def test_LeastSquares(loss, verbose):
rng = np.random.default_rng(1)
x = np.linspace(0, 1, 1000)
ye = 0.1
y = rng.normal(2 * x + 1, ye)
def model(x, a, b):
return a + b * x
cost = LeastSquares(x, y, ye, model, loss=loss, verbose=verbose)
assert cost.ndata == len(x)
m = Minuit(cost, a=0, b=0)
m.migrad()
assert_allclose(m.values, (1, 2), rtol=0.05)
assert cost.loss == loss
if loss != "linear":
cost.loss = "linear"
assert cost.loss != loss
m.migrad()
assert_allclose(m.values, (1, 2), rtol=0.05)
assert m.ndof == len(x) - 2
assert_allclose(m.fmin.reduced_chi2, 1, atol=5e-2)
def test_LeastSquares_bad_input():
with pytest.raises(ValueError):
LeastSquares([1, 2], [1], [1], lambda x, a: 0)
with pytest.raises(ValueError):
LeastSquares([1, 2], [1, 2], [1], lambda x, a: 0)
with pytest.raises(ValueError):
LeastSquares([1], [1], [1], lambda x, a: 0, loss="foo")
def test_addable_cost_1():
def model1(x, a):
return a + x
def model2(x, b, a):
return a + b * x
def model3(x, c):
return c
lsq1 = LeastSquares(1, 2, 3, model1)
assert lsq1.func_code.co_varnames == ("a", )
lsq2 = LeastSquares(1, 3, 4, model2)
assert lsq2.func_code.co_varnames == ("b", "a")
lsq3 = LeastSquares(1, 1, 1, model3)
assert lsq3.func_code.co_varnames == ("c", )
lsq12 = lsq1 + lsq2
assert lsq12._items == [lsq1, lsq2]
assert isinstance(lsq12, CostSum)
assert isinstance(lsq1, LeastSquares)
assert isinstance(lsq2, LeastSquares)
assert lsq12.func_code.co_varnames == ("a", "b")
assert lsq12.ndata == 2
assert lsq12(1, 2) == lsq1(1) + lsq2(2, 1)
m = Minuit(lsq12, a=0, b=0)
m.migrad()
assert m.parameters == ("a", "b")
assert_allclose(m.values, (1, 2))
assert_allclose(m.errors, (3, 5))
assert_allclose(m.covariance, ((9, -9), (-9, 25)), atol=1e-10)
lsq121 = lsq12 + lsq1
assert lsq121._items == [lsq1, lsq2, lsq1]
assert lsq121.func_code.co_varnames == ("a", "b")
assert lsq121.ndata == 3
lsq312 = lsq3 + lsq12
assert lsq312._items == [lsq3, lsq1, lsq2]
assert lsq312.func_code.co_varnames == ("c", "a", "b")
assert lsq312.ndata == 3
lsq31212 = lsq312 + lsq12
assert lsq31212._items == [lsq3, lsq1, lsq2, lsq1, lsq2]
assert lsq31212.func_code.co_varnames == ("c", "a", "b")
assert lsq31212.ndata == 5
lsq31212 += lsq1
assert lsq31212._items == [lsq3, lsq1, lsq2, lsq1, lsq2, lsq1]
assert lsq31212.func_code.co_varnames == ("c", "a", "b")
assert lsq31212.ndata == 6
def test_LeastSquares_mask():
c = LeastSquares([1, 2, 3], [3, np.nan, 4], [1, 1, 1], lambda x, a: x + a)
assert c.ndata == 3
assert np.isnan(c(0)) == True
m = Minuit(c, 1)
assert m.ndof == 2
m.migrad()
assert not m.valid
c.mask = np.arange(3) != 1
assert np.isnan(c(0)) == False
assert c.ndata == 2
assert m.ndof == 1
m.migrad()
assert m.valid
assert_equal(m.values, [1.5])
def test_addable_cost_3():
def line_np(x, par):
return par[0] + par[1] * x
lsq = LeastSquares([1, 2, 3], [3, 4, 5], 1, line_np)
con = NormalConstraint("par", (1, 1), (1, 1))
cs = sum([lsq, con])
assert cs((1, 1)) == pytest.approx(3)
cs = 1.5 + lsq + con
assert cs((1, 1)) == pytest.approx(4.5)
def test_LeastSquares(loss, verbose):
np.random.seed(1)
x = np.random.rand(20)
y = 2 * x + 1
ye = 0.1
y += ye * np.random.randn(len(y))
def model(x, a, b):
return a + b * x
cost = LeastSquares(x, y, ye, model, loss=loss, verbose=verbose)
m = Minuit(cost, a=0, b=0)
m.migrad()
assert_allclose(m.values, (1, 2), rtol=0.03)
assert cost.loss == loss
if loss != "linear":
cost.loss = "linear"
assert cost.loss != loss
m.migrad()
assert_allclose(m.values, (1, 2), rtol=0.02)
def fit(self, index, n_bins=100, data_color=None, fit_color=None, box_color=None):
data, data_errs, bins = self.get_histogram_by_index(index, n_bins)
parameters = {
'mu':0.02,
's':1/250,
'c':0.004,
'N':0.35,
}
parameters_options = {
'mu' : ([0, 1], 0.01),
's' : ([0,1], 1/25),
'c' : ([0,1], 0.01),
'N' : ([0,1], 0.05),
}
m = Minuit(LeastSquares(bins, data, data_errs, RegEff.sigFunc), **parameters)
for par in m.parameters:
m.limits[par], m.errors[par] = parameters_options[par]
m.migrad()
if not(m.accurate):
warnings.warn('Minuit troubles')
if self.fit_results is None:
columns = []
columns += m.parameters
columns += ( tuple(map(lambda x: f'{x}_err', m.parameters)) + ('eff0', 'eff0_err') )
self.fit_results = pd.DataFrame(columns=columns)
eff0 = RegEff.sigFunc(0, *m.values)
eff0_err = RegEff.sigFunc(0, *(np.array(m.values)+np.array(m.errors))) - eff0
temp_ser = pd.Series(list(m.values) + list(m.errors) + [eff0, eff0_err], index=self.fit_results.columns, name=self.index2energy(index))
if temp_ser.name in self.fit_results.index:
self.fit_results.drop(temp_ser.name, axis=0, inplace=True)
self.fit_results = self.fit_results.append(temp_ser)
fig, ax = plt.subplots()
xx = np.linspace(0, np.max(bins), 100)
ax.errorbar(bins, data, yerr=data_errs, fmt='.', color=data_color)
ax.plot(xx, RegEff.sigFunc(xx, *m.values), color=fit_color)
my_style(title=f'Registration eff. vs rad. photon energy ($\sqrt{{s}}$ = {self.index2energy(index)*2e-3:.3f} GeV)', xlim=(0, np.max(bins)), ylim=(0, None),
xtitle='$E_{\\gamma}$, GeV', ytitle='$\\varepsilon_{reg}$')
values_dict = dict(zip(m.parameters, m.values))
chi2, ndf = m.fval, len(bins)-len(m.parameters)-1
s = f'$\\chi^2$ / ndf = {chi2:.2f} / {ndf}\n'
s += f'p-value: {1-stats.chi2.cdf(chi2, ndf):.2f}\n'
for var, val, err, fixed in zip(m.parameters, m.values, m.errors, m.fixed):
if fixed:
s += f'{var} = {val:1.3f}\n'
else:
s += f'{var} = {val:1.3f}$\\pm${err:.4f}\n'
props = dict(boxstyle='square', facecolor=box_color, alpha=0.5)
ax.text(0.65, 0.95, s.strip(), transform=ax.transAxes,
verticalalignment='top', bbox=props)
return
def test_NormalConstraint_1():
def model(x, a):
return a
lsq1 = LeastSquares(0, 1, 1, model)
lsq2 = lsq1 + NormalConstraint("a", 1, 0.1)
assert lsq1.func_code.co_varnames == ("a",)
assert lsq2.func_code.co_varnames == ("a",)
m = Minuit(lsq1, 0)
m.migrad()
assert_allclose(m.values, (1,), atol=1e-2)
assert_allclose(m.errors, (1,), rtol=1e-2)
m = Minuit(lsq2, 0)
m.migrad()
assert_allclose(m.values, (1,), atol=1e-2)
assert_allclose(m.errors, (0.1,), rtol=1e-2)
def test_LeastSquares_properties():
def model(x, a):
return a
c = LeastSquares(1, 2, 3, model)
assert_equal(c.x, [1])
assert_equal(c.y, [2])
assert_equal(c.yerror, [3])
assert c.model is model
with pytest.raises(AttributeError):
c.model = model
with pytest.raises(ValueError):
c.x = [1, 2]
with pytest.raises(ValueError):
c.y = [1, 2]
with pytest.raises(ValueError):
c.yerror = [1, 2]
TCR2 = 1 / ((1 / TCS2) + (1 / TAUR))
JTOT1 = TCR1 / (1 + numpy.power((freq1 * TCR1), 2))
JTOT2 = TCR2 / (1 + numpy.power((freq2 * TCR2), 2))
RR1 = CMR * (
(3 * JTOT1) +
(7 * JTOT2)) + (CMS * TCS2) / (1 + numpy.power(freq2 * TCS2, 2))
T1M = 1 / RR1 # T1m
R1rotSS = PROPR * (
(CONC / 55.55) * SOLV) / (T1M + TAUM) #PROPR # Y de R1
# return x
# print(R1trans + R1rot)
return R1trans + R1rotSS
data_yerr = 0.000001
least_squares = LeastSquares(rawdata_x, rawdata_y, data_yerr, line)
# pass starting values for a and b
# print("coucou1")
m = Minuit(
least_squares,
CONC=float(params["CONC"]["value"]),
SOLV=float(params["SOLV"]["value"]),
PROPR=float(params["PROPR"]["value"]),
SPIN=float(params["SPIN"]["value"]),
B=float(params["B"]["value"]),
DIF=float(params["DIF"]["value"]),
TAUS0=float(params["TAUS0"]["value"]),
TAUV=float(params["TAUV"]["value"]),
PROPT=float(params["PROPT"]["value"]),
gl=float(params["gl"]["value"]),
TAUM=float(params["TAUM"]["value"]),
plt.xlabel('$t_{decay}$ (s)')
plt.ylabel('Entries')
plt.title('Decay time distribution')
centers = bins[:-1] + np.diff(bins) / 2
gamma_init = 100.
n0_init = n[0]
#l = 1./gamma
def special_exp(x, n0, gamma):
y = n0 * np.exp(-centers / (gamma * piCnst.lifetime()))
return y
#plt.plot(centers, y, '-', color='b')
least_squares = LeastSquares(centers, n, yerror=np.sqrt(n), model=special_exp)
m = Minuit(least_squares, n0=n0_init, gamma=gamma_init)
m.migrad()
print(m.hesse())
plt.plot(centers,
special_exp(centers, m.values[0], m.values[1]),
color='b',
label='fit')
#plt.show()
plt.savefig('Scratch/nuSTORMTrfLine/nuSTORMTrfLineTst_4_tdec.pdf')
plt.close()
n, bins, patches = plt.hist(s_dcy_pi, bins=50, color='y')
plt.xlabel('s decay (m)')
plt.ylabel('Entries')
plt.title('Decay point distribution')
print(error)
errbar = np.array(error)
err = sem(avg)
x_data = len
y = avg
f = plt.figure()
f.set_figwidth(10)
f.set_figheight(10)
def line(x, a, b):
return a + b * x
least_squares = LeastSquares(x_data, y, error, line)
m = Minuit(least_squares, a=0, b=0)
m.migrad() # finds minimum of least_squares function
m.hesse()
plt.plot(np.linspace(0.35, 2.00),
line(np.linspace(0.35, 2.00), *m.values),
label="fit")
plt.errorbar(x_data, y, yerr=error, fmt="o", label="data")
print(x_data)
print(m.nfit)
print(m.fval)
length = 7
r = m.fval / (length - m.nfit)
fit_info = [
eid_other.append(i[0]) P = pd.DataFrame(eid_p) if not P.empty: P.columns = ['EventID'] P_DFRONT = pd.merge(P,DATA_FRONT, on='EventID') P_DBACK = pd.merge(P,DATA_BACK, on='EventID') P_DDIFF = pd.merge(P,DATA_DIFFERENCE, on='EventID') P_DDIFF = P_DDIFF.dropna() P_DBACK = P_DBACK.dropna() doiList = P_DBACK.gammaxpos.tolist() backCountsList = P_DBACK.Back_Counts.tolist() diffCountsList = P_DDIFF.Difference_Counts.tolist() k = Minuit(LeastSquares(diffCountsList, doiList, 10.0, Line), m = 0.02, b = 0) k.migrad() k.hesse() fig, axs = plt.subplots() crystalLength = 30 nChoices = [5] refractiveIndex = 1.82 for index in range(len(nChoices)): nthPhotonTimes = [] backTriggers = [] frontTriggers = [] doiList = [] doiTruthList = []
variancesOverEnergy.append(varianceOverEnergy)
photopeakEnergies = [i for i in eventEnergies if i > 7500]
numBins = 50
fig, ax = plt.subplots()
hist, xedges = np.histogram(eventEnergies, bins=100)
photoPeak = xedges[hist.argmax()]
(binCounts, bins,
patches) = ax.hist(photopeakEnergies,
bins=numBins,
range=[photoPeak - 1000, photoPeak + 1000])
binCenters = np.linspace(min(bins), max(bins), numBins)
k = Minuit(LeastSquares(binCenters, binCounts, 10.0, gauss),
a=100,
mu=photoPeak,
sigma=100,
c=0)
k.migrad()
k.hesse()
energyResolution = k.values[2] / k.values[1] * 100
fitPoints = np.linspace(min(bins), max(bins), 1000)
ax.plot(fitPoints, gauss(fitPoints, *k.values[0:4]), color='k')
ax.text(0.7, 0.9, "Data Stats:", weight='bold', transform=ax.transAxes)
ax.text(0.7,
0.85,
"mean: " + format(np.mean(photopeakEnergies), "5.4f"),
transform=ax.transAxes)
new_mag = []
for i in range(len(x_chunk)):
if np.abs(x_chunk[i] - np.median(x_chunk)
) < 2 * 1.428 * stats.median_absolute_deviation(
x_chunk - np.median(x_chunk)):
new_chunk.append(x_chunk[i])
newt_chunk.append(t_chunk[i])
new_chunk1.append(ra_chunk[i])
new_chunk2.append(dec_chunk[i])
new_mag.append(mag_chunk[i])
new_chunk3.append(raerr_chunk[i])
new_chunk4.append(decerr_chunk[i])
#Run Minuit on outlier-free ra and dec chunks
least_squares = LeastSquares(newt_chunk, new_chunk1, new_chunk3, line)
m = Minuit(least_squares, a=0, b=0)
m.migrad()
m.hesse()
least_squares1 = LeastSquares(newt_chunk, new_chunk2, new_chunk4, line)
m1 = Minuit(least_squares1, a=0, b=0)
m1.migrad()
m1.hesse()
#Run linear regression with scipy.stats
slope, intercept, r_value, p_value, std_err = stats.linregress(
def fit_freezeout(dict_yield,**kwargs):
"""
Extract freeze out parameters by fitting final heavy ion data (dN/dy)
given in dict_yield. Construct ratios of different particles.
"""
# additional plots of chi^2 (takes time)
try:
chi2_plot = kwargs['chi2_plot']
except:
chi2_plot = False # default
# consider decay from unstable particles in the calculation of densities?
try:
freezeout_decay = kwargs['freezeout_decay']
except:
freezeout_decay = True
# apply fit to both yields and ratios?
try:
method = kwargs['method']
except:
method = 'all'
# consider integration over mass?
try:
offshell = kwargs['offshell']
except:
offshell = False # default
# evaluate freeze out parameters for which EoS? full or strangeness neutrality ns0 ?
try:
EoS = kwargs['EoS']
except:
EoS = 'all' # default
# we fit the HRG EoS to the ratios of particle yields as list_part1/list_part2
# as in BES STAR paper: PHYSICAL REVIEW C 96, 044904 (2017)
list_part1 = ['pi-','K-','p~','Lambda~','Xi~+','K-','p~','Lambda','Xi~+']
list_part2 = ['pi+','K+','p','Lambda','Xi-','pi-','pi-','pi-','pi-']
# unique list of particles (for the yields)
list_part = ['pi+','pi-','K+','K-','p','p~','Lambda','Lambda~','Xi-','Xi~+']
# construct yields from input
data_yields = []
err_yields = []
final_part = []
for part in list_part:
try:
# check if the particles are given in dict_yield
if(dict_yield[part]!=None and dict_yield[part]>0.):
data_yields.append(dict_yield[part])
err_yields.append(dict_yield[part+'_err'])
final_part.append(part)
except:
pass
# construct ratios from input yields
data_ratios = []
err_ratios = []
final_part1 = []
final_part2 = []
# loop over particles in list_part1 and list_part2
for part1,part2 in zip(list_part1,list_part2):
try:
# check if the particles are given in dict_yield
if(dict_yield[part1]!=None and dict_yield[part1]>0. and dict_yield[part2]!=None and dict_yield[part2]>0.):
ratio = dict_yield[part1]/dict_yield[part2]
data_ratios.append(ratio)
err_ratios.append(abs(ratio)*np.sqrt((dict_yield[part1+'_err']/dict_yield[part1])**2.+(dict_yield[part2+'_err']/dict_yield[part2])**2.))
final_part1.append(part1)
final_part2.append(part2)
except:
pass
def f_yields(x,T,muB,muQ,muS,gammaS,dVdy):
"""
Calculate the particle yields for fixed T,muB,muQ,muS,gammaS,volume
x is a dummy argument
"""
result = np.zeros(len(final_part))
# calculate all densities
result_HRG = HRG_freezout(T,muB,muQ,muS,gammaS,EoS='full',**kwargs)
# loop over particles
for i,part in enumerate(final_part):
yval = result_HRG[part]
#print('part,yval=',part,yval)
# if no decays, then Sigma0 should be added to Lambda
# if decays are activated, then Sigma0 decays to Lambda
if(not(freezeout_decay)):
# include Sigma0 with Lambda
if(part=='Lambda'):
yval += result_HRG['Sigma0']
# include Sigma~0 with Lambda~
elif(part=='Lambda~'):
yval += result_HRG['Sigma~0']
# number of particles
result[i] = yval*T**3.*dVdy/(0.197**3.)
# return the list of yields
return result
def f_yields_nS0(x,T,muB,gammaS,dVdy):
"""
Calculate the particle yields for fixed T,muB,gammaS,volume
x is a dummy argument
"""
result = np.zeros(len(final_part))
# calculate all densities
result_HRG = HRG_freezout(T,muB,0.,0.,gammaS,EoS='nS0',**kwargs)
# loop over particles
for i,part in enumerate(final_part):
yval = result_HRG[part]
#print('part,yval=',part,yval)
# if no decays, then Sigma0 should be added to Lambda
# if decays are activated, then Sigma0 decays to Lambda
if(not(freezeout_decay)):
# include Sigma0 with Lambda
if(part=='Lambda'):
yval += result_HRG['Sigma0']
# include Sigma~0 with Lambda~
elif(part=='Lambda~'):
yval += result_HRG['Sigma~0']
# number of particles
result[i] = yval*T**3.*dVdy/(0.197**3.)
# return the list of yields
return result
def f_ratios(x,T,muB,muQ,muS,gammaS):
"""
Calculate the ratios of particle yields for fixed T,muB,muQ,muS,gammaS
x is a dummy argument
"""
result = np.zeros(len(data_ratios))
# calculate all densities
result_HRG = HRG_freezout(T,muB,muQ,muS,gammaS,EoS='full',**kwargs)
# loop over different ratios
for i,(part1,part2) in enumerate(zip(final_part1,final_part2)):
yval1 = result_HRG[part1]
yval2 = result_HRG[part2]
#print('part,yval1=',part1,yval1)
#print('part,yval2=',part2,yval2)
# if no decays, then Sigma0 should be added to Lambda
# if decays are activated, then Sigma0 decays to Lambda
if(not(freezeout_decay)):
# include Sigma0 with Lambda
if(part1=='Lambda'):
yval1 += result_HRG['Sigma0']
# include Sigma~0 with Lambda~
elif(part1=='Lambda~'):
yval1 += result_HRG['Sigma~0']
# include Sigma0 with Lambda
if(part2=='Lambda'):
yval2 += result_HRG['Sigma0']
# include Sigma~0 with Lambda~
elif(part2=='Lambda~'):
yval2 += result_HRG['Sigma~0']
# ratio of particle1/particle2
result[i] = yval1/yval2
# return the list of ratios
return result
def f_ratios_nS0(x,T,muB,gammaS):
"""
Calculate the ratios of particle yields for fixed T,muB,gammaS
x is a dummy argument
"""
result = np.zeros(len(data_ratios))
# calculate all densities
result_HRG = HRG_freezout(T,muB,0.,0.,gammaS,EoS='nS0',**kwargs)
# loop over different ratios
for i,(part1,part2) in enumerate(zip(final_part1,final_part2)):
yval1 = result_HRG[part1]
yval2 = result_HRG[part2]
#print('part,yval1=',part1,yval1)
#print('part,yval2=',part2,yval2)
# if no decays, then Sigma0 should be added to Lambda
# if decays are activated, then Sigma0 decays to Lambda
if(not(freezeout_decay)):
# include Sigma0 with Lambda
if(part1=='Lambda'):
yval1 += result_HRG['Sigma0']
# include Sigma~0 with Lambda~
elif(part1=='Lambda~'):
yval1 += result_HRG['Sigma~0']
# include Sigma0 with Lambda
if(part2=='Lambda'):
yval2 += result_HRG['Sigma0']
# include Sigma~0 with Lambda~
elif(part2=='Lambda~'):
yval2 += result_HRG['Sigma~0']
# ratio of particle1/particle2
result[i] = yval1/yval2
# return the list of ratios
return result
# initialize the parameters
# which parameters to be fixed?
fix_T=False
fix_muB=False
fix_muQ=False
fix_muS=False
fix_gammaS=False
fix_dVdy=False
# first guesses for T,muB,muQ,muS,gammaS,dVdy
guess = (0.150, 0.05, 0., 0.05, 1., 2000.)
# bounds
bounds = ((0.100, 0.200), (0, 0.6), (-0.2,0.2), (0,0.2), (0.0,1.2), (100.,10000.))
# fit with yields
if((EoS=='all' or EoS=='full') and (method=='all' or method=='yields')):
# x-values, just the indexes of ratios [1,2,...,N_particles]
xyields = np.arange(len(final_part))
# initialize Minuit least_squares class
least_squares = LeastSquares(xyields, data_yields, err_yields, f_yields)
m = Minuit(least_squares, T=guess[0], muB=guess[1], muQ=guess[2], muS=guess[3], gammaS=guess[4], dVdy=guess[5],
limit_T=bounds[0],limit_muB=bounds[1],limit_muQ=bounds[2],limit_muS=bounds[3],limit_gammaS=bounds[4],limit_dVdy=bounds[5],
fix_T=fix_T,fix_muB=fix_muB,fix_muQ=fix_muQ,fix_muS=fix_muS,fix_gammaS=fix_gammaS,fix_dVdy=fix_dVdy)
m.migrad() # finds minimum of least_squares function
m.hesse() # computes errors
#print(m.params) # minuit output
# display values and errors
popt1 = m.values.values()
perr1 = m.errors.values()
print('\nfit from yields, full EoS:')
fit_string1 = f'$T_{{ch}}={popt1[0]:.4f} \pm {perr1[0]:.4f}\ GeV$\
\n$\mu_{{B}}={popt1[1]:.4f} \pm {perr1[1]:.4f}\ GeV$\
\n$\mu_{{Q}}={popt1[2]:.4f} \pm {perr1[2]:.4f}\ GeV$\
\n$\mu_{{S}}={popt1[3]:.4f} \pm {perr1[3]:.4f}\ GeV$\
\n$\gamma_{{S}}={popt1[4]:.2f} \pm {perr1[4]:.2f}$\
\n$dV/dy={popt1[5]:.1f} \pm {perr1[5]:.1f} \ fm^3$'
print(fit_string1)
thermo = HRG(popt1[0],popt1[1],popt1[2],popt1[3],gammaS=popt1[4],offshell=offshell)
snB1 = thermo['s']/thermo['n_B']
snB1_err = 0.
# derivative wrt T
thermoT1 = HRG(popt1[0]+perr1[0]/2.,popt1[1],popt1[2],popt1[3],gammaS=popt1[4],offshell=offshell)
thermoT2 = HRG(popt1[0]-perr1[0]/2.,popt1[1],popt1[2],popt1[3],gammaS=popt1[4],offshell=offshell)
if(thermoT1['n_B']!=0. and thermoT2['n_B']!=0.):
snB1_err += (thermoT1['s']/thermoT1['n_B']-thermoT2['s']/thermoT2['n_B'])**2.
# derivative wrt mu_B
thermomuB1 = HRG(popt1[0],popt1[1]+perr1[1]/2.,popt1[2],popt1[3],gammaS=popt1[4],offshell=offshell)
thermomuB2 = HRG(popt1[0],popt1[1]-perr1[1]/2.,popt1[2],popt1[3],gammaS=popt1[4],offshell=offshell)
if(thermomuB1['n_B']!=0. and thermomuB2['n_B']!=0.):
snB1_err += (thermomuB1['s']/thermomuB1['n_B']-thermomuB2['s']/thermomuB2['n_B'])**2.
# derivative wrt mu_Q
thermomuQ1 = HRG(popt1[0],popt1[1],popt1[2]+perr1[2]/2.,popt1[3],gammaS=popt1[4],offshell=offshell)
thermomuQ2 = HRG(popt1[0],popt1[1],popt1[2]-perr1[2]/2.,popt1[3],gammaS=popt1[4],offshell=offshell)
if(thermomuQ1['n_B']!=0. and thermomuQ2['n_B']!=0.):
snB1_err += (thermomuQ1['s']/thermomuQ1['n_B']-thermomuQ2['s']/thermomuQ2['n_B'])**2.
# derivative wrt mu_S
thermomuS1 = HRG(popt1[0],popt1[1],popt1[2],popt1[3]+perr1[3]/2.,gammaS=popt1[4],offshell=offshell)
thermomuS2 = HRG(popt1[0],popt1[1],popt1[2],popt1[3]-perr1[3]/2.,gammaS=popt1[4],offshell=offshell)
if(thermomuS1['n_B']!=0. and thermomuS2['n_B']!=0.):
snB1_err += (thermomuS1['s']/thermomuS1['n_B']-thermomuS2['s']/thermomuS2['n_B'])**2.
# derivative wrt gamma_S
thermogammaS1 = HRG(popt1[0],popt1[1],popt1[2],popt1[3],gammaS=popt1[4]+perr1[4]/2.,offshell=offshell)
thermogammaS2 = HRG(popt1[0],popt1[1],popt1[2],popt1[3],gammaS=popt1[4]-perr1[4]/2.,offshell=offshell)
if(thermogammaS1['n_B']!=0. and thermogammaS2['n_B']!=0.):
snB1_err += (thermogammaS1['s']/thermogammaS1['n_B']-thermogammaS2['s']/thermogammaS2['n_B'])**2.
# error as sqrt((df/dT)**2. dT+(df/dmuB)**2.+...) with f = s/n_B
snB1_err = np.sqrt(snB1_err)
print(f's/n_B = {snB1} \pm {snB1_err}')
# evaluate the chi^2 values for each parameter
if(chi2_plot):
dT, fT = m.profile('T')
dmuB, fmuB = m.profile('muB')
dmuQ, fmuQ = m.profile('muQ')
dmuS, fmuS = m.profile('muS')
dgammaS, fgammaS = m.profile('gammaS')
ddVdy, fdVdy = m.profile('dVdy')
output_chi21 = [[dT,fT],[dmuB,fmuB],[dmuQ,fmuQ],[dmuS,fmuS],[dgammaS,fgammaS],[ddVdy,fdVdy]]
else:
output_chi21 = None
output_yields = {'fit_yields':np.array(list(zip(popt1,perr1))),\
'fit_string_yields':fit_string1,\
'result_yields':f_yields(xyields,*popt1),\
'data_yields':np.array(list(zip(data_yields,err_yields))),\
'particle_yields':list(latex(final_part)),\
'chi2_yields':output_chi21,\
'snB_yields':np.array([snB1,snB1_err])}
else:
output_yields = {}
# fit with yields
# strangeness neutrality
if((EoS=='all' or EoS=='nS0') and (method=='all' or method=='yields')):
# x-values, just the indexes of ratios [1,2,...,N_particles]
xyields = np.arange(len(final_part))
# initialize Minuit least_squares class
least_squares = LeastSquares(xyields, data_yields, err_yields, f_yields_nS0)
m = Minuit(least_squares, T=guess[0], muB=guess[1], gammaS=guess[4], dVdy=guess[5],
limit_T=bounds[0],limit_muB=bounds[1],limit_gammaS=bounds[4],limit_dVdy=bounds[5],
fix_T=fix_T,fix_muB=fix_muB,fix_gammaS=fix_gammaS,fix_dVdy=fix_dVdy)
m.migrad() # finds minimum of least_squares function
m.hesse() # computes errors
#print(m.params) # minuit output
# display values and errors
popt1 = m.values.values()
perr1 = m.errors.values()
thermo = EoS_nS0(HRG,popt1[0],popt1[1],gammaS=popt1[2],offshell=offshell)
print('\nfit from yields, nS0 EoS:')
fit_string1 = f'$T_{{ch}}={popt1[0]:.4f} \pm {perr1[0]:.4f}\ GeV$\
\n$\mu_{{B}}={popt1[1]:.4f} \pm {perr1[1]:.4f}\ GeV$\
\n$\gamma_{{S}}={popt1[2]:.2f} \pm {perr1[2]:.2f}$\
\n$dV/dy={popt1[3]:.1f} \pm {perr1[3]:.1f} \ fm^3$\
\n$\mu_{{Q}}={thermo["muQ"]:.4f}\ GeV$\
\n$\mu_{{S}}={thermo["muS"]:.4f}\ GeV$'
print(fit_string1)
snB1 = thermo['s']/thermo['n_B']
snB1_err = 0.
# derivative wrt T
thermoT1 = EoS_nS0(HRG,popt1[0]+perr1[0]/2.,popt1[1],gammaS=popt1[2],offshell=offshell)
thermoT2 = EoS_nS0(HRG,popt1[0]-perr1[0]/2.,popt1[1],gammaS=popt1[2],offshell=offshell)
if(thermoT1['n_B']!=0. and thermoT2['n_B']!=0.):
snB1_err += (thermoT1['s']/thermoT1['n_B']-thermoT2['s']/thermoT2['n_B'])**2.
# derivative wrt mu_B
thermomuB1 = EoS_nS0(HRG,popt1[0],popt1[1]+perr1[1]/2.,gammaS=popt1[2],offshell=offshell)
thermomuB2 = EoS_nS0(HRG,popt1[0],popt1[1]-perr1[1]/2.,gammaS=popt1[2],offshell=offshell)
if(thermomuB1['n_B']!=0. and thermomuB2['n_B']!=0.):
snB1_err += (thermomuB1['s']/thermomuB1['n_B']-thermomuB2['s']/thermomuB2['n_B'])**2.
# derivative wrt gamma_S
thermogammaS1 = EoS_nS0(HRG,popt1[0],popt1[1],gammaS=popt1[2]+perr1[2]/2.,offshell=offshell)
thermogammaS2 = EoS_nS0(HRG,popt1[0],popt1[1],gammaS=popt1[2]-perr1[2]/2.,offshell=offshell)
if(thermogammaS1['n_B']!=0. and thermogammaS2['n_B']!=0.):
snB1_err += (thermogammaS1['s']/thermogammaS1['n_B']-thermogammaS2['s']/thermogammaS2['n_B'])**2.
# error as sqrt((df/dT)**2. dT+(df/dmuB)**2.+...) with f = s/n_B
snB1_err = np.sqrt(snB1_err)
print(f's/n_B = {snB1} \pm {snB1_err}')
# evaluate the chi^2 values for each parameter
if(chi2_plot):
dT, fT = m.profile('T')
dmuB, fmuB = m.profile('muB')
dgammaS, fgammaS = m.profile('gammaS')
ddVdy, fdVdy = m.profile('dVdy')
output_chi21 = [[dT,fT],[dmuB,fmuB],[dgammaS,fgammaS],[ddVdy,fdVdy]]
else:
output_chi21 = None
result_yields_nS0 = f_yields_nS0(xyields,*popt1)
Tch,muB,gammaS,dVdy = popt1
Tch_err,muB_err,gammaS_err,dVdy_err = perr1
popt1 = np.array([Tch,muB,thermo['muQ'],thermo['muS'],gammaS,dVdy])
perr1 = np.array([Tch_err,muB_err,0.,0.,gammaS_err,dVdy_err])
output_yields_nS0 = {'fit_yields_nS0':np.array(list(zip(popt1,perr1))),\
'fit_string_yields_nS0':fit_string1,\
'result_yields_nS0':result_yields_nS0,\
'data_yields':np.array(list(zip(data_yields,err_yields))),\
'particle_yields':list(latex(final_part)),\
'chi2_yields_nS0':output_chi21,\
'snB_yields_nS0':np.array([snB1,snB1_err])}
else:
output_yields_nS0 = {}
# fit with ratios
if((EoS=='all' or EoS=='full') and (method=='all' or method=='ratios')):
# x-values, just the indexes of ratios [1,2,...,N_ratios]
xratios = np.arange(len(data_ratios))
# initialize Minuit least_squares class
least_squares = LeastSquares(xratios, data_ratios, err_ratios, f_ratios)
m = Minuit(least_squares, T=guess[0], muB=guess[1], muQ=guess[2], muS=guess[3], gammaS=guess[4],
limit_T=bounds[0],limit_muB=bounds[1],limit_muQ=bounds[2],limit_muS=bounds[3],limit_gammaS=bounds[4],
fix_T=fix_T,fix_muB=fix_muB,fix_muQ=fix_muQ,fix_muS=fix_muS,fix_gammaS=fix_gammaS)
m.migrad() # finds minimum of least_squares function
m.hesse() # computes errors
#print(m.params) # minuit output
# display values and errors
popt2 = m.values.values()
perr2 = m.errors.values()
print('\nfit from ratios, full EoS:')
fit_string2 = f'$T_{{ch}}={popt2[0]:.4f} \pm {perr2[0]:.4f}\ GeV$\
\n$\mu_{{B}}={popt2[1]:.4f} \pm {perr2[1]:.4f}\ GeV$\
\n$\mu_{{Q}}={popt2[2]:.4f} \pm {perr2[2]:.4f}\ GeV$\
\n$\mu_{{S}}={popt2[3]:.4f} \pm {perr2[3]:.4f}\ GeV$\
\n$\gamma_{{S}}={popt2[4]:.2f} \pm {perr2[4]:.2f}$'
print(fit_string2)
thermo = HRG(popt2[0],popt2[1],popt2[2],popt2[3],gammaS=popt2[4],offshell=offshell)
snB2 = thermo['s']/thermo['n_B']
snB2_err = 0.
# derivative wrt T
thermoT1 = HRG(popt2[0]+perr2[0]/2.,popt2[1],popt2[2],popt2[3],gammaS=popt2[4],offshell=offshell)
thermoT2 = HRG(popt2[0]-perr2[0]/2.,popt2[1],popt2[2],popt2[3],gammaS=popt2[4],offshell=offshell)
if(thermoT1['n_B']!=0. and thermoT2['n_B']!=0.):
snB2_err += (thermoT1['s']/thermoT1['n_B']-thermoT2['s']/thermoT2['n_B'])**2.
# derivative wrt mu_B
thermomuB1 = HRG(popt2[0],popt2[1]+perr2[1]/2.,popt2[2],popt2[3],gammaS=popt2[4],offshell=offshell)
thermomuB2 = HRG(popt2[0],popt2[1]-perr2[1]/2.,popt2[2],popt2[3],gammaS=popt2[4],offshell=offshell)
if(thermomuB1['n_B']!=0. and thermomuB2['n_B']!=0.):
snB2_err += (thermomuB1['s']/thermomuB1['n_B']-thermomuB2['s']/thermomuB2['n_B'])**2.
# derivative wrt mu_Q
thermomuQ1 = HRG(popt2[0],popt2[1],popt2[2]+perr2[2]/2.,popt2[3],gammaS=popt2[4],offshell=offshell)
thermomuQ2 = HRG(popt2[0],popt2[1],popt2[2]-perr2[2]/2.,popt2[3],gammaS=popt2[4],offshell=offshell)
if(thermomuQ1['n_B']!=0. and thermomuQ2['n_B']!=0.):
snB2_err += (thermomuQ1['s']/thermomuQ1['n_B']-thermomuQ2['s']/thermomuQ2['n_B'])**2.
# derivative wrt mu_S
thermomuS1 = HRG(popt2[0],popt2[1],popt2[2],popt2[3]+perr2[3]/2.,gammaS=popt2[4],offshell=offshell)
thermomuS2 = HRG(popt2[0],popt2[1],popt2[2],popt2[3]-perr2[3]/2.,gammaS=popt2[4],offshell=offshell)
if(thermomuS1['n_B']!=0. and thermomuS2['n_B']!=0.):
snB2_err += (thermomuS1['s']/thermomuS1['n_B']-thermomuS2['s']/thermomuS2['n_B'])**2.
# derivative wrt gamma_S
thermogammaS1 = HRG(popt2[0],popt2[1],popt2[2],popt2[3],gammaS=popt2[4]+perr2[4]/2.,offshell=offshell)
thermogammaS2 = HRG(popt2[0],popt2[1],popt2[2],popt2[3],gammaS=popt2[4]-perr2[4]/2.,offshell=offshell)
if(thermogammaS1['n_B']!=0. and thermogammaS2['n_B']!=0.):
snB2_err += (thermogammaS1['s']/thermogammaS1['n_B']-thermogammaS2['s']/thermogammaS2['n_B'])**2.
# error as sqrt((df/dT)**2. dT+(df/dmuB)**2.+...) with f = s/n_B
snB2_err = np.sqrt(snB2_err)
print(f's/n_B = {snB2} \pm {snB2_err}')
# evaluate the chi^2 values for each parameter
if(chi2_plot):
dT, fT = m.profile('T')
dmuB, fmuB = m.profile('muB')
dmuQ, fmuQ = m.profile('muQ')
dmuS, fmuS = m.profile('muS')
dgammaS, fgammaS = m.profile('gammaS')
output_chi22 = [[dT,fT],[dmuB,fmuB],[dmuQ,fmuQ],[dmuS,fmuS],[dgammaS,fgammaS]]
else:
output_chi22 = None
output_ratios = {'fit_ratios':np.array(list(zip(popt2,perr2))),\
'fit_string_ratios':fit_string2,\
'result_ratios':f_ratios(xratios,*popt2),\
'data_ratios':np.array(list(zip(data_ratios,err_ratios))),\
'particle_ratios':list(zip(latex(final_part1),latex(final_part2))),\
'chi2_ratios':output_chi22,\
'snB_ratios':np.array([snB2,snB2_err])}
else:
output_ratios = {}
# fit with ratios
if((EoS=='all' or EoS=='nS0') and (method=='all' or method=='ratios')):
# x-values, just the indexes of ratios [1,2,...,N_ratios]
xratios = np.arange(len(data_ratios))
# initialize Minuit least_squares class
least_squares = LeastSquares(xratios, data_ratios, err_ratios, f_ratios_nS0)
m = Minuit(least_squares, T=guess[0], muB=guess[1], gammaS=guess[4],
limit_T=bounds[0],limit_muB=bounds[1],limit_gammaS=bounds[4],
fix_T=fix_T,fix_muB=fix_muB,fix_gammaS=fix_gammaS)
m.migrad() # finds minimum of least_squares function
m.hesse() # computes errors
#print(m.params) # minuit output
# display values and errors
popt2 = m.values.values()
perr2 = m.errors.values()
thermo = EoS_nS0(HRG,popt2[0],popt2[1],gammaS=popt2[2],offshell=offshell)
print('\nfit from ratios, nS0 EoS:')
fit_string2 = f'$T_{{ch}}={popt2[0]:.4f} \pm {perr2[0]:.4f}\ GeV$\
\n$\mu_{{B}}={popt2[1]:.4f} \pm {perr2[1]:.4f}\ GeV$\
\n$\gamma_{{S}}={popt2[2]:.2f} \pm {perr2[2]:.2f}$\
\n$\mu_{{Q}}={thermo["muQ"]:.4f}\ GeV$\
\n$\mu_{{S}}={thermo["muS"]:.4f}\ GeV$'
print(fit_string2)
snB2 = thermo['s']/thermo['n_B']
snB2_err = 0.
# derivative wrt T
thermoT1 = EoS_nS0(HRG,popt2[0]+perr2[0]/2.,popt2[1],gammaS=popt2[2],offshell=offshell)
thermoT2 = EoS_nS0(HRG,popt2[0]-perr2[0]/2.,popt2[1],gammaS=popt2[2],offshell=offshell)
if(thermoT1['n_B']!=0. and thermoT2['n_B']!=0.):
snB2_err += (thermoT1['s']/thermoT1['n_B']-thermoT2['s']/thermoT2['n_B'])**2.
# derivative wrt mu_B
thermomuB1 = EoS_nS0(HRG,popt2[0],popt2[1]+perr2[1]/2.,gammaS=popt2[2],offshell=offshell)
thermomuB2 = EoS_nS0(HRG,popt2[0],popt2[1]-perr2[1]/2.,gammaS=popt2[2],offshell=offshell)
if(thermomuB1['n_B']!=0. and thermomuB2['n_B']!=0.):
snB2_err += (thermomuB1['s']/thermomuB1['n_B']-thermomuB2['s']/thermomuB2['n_B'])**2.
# derivative wrt gamma_S
thermogammaS1 = EoS_nS0(HRG,popt2[0],popt2[1],gammaS=popt2[2]+perr2[2]/2.,offshell=offshell)
thermogammaS2 = EoS_nS0(HRG,popt2[0],popt2[1],gammaS=popt2[2]-perr2[2]/2.,offshell=offshell)
if(thermogammaS1['n_B']!=0. and thermogammaS2['n_B']!=0.):
snB2_err += (thermogammaS1['s']/thermogammaS1['n_B']-thermogammaS2['s']/thermogammaS2['n_B'])**2.
# error as sqrt((df/dT)**2. dT+(df/dmuB)**2.+...) with f = s/n_B
snB2_err = np.sqrt(snB2_err)
print(f's/n_B = {snB2} \pm {snB2_err}')
# evaluate the chi^2 values for each parameter
if(chi2_plot):
dT, fT = m.profile('T')
dmuB, fmuB = m.profile('muB')
dgammaS, fgammaS = m.profile('gammaS')
output_chi22 = [[dT,fT],[dmuB,fmuB],[dgammaS,fgammaS]]
else:
output_chi22 = None
result_ratios_nS0 = f_ratios_nS0(xratios,*popt2)
Tch,muB,gammaS = popt2
Tch_err,muB_err,gammaS_err = perr2
popt2 = np.array([Tch,muB,thermo['muQ'],thermo['muS'],gammaS])
perr2 = np.array([Tch_err,muB_err,0.,0.,gammaS_err])
output_ratios_nS0 = {'fit_ratios_nS0':np.array(list(zip(popt2,perr2))),\
'fit_string_ratios_nS0':fit_string2,\
'result_ratios_nS0':result_ratios_nS0,\
'data_ratios':np.array(list(zip(data_ratios,err_ratios))),\
'particle_ratios':list(zip(latex(final_part1),latex(final_part2))),\
'chi2_ratios_nS0':output_chi22,\
'snB_ratios_nS0':np.array([snB2,snB2_err])}
else:
output_ratios_nS0 = {}
output = {}
output.update(output_yields)
output.update(output_ratios)
output.update(output_yields_nS0)
output.update(output_ratios_nS0)
return output
cache = []
# initilize model
model = Quarks(boundary_type=boundary_type)
chi_squared_threshold = 10.
N = 100 # number of trials
x = np.array([None])
# 2-step optimization process
# fit masses then fit full
for i in tqdm(range(N)):
# Step 1: fitting the masses only
params = model.generate_random_inputs(c_min=1., c_max=5.)
least_squares = LeastSquares(x, model.output_values[:, :6],
model.output_errors[:, :6],
model.get_output_masses)
optimizer = Minuit(least_squares, params, name=model.input_names)
optimizer.limits = model.input_limits
optimizer.fixed[:36] = True
try:
optimizer.migrad()
optimizer.hesse()
except ValueError:
pass
# Step 2: fitting all at once
# Only run if step 1 is error-free
if optimizer.fval:
params_2 = np.array(optimizer.values) # feed forward
y_2 = model.get_output_full(x, params_2)
def test_LeastSquares_mask():
c = LeastSquares([1, 2, 3], [3, np.nan, 4], [1, 1, 1], lambda x, a: x + a)
assert np.isnan(c(0)) == True
c.mask = np.arange(3) != 1
assert np.isnan(c(0)) == False
# elif whatDetector == 'Back':
# ax1 = P_DBACK.plot(kind='scatter', y ='gammaxpos', x='Back_Counts', label = 'phot',color='b')
# elif whatDetector == 'Difference':
# ax1 = P_DDIFF.plot(kind='scatter', y ='gammaxpos', x='Difference_Counts', label = 'phot',color='b')
# elif whatDetector == 'Aug':
# ax1 = P_DAUG.plot(kind='scatter', y ='gammaxpos', x='Augmented_Difference_Counts', label = 'phot',color='b')
P_DDIFF = P_DDIFF.dropna()
doiListPhot = P_DDIFF.gammaxpos.tolist()
differenceCountsPhot = P_DDIFF.Difference_Counts.tolist()
DATA_DIFFERENCE = DATA_DIFFERENCE.dropna()
doiList = DATA_DIFFERENCE.gammaxpos.tolist()
differenceCounts = DATA_DIFFERENCE.Difference_Counts.tolist()
m = Minuit(LeastSquares(differenceCountsPhot, doiListPhot, 10.0, Line),
m=-500,
b=3000)
m.migrad()
m.hesse()
# print(m.values)
# x = range(int(min(differenceCounts)), int(max(differenceCounts)))
# y = [Line(k, *m.values[0:2]) for k in x]
# ax1.plot(x, y, color = 'k')
# C = pd.DataFrame(eid_c)
# if not C.empty:
# C.columns = ['EventID']
# C_DFRONT = pd.merge(C,DATA_FRONT, on='EventID')
# C_DBACK = pd.merge(C,DATA_BACK, on='EventID')
# C_DDIFF = pd.merge(C,DATA_DIFFERENCE, on='EventID')
# C_DDIFF = pd.merge(C,DATA_DIFFERENCE, on='EventID')
dppLg = np.zeros_like(dppHg)
pedestalLg = np.zeros_like(pedestalHg)
if GUI:
fig, ax = plt.subplots()
for r in range(row):
for c in range(col):
channelHgPe = matrixHg[r, c, :]
channelLgADC = matrixLg[r, c, :]
x = channelHgPe[(channelHgPe > INF) & (channelHgPe < SUP)]
y = channelLgADC[(channelHgPe > INF) & (channelHgPe < SUP)]
lsq = LeastSquares(x, y, np.ones_like(y), line)
fit = Minuit(lsq, m=1, q=60)
fit.migrad()
fit.hesse()
dppLg[r, c] = fit.values["m"]
pedestalLg[r, c] = fit.values["q"]
print(
f"Channel {r} - {c} ADC/pe: {fit.values[0]:.2f} +/- {fit.errors[0]:.2f} Pedestal: {fit.values[1]:.2f} +/- {fit.errors[1]:.2f}"
)
if GUI:
xFit = np.arange(channelHgPe.min(), channelHgPe.max(), 0.1)
yFit = line(xFit, *fit.values)
par_b = np.random.multivariate_normal(fit.values,
fit.covariance,