def __init__(self, scenario_flag = "Freeway_Free"):
"""
Totally five scenarios are supported here:
Freeway_Night, Freeway_Free, Freeway_Rush;
Urban_Peak, Urban_Nonpeak.
The PDFs of the vehicle speed and the inter-vehicle space are adapted
from existing references.
"""
if scenario_flag == "Freeway_Night":
self.headway_random = expon(0.0, 1.0/256.41)
meanSpeed = 30.93 #m/s
stdSpeed = 1.2 #m/s
elif scenario_flag == "Freeway_Free":
self.headway_random = lognorm(0.75, 0.0, np.exp(3.4))
meanSpeed = 29.15 #m/s
stdSpeed = 1.5 #m/s
elif scenario_flag == "Freeway_Rush":
self.headway_random = lognorm(0.5, 0.0, np.exp(2.5))
meanSpeed = 10.73 #m/s
stdSpeed = 2.0 #m/s
elif scenario_flag == "Urban_Peak":
scale = 1.096
c = 0.314
loc = 0.0
self.headway_random = fisk(c, loc, scale)
meanSpeed = 6.083 #m/s
stdSpeed = 1.2 #m/s
elif scenario_flag == "Urban_Nonpeak":
self.headway_random = lognorm(0.618, 0.0, np.exp(0.685))
meanSpeed = 12.86 #m/s
stdSpeed = 1.5 #m/s
else:
raise
self.speed_random = norm(meanSpeed, stdSpeed)
def main(options):
"""
The main function.
"""
with open(options.results, 'rb') as fd:
results = pickle.load(fd)
for key in results.keys():
print '=' * 80
print key, ':'
print str(results[key])
print '=' * 80
if options.catalysis is None:
return
log_q = results['log_q']
print 'Median\t95\% Interval'
for i in xrange(log_q.mu.shape[1]):
mu = log_q.mu[0, i]
s = np.sqrt(log_q.C[0, i, i])
if i == log_q.mu.shape[1] - 1:
rv = stats.lognorm(s, scale=np.exp(mu))
else:
rv = stats.lognorm(s, scale=np.exp(mu)/180.)
I = rv.interval(0.95)
print '{0:1.4f} & ({1:1.4f}, {2:1.4f}) \\\\'.format(rv.median(), I[0], I[1])
def plot_multiplicative(self, T, npaths=25, show_trend=True):
"""
Plots for the multiplicative decomposition
"""
# Pull out right sizes so we know how to increment
nx, nk, nm = self.nx, self.nk, self.nm
# Matrices for the multiplicative decomposition
nu_tilde, H, g = self.multiplicative_decomp()
# Allocate space (nm is the number of functionals - we want npaths for each)
mpath_mult = np.empty((nm*npaths, T))
mbounds_mult = np.empty((nm*2, T))
spath_mult = np.empty((nm*npaths, T))
sbounds_mult = np.empty((nm*2, T))
tpath_mult = np.empty((nm*npaths, T))
ypath_mult = np.empty((nm*npaths, T))
# Simulate for as long as we wanted
moment_generator = self.lss.moment_sequence()
# Pull out population moments
for t in range (T):
tmoms = next(moment_generator)
ymeans = tmoms[1]
yvar = tmoms[3]
# Lower and upper bounds - for each multiplicative functional
for ii in range(nm):
li, ui = ii*2, (ii+1)*2
Mdist = lognorm(np.asscalar(np.sqrt(yvar[nx+nm+ii, nx+nm+ii])),
scale=np.asscalar( np.exp( ymeans[nx+nm+ii]- \
t*(.5)*np.expand_dims(np.diag(H @ H.T),1)[ii])))
Sdist = lognorm(np.asscalar(np.sqrt(yvar[nx+2*nm+ii, nx+2*nm+ii])),
scale = np.asscalar( np.exp(-ymeans[nx+2*nm+ii])))
mbounds_mult[li:ui, t] = Mdist.ppf([.01, .99])
sbounds_mult[li:ui, t] = Sdist.ppf([.01, .99])
# Pull out paths
for n in range(npaths):
x, y = self.lss.simulate(T)
for ii in range(nm):
ypath_mult[npaths*ii+n, :] = np.exp(y[nx+ii, :])
mpath_mult[npaths*ii+n, :] = np.exp(y[nx+nm + ii, :] - np.arange(T)*(.5)*np.expand_dims(np.diag(H @ H.T),1)[ii])
spath_mult[npaths*ii+n, :] = 1/np.exp(-y[nx+2*nm + ii, :])
tpath_mult[npaths*ii+n, :] = np.exp(y[nx+3*nm + ii, :] + np.arange(T)*(.5)*np.expand_dims(np.diag(H @ H.T),1)[ii])
mult_figs = []
for ii in range(nm):
li, ui = npaths*(ii), npaths*(ii+1)
LI, UI = 2*(ii), 2*(ii+1)
mult_figs.append(self.plot_given_paths(T, ypath_mult[li:ui,:], mpath_mult[li:ui,:],
spath_mult[li:ui,:], tpath_mult[li:ui,:],
mbounds_mult[LI:UI,:], sbounds_mult[LI:UI,:], 1,
show_trend=show_trend))
mult_figs[ii].suptitle( r'Multiplicative decomposition of $y_{%s}$' % str(ii+1), fontsize=14)
return mult_figs
def estimate_distribution(self,index_stats,queries,qrel=None):
self._estimate_para(index_stats,queries,qrel)
for qid in self._run.ranking:
self._rel_distribution[qid] = lognorm(self._sigma1[qid],scale = math.exp(self._mu1[qid]))
self._non_rel_distribution[qid] = lognorm(self._sigma0[qid],scale = math.exp(self._mu0[qid]))
def test__validate_input():
"""Testing validation of inputs."""
# valid inputs must be an instance of the Input class
invalid_workers = stats.lognorm(s=1.0)
invalid_firms = stats.lognorm(s=1.0)
with nose.tools.assert_raises(AttributeError):
models.Model('positive', invalid_workers, invalid_firms,
production=valid_F, params=valid_F_params)
def __init__(self,
gamma=2,
beta=0.95,
alpha=0.90,
sigma=0.1,
grid_size=100):
self.gamma = gamma
self.beta = beta
self.alpha = alpha
self.sigma = sigma
# == Set the grid interval to contain most of the mass of the
# stationary distribution of the consumption endowment == #
ssd = self.sigma / np.sqrt(1 - self.alpha**2)
grid_min, grid_max = np.exp(-4 * ssd), np.exp(4 * ssd)
self.grid = np.linspace(grid_min, grid_max, grid_size)
self.grid_size = grid_size
# == set up distribution for shocks == #
self.phi = lognorm(sigma)
self.draws = self.phi.rvs(500)
# == h(y) = beta * int G(y,z)^(1-gamma) phi(dz) == #
self.h = np.empty(self.grid_size)
for i, y in enumerate(self.grid):
self.h[i] = beta * np.mean((y**alpha * self.draws)**(1 - gamma))
def __init__(self, mu, sigma):
self.mu = mu
self.sigma = sigma
# set dist before calling super's __init__
self.dist = st.lognorm(sigma, scale=exp(mu))
super(LogNormal, self).__init__()
def log10norm(x, mu, sigma=1.0):
""" Scale scipy lognorm from natural log to base 10
x : input parameter
mu : mean of the underlying log10 gaussian
sigma : variance of underlying log10 gaussian
"""
return stats.lognorm(sigma * np.log(10), scale=mu).pdf(x)
def plot(vals, name, bins=100, power=1, nmu=None, nstd=None):
"""Function accepts a dictionary of orf length - frequency pairs, and the length of the
ORF of interest, also optional plot flag for if data histogram should be plotted. Fits a
lognormal distribution to the orf length data. Returns dictionaries of the probabilites of
each length, the Predicted p-value for each length based on log normal, the observed
p-value for each length, and the p-value for the length of interest.
"""
# mu, std = log_normal(vals)
loged = np.log(vals)
if not nmu and not nstd:
nmu, nstd = np.mean(loged), np.std(loged)
lgn = lognorm([nstd], scale=math.e ** nmu)
# Plot the fit line
f, (ax1, ax2) = plt.subplots(1, 2, sharey=False)
ax1.scatter(range(len(vals)), sorted(vals))
hi, pos, patch = ax2.hist(vals, bins, normed=True)
x = np.linspace(min(vals), max(vals), 500)
y1 = lgn.pdf(x)
# y2 = n.pdf(x) ** power
ax2.plot(x, y1, color="green", lw=3.0)
# ax2.plot(x, y2, color='red', lw=3.0)
plt.text(
0.4,
max(hi) * 3 / 4,
"E(X) = {:4f}\nVAR(X) = {:4f}\nSTD(X) = {:4f}".format(np.mean(vals), np.var(vals), np.std(vals)),
fontsize=8,
)
plt.savefig(name)
plt.close()
def particlesInVolumeLogNorm(vol_frac, mu, sigma, particle_diameters):
'''
Function that calculates particle densities in a volume element.
The particles are diameters are log-normally distributed (sigma, mu)
and they have a given volume fraction.
'''
D = particle_diameters
# Calculate particle density(particles per um ^ 3)
N = lognorm(sigma, scale=np.exp(mu))
# Weight factors of each particle size
pdf = N.pdf(D)
# Volume of particle having radius R[m ^ 3]
Vsph = 4.0 / 3.0 * np.pi * (D / 2.0) ** 3.0
# Particle volumes multiplied with weight factors = > volume distribution
WV = pdf * Vsph
# Total volume of the volume distribution
Vtot = np.trapz(WV, D)
# Number of particles in um ^ 3
n_part = vol_frac / Vtot
print('Number of particles in cubic micrometer = %.18f' % n_part)
# Check, should give the volume fraction in %
print("Volume fraction was: %.1f %%" %
(np.trapz(n_part * pdf * Vsph, D) * 100))
bins = pdf * (D[1] - D[0])
# print(bins.sum())
return(n_part * bins)
def __generateMieEffective(self,
n_particle,
n_host,
particle_mu,
particle_sigma,
effective_model=True,
wavelen_n=1000,
wavelen_max=1100.0,
wavelen_min=100.0,
particle_n=20,
particle_max=20.0,
particle_min=1.0):
'''
Private function.
Generates new effective mie-data file for the database.
'''
if particle_n < 10:
print(
"Too few particles to calculate \
effective model: particle_n < 10")
exit()
n_x_rv = 10000
n_tht = 91
wavelengths = np.linspace(wavelen_min, wavelen_max, wavelen_n) / 1000.0
p_diameters = np.linspace(particle_min, particle_max, particle_n)
o_f = ("mie_eff_p-%dum-%dum-%d_" % (particle_min,
particle_max,
particle_n) +
'np-%s_nh-%.2f_' % (n_particle.__format__('.2f'),
n_host) +
'wave-%.1fnm-%.1fnm-%d' % (wavelen_min,
wavelen_max,
wavelen_n) +
'.hdf5')
o_f = baseDir + '/' + o_f
# Calculate particle distribution
N = lognorm(particle_sigma, scale=np.exp(particle_mu))
# Weight factors of each particle size
pdf = N.pdf(p_diameters)
pdf /= pdf.sum()
weight = dict(zip(p_diameters, pdf))
df = 0
df = mie.generateMieDataEffective(wavelengths,
p_normed_weights_dict=weight,
number_of_rvs=n_x_rv,
number_of_theta_angles=n_tht,
n_particle=n_particle,
n_silicone=n_host,
p_diameters=p_diameters)
print(df.info())
mie.saveMieDataToHDF5([df],
particle_diameters=[p_diameters.mean()],
out_fname=o_f,
wavelengths=wavelengths * 1000.0)
return(o_f)
def lognorm(mu=1,sigma=1,phi=0):
''' Y ~ log(X)+phi
X ~ Normal(mu,sigma)
mu - mean of X
sigma - standard deviation of X
'''
return stats.lognorm(sigma,loc=-phi,scale=np.exp(mu))
def test_ss_wage_flexible(self):
w_grid = np.linspace(0.40000000000000002, 3.5, 40)
sigma = .4
mu = -(sigma ** 2) / 2
ln_dist = lognorm(sigma, scale=np.exp(-(sigma) ** 2 / 2))
zl, zh = ln_dist.ppf(.05), ln_dist.ppf(.95)
z_grid = np.linspace(zl, zh, 22)
params = {
"lambda_": [0.0, "degree of rigidity"],
"pi": [0.02, "target inflation"],
"eta": [2.5, "elas. of subs among labor types"],
"gamma": [0.5, "frisch elas. of labor supply"],
"wl": [0.4, "wage lower bound"],
"wu": [3.5, "wage upper bound"],
"wn": [40, "wage grid point"],
"beta": [0.97, "disount factor. check this"],
"tol": [10e-6, "error tolerance for iteration"],
"sigma": [sigma, "standard dev. of underlying normal dist"],
'z_grid': (z_grid, 'a'),
'w_grid': (w_grid, 'a'),
'full_ln_dist': (ln_dist, 'a'),
'mu': (mu, 'mean of underlying nomral distribution.')}
res_dict = run_one(params)
expected = Interp(z_grid, ss_wage_flexible(params, shock=z_grid))
actual = res_dict['ws']
print(expected.Y)
print(actual.Y)
np.testing.assert_almost_equal(actual.Y, expected.Y, 5)
def get_population_density_lognorm(size, upper, lower, log_mean, log_sd, mean, sd, position_marker): '''This :returns a value of a lognormal population distribution :param size: total size :type size: float :param upper: upper value of bin :type upper: float :param lower: lower value of bin :type lower: float :param log_mean: log mean :type log_mean: float :param log_sd: log standard deviation :type log_sd: float :param mean: mean :type mean: float :param sd: standard deviation :type sd: float :param position_marker: is the last/first bin of samples or not, -1: first bin; 1: last bin; 0:any bin between the first and the last :type position_marker: int :returns: population density ''' distribution = lognorm(loc=log_sd,scale=log_mean) if position_marker: cdf1 = 1 lower = upper else: cdf1 = logncdf(upper,log_mean,log_sd) cdf2 = logncdf(lower,log_mean,log_sd) posibility_space = cdf1 - cdf2 population = size * posibility_space population_int = population return population_int;
def test_sklearn_():
'''
Test whether the booster indeed gets updated
:return:
'''
Xtrain = np.random.randn(100,10)
ytrain = np.random.randint(0,2,100)
Xval = np.random.randn(20, 10)
yval = np.random.randint(0, 2, 20)
classifier = SHSklearnEstimator(model=RandomForestClassifier(n_estimators=4),\
ressource_name='n_estimators')
param_grid = {'max_depth': randint(1,10),
'min_impurity_decrease':lognorm(0.1)
}
scoring = make_scorer(accuracy_score)
successiveHalving = SuccessiveHalving(
estimator=classifier,
n = 10,
r = 100,
param_grid=param_grid,
ressource_name='n_estimators',
scoring=scoring,
n_jobs=1,
cv=None,
seed=0
)
T = successiveHalving.apply(Xtrain,ytrain,Xval,yval)
print(T)
assert(True)
def __init__(self, gamma, beta, alpha, sigma, grid=None):
self.gamma = gamma
self.beta = beta
self.alpha = alpha
self.sigma = sigma
# == set up grid == #
if grid is None:
(self.grid, self.grid_min,
self.grid_max, self.grid_size) = self._new_grid()
else:
self.grid = np.asarray(grid)
self.grid_min = min(grid)
self.grid_max = max(grid)
self.grid_size = len(grid)
# == set up distribution for shocks == #
self.phi = lognorm(sigma)
# == set up integration bounds. 4 Standard deviations. Make them
# private attributes b/c users don't need to see them, but we
# only want to compute them once. == #
self._int_min = np.exp(-4.0 * sigma)
self._int_max = np.exp(4.0 * sigma)
# == Set up h from the Lucas Operator == #
self.h = self._init_h()
def testTransformedDistribution(self):
g = ops.Graph()
with g.as_default():
mu = 3.0
sigma = 2.0
# Note: the Jacobian callable only works for this example; more generally
# you may or may not need a reduce_sum.
log_normal = self._cls()(
distribution=ds.Normal(loc=mu, scale=sigma),
bijector=bs.Exp(event_ndims=0))
sp_dist = stats.lognorm(s=sigma, scale=np.exp(mu))
# sample
sample = log_normal.sample(100000, seed=235)
self.assertAllEqual([], log_normal.event_shape)
with self.test_session(graph=g):
self.assertAllEqual([], log_normal.event_shape_tensor().eval())
self.assertAllClose(
sp_dist.mean(), np.mean(sample.eval()), atol=0.0, rtol=0.05)
# pdf, log_pdf, cdf, etc...
# The mean of the lognormal is around 148.
test_vals = np.linspace(0.1, 1000., num=20).astype(np.float32)
for func in [[log_normal.log_prob, sp_dist.logpdf],
[log_normal.prob, sp_dist.pdf],
[log_normal.log_cdf, sp_dist.logcdf],
[log_normal.cdf, sp_dist.cdf],
[log_normal.survival_function, sp_dist.sf],
[log_normal.log_survival_function, sp_dist.logsf]]:
actual = func[0](test_vals)
expected = func[1](test_vals)
with self.test_session(graph=g):
self.assertAllClose(expected, actual.eval(), atol=0, rtol=0.01)
def __init__(self, gamma=2, beta=0.95, alpha=0.90, sigma=0.1, grid=None):
self.gamma = gamma
self.beta = beta
self.alpha = alpha
self.sigma = sigma
# == set up grid == #
if grid is None:
(self.grid, self.grid_min,
self.grid_max, self.grid_size) = self._new_grid()
else:
self.grid = np.asarray(grid)
self.grid_min = min(grid)
self.grid_max = max(grid)
self.grid_size = len(grid)
# == set up distribution for shocks == #
self.phi = lognorm(sigma)
# == set up integration bounds. 4 Standard deviations.
self._int_min = np.exp(-4.0 * sigma)
self._int_max = np.exp(4.0 * sigma)
# == initial h to iterate from == #
self.h = self._init_h()
def set_distribution(self, mean, mode):
"""
Create lognormal distribution from given mean and mode.
Distances are converted to km to prevent overflow.
"""
scale = np.exp(mean)
s = np.sqrt(np.log(scale / float(mode)))
return scs.lognorm(s=s, scale=scale)
def lognorm_mean(mean, sigma):
""" returns a lognormal distribution parameterized by its mean and a spread
parameter `sigma` """
if sigma == 0:
return DeterministicDistribution(mean)
else:
mu = mean * np.exp(-0.5 * sigma**2)
return stats.lognorm(scale=mu, s=sigma)
def lognorm_mean_var(mean, variance):
""" returns a lognormal distribution parameterized by its mean and its
variance. """
if variance == 0:
return DeterministicDistribution(mean)
else:
scale, sigma = lognorm_mean_var_to_mu_sigma(mean, variance, 'scipy')
return stats.lognorm(scale=scale, s=sigma)
def estimate_smoothG_cutoff_lognorm_robust(smoothG, fdr=0.05, independent=False, modefunc=half_sample_mode, madmult=5.2):
lmu, ls2 = robust_lognormal_mean_var(smoothG, modefunc=modefunc, madmult=madmult)
nulldist = stats.lognorm(math.sqrt(ls2),scale=math.exp(lmu))
pvals = [nulldist.sf(i) for i in smoothG]
pcutoff = BH_fdr_procedure(pvals, fdr, independent=independent)
if pcutoff is None:
return None, None
gcutoff = nulldist.isf(pcutoff)
return pcutoff, gcutoff
def __init__(self, mu, sigma, a, b):
super(Lognormal, self).__init__()
self.__mu = mu
self.__sigma = sigma
self._dist = lognorm(sigma, scale=mu)
self.__a = a
self.__b = b
def test__validate_input():
"""Testing validation of inputs."""
# valid inputs must be an instance of the Input class
invalid_input = stats.lognorm(s=1.0)
with nose.tools.assert_raises(AttributeError):
mod = model.AssortativeMatchingModelLike()
mod.input2 = invalid_input
def __init__(self, mu, sigma, bounds=None):
self.mu = mu
self.sigma = sigma
self.scale = np.exp(mu)
self.log_s = np.log(sigma)
self.distribution = lognorm(sigma, scale=np.exp(mu))
self._bounds = (0, np.inf)
super().__init__(self)
def __init__(self, lossType = "Large",
sevDist = ["lognorm", 0, 1],
freqDist = [ "poisson", 1 ]
):
self.sevDist = None
self.freqDist = None
if lossType == "Cat":
#do the thing for cat losses
self.sevDist = sp.lognorm(sevDist[2], scale = np.exp(sevDist[1]))
elif lossType == "Att":
self.sevDist = sp.lognorm(sevDist[2], scale = np.exp(sevDist[1]))
self.freqDist = None
elif lossType == "Large":
if sevDist[0] == "lognorm" or sevDist[0] == "lognormal":
self.sevDist = sp.lognorm(sevDist[2], scale = np.exp(sevDist[1]))
elif sevDist[0] == "gamma":
self.sevDist = sp.gamma(sevDist[1], scale = sevDist[2])
self.freqDist = sp.poisson(freqDist[1])
def estimate_smoothG_cutoff_lognorm_theory(smoothG, tmean, tvar, fdr=0.05, independent=False):
tmean, tvar = float(tmean), float(tvar)
lmu, ls2 = lognormal_mean_var(tmean, tvar)
nulldist = stats.lognorm(math.sqrt(ls2),scale=math.exp(lmu))
pvals = [nulldist.sf(i) for i in smoothG]
pcutoff = BH_fdr_procedure(pvals, fdr, independent=independent)
if pcutoff is None:
return None, None
gcutoff = nulldist.isf(pcutoff)
return pcutoff, gcutoff
def lognormal_diff(tau, amp, mu, sigma):
print amp, mu, sigma
dist = lognorm([sigma], loc=mu * 1000)
n = 10000
# taus = dist.rvs(n)
# (a,b) = dist.interval(0.9)
(a, b) = (max(1e-4, mu - sigma), mu + 100 * sigma)
taus = np.logspace(np.log(a), np.log(b), n)
G = amp * np.sum(dist.pdf(taus) * np.exp(-tau[:, newaxis] / taus[newaxis, :]), axis=1)
return G
def choose(self):
if self.user_class == 'HF':
self.name = "Log-norm"
peak_hours_for_iat_hf = [1, 2, 3, 4, 5, 6]
if self.hour in peak_hours_for_iat_hf:
lognorm_shape, lognorm_scale, lognorm_location = 4.09174469261446, 1.12850165892419, 4.6875
else:
lognorm_shape, lognorm_scale, lognorm_location = 3.93740014906562, 0.982210300411203, 3
return lognorm(lognorm_shape, loc=lognorm_location, scale=lognorm_scale)
elif self.user_class == 'HO':
self.name = "Gamma"
peak_hours_for_iat_ho = [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]
if self.hour in peak_hours_for_iat_ho:
gamma_shape, gamma_rate, gamma_location = 1.25170029089175, 0.00178381168026473, 0.5
else:
gamma_shape, gamma_rate, gamma_location = 1.20448161464647, 0.00177591076721503, 0.5
return gamma(gamma_shape, loc=gamma_location, scale=1. / gamma_rate)
elif self.user_class == 'MF':
self.name = "Gamma"
peak_hours_for_iat_mf = [1, 2, 3, 4, 5, 6, 7, 22, 23]
if self.hour in peak_hours_for_iat_mf:
gamma_shape, gamma_rate, gamma_location = 2.20816848575484, 0.00343216949000565, 1
else:
gamma_shape, gamma_rate, gamma_location = 2.03011412986896, 0.00342699308280547, 1
return gamma(gamma_shape, loc=gamma_location, scale=1. / gamma_rate)
elif self.user_class == 'MO':
self.name = "Gamma"
peak_hours_for_iat_mo = [1, 2, 3, 4, 5, 6]
if self.hour in peak_hours_for_iat_mo:
gamma_shape, gamma_rate, gamma_location = 1.29908195595742, 0.00163527376977441, 0.5
else:
gamma_shape, gamma_rate, gamma_location = 1.19210494792398, 0.00170354443324898, 0.5
return gamma(gamma_shape, loc=gamma_location, scale=1. / gamma_rate)
elif self.user_class == 'LF':
peak_hours_for_iat_lf = [1, 2, 3, 4, 5, 6, 7]
if self.hour in peak_hours_for_iat_lf:
self.name = "Gamma"
gamma_shape, gamma_rate, gamma_location = 1.79297773527656, 0.00191590321039876, 2
return gamma(gamma_shape, loc=gamma_location, scale=1. / gamma_rate)
else:
self.name = "Weibull"
weibull_c_shape, weibull_scale, weibull_location = 1.1988117443903, 827.961760834184, 1
return weibull_min(weibull_c_shape, loc=weibull_location, scale=weibull_scale)
elif self.user_class == 'LO':
peak_hours_for_iat_lo = [2, 3, 4, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20]
if self.hour in peak_hours_for_iat_lo:
self.name = "Weibull"
weibull_c_shape, weibull_scale, weibull_location = 0.850890858519732, 548.241539446292, 1
return weibull_min(weibull_c_shape, loc=weibull_location, scale=weibull_scale)
else:
self.name = "Gamma"
gamma_shape, gamma_rate, gamma_location = 0.707816241615835, 0.00135537879658998, 1
return gamma(gamma_shape, loc=gamma_location, scale=1. / gamma_rate)
else:
raise Exception('The user class %s does not exist' % self.user_class)
def log_normal(mean, mode):
"""Creating log normal, by first calculating
sigma and mu by manipulating these equations:
- mode = np.exp(mu - sig**2)
- mean = np.exp(mu + (sig**2/2))
then using the scipy.stats package.
"""
sigma = np.sqrt((2. / 3.) * (np.log(mean) - np.log(mode)))
mu = ((2. * np.log(mean)) + np.log(mode)) / 3.
lognorm = stats.lognorm(sigma, loc=0., scale=np.exp(mu))
return lognorm
def solve_compound(solFunc,
parameters,
hyperparameter,
N,
parIdx=3,
distribution='normal',
recurrence=False,
precision=50):
"""Obtain a compound distribution for the model in solfunc.
Arguments:
solFunc -- The solution function over which to compound
parameters -- List of parameters accepted by solFunc
hyperparameter -- Standard deviation of the compounding distribution
N -- Maximal mRNA copy number. The distribution is evaluated for n=0:N-1
Keyword arguments:
parIdx -- Index of the parameter over which the solution is compunded
distribution -- String specifying the type of compounding distribution
recurrence -- Boolean specifying if compounding is over recurrence terms
precision -- Integer specifying the precision used by the Decimal class
"""
# Specify some hyperparameters governing integration accuracy
cdfMax = 0.999
nTheta = 200
# Set up the parameter distribution
m, s = parameters[parIdx], hyperparameter
if distribution == 'normal':
a, b = (0 - m) / s, 10000
dist = st.truncnorm(a, b, m, s)
elif distribution == 'gamma':
theta = s**2 / m
k = (m / s)**2
dist = st.gamma(k, scale=theta)
elif distribution == 'lognormal':
mu = np.log(m / np.sqrt(1 + (s / m)**2))
sg = np.sqrt(np.log(1 + (s / m)**2))
dist = st.lognorm(s=sg, scale=np.exp(mu))
else:
print('Invalid distribution selected')
return
# Set up parameter vector
thetMax = dist.ppf(cdfMax)
thetMin = dist.ppf(1 - cdfMax)
thetVec = np.linspace(thetMin, thetMax, nTheta)
dThet = thetVec[1] - thetVec[0]
P = np.zeros(N)
parMod = deepcopy(parameters)
# If operating on the recurrence terms, need to comnvert to Decimal
if recurrence:
P = np.array([Decimal(p) for p in P])
dThet = Decimal(dThet)
# Evaluate distribution for each theta and add contribution
for thet in thetVec:
parMod[parIdx] = thet
if recurrence:
P += np.array(solFunc(parMod, N, precision=precision)) * Decimal(
dist.pdf(thet))
else:
P += solFunc(parMod, N) * dist.pdf(thet)
P *= dThet
return P
from pyNetica import Node, Network
from scipy import stats
import numpy as np
import itertools
import sys
from bnexample1_funcs import form2y
# random variables
rvX1 = stats.lognorm(1., scale=np.exp(0))
rvX3 = stats.lognorm(1., scale=np.exp(3*np.sqrt(2)))
# create nodes
x1 = Node("X1", parents=None, rvname='lognormal', rv=rvX1)
x2 = Node("X2", parents=[x1], rvname='continuous')
y = Node("Y", parents=[x2], rvname='discrete')
# discretize continuous rv
x1num = 5
x2num = 5
m = x1.rv.stats('m'); s = np.sqrt(x1.rv.stats('v'))
#lb = np.maximum(0, m-2*s); ub = m+2*s
lb = 0.; ub = m+1.5*s
x1names = x1.discretize(lb, ub, x1num, infinity='+')
x2names = x2.discretize(lb*10., ub*10., x2num, infinity='+')
# calculate and assign CPT
# node X1
x1cpt = x1.rv.cdf(x1.bins[1:]) - x1.rv.cdf(x1.bins[:-1])
x1cpt = x1cpt[np.newaxis,:]
x1.assign_cpt(x1cpt, statenames=x1names)
def get_random_rect_sz_HARDCODE():
shape, scale = 0.7635779560378387, 0.07776496289182451
dist = stats.lognorm(shape, 0.0, scale)
size = dist.rvs()
size = size * 0.9671784150570207 + 0.007142151004612083
return (size)
def errfunc(mu_, sig_):
N = lognorm(sig_, scale=np.exp(mu_))
# minimize ze difference between D10 and D90 to cumulative function
# Weight the D10 more by 2*
zero = 2 * np.abs(0.1 - N.cdf(D10)) + np.abs(0.9 - N.cdf(D90))
return (zero)
# == NON-UNIFORM SIMULATION =========================
'''
Simulate an array of N non-uniform droplets being linearly cooled.
steps:
1. Generate N areas from a given distribution
2. Generate N uniformly distributed random numbers in [0,1)
3. Multiply each area by J_HET and generate the liquid probability curve
as a function of temperature for that freezing rate.
4. Map the corresponding random number to the liquid probability curve
corresponding to the given droplet.
'''
fig, ax = plt.subplots(1, figsize=(7, 5))
rv = lognorm(1.5)
LOWER, UPPER = rv.ppf(0.001) / SCALER, rv.ppf(0.999) / SCALER
areas = rv.rvs(N) / SCALER # [cm^2]
ps = np.random.random(N) # probability for each droplet
mean_area = rv.mean() / SCALER
std_area = rv.std() / SCALER
Ts = T_freeze(ps, areas, B, T_0) # Simulated freezing temperatures
data = np.c_[areas, ps, Ts]
Ts.sort()
frac = [i / N for i in range(1, N + 1)] # Liquid proportion
Ts_fit = np.linspace(Ts[0], Ts[-1], 250)
def ln_log10norm(x, mu, sigma=1.0):
""" Natural log of base 10 lognormal """
return np.log(stats.lognorm(sigma * np.log(10), scale=mu).pdf(x))
def lognorm(x, mu, sigma=1.0):
""" Log-normal function from scipy """
return stats.lognorm(sigma, scale=mu).pdf(x)
try:
from ISP_mystyle import setFonts, showData
except ImportError:
# Ensure correct performance otherwise
def setFonts(*options):
return
def showData(*options):
plt.show()
return
# Generate the data
x = np.logspace(-9, 1, 1001) + 1e-9
lnd = stats.lognorm(2)
y = lnd.pdf(x)
# Generate 2 plots, side-by-side
sns.set_style('ticks')
setFonts(18)
fig, axs = plt.subplots(1, 2, sharey=True)
sns.set_context('poster')
# Left plot: linear scale on x-axis
axs[0].plot(x, y)
axs[0].set_xlim(-0.5, 8)
axs[0].set_xlabel('x')
axs[0].set_ylabel('pdf(x)')
# Right plot: logarithmic scale on x-axis
# in incomes.txt came from the distribution in part (b)
log_lik_h0 = log_lik_norm(income, mu, sigma, cutoff)
log_lik_mle = log_lik_norm(income, mu_MLE, sig_MLE, cutoff)
LR_val = 2 * (log_lik_mle - log_lik_h0)
pval_h0 = 1.0 - sts.chi2.cdf(LR_val, 2) #area under the graph
print('1-d. Chi squared of H0 with 2 degrees of freedom p-value is ', pval_h0)
print(
'P-value is in the rejection area so that we can conclude that the data \n in income.txt\
is not came from the distribution in part(b).')
print("")
# 1 - e
# According to the part (c), estimated the probability
lognorm_mle = sts.lognorm(s=sig_MLE, scale=np.exp(mu_MLE))
cdf_mle_100k = lognorm_mle.cdf(100000)
cdf_mle_75k = lognorm_mle.cdf(75000)
gt_than_100k = 1 - cdf_mle_100k
ls_than_75k = cdf_mle_75k
print(
'1-e. The probability that the student will earn more than $100,000 is \n {:.2f}%.'
.format(gt_than_100k * 100))
print(
'The probability that the student will earn less than $75,000 is \n {:.2f}%.'
.format(ls_than_75k * 100))
print("")
print("")
'''
def __call__(self, mean, stddev):
func = lognorm(scale=np.exp(mean), s=stddev)
return func.cdf
# In[85]:
#4
for parametro in informacoes:
a = sc.probplot(parametro.ordem,
dist=sc.expon(scale=(1 / parametro.eLambda)),
plot=plot)
plot.title('Exponencial x %s' % parametro.nome)
plot.show()
b = sc.probplot(parametro.ordem,
dist=sc.norm(loc=parametro.media, scale=parametro.var),
plot=plot)
plot.title('Normal x %s' % parametro.nome)
plot.show()
c = sc.probplot(parametro.ordem,
dist=sc.lognorm(s=(parametro.logvar)**0.5,
scale=math.exp(parametro.logmedia)),
plot=plot)
plot.title('Lognormal x %s' % parametro.nome)
plot.show()
d = sc.probplot(parametro.ordem,
dist=sc.weibull_min(c=parametro.wshape,
loc=parametro.wloc,
scale=parametro.wscale),
plot=plot)
plot.title('Weibull x %s' % parametro.nome)
plot.show()
# In[86]:
#5
d = 1.36 / ((len(idade.dados))**0.5) #d adequado para a situação
def saturation(self):
""" Upper bound on support. """
return st.lognorm(self.sigma, scale=np.exp(self.mu)).ppf(0.999)
def saturation(self):
""" Upper bound on support. """
return st.lognorm(self.loc[2], scale=np.exp(self.scale[2])).ppf(0.999)
# specify prior distributions using stats.scipy for each parameter (independently)
# available options (univariate): https://docs.scipy.org/doc/scipy/reference/stats.html
from scipy import stats
from spux.distributions.tensor import Tensor
from spux.utils import transforms
distributions = {}
# model parameters
distributions['drift'] = stats.uniform(loc=-1, scale=2)
distributions['volatility'] = stats.uniform(loc=0.2, scale=1)
# observational error model parameters
distributions['error'] = stats.lognorm(**transforms.logmeanstd(logm=1, logs=1))
# construct a joint distribution for a vector of independent parameters by tensorization
prior = Tensor(distributions)
from units import units
prior.setup(units=units['parameters'])
import numpy as np from utils import ContinuousDistribution, DiscreteDistribution from MDP.mdp_solver import ValueIteration # # searching robot environment # state_names = ['high', 'low'] # action_names = ['wait', 'recharge', 'search'] # P = np.array([[[1, 0], [1, 0], [0.8, 0.2]], [[0, 1], [1, 0], [0.6, 0.4]]]) # R = np.array([[[2, 0], [0, 0], [5, 5]], [[0, 2], [0, 0], [-3, 5]]]) # bidding MDP n_bidders = 10 dst = stats.lognorm(s=0.5, loc=0, scale=np.exp(1)) dst = stats.uniform(0,10) dist = ContinuousDistribution(dst) dst = stats.geom(p=0.3) dist = DiscreteDistribution(dst) print(dist.exp_fos(n_bidders)) state_names = ['win', 'lose'] budget = 10 states = np.arange(budget+1) actions = np.arange(budget+1) P = np.zeros((states.size, actions.size, states.size)) R = np.zeros((states.size, actions.size, states.size))
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri May 29 22:30:05 2020
@author: huangxiaoyi
"""
import numpy as np
import scipy.stats as st
import matplotlib.pyplot as plt
a = np.linspace(0,50,25)
val = st.lognorm(1,1).pdf(a)#very useful lib to calculate density
val2 = st.lognorm(2,1).pdf(a)
val3 = st.lognorm(3,1).pdf(a)
fig, ax = plt.subplots()
ax.plot(val,'g--',label='m=1')
ax.plot(val2,'b:',label='m=2')
ax.plot(val3,'r',label='m=3')
legend = ax.legend(loc='upper right', shadow=True)
plt.xlabel('success')
plt.ylabel('probability')
cdf = st.lognorm(1,1).cdf(a)##compute culmulated probability density
cdf2 = st.lognorm(2,1).cdf(a)
cdf3 = st.lognorm(3,1).cdf(a)
fig2, bx = plt.subplots()
bx.plot(cdf,'g--',label='m=1')
bx.plot(cdf2,'b:',label='m=2')
bx.plot(cdf3,'r',label='m=3')
legend = bx.legend(loc='upper right', shadow=True)
plt.xlabel('success')
def lognorm(mu: float, sigma2: float):
assert sigma2 > 0
return stats.lognorm(s=np.sqrt(sigma2), scale=np.exp(mu))
def survival_times(self):
# base the survival times upon the parameters mu and sigma
return {state: lognorm(s=self.s[self._ix[state]], loc=0, scale=self.scale[self._ix[state]]) for state in self.states}
def __call__(self, x):
""" Log-normal function from scipy """
return stats.lognorm(self._sigma, scale=self._mu).pdf(x * self.j_ref())
s = 0.954 mean, var, skew, kurt = lognorm.stats(s, moments='mvsk') # Display the probability density function (``pdf``): x = np.linspace(lognorm.ppf(0.01, s), lognorm.ppf(0.99, s), 100) ax.plot(x, lognorm.pdf(x, s), 'r-', lw=5, alpha=0.6, label='lognorm pdf') # Alternatively, the distribution object can be called (as a function) # to fix the shape, location and scale parameters. This returns a "frozen" # RV object holding the given parameters fixed. # Freeze the distribution and display the frozen ``pdf``: rv = lognorm(s) ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf') # Check accuracy of ``cdf`` and ``ppf``: vals = lognorm.ppf([0.001, 0.5, 0.999], s) np.allclose([0.001, 0.5, 0.999], lognorm.cdf(vals, s)) # True # Generate random numbers: r = lognorm.rvs(s, size=1000) # And compare the histogram: ax.hist(r, normed=True, histtype='stepfilled', alpha=0.2)
def lognormal(media, varianza):
from scipy.stats import lognorm
return lognorm(media, varianza)
import cmdstanpy
import os
cmdstanpy.utils.cxx_toolchain_path()
#%% [markdown]
## Generate Claims
# Simple generator of lognormal claims
#%%
# parameters
mu = 0.5
sigma = 1
dist = stats.lognorm(np.exp(mu), sigma)
# generate claims
claims = dist.rvs(size=1000)
# graph
sns.distplot(claims)
#%% [markdown]
# \begin{aligned}
# X_i & \sim LN(mu, sigma) \\
# mu & \sim N( \mu_{mu}, 1 ) \\
# sigma & \sim exp( \lambda_{sigma} ) \\
# \mu_{mu} & = 1 \\
# \lambda_{sigma} & = 1 \\
# \end{aligned}
### TUNE HYPERPARAMETERS HERE ###
CONFIG = {
"env": "Taxi-v3",
"total_eps": 100000,
"eps_max_steps": 50,
"eval_episodes": 500,
"eval_freq": 1000,
"gamma": 0.99,
"alpha": 0.15,
"epsilon": 0.9,
}
if __name__ == "__main__":
# env = gym.make(CONFIG["env"])
dist = ContinuousDistribution(stats.lognorm(s=0.5, loc=0, scale=np.exp(0.25)))
n_bidders = 10
env = my_envs.AuctionEnvV1(dist, maxbudget=25, n_bidders=n_bidders, maxsteps=CONFIG["eps_max_steps"], action_granularity=0.25)
total_reward, evaluation_return_means, evaluation_negative_returns, q_table, obs_counter, episode_lens = train(env, CONFIG)
np.save("Qlearning_qtable.npy", q_table)
np.save("Qlearning_obscount.npy", obs_counter)
np.save("Qlearning_epslens.npy", episode_lens)
print()
print(f"Total reward over training: {total_reward}\n")
arr = np.array(evaluation_return_means)
fig = plt.figure(figsize=(6,5))
ax1 = fig.add_subplot(311)
ax2 = fig.add_subplot(312)
ax3 = fig.add_subplot(313, sharex=ax2)
[Normal, Gamma, Beta, InverseGamma, LogNormal])
def test_prior_equality(Prior):
assert Prior() == Prior()
@pytest.mark.parametrize(
'Prior, log, dlog, scipy_fun',
[
(Normal, -0.9639385332046727, -0.3, stats.norm(loc=0, scale=1)),
(Beta, 0.27990188513281833, 3.8095238095238098, stats.beta(a=3, b=3)),
(Gamma, -3.4010927892118175, 5.666666666666667,
stats.gamma(a=3, scale=1 / 1)),
(InverseGamma, 0.7894107034104656, -2.222222222222223,
stats.invgamma(a=3, scale=1)),
(LogNormal, -0.43974098565696607, 0.6799093477531204,
stats.lognorm(loc=0, s=1)),
],
)
def test_log_pdf(Prior, log, dlog, scipy_fun, N):
prior = Prior()
rvs = prior.random(N)
x = np.random.uniform()
assert prior.log_pdf(0.3) == pytest.approx(log)
assert prior.dlog_pdf(0.3) == pytest.approx(dlog)
assert prior.mean == pytest.approx(np.mean(rvs),
abs=3 * np.std(rvs) / np.sqrt(N))
assert prior.log_pdf(x) == pytest.approx(scipy_fun.logpdf(x))
@pytest.mark.parametrize('Prior',
print("Суженное множество:")
print("p=", p)
print("delta=", delta)
print("m1=", m1)
# plotting bar chart
X = np.array([(delta[j] + delta[j + 1]) / 2 for j in range(m1)])
Y = np.array([p[j] / (delta[j + 1] - delta[j]) for j in range(m1)])
fig = plt.figure(dpi=100)
plt.bar(X, Y, 1)
# set interval min=-inf; max=inf
delta[0] = -np.inf
delta[-1] = np.inf
# setting distribution type
if data['low'] == 'lognorm':
mu, sigma = np.log(x).mean(), np.sqrt(np.log(x).var())
dist = stats.lognorm(sigma, scale=np.exp(mu))
print(mu, sigma)
elif data['low'] == 'exp':
la = 1 / x.mean()
dist = stats.expon(scale=1 / la)
print(la)
else:
dist = stats.uniform(a, b)
print(a, b)
# setting real percentage of fall into intervals multiply by N
nt = np.array(
[dist.cdf(delta[j + 1]) - dist.cdf(delta[j]) for j in range(m1 - 1)]) * N
print("nt", nt)
# calculating chi
chi = np.array([(p[j] - nt[j])**2 / nt[j] for j in range(m1 - 1)]).sum()
# finding table value
_DIST_MAP = {
dist.BernoulliProbs: lambda probs: osp.bernoulli(p=probs),
dist.BernoulliLogits: lambda logits: osp.bernoulli(p=_to_probs_bernoulli(logits)),
dist.Beta: lambda con1, con0: osp.beta(con1, con0),
dist.BinomialProbs: lambda probs, total_count: osp.binom(n=total_count, p=probs),
dist.BinomialLogits: lambda logits, total_count: osp.binom(n=total_count, p=_to_probs_bernoulli(logits)),
dist.Cauchy: lambda loc, scale: osp.cauchy(loc=loc, scale=scale),
dist.Chi2: lambda df: osp.chi2(df),
dist.Dirichlet: lambda conc: osp.dirichlet(conc),
dist.Exponential: lambda rate: osp.expon(scale=np.reciprocal(rate)),
dist.Gamma: lambda conc, rate: osp.gamma(conc, scale=1./rate),
dist.HalfCauchy: lambda scale: osp.halfcauchy(scale=scale),
dist.HalfNormal: lambda scale: osp.halfnorm(scale=scale),
dist.InverseGamma: lambda conc, rate: osp.invgamma(conc, scale=rate),
dist.LogNormal: lambda loc, scale: osp.lognorm(s=scale, scale=np.exp(loc)),
dist.MultinomialProbs: lambda probs, total_count: osp.multinomial(n=total_count, p=probs),
dist.MultinomialLogits: lambda logits, total_count: osp.multinomial(n=total_count,
p=_to_probs_multinom(logits)),
dist.MultivariateNormal: _mvn_to_scipy,
dist.LowRankMultivariateNormal: _lowrank_mvn_to_scipy,
dist.Normal: lambda loc, scale: osp.norm(loc=loc, scale=scale),
dist.Pareto: lambda alpha, scale: osp.pareto(alpha, scale=scale),
dist.Poisson: lambda rate: osp.poisson(rate),
dist.StudentT: lambda df, loc, scale: osp.t(df=df, loc=loc, scale=scale),
dist.Uniform: lambda a, b: osp.uniform(a, b - a),
}
CONTINUOUS = [
T(dist.Beta, 1., 2.),
def get_random_rect_sz(min_x, max_x, shape, loc, scale):
dist = stats.lognorm(shape, loc, scale)
size = dist.rvs()
size = size * (max_x - min_x) + min_x
return (size)
def check_one_value(params): # in prior_samples:
logLstar, logPhiStar, alpha = params
logLmin = 8.5
#distro=gamma(alpha,loc=0,scale=10**logLstar) #this choice of alpha means that the LF form is NOT same as Mike's but rather has alpha in the exponent when written as dN/dV/dlogL
vol_COS = 20189.
vol_GN = 131042.
normaliz = fp.gammainc(alpha, 10**(logLmin - logLstar))
Numexp_COS = 10**(
logPhiStar
) * normaliz * vol_COS #*(1-distro.cdf(1e9)) #This is how many galaxies in volume vol, are expected on average
Numexp_GN = 10**(logPhiStar) * normaliz * vol_GN
#plt.loglog(np.logspace(9,12,100),distro.pdf(np.logspace(9,12,100)))
N_to_use_COS = poisson.rvs(Numexp_COS)
N_to_use_GN = poisson.rvs(Numexp_GN)
Lprimes_COS = simulate_schechter_distribution(
alpha, 10**logLstar, 10**logLmin,
N_to_use_COS) #distro.rvs(size=N_to_use_COS)
Lprimes_GN = simulate_schechter_distribution(
alpha, 10**logLstar, 10**logLmin,
N_to_use_GN) #distro.rvs(size=N_to_use_GN)
#while(np.any(Lprimes<1e9)):
# Lprimes=distro.rvs(size=N_to_use)
freq_list_COS = 31 + 8 * np.random.random(N_to_use_COS)
freq_list_GN = 30 + 8 * np.random.random(N_to_use_GN)
sdv_list_COS = Lprimes_COS / L_prime_freq_conversion[(
(freq_list_COS - 30) / 9.0e-5).astype(int)]
sdv_list_GN = Lprimes_GN / L_prime_freq_conversion[(
(freq_list_GN - 30) / 9.0e-5).astype(int)]
#sdv_list_COS=np.array([Lprimes_COS[idx]/calc_L_prime(1,fre) for idx,fre in enumerate(freq_list_COS)])
#sdv_list_GN=np.array([Lprimes_GN[idx]/calc_L_prime(1,fre) for idx,fre in enumerate(freq_list_GN)])
spat_real_COS = np.random.choice(3,
size=N_to_use_COS,
replace=True,
p=[0.88, 0.1, 0.02])
freq_real_COS = np.random.choice(3,
size=N_to_use_COS,
replace=True,
p=[0.34, 0.33, 0.33])
spat_real_GN = np.random.choice(3,
size=N_to_use_GN,
replace=True,
p=[0.88, 0.1, 0.02])
freq_real_GN = np.random.choice(3,
size=N_to_use_GN,
replace=True,
p=[0.34, 0.33, 0.33])
compl_params_fit_COS = np.array([[[0.51093145, 0.02771134],
[0.41731388, 0.03699222],
[0.48504448, 0.04833295]],
[[0.52961387, 0.06536336],
[0.47647305, 0.09091878],
[0.43582843, 0.11752236]],
[[0.48816207, 0.1055706],
[0.41942854, 0.15440935],
[0.43130629, 0.21278495]]])
compl_params_fit_GN = np.array([[[0.30244889, 0.0647361],
[0.19111455, 0.0863606],
[0.26355572, 0.11940371]],
[[0.34815344, 0.11987698],
[0.3085827, 0.17502077],
[0.3268172, 0.23117797]],
[[0.37420752, 0.21330359],
[0.30220447, 0.30313399],
[0.29627785, 0.40176673]]])
myfit = lambda f, d, f0: max(0, 1 - (1. / (f + d) * np.exp(-f / f0)))
completenesses_COS = [
myfit(sdv, *compl_params_fit_COS[spat, freq])
for sdv, spat, freq in zip(sdv_list_COS, spat_real_COS, freq_real_COS)
]
completenesses_GN = [
myfit(sdv, *compl_params_fit_GN[spat, freq])
for sdv, spat, freq in zip(sdv_list_GN, spat_real_GN, freq_real_GN)
]
observed_COS = np.random.random(size=N_to_use_COS) < completenesses_COS
Nobs_COS = np.sum(observed_COS)
observed_GN = np.random.random(size=N_to_use_GN) < completenesses_GN
Nobs_GN = np.sum(observed_GN)
#now take care of the real candidates
purities_COS = np.array([
max(0, obj.purity *
np.random.normal(loc=1., scale=1.)) if obj.purity < 1 else 1
for obj in objects_COS
])
purities_GN = np.array([
max(0, obj.purity *
np.random.normal(loc=1., scale=1.)) if obj.purity < 1 else 1
for obj in objects_GN
])
#purities_COS=np.array([np.random.random()*obj.purity if obj.purity<1 else 1 for obj in objects_COS ])
#purities_GN=np.array([np.random.random()*obj.purity if obj.purity<1 else 1 for obj in objects_GN ])
selected_candidates_COS = np.random.random(
size=len(objects_COS)) < purities_COS
Nselected_COS = np.sum(selected_candidates_COS)
selected_candidates_GN = np.random.random(
size=len(objects_GN)) < purities_GN
Nselected_GN = np.sum(selected_candidates_GN)
#print N_to_use_COS,N_to_use_GN,Nobs_COS,Nobs_GN,'real:',Nselected_COS,Nselected_GN
if np.absolute(Nselected_COS - Nobs_COS) <= 1 and np.absolute(
Nselected_GN - Nobs_GN) <= 1 and Nobs_GN > 0:
#print 'Match!'
Lprime_observed_real_COS = np.array([
obj.L_prime for idx, obj in enumerate(objects_COS)
if selected_candidates_COS[idx]
])
Lprime_observed_real_GN = np.array([
obj.L_prime for idx, obj in enumerate(objects_GN)
if selected_candidates_GN[idx]
])
SNRbins = np.arange(4, 7, .1)
SNRbin_idx = np.digitize(5.5, SNRbins) - 1 #I set this to 5.5
observed_Lprime_COS = []
for idx in range(Nobs_COS):
inj_spa_COS = spat_real_COS[observed_COS][idx]
#inj_fre=freq_real[observed][idx]
spat_distrib_COS = [
np.mean([
likelihood_COS[inj_spa_COS][key][SNR_b]
for SNR_b in range(SNRbin_idx - 3, SNRbin_idx + 3)
]) for key in [-1, 0, 2, 4, 6, 8, 10, 12]
]
spat_obs_idx_COS = min(
5,
np.random.choice(8, size=1, replace=True,
p=spat_distrib_COS)[0])
spat_obs_COS = [-1, 0, 2, 4, 6, 8][spat_obs_idx_COS]
#freq_distrib=[np.mean([likelihood_freq[inj_fre][key][SNR_b] for SNR_b in range(SNRbin_idx-3,SNRbin_idx+3)]) for key in [4,8,12,16,20]]
#freq_obs=[4,8,12,16,20][np.random.choice(5, size=1, replace=True, p=freq_distrib)[0]]
#for the given intrinsic and observed properties, and the SNR=5.5, what flux ratio do we expect?
lognorm_par_COS = lognorm_params_given_inj_and_meas_COS[
spat_obs_idx_COS, inj_spa_COS]
from scipy.stats import lognorm
flux_correct_COS = lognorm(s=lognorm_par_COS[1],
scale=np.exp(lognorm_par_COS[0])).rvs()
observed_flux_COS = sdv_list_COS[observed_COS][
idx] * flux_correct_COS
observed_Lprime_COS.append(Lprimes_COS[observed_COS][idx] *
flux_correct_COS)
observed_Lprime_GN = []
for idx in range(Nobs_GN):
inj_spa_GN = spat_real_GN[observed_GN][idx]
#inj_fre=freq_real[observed][idx]
spat_distrib_GN = [
np.mean([
likelihood_GN[inj_spa_GN][key][SNR_b]
for SNR_b in range(SNRbin_idx - 3, SNRbin_idx + 3)
]) for key in [-1, 0, 2, 4, 6, 8, 10]
]
spat_obs_idx_GN = min(
5,
np.random.choice(7, size=1, replace=True,
p=spat_distrib_GN)[0])
spat_obs_GN = [-1, 0, 2, 4, 6, 8][spat_obs_idx_GN]
#freq_distrib=[np.mean([likelihood_freq[inj_fre][key][SNR_b] for SNR_b in range(SNRbin_idx-3,SNRbin_idx+3)]) for key in [4,8,12,16,20]]
#freq_obs=[4,8,12,16,20][np.random.choice(5, size=1, replace=True, p=freq_distrib)[0]]
#for the given intrinsic and observed properties, and the SNR=5.5, what flux ratio do we expect?
lognorm_par_GN = lognorm_params_given_inj_and_meas_GN[
spat_obs_idx_GN, inj_spa_GN]
from scipy.stats import lognorm
flux_correct_GN = lognorm(s=lognorm_par_GN[1],
scale=np.exp(lognorm_par_GN[0])).rvs()
observed_flux_GN = sdv_list_GN[observed_GN][idx] * flux_correct_GN
observed_Lprime_GN.append(Lprimes_GN[observed_GN][idx] *
flux_correct_GN)
allmatched = True
for obs_real_Lprime in Lprime_observed_real_COS:
if np.min(
np.absolute(obs_real_Lprime -
np.array(observed_Lprime_COS)) /
obs_real_Lprime) > .2:
#print np.min(np.absolute(obs_real_Lprime-np.array(observed_Lprime_COS))/obs_real_Lprime)
allmatched = False
for obs_real_Lprime in Lprime_observed_real_GN:
if np.min(
np.absolute(obs_real_Lprime - np.array(observed_Lprime_GN))
/ obs_real_Lprime) > .2:
#print np.min(np.absolute(obs_real_Lprime-np.array(observed_Lprime_GN))/obs_real_Lprime)
allmatched = False
if allmatched:
#print 'amazing this works!'#,'real:',Lprime_observed_real,'simul:',observed_Lprime
return params
def d_lnorm(meanlog, sdlog):
return SpDouble(sts.lognorm(s=np.exp(sdlog),
scale=np.exp(np.exp(meanlog))))
def plot_multiplicative(self, T, npaths=25, show_trend=True):
"""
Plots for the multiplicative decomposition
"""
# Pull out right sizes so we know how to increment
nx, nk, nm = self.nx, self.nk, self.nm
# Matrices for the multiplicative decomposition
nu_tilde, H, g = self.multiplicative_decomp()
# Allocate space (nm is the number of functionals - we want npaths for each)
mpath_mult = np.empty((nm * npaths, T))
mbounds_mult = np.empty((nm * 2, T))
spath_mult = np.empty((nm * npaths, T))
sbounds_mult = np.empty((nm * 2, T))
tpath_mult = np.empty((nm * npaths, T))
ypath_mult = np.empty((nm * npaths, T))
# Simulate for as long as we wanted
moment_generator = self.lss.moment_sequence()
# Pull out population moments
for t in range(T):
tmoms = next(moment_generator)
ymeans = tmoms[1]
yvar = tmoms[3]
# Lower and upper bounds - for each multiplicative functional
for ii in range(nm):
li, ui = ii * 2, (ii + 1) * 2
Mdist = lognorm(np.asscalar(np.sqrt(yvar[nx+nm+ii, nx+nm+ii])),
scale=np.asscalar( np.exp( ymeans[nx+nm+ii]- \
t*(.5)*np.expand_dims(np.diag(H @ H.T),1)[ii])))
Sdist = lognorm(np.asscalar(
np.sqrt(yvar[nx + 2 * nm + ii, nx + 2 * nm + ii])),
scale=np.asscalar(
np.exp(-ymeans[nx + 2 * nm + ii])))
mbounds_mult[li:ui, t] = Mdist.ppf([.01, .99])
sbounds_mult[li:ui, t] = Sdist.ppf([.01, .99])
# Pull out paths
for n in range(npaths):
x, y = self.lss.simulate(T)
for ii in range(nm):
ypath_mult[npaths * ii + n, :] = np.exp(y[nx + ii, :])
mpath_mult[npaths * ii + n, :] = np.exp(
y[nx + nm + ii, :] - np.arange(T) *
(.5) * np.expand_dims(np.diag(H @ H.T), 1)[ii])
spath_mult[npaths * ii +
n, :] = 1 / np.exp(-y[nx + 2 * nm + ii, :])
tpath_mult[npaths * ii + n, :] = np.exp(
y[nx + 3 * nm + ii, :] + np.arange(T) *
(.5) * np.expand_dims(np.diag(H @ H.T), 1)[ii])
mult_figs = []
for ii in range(nm):
li, ui = npaths * (ii), npaths * (ii + 1)
LI, UI = 2 * (ii), 2 * (ii + 1)
mult_figs.append(
self.plot_given_paths(T,
ypath_mult[li:ui, :],
mpath_mult[li:ui, :],
spath_mult[li:ui, :],
tpath_mult[li:ui, :],
mbounds_mult[LI:UI, :],
sbounds_mult[LI:UI, :],
1,
show_trend=show_trend))
mult_figs[ii].suptitle(
r'Multiplicative decomposition of $y_{%s}$' % str(ii + 1),
fontsize=14)
return mult_figs