def fit(self):
numberOfParameters = len(self.samples)
gMinuit = TMinuit(numberOfParameters)
if self.method == 'logLikelihood': # set function for minimisation
gMinuit.SetFCN(self.logLikelihood)
gMinuit.SetMaxIterations(1000000000000)
# set Minuit print level
# printlevel = -1 quiet (also suppress all warnings)
# = 0 normal
# = 1 verbose
# = 2 additional output giving intermediate results.
# = 3 maximum output, showing progress of minimizations.
gMinuit.SetPrintLevel(-1)
# Error definition: 1 for chi-squared, 0.5 for negative log likelihood
# SETERRDEF<up>: Sets the value of UP (default value= 1.), defining parameter errors.
# Minuit defines parameter errors as the change in parameter value required to change the function value by UP.
# Normally, for chisquared fits UP=1, and for negative log likelihood, UP=0.5.
gMinuit.SetErrorDef(0.5)
# error flag for functions passed as reference.set to as 0 is no error
errorFlag = Long(2)
N_min = 0
N_max = self.fit_data_collection.max_n_data() * 2
param_index = 0
# MNPARM
# Implements one parameter definition:
# mnparm(k, cnamj, uk, wk, a, b, ierflg)
# K (external) parameter number
# CNAMK parameter name
# UK starting value
# WK starting step size or uncertainty
# A, B lower and upper physical parameter limits
# and sets up (updates) the parameter lists.
# Output: IERFLG =0 if no problems
# >0 if MNPARM unable to implement definition
for sample in self.samples: # all samples but data
if self.n_distributions > 1:
gMinuit.mnparm(
param_index, sample,
self.normalisation[self.distributions[0]][sample], 10.0,
N_min, N_max, errorFlag)
else:
gMinuit.mnparm(param_index, sample, self.normalisation[sample],
10.0, N_min, N_max, errorFlag)
param_index += 1
arglist = array('d', 10 * [0.])
# minimisation strategy: 1 standard, 2 try to improve minimum (a bit slower)
arglist[0] = 2
# minimisation itself
# SET STRategy<level>: Sets the strategy to be used in calculating first and second derivatives and in certain minimization methods.
# In general, low values of <level> mean fewer function calls and high values mean more reliable minimization.
# Currently allowed values are 0, 1 (default), and 2.
gMinuit.mnexcm("SET STR", arglist, 1, errorFlag)
gMinuit.Migrad()
gMinuit.mnscan(
) # class for minimization using a scan method to find the minimum; allows for user interaction: set/change parameters, do minimization, change parameters, re-do minimization etc.
gMinuit.mnmatu(1) # prints correlation matrix (always needed)
self.module = gMinuit
self.performedFit = True
if not self.module:
raise Exception(
'No fit results available. Please run fit method first')
results = {}
param_index = 0
for sample in self.samples:
temp_par = Double(0)
temp_err = Double(0)
self.module.GetParameter(param_index, temp_par, temp_err)
if (math.isnan(temp_err)):
self.logger.warning(
'Template fit error is NAN, setting to sqrt(N).')
temp_err = math.sqrt(temp_par)
# gMinuit.Command("SCAn %i %i %i %i" % ( param_index, 100, N_min, N_total ) );
# scan = gMinuit.GetPlot()
# results[sample] = ( temp_par, temp_err, scan )
results[sample] = (temp_par, temp_err)
param_index += 1
# # gMinuit.Command("CONtour 1 2 3 50")
# gMinuit.SetErrorDef(1)
# results['contour'] = [gMinuit.Contour(100, 0, 1)]
# gMinuit.SetErrorDef(4)
# results['contour'].append(gMinuit.Contour(100, 0, 1))
self.results = results
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
def signalfit(data_hist, signalfunction, signalname, process):
binning = HistBinsToList(data_hist)
data_x = HistToList(data_hist)
data_error = HistErrorList(data_hist)
parfunction = signalfunction.GetNumberFreeParameters()
partot = signalfunction.GetNumberFreeParameters()
print partot
### 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):
# continue
bincen = binning[ibin]
mu_x = 0
data = data_x[ibin]
if data_error[ibin] == 0:
continue
#if data<0.1:
# continue
if signalname == "CrystalBall":
if par[3] < 0:
mu_x = 0
else:
t = (bincen - par[2]) / (par[3])
if (par[0] < 0):
t = -t
absAlpha = abs(par[0])
if (t >= -absAlpha):
mu_x = par[4] * exp(-0.5 * t * t)
else:
nDivAlpha = par[1] / absAlpha
AA = exp(-0.5 * absAlpha * absAlpha)
B = nDivAlpha - absAlpha
arg = nDivAlpha / (B - t)
mu_x = par[4] * (arg**par[1])
if signalname == "CrystalBallGaus":
if par[3] < 0:
mu_x = 0
else:
t = (bincen - par[2]) / (par[3])
if (par[0] < 0):
t = -t
absAlpha = abs(par[0])
if (t >= -absAlpha):
mu_x = par[4] * exp(-0.5 * t * t +
exp(-(bincen - par[5])**2 /
(2 * par[6]**2)))
else:
nDivAlpha = par[1] / absAlpha
AA = exp(-0.5 * absAlpha * absAlpha)
B = nDivAlpha - absAlpha
arg = nDivAlpha / (B - t)
mu_x = par[4] * (arg**par[1] +
exp(-(bincen - par[5])**2 /
(2 * par[6]**2)))
#print mu_x, data, data_error[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 = [125.0] * partot
step = [0.1] * partot
upper = [1000000] * partot
lower = [-100] * partot
varname = []
lower[3] = 0
lower[4] = 0
lower[1] = 0
vstart[4] = data_hist.Integral()
if process == "signal":
vstart[2] = 125
lower[2] = 110
upper[2] = 140
vstart[3] = 10
lower[3] = 2
upper[3] = 25
if len(vstart) > 5:
vstart[5] = 125
lower[5] = 110
upper[5] = 140
vstart[6] = 10
lower[6] = 5
upper[6] = 20
if process == "z":
vstart[2] = 90
lower[2] = 70
upper[2] = 110
vstart[3] = 10
lower[3] = 2
upper[3] = 30
if len(vstart) > 5:
vstart[5] = 90
lower[5] = 70
upper[5] = 110
vstart[6] = 10
lower[6] = 2
upper[6] = 30
for i in range(parfunction):
varname.append("p" + str(i))
for i in range(partot):
gMinuit.mnparm(i, varname[i], vstart[i], step[i], lower[i], upper[i],
ierflag)
# 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(signalfunction.GetNumberFreeParameters()):
signalfunction.SetParameter(p, fitval[p])
print "fit uncert", fiterr_p[p]
signalfunction.SetChisquare(fmin_p[0])
print fmin_p[0]
return fitval[partot - 1], fitval[partot - 2]
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 MinimizerROOTTMinuit(MinimizerBase):
def __init__(self,
parameter_names,
parameter_values,
parameter_errors,
function_to_minimize,
tolerance=1e-9,
errordef=MinimizerBase.ERRORDEF_CHI2,
strategy=1):
self._strategy = strategy
self._par_bounds = np.array([None] * len(parameter_names))
self._par_fixed = np.array([False] * len(parameter_names))
self.reset() # sets self.__gMinuit and caches to None
super(MinimizerROOTTMinuit,
self).__init__(parameter_names=parameter_names,
parameter_values=parameter_values,
parameter_errors=parameter_errors,
function_to_minimize=function_to_minimize,
tolerance=tolerance,
errordef=errordef)
# -- private methods
def _save_state(self):
if self._par_val is None:
self._save_state_dict["par_val"] = self._par_val
else:
self._save_state_dict["par_val"] = np.array(self._par_val)
if self._par_err is None:
self._save_state_dict["par_err"] = self._par_err
else:
self._save_state_dict["par_err"] = np.array(self._par_err)
self._save_state_dict['par_fixed'] = np.array(self._par_fixed)
self._save_state_dict['gMinuit'] = self.__gMinuit
super(MinimizerROOTTMinuit, self)._save_state()
def _load_state(self):
self.reset()
self._par_val = self._save_state_dict["par_val"]
if self._par_val is not None:
self._par_val = np.array(self._par_val)
self._par_err = self._save_state_dict["par_err"]
if self._par_err is not None:
self._par_err = np.array(self._par_err)
self._par_fixed = np.array(self._save_state_dict['par_fixed'])
self.__gMinuit = self._save_state_dict['gMinuit']
# call the function to propagate the changes to the nexus:
self._func_handle(*self.parameter_values)
super(MinimizerROOTTMinuit, self)._load_state()
def _recreate_gMinuit(self):
self.__gMinuit = TMinuit(self.num_pars)
self.__gMinuit.SetPrintLevel(-1)
self.__gMinuit.mncomd("SET STRATEGY {}".format(self._strategy),
ctypes.c_int(0))
self.__gMinuit.SetFCN(self._minuit_fcn)
self.__gMinuit.SetErrorDef(self._err_def)
# set gMinuit parameters
error_code = ctypes.c_int(0)
for _pid, (_pn, _pv, _pe) in enumerate(
zip(self._par_names, self._par_val, self._par_err)):
self.__gMinuit.mnparm(_pid, _pn, _pv, 0.1 * _pe, 0, 0, error_code)
err_code = ctypes.c_int(0)
# set fixed parameters
for _par_id, _pf in enumerate(self._par_fixed):
if _pf:
self.__gMinuit.mnfixp(_par_id, err_code)
# set parameter limits
for _par_id, _pb in enumerate(self._par_bounds):
if _pb is not None:
_lo_lim, _up_lim = _pb
self.__gMinuit.mnexcm(
"SET LIM", arr('d', [_par_id + 1, _lo_lim, _up_lim]), 3,
error_code)
def _get_gMinuit(self):
if self.__gMinuit is None:
self._recreate_gMinuit()
return self.__gMinuit
def _migrad(self, max_calls=6000):
# need to set the FCN explicitly before every call
self._get_gMinuit().SetFCN(self._minuit_fcn)
error_code = ctypes.c_int(0)
self._get_gMinuit().mnexcm("MIGRAD",
arr('d', [max_calls, self.tolerance]), 2,
error_code)
def _minuit_fcn(self, number_of_parameters, derivatives, f, parameters,
internal_flag):
"""
This is actually a function called in *ROOT* and acting as a C wrapper
for our `FCN`, which is implemented in Python.
This function is called by `Minuit` several times during a fitters. It
doesn't return anything but modifies one of its arguments (*f*).
This is *ugly*, but it's how *ROOT*'s ``TMinuit`` works. Its argument
structure is fixed and determined by `Minuit`:
**number_of_parameters** : int
The number of parameters of the current fitters
**derivatives** : C array
If the user chooses to calculate the first derivative of the
function inside the `FCN`, this value should be written here. This
interface to `Minuit` ignores this derivative, however, so
calculating this inside the `FCN` has no effect (yet).
**f** : C array
The desired function value is in f[0] after execution.
**parameters** : C array
A C array of parameters. Is cast to a Python list
**internal_flag** : int
A flag allowing for different behaviour of the function.
Can be any integer from 1 (initial run) to 4(normal run). See
`Minuit`'s specification.
"""
# Retrieve the parameters from the C side of ROOT and
# store them in a Python list -- resource-intensive
# for many calls, but can't be improved (yet?)
parameter_list = np.frombuffer(parameters,
dtype=float,
count=self.num_pars)
# call the Python implementation of FCN.
f[0] = self._func_wrapper(*parameter_list)
def _calculate_asymmetric_parameter_errors(self):
self._get_gMinuit().mnmnos()
_asymm_par_errs = np.zeros(shape=(self.num_pars, 2))
for _n in range(self.num_pars):
_number = Long(_n)
_eplus = ctypes.c_double(0)
_eminus = ctypes.c_double(0)
_eparab = ctypes.c_double(0)
_gcc = ctypes.c_double(0)
self._get_gMinuit().mnerrs(_number, _eplus, _eminus, _eparab, _gcc)
_asymm_par_errs[_n, 0] = _eminus.value
_asymm_par_errs[_n, 1] = _eplus.value
self.minimize()
return _asymm_par_errs
def _get_fit_info(self, info):
'''Retrieves other info from `Minuit`.
**info** : string
Information about the fit to retrieve.
This can be any of the following:
- ``'fcn'``: `FCN` value at minimum,
- ``'edm'``: estimated distance to minimum
- ``'err_def'``: `Minuit` error matrix status code
- ``'status_code'``: `Minuit` general status code
'''
# declare vars in which to retrieve other info
fcn_at_min = ctypes.c_double(0)
edm = ctypes.c_double(0)
err_def = ctypes.c_double(0)
n_var_param = ctypes.c_int(0)
n_tot_param = ctypes.c_int(0)
status_code = ctypes.c_int(0)
# Tell TMinuit to update the variables declared above
self.__gMinuit.mnstat(fcn_at_min, edm, err_def, n_var_param,
n_tot_param, status_code)
if info == 'fcn':
return fcn_at_min.value
elif info == 'edm':
return edm.value
elif info == 'err_def':
return err_def.value
elif info == 'status_code':
return status_code.value
else:
raise ValueError("Unknown fit info: %s" % info)
# -- public properties
@property
def hessian(self):
if not self.did_fit:
return None
if self._hessian is None:
_submat = self._remove_zeroes_for_fixed(self.cov_mat)
_submat_inv = 2.0 * self.errordef * np.linalg.inv(_submat)
self._hessian = self._fill_in_zeroes_for_fixed(_submat_inv)
return self._hessian.copy()
@property
def cov_mat(self):
if not self.did_fit:
return None
if self._par_cov_mat is None:
_n_pars_total = self.num_pars
_tmp_mat_array = arr('d', [0.0] * (_n_pars_total**2))
# get parameter covariance matrix from TMinuit
self._get_gMinuit().mnemat(_tmp_mat_array, _n_pars_total)
# reshape into 2D array
_sub_cov_mat = np.asarray(np.reshape(
_tmp_mat_array, (_n_pars_total, _n_pars_total)),
dtype=np.float)
_num_pars_free = np.sum(np.invert(self._par_fixed))
_sub_cov_mat = _sub_cov_mat[:_num_pars_free, :_num_pars_free]
self._par_cov_mat = self._fill_in_zeroes_for_fixed(_sub_cov_mat)
return self._par_cov_mat.copy()
@property
def hessian_inv(self):
if not self.did_fit:
return None
if self._hessian_inv is None:
self._hessian_inv = self.cov_mat / (2.0 * self.errordef)
return self._hessian_inv.copy()
@property
def parameter_values(self):
return self._par_val.copy()
@parameter_values.setter
def parameter_values(self, new_values):
self._par_val = np.array(new_values)
self.reset()
@property
def parameter_errors(self):
return self._par_err.copy()
@parameter_errors.setter
def parameter_errors(self, new_errors):
_err_array = np.array(new_errors)
if not np.all(_err_array > 0):
raise ValueError("All parameter errors must be > 0! Received: %s" %
new_errors)
self._par_err = _err_array
self.reset()
# -- private "properties"
# -- public methods
def reset(self):
super(MinimizerROOTTMinuit, self).reset()
self.__gMinuit = None
def set(self, parameter_name, parameter_value):
if parameter_name not in self._par_names:
raise ValueError("No parameter named '%s'!" % (parameter_name, ))
_par_id = self.parameter_names.index(parameter_name)
self._par_val[_par_id] = parameter_value
self.reset()
def fix(self, parameter_name):
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if self._par_fixed[_par_id]:
return # par is already fixed
self._par_fixed[_par_id] = True
if self.__gMinuit is not None:
# also update Minuit instance
err_code = ctypes.c_int(0)
self.__gMinuit.mnfixp(_par_id, err_code)
# self.__gMinuit.mnexcm("FIX",
# arr('d', [_par_id+1]), 1, error_code)
self._invalidate_cache()
def is_fixed(self, parameter_name):
_par_id = self.parameter_names.index(parameter_name)
return self._par_fixed[_par_id]
def release(self, parameter_name):
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if not self._par_fixed[_par_id]:
return # par is already released
self._par_fixed[_par_id] = False
if self.__gMinuit is not None:
# also update Minuit instance
self.__gMinuit.mnfree(-_par_id - 1)
# self.__gMinuit.mnexcm("RELEASE",
# arr('d', [_par_id+1]), 1, error_code)
self._invalidate_cache()
def limit(self, parameter_name, parameter_bounds):
assert len(parameter_bounds) == 2
if parameter_bounds[0] is None or parameter_bounds[1] is None:
raise MinimizerROOTTMinuitException(
"Cannot define one-sided parameter limits when using the ROOT TMinuit Minimizer."
)
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if self._par_bounds[_par_id] == parameter_bounds:
return # same limits already set
if self._par_val[_par_id] < parameter_bounds[0]:
self.set(parameter_name, parameter_bounds[0])
elif self._par_val[_par_id] > parameter_bounds[1]:
self.set(parameter_name, parameter_bounds[1])
self._par_bounds[_par_id] = parameter_bounds
if self.__gMinuit is not None:
_lo_lim, _up_lim = self._par_bounds[_par_id]
# also update Minuit instance
error_code = ctypes.c_int(0)
self.__gMinuit.mnexcm("SET LIM",
arr('d', [_par_id + 1, _lo_lim, _up_lim]), 3,
error_code)
self._did_fit = False
self._invalidate_cache()
def unlimit(self, parameter_name):
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if self._par_bounds[_par_id] is None:
return # parameter is already unlimited
self._par_bounds[_par_id] = None
if self.__gMinuit is not None:
# also update Minuit instance
error_code = ctypes.c_int(0)
self.__gMinuit.mnexcm("SET LIM", arr('d', [_par_id + 1]), 1,
error_code)
self._did_fit = False
self._invalidate_cache()
def minimize(self, max_calls=6000):
if np.all(self._par_fixed):
raise MinimizerROOTTMinuitException(
"Cannot perform a fit if all parameters are fixed!")
self._migrad(max_calls=max_calls)
# retrieve fitters parameters
self._par_val = np.zeros(self.num_pars)
self._par_err = np.zeros(self.num_pars)
_pv, _pe = ctypes.c_double(0), ctypes.c_double(0)
for _par_id in six.moves.range(0, self.num_pars):
self.__gMinuit.GetParameter(_par_id, _pv,
_pe) # retrieve fit result
self._par_val[_par_id] = _pv.value
self._par_err[_par_id] = _pe.value
self._did_fit = True
def contour(self,
parameter_name_1,
parameter_name_2,
sigma=1.0,
**minimizer_contour_kwargs):
if not self.did_fit:
raise MinimizerROOTTMinuitException(
"Need to perform a fit before calling contour()!")
_numpoints = minimizer_contour_kwargs.pop("numpoints", 100)
if minimizer_contour_kwargs:
raise MinimizerROOTTMinuitException(
"Unknown parameters: {}".format(minimizer_contour_kwargs))
_id_1 = self.parameter_names.index(parameter_name_1)
_id_2 = self.parameter_names.index(parameter_name_2)
self.__gMinuit.SetErrorDef(sigma**2)
_t_graph = self.__gMinuit.Contour(_numpoints, _id_1, _id_2)
self.__gMinuit.SetErrorDef(self._err_def)
_x_buffer, _y_buffer = _t_graph.GetX(), _t_graph.GetY()
_N = _t_graph.GetN()
_x = np.frombuffer(_x_buffer, dtype=float, count=_N)
_y = np.frombuffer(_y_buffer, dtype=float, count=_N)
self._func_handle(*self.parameter_values)
return ContourFactory.create_xy_contour((_x, _y), sigma)
def profile(self,
parameter_name,
bins=21,
bound=2,
args=None,
subtract_min=False):
if not self.did_fit:
raise MinimizerROOTTMinuitException(
"Need to perform a fit before calling profile()!")
MAX_ITERATIONS = 6000
_error_code = ctypes.c_int(0)
_minuit_id = Long(self.parameter_names.index(parameter_name) + 1)
_par_min = ctypes.c_double(0)
_par_err = ctypes.c_double(0)
self.__gMinuit.GetParameter(_minuit_id - 1, _par_min, _par_err)
_par_min = _par_min.value
_par_err = _par_err.value
_x = np.linspace(start=_par_min - bound * _par_err,
stop=_par_min + bound * _par_err,
num=bins,
endpoint=True)
self.__gMinuit.mnexcm("FIX", arr('d', [_minuit_id]), 1, _error_code)
_y = np.zeros(bins)
for i in range(bins):
self.__gMinuit.mnexcm("SET PAR",
arr('d',
[_minuit_id, Double(_x[i])]), 2,
_error_code)
self.__gMinuit.mnexcm("MIGRAD",
arr('d', [MAX_ITERATIONS, self.tolerance]),
2, _error_code)
_y[i] = self._get_fit_info("fcn")
self.__gMinuit.mnexcm("RELEASE", arr('d', [_minuit_id]), 1,
_error_code)
self._migrad()
self.__gMinuit.mnexcm("SET PAR",
arr('d',
[_minuit_id, Double(_par_min)]), 2,
_error_code)
if subtract_min:
_y -= self.function_value
return np.asarray((_x, _y))
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()
class MinimizerROOTTMinuit(MinimizerBase):
def __init__(self,
parameter_names, parameter_values, parameter_errors,
function_to_minimize, strategy = 1):
self._par_names = parameter_names
self._strategy = strategy
self._func_handle = function_to_minimize
self._err_def = 1.0
self._tol = 0.001
# initialize the minimizer parameter specification
self._minimizer_param_dict = {}
assert len(parameter_names) == len(parameter_values) == len(parameter_errors)
self._par_val = []
self._par_err = []
self._par_fixed_mask = []
self._par_limits = []
for _pn, _pv, _pe in zip(parameter_names, parameter_values, parameter_errors):
self._par_val.append(_pv)
self._par_err.append(_pe)
self._par_fixed_mask.append(False)
self._par_limits.append(None)
# TODO: limits/fixed parameters
self.__gMinuit = None
# cache for calculations
self._hessian = None
self._hessian_inv = None
self._fval = None
self._par_cov_mat = None
self._par_cor_mat = None
self._par_asymm_err = None
self._fmin_struct = None
self._pars_contour = None
self._min_result_stale = True
self._printed_inf_cost_warning = False
# -- private methods
# def _invalidate_cache(self):
# self._par_val = None
# self._par_err = None
# self._hessian = None
# self._hessian_inv = None
# self._fval = None
# self._par_cov_mat = None
# self._par_cor_mat = None
# self._par_asymm_err_dn = None
# self._par_asymm_err_up = None
# self._fmin_struct = None
# self._pars_contour = None
def _recreate_gMinuit(self):
self.__gMinuit = TMinuit(self.n_pars)
self.__gMinuit.SetPrintLevel(-1)
self.__gMinuit.mncomd("SET STRATEGY {}".format(self._strategy), Long(0))
self.__gMinuit.SetFCN(self._minuit_fcn)
self.__gMinuit.SetErrorDef(self._err_def)
# set gMinuit parameters
error_code = Long(0)
for _pid, (_pn, _pv, _pe) in enumerate(zip(self._par_names, self._par_val, self._par_err)):
self.__gMinuit.mnparm(_pid,
_pn,
_pv,
0.1 * _pe,
0, 0, error_code)
err_code = Long(0)
# set fixed parameters
for _par_id, _pf in enumerate(self._par_fixed_mask):
if _pf:
self.__gMinuit.mnfixp(_par_id, err_code)
# set parameter limits
for _par_id, _pl in enumerate(self._par_limits):
if _pl is not None:
_lo_lim, _up_lim = _pl
self.__gMinuit.mnexcm("SET LIM",
arr('d', [_par_id + 1, _lo_lim, _up_lim]), 3, error_code)
def _get_gMinuit(self):
if self.__gMinuit is None:
self._recreate_gMinuit()
return self.__gMinuit
def _migrad(self, max_calls=6000):
# need to set the FCN explicitly before every call
self._get_gMinuit().SetFCN(self._minuit_fcn)
error_code = Long(0)
self._get_gMinuit().mnexcm("MIGRAD",
arr('d', [max_calls, self.tolerance]),
2, error_code)
def _hesse(self, max_calls=6000):
# need to set the FCN explicitly before every call
self._get_gMinuit().SetFCN(self._minuit_fcn)
error_code = Long(0)
self._get_gMinuit().mnexcm("HESSE", arr('d', [max_calls]), 1, error_code)
def _minuit_fcn(self,
number_of_parameters, derivatives, f, parameters, internal_flag):
"""
This is actually a function called in *ROOT* and acting as a C wrapper
for our `FCN`, which is implemented in Python.
This function is called by `Minuit` several times during a fitters. It
doesn't return anything but modifies one of its arguments (*f*).
This is *ugly*, but it's how *ROOT*'s ``TMinuit`` works. Its argument
structure is fixed and determined by `Minuit`:
**number_of_parameters** : int
The number of parameters of the current fitters
**derivatives** : C array
If the user chooses to calculate the first derivative of the
function inside the `FCN`, this value should be written here. This
interface to `Minuit` ignores this derivative, however, so
calculating this inside the `FCN` has no effect (yet).
**f** : C array
The desired function value is in f[0] after execution.
**parameters** : C array
A C array of parameters. Is cast to a Python list
**internal_flag** : int
A flag allowing for different behaviour of the function.
Can be any integer from 1 (initial run) to 4(normal run). See
`Minuit`'s specification.
"""
# Retrieve the parameters from the C side of ROOT and
# store them in a Python list -- resource-intensive
# for many calls, but can't be improved (yet?)
parameter_list = np.frombuffer(parameters,
dtype=float,
count=self.n_pars)
# call the Python implementation of FCN.
f[0] = self._func_wrapper(*parameter_list)
def _insert_zeros_for_fixed(self, submatrix):
"""
Takes the partial error matrix (submatrix) and adds
rows and columns with 0.0 where the fixed
parameters should go.
"""
_mat = submatrix
# reduce the matrix before inserting zeros
_n_pars_free = self.n_pars_free
_mat = _mat[0:_n_pars_free,0:_n_pars_free]
_fparam_ids = [_par_id for _par_id, _p in enumerate(self._par_fixed_mask) if _p]
for _id in _fparam_ids:
_mat = np.insert(np.insert(_mat, _id, 0., axis=0), _id, 0., axis=1)
return _mat
# -- public properties
def get_fit_info(self, info):
'''Retrieves other info from `Minuit`.
**info** : string
Information about the fit to retrieve.
This can be any of the following:
- ``'fcn'``: `FCN` value at minimum,
- ``'edm'``: estimated distance to minimum
- ``'err_def'``: `Minuit` error matrix status code
- ``'status_code'``: `Minuit` general status code
'''
# declare vars in which to retrieve other info
fcn_at_min = Double(0)
edm = Double(0)
err_def = Double(0)
n_var_param = Long(0)
n_tot_param = Long(0)
status_code = Long(0)
# Tell TMinuit to update the variables declared above
self.__gMinuit.mnstat(fcn_at_min,
edm,
err_def,
n_var_param,
n_tot_param,
status_code)
if info == 'fcn':
return fcn_at_min
elif info == 'edm':
return edm
elif info == 'err_def':
return err_def
elif info == 'status_code':
try:
return D_MATRIX_ERROR[status_code]
except:
return status_code
@property
def n_pars(self):
return len(self.parameter_names)
@property
def n_pars_free(self):
return len([_p for _p in self._par_fixed_mask if not _p])
@property
def errordef(self):
return self._err_def
@errordef.setter
def errordef(self, err_def):
assert err_def > 0
self._err_def = err_def
if self.__gMinuit is not None:
self.__gMinuit.set_errordef(err_def)
self._min_result_stale = True
@property
def tolerance(self):
return self._tol
@tolerance.setter
def tolerance(self, tolerance):
assert tolerance > 0
self._tol = tolerance
self._min_result_stale = True
@property
def hessian(self):
# TODO: cache this
return 2.0 * self.errordef * np.linalg.inv(self.cov_mat)
@property
def cov_mat(self):
if self._min_result_stale:
raise MinimizerROOTTMinuitException("Cannot get cov_mat: Minimizer result is outdated.")
if self._par_cov_mat is None:
_n_pars_total = self.n_pars
_n_pars_free = self.n_pars_free
_tmp_mat_array = arr('d', [0.0]*(_n_pars_total**2))
# get parameter covariance matrix from TMinuit
self.__gMinuit.mnemat(_tmp_mat_array, _n_pars_total)
# reshape into 2D array
_sub_cov_mat = np.asarray(
np.reshape(
_tmp_mat_array,
(_n_pars_total, _n_pars_total)
)
)
self._par_cov_mat = self._insert_zeros_for_fixed(_sub_cov_mat)
return self._par_cov_mat
@property
def cor_mat(self):
if self._min_result_stale:
raise MinimizerROOTTMinuitException("Cannot get cor_mat: Minimizer result is outdated.")
if self._par_cor_mat is None:
_cov_mat = self.cov_mat
# TODO: use CovMat object!
# Note: for zeros on cov_mat diagonals (which occur for fixed parameters) -> overwrite with 1.0
_sqrt_diag = np.array([_err if _err>0 else 1.0 for _err in np.sqrt(np.diag(_cov_mat))])
self._par_cor_mat = np.asarray(_cov_mat) / np.outer(_sqrt_diag, _sqrt_diag)
return self._par_cor_mat
@property
def hessian_inv(self):
return self.cov_mat / 2.0 / self.errordef
@property
def parameter_values(self):
return self._par_val
@property
def parameter_errors(self):
return self._par_err
@property
def parameter_names(self):
return self._par_names
# -- private "properties"
# -- public methods
def fix(self, parameter_name):
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if self._par_fixed_mask[_par_id]:
return # par is already fixed
self._par_fixed_mask[_par_id] = True
if self.__gMinuit is not None:
# also update Minuit instance
err_code = Long(0)
self.__gMinuit.mnfixp(_par_id, err_code)
# self.__gMinuit.mnexcm("FIX",
# arr('d', [_par_id+1]), 1, error_code)
self._min_result_stale = True
def fix_several(self, parameter_names):
for _pn in parameter_names:
self.fix(_pn)
def release(self, parameter_name):
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if not self._par_fixed_mask[_par_id]:
return # par is already released
self._par_fixed_mask[_par_id] = False
if self.__gMinuit is not None:
# also update Minuit instance
self.__gMinuit.mnfree(-_par_id-1)
# self.__gMinuit.mnexcm("RELEASE",
# arr('d', [_par_id+1]), 1, error_code)
self._min_result_stale = True
def release_several(self, parameter_names):
for _pn in parameter_names:
self.release(_pn)
def limit(self, parameter_name, parameter_bounds):
assert len(parameter_bounds) == 2
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if self._par_limits[_par_id] == parameter_bounds:
return # same limits already set
self._par_limits[_par_id] = parameter_bounds
if self.__gMinuit is not None:
_lo_lim, _up_lim = self._par_limits[_par_id]
# also update Minuit instance
error_code = Long(0)
self.__gMinuit.mnexcm("SET LIM",
arr('d', [_par_id+1, _lo_lim, _up_lim]), 3, error_code)
self._min_result_stale = True
def unlimit(self, parameter_name):
# set local flag
_par_id = self.parameter_names.index(parameter_name)
if self._par_limits[_par_id] is None:
return # parameter is already unlimited
self._par_limits[_par_id] = None
if self.__gMinuit is not None:
# also update Minuit instance
error_code = Long(0)
self.__gMinuit.mnexcm("SET LIM",
arr('d', [_par_id+1]), 1, error_code)
self._min_result_stale = True
def minimize(self, max_calls=6000):
self._migrad(max_calls=max_calls)
# retrieve fitters parameters
self._par_val = []
self._par_err = []
_pv, _pe = Double(0), Double(0)
for _par_id in six.moves.range(0, self.n_pars):
self.__gMinuit.GetParameter(_par_id, _pv, _pe) # retrieve fitresult
self._par_val.append(float(_pv))
self._par_err.append(float(_pe))
self._min_result_stale = False
def contour(self, parameter_name_1, parameter_name_2, sigma=1.0, **minimizer_contour_kwargs):
if self.__gMinuit is None:
raise MinimizerROOTTMinuitException("Need to perform a fit before calling contour()!")
_numpoints = minimizer_contour_kwargs.pop("numpoints", 100)
if minimizer_contour_kwargs:
raise MinimizerROOTTMinuitException("Unknown parameters: {}".format(minimizer_contour_kwargs))
_id_1 = self.parameter_names.index(parameter_name_1)
_id_2 = self.parameter_names.index(parameter_name_2)
self.__gMinuit.SetErrorDef(sigma ** 2)
_t_graph = self.__gMinuit.Contour(_numpoints, _id_1, _id_2)
self.__gMinuit.SetErrorDef(self._err_def)
_x_buffer, _y_buffer = _t_graph.GetX(), _t_graph.GetY()
_N = _t_graph.GetN()
_x = np.frombuffer(_x_buffer, dtype=float, count=_N)
_y = np.frombuffer(_y_buffer, dtype=float, count=_N)
self._func_handle(*self.parameter_values)
return ContourFactory.create_xy_contour((_x, _y), sigma)
def profile(self, parameter_name, bins=21, bound=2, args=None, subtract_min=False):
if self.__gMinuit is None:
raise MinimizerROOTTMinuitException("Need to perform a fit before calling profile()!")
MAX_ITERATIONS = 6000
_error_code = Long(0)
_minuit_id = Long(self.parameter_names.index(parameter_name) + 1)
_par_min = Double(0)
_par_err = Double(0)
self.__gMinuit.GetParameter(_minuit_id - 1, _par_min, _par_err)
_x = np.linspace(start=_par_min - bound * _par_err, stop=_par_min + bound * _par_err, num=bins, endpoint=True)
self.__gMinuit.mnexcm("FIX", arr('d', [_minuit_id]), 1, _error_code)
_y = np.zeros(bins)
for i in range(bins):
self.__gMinuit.mnexcm("SET PAR", arr('d', [_minuit_id, Double(_x[i])]), 2, _error_code)
self.__gMinuit.mnexcm("MIGRAD", arr('d', [MAX_ITERATIONS, self.tolerance]), 2, _error_code)
_y[i] = self.get_fit_info("fcn")
self.__gMinuit.mnexcm("RELEASE", arr('d', [_minuit_id]), 1, _error_code)
self._migrad()
self.__gMinuit.mnexcm("SET PAR", arr('d', [_minuit_id, Double(_par_min)]), 2, _error_code)
return np.asarray((_x, _y))
