 - 1. / 4.)
def calculate_yg_van_regemorter(atomic_data, t_electrons,
continuum_interaction_species):
"""
Calculate collision strengths in the van Regemorter approximation.
This function calculates thermally averaged effective collision
strengths (divided by the statistical weight of the lower level)
Y_ij / g_i using the van Regemorter approximation.
Parameters
----------
atomic_data : tardis.io.atom_data.AtomData
t_electrons : numpy.ndarray
continuum_interaction_species : pandas.MultiIndex
Returns
-------
pandas.DataFrame
Thermally averaged effective collision strengths
(divided by the statistical weight of the lower level) Y_ij / g_i
Notes
-----
See Eq. 9.58 in [2].
References
----------
.. [1] van Regemorter, H., “Rate of Collisional Excitation in Stellar
Atmospheres.”, The Astrophysical Journal, vol. 136, p. 906, 1962.
doi:10.1086/147445.
.. [2] Hubeny, I. and Mihalas, D., "Theory of Stellar Atmospheres". 2014.
"""
I_H = atomic_data.ionization_data.loc[(1, 1)]
mask_selected_species = atomic_data.lines.index.droplevel(
["level_number_lower",
"level_number_upper"]).isin(continuum_interaction_species)
lines_filtered = atomic_data.lines[mask_selected_species]
f_lu = lines_filtered.f_lu.values
nu_lines = lines_filtered.nu.values
yg = f_lu * (I_H / (H * nu_lines))**2
coll_const = A0**2 * np.pi * np.sqrt(8 * K_B / (np.pi * M_E))
yg = 14.5 * coll_const * t_electrons * yg[:, np.newaxis]
u0 = nu_lines[np.newaxis].T / t_electrons * (H / K_B)
gamma = 0.276 * np.exp(u0) * expn(1, u0)
gamma[gamma < 0.2] = 0.2
yg *= u0 * gamma / BETA_COLL
yg = pd.DataFrame(yg, index=lines_filtered.index, columns=t_electrons)
return yg
def custom_structure(kn):
"""
The mfp shrinkage calculation for your own structure.
you should implement this function on your own.
Args:
kn (float): The Knudsen number.
:param kn:
:return:
"""
e5 = sc.expn(5, 1 / kn)
return 1 + 3. * kn * (e5 - 1. / 4.)
def GetSpec(specType):
"""
Given a 2FGL Spectral type return lambdas for the spectrum and integrated spectrum
:param specType: Can be 'PowerLaw','PLExpCutoff', or 'LogParabola'
:returns Spec,IntegratedSpec: the spectrum and integrated spectrum. See function def for param ordering.
"""
if specType == 'PowerLaw':
Spec = lambda e, gamma: e**-gamma
IntegratedSpec = lambda e1, e2, gamma: (e1*e2)**-gamma * (e1*e2**gamma - e1**gamma*e2)/(gamma-1)
elif specType == 'PLExpCutoff':
Spec = lambda e, gamma, cutoff: e**-gamma * np.exp(-e/cutoff)
IntegratedSpec = lambda e1, e2, gamma, cutoff: (e1**(1-gamma)*expn(gamma, e1/cutoff)
-e2**(1-gamma)*expn(gamma, e2/cutoff))
elif specType == 'LogParabola':
Spec = lambda e, alpha, beta, pivot: (e/pivot)**-(alpha+beta*np.log(e/pivot))
IntegratedSpec = lambda e1, e2, alpha, beta, pivot: quad(Spec, e1, e2, args=(alpha, beta, pivot))[0]
else:
raise Exception("Spectral type not supported.")
return Spec, IntegratedSpec
def EvalWellFunction(self, u, rB):
'''Evaluates the Hantush-Jacob well function.
u dimensionless time
rB dimensionless radius'''
#return zero for large u to avoid numerical issues
if u > 14:
return 0.0
#set number of terms used in summation. as u increases more
#terms are needed
if u <= 2:
endmember = 10
elif u <= 7:
endmember = 20
else:
endmember = 30
#compute temporary variable
r4B = rB**2 / 4.0
#compute summation term
last_term = 0.0
for i in range(1,endmember):
for j in range(1,i+1):
last_term += (-1)**(i+j) * spy.factorial(i - j + 1) / \
(spy.factorial(i+2))**2 * u**(i-j) * r4B**j
#for rB values close to 0 one term is dropped to avoid numerical
#problems
if abs(sci.iv(0.0,rB) - 1.0) < 1e-15:
WellFuncHJ = 2.0 * sci.kv(0.0,rB) \
- sci.iv(0.0,rB) * sci.expn(1,r4B / u) \
+ mth.exp(-1.0 * r4B / u) * (0.5772156649015328606 \
+ mth.log(u) + sci.expn(1,u) - u - u**2 * last_term)
else:
#full expression
WellFuncHJ = 2.0 * sci.kv(0.0,rB) \
- sci.iv(0.0,rB) * sci.expn(1,r4B / u) \
+ mth.exp(-1.0 * r4B / u) * (0.5772156649015328606 \
+ mth.log(u) + sci.expn(1,u) - u + u * (sci.iv(0.0,rB) - 1.0) \
/ r4B - u**2 * last_term)
return WellFuncHJ
def exp_expn(n, x):
""" Returns :math:`e^x E_n(x)`.
The exponential integral :math:`E_n(x)` is defined as
.. math::
E_n(x) \\equiv \\int_1^\\infty dt\\, \\frac{e^{-xt}}{t^n}
Circumvents overflow error in ``np.exp`` by expanding the exponential integral in a series to the 5th or 6th order.
Parameters
----------
n : {1,2}
The order of the exponential integral.
x : ndarray
The argument of the function.
Returns
-------
ndarray
The value of :math:`e^x E_n(x)`.
"""
import scipy.special as sp
x_flt64 = np.array(x, dtype='float64')
low = x < 700
high = ~low
expr = np.zeros_like(x)
if np.any(low):
expr[low] = np.exp(x[low]) * sp.expn(n, x_flt64[low])
if np.any(high):
if n == 1:
# The relative error is roughly 1e-15 for 700, smaller for larger arguments.
expr[high] = (1 / x[high] - 1 / x[high]**2 + 2 / x[high]**3 -
6 / x[high]**4 + 24 / x[high]**5)
elif n == 2:
# The relative error is roughly 6e-17 for 700, smaller for larger arguments.
expr[high] = (1 / x[high] - 2 / x[high]**2 + 6 / x[high]**3 -
24 / x[high]**4 + 120 / x[high]**5 -
720 / x[high]**6)
else:
raise TypeError('only supports n = 1 or 2 for x > 700.')
return expr
def xi(gamma, tau):
"""
Calculate Equation (14) of Line et al. (2013) Apj 775, 137
Parameters:
-----------
gamma: Float
Visible-to-thermal stream Planck mean opacity ratio.
tau: 1D float ndarray
Gray IR optical depth.
Modification History:
---------------------
2014-12-10 patricio Initial implemetation.
"""
return (2.0/3) * (1 + (1/gamma) * (1 + (0.5*gamma*tau-1)*np.exp(-gamma*tau)) +
gamma*(1 - 0.5*tau**2) * sp.expn(2, gamma*tau) )
def exp_int(s, x):
r"""The exponential integral :math:`E_s(x)`
Given by: :math:`E_s(x) = \int_1^\infty \frac{e^{-xt}}{t^s}\,\mathrm dt`
Parameters
----------
s : :class:`float`
exponent in the integral
x : :class:`numpy.ndarray`
input values
"""
if np.isclose(s, 1):
return sps.exp1(x)
if np.isclose(s, np.around(s)) and s > -1:
return sps.expn(int(np.around(s)), x)
return inc_gamma(1 - s, x) * x**(s - 1)
def H_0_src(src_func, a_array, tau_array):
"""
given an array of optical depths, the emergent H is calculated
This is calculated assuming a given source function and using the exp int
Also assume no incident radiation
src_func: a function for the source function
a_array: an array containing the a_n coeficients for the source function
tau_array: an array of tau values to use for the integration
(in reality, only the max and min values and the number of points)
"""
min_tau = min(tau_array)
sampling = len(tau_array)
max_tau = max(tau_array)
return 0.5 * trap_log(lambda t: src_func(t, a_array) * sc.expn(2, t),
min_tau, max_tau, sampling)
def inc_gamma(s, x):
r"""Calculate the (upper) incomplete gamma function.
Given by: :math:`\Gamma(s,x) = \int_x^{\infty} t^{s-1}\,e^{-t}\,{\rm d}t`
Parameters
----------
s : :class:`float`
exponent in the integral
x : :class:`numpy.ndarray`
input values
"""
if np.isclose(s, 0):
return sps.exp1(x)
if np.isclose(s, np.around(s)) and s < -0.5:
return x**(s - 1) * sps.expn(int(1 - np.around(s)), x)
if s < 0:
return (inc_gamma(s + 1, x) - x**s * np.exp(-x)) / s
return sps.gamma(s) * sps.gammaincc(s, x)
def G_function_ILS(Fo):
"""
Infinite Line Source solution
Fo = Fourier number
Reference:
----------
Lamarche and Beauchamp (2007). A new contribution to the finite
line-source model for geothermal boreholes. Energy and
Building, 39:188-198.
"""
if Fo == 0:
G_ILS = 0
else:
G_ILS = 1 / (4 * pi) * special.expn(1, 1 /
(4 * Fo)) # Exponential integral
return G_ILS
def u_s(r_x, alpha, r_t0, m, M, sigma, alpha_hod, A, M_1, gamma_1, gamma_2, b_0, b_1, b_2): """ NFW for smaller scales, more to the center, exponential decline for the outer regions, which can be varied with alpha parameter! r_t can be changed! Fedeli -> 0.03 """ r_t = r_t0 * r_x[-1] x = r_x/r_t x_delta = r_x[-1]/r_t nu_alpha = 1.0 - (2.0/alpha) # absolute value, yes / no? - still not completely solved! BE AWARE! E_alpha = sp.expn(np.absolute(nu_alpha), (x_delta ** alpha)) G_alpha = sp.gamma(1.0 - nu_alpha) rho_t = (M*f_stars(m, M, sigma, alpha_hod, A, M_1, gamma_1, gamma_2, b_0, b_1, b_2)*alpha)/(4.0*np.pi*(r_t**3.0)*(G_alpha - (x_delta**2.0)*E_alpha)) profile = (rho_t/x) * np.exp(-(x**alpha)) return profile
def one_source(x0, y0, mag, rad, core, grid, type=0):
r = fromfunction(lambda x,y: sqrt((x-x0)**2 + (y-y0)**2), grid)
if type == 0:
# log sources
#[ 1.60121182e-06 7.82761030e+03 -6.36886579e-01]
s = mag*log(rad/r) + core #mag*log(1/(rad+r))+core
elif type == 1:
# from the 3d diffusion green's function
#[ 3.24852149e-05 8.97514165e+00 -6.11534255e-02]
s = mag*funcs.erf(r/rad)/r + core
elif type == 2:
# just a plain 'ol gaussian
s = mag*exp(-r**2/rad) + core
elif type == 3:
# from the 2d green's function
#[ 5.99160034e-06 2.39560167e+01 9.78734951e-03]
s = mag*funcs.expn(2,r/rad) + core
else:
s = mag/(r+rad) + core
return s
def single(self, freqs, atm, b, alpha, orientation=None, taulimit=20.0, plot= None, verbose = None, discAverage = False, normW4plot=True):
"""This computes the brightness temperature along one ray path"""
if verbose is None:
verbose = self.verbose
if plot is None:
plot = self.plot
# get path lengths (ds_layer) vs layer number (num_layer) - currently frequency independent refractivity
self.path = ray.compute_ds(atm,b,orientation,gtype=None,verbose=verbose,plot=plot)
if self.path.ds == None:
print 'Off planet'
self.Tb = []
for j in range(len(freqs)):
self.Tb.append(utils.T_cmb)
return self.Tb
# these profiles are saved
self.tau = []
self.W = []
self.Tb_lyr = []
# temporary arrays
taus = []
Tbs = []
Ws = []
# initialize
for j in range(len(freqs)):
taus.append(0.0)
Tbs.append(0.0)
Ws.append(0.0)
self.tau.append(taus)
self.W.append(Ws)
self.Tb_lyr.append(Tbs)
if alpha.config.Doppler:
P = atm.gas[atm.config.C['P']]
T = atm.gas[atm.config.C['T']]
alphaUnits = 'invcm'
#--debug--#self.debugDoppler = []
print ''
for i in range( len(self.path.ds)-1 ):
ds = self.path.ds[i]*utils.Units[utils.processingAtmLayerUnit]/utils.Units['cm']
taus = []
Ws = []
Tbs = []
ii = self.path.layer4ds[i]
ii1= self.path.layer4ds[i+1]
for j,f in enumerate(freqs):
if not alpha.config.Doppler:
a1 = self.layerAlpha[j][ii1]
a0 = self.layerAlpha[j][ii]
else:
fshifted=[[f/self.path.doppler[i]],[f/self.path.doppler[i+1]]]
#--debug--#self.debugDoppler.append(fshifted[0][0])
print '\rdoppler corrected frequency at layer',i,
a1 = alpha.getAlpha(fshifted[0],T[ii1],P[ii1],atm.gas[:,ii1],atm.config.C,atm.cloud[:,ii1],atm.config.Cl,units=alphaUnits,verbose=False)
a0 = alpha.getAlpha(fshifted[1],T[ii],P[ii],atm.gas[:,ii],atm.config.C,atm.cloud[:,ii],atm.config.Cl,units=alphaUnits,verbose=False)
dtau = (a0 + a1)*ds/2.0
taus.append(self.tau[i][j] + dtau) # this is tau_(i+1)
T1 = atm.gas[atm.config.C['T']][ii1]
T0 = atm.gas[atm.config.C['T']][ii]
if discAverage==True:
Ws.append( 2.0*a1*ss.expn(2,taus[j]) ) # this is W_(i+1) for disc average
# dTb = ( T1*ss.expn(2,taus[j])/scriptR(T1,freqs[j]) + T0*ss.expn(2,self.tau[ii][j])/scriptR(T0,freqs[j]) )*dtau
# Tbs.append( self.Tb_lyr[i][j] + dTb )
else:
Ws.append( a1*math.exp(-taus[j]) ) # this is W_(i+1) for non disc average
dTb = ( T1*Ws[j]/scriptR(T1,freqs[j]) + T0*self.W[i][j]/scriptR(T0,freqs[j]) )*ds/2.0
Tbs.append( self.Tb_lyr[i][j] + dTb)
self.tau.append(taus)
self.W.append(Ws)
self.Tb_lyr.append(Tbs)
print ''
# final spectrum
self.Tb = []
for j in range(len(freqs)):
top_Tb_lyr = self.Tb_lyr[-1][j]
if top_Tb_lyr < utils.T_cmb:
top_Tb_lyr = utils.T_cmb
self.Tb.append(top_Tb_lyr)
self.tau = np.array(self.tau).transpose()
self.W = np.array(self.W).transpose()
self.Tb_lyr = np.array(self.Tb_lyr).transpose()
try:
if plot:
# save a local copy of
self.P = atm.gas[atm.config.C['P']][0:len(self.W[0])]
self.z = atm.gas[atm.config.C['Z']][0:len(self.W[0])]
#####-----Weigthing functions
plt.figure('radtran')
plt.subplot(121)
for i,f in enumerate(freqs):
#label=r'$\tau$: %.1f GHz' % (f)
#plt.semilogy(self.tau[i],self.P,label=label)
if normW4plot:
wplot = self.W[i]/np.max(self.W[i])
else:
wplot = self.W[i]
label=r'$W$: %.1f GHz' % (f)
label=r'%.1f cm' % (30.0/f)
#label=r'%.0f$^o$' % ((180.0/math.pi)*math.asin(b[0]))
plt.semilogy(wplot,self.P,label=label,linewidth=3)
#label=r'Tlyr$_b$: %.1f GHz' % (f)
#plt.semilogy(self.Tb_lyr[i],self.P,label=label)
plt.legend()
plt.axis(ymin=100.0*math.ceil(self.P[-1]/100.0), ymax=1.0E-7*math.ceil(self.P[0]/1E-7))
#plt.xlabel('units')
plt.ylabel('P [bars]')
#####-----Alpha
plt.figure('alpha')
for i,f in enumerate(freqs):
label=r'$\alpha$: %.1f GHz' % (f)
label=r'%.1f cm' % (30.0/f)
pl = list(self.layerAlpha[i])
del pl[0]
#delete because alpha is at the layer boundaries, so there are n+1 of them
plt.loglog(pl,self.P,label=label)
plt.legend()
v = list(plt.axis())
v[2] = 100.0*math.ceil(self.P[-1]/100.0)
v[3] = 1.0E-7*math.ceil(self.P[0]/1E-7)
plt.axis(v)
#plt.legend()
#plt.xlabel('units')
plt.ylabel('P [bars]')
#####-----Brightness temperature
plt.figure('brightness')
lt = '-'
if (len(self.Tb)==1):
lt = 'o'
plt.plot(freqs,self.Tb,lt)
plt.xlabel('Frequency [GHz]')
plt.ylabel('Brightness temperature [K]')
except:
print 'Plotting broke'
del taus, Tbs, Ws
return self.Tb
###-----------------------------------
### p11
from scipy.integrate import quad
def integrand(t,n,x):
return exp(-x*t) / t**n
def expint(n,x):
return quad(integrand, 1, Inf, args=(n, x))[0]
vec_expint = vectorize(expint)
vec_expint(3, arange(1.0, 4.0, 0.5))
special.expn(3, arange(1.0, 4.0, 0.5))
result = quad(lambda x:expint(3, x), 0, inf)
print result
I3 = 1.0/3.0
print I3
print I3 - result[0]
###-----------------------------------
### 11
from scipy.integrate import quad, dblquad
def I(n):
return dblquad(lambda t, x: exp(-x*t) / t**n, 0, Inf, lambda x: 1, lambda x: Inf)
def matchlogtoexpn_score(p):
m, r0, off = p
return ((funcs.expn(2,rr/20.) - m*log(r0/rr) + off)**2).sum()
tau_start = 0.
tau_end = 1.0
sigma = 100
x_start = tau_start/sigma
x_end = tau_end/sigma
dx = x_end - x_start
psi_inc = 500
print("In MFP: ", sigma*(x_end - x_start))
#Compute values for multiple cells
for i in range(4):
print(x_start,x_end)
psi_x2 = lambda x: 6.*psi_inc*(expn(3,sigma*x) - 0.5*expn(2,sigma*x))
phi_avg =psi_inc/(dx)*quadrature(lambda x: expn(2,sigma*x),x_start,x_end,tol=1.E-12,maxiter=500)[0]
phi_eval = lambda x: 1/(sigma*(dx))*6.*psi_inc*(0.5*expn(3,sigma*x) - expn(4,sigma*x))
phi_mu = phi_eval(x_end) - phi_eval(x_start)
phi_x_int = lambda x: 6.*psi_inc/(dx*dx)*(x-0.5*(x_start+x_end))*expn(2,sigma*x)
phi_x = quadrature(lambda x: phi_x_int(x),x_start,x_end,tol=1.E-12,maxiter=500)[0]
print("---Results for %f < x < %f ---")
print("Moments: ",phi_avg,phi_x,phi_mu)
print("Corner values = ",phi_avg+phi_x-phi_mu,phi_avg-phi_x-phi_mu)
print("Phi_avg outflow = ",phi_avg+phi_x)
print("")
x_start += dx
x_end += dx
def time_expn_large_n(self):
expn(self.n, self.x)
def baz(r):
from scipy.special import expn
x1 = (R-r)/L
x2 = (r+R)/L
return r*(-expn(1,x1) + expn(1,x2))
def single(self, freqs, atm, b, alpha, orientation=None, taulimit=20.0, discAverage=False, normW4plot=True):
"""This computes the brightness temperature along one ray path"""
if self.layerAlpha is None:
self.layerAbsorption(freqs, atm, alpha)
# get path lengths (ds_layer) vs layer number (num_layer) - currently frequency independent refractivity
print_meta = (self.verbose == 'loud')
travel = ray.compute_ds(atm, b, orientation, gtype=None, verbose=print_meta, plot=self.plot)
self.travel = travel
if travel.ds is None:
print('Off planet')
self.Tb = []
for j in range(len(freqs)):
self.Tb.append(utils.T_cmb)
return self.Tb
# set and initialize arrays
integrated_W = [0.0 for f in freqs]
self.tau = [[0.0 for f in freqs]]
self.Tb_lyr = [[0.0 for f in freqs]]
self.W = [[0.0 for f in freqs]]
P_layers = atm.gas[atm.config.C['P']]
T_layers = atm.gas[atm.config.C['T']]
z_layers = atm.gas[atm.config.C['Z']]
self.P = [P_layers[travel.layer4ds[0]]]
self.z = [z_layers[travel.layer4ds[0]]]
for i in range(len(travel.ds) - 1):
ds = travel.ds[i] * utils.Units[utils.atmLayerUnit] / utils.Units['cm']
taus = []
Ws = []
Tbs = []
ii = travel.layer4ds[i]
ii1 = travel.layer4ds[i + 1]
T1 = T_layers[ii1]
T0 = T_layers[ii]
self.P.append((P_layers[ii] + P_layers[ii1]) / 2.0)
self.z.append((z_layers[ii] + z_layers[ii1]) / 2.0)
if self.layerAlpha is None:
print("is None at ", i)
for j, f in enumerate(freqs):
if not alpha.config.Doppler:
a1 = self.layerAlpha[j][ii1]
a0 = self.layerAlpha[j][ii]
else:
print("\n\nDoppler currently broken since the getAlpha call is different.")
fshifted = [[f / travel.doppler[i]], [f / travel.doppler[i + 1]]]
print('\rdoppler corrected frequency at layer', i, end='')
a1 = alpha.getAlpha(fshifted[0], T_layers[ii1], P_layers[ii1], atm.gas[:, ii1], atm.config.C, atm.cloud[:, ii1],
atm.config.Cl, units=utils.alphaUnit)
a0 = alpha.getAlpha(fshifted[1], T_layers[ii], P_layers[ii], atm.gas[:, ii], atm.config.C, atm.cloud[:, ii],
atm.config.Cl, units=utils.alphaUnit)
dtau = (a0 + a1) * ds / 2.0
taus.append(self.tau[i][j] + dtau) # this is tau_(i+1)
if discAverage is True:
Ws.append(2.0 * a1 * ss.expn(2, taus[j])) # this is W_(i+1) for disc average
else:
Ws.append(a1 * math.exp(-taus[j])) # this is W_(i+1) for non disc average
integrated_W[j] += (Ws[j] + self.W[i][j]) * ds / 2.0
dTb = (T1 * Ws[j] + T0 * self.W[i][j]) * ds / 2.0
Tbs.append(self.Tb_lyr[i][j] + dTb)
self.tau.append(taus)
self.W.append(Ws)
self.Tb_lyr.append(Tbs)
# final spectrum
self.Tb = []
for j in range(len(freqs)):
top_Tb_lyr = self.Tb_lyr[-1][j]
if top_Tb_lyr < utils.T_cmb:
top_Tb_lyr = utils.T_cmb
else:
top_Tb_lyr /= integrated_W[j] # Normalize by integrated weights (makes assumptions)
if integrated_W[j] < 0.96 and self.verbose:
print("Weight correction at {:.2f} is {:.4f} (showing below 0.96)".format(freqs[j], integrated_W[j]))
self.Tb.append(top_Tb_lyr)
self.tau = np.array(self.tau).transpose()
self.W = np.array(self.W).transpose()
self.Tb_lyr = np.array(self.Tb_lyr).transpose()
self.P = np.array(self.P)
self.z = np.array(self.z)
if self.plot:
# ####-----Weigthing functions
plt.figure('INT_W')
plt.plot(freqs, integrated_W)
plt.title('Integrated weighting function')
plt.xlabel('Frequency [GHz]')
plt.figure('radtran')
plt.subplot(121)
for i, f in enumerate(freqs):
if normW4plot:
wplot = self.W[i] / np.max(self.W[i])
else:
wplot = self.W[i]
if self.output_type == 'frequency':
label = (r'{:.1f} GHz').format(f)
else:
label = (r'{:.1f} cm').format(30.0 / f)
plt.semilogy(wplot, self.P, label=label, linewidth=3)
plt.legend()
plt.axis(ymin=100.0 * math.ceil(np.max(self.P) / 100.0), ymax=1.0E-7 * math.ceil(np.min(self.P) / 1E-7))
plt.ylabel('P [bars]')
# ####-----Alpha
plt.figure('alpha')
for i, f in enumerate(freqs):
if self.output_type == 'frequency':
label = (r'$\alpha$: {:.1f} GHz').format(f)
else:
label = (r'{:.1f} cm').format(30.0 / f)
pl = list(self.layerAlpha[i])
del pl[0]
plt.loglog(pl, self.P, label=label)
plt.legend()
v = list(plt.axis())
v[2] = 100.0 * math.ceil(np.max(self.P) / 100.0)
v[3] = 1.0E-7 * math.ceil(np.min(self.P) / 1E-7)
plt.axis(v)
plt.ylabel('P [bars]')
# ####-----Brightness temperature
plt.figure('brightness')
lt = '-'
if (len(self.Tb) == 1):
lt = 'o'
plt.plot(freqs, self.Tb, lt)
plt.xlabel('Frequency [GHz]')
plt.ylabel('Brightness temperature [K]')
del taus, Tbs, Ws
return self.Tb
from scipy.special import expn import numpy as np ## http://docs.scipy.org/doc/scipy/reference/tutorial/integrate.html ## http://docs.scipy.org/doc/scipy/reference/generated/scipy.special.expn.html ## Siempre el primer arg es 1, el segundo valor va a ser lo que se ponga en Matlab res=expn(1,1.0) print "valor: ", res
