def test_start():
m = minuit(fn, x, y, start=[1,2,3,4,5])
assert_equal(m.values['e'], 5, 'minuit start assignment named')
m = minuit(fn2, x, y, start=[1,2,3,4,5])
assert_equal(m.values['x4'], 5, 'minuit start assignment unnamed')
m = minuit(fn, x, y, e=5)
assert_equal(m.values['e'], 5, 'minuit start assignment single named')
m = minuit(fn, x, y)
assert_equal(m.values['e'], 1, 'minuit start default param named')
def test_limit_broadcast():
m = minuit(fn, x, y, limit=[0,5])
limits_all = [m.limits[k][1] == 5 for k in 'abcde']
assert_equal(all(limits_all), True, 'minuit limits broadcasting')
limits_all = [m.limits[k][0] == 0 for k in 'abcde']
assert_equal(all(limits_all), True, 'minuit limits broadcasting')
def _fit_single_minuit(fn, x, y, dy, fixed, do_minos=True, **kwargs):
"""
Fit data with minuit minimizer
"""
# set up minuit inputs
bounds = np.array(kwargs['bounds']).T
kwargs_minuit = {'start':kwargs['p0'],
'limit':bounds,
'fix':fixed,
'print_level':kwargs.get('print_level', 0),
}
name = kwargs.get('name', None)
if name is None:
name = inspect.getfullargspec(fn).args
if 'self' in name: name.remove('self')
if len(name) == len(kwargs['p0']): kwargs_minuit['name'] = name
else:
kwargs_minuit['name'] = name
m = minuit(fn, x, y, dy, **kwargs_minuit)
m.migrad()
# get errors
if do_minos:
try:
m.minos()
names = list(m.mname)
mlower = np.abs(m.mlower)
mupper = m.mupper
# insert errors of zero for fixed parameters
lower = [mlower[names.index(p)] if not m.fixed[p] else 0 for p in m.parameters]
upper = [mupper[names.index(p)] if not m.fixed[p] else 0 for p in m.parameters]
except RuntimeError as errmsg: # migrad did not converge
print(errmsg)
err = m.errors
lower, upper = (err, err)
else:
m.hesse()
err = m.errors
lower, upper = (err, err)
# get parameters
par = m.values
try:
cov = m.covariance
except RuntimeError:
cov = None
dof = len(y) - len(kwargs['p0'])
chi = m.fval/dof
return (par, cov, lower, upper, chi, m)
def test_limit_named_and_list_assign():
m = minuit(fn, x, y, limit_e=[1,2], limit=[0,5])
assert_equal(m.limits['e'][0], 1, 'minuit limits 0 list and named assignment')
assert_equal(m.limits['e'][1], 2, 'minuit limits 1 list and named assignment')
others = [m.limits[k][0]==0 for k in 'abcd']
assert_equal(all(others), True, 'minuit limits 0 list and named assignment')
others = [m.limits[k][1]==5 for k in 'abcd']
assert_equal(all(others), True, 'minuit limits 1 list and named assignment')
def test_limit_named_assign():
m = minuit(fn, x, y, limit_e=[0,5])
assert_equal(m.limits['e'][0], 0, 'minuit limits 0 named assignment')
assert_equal(m.limits['e'][1], 5, 'minuit limits 1 named assignment')
def _do_fit(self, text):
# save model text
self.text= text[-1]
# get fit data
xstr = self.xaxis.get()
ystr = self.yaxis.get()
# Make model
parnames = self.output_par_text.get('1.0', END).split('\n')[:-1]
parstr = ', '.join(parnames)
eqn = text[-1].split('=')[-1]
model = 'lambda x, %s : %s' % (parstr, eqn)
self.logger.info('Fitting model %s for x="%s", y="%s"', model, xstr, ystr)
self.model_fn = eval(model)
npar = len(parnames)
# set up p0, bounds
p0 = self.new_par['p0'].values
blo = self.new_par['blo'].values
bhi = self.new_par['bhi'].values
p0 = list(map(float, p0))
blo = list(map(float, blo))
bhi = list(map(float, bhi))
# get data to fit
xvals, xerrs_l, xerrs_h = self._get_data(xstr)
yvals, yerrs_l, yerrs_h = self._get_data(ystr)
# minimize
m = minuit(self.model_fn, xvals, yvals,
dy = yerrs_h,
dx = xerrs_h,
dy_low = yerrs_l,
dx_low = xerrs_l,
name = parnames,
print_level = 0,
limit = np.array([blo, bhi]).T,
start = p0,
)
m.migrad()
m.hesse()
m.minos()
# print fitting quality
try:
print(m.fmin)
print(m.params)
print(m.merrors)
except UnicodeEncodeError:
pass
# get results
par = m.values
self.par = par
n = len(m.merrors)
if npar == 1:
std_l = np.array([m.merrors[i].lower for i in range(n)])
std_h = np.array([std_l])
else:
std_l = np.array([m.merrors[i].lower for i in range(n)])
std_h = np.array([m.merrors[i].upper for i in range(n)])
# chi2
chi = m.chi2
self.chi_label['text'] = 'ChiSq: %.2f' % np.around(chi, 2)
self.chi = chi
self.logger.info('Fit model results: %s, Errors-: %s, Errors+: %s',
str(par), str(std_l), str(std_h))
self.bfit.plt.figure('param')
self.draw_data()
self.draw_model()
return (par, std_l, std_h)
def _do_migrad(self, master_fn, master_fnprime, do_minos, p0_first,
**fitargs):
# set args
limit = fitargs.get('bounds', None)
if limit is not None:
limit = np.array(limit).T
kwargs_minuit = {
'start': p0_first,
'limit': limit,
'print_level': fitargs.get('print_level', 1),
}
# get minuit obj
m = minuit(master_fn,
self.xcat,
self.ycat,
dy=self.dycat,
dx=self.dxcat,
dy_low=self.dycat_low,
dx_low=self.dxcat_low,
fn_prime=master_fnprime,
**kwargs_minuit)
self.ls = m.ls
self.minuit = m
# minimize
try:
m.migrad()
except UnicodeEncodeError: # can't print on older machines
pass
# check minimum
if not m.fmin.is_valid:
raise RuntimeError('Minuit failed to converge to a valid minimum')
# get errors
if do_minos:
try:
m.minos()
except UnicodeEncodeError: # can't print on older machines
pass
lower = np.abs(m.mlower)
upper = m.mupper
else:
try:
m.hesse()
except UnicodeEncodeError: # can't print on older machines
pass
lower = m.errors
upper = lower
# get output
par = m.values
cov = m.covariance
return (par, lower, upper, cov)
def test_fix_named_and_list_assign():
m = minuit(fn, x, y, fix_e=False, fix=True)
assert_equal(m.fixed['e'], False, 'minuit fixed list and named assignment')
others = [m.fixed[k] for k in 'abcd']
assert_equal(all(others), True, 'minuit fixed list and named assignment')
def test_fix_named_assign():
m = minuit(fn, x, y, fix_e=True)
assert_equal(m.fixed['e'], True, 'minuit fixed named assignment')
fixed_other = [m.fixed[k] for k in 'abcd']
assert_equal(any(fixed_other), False, 'minuit fixed named assignment, other')
def test_fix_broadcast():
m = minuit(fn, x, y, fix=True)
assert_equal(m.fixed['e'], True, 'minuit fixed broadcasting')
def test_fix_assign():
m = minuit(fn, x, y, fix=[True, True, True, True, True])
assert_equal(m.fixed['e'], True, 'minuit fixed assignment')
def test_name_default():
m = minuit(fn2, x, y, name=['a', 'b', 'c', 'd', 'e'])
assert_equal(m.values['e'], 1, 'minuit start default param unnamed')
def test_name_assign():
m = minuit(fn2, x, y, name=['a', 'b', 'c', 'd', 'e'])
assert m.values['e'], 'minuit name assignment'
def test_limit_assign():
m = minuit(fn, x, y, limit=[[0,1],[0,2],[0,3],[0,4],[0,5]])
assert_equal(m.limits['e'][1], 5, 'minuit limits assignment')
def test_error_named_and_list_assign():
m = minuit(fn, x, y, error_e=5, error=1)
assert_equal(m.errors['e'], 5, 'minuit errors list and named assignment')
others = [m.errors[k]==1 for k in 'abcd']
assert_equal(all(others), True, 'minuit errors list and named assignment')
def test_error_named_assign():
m = minuit(fn, x, y, error_e=5)
assert_equal(m.errors['e'], 5, 'minuit errors named assignment')
def test_error_broadcast():
m = minuit(fn, x, y, error=5)
errors_all = [m.errors[k] == 5 for k in 'abcde']
assert_equal(all(errors_all), True, 'minuit errors broadcasting')
def test_error_assign():
m = minuit(fn, x, y, error=[1,2,3,4,5])
assert_equal(m.errors['e'], 5, 'minuit errors assignment')