from iminuit import Minuit
def cost(x, y, z):
return (x - 1) ** 2 + (y - x) ** 2 + (z - 2) ** 2
cost.errordef = Minuit.LEAST_SQUARES
m = Minuit(cost, x=0, y=0, z=0)
m.migrad()
m.draw_mnprofile("y")
def test_typo():
with pytest.raises(RuntimeError):
Minuit(func4, printlevel=0)
def test_minos_single_nonsense_variable():
m = Minuit(func3, pedantic=False, print_level=0)
m.migrad()
with pytest.raises(RuntimeError):
m.minos('nonsense')
def fit_ringdown(int_index):
#print fterm_prior, fterm_prior_width
t_mean = np.mean(all_time[int_index])
t_last = np.max(all_time[int_index]) + 0.25
# bu.progress_bar(i, last_ind+1)
fit_inds = all_time_flat < t_last
derp_inds = all_time_flat < fit_end_time
npts = np.sum(fit_inds)
xdat = all_time_flat[fit_inds]
ydat = all_freq_flat[fit_inds]
yerr = all_freq_err_flat[fit_inds]
#yerr = np.sqrt(ydat)
#yerr = np.random.randn(npts) * np.std(yerr) + np.mean(yerr)
if priors:
fterm_init = prior_data[0]
def chisquare_1d(tau, fterm):
resid = ydat - fit_fun(xdat, t0_line, tau, fterm)
prior = (fterm - prior_data[0])**2 / prior_data[1]**2
chisq = (1.0 / (npts - 1.0)) * np.sum(resid**2 / yerr**2)
return chisq + prior
elif manual_priors:
fterm_init = fterm_prior
def chisquare_1d(tau, fterm):
resid = ydat - fit_fun(xdat, t0_line, tau, fterm)
prior = (fterm - fterm_prior)**2 / fterm_prior_width**2
chisq = (1.0 / (npts - 1.0)) * np.sum(resid**2 / yerr**2)
return chisq + prior
else:
fterm_init = 0.0
def chisquare_1d(tau, fterm):
resid = ydat - fit_fun(xdat, t0_line, tau, fterm)
chisq = (1.0 / (npts - 1.0)) * np.sum(resid**2 / yerr**2)
return chisq
# m=Minuit(chisquare_1d,
# f0=50000.0,
# tau = 1500.0, # set start parameter
# limit_tau = (500.0, 4000.0), # if you want to limit things
# #fix_a = "True", # you can also fix it
# fopt = 1000.0,
# limit_fopt = (0.0, 10000.0),
# errordef = 1,
# print_level = 0,
# pedantic=False)
# m.migrad(ncall=500000)
m2 = Minuit(
chisquare_1d,
#t0 = 0.0,
#fix_t0 = t0_line,
#limit_t0 = (-5, 5),
tau=two_point_tau, # set start parameter
#fix_tau = True,
#limit_tau = (500.0, 4000.0), # if you want to limit things
fterm=fterm_init, # set start parameter
fix_fterm=fix_fterm,
# limit_tau = (500.0, 4000.0), # if you want to limit things
#fix_a = "True", # you can also fix it
# limit_fopt = (0.0, 10000.0),
errordef=1,
print_level=0,
pedantic=False)
m2.migrad(ncall=500000)
# plt.figure()
# m.draw_mnprofile('tau', bound = 3, bins = 50)
# plt.figure()
# m2.draw_mnprofile('tau', bound = 3, bins = 50)
# plt.show()
# p0 = [f0, 1500.0, 1000.0]
# popt = [m2.values['t0'], m2.values['tau'], m2.values['fterm']]
# # print tau_many
# # print tau_many_2
# if m.values['tau'] < 1200:
# plt.figure()
# plt.plot(all_time_flat[derp_inds], all_freq_flat[derp_inds])
# plt.plot(all_time_flat[fit_inds], all_freq_flat[fit_inds])
# plt.plot(all_time_flat[derp_inds], exp_decay(all_time_flat[derp_inds], *p0), '--', \
# color='k', lw=4, alpha=0.5)
# plt.plot(all_time_flat[derp_inds], exp_decay(all_time_flat[derp_inds], *popt), '--', \
# color='r', lw=4, alpha=0.5)
# plt.figure()
# plt.plot(yerr)
# plt.show()
try:
minos = m2.minos()
return [t_mean, minos['tau']['min'], minos['tau']['upper'], \
minos['tau']['lower'], minos['fterm']['min']]
except:
return [t_mean, m2.values['tau'], m2.errors['tau'], \
m2.errors['tau'], m2.values['fterm']]
m = Minuit(
least_squares,
CONC=params["CONC"]["value"],
SPIN=params["SPIN"]["value"],
B=params["B"]["value"],
DIF=params["DIF"]["value"],
TAUS0=params["TAUS0"]["value"],
TAUV=params["TAUV"]["value"],
PROPT=params["PROPT"]["value"],
gl=params["gl"]["value"],
limit_CONC=(float(params["CONC"]["minM"]),
float(params["CONC"]["maxM"])),
limit_SPIN=(float(params["SPIN"]["minM"]),
float(params["SPIN"]["maxM"])),
limit_B=(float(params["B"]["minM"]), float(params["B"]["maxM"])),
limit_DIF=(float(params["DIF"]["minM"]), float(params["DIF"]["maxM"])),
limit_TAUS0=(float(params["TAUS0"]["minM"]),
float(params["TAUS0"]["maxM"])),
limit_TAUV=(float(params["TAUV"]["minM"]),
float(params["TAUV"]["maxM"])),
limit_PROPT=(float(params["PROPT"]["minM"]),
float(params["PROPT"]["maxM"])),
limit_gl=(float(params["gl"]["minM"]), float(params["gl"]["maxM"])),
fix_CONC=params["CONC"]["fixed"],
fix_SPIN=params["SPIN"]["fixed"],
fix_B=params["B"]["fixed"],
fix_DIF=params["DIF"]["fixed"],
fix_TAUS0=params["TAUS0"]["fixed"],
fix_TAUV=params["TAUV"]["fixed"],
fix_PROPT=params["PROPT"]["fixed"],
fix_gl=params["gl"]["fixed"],
)
def minimise(self, params, step, limits, minimiser_name="minuit"):
"""
Parameters
----------
params
step
limits
minimiser_name
Returns
-------
"""
if minimiser_name == "minuit":
min = Minuit(self.get_likelihood,
print_level=1,
source_x=params[0],
error_source_x=step[0],
limit_source_x=limits[0],
source_y=params[1],
error_source_y=step[1],
limit_source_y=limits[1],
core_x=params[2],
error_core_x=step[2],
limit_core_x=limits[2],
core_y=params[3],
error_core_y=step[3],
limit_core_y=limits[3],
energy=params[4],
error_energy=step[4],
limit_energy=limits[4],
x_max_scale=params[5], error_x_max_scale=step[5],
limit_x_max_scale=limits[5],
fix_x_max_scale=False,
errordef=1)
min.migrad()
min.tol *= 1000
min.set_strategy(0)
# Perform minimisation
fit_params = min.values
errors = min.errors
return (fit_params["source_x"], fit_params["source_y"], fit_params["core_x"],
fit_params["core_y"], fit_params["energy"], fit_params[
"x_max_scale"]),\
(errors["source_x"], errors["source_y"], errors["core_x"],
errors["core_x"], errors["energy"], errors["x_max_scale"])
elif minimiser_name in ("lm", "trf", "dogleg"):
self.array_return = True
min = least_squares(self.get_likelihood_min, params,
method=minimiser_name,
x_scale=step,
xtol=1e-10,
ftol=1e-10
)
return min.x, (0, 0, 0, 0, 0, 0)
else:
min = minimize(self.get_likelihood_min, params,
method=minimiser_name,
bounds=limits
)
return min.x, (0, 0, 0, 0, 0, 0)
prob = np.loadtxt(f'{photon_base_path}/prob{i:03.0f}.dat')
for j in range(nsim):
loglikes[j, 0] = - gta.like()
p = prob[j]
def cost_func_alps(norm, alpha, beta):
dnde = p * norm * 1.0e-11 * np.power((x / Eb) , -(alpha + beta * 1.0e-1 * np.log((x / Eb))))
gta.set_source_dnde(source, dnde)
return gta.like()
def cost_func(norm, alpha, beta):
dnde = norm * 1.0e-11 * np.power((x / Eb) , -(alpha + beta * 1.0e-1 * np.log((x / Eb))))
gta.set_source_dnde(source, dnde)
return gta.like()
m = Minuit(cost_func_alps, errordef=0.5, norm=norm, alpha=alpha, beta=beta,\
error_norm=norm_err, error_alpha=alpha_err, error_beta=beta_err,\
limit_norm=(0, 100), limit_alpha=(-5, 5), limit_beta=(-5, 10), print_level=1)
r = m.migrad()
loglikes[j, 1] = -gta.like()
gta.fit(opimizer='NEWMINUIT', reoptimize=True)
loglikes[j, 2] = -gta.like()
m = Minuit(cost_func_alps, errordef=0.5, norm=norm, alpha=alpha, beta=beta,\
error_norm=norm_err, error_alpha=alpha_err, error_beta=beta_err,\
limit_norm=(0, 100), limit_alpha=(-5, 5), limit_beta=(-5, 10), print_level=1)
r = m.migrad()
loglikes[j, 3] = -gta.like()
gta.fit(opimizer='NEWMINUIT', reoptimize=True)
loglikes[j, 4] = -gta.like()
try:
gta.load_roi(roi_file)
except:
def chi2_fit(func,
x,
y,
yerr,
get_values=False,
pedantic=False,
print_level=0,
latex_format=False,
**kwdarg):
'''
ChiSquare fit of a given function to a given data set.
Returns the fitted parameters for further plotting.
**kwdarg allows the user to specify initial parameter
values and fix values using the syntax from Minuit
'''
chi2obj = Chi2Regression(func, x, y, yerr)
minuit_obj = Minuit(chi2obj,
pedantic=pedantic,
print_level=print_level,
**kwdarg)
minuit_obj.migrad()
if (not minuit_obj.get_fmin().is_valid): # Check if the fit converged
print(" WARNING: The ChiSquare fit DID NOT converge!!!")
Chi2_value = minuit_obj.fval # The Chi2 value
NvarModel = len(minuit_obj.args)
Ndof = len(x) - NvarModel
ProbChi2 = stats.chi2.sf(Chi2_value, Ndof)
if latex_format:
print(
r'''----------------------------------------------------------------------------------
NB! Units, caption, label and sometimes parameter names must be changed in LaTex.
----------------------------------------------------------------------------------
\begin{table}[b]
\centering
\begin{tabular}{lrr}
\hline
\hline
Parameter & Value (Unit) & Unc. (Unit) \\
\hline''')
for name in minuit_obj.parameters:
print(
f' ${name}$ & ${minuit_obj.values[name]:.5f}$ & ${minuit_obj.errors[name]:.5f}$ \\\ '
)
print(r''' \hline
\hline''')
print(
r' $\chi^2$-value = {0:.3f} & Ndof = {1} & $\chi^2$-prob = {2:.3f} \\'
.format(Chi2_value, Ndof, ProbChi2))
print(r''' \hline
\hline
\end{tabular}
\caption{Results of $\chi^2$-fit.}
\label{tab:chi2_fit}
\end{table}''')
else:
print(f'''
_____________________________________________________
-----------------------------------------------------
ChiSquare Fit Results
-----------------------------------------------------
Chi2-value = {Chi2_value:.3f}
Ndof = {Ndof}
Chi2-prob = {ProbChi2:.2%}
-----------------------------------------------------''')
for name in minuit_obj.parameters:
print(
f'\n Chi2 Fit result: {name} = {minuit_obj.values[name]:.5f} +/- {minuit_obj.errors[name]:.5f}'
)
print(' _____________________________________________________')
if get_values:
return minuit_obj.args, Chi2_value, Ndof, ProbChi2
else:
return minuit_obj.args
def minuit():
m = Minuit(lambda x: x**2, pedantic=False)
m.migrad()
return m
def fit_muon(self, centre_x, centre_y, radius, pixel_x, pixel_y, image):
"""
Parameters
----------
centre_x: float
Centre of muon ring in the field of view from circle fitting
centre_y: float
Centre of muon ring in the field of view from circle fitting
radius: float
Radius of muon ring from circle fitting
pixel_x: ndarray
X position of pixels in image from circle fitting
pixel_y: ndarray
Y position of pixel in image from circle fitting
image: ndarray
Amplitude of image pixels
Returns
-------
MuonIntensityParameters
"""
# First store these parameters in the class so we can use them in minimisation
self.image = image
self.pixel_x = pixel_x.to(u.deg)
self.pixel_y = pixel_y.to(u.deg)
self.unit = pixel_x.unit
radius.to(u.deg)
centre_x.to(u.deg)
centre_y.to(u.deg)
# Return interesting stuff
fitoutput = MuonIntensityParameter()
init_params = {}
init_errs = {}
init_constrain = {}
init_params['impact_parameter'] = 4.
init_params['phi'] = 0.
init_params['radius'] = radius.value
init_params['centre_x'] = centre_x.value
init_params['centre_y'] = centre_y.value
init_params['ring_width'] = 0.1
init_params['optical_efficiency_muon'] = 0.1
init_errs['error_impact_parameter'] = 2.
init_constrain['limit_impact_parameter'] = (0., 25.)
init_errs['error_phi'] = 0.1
init_errs['error_ring_width'] = 0.001 * radius.value
init_errs['error_optical_efficiency_muon'] = 0.05
init_constrain['limit_phi'] = (-np.pi, np.pi)
init_constrain['fix_radius'] = True
init_constrain['fix_centre_x'] = True
init_constrain['fix_centre_y'] = True
init_constrain['limit_ring_width'] = (0., 1.)
#init_constrain['limit_optical_efficiency_muon'] = (0., 1.) # Unneeded constraint - and misleading in case of changes leading to >1 values!
logger.debug("radius = %3.3f pre migrad", radius)
# Create Minuit object with first guesses at parameters
# strip away the units as Minuit doesnt like them
minuit = Minuit(
self.likelihood,
# forced_parameters=parameter_names,
**init_params,
**init_errs,
**init_constrain,
errordef=0.1,
print_level=0,
pedantic=False
)
# Perform minimisation
minuit.migrad()
# Get fitted values
fit_params = minuit.values
fitoutput.impact_parameter = fit_params['impact_parameter'] * u.m
# fitoutput.phi = fit_params['phi']*u.rad
fitoutput.impact_parameter_pos_x = fit_params['impact_parameter'] * np.cos(
fit_params['phi'] * u.rad) * u.m
fitoutput.impact_parameter_pos_y = fit_params['impact_parameter'] * np.sin(
fit_params['phi'] * u.rad) * u.m
fitoutput.ring_width = fit_params['ring_width'] * self.unit
fitoutput.optical_efficiency_muon = fit_params['optical_efficiency_muon']
fitoutput.prediction = self.prediction
return fitoutput
def gauss_pdf(x, mu, sigma):
"""Normalized Gaussian"""
return 1 / np.sqrt(2 * np.pi) / sigma * np.exp(
-(x - mu)**2 / 2. / sigma**2)
def gauss_extended(x, N, mu, sigma):
"""Non-normalized Gaussian"""
return N * gauss_pdf(x, mu, sigma)
chi_A_ill = Chi2Regression(gauss_extended, x, y, sy)
minuit_ill = Minuit(chi_A_ill,
pedantic=False,
N=len(A_ill),
mu=A_ill_mean,
sigma=A_ill_sigma)
minuit_ill.migrad()
print(minuit_ill.fval)
#Ndof = 120-*minuit_ill.args
prob = stats.chi2.sf(minuit_ill.fval, (65 - len(minuit_ill.args)))
print(prob)
xaxis = np.linspace(0.0, 30, 1000)
yaxis = gauss_extended(xaxis, *minuit_ill.args)
names = [
'Distribution of A ill:', 'Entries', 'Mean', 'RMS', "Chi2/Ndof", "Prob"
]
values = [
"", "{:d}".format(len(A_ill)), "{:.3f}".format(x.mean()),
chisq = 0
for t in range(24, len(epos), 1):
model_PWN = eta * funcinterpolate(epos[t], gamma)
model_DM = np.power(epos[t],3.)*sigma_v_normalization*DM.DM_spectrum(epos[t], DM_mass, channel)[0]/np.power(10.,-26)
model_sec = PWN.flux_secondary(epos[t], normalization_sec)
model_tot = model_PWN + model_sec + model_DM
chisq = chisq + np.power((model_tot - pos[t]) / errortot_pos[t], 2.)
return chisq
# Define an empty array of chisquare values from the the cross section array
chisquare_arr = np.zeros((len(channel_arr), len(sigma_exp_arr)))
upperlim_arr = np.zeros((len(channel_arr)))
for i, DMchannel in enumerate(channel_arr):
for j, sigma_exp in enumerate(sigma_exp_arr):
m = Minuit(f_BPL_DM, par0=0.06, par1=1.44, par2=1.26, par3=sigma_exp)
m.errors['par0'] = 0.06
m.errors['par1'] = 0.03
m.errors['par2'] = 0.02
m.errors['par3'] = 1e-4
m.limits['par0'] = (-10.0, 10.)
m.limits['par1'] = (0., 5.)
m.limits['par2'] = (0.1, 10.)
m.limits['par3'] = (-29, 20)
m.fixed['par3'] = True
m.errordef = 1
m.migrad()
print('value', m.values)
print('error', m.errors)
print('fval', m.fval)
chisquare_arr[i, j] = m.fval
def main():
global Count
x0 = np.array([
0.301670059774, 0.994252132593, 0.00230538402151, 0.00590002382274,
0.8945971901, 0.464840905602, 8.25381559741, 3.94217843788,
NearMean[0], NearMean[1], NearMean[2], FarMean[0], FarMean[1],
FarMean[2], OldFarMean[0], OldFarMean[1], OldFarMean[2],
0.00453978243062, 0.10091505595897542, 0.0024079639515751355
])
print "Make sure you have the proton normalization for the fiducial cut and the spill in/spill out normalization correctly."
print "Minimizing"
#res = minimize(SimplexFunc, x0, method='Powell', options={'xtol': 1e-8, 'disp': True})
Count = 0
#LOOK AT NEAR CUT
print "MAKE SURE NEARDET IS SET TO TRUE IF NEAR DETECTOR ANALYSIS and UNCOMMENT OUT LIKELIHOODS"
m = Minuit(
LogLikelihood,
SSTT13=0.12054415908568761,
M13=0.0025043194579322248,
Li9Rate=1.1244941107796325,
FNSMRate=0.43741890871782574,
NearLi9Rate=7.901068678691314,
NearFNSMRate=3.7788535947724244,
error_SSTT13=5.,
limit_SSTT13=(0., 1.),
limit_M13=(0., 1.),
limit_Li9Rate=(0., 10.),
limit_FNSMRate=(0., 1.),
limit_NearLi9Rate=(0., 10.),
limit_NearFNSMRate=(0., 10.),
error_Li9Rate=4.,
error_FNSMRate=4.,
error_M13=2.e-2,
error_NearLi9Rate=4.,
error_NearFNSMRate=4.,
errordef=1.,
#fix_NearLi9Rate=True, fix_NearFNSMRate = True,
BumpNorm=0.011238038728963017,
error_BumpNorm=1.,
fix_BumpNorm=True,
NearNorm_A=3.969585771201878e-11,
NearNorm_B=0.0,
NearNorm_C=0.0,
limit_NearNorm_A=(0., 1.),
limit_NearNorm_B=(0., 1.),
#limit_NearNorm_A=(0., 10.), limit_NearNorm_B=(0., 10.), limit_NearNorm_C=(0., 10.),
NearAcc=0.575028741826883,
error_NearAcc=1.5,
#fix_NearAcc=True,
error_NearNorm_A=4.,
error_NearNorm_B=4.,
error_NearNorm_C=5.,
#fix_NearNorm_A=True,
fix_NearNorm_B=True,
fix_NearNorm_C=True,
#fix_NearLi9Rate=True, fix_NearFNSMRate=True,
Near_A=-0.004116474803739965,
Near_B=1.0018032274975033,
Near_C=-1.7993784835962714e-07,
error_Near_A=3.,
error_Near_B=.1,
error_Near_C=1.e-5,
Far_A=-0.012606607718833054,
Far_B=1.0056769330102382,
Far_C=-3.662679490821011e-08,
error_Far_A=1.,
error_Far_B=.1,
error_Far_C=1.e-5,
Old_Far_A=-0.012601515890730806,
Old_Far_B=1.0056896190670936,
Old_Far_C=-1.0659506576591107e-07,
error_Old_Far_A=1.,
error_Old_Far_B=.1,
#Near_A = NearMean[0], Near_B = NearMean[1], Near_C = NearMean[2], error_Near_A = 3., error_Near_B=.1, error_Near_C=1.e-5,
#Far_A = FarMean[0], Far_B = FarMean[1], Far_C = FarMean[2], error_Far_A = 1., error_Far_B=.1, error_Far_C=1.e-5,
#Old_Far_A = OldFarMean[0], Old_Far_B = OldFarMean[1], Old_Far_C = OldFarMean[2], error_Old_Far_A = 1., error_Old_Far_B=.1, error_Old_Far_C=1.e-5,
#fix_Near_A=True, fix_Near_B=True, fix_Near_C=True,
#fix_Far_A=True, fix_Far_B=True, fix_Far_C=True, fix_Old_Far_A=True, fix_Old_Far_B=True, fix_Old_Far_C=True
#fix_SSTT13=True, fix_M13=True, fix_Li9Rate=True, fix_FNSMRate=True, fix_NearLi9Rate=True,
#fix_Near_A=True, fix_Near_B=True, fix_Near_C=True,
#fix_Far_A=True, fix_Far_B=True, fix_Far_C=True, fix_Old_Far_A=True,
#fix_Old_Far_B=True, fix_Old_Far_C=True,
limit_Near_A=(NearMean[0] - 5. * np.sqrt(NearCov[0][0]),
NearMean[0] + 5. * np.sqrt(NearCov[0][0])),
limit_Near_B=(NearMean[1] - 5. * np.sqrt(NearCov[1][1]),
NearMean[1] + 5. * np.sqrt(NearCov[1][1])),
limit_Near_C=(NearMean[2] - 5. * np.sqrt(NearCov[2][2]),
NearMean[2] + 5. * np.sqrt(NearCov[2][2])),
limit_Far_A=(FarMean[0] - 5. * np.sqrt(FarCov[0][0]),
FarMean[0] + 5. * np.sqrt(FarCov[0][0])),
limit_Far_B=(FarMean[1] - 5. * np.sqrt(FarCov[1][1]),
FarMean[1] + 5. * np.sqrt(FarCov[1][1])),
limit_Far_C=(FarMean[2] - 5. * np.sqrt(FarCov[2][2]),
FarMean[2] + 5. * np.sqrt(FarCov[2][2])),
limit_Old_Far_A=(OldFarMean[0] - 5. * np.sqrt(OldFarCov[0][0]),
OldFarMean[0] + 5. * np.sqrt(OldFarCov[0][0])),
limit_Old_Far_B=(OldFarMean[1] - 5. * np.sqrt(OldFarCov[1][1]),
OldFarMean[1] + 5. * np.sqrt(OldFarCov[1][1])),
limit_Old_Far_C=(OldFarMean[2] - 5. * np.sqrt(OldFarCov[2][2]),
OldFarMean[2] + 5. * np.sqrt(OldFarCov[2][2])))
m.migrad()
m.print_param()
print('value', m.values)
print('covariance', m.covariance)
#m.profile('SSTT13')
mi = .07
ma = .14
d = .001
N = int((ma - mi) / d)
'''
a0=-3000,
error_a0=100,
alphas=1.18400000e-01,
fix_alphas=True,
invalpha=1.27944000e+02,
fix_invalpha=True,
m0=400,
error_m0=100,
m12=900,
error_m12=100,
mb=4.18000000e+00,
fix_mb=True,
mt=1.74500000e+02,
fix_mt=True,
signmu=1,
fix_signmu=True,
tanb=11,
error_tanb=3,
lambda=0.1,
error_lambda=0.1,
errordef=1,
)
# Set Minuit likelihood function.
m = Minuit(chisquared, **kwdarg)
# Run migrad.
m.migrad()
print m.values
print m.errors
def get_corrfunc(x, x_err=None, n_frac=2, viz=True, model=False, est=False):
"""
Auto correlation of a signal and mean estimation
Parameters
x : samples of the first variable
x_err : error vector for the first variable
n_frac : number of pixels over which to estiamte correlation wrt
the size of the samples
viz : plot the correlation function
model : model the correlation function
est : Get estimates on the best-fit values using the covariance
matrices estmated
Returns:
loc, sig : the mean and uncertainty on the location parameter
"""
npp = len(x)
coef = [
np.corrcoef(x[:npp - j], x[j:])[0, 1] for j in range(npp // n_frac)
]
if viz:
fig, ax = plt.subplots(1)
ax.plot(coef, '-k')
if model:
def model_func(x, cl):
# A simple exponential model
return np.exp(-x / cl)
popt, __ = curve_fit(model_func,
np.arange(npp // n_frac)[:20], coef[:20])
if viz:
x_plot = np.linspace(0, 50, 50)
ax.plot(x_plot, model_func(x_plot, *popt), '-r')
ax.text(10, 0.8, "$r_{x_0}=%.1f$" % popt[0])
ax.set_xlim(0, 50)
if est:
if x_err is None:
raise TypeError("Requires errorbars on the samples")
# Obtain band-diagonal correlation matrix
from scipy.linalg import toeplitz
Xi = toeplitz(model_func(np.arange(npp), *popt))
# Covariance matrix from errorbars and correlation matrix
# C = D * Xi * D.T
cov = np.diag(x_err).dot(Xi.dot(np.diag(x_err)))
# Minimization using iminuit
from iminuit import Minuit
ico = np.linalg.inv(cov)
def chi2(mu):
dyi = x - mu
return dyi.T.dot(ico.dot(dyi))
mm = Minuit(chi2,
mu=x.mean(),
error_mu=x.std(),
fix_mu=False,
errordef=1.,
print_level=-1)
mm.migrad()
loc, sig = mm.values["mu"], mm.errors["mu"]
if viz:
fig, ax = plt.subplots(figsize=(9, 3))
ax.plot(x)
ax.fill_between(np.arange(npp),
loc + sig,
loc - sig,
color='r',
alpha=0.2)
return loc, sig
def test_default_errordef():
with pytest.warns(DeprecationWarning):
Minuit(Fcn(), pedantic=False)
def fit_model(charges, model, startparams=None, \
rej_outliers=False, nbins=200, \
silent=False,\
parameter_text=((r"$\mu_{{SPE}}$& {:4.2e}\\", 5),),
use_minuit=False,\
normalize=True,\
**kwargs):
"""
Standardazied fitting routine
Args:
charges (np.ndarray): Charges obtained in a measurement (no histogram)
model (pyevsel.fitting.Model): A model to fit to the data
startparams (tuple): initial parameters to model, or None for first guess
Keyword Args:
rej_outliers (bool): Remove extreme outliers from data
nbins (int): Number of bins
parameter_text (tuple): will be passed to model.plot_result
use_miniuit (bool): use minuit to minimize startparams for best
chi2
normalize (bool): normalize data before fitting
silent (bool): silence output
Returns:
tuple
"""
if rej_outliers:
charges = reject_outliers(charges)
if use_minuit:
from iminuit import Minuit
# FIXME!! This is too ugly. Minuit wants named parameters ... >.<
assert len(startparams) < 10; "Currently more than 10 paramters are not supported for minuit fitting!"
assert model.all_coupled, "Minuit fitting can only be done for models with all parmaters coupled!"
names = ["a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k"]
funcstring = "def do_min("
for i,__ in enumerate(startparams):
funcstring += names[i] + ","
funcstring = funcstring[:-1] + "):\n"
funcstring += "\tmodel.startparams = ("
for i,__ in enumerate(startparams):
funcstring += names[i] + ","
funcstring = funcstring[:-1] + ")\n"
funcstring += "\tmodel.fit_to_data(charges, nbins, silent=True, **kwargs)"
funcstring += "\treturn model.chi2_ndf"
#def do_min(a, b, c, d, e, f, g, h, i, j, k): #FIXME!!!
# model.startparams = (a, b, c, d, e, f, g, h, i, j, k)
# model.fit_to_data(charges, nbins, silent=True, **kwargs)
# return model.chi2_ndf
exec(funcstring)
bnd = kwargs["bounds"]
if "bounds" in kwargs:
min_kwargs = dict()
for i,__ in enumerate(startparams):
min_kwargs["limit_" + names[i]] =(bnd[0][i],bnd[1][i])
m = Minuit(do_min, **min_kwargs)
#m = Minuit(do_min, limit_a=(bnd[0][0],bnd[1][0]),
# limit_b=(bnd[0][1],bnd[1][1]),
# limit_c=(bnd[0][2],bnd[1][2]),
# limit_d=(bnd[0][3],bnd[1][3]),
# limit_e=(bnd[0][4],bnd[1][4]),
# limit_f=(bnd[0][5],bnd[1][5]),
# limit_g=(bnd[0][6],bnd[1][6]),
# limit_h=(bnd[0][7],bnd[1][7]),
# limit_i=(bnd[0][8],bnd[1][8]),
# limit_j=(bnd[0][9],bnd[1][9]),
# limit_k=(bnd[0][10],bnd[1][10]))
else:
m = Minuit(do_min)
# hand over the startparams
for key, value in zip(["a","b","c","d","e","f","g","h","i","j"], startparams):
m.values[key] = value
m.migrad()
else:
model.startparams = startparams
model.fit_to_data(charges, nbins,normalize=normalize, silent=silent, **kwargs)
# check for named tuple
if hasattr(startparams, "_make"): # duck typing
best_fit_params = startparams._make(model.best_fit_params)
else:
best_fit_params = model.best_fit_params
print("Best fit parameters {}".format(best_fit_params))
return model
"""Use iminuit to find the minimum of a 3D scalar field"""
from vedo import show, Point, Line, printc
from iminuit import Minuit
# pip install iminuit # https://github.com/scikit-hep/iminuit
import numpy as np
def fcn(x, y, z):
f = (x - 4)**4 + (y - 3)**4 + (z - 2)**2
if not vals or f < vals[-1]:
path.append([x, y, z])
vals.append(f)
return f
paths = []
for x, y, z in np.random.rand(200, 3) * 3:
path, vals = [], []
m = Minuit(fcn, x=x, y=y, z=z)
m.errordef = m.LEAST_SQUARES
# m.simplex() # run simplex optimiser
m.migrad() # run migrad optimiser
line = Line(path).cmap('jet_r', vals).lw(2).alpha(0.25)
paths.append(line)
printc('Last optimization output:', c='green7', invert=1)
printc(m, c='green7', italic=1)
show(paths, Point([4, 3, 2]), __doc__, axes=1).close()
def __call__(self,
tel_id,
center_x,
center_y,
radius,
image,
pedestal,
mask=None):
"""
Parameters
----------
center_x: Angle quantity
Initial guess for muon ring center in telescope frame
center_y: Angle quantity
Initial guess for muon ring center in telescope frame
radius: Angle quantity
Radius of muon ring from circle fitting
pixel_x: ndarray
X position of pixels in image from circle fitting
pixel_y: ndarray
Y position of pixel in image from circle fitting
image: ndarray
Amplitude of image pixels
mask: ndarray
mask marking the pixels to be used in the likelihood fit
Returns
-------
MuonEfficiencyContainer
"""
telescope = self.subarray.tel[tel_id]
if telescope.optics.num_mirrors != 1:
raise NotImplementedError(
"Currently only single mirror telescopes"
f" are supported in {self.__class__.__name__}")
negative_log_likelihood = build_negative_log_likelihood(
image,
telescope,
mask,
oversampling=self.oversampling.tel[tel_id],
min_lambda=self.min_lambda_m.tel[tel_id] * u.m,
max_lambda=self.max_lambda_m.tel[tel_id] * u.m,
spe_width=self.spe_width.tel[tel_id],
pedestal=pedestal,
hole_radius=self.hole_radius_m.tel[tel_id] * u.m,
)
initial_guess = create_initial_guess(center_x, center_y, radius,
telescope)
step_sizes = {}
step_sizes["error_impact_parameter"] = 0.5
step_sizes["error_phi"] = np.deg2rad(0.5)
step_sizes["error_ring_width"] = 0.001 * radius.to_value(u.rad)
step_sizes["error_optical_efficiency_muon"] = 0.05
constraints = {}
constraints["limit_impact_parameter"] = (0, None)
constraints["limit_phi"] = (-np.pi, np.pi)
constraints["fix_radius"] = True
constraints["fix_center_x"] = True
constraints["fix_center_y"] = True
constraints["limit_ring_width"] = (0.0, None)
constraints["limit_optical_efficiency_muon"] = (0.0, None)
# Create Minuit object with first guesses at parameters
# strip away the units as Minuit doesnt like them
minuit = Minuit(
negative_log_likelihood,
# forced_parameters=parameter_names,
**initial_guess,
**step_sizes,
**constraints,
errordef=0.5,
print_level=0,
pedantic=True,
)
# Perform minimisation
minuit.migrad()
# Get fitted values
result = minuit.values
return MuonEfficiencyContainer(
impact=result["impact_parameter"] * u.m,
impact_x=result["impact_parameter"] * np.cos(result["phi"]) * u.m,
impact_y=result["impact_parameter"] * np.sin(result["phi"]) * u.m,
width=u.Quantity(np.rad2deg(result["ring_width"]), u.deg),
optical_efficiency=result["optical_efficiency_muon"],
)
def fit_sample(df_mbinfos, j):
df_results = pd.DataFrame(columns=\
['accountid','principal','oriinuldegdel','term','month0','month1',
'rate_mean','rate_error','month0_mean','month1_mean','fval','payment_pred',
'grace4','month3','month4','fval3','fval4',
'payment_prin_mean3'])
i = 0
accountid, principal, term, months, oriinuldegdel = create_prod_df(
df_mbinfos, j)
print(accountid, principal, term, months, oriinuldegdel)
global term_corr
term_corr = term
global principal_corr
principal_corr = principal
months_corr = [month + 0 for month in months]
months_corr = months_corr[-1:]
print(months_corr, principal_corr)
global oriinuldegdel_corr
oriinuldegdel_corr = oriinuldegdel[-1:]
months_min = months[0] - 1
months_max = months[0] + 1
if months_min < 0:
months_min = 0
start = time.time()
m1 = Minuit(
func_total_LL_two,
rate=18.0,
error_rate=0.1,
limit_rate=(12, 25),
month0=months[0],
error_month0=0.1,
limit_month0=(months_min, months_max),
#month1=months[0], error_month1=1.0, limit_month1=(months[1]-1, months[1]+1),
#term=term, error_term=1.0, limit_term=(term-2,term+2),
errordef=1)
m1.migrad()
end = time.time()
print("m1 {} {}".format(j, end - start))
start = time.time()
m2 = Minuit(
func_total_LL_two,
rate=8.0,
error_rate=0.1,
limit_rate=(3, 10),
month0=months[0],
error_month0=1.0,
limit_month0=(months_min, months_max),
#month1=months[0], error_month1=1.0, limit_month1=(months[1]-1, months[1]+1),
#term=term, error_term=1.0, limit_term=(term-2, term+2),
errordef=1)
m2.migrad()
end = time.time()
print("m2 {} {}".format(j, end - start))
start = time.time()
m3 = Minuit(
func_principal_LL_one,
#grace=0.0, error_grace=0.1, limit_grace=(0.0, 12.0),
month0=months[0],
error_month0=0.1,
limit_month0=(months_min, months_max),
#month1=months[0], error_month1=1.0, limit_month1=(months[1]-1, months[1]+1),
#term=term, error_term=1.0, limit_term=(term-2, term+2),
errordef=1)
m3.migrad()
end = time.time()
print("m3 {} {}".format(j, end - start))
fval1 = float(m1.get_fmin()['fval'])
fval2 = float(m2.get_fmin()['fval'])
log_fval1 = np.log(fval1 + 1)
log_fval2 = np.log(fval2 + 1)
log_fval_ratio = log_fval1 / log_fval2
month0_mean = months[0]
month1_mean = 0 #months[1]
fval3 = float(m3.get_fmin()['fval'])
month3 = round(float(m3.fitarg['month0']))
payment_prin_mean3 = float(principal) * 0.20 / 12.0 + float(
principal) / term_corr
payment_prin_max3 = float(principal) * 0.25 / 12.0 + float(
principal) / term_corr
if log_fval_ratio > 50.0:
error_rate = float(m2.fitarg['error_rate'])
rate_mean = float(m2.fitarg['rate'])
month0_mean = round(float(m2.fitarg['month0']))
#month1_mean = round(float(m2.fitarg['month0'])+months[1]-months[0])
fval = float(m2.get_fmin()['fval'])
else:
error_rate = float(m1.fitarg['error_rate'])
rate_mean = float(m1.fitarg['rate'])
month0_mean = round(float(m1.fitarg['month0']))
#month1_mean = round(float(m1.fitarg['month0'])+months[1]-months[0])
fval = float(m1.get_fmin()['fval'])
df_results.loc[i, 'accountid'] = accountid
df_results.loc[i, 'principal'] = float(principal)
df_results.loc[i, 'oriinuldegdel'] = oriinuldegdel_corr
df_results.loc[i, 'term'] = float(term_corr)
df_results.loc[i, 'month0'] = months[0]
df_results.loc[i, 'month1'] = 0 #months[1]
df_results.loc[i, 'rate_error'] = error_rate
df_results.loc[i, 'rate_mean'] = rate_mean
df_results.loc[i, 'month0_mean'] = month0_mean
df_results.loc[i, 'month1_mean'] = month1_mean
df_results.loc[i, 'fval'] = fval
payment_pred=df_results.loc[i:i].apply\
(lambda row: utils.pmt(row['principal'],row['term'],row['rate_mean']),\
axis=1).tolist()[0]
df_results.loc[i:i, 'payment_pred'] = payment_pred
df_results.loc[i, 'month3'] = round(float(m3.fitarg['month0']))
df_results.loc[i, 'fval3'] = fval3
df_results.loc[i, 'payment_prin_mean3'] = payment_prin_mean3
df_results.loc[i, 'payment_prin_max3'] = payment_prin_max3
i = i + 1
columns_float = [
'principal', 'term', 'rate_mean', 'rate_error', 'fval', 'fval3',
'payment_pred'
]
df_results[columns_float] = df_results[columns_float].astype(float)
return df_results
# m.migrad(ncall=500000)
# plt.figure()
# m.draw_mnprofile('tau', bound = 50, bins = 50)
two_point_tau = np.mean(two_point_estimates[-1])
two_point_tau_err = np.std(two_point_estimates[-1])
print(two_point_tau)
m = Minuit(
chisquare_1d_2,
#t0 = 0,
#fix_t0 = t0_line,
#limit_t0 = (-5, 5),
#tau = 2000.0, # set start parameter
tau=two_point_tau,
#limit_tau = (500.0, 4000.0), # if you want to limit things
#fix_tau = True,
#fix_a = "True", # you can also fix it
fterm=fterm_prior,
#limit_fopt = (0.0, 10000.0),
errordef=1,
print_level=0,
pedantic=False)
m.migrad(ncall=500000)
minos = m.minos()
# plt.figure()
# m.draw_mnprofile('tau', bound = 5, bins = 50)
# plt.show()
print()
print(file)
#signature dynamically
self.func_code = make_func_code(f_sig[1:])#docking off independent variable
self.func_defaults = None #this keeps np.vectorize happy
def __call__(self,*arg):
#notice that it accept variable length
#positional arguments
chi2 = sum((y-self.f(x,*arg))**2 for x,y in zip(self.x,self.y))
return chi2
def gaussian3(x,p1,p2,p3):
g=(p1*exp(-(x-440)**2)+p2*exp(-(x-530)**2)+p3*exp(-(x-620)**2))
return g/sqrt(pi)
comp3=Chi2Functor(gaussian3,x,y)
describe(comp3)
m=Minuit(comp3,p1=1,p2=1,p3=1)
m.migrad();
print(m.values)
sample_spd_fit = {i:gaussian3(i,m.values['p1'],m.values['p2'],m.values['p3']) for i in x }
spd_fit = colour.SpectralPowerDistribution(sample_spd_fit)
XYZf = colour.spectral_to_XYZ(spd_fit, cmfs)
xy = colour.XYZ_to_xy(XYZ) # Conversion to correlated colour temperature in K.
xyf = colour.XYZ_to_xy(XYZf)
print("XYZ: ",XYZ)
print(xy)
print("XYZf: ",XYZf)
print(xyf)
#print(colour.delta_E(XYZ,XYZf))
# Plotting the *CIE 1931 Chromaticity Diagram*.
Hist_HitMiss_error = np.sqrt(Hist_HitMiss)
Hist_HitMiss_indexes = Hist_HitMiss > 0 # Produce a new histogram, using only bins with non-zero entries
#----------------------------------------------------------------------------------
# Plot histograms on screen:
#----------------------------------------------------------------------------------
fig, ax = plt.subplots(figsize=(10, 5))
ax.set_xlabel("Random number")
ax.set_ylabel("Frequency")
chi2_object_hitmiss = Chi2Regression(
fit_function, Hist_HitMiss_centers[Hist_HitMiss_indexes],
Hist_HitMiss[Hist_HitMiss_indexes],
Hist_HitMiss_error[Hist_HitMiss_indexes])
minuit_hitmiss = Minuit(chi2_object_hitmiss, p0=20.0, pedantic=False)
minuit_hitmiss.migrad()
chi2_hitmiss = minuit_hitmiss.fval
ndof_hitmiss = chi2_object_hitmiss.ndof
prob_hitmiss = stats.chi2.sf(chi2_hitmiss, ndof_hitmiss)
p0 = minuit_hitmiss.args
x_fit = np.linspace(xmin, xmax, 1000)
y_fit_simple = fit_function(x_fit, p0)
#ax.plot(x_fit, y_fit_simple, 'b-')
names = ['Hit & Miss:', 'Entries', 'Mean', 'RMS']
values = [
"",
def minimise(self, params, step, limits, minimiser_name="minuit", max_calls=0):
"""
Parameters
----------
params: ndarray
Seed parameters for fit
step: ndarray
Initial step size in the fit
limits: ndarray
Fit bounds
minimiser_name: str
Name of minimisation method
max_calls: int
Maximum number of calls to minimiser
Returns
-------
tuple: best fit parameters and errors
"""
limits = np.asarray(limits)
if minimiser_name == "minuit":
self.min = Minuit(
self.get_likelihood,
print_level=1,
source_x=params[0],
error_source_x=step[0],
limit_source_x=limits[0],
fix_source_x=False,
source_y=params[1],
error_source_y=step[1],
limit_source_y=limits[1],
fix_source_y=False,
core_x=params[2],
error_core_x=step[2],
limit_core_x=limits[2],
fix_core_x=False,
core_y=params[3],
error_core_y=step[3],
limit_core_y=limits[3],
fix_core_y=False,
energy=params[4],
error_energy=step[4],
limit_energy=limits[4],
fix_energy=False,
x_max_scale=params[5],
error_x_max_scale=step[5],
limit_x_max_scale=limits[5],
fix_x_max_scale=False,
goodness_of_fit=False,
fix_goodness_of_fit=True,
errordef=1,
)
self.min.tol *= 1000
self.min.set_strategy(1)
migrad = self.min.migrad()
fit_params = self.min.values
errors = self.min.errors
return (
(
fit_params["source_x"],
fit_params["source_y"],
fit_params["core_x"],
fit_params["core_y"],
fit_params["energy"],
fit_params["x_max_scale"],
),
(
errors["source_x"],
errors["source_y"],
errors["core_x"],
errors["core_x"],
errors["energy"],
errors["x_max_scale"],
),
self.min.fval,
)
elif "nlopt" in minimiser_name:
import nlopt
opt = nlopt.opt(nlopt.LN_BOBYQA, 6)
opt.set_min_objective(self.get_likelihood_nlopt)
opt.set_initial_step(step)
opt.set_lower_bounds(np.asarray(limits).T[0])
opt.set_upper_bounds(np.asarray(limits).T[1])
opt.set_xtol_rel(1e-3)
if max_calls:
opt.set_maxeval(max_calls)
x = opt.optimize(np.asarray(params))
return x, (0, 0, 0, 0, 0, 0), self.get_likelihood_min(x)
elif minimiser_name in ("lm", "trf", "dogleg"):
self.array_return = True
min = least_squares(
self.get_likelihood_min,
params,
method=minimiser_name,
x_scale=step,
xtol=1e-10,
ftol=1e-10,
)
return min.x, (0, 0, 0, 0, 0, 0), self.get_likelihood_min(min.x)
else:
min = minimize(
self.get_likelihood_min,
np.array(params),
method=minimiser_name,
bounds=limits,
options={"disp": False},
tol=1e-5,
)
return np.array(min.x), (0, 0, 0, 0, 0, 0), self.get_likelihood_min(min.x)
capthick=1)
ax1.set_title('Assignemnt 5.2 - Histogram of residuals with a Gaussian fit')
ax1.set_xlabel('Residual')
ax1.set_ylabel('Frequency / binwidth = 0.01')
# Draw Gaussian:
# -------------
def func_Gaussian(x, N, mu, sigma):
return N * stats.norm.pdf(x, mu, sigma)
Chi2_Gaussian = Chi2Regression(func_Gaussian, x, y, sy)
minuit_Gaussian = Minuit(Chi2_Gaussian,
pedantic=False,
N=len(y),
mu=mu,
sigma=std)
minuit_Gaussian.migrad() # perform the actual fit
chi2_gaussian = minuit_Gaussian.fval
ndof_gaussian = len(x) - len(minuit_Gaussian.args)
prob_gaussian = stats.chi2.sf(chi2_gaussian, ndof_gaussian)
xaxis = np.linspace(xmin, xmax, 1000)
yaxis = func_Gaussian(xaxis, *minuit_Gaussian.args)
ax1.plot(xaxis, yaxis, '-', label='Gaussian distribution fit')
names = [
'Entries', 'Mean', 'Std Dev', 'Chi2/ndf', 'Prob', 'N fit', 'mu fit',
'sigma fit'
def run_actual_fit(t, y, sy, cfg, dt, ts):
debug = False
# debug = True
# np.random.seed(cfg.ID)
np.random.seed(42)
if debug:
reload(SIR)
print("delete this")
# reload(SIR)
normal_priors = dict(
# multiplier=0,
# lambda_E={'mean': cfg.lambda_E, 'std': cfg.lambda_E/10},
# lambda_I={'mean': cfg.lambda_I, 'std': cfg.lambda_I/10},
# beta= {'mean': 0.01, 'std': 0.05},
)
p0 = dict(
lambda_E=cfg.lambda_E,
lambda_I=cfg.lambda_I,
beta=cfg.beta,
tau=0,
)
bounds = dict(
limit_lambda_E=(1e-6, None),
limit_lambda_I=(1e-6, None),
limit_beta=(1e-6, None),
)
fix = dict(
fix_lambda_E=True,
fix_lambda_I=True,
)
fit_object = SIR.FitSIR(t, y, sy, normal_priors, cfg, dt=dt, ts=ts)
minuit = Minuit(
fit_object,
pedantic=False,
print_level=0,
**p0,
**bounds,
**fix,
errordef=Minuit.LEAST_SQUARES,
)
minuit.migrad()
fit_object.set_minuit(minuit)
fit_object, fit_failed = refit_if_needed(fit_object,
cfg,
bounds,
fix,
minuit,
debug=debug)
return fit_object, fit_failed
def test_minos_single_no_migrad():
m = Minuit(func3, pedantic=False, print_level=0)
with pytest.raises(RuntimeError):
m.minos('x')
-0.190318, 3.5303, 0.504813)
initialErrors = (0.1, 10., 10., 0.1, 0.1, 0.3, 0.5, 1., 1., 1., 1., 1., 1.,
0.1)
# searchLimits=((0.0001,2.),(0.01,80), (0.0,400), None,None,
# (-2.,2.),(-0.99,2.5), (-10.,10.),
# (-20.,20.),(-0.99,6.), (-15.,15.),
# (-5.,5.),(-0.99,8), None)
searchLimits = ((0, None), (0, None), (0, None), None, None, (-5., 5.),
(-0.99, 30), (-30., 30.), (-5., 5.), (-0.99, 60.), (-30., 30.),
(-5., 15.), (-0.99, 30.), (-5, 5))
parametersToMinimize = (False, False, False, True, True, False, False, False,
False, False, False, False, False, False)
m = Minuit(chi_2, initialValues)
m.errors = initialErrors
m.limits = searchLimits
m.fixed = parametersToMinimize
m.errordef = 1
print(m.params)
m.tol = 0.0001 * totalN * 10000 ### the last 0.0001 is to compensate MINUIT def
m.strategy = 1
#%%
# m.tol=0.0001*totalN*10000 ### the last 0.0001 is to compensate MINUIT def
# m.strategy=1
def setup(self):
self.m = Minuit(func3, print_level=0, pedantic=False)
self.m.migrad()
self.m.hesse()
self.m.minos()
def predict(self, shower_seed, energy_seed):
"""
Parameters
----------
source_x: float
Initial guess of source position in the nominal frame
source_y: float
Initial guess of source position in the nominal frame
core_x: float
Initial guess of the core position in the tilted system
core_y: float
Initial guess of the core position in the tilted system
energy: float
Initial guess of energy
Returns
-------
Shower object with fit results
"""
horizon_seed = HorizonFrame(az=shower_seed.az, alt=shower_seed.alt)
nominal_seed = horizon_seed.transform_to(
NominalFrame(array_direction=self.array_direction))
source_x = nominal_seed.x.to(u.rad).value
source_y = nominal_seed.y.to(u.rad).value
ground = GroundFrame(x=shower_seed.core_x,
y=shower_seed.core_y,
z=0 * u.m)
tilted = ground.transform_to(
TiltedGroundFrame(pointing_direction=self.array_direction))
tilt_x = tilted.x.to(u.m).value
tilt_y = tilted.y.to(u.m).value
lower_en_limit = energy_seed.energy * 0.1
if lower_en_limit < 0.04 * u.TeV:
lower_en_limit = 0.04 * u.TeV
# Create Minuit object with first guesses at parameters, strip away the
# units as Minuit doesnt like them
min = Minuit(self.get_likelihood,
print_level=1,
source_x=source_x,
error_source_x=0.01 / 57.3,
fix_source_x=False,
limit_source_x=(source_x - 0.5 / 57.3,
source_x + 0.5 / 57.3),
source_y=source_y,
error_source_y=0.01 / 57.3,
fix_source_y=False,
limit_source_y=(source_y - 0.5 / 57.3,
source_y + 0.5 / 57.3),
core_x=tilt_x,
error_core_x=10,
limit_core_x=(tilt_x - 200, tilt_x + 200),
core_y=tilt_y,
error_core_y=10,
limit_core_y=(tilt_y - 200, tilt_y + 200),
energy=energy_seed.energy.value,
error_energy=energy_seed.energy.value * 0.05,
limit_energy=(lower_en_limit.value,
energy_seed.energy.value * 10.),
x_max_scale=1,
error_x_max_scale=0.1,
limit_x_max_scale=(0.5, 2),
fix_x_max_scale=False,
errordef=1)
min.tol *= 1000
min.strategy = 0
# Perform minimisation
migrad = min.migrad()
fit_params = min.values
errors = min.errors
# print(migrad)
# print(min.minos())
# container class for reconstructed showers '''
shower_result = ReconstructedShowerContainer()
nominal = NominalFrame(x=fit_params["source_x"] * u.rad,
y=fit_params["source_y"] * u.rad,
array_direction=self.array_direction)
horizon = nominal.transform_to(HorizonFrame())
shower_result.alt, shower_result.az = horizon.alt, horizon.az
tilted = TiltedGroundFrame(x=fit_params["core_x"] * u.m,
y=fit_params["core_y"] * u.m,
pointing_direction=self.array_direction)
ground = project_to_ground(tilted)
shower_result.core_x = ground.x
shower_result.core_y = ground.y
shower_result.is_valid = True
shower_result.alt_uncert = np.nan
shower_result.az_uncert = np.nan
shower_result.core_uncert = np.nan
zenith = 90 * u.deg - self.array_direction[0]
shower_result.h_max = fit_params["x_max_scale"] * \
self.get_shower_max(fit_params["source_x"],
fit_params["source_y"],
fit_params["core_x"],
fit_params["core_y"],
zenith.to(u.rad).value)
shower_result.h_max_uncert = errors["x_max_scale"] * shower_result.h_max
shower_result.goodness_of_fit = np.nan
shower_result.tel_ids = list(self.image.keys())
energy_result = ReconstructedEnergyContainer()
energy_result.energy = fit_params["energy"] * u.TeV
energy_result.energy_uncert = errors["energy"] * u.TeV
energy_result.is_valid = True
energy_result.tel_ids = list(self.image.keys())
# Return interesting stuff
return shower_result, energy_result
