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Improved prior fit (#161)
* refactor: merged combined fit and prior fit without breaking the routine. Fitting with priors does not work yet. * refactor: correlated fits without priors work now. * refactor: prior error propagation and dof fixed. * refactor: old prior fit implementation moved to tests. * refactor: moved _extract_val_and_dval out of least_squares. * refactor: comment removed. * tests: additional tests and exceptions added. * tests: test for constrained prior fit added. * docs: least_squares docstring extended. * fix: linting errors fixed. * feat: additional if cause for fits without priors added to achieve original speed. * tests: test_constrained_and_prior_fit fixed. * fix: fix array cast of least_squares dict mode. * tests: test for lists in dict fit added. * fix: additional asarray added in resplot. Co-authored-by: Simon Kuberski <simon.kuberski@uni-muenster.de>
This commit is contained in:
Fabian Joswig
GitHub
parent
82cd2f11ea
commit
839d9214ed
3 changed files with 549 additions and 364 deletions
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@ -6,6 +6,9 @@ import scipy.optimize
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from scipy.odr import ODR, Model, RealData
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from scipy.linalg import cholesky
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from scipy.stats import norm
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import iminuit
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from autograd import jacobian
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from autograd import hessian
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import pyerrors as pe
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import pytest
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@ -410,6 +413,19 @@ def test_prior_fit():
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fitp = pe.fits.least_squares([0, 1], y, f, priors=y, resplot=True, qqplot=True)
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def test_vs_old_prior_implementation():
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x = np.arange(1, 5)
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y = [pe.pseudo_Obs(2 * i + 1.1 + np.random.normal(0.0, 0.1), .1, 't') for i in x]
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[o.gm() for o in y];
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def fitf(a, x):
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return a[0] * x + a[1]
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priors = [pe.cov_Obs(1.10, 0.01 ** 2, "p0"), pe.cov_Obs(1.1, 0.3 ** 2, "p1")]
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pr = pe.fits.least_squares(x, y, fitf, priors=priors, method="migrad")
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fr = old_prior_fit(x, y, fitf, priors=priors)
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assert pr[0] == fr[0]
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assert pr[1] == fr[1]
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def test_correlated_fit_covobs():
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x1 = pe.cov_Obs(1.01, 0.01 ** 2, 'test1')
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x2 = pe.cov_Obs(2.01, 0.01 ** 2, 'test2')
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@ -924,6 +940,123 @@ def test_x_multidim_fit():
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pe.fits.least_squares(x, y, fitf)
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def test_priors_dict_vs_list():
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x = np.arange(1, 5)
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y = [pe.pseudo_Obs(2 * i + 1.1 + np.random.normal(0.0, 0.01), .01, 't') for i in x]
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[o.gm() for o in y];
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def fitf(a, x):
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return a[0] * x + a[1]
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priors = [pe.cov_Obs(1.0, 0.0001 ** 2, "p0"), pe.cov_Obs(1.1, 0.8 ** 2, "p1")]
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pr1 = pe.fits.least_squares(x, y, fitf, priors=priors)
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prd = {0: priors[0],
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1: priors[1]}
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pr2 = pe.fits.least_squares(x, y, fitf, priors=prd)
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prd = {1: priors[1],
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0: priors[0]}
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pr3 = pe.fits.least_squares(x, y, fitf, priors=prd)
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assert (pr1[0] - pr2[0]).is_zero(1e-6)
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assert (pr1[1] - pr2[1]).is_zero(1e-6)
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assert (pr1[0] - pr3[0]).is_zero(1e-6)
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assert (pr1[1] - pr3[1]).is_zero(1e-6)
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def test_not_all_priors_set():
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x = np.arange(1, 5)
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y = [pe.pseudo_Obs(2 * i + 1.1 + np.random.normal(0.0, 0.01), .01, 't') for i in x]
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[o.gm() for o in y];
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def fitf(a, x):
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return a[0] * x + a[1] + a[2] * x ** 2
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priors = [pe.cov_Obs(2.0, 0.1 ** 2, "p0"), pe.cov_Obs(2, 0.8 ** 2, "p2")]
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prd = {0: priors[0],
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2: priors[1]}
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pr1 = pe.fits.least_squares(x, y, fitf, priors=prd)
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prd = {2: priors[1],
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0: priors[0]}
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pr2 = pe.fits.least_squares(x, y, fitf, priors=prd)
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assert (pr1[0] - pr2[0]).is_zero(1e-6)
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assert (pr1[1] - pr2[1]).is_zero(1e-6)
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assert (pr1[2] - pr2[2]).is_zero(1e-6)
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def test_force_fit_on_prior():
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x = np.arange(1, 10)
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y = [pe.pseudo_Obs(2 + np.random.normal(0.0, 0.1), .1, 't') for i in x]
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[o.gm() for o in y];
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def fitf(a, x):
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return a[0]
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prd = {0: pe.cov_Obs(0.0, 0.0000001 ** 2, "prior0")}
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pr = pe.fits.least_squares(x, y, fitf, priors=prd)
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pr.gm()
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diff = prd[0] - pr[0]
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diff.gm()
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assert diff.is_zero_within_error(5)
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def test_constrained_and_prior_fit():
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for my_constant in [pe.pseudo_Obs(5.0, 0.00000001, "test"),
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pe.pseudo_Obs(6.5, 0.00000001, "test"),
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pe.pseudo_Obs(6.5, 0.00000001, "another_ensmble")]:
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dim = 10
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x = np.arange(dim)
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y = -0.06 * x + 5 + np.random.normal(0.0, 0.3, dim)
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yerr = [0.3] * dim
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oy = []
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for i, item in enumerate(x):
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oy.append(pe.pseudo_Obs(y[i], yerr[i], 'test'))
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def func(a, x):
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y = a[0] * x + a[1]
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return y
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# Fit with constrained parameter
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out = pe.least_squares(x, oy, func, priors={1: my_constant}, silent=True)
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out.gm()
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def alt_func(a, x):
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y = a[0] * x
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return y
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alt_y = np.array(oy) - my_constant
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[o.gm() for o in alt_y]
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# Fit with the constant subtracted from the data
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alt_out = pe.least_squares(x, alt_y, alt_func, silent=True)
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alt_out.gm()
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assert np.isclose(out[0].value, alt_out[0].value, atol=1e-5, rtol=1e-6)
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assert np.isclose(out[0].dvalue, alt_out[0].dvalue, atol=1e-5, rtol=1e-6)
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assert np.isclose(out.chisquare_by_dof, alt_out.chisquare_by_dof, atol=1e-5, rtol=1e-6)
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def test_resplot_lists_in_dict():
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xd = {
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'a': [1, 2, 3],
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'b': [1, 2, 3],
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}
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yd = {
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'a': [pe.pseudo_Obs(i, .1*i, 't') for i in range(1, 4)],
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'b': [pe.pseudo_Obs(2*i**2, .1*i**2, 't') for i in range(1, 4)]
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}
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[[o.gamma_method() for o in y] for y in yd.values()]
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fd = {
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'a': lambda a, x: a[0] + a[1] * x,
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'b': lambda a, x: a[0] + a[2] * x**2,
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}
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fitp = pe.fits.least_squares(xd, yd, fd, resplot=True)
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def fit_general(x, y, func, silent=False, **kwargs):
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"""Performs a non-linear fit to y = func(x) and returns a list of Obs corresponding to the fit parameters.
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@ -1021,3 +1154,126 @@ def fit_general(x, y, func, silent=False, **kwargs):
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for n in range(n_parms):
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res.append(pe.derived_observable(do_the_fit, obs, function=func, xerr=xerr, yerr=yerr, x_constants=x_constants, num_grad=True, n=n, **kwargs))
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return res
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def old_prior_fit(x, y, func, priors, silent=False, **kwargs):
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output = pe.fits.Fit_result()
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output.fit_function = func
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x = np.asarray(x)
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if not callable(func):
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raise TypeError('func has to be a function.')
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for i in range(100):
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try:
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func(np.arange(i), 0)
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except TypeError:
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continue
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except IndexError:
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continue
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else:
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break
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else:
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raise RuntimeError("Fit function is not valid.")
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n_parms = i
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if n_parms != len(priors):
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raise Exception('Priors does not have the correct length.')
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def extract_val_and_dval(string):
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split_string = string.split('(')
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if '.' in split_string[0] and '.' not in split_string[1][:-1]:
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factor = 10 ** -len(split_string[0].partition('.')[2])
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else:
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factor = 1
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return float(split_string[0]), float(split_string[1][:-1]) * factor
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loc_priors = []
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for i_n, i_prior in enumerate(priors):
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if isinstance(i_prior, pe.Obs):
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loc_priors.append(i_prior)
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else:
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loc_val, loc_dval = extract_val_and_dval(i_prior)
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loc_priors.append(pe.cov_Obs(loc_val, loc_dval ** 2, '#prior' + str(i_n) + f"_{np.random.randint(2147483647):010d}"))
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output.priors = loc_priors
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if not silent:
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print('Fit with', n_parms, 'parameter' + 's' * (n_parms > 1))
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y_f = [o.value for o in y]
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dy_f = [o.dvalue for o in y]
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if np.any(np.asarray(dy_f) <= 0.0):
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raise Exception('No y errors available, run the gamma method first.')
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p_f = [o.value for o in loc_priors]
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dp_f = [o.dvalue for o in loc_priors]
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if np.any(np.asarray(dp_f) <= 0.0):
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raise Exception('No prior errors available, run the gamma method first.')
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if 'initial_guess' in kwargs:
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x0 = kwargs.get('initial_guess')
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if len(x0) != n_parms:
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raise Exception('Initial guess does not have the correct length.')
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else:
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x0 = p_f
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def chisqfunc(p):
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model = func(p, x)
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chisq = anp.sum(((y_f - model) / dy_f) ** 2) + anp.sum(((p_f - p) / dp_f) ** 2)
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return chisq
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if not silent:
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print('Method: migrad')
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m = iminuit.Minuit(chisqfunc, x0)
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m.errordef = 1
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m.print_level = 0
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if 'tol' in kwargs:
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m.tol = kwargs.get('tol')
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else:
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m.tol = 1e-4
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m.migrad()
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params = np.asarray(m.values)
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output.chisquare_by_dof = m.fval / len(x)
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output.method = 'migrad'
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if not silent:
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print('chisquare/d.o.f.:', output.chisquare_by_dof)
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if not m.fmin.is_valid:
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raise Exception('The minimization procedure did not converge.')
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hess = hessian(chisqfunc)(params)
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hess_inv = np.linalg.pinv(hess)
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def chisqfunc_compact(d):
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model = func(d[:n_parms], x)
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chisq = anp.sum(((d[n_parms: n_parms + len(x)] - model) / dy_f) ** 2) + anp.sum(((d[n_parms + len(x):] - d[:n_parms]) / dp_f) ** 2)
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return chisq
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jac_jac = hessian(chisqfunc_compact)(np.concatenate((params, y_f, p_f)))
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deriv = -hess_inv @ jac_jac[:n_parms, n_parms:]
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result = []
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for i in range(n_parms):
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result.append(pe.derived_observable(lambda x, **kwargs: (x[0] + np.finfo(np.float64).eps) / (y[0].value + np.finfo(np.float64).eps) * params[i], list(y) + list(loc_priors), man_grad=list(deriv[i])))
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output.fit_parameters = result
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output.chisquare = chisqfunc(np.asarray(params))
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if kwargs.get('resplot') is True:
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residual_plot(x, y, func, result)
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if kwargs.get('qqplot') is True:
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qqplot(x, y, func, result)
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return output
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@ -1085,7 +1085,7 @@ def test_non_overlapping_missing_cnfgs():
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average = (even + odd) / 2
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average.gm(S=0)
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assert np.isclose(full.value, average.value)
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assert np.isclose(full.dvalue, average.dvalue, rtol=0.01)
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assert np.isclose(full.dvalue, average.dvalue, rtol=0.02)
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def test_non_overlapping_operations():
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