class Minuit(object):
"""A wrapper class to initialize a minuit object with a numpy array.
Positional args:
myFCN : A python callable
params : An array (or other python sequence) of parameters
Keyword args:
limits [None] : a nested sequence of (lower_limit,upper_limit) for each parameter.
steps [[.1]*npars] : Estimated errors for the parameters, used as an initial step size.
tolerance [.001] : Tolerance to test for convergence. Minuit considers convergence to be
when the estimated distance to the minimum (edm) is <= .001*up*tolerance,
or 5e-7 by default.
up [.5] : Change in the objective function that determines 1-sigma error. .5 if
the objective function is -log(Likelihood), 1 for chi-squared.
max_calls [10000] : Maximum number of calls to the objective function.
param_names ['p0','p1',...] : a list of names for the parameters
args [()] : a tuple of extra arguments to pass to myFCN and gradient.
gradient [None] : a function that takes a list of parameters and returns a list of
first derivatives of myFCN. Assumed to take the same args as myFCN.
force_gradient [0] : Set to 1 to force Minuit to use the user-provided gradient function.
strategy[1] : Strategy for minuit to use, from 0 (fast) to 2 (safe)
fixed [False, False, ...] : If passed, an array of all the parameters to fix
"""
def __init__(self, myFCN, params, **kwargs):
from ROOT import TMinuit, Long, Double
self.limits = np.zeros((len(params), 2))
self.steps = .04 * np.ones(
len(params)) # about 10 percent in log10 space
self.tolerance = .001
self.maxcalls = 10000
self.printMode = 0
self.up = 0.5
self.param_names = ['p%i' % i for i in xrange(len(params))]
self.erflag = Long()
self.npars = len(params)
self.args = ()
self.gradient = None
self.force_gradient = 0
self.strategy = 1
self.fixed = np.zeros_like(params)
self.__dict__.update(kwargs)
self.params = np.asarray(params, dtype='float')
self.fixed = np.asarray(self.fixed, dtype=bool)
self.fcn = FCN(myFCN,
self.params,
args=self.args,
gradient=self.gradient)
self.fval = self.fcn.fval
self.minuit = TMinuit(self.npars)
self.minuit.SetPrintLevel(self.printMode)
self.minuit.SetFCN(self.fcn)
if self.gradient:
self.minuit.mncomd('SET GRA %i' % (self.force_gradient),
self.erflag)
self.minuit.mncomd('SET STR %i' % self.strategy, Long())
for i in xrange(self.npars):
if self.limits[i][0] is None: self.limits[i][0] = 0.0
if self.limits[i][1] is None: self.limits[i][1] = 0.0
self.minuit.DefineParameter(i, self.param_names[i], self.params[i],
self.steps[i], self.limits[i][0],
self.limits[i][1])
self.minuit.SetErrorDef(self.up)
for index in np.where(self.fixed)[0]:
self.minuit.FixParameter(int(index))
def minimize(self, method='MIGRAD'):
from ROOT import TMinuit, Long, Double
self.minuit.mncomd(
'%s %i %f' % (method, self.maxcalls, self.tolerance), self.erflag)
for i in xrange(self.npars):
val, err = Double(), Double()
self.minuit.GetParameter(i, val, err)
self.params[i] = val
self.fval = self.fcn.fcn(self.params)
return (self.params, self.fval)
def errors(self, method='HESSE'):
"""method ['HESSE'] : how to calculate the errors; Currently, only 'HESSE' works."""
if not np.any(self.fixed):
mat = np.zeros(self.npars**2)
if method == 'HESSE':
self.minuit.mnhess()
else:
raise Exception("Method %s not recognized." % method)
self.minuit.mnemat(mat, self.npars)
return mat.reshape((self.npars, self.npars))
else:
# Kind of ugly, but for fixed parameters, you need to expand out the covariance matrix.
nf = int(np.sum(~self.fixed))
mat = np.zeros(nf**2)
if method == 'HESSE':
self.minuit.mnhess()
else:
raise Exception("Method %s not recognized." % method)
self.minuit.mnemat(mat, nf)
# Expand out the covariance matrix.
cov = np.zeros((self.npars, self.npars))
cov[np.outer(~self.fixed, ~self.fixed)] = np.ravel(mat)
return cov
def uncorrelated_minos_error(self):
""" Kind of a kludge, but a compromise between the speed of
HESSE errors and the accuracy of MINOS errors. It accounts
for non-linearities in the likelihood by varying each function
until the value has fallen by the desired amount using hte
MINOS code. But does not account for correlations between
the parameters by fixing all other parameters during the
minimzation.
Again kludgy, but what is returned is an effective covariance
matrix. The diagonal errors are calcualted by averaging the
upper and lower errors and the off diagonal terms are set
to 0. """
cov = np.zeros((self.npars, self.npars))
# fix all parameters
for i in range(self.npars):
self.minuit.FixParameter(int(i))
# loop over free paramters getting error
for i in np.where(self.fixed == False)[0]:
self.minuit.Release(int(i))
# compute error
self.minuit.mnmnos()
low, hi, parab, gcc = ROOT.Double(), ROOT.Double(), ROOT.Double(
), ROOT.Double()
# get error
self.minuit.mnerrs(int(i), low, hi, parab, gcc)
cov[i, i] = ((abs(low) + abs(hi)) / 2.0)**2
self.minuit.FixParameter(int(i))
for i, fixed in enumerate(self.fixed):
if fixed:
self.minuit.FixParameter(int(i))
else:
self.minuit.Release(int(i))
return cov
class Fits:
def __init__(self):
self.p_n = [
0,
] * 100
self.e_n = [
0,
] * 100
self.stored_parameters = [
0,
] * 100
self.num_bins = 0
self.xmins = []
self.xmaxes = []
self.data = []
self.errors = []
self.data_fits = []
self.model_scale_values = []
self.final = False
self.exclude_regions = ((0, 0), )
self.col1 = 1
self.col2 = TColor.GetColor(27, 158, 119)
self.col3 = TColor.GetColor(217, 95, 2)
self.col4 = TColor.GetColor(117, 112, 179)
def run_mass_fit(self, peak_scale_initial, mass=0):
self.gMinuit = TMinuit(30)
self.gMinuit.SetPrintLevel(-1)
self.gMinuit.SetFCN(self.Fitfcn_max_likelihood)
arglist = array("d", [
0,
] * 10)
ierflg = ROOT.Long(0)
arglist[0] = ROOT.Double(1)
# peak_scale_initial = ROOT.Double(peak_scale_initial)
tmp = array("d", [
0,
])
self.gMinuit.mnexcm("SET NOWarnings", tmp, 0, ierflg)
self.gMinuit.mnexcm("SET ERR", arglist, 1, ierflg)
self.gMinuit.mnparm(0, "p1", 5e-6, 1e-7, 0, 0, ierflg)
self.gMinuit.mnparm(1, "p2", 10, 10, 0, 0, ierflg)
self.gMinuit.mnparm(2, "p3", -5.3, 1, 0, 0, ierflg)
self.gMinuit.mnparm(3, "p4", -4e-2, 1e-2, 0, 0, ierflg)
self.gMinuit.mnparm(4, "p5", peak_scale_initial,
peak_scale_initial / 50, 0, 0, ierflg)
self.background_fit_only = [
0,
] * len(self.data)
arglist[0] = ROOT.Double(0)
arglist[1] = ROOT.Double(0)
#self.exclude_regions = ((2.2, 3.3),)
self.gMinuit.FixParameter(2)
self.gMinuit.FixParameter(3)
self.gMinuit.FixParameter(4)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
self.gMinuit.Release(2)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
self.gMinuit.Release(3)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
# Find an actual best fit
#self.exclude_regions = ((0, 2), (3.3, 100),)
self.gMinuit.FixParameter(0)
self.gMinuit.FixParameter(1)
self.gMinuit.FixParameter(2)
self.gMinuit.FixParameter(3)
self.gMinuit.Release(4)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
self.exclude_regions = ()
self.gMinuit.Release(0)
self.gMinuit.Release(1)
self.gMinuit.Release(2)
self.gMinuit.Release(3)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
best_fit_value = ROOT.Double(0)
self.gMinuit.mnstat(best_fit_value, ROOT.Double(0), ROOT.Double(0),
ROOT.Long(0), ROOT.Long(0), ROOT.Long(0))
#print("Best fit value", best_fit_value)
# And prepare for iterating over fit values for N injected events
self.gMinuit.Release(0)
self.gMinuit.Release(1)
self.gMinuit.Release(2)
self.gMinuit.Release(3)
self.exclude_regions = ()
#self.data_fits = no_peak_data_fits
x_values = []
y_values = []
fitted_N = ROOT.Double(0)
self.gMinuit.GetParameter(4, fitted_N, ROOT.Double(0))
best_fit_likelihood = self.calc_likelihood(fitted_N)
step = 5
if int(mass) >= 4000:
step = 1
if int(mass) >= 5000:
step = 0.2
if int(mass) >= 6000:
step = 0.1
if int(mass) >= 6500:
step = 0.05
N = 0
while N < 5000:
start_sum = sum([math.exp(-a) for a in y_values])
fit_likelihood = self.calc_likelihood(N)
x_values.append(N)
y_values.append(fit_likelihood - best_fit_likelihood)
probabilities = [math.exp(-a) for a in y_values]
end_sum = sum(probabilities)
max_prob = max(probabilities)
normalised_probabilities = [a / max_prob for a in probabilities]
if N / step > 50 and all(
[v > 0.99 for v in normalised_probabilities]):
print(
"Probability=1 everywhere, probably something wrong with fit"
)
print(normalised_probabilities)
return None, None
# if new value changes total by less than 0.1%, end loop
if N > 0 and (end_sum - start_sum) / start_sum < 0.0001:
print("Iterated up to {0}".format(N))
break
N += step
self.iflag = int(ierflg)
return x_values, y_values
def Fitfcn_max_likelihood(self, npar, gin, fcnVal, par, iflag):
likelihood = 0
mf = ROOT.MyMassSpectrum()
mf.SetParameters(par)
ig = GaussIntegrator()
ig.SetFunction(mf)
ig.SetRelTolerance(0.00001)
for i in range(0, self.num_bins):
for lower, higher in self.exclude_regions:
if lower < self.xmins[i] < higher:
continue
model_val = ig.Integral(self.xmins[i], self.xmaxes[i]) / (
self.xmaxes[i] - self.xmins[i])
self.background_fit_only[i] = model_val
model_val += self.model_scale_values[i] * par[4]
self.data_fits[i] = model_val
likelihood += model_val - self.data[i]
if self.data[i] > 0 and model_val > 0:
likelihood += self.data[i] * (math.log(self.data[i]) -
math.log(model_val))
fcnVal[0] = likelihood
def calc_likelihood(self, peak_scale):
like = 0
for i in range(0, self.num_bins):
if self.data_fits[i] <= 0:
continue
p = peak_scale * self.model_scale_values[i]
tmp = ROOT.TMath.PoissonI(self.data[i],
self.background_fit_only[i] + p)
#if peak_scale == 40000:
# print(i, "\txmin", self.xmins[i], "\tdata", self.data[i], "\tdata_fit", self.data_fits[i], "\tp", p, "\tdata_fit+p", self.data_fits[i]+p)
if tmp == 0:
print("tmp == 0 here")
logtmp = math.log(sys.float_info.min)
else:
logtmp = math.log(tmp)
like += logtmp
return -like
def main():
global freqs_hz, pv, sigq, sigu
parser = OptionParser(usage)
parser.add_option("-r", "--rm", type="float", dest="rm", default=0.,
help="Estimate of the RM")
parser.add_option("-n", "--norm", action="store_true", dest="norm",
default=False, help="Verbose mode")
parser.add_option("-b", "--baseline", action="store_true", dest="baseline",
default=False, help="Fit for a baseline")
parser.add_option("-f", "--nofit", action="store_true", dest="nofit",
default=False, help="Don't fit for the RM with Minuit")
parser.add_option("-c", "--clean", action="store_true", dest="clean",
default=False, help="Clean the baseline")
(opts, args) = parser.parse_args()
#if opts.help:
# print full_usage
arch = psrchive.Archive_load(sys.argv[1])
arch.tscrunch()
arch.bscrunch(2)
#arch.fscrunch(2)
arch.dedisperse()
arch.remove_baseline()
arch.convert_state('Stokes')
arch.centre_max_bin()
#arch.rotate(0.5)
data = arch.get_data()
MJD = arch.get_first_Integration().get_epoch().strtempo()
w = arch.get_weights().sum(0)
I = data[:,0,:,:].mean(0)
Q = data[:,1,:,:].mean(0)
U = data[:,2,:,:].mean(0)
#V = data[:,3,:,:].mean(0)
I = ma.masked_array(I)
Q = ma.masked_array(Q)
U = ma.masked_array(U)
#V = ma.masked_array(V)
I[w==0] = np.ma.masked
Q[w==0] = np.ma.masked
U[w==0] = np.ma.masked
# Get Freqs
nchan = arch.get_nchan()
freqs = np.zeros(nchan)
for i in range(nchan):
freqs[i] = arch.get_Profile(0,0,i).get_centre_frequency()
## Determine phase range
arch.fscrunch()
arch.tscrunch()
arch.pscrunch()
prof = arch.get_Profile(0,0,0)
#print prof.get_amps()
lowbin, hibin = get_pulse_range(arch)
#lowbin, hibin = 458,531
#lowbin, hibin = 20,120
if opts.clean:
for n in range(nchan):
if n%20: continue
baseline_idx = np.append(np.arange(0, lowbin), np.arange(hibin, arch.get_nbin()))
baseline_dat = I[n][baseline_idx]
print n, baseline_idx, baseline_dat
poly = np.polyfit(baseline_idx, baseline_dat, 1)
p = np.poly1d(poly)
pylab.plot(I[n])
I[n] = I[n] - p(np.arange(0, arch.get_nbin()))
pylab.plot(I[n])
pylab.show()
for ii, wx in enumerate(w):
I[ii] *= wx/np.max(w)
Q[ii] *= wx/np.max(w)
U[ii] *= wx/np.max(w)
#V[ii] *= wx
if opts.norm:
print "Will normalize by the rms of the noise"
scale = np.std(I, axis=1) / np.max(np.std(I, axis=1))
for ii, s in enumerate(scale):
I[ii,:] /= s
Q[ii,:] /= s
U[ii,:] /= s
#Q = Q / scale
#U = U / scale
freq_lo = freqs[0]
freq_hi = freqs[-1]
lowphase = lowbin / float(arch.get_nbin())
hiphase = hibin / float(arch.get_nbin())
#lowphase= 0.48
#hiphase = 0.515
#lowphase = 0.515
#hiphase = 0.54
print "Pulse phase window: ", lowphase, hiphase
#pylab.plot(np.sum(I), axis)
#pylab.show()
# 2D plot
f = pylab.figure()
pylab.subplot(321)
#print np.sum(I,axis=0)
#pylab.plot(np.sum(I, axis=0))
pylab.plot(prof.get_amps())
pylab.xlim([0, arch.get_nbin()])
f.text( .5, 0.95, r'%s'%os.path.split(sys.argv[1])[1], horizontalalignment='center')
pylab.subplot(323)
pylab.axis([0,1,freq_lo,freq_hi])
pylab.imshow(I,extent=(0,1,freq_lo,freq_hi), origin='lower', aspect='auto', vmax=I.max()/1.5, vmin=I.min()/1.5)
pylab.xlabel('Pulse phase')
pylab.ylabel('Frequency (MHz)')
# Compute errors of Q and U
sigq = np.std(Q[:,lowbin:hibin], axis=1) / np.sqrt(hibin-lowbin)
sigu = np.std(U[:,lowbin:hibin], axis=1) / np.sqrt(hibin-lowbin)
#sigq = np.std(Q[:,:], axis=1)
#sigu = np.std(U[:,:], axis=1)
pylab.plot([lowphase,lowphase], [freq_lo, freq_hi], 'r--')
pylab.plot([hiphase,hiphase], [freq_lo, freq_hi], 'r--')
freqs_hz = freqs * 1e6
# Select phase range
lowbin = int(lowphase * arch.get_nbin())
hibin = int(hiphase * arch.get_nbin())
dat = Q + 1j * U
pv = dat[:,lowbin:hibin].mean(1) # Select phase range and average
#rhos = np.arange(-90000, 90000, 10)
rhos = np.arange(-2000, 2000, 1)
res = np.absolute(getL(rhos, pv))
# Plot I f(RM)
pylab.subplot(324)
pylab.plot(rhos, res, 'b-')
pylab.xlabel('RM')
pylab.ylabel('I')
# Plot Q
pylab.subplot(325)
pylab.errorbar(freqs, np.real(pv), yerr=sigq, ls='None')
pylab.plot(freqs, np.real(pv), 'bo')
pylab.xlabel('Frequency (MHz)')
pylab.ylabel('Q')
# Plot U
pylab.subplot(326)
pylab.errorbar(freqs, np.imag(pv), yerr=sigu, ls='None')
pylab.plot(freqs, np.imag(pv), 'bo')
pylab.xlabel('Frequency (MHz)')
pylab.ylabel('U')
# Should get the initial RM
if opts.rm:
initial_RM = -opts.rm
else:
initial_RM = -rhos[np.argmax(res)]
print "Will use initial RM", initial_RM
initial_L = getL(np.array([initial_RM]), pv) / (hibin-lowbin)
if not opts.nofit:
# Minuit part
gMinuit = TMinuit(5)
#gMinuit.SetErrorDef(1) # 1-Sigma Error
gMinuit.SetErrorDef(4) # 2-Sigma Error
gMinuit.SetFCN(fcn)
arglist = arr('d', 2*[0.01])
ierflg = Long(0)
#arglist[0] = 1
#gMinuit.mnexcm("SET ERR", arglist ,1,ierflg)
# Set initial parameter values for fit
vstart = arr( 'd', (np.real(initial_L), np.imag(initial_L), initial_RM) )
#vstart = arr( 'd', (2*np.real(initial_L), 2*np.imag(initial_L), initial_RM) )
# Set step size for fit
step = arr( 'd', (0.001, 0.001, 0.001) )
# Define the parameters for the fit
gMinuit.mnparm(0, "Qf", vstart[0], step[0], 0,0,ierflg)
gMinuit.mnparm(1, "Uf", vstart[1], step[1], 0,0,ierflg)
gMinuit.mnparm(2, "RM", vstart[2], step[2], 0,0,ierflg)
gMinuit.mnparm(3, "a", 0.0, step[2], 0,0,ierflg)
gMinuit.mnparm(4, "b", 0.0, step[2], 0,0,ierflg)
#gMinuit.FixParameter(2)
if not opts.baseline:
gMinuit.FixParameter(3)
gMinuit.FixParameter(4)
arglist[0] = 6000 # Number of calls to FCN before giving up.
arglist[1] = 0.1 # Tolerance
gMinuit.mnexcm("MIGRAD", arglist ,2,ierflg)
amin, edm, errdef = Double(0.18), Double(0.19), Double(1.0)
nvpar, nparx, icstat = Long(1), Long(2), Long(3)
gMinuit.mnstat(amin,edm,errdef,nvpar,nparx,icstat);
gMinuit.mnmnos();
gMinuit.mnprin(3,amin);
finalQ, finalQ_err = Double(0), Double(0)
finalU, finalU_err = Double(0), Double(0)
finalRM, finalRM_err = Double(0), Double(0)
A, A_err = Double(0), Double(0)
B, B_err = Double(0), Double(0)
print "\n\n"
gMinuit.GetParameter(0, finalQ, finalQ_err)
gMinuit.GetParameter(1, finalU, finalU_err)
gMinuit.GetParameter(2, finalRM, finalRM_err)
gMinuit.GetParameter(3, A, A_err)
gMinuit.GetParameter(4, B, B_err)
finalRM *= -1.
print finalQ, finalU
line1 = "Final RM: %.1f"%(finalRM) + "(+/-) %.1f "%(finalRM_err) + " (2-sig) "
line2 = "Chi**2r = %.2f"%(get_chi2((finalQ,finalU,-finalRM,A,B)) / ( 2*pv.size - 3 - 1 -2))
print line1
print line2
f.text( .5, 0.92, line1 + line2, horizontalalignment='center')
print MJD, np.mean(freqs), finalRM, finalRM_err, get_chi2((finalQ,finalU,finalRM,A,B)), 2*pv.count()
# Plot best fit model
finalRM *= -1.
pylab.subplot(325)
pylab.plot(freqs, np.real( -A+getPV(finalQ+1j*finalU, finalRM) ))
pylab.subplot(326)
pylab.plot(freqs, np.imag( -B+getPV(finalQ+1j*finalU, finalRM) ))
pylab.show()
def bkgfit(data_hist,
bkgfunction,
bkgname,
doFloatZ=False,
signal_hist=None,
z_hist=None):
isBkgPlusZFit = False
isSpuriousFit = False
binning = HistBinsToList(data_hist)
data_x = HistToList(data_hist)
data_error = HistErrorList(data_hist)
z_x = []
signal_x = []
if z_hist != None:
isBkgPlusZFit = True
z_x = HistToList(z_hist)
if signal_hist != None:
isSpuriousFit = True
signal_x = HistToList(signal_hist)
parfunction = bkgfunction.GetNumberFreeParameters()
partot = bkgfunction.GetNumberFreeParameters() + 2
### the fucntion used for TMinuit
def fcn(npar, gin, f, par, ifag):
L = 0
# calculate likelihood, input par[0] is the N_B, par[1] is N_C, par[2] is N_L
for ibin in range(len(binning)):
if (data_x[ibin] < 0.5):
continue
bincen = binning[ibin]
bkg = 0
data = data_x[ibin]
if bkgname == "BernsteinO2":
bkg = (par[0] * (1 - (bincen - fit_start) / fit_range)**2 +
2 * par[1] * (1 - (bincen - fit_start) / fit_range) *
((bincen - fit_start) / fit_range) + par[2] *
((bincen - fit_start) / fit_range)**2)
if bkgname == "BernsteinO3":
bkg = par[0] * (1 - (
(bincen - fit_start) / fit_range))**3 + par[1] * (
3 * ((bincen - fit_start) / fit_range) *
(1 -
((bincen - fit_start) / fit_range))**2) + par[2] * (
3 * ((bincen - fit_start) / fit_range)**2 *
(1 -
((bincen - fit_start) / fit_range))) + par[3] * (
(bincen - fit_start) / fit_range)**3
if bkgname == "BernsteinO4":
bkg = par[0] * (1 - (
(bincen - fit_start) / fit_range))**4 + par[1] * (
4 * ((bincen - fit_start) / fit_range) *
(1 -
((bincen - fit_start) / fit_range))**3) + par[2] * (
6 * ((bincen - fit_start) / fit_range)**2 *
(1 - ((bincen - fit_start) / fit_range))**2
) + par[3] * (
4 * ((bincen - fit_start) / fit_range)**3 *
(1 -
((bincen - fit_start) / fit_range))) + par[4] * (
(bincen - fit_start) / fit_range)**4
if bkgname == "BernsteinO5":
bkg = par[0] * (1 - (
(bincen - fit_start) / fit_range))**5 + par[1] * (5 * (
(bincen - fit_start) / fit_range) * (1 - (
(bincen - fit_start) / fit_range))**4) + par[2] * (
10 * ((bincen - fit_start) / fit_range)**2 *
(1 - ((bincen - fit_start) / fit_range))**3
) + par[3] * (10 * (
(bincen - fit_start) / fit_range)**3 * (1 - (
(bincen - fit_start) / fit_range
))**2) + par[4] * (5 * (
(bincen - fit_start) / fit_range)**4 *
(1 -
((bincen - fit_start) /
fit_range))) + par[5] * (
(bincen - fit_start) /
fit_range)**5
if bkgname == "BernsteinO6":
bkg = (par[0] * (1 - ((bincen - fit_start) / fit_range))**6 +
par[1] * (6 * ((bincen - fit_start) / fit_range)**1 *
(1 - ((bincen - fit_start) / fit_range))**5) +
par[2] * (15 * ((bincen - fit_start) / fit_range)**2 *
(1 - ((bincen - fit_start) / fit_range))**4) +
par[3] * (20 * ((bincen - fit_start) / fit_range)**3 *
(1 - ((bincen - fit_start) / fit_range))**3) +
par[4] * (15 * ((bincen - fit_start) / fit_range)**4 *
(1 - ((bincen - fit_start) / fit_range))**2) +
par[5] * (6 * ((bincen - fit_start) / fit_range)**5 *
(1 - ((bincen - fit_start) / fit_range))**1) +
par[6] * ((bincen - fit_start) / fit_range)**6)
if bkgname == "ExpoBernsteinO2":
try:
bkg = exp(par[0] * (bincen - fit_start) / fit_range) * (
par[1] *
(1 -
(bincen - fit_start) / fit_range)**2 + 2 * par[2] *
(1 - (bincen - fit_start) / fit_range) *
((bincen - fit_start) / fit_range) + par[3] *
((bincen - fit_start) / fit_range)**2)
except OverflowError:
bkg = 0
if bkgname == "ExpoBernsteinO3":
try:
bkg = exp(par[0] * (bincen - fit_start) / fit_range) * (
par[1] *
(1 - ((bincen - fit_start) / fit_range))**3 + par[2] *
(3 * ((bincen - fit_start) / fit_range) *
(1 -
((bincen - fit_start) / fit_range))**2) + par[3] *
(3 * ((bincen - fit_start) / fit_range)**2 *
(1 - ((bincen - fit_start) / fit_range))) + par[4] *
((bincen - fit_start) / fit_range)**3)
except OverflowError:
bkg = 0
if bkgname == "ExpoBernsteinO4":
try:
bkg = exp(par[0] * (bincen - fit_start) / fit_range) * (
par[1] *
(1 - ((bincen - fit_start) / fit_range))**4 + par[2] *
(4 * ((bincen - fit_start) / fit_range) *
(1 -
((bincen - fit_start) / fit_range))**3) + par[3] *
(6 * ((bincen - fit_start) / fit_range)**2 *
(1 -
((bincen - fit_start) / fit_range))**2) + par[4] *
(4 * ((bincen - fit_start) / fit_range)**3 *
(1 - ((bincen - fit_start) / fit_range))) + par[5] *
((bincen - fit_start) / fit_range)**4)
except OverflowError:
bkg = 0
if bkgname == "ExpoBernsteinO5":
try:
bkg = exp(par[0] * (bincen - fit_start) / fit_range) * (
par[1] *
(1 - ((bincen - fit_start) / fit_range))**5 + par[2] *
(5 * ((bincen - fit_start) / fit_range) *
(1 -
((bincen - fit_start) / fit_range))**4) + par[3] *
(10 * ((bincen - fit_start) / fit_range)**2 *
(1 -
((bincen - fit_start) / fit_range))**3) + par[4] *
(10 * ((bincen - fit_start) / fit_range)**3 *
(1 -
((bincen - fit_start) / fit_range))**2) + par[5] *
(5 * ((bincen - fit_start) / fit_range)**4 *
(1 - ((bincen - fit_start) / fit_range))) + par[6] *
((bincen - fit_start) / fit_range)**5)
except OverflowError:
bkg = 0
if bkgname == "ExpoPolO2":
bkg = exp(-(par[0] + par[1] *
((bincen - fit_start) / fit_range) + par[2] *
((bincen - fit_start) / fit_range)**2))
if bkgname == "ExpoPolO3":
bkg = exp(-(par[0] + par[1] *
((bincen - fit_start) / fit_range) + par[2] *
((bincen - fit_start) / fit_range)**2 + par[3] *
((bincen - fit_start) / fit_range)**3))
if bkgname == "ExpoPolO4":
bkg = exp(-(par[0] + par[1] *
((bincen - fit_start) / fit_range) + par[2] *
((bincen - fit_start) / fit_range)**2 + par[3] *
((bincen - fit_start) / fit_range)**3 + par[4] *
((bincen - fit_start) / fit_range)**4))
mu_x = bkg
#if isBkgPlusZFit:
# mu_x = mu_x + (par[partot-1] *z_x[ibin])
if isSpuriousFit:
mu_x = mu_x + par[partot - 2] * signal_x[ibin]
#L = L + mu_x - data*log(mu_x)
L = L + ((mu_x - data) / data_error[ibin])**2
f[0] = L
# initialize the TMinuit object
arglist_p = 10 * [0]
arglist = array.array('d')
arglist.fromlist(arglist_p)
ierflag = Long(0)
maxiter = 1000000000
arglist_p = [1]
gMinuit = TMinuit(partot)
gMinuit.mnexcm('SET PRIntout', arglist, 0, ierflag)
gMinuit.SetPrintLevel(1)
gMinuit.SetErrorDef(1.0)
gMinuit.SetFCN(fcn)
arglist_p = [2]
arglist = array.array('d')
arglist.fromlist(arglist_p)
gMinuit.mnexcm('SET STRategy', arglist, 1, ierflag)
arglist_p = [maxiter, 0.0000001]
arglist = array.array('d')
arglist.fromlist(arglist_p)
gMinuit.mnexcm('MIGrad', arglist, 2, ierflag)
gMinuit.SetMaxIterations(maxiter)
# initialize fitting the variables
vstart = [100.0] * partot
# start alpha_z with 1
vstart[partot - 1] = 1.0
vstart[partot - 2] = 0
step = [0.1] * partot
upper = [100000] * partot
lower = [0.1] * partot
varname = []
if "ExpoPol" in bkgname:
upper = [1000] * partot
lower = [-1000] * partot
if "ExpoBernstein" in bkgname:
vstart[0] = -1
upper[0] = 0
lower[0] = -10
for i in range(parfunction):
varname.append("p" + str(i))
varname.append("alpha_sig")
varname.append("alpha_z")
if doFloatZ:
vstart[partot - 1] = 1.0
upper[partot - 1] = 2
lower[partot - 1] = 0
step[partot - 1] = 0.01
if isSpuriousFit:
upper[partot - 2] = 10.0
lower[partot - 2] = -10.0
step[partot - 2] = 0.1
vstart[partot - 2] = 1
for i in range(partot):
gMinuit.mnparm(i, varname[i], vstart[i], step[i], lower[i], upper[i],
ierflag)
if not isSpuriousFit:
vstart[partot - 2] = 0
gMinuit.FixParameter(partot - 2)
if not doFloatZ:
lower[partot - 1] = 1
upper[partot - 1] = 1
gMinuit.FixParameter(partot - 1)
if not isBkgPlusZFit:
vstart[partot - 1] = 0.0
gMinuit.FixParameter(partot - 1)
# fitting procedure
migradstat = gMinuit.Command('MIGrad ' + str(maxiter) + ' ' + str(0.001))
improvestat = gMinuit.Command('IMProve ' + str(maxiter) + ' ' + str(0.01))
for i in range(partot):
arglist_p.append(i + 1)
arglist = array.array('d')
arglist.fromlist(arglist_p)
#gMinuit.mnmnos()
# get fitting parameters
fitval_p = [Double(0)] * partot
fiterr_p = [Double(0)] * partot
errup_p = [Double(0)] * partot
errdown_p = [Double(0)] * partot
eparab_p = [Double(0)] * partot
gcc_p = [Double(0)] * partot
fmin_p = [Double(0)]
fedm_p = [Double(0)]
errdef_p = [Double(0)]
npari_p = Long(0)
nparx_p = Long(0)
istat_p = Long(0)
fitval = array.array('d')
fiterr = array.array('d')
errup = array.array('d')
errdown = array.array('d')
eparab = array.array('d')
gcc = array.array('d')
for i in range(partot):
gMinuit.GetParameter(i, fitval_p[i], fiterr_p[i])
fitval.append(fitval_p[i])
fiterr.append(fiterr_p[i])
errup.append(errup_p[i])
errdown.append(errdown_p[i])
eparab.append(eparab_p[i])
gcc.append(gcc_p[i])
gMinuit.mnstat(fmin_p[0], fedm_p[0], errdef_p[0], npari_p, nparx_p,
istat_p)
for p in range(bkgfunction.GetNumberFreeParameters()):
bkgfunction.SetParameter(p, fitval[p])
print "fit uncert", fiterr_p[p]
bkgfunction.SetChisquare(fmin_p[0])
return fitval[partot - 1], fitval[partot - 2]
class Fits:
def __init__(self):
self.p_n = [
0,
] * 100
self.e_n = [
0,
] * 100
self.stored_parameters = [
0,
] * 100
self.num_bins = 0
self.xmins = []
self.xmaxes = []
self.data = []
self.errors = []
self.data_fits = []
self.model_scale_values = []
self.final = False
self.exclude_regions = ((0, 0), )
self.col1 = 1
self.col2 = TColor.GetColor(27, 158, 119)
self.col3 = TColor.GetColor(217, 95, 2)
self.col4 = TColor.GetColor(117, 112, 179)
def run_mass_fit(self, peak_scale_initial):
self.gMinuit = TMinuit(30)
self.gMinuit.SetPrintLevel(-1)
self.gMinuit.SetFCN(self.Fitfcn_max_likelihood)
self.fit_failed = False
arglist = array("d", [
0,
] * 10)
ierflg = ROOT.Long(0)
arglist[0] = ROOT.Double(1)
# peak_scale_initial = ROOT.Double(peak_scale_initial)
tmp = array("d", [
0,
])
self.gMinuit.mnexcm("SET NOWarnings", tmp, 0, ierflg)
self.gMinuit.mnexcm("SET ERR", arglist, 1, ierflg)
self.gMinuit.mnparm(0, "p1", 30, 20, 0, 100, ierflg)
self.gMinuit.mnparm(1, "p2", 10, 1, 0, 0, ierflg)
self.gMinuit.mnparm(2, "p3", -5.3, 1, 0, 0, ierflg)
self.gMinuit.mnparm(3, "p4", -4e-2, 1e-2, 0, 0, ierflg)
self.gMinuit.mnparm(4, "p5", peak_scale_initial, 1, 0, 10000, ierflg)
self.background_fit_only = [
0,
] * len(self.data)
arglist[0] = ROOT.Double(0)
arglist[1] = ROOT.Double(0)
#self.exclude_regions = ((2.2, 3.3),)
self.gMinuit.FixParameter(1)
self.gMinuit.FixParameter(2)
self.gMinuit.FixParameter(3)
self.gMinuit.FixParameter(4)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
print("Run fit 0")
if self.fit_failed:
print("Fit failed, returning")
return None, None
self.gMinuit.Release(1)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
print("Run fit 1")
if self.fit_failed:
print("Fit failed, returning")
return None, None
self.gMinuit.Release(2)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
print("Run fit 2")
if self.fit_failed:
print("Fit failed, returning")
return None, None
self.gMinuit.Release(3)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
print("Run fit 3")
if self.fit_failed:
print("Fit failed, returning")
return None, None
# Find an actual best fit
#self.exclude_regions = ((0, 2), (3.3, 100),)
self.gMinuit.FixParameter(0)
self.gMinuit.FixParameter(1)
self.gMinuit.FixParameter(2)
self.gMinuit.FixParameter(3)
self.gMinuit.Release(4)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
print("Run fit 4")
if self.fit_failed:
print("Fit failed, returning")
return None, None
self.exclude_regions = ()
self.gMinuit.Release(0)
self.gMinuit.Release(1)
self.gMinuit.Release(2)
self.gMinuit.Release(3)
self.gMinuit.mnexcm("simplex", arglist, 2, ierflg)
self.gMinuit.mnexcm("MIGRAD", arglist, 2, ierflg)
print("Run last fitting stage")
if self.fit_failed:
print("Fit failed, returning")
return None, None
best_fit_value = ROOT.Double(0)
self.gMinuit.mnstat(best_fit_value, ROOT.Double(0), ROOT.Double(0),
ROOT.Long(0), ROOT.Long(0), ROOT.Long(0))
#print("Best fit value", best_fit_value)
# And prepare for iterating over fit values for N injected events
self.gMinuit.Release(0)
self.gMinuit.Release(1)
self.gMinuit.Release(2)
self.gMinuit.Release(3)
self.exclude_regions = ()
#self.data_fits = no_peak_data_fits
x_values = []
y_values = []
for i in range(0, 5):
p = ROOT.Double(0)
self.gMinuit.GetParameter(i, p, ROOT.Double(0))
print("Parameter", i, p)
fitted_N = ROOT.Double(0)
self.gMinuit.GetParameter(4, fitted_N, ROOT.Double(0))
best_fit_likelihood = self.calc_likelihood(fitted_N)
self.iflag = int(ierflg)
print("iflag:", self.iflag)
step = 5
if int(MASS_FILE) >= 4000:
step = 1
if int(MASS_FILE) >= 5000:
step = 0.2
if int(MASS_FILE) >= 6000:
step = 0.1
if int(MASS_FILE) >= 6500:
step = 0.1
N = 0
print("About to start likelihood testing loop")
while N < 10000:
start_sum = sum([math.exp(-a) for a in y_values])
fit_likelihood = self.calc_likelihood(N)
if fit_likelihood is None:
print("Bad fit_likelihood")
return None, None
x_values.append(N)
y_values.append(fit_likelihood - best_fit_likelihood)
probabilities = [math.exp(-a) for a in y_values]
end_sum = sum(probabilities)
max_prob = max(probabilities)
if max_prob == 0:
print("max_prob == 0")
return None, None
normalised_probabilities = [a / max_prob for a in probabilities]
if N / step > 50 and all(
[v > 0.99 for v in normalised_probabilities]):
print(
"Probability=1 everywhere, probably something wrong with fit"
)
print(normalised_probabilities)
return None, None
# if new value changes total by less than 0.1%, end loop
if N > 0 and (end_sum - start_sum) / start_sum < 0.0001:
print("Iterated up to {0}".format(N))
break
N += step
self.iflag = int(ierflg)
return x_values, y_values
def Fitfcn_max_likelihood(self, npar, gin, fcnVal, par, iflag):
likelihood = 0
mf = ROOT.MyMassSpectrum()
mf.SetParameters(par)
ig = GaussIntegrator()
ig.SetFunction(mf)
ig.SetRelTolerance(0.00001)
for i in range(0, self.num_bins):
for lower, higher in self.exclude_regions:
if lower < self.xmins[i] < higher:
continue
model_val = ig.Integral(self.xmins[i], self.xmaxes[i]) / (
self.xmaxes[i] - self.xmins[i])
self.background_fit_only[i] = model_val
model_val += self.model_scale_values[i] * par[4]
self.data_fits[i] = model_val
mv = model_val
di = self.data[i]
#print("mv", mv, "di", di)
#sys.stdout.flush()
if di > 1e10 or math.isinf(mv) or math.isnan(mv):
self.fit_failed = True
return
likelihood += mv - di
if di > 0 and mv > 0:
likelihood += di * (TMath.Log(di) - TMath.Log(mv))
#sys.stderr.flush()
fcnVal[0] = likelihood
def calc_likelihood(self, peak_scale):
like = 0
for i in range(0, self.num_bins):
if self.data_fits[i] <= 0:
continue
p = peak_scale * self.model_scale_values[i]
tmp = ROOT.TMath.PoissonI(self.data[i],
self.background_fit_only[i] + p)
if tmp == 0:
return None
print("tmp == 0 here")
logtmp = math.log(sys.float_info.min)
else:
logtmp = math.log(tmp)
like += logtmp
return -like
