def test_constraints(self):
# constraints should work during fitting
self.p[0].value = 5.4
self.p[1].constraint = -0.203 * self.p[0]
assert_equal(self.p[1].value, self.p[0].value * -0.203)
res = self.mcfitter.fit()
assert_(res.success)
assert_equal(len(self.objective.varying_parameters()), 1)
# lnsigma is parameters[0]
assert_(self.p[0] is self.objective.parameters.flattened()[0])
assert_(self.p[1] is self.objective.parameters.flattened()[1])
assert_almost_equal(self.p[0].value, res.x[0])
assert_almost_equal(self.p[1].value, self.p[0].value * -0.203)
# check that constraints work during sampling
# the CurveFitter has to be set up again if you change how the
# parameters are being fitted.
mcfitter = CurveFitter(self.objective)
assert_(mcfitter.nvary == 1)
mcfitter.sample(5)
assert_equal(self.p[1].value, self.p[0].value * -0.203)
# the constrained parameters should have a chain
assert_(self.p[0].chain is not None)
assert_(self.p[1].chain is not None)
assert_allclose(self.p[1].chain, self.p[0].chain * -0.203)
def setup(self):
pth = os.path.dirname(os.path.abspath(refnx.reflect.__file__))
e361 = RD(os.path.join(pth, 'test', 'e361r.txt'))
sio2 = SLD(3.47, name='SiO2')
si = SLD(2.07, name='Si')
d2o = SLD(6.36, name='D2O')
polymer = SLD(1, name='polymer')
# e361 is an older dataset, but well characterised
structure361 = si | sio2(10, 4) | polymer(200, 3) | d2o(0, 3)
model361 = ReflectModel(structure361, bkg=2e-5)
model361.scale.vary = True
model361.bkg.vary = True
model361.scale.range(0.1, 2)
model361.bkg.range(0, 5e-5)
model361.dq = 5.
# d2o
structure361[-1].sld.real.vary = True
structure361[-1].sld.real.range(6, 6.36)
structure361[1].thick.vary = True
structure361[1].thick.range(5, 20)
structure361[2].thick.vary = True
structure361[2].thick.range(100, 220)
structure361[2].sld.real.vary = True
structure361[2].sld.real.range(0.2, 1.5)
e361.x_err = None
objective = Objective(model361, e361)
self.fitter = CurveFitter(objective, nwalkers=200)
self.fitter.initialise('jitter')
class curvefitter(Benchmark):
repeat = 3
def setup(self):
# Reproducible results!
np.random.seed(123)
m_true = -0.9594
b_true = 4.294
f_true = 0.534
m_ls = -1.1040757010910947
b_ls = 5.4405552502319505
# Generate some synthetic data from the model.
N = 50
x = np.sort(10 * np.random.rand(N))
y_err = 0.1 + 0.5 * np.random.rand(N)
y = m_true * x + b_true
y += np.abs(f_true * y) * np.random.randn(N)
y += y_err * np.random.randn(N)
data = Data1D(data=(x, y, y_err))
p = Parameter(b_ls, 'b', vary=True, bounds=(-100, 100))
p |= Parameter(m_ls, 'm', vary=True, bounds=(-100, 100))
model = Model(p, fitfunc=line)
objective = Objective(model, data)
self.mcfitter = CurveFitter(objective)
self.mcfitter.initialise('prior')
def time_sampler(self):
# to get an idea of how fast the actual sampling is.
# i.e. the overhead of objective.lnprob, objective.lnprior, etc
self.mcfitter.sampler.run_mcmc(self.mcfitter._state, 100)
def NIST_runner(
dataset,
method="least_squares",
chi_atol=1e-5,
val_rtol=1e-2,
err_rtol=6e-3,
):
NIST_dataset = ReadNistData(dataset)
x, y = (NIST_dataset["x"], NIST_dataset["y"])
if dataset == "Nelson":
y = np.log(y)
params = NIST_dataset["start"]
fitfunc = NIST_Models[dataset][0]
model = Model(params, fitfunc)
objective = Objective(model, (x, y))
fitter = CurveFitter(objective)
result = fitter.fit(method=method)
assert_allclose(objective.chisqr(),
NIST_dataset["sum_squares"],
atol=chi_atol)
certval = NIST_dataset["cert_values"]
assert_allclose(result.x, certval, rtol=val_rtol)
if "stderr" in result:
certerr = NIST_dataset["cert_stderr"]
assert_allclose(result.stderr, certerr, rtol=err_rtol)
def test_mcmc(self):
self.mcfitter.sample(steps=50, nthin=1, verbose=False)
assert_equal(self.mcfitter.nvary, 2)
# smoke test for corner plot
self.mcfitter.objective.corner()
# we're not doing Parallel Tempering here.
assert_(self.mcfitter._ntemps == -1)
assert_(isinstance(self.mcfitter.sampler, emcee.EnsembleSampler))
# should be able to multithread
mcfitter = CurveFitter(self.objective, nwalkers=50)
res = mcfitter.sample(steps=33, nthin=2, verbose=False, pool=2)
# check that the autocorrelation function at least runs
acfs = mcfitter.acf(nburn=10)
assert_equal(acfs.shape[-1], mcfitter.nvary)
# check chain shape
assert_equal(mcfitter.chain.shape, (33, 50, 2))
# assert_equal(mcfitter._lastpos, mcfitter.chain[:, -1, :])
assert_equal(res[0].chain.shape, (33, 50))
# if the number of parameters changes there should be an Exception
# raised
from pytest import raises
with raises(RuntimeError):
self.p[0].vary = False
self.mcfitter.sample(1)
# can fix by making the sampler again
self.mcfitter.make_sampler()
self.mcfitter.sample(1)
def NIST_runner(dataset, method='leastsq', chi_atol=1e-5,
val_rtol=1e-2, err_rtol=0.01):
NIST_dataset = ReadNistData(dataset)
x, y = (NIST_dataset['x'], NIST_dataset['y'])
if dataset == 'Nelson':
y = np.log(y)
params = NIST_dataset['start']
fitfunc = Models[dataset][0]
fitter = CurveFitter(fitfunc, (x, y), params)
result = fitter.fit(method, params)
assert_allclose(result.chisqr, NIST_dataset['sum_squares'], atol=chi_atol)
thisval = values(result.params)
certval = NIST_dataset['cert_values']
assert_allclose(thisval, certval, rtol=val_rtol)
if result.errorbars:
thiserr = np.array([result.params[par].stderr for par in result.params])
certerr = NIST_dataset['cert_stderr']
assert_allclose(thiserr, certerr, rtol=err_rtol)
def setup(self):
# Reproducible results!
np.random.seed(123)
m_true = -0.9594
b_true = 4.294
f_true = 0.534
m_ls = -1.1040757010910947
b_ls = 5.4405552502319505
# Generate some synthetic data from the model.
N = 50
x = np.sort(10 * np.random.rand(N))
y_err = 0.1 + 0.5 * np.random.rand(N)
y = m_true * x + b_true
y += np.abs(f_true * y) * np.random.randn(N)
y += y_err * np.random.randn(N)
data = Data1D(data=(x, y, y_err))
p = Parameter(b_ls, 'b', vary=True, bounds=(-100, 100))
p |= Parameter(m_ls, 'm', vary=True, bounds=(-100, 100))
model = Model(p, fitfunc=line)
self.objective = Objective(model, data)
self.mcfitter = CurveFitter(self.objective)
self.mcfitter_t = CurveFitter(self.objective, ntemps=20)
self.mcfitter.initialise('prior')
self.mcfitter_t.initialise('prior')
def NIST_runner(dataset, method='least_squares', chi_atol=1e-5,
val_rtol=1e-2, err_rtol=5e-3):
NIST_dataset = ReadNistData(dataset)
x, y = (NIST_dataset['x'], NIST_dataset['y'])
if dataset == 'Nelson':
y = np.log(y)
params = NIST_dataset['start']
fitfunc = NIST_Models[dataset][0]
model = Model(params, fitfunc)
objective = Objective(model, (x, y))
fitter = CurveFitter(objective)
result = fitter.fit(method=method)
assert_allclose(objective.chisqr(),
NIST_dataset['sum_squares'],
atol=chi_atol)
certval = NIST_dataset['cert_values']
assert_allclose(result.x, certval, rtol=val_rtol)
if 'stderr' in result:
certerr = NIST_dataset['cert_stderr']
assert_allclose(result.stderr, certerr, rtol=err_rtol)
def test_all_minimisers(self):
"""test minimisers against the Gaussian fit"""
f = CurveFitter(self.objective)
methods = [
"differential_evolution",
"L-BFGS-B",
"least_squares",
"shgo",
"dual_annealing",
]
for method in methods:
self.objective.setp(self.p0)
opts = {}
if method in ["differential_evolution", "dual_annealing"]:
opts = {"seed": 1}
res = f.fit(method=method, **opts)
assert_allclose(res.x, self.best_weighted, rtol=0.005)
# smoke test to check that we can use nlpost
self.objective.setp(self.p0)
logp0 = self.objective.logp()
# check that probabilities are calculated correctly
assert_allclose(
self.objective.logpost(),
self.objective.logp() + self.objective.logl(),
)
assert_allclose(self.objective.nlpost(), -self.objective.logpost())
assert_allclose(self.objective.nlpost(self.p0),
-self.objective.logpost(self.p0))
# if the priors are all uniform then the only difference between
# logpost and logl is a constant. A minimiser should converge on the
# same answer. The following tests examine that.
# The test works for dual_annealing, but not for differential
# evolution, not sure why that is.
self.objective.setp(self.p0)
res1 = f.fit(method="dual_annealing", seed=1)
assert_almost_equal(res1.x, self.best_weighted, 3)
nll1 = self.objective.nll()
nlpost1 = self.objective.nlpost()
self.objective.setp(self.p0)
res2 = f.fit(method="dual_annealing", target="nlpost", seed=1)
assert_almost_equal(res2.x, self.best_weighted, 3)
nll2 = self.objective.nll()
nlpost2 = self.objective.nlpost()
assert_allclose(nlpost1, nlpost2, atol=0.001)
assert_allclose(nll1, nll2, atol=0.001)
# these two priors are calculated for different parameter values
# (before and after the fit) they should be the same because all
# the parameters have uniform priors.
assert_almost_equal(self.objective.logp(), logp0)
def test_reflectivity_fit(self):
# a smoke test to make sure the reflectivity fit proceeds
model = self.model361
objective = Objective(model,
(self.qvals361, self.rvals361, self.evals361),
transform=Transform('logY'))
fitter = CurveFitter(objective)
with np.errstate(invalid='raise'):
fitter.fit('differential_evolution')
def test_mcmc_pt(self):
if not _HAVE_PTSAMPLER:
return
# smoke test for parallel tempering
mcfitter = CurveFitter(self.objective, ntemps=10, nwalkers=50)
assert_equal(mcfitter.sampler.ntemps, 10)
res = mcfitter.sample(steps=30, nthin=2, verbose=False, pool=0)
assert_equal(mcfitter.chain.shape, (30, 10, 50, 2))
assert_equal(res[0].chain.shape, (30, 50))
assert_equal(mcfitter.chain[:, 0, :, 0], res[0].chain)
assert_equal(mcfitter.chain[:, 0, :, 1], res[1].chain)
def test_run():
print("\n\n\n")
from refnx.dataset import Data1D
from refnx.dataset import ReflectDataset
import refnx
import data_in
data = data_in.data_in('d2o/29553_54.dat')
# dataset = data # ...
data = Data1D(data)
from make_egg import bsla_thesis
# air = SLD(0)
# air = air(0,0)
bt = bsla_thesis()
bt.interface_protein_solvent.setp(vary=True, bounds=(11, 40))
bt.protein_length.setp(vary=True, bounds=(25, 55))
bt.number_of_water_molecules.setp(vary=True, bounds=(1, 10000))
bt.interface_width_air_solvent.setp(vary=True, bounds=(0.001, 30))
#bt.interface_width_protein_solvent.setp(vary=True, bounds=(0, 5))
bt.sld_of_protein.setp(vary=True, bounds=(1.92, 6.21)) # *(10**(-6))
bt.d2o_to_h2o_ratio.setp(vary=True, bounds=(0, 1))
# if isinstance(bt, Component):
# print("it is comp")
# if isinstance(bt, Structure):
# print("it is")
#print(bt.parameters)
# d2o = 1.9185/0.3
# h2o = -0.1635/0.3
# solvent = SLD((bt.d2o_to_h2o_ratio.value*d2o + (1-bt.d2o_to_h2o_ratio.value)*h2o))
# solvent = solvent(0,0)
# from refnx.reflect import Structure
# structure = air|bt|solvent
# structure.name = "bsla"
from refnx.reflect import ReflectModel
model = ReflectModel(bt) #structure)
from refnx.analysis import Transform, CurveFitter, Objective
objective = Objective(model, data)
fitter = CurveFitter(objective)
fitter.fit('differential_evolution')
import matplotlib.pyplot as plt
#%matplotlib notebook
# plt.plot(*bt.sld_profile())
objective.plot()
plt.yscale('log')
plt.xscale('log')
plt.xlabel('Q')
plt.ylabel('Reflectivity')
plt.legend()
print(bt)
plt.show()
def test_all_minimisers(self):
"""test minimisers against the Gaussian fit"""
f = CurveFitter(self.objective)
methods = ['differential_evolution', 'L-BFGS-B', 'least_squares']
if hasattr(sciopt, 'shgo'):
methods.append('shgo')
if hasattr(sciopt, 'dual_annealing'):
methods.append('dual_annealing')
for method in methods:
self.objective.setp(self.p0)
res = f.fit(method=method)
assert_almost_equal(res.x, self.best_weighted, 3)
# smoke test to check that we can use nlpost
self.objective.setp(self.p0)
logp0 = self.objective.logp()
# check that probabilities are calculated correctly
assert_allclose(self.objective.logpost(),
self.objective.logp() + self.objective.logl())
assert_allclose(self.objective.nlpost(), -self.objective.logpost())
# if the priors are all uniform then the only difference between
# logpost and logl is a constant. A minimiser should converge on the
# same answer. The following tests examine that.
# The test works for dual_annealing, but not for differential
# evolution, not sure why that is.
self.objective.setp(self.p0)
res1 = f.fit(method='dual_annealing', seed=1)
assert_almost_equal(res1.x, self.best_weighted, 3)
nll1 = self.objective.nll()
nlpost1 = self.objective.nlpost()
self.objective.setp(self.p0)
res2 = f.fit(method='dual_annealing', target='nlpost', seed=1)
assert_almost_equal(res2.x, self.best_weighted, 3)
nll2 = self.objective.nll()
nlpost2 = self.objective.nlpost()
assert_allclose(nlpost1, nlpost2, atol=0.001)
assert_allclose(nll1, nll2, atol=0.001)
# these two priors are calculated for different parameter values
# (before and after the fit) they should be the same because all
# the parameters have uniform priors.
assert_almost_equal(self.objective.logp(), logp0)
def test_best_unweighted(self):
self.objective.weighted = False
f = CurveFitter(self.objective, nwalkers=100)
res = f.fit()
output = res.x
assert_almost_equal(self.objective.chisqr(),
self.best_unweighted_chisqr)
assert_almost_equal(output, self.best_unweighted, 5)
# compare the residuals
res = self.data.y - self.model(self.data.x)
assert_equal(self.objective.residuals(), res)
# compare objective._covar to the best_unweighted_errors
uncertainties = np.array([param.stderr for param in self.params])
assert_almost_equal(uncertainties, self.best_unweighted_errors, 3)
def test_reflectivity_emcee(self):
model = self.model361
model.dq = 5.
objective = Objective(model,
(self.qvals361, self.rvals361, self.evals361),
transform=Transform('logY'))
fitter = CurveFitter(objective, nwalkers=100)
assert_(len(objective.generative().shape) == 1)
assert_(len(objective.residuals().shape) == 1)
res = fitter.fit('least_squares')
res_mcmc = fitter.sample(steps=5, nthin=10, random_state=1,
verbose=False)
mcmc_val = [mcmc_result.median for mcmc_result in res_mcmc]
assert_allclose(mcmc_val, res.x, rtol=0.05)
def curvefitter(self):
"""
class:`CurveFitter` : Object for fitting the data based on the
objective.
"""
if self.objective is not None and self._curvefitter is None:
self._curvefitter = CurveFitter(self.objective)
return self._curvefitter
def setup_method(self):
# Reproducible results!
np.random.seed(123)
self.m_true = -0.9594
self.b_true = 4.294
self.f_true = 0.534
self.m_ls = -1.1040757010910947
self.b_ls = 5.4405552502319505
# Generate some synthetic data from the model.
N = 50
x = np.sort(10 * np.random.rand(N))
y_err = 0.1 + 0.5 * np.random.rand(N)
y = self.m_true * x + self.b_true
y += np.abs(self.f_true * y) * np.random.randn(N)
y += y_err * np.random.randn(N)
self.data = Data1D(data=(x, y, y_err))
self.p = Parameter(self.b_ls, 'b', vary=True, bounds=(-100, 100))
self.p |= Parameter(self.m_ls, 'm', vary=True, bounds=(-100, 100))
self.model = Model(self.p, fitfunc=line)
self.objective = Objective(self.model, self.data)
assert_(len(self.objective.varying_parameters()) == 2)
mod = np.array([4.78166609, 4.42364699, 4.16404064, 3.50343504,
3.4257084, 2.93594347, 2.92035638, 2.67533842,
2.28136038, 2.19772983, 1.99295496, 1.93748334,
1.87484436, 1.65161016, 1.44613461, 1.11128101,
1.04584535, 0.86055984, 0.76913963, 0.73906649,
0.73331407, 0.68350418, 0.65216599, 0.59838566,
0.13070299, 0.10749131, -0.01010195, -0.10010155,
-0.29495372, -0.42817431, -0.43122391, -0.64637715,
-1.30560686, -1.32626428, -1.44835768, -1.52589881,
-1.56371158, -2.12048349, -2.24899179, -2.50292682,
-2.53576659, -2.55797996, -2.60870542, -2.7074727,
-3.93781479, -4.12415366, -4.42313742, -4.98368609,
-5.38782395, -5.44077086])
self.mod = mod
self.mcfitter = CurveFitter(self.objective)
def test_mcmc(self):
self.mcfitter.sample(steps=50, nthin=1, verbose=False)
# we're not doing Parallel Tempering here.
assert_(self.mcfitter._ntemps == -1)
assert_(isinstance(self.mcfitter.sampler, emcee.EnsembleSampler))
# should be able to multithread
mcfitter = CurveFitter(self.objective, nwalkers=50)
res = mcfitter.sample(steps=33, nthin=2, verbose=False, pool=2)
# check that the autocorrelation function at least runs
acfs = mcfitter.acf(nburn=10)
assert_equal(acfs.shape[-1], mcfitter.nvary)
# check chain shape
assert_equal(mcfitter.chain.shape, (33, 50, 2))
# assert_equal(mcfitter._lastpos, mcfitter.chain[:, -1, :])
assert_equal(res[0].chain.shape, (33, 50))
def test_modelvals_degenerate_layers(self):
# try fitting dataset with a deposited layer split into two degenerate
# layers
fname = os.path.join(self.pth, "c_PLP0011859_q.txt")
dataset = ReflectDataset(fname)
sio2 = SLD(3.47, name="SiO2")
si = SLD(2.07, name="Si")
d2o = SLD(6.36, name="D2O")
polymer = SLD(2.0, name="polymer")
sio2_l = sio2(30, 3)
polymer_l = polymer(125, 3)
structure = si | sio2_l | polymer_l | polymer_l | d2o(0, 3)
polymer_l.thick.setp(value=125, vary=True, bounds=(0, 250))
polymer_l.rough.setp(value=4, vary=True, bounds=(0, 8))
structure[-1].rough.setp(vary=True, bounds=(0, 6))
sio2_l.rough.setp(value=3.16, vary=True, bounds=(0, 8))
model = ReflectModel(structure, bkg=2e-6)
objective = Objective(model,
dataset,
use_weights=False,
transform=Transform("logY"))
model.scale.setp(vary=True, bounds=(0, 2))
model.bkg.setp(vary=True, bounds=(0, 8e-6))
slabs = structure.slabs()
assert_equal(slabs[2, 0:2], slabs[3, 0:2])
assert_equal(slabs[2, 3], slabs[3, 3])
assert_equal(slabs[1, 3], sio2_l.rough.value)
f = CurveFitter(objective)
f.fit(method="differential_evolution", seed=1, maxiter=3)
slabs = structure.slabs()
assert_equal(slabs[2, 0:2], slabs[3, 0:2])
assert_equal(slabs[2, 3], slabs[3, 3])
def test_globalfitting(self):
# smoke test for can the global fitting run?
# also tests that global fitting gives same output as
# normal fitting (for a single dataset)
self.model.scale.setp(vary=True, bounds=(0.1, 2))
self.model.bkg.setp(vary=True, bounds=(1e-10, 8e-6))
self.structure[-1].rough.setp(vary=True, bounds=(0.2, 6))
self.sio2_l.thick.setp(vary=True, bounds=(0.2, 80))
self.polymer_l.thick.setp(bounds=(0.01, 400), vary=True)
self.polymer_l.sld.real.setp(vary=True, bounds=(0.01, 4))
self.objective.transform = Transform('logY')
starting = np.array(self.objective.parameters)
with np.errstate(invalid='raise'):
g = CurveFitter(self.global_objective)
res_g = g.fit()
# need the same starting point
self.objective.setp(starting)
f = CurveFitter(self.objective)
res_f = f.fit()
# individual and global should give the same fit.
assert_almost_equal(res_g.x, res_f.x)
def make_model(names, bs, thicks, roughs, fig_i, data, show=False, mcmc=False):
extent = sum(
thicks[:, 0]) # (float or Parameter) – Total extent of spline region
vs = array(
bs
)[:,
0] #(Sequence of float/Parameter) – the real part of the SLD values of each of the knots.
dz = cum_sum(
array(thicks[:, 0])
) #(Sequence of float/Parameter) – the lateral offset between successive knots.
print(dz)
name = "number of nots " + str(len(names)) #(str) – Name of component
component = Spline(extent, vs, dz, name)
front = SLD(0)
front = front(0, 0)
back = SLD(0)
back = back(0, 0)
structure = front | component | back
model = ReflectModel(structure, bkg=3e-6, dq=5.0)
objective = Objective(model, data, transform=Transform('logY'))
fitter = CurveFitter(objective)
fitter.fit('differential_evolution')
return structure, fitter, objective, fig_i + 1
def test_best_weighted(self):
assert_equal(len(self.objective.varying_parameters()), 4)
self.objective.setp(self.p0)
f = CurveFitter(self.objective, nwalkers=100)
res = f.fit('least_squares', jac='3-point')
output = res.x
assert_almost_equal(output, self.best_weighted, 3)
assert_almost_equal(self.objective.chisqr(),
self.best_weighted_chisqr, 5)
# compare the residuals
res = (self.data.y - self.model(self.data.x)) / self.data.y_err
assert_equal(self.objective.residuals(), res)
# compare objective.covar to the best_weighted_errors
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.005)
# we're also going to try the checkpointing here.
checkpoint = os.path.join(self.tmpdir, 'checkpoint.txt')
# compare samples to best_weighted_errors
np.random.seed(1)
f.sample(steps=101, random_state=1, verbose=False, f=checkpoint)
process_chain(self.objective, f.chain, nburn=50, nthin=10)
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.07)
# test that the checkpoint worked
check_array = np.loadtxt(checkpoint)
check_array = check_array.reshape(101, f._nwalkers, f.nvary)
assert_allclose(check_array, f.chain)
# test loading the checkpoint
chain = load_chain(checkpoint)
assert_allclose(chain, f.chain)
f.initialise('jitter')
f.sample(steps=2, nthin=4, f=checkpoint, verbose=False)
assert_equal(f.chain.shape[0], 2)
def make_model(names, bs, thicks, roughs, fig_i, data, show=False, mcmc=False):
no_layers = len(bs)
layers = []
for i in range(no_layers):
names.append('layer' + str(i))
for i in range(no_layers):
sld = SLD(bs[i], name=names[i])
layers.append(sld(thicks[i], roughs[i]))
layers[0].thick.setp(vary=True, bounds=(thicks[i] - 1, thicks[i] + 1))
layers[0].sld.real.setp(vary=True, bounds=(bs[i] - 1, bs[i] + 1))
for layer in layers[1:]:
layer.thick.setp(vary=True, bounds=(thicks[i] - 1, thicks[i] + 1))
layer.sld.real.setp(vary=True, bounds=(bs[i] - 1, bs[i] + 1))
layer.rough.setp(vary=True, bounds=(0, 5))
structure = layers[0]
for layer in layers[1:]:
structure |= layer
print(structure)
model = ReflectModel(structure, bkg=3e-6, dq=5.0)
#model.scale.setp(bounds=(0.6, 1.2), vary=True)
#model.bkg.setp(bounds=(1e-9, 9e-6), vary=True)
objective = Objective(model, data, transform=Transform('logY'))
fitter = CurveFitter(objective)
if mcmc:
fitter.sample(1000)
process_chain(objective, fitter.chain, nburn=300, nthin=100)
else:
fitter.fit('differential_evolution')
print(objective.parameters)
if show:
plt.figure(fig_i)
plt.plot(*structure.sld_profile())
plt.ylabel('SLD /$10^{-6} \AA^{-2}$')
plt.xlabel('distance / $\AA$')
return structure, fitter, objective, fig_i + 1
def test_globalfitting(self):
# smoke test for can the global fitting run?
# also tests that global fitting gives same output as
# normal fitting (for a single dataset)
self.model.scale.setp(vary=True, bounds=(0.1, 2))
self.model.bkg.setp(vary=True, bounds=(1e-10, 8e-6))
self.structure[-1].rough.setp(vary=True, bounds=(0.2, 6))
self.sio2_l.thick.setp(vary=True, bounds=(0.2, 80))
self.polymer_l.thick.setp(bounds=(0.01, 400), vary=True)
self.polymer_l.sld.real.setp(vary=True, bounds=(0.01, 4))
self.objective.transform = Transform('logY')
with np.errstate(invalid='raise'):
g = CurveFitter(self.global_objective)
res_g = g.fit(method='differential_evolution', seed=1, maxiter=10)
f = CurveFitter(self.objective)
res_f = f.fit(method='differential_evolution', seed=1, maxiter=10)
# individual and global should give the same fit. Because we use DE
# there is no dependence on starting point, so long as we set a
# seed.
assert_almost_equal(res_g.x, res_f.x)
def test_mcmc_pt(self):
# smoke test for parallel tempering
x = np.array(self.objective.parameters)
mcfitter = CurveFitter(self.objective, ntemps=10, nwalkers=50)
assert_equal(mcfitter.sampler.ntemps, 10)
# check that the parallel sampling works
# and that chain shape is correct
res = mcfitter.sample(steps=5, nthin=2, verbose=False, pool=-1)
assert_equal(mcfitter.chain.shape, (5, 10, 50, 2))
assert_equal(res[0].chain.shape, (5, 50))
assert_equal(mcfitter.chain[:, 0, :, 0], res[0].chain)
assert_equal(mcfitter.chain[:, 0, :, 1], res[1].chain)
chain = np.copy(mcfitter.chain)
# the sampler should store the probability
assert_equal(mcfitter.logpost.shape, (5, 10, 50))
assert_allclose(mcfitter.logpost, mcfitter.sampler._ptchain.logP)
logprobs = mcfitter.logpost
highest_prob_loc = np.argmax(logprobs[:, 0])
idx = np.unravel_index(highest_prob_loc, logprobs[:, 0].shape)
idx = list(idx)
idx.insert(1, 0)
idx = tuple(idx)
assert_equal(idx, mcfitter.index_max_prob)
pvals = mcfitter.chain[idx]
assert_allclose(logprobs[idx], self.objective.logpost(pvals))
# try resetting the chain
mcfitter.reset()
# test for reproducible operation
self.objective.setp(x)
mcfitter = CurveFitter(self.objective, ntemps=10, nwalkers=50)
mcfitter.initialise("jitter", random_state=1)
mcfitter.sample(steps=5, nthin=2, verbose=False, random_state=2)
chain = np.copy(mcfitter.chain)
self.objective.setp(x)
mcfitter = CurveFitter(self.objective, ntemps=10, nwalkers=50)
mcfitter.initialise("jitter", random_state=1)
mcfitter.sample(steps=5, nthin=2, verbose=False, random_state=2)
chain2 = np.copy(mcfitter.chain)
assert_allclose(chain2, chain)
n = l.reshape(timesteps, sim.layers.shape[1]-layers_to_cut, sim.layers.shape[2])
data_dir = '../data/reflectometry2/dspc_{}/'.format(surface_pressure)
dataset = ReflectDataset(os.path.join(data_dir, '{}{}.dat'.format(contrast, surface_pressure)))
refy = np.zeros((n.shape[0], dataset.x.size))
sldy = []
chi = np.zeros((n.shape[0]))
print(n.shape[0])
for i in range(n.shape[0]):
sim.av_layers = n[i, :, :]
model = ReflectModel(sim)
model.scale.setp(1, vary=True, bounds=(0.00000001, np.inf))
model.bkg.setp(dataset.y[-1], vary=False)
objective = Objective(model, dataset, transform=Transform('YX4'))
fitter = CurveFitter(objective)
res = fitter.fit()
refy[i] = model(dataset.x, x_err=dataset.x_err)*(dataset.x)**4
sldy.append(sim.sld_profile()[1])
chi[i] = objective.chisqr()
all_chi = np.append(all_chi, objective.chisqr())
if i == 0:
ax1.errorbar(dataset.x,
dataset.y*(dataset.x)**4 * 10**(ci-1),
yerr=dataset.y_err*(
dataset.x)**4 * 10**(ci-1),
linestyle='', marker='o',
color=sns.color_palette()[ci])
if i % 5 == 0:
ax1.plot(dataset.x,
model(dataset.x,
def test_multipledataset_corefinement(self):
# test corefinement of three datasets
data361 = ReflectDataset(os.path.join(self.pth, 'e361r.txt'))
data365 = ReflectDataset(os.path.join(self.pth, 'e365r.txt'))
data366 = ReflectDataset(os.path.join(self.pth, 'e366r.txt'))
si = SLD(2.07, name='Si')
sio2 = SLD(3.47, name='SiO2')
d2o = SLD(6.36, name='d2o')
h2o = SLD(-0.56, name='h2o')
cm3 = SLD(3.47, name='cm3')
polymer = SLD(1, name='polymer')
structure361 = si | sio2(10, 4) | polymer(200, 3) | d2o(0, 3)
structure365 = si | structure361[1] | structure361[2] | cm3(0, 3)
structure366 = si | structure361[1] | structure361[2] | h2o(0, 3)
structure365[-1].rough = structure361[-1].rough
structure366[-1].rough = structure361[-1].rough
structure361[1].thick.setp(vary=True, bounds=(0, 20))
structure361[2].thick.setp(value=200., bounds=(200., 250.), vary=True)
structure361[2].sld.real.setp(vary=True, bounds=(0, 2))
structure361[2].vfsolv.setp(value=5., bounds=(0., 100.), vary=True)
model361 = ReflectModel(structure361, bkg=2e-5)
model365 = ReflectModel(structure365, bkg=2e-5)
model366 = ReflectModel(structure366, bkg=2e-5)
model361.bkg.setp(vary=True, bounds=(1e-6, 5e-5))
model365.bkg.setp(vary=True, bounds=(1e-6, 5e-5))
model366.bkg.setp(vary=True, bounds=(1e-6, 5e-5))
objective361 = Objective(model361, data361)
objective365 = Objective(model365, data365)
objective366 = Objective(model366, data366)
global_objective = GlobalObjective(
[objective361, objective365, objective366])
# are the right numbers of parameters varying?
assert_equal(len(global_objective.varying_parameters()), 7)
# can we set the parameters?
global_objective.setp(np.array([1e-5, 10, 212, 1, 10, 1e-5, 1e-5]))
f = CurveFitter(global_objective)
f.fit()
indiv_chisqr = np.sum(
[objective.chisqr() for objective in global_objective.objectives])
# the overall chi2 should be sum of individual chi2
global_chisqr = global_objective.chisqr()
assert_almost_equal(global_chisqr, indiv_chisqr)
# now check that the parameters were held in common correctly.
slabs361 = structure361.slabs()
slabs365 = structure365.slabs()
slabs366 = structure366.slabs()
assert_equal(slabs365[0:2, 0:5], slabs361[0:2, 0:5])
assert_equal(slabs366[0:2, 0:5], slabs361[0:2, 0:5])
assert_equal(slabs365[-1, 3], slabs361[-1, 3])
assert_equal(slabs366[-1, 3], slabs361[-1, 3])
# check that the residuals are the correct lengths
res361 = objective361.residuals()
res365 = objective365.residuals()
res366 = objective366.residuals()
res_global = global_objective.residuals()
assert_allclose(res_global[0:len(res361)], res361, rtol=1e-5)
assert_allclose(res_global[len(res361):len(res361) + len(res365)],
res365,
rtol=1e-5)
assert_allclose(res_global[len(res361) + len(res365):],
res366,
rtol=1e-5)
repr(global_objective)
def test_mcmc_init(self):
# smoke test for sampler initialisation
# TODO check that the initialisation worked.
# reproducible initialisation with random_state dependents
self.mcfitter.initialise("prior", random_state=1)
starting_pos = np.copy(self.mcfitter._state.coords)
self.mcfitter.initialise("prior", random_state=1)
starting_pos2 = self.mcfitter._state.coords
assert_equal(starting_pos, starting_pos2)
self.mcfitter.initialise("jitter", random_state=1)
starting_pos = np.copy(self.mcfitter._state.coords)
self.mcfitter.initialise("jitter", random_state=1)
starting_pos2 = self.mcfitter._state.coords
assert_equal(starting_pos, starting_pos2)
mcfitter = CurveFitter(self.objective, nwalkers=100)
mcfitter.initialise("covar")
assert_equal(mcfitter._state.coords.shape, (100, 2))
mcfitter.initialise("prior")
assert_equal(mcfitter._state.coords.shape, (100, 2))
mcfitter.initialise("jitter")
assert_equal(mcfitter._state.coords.shape, (100, 2))
# initialise with last position
mcfitter.sample(steps=1)
chain = mcfitter.chain
mcfitter.initialise(pos=chain[-1])
assert_equal(mcfitter._state.coords.shape, (100, 2))
# initialise with chain
mcfitter.sample(steps=2)
chain = mcfitter.chain
mcfitter.initialise(pos=chain)
assert_equal(mcfitter._state.coords, chain[-1])
# initialise with chain if it's never been run before
mcfitter = CurveFitter(self.objective, nwalkers=100)
mcfitter.initialise(chain)
# initialise for Parallel tempering
mcfitter = CurveFitter(self.objective, ntemps=20, nwalkers=100)
mcfitter.initialise("covar")
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
mcfitter.initialise("prior")
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
mcfitter.initialise("jitter")
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
# initialise with last position
mcfitter.sample(steps=1)
chain = mcfitter.chain
mcfitter.initialise(pos=chain[-1])
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
# initialise with chain
mcfitter.sample(steps=2)
chain = mcfitter.chain
mcfitter.initialise(pos=np.copy(chain))
assert_equal(mcfitter._state.coords, chain[-1])
# initialise with chain if it's never been run before
mcfitter = CurveFitter(self.objective, nwalkers=100, ntemps=20)
mcfitter.initialise(chain)
def test_best_weighted(self):
assert_equal(len(self.objective.varying_parameters()), 4)
self.objective.setp(self.p0)
f = CurveFitter(self.objective, nwalkers=100)
res = f.fit("least_squares", jac="3-point")
output = res.x
assert_almost_equal(output, self.best_weighted, 3)
assert_almost_equal(self.objective.chisqr(), self.best_weighted_chisqr,
5)
# compare the residuals
res = (self.data.y - self.model(self.data.x)) / self.data.y_err
assert_equal(self.objective.residuals(), res)
# compare objective.covar to the best_weighted_errors
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.005)
# we're also going to try the checkpointing here.
checkpoint = os.path.join(self.tmpdir, "checkpoint.txt")
# compare samples to best_weighted_errors
np.random.seed(1)
f.sample(steps=201, random_state=1, verbose=False, f=checkpoint)
process_chain(self.objective, f.chain, nburn=50, nthin=10)
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.07)
# test that the checkpoint worked
check_array = np.loadtxt(checkpoint)
check_array = check_array.reshape(201, f._nwalkers, f.nvary)
assert_allclose(check_array, f.chain)
# test loading the checkpoint
chain = load_chain(checkpoint)
assert_allclose(chain, f.chain)
f.initialise("jitter")
f.sample(steps=2, nthin=4, f=checkpoint, verbose=False)
assert_equal(f.chain.shape[0], 2)
# we should be able to produce 2 * 100 steps from the generator
g = self.objective.pgen(ngen=20000000000)
s = [i for i, a in enumerate(g)]
assert_equal(np.max(s), 200 - 1)
g = self.objective.pgen(ngen=200)
pvec = next(g)
assert_equal(pvec.size, len(self.objective.parameters.flattened()))
# check that all the parameters are returned via pgen, not only those
# being varied.
self.params[0].vary = False
f = CurveFitter(self.objective, nwalkers=100)
f.initialise("jitter")
f.sample(steps=2, nthin=4, f=checkpoint, verbose=False)
g = self.objective.pgen(ngen=100)
pvec = next(g)
assert_equal(pvec.size, len(self.objective.parameters.flattened()))
# the following test won't work because of emcee/gh226.
# chain = load_chain(checkpoint)
# assert_(chain.shape == f.chain.shape)
# assert_allclose(chain, f.chain)
# try reproducing best fit with parallel tempering
self.params[0].vary = True
f = CurveFitter(self.objective, nwalkers=100, ntemps=10)
f.fit("differential_evolution", seed=1)
f.sample(steps=201, random_state=1, verbose=False)
process_chain(self.objective, f.chain, nburn=50, nthin=15)
print(self.params[0].chain.shape, self.params[0].chain)
uncertainties = [param.stderr for param in self.params]
assert_allclose(uncertainties, self.best_weighted_errors, rtol=0.07)
def test_pickle(self):
# tests if a CurveFitter can be pickled/unpickled.
f = CurveFitter(self.objective)
pkl = pickle.dumps(f)
g = pickle.loads(pkl)
g._check_vars_unchanged()
class TestCurveFitter(object):
def setup_method(self):
# Reproducible results!
np.random.seed(123)
self.m_true = -0.9594
self.b_true = 4.294
self.f_true = 0.534
self.m_ls = -1.1040757010910947
self.b_ls = 5.4405552502319505
# Generate some synthetic data from the model.
N = 50
x = np.sort(10 * np.random.rand(N))
y_err = 0.1 + 0.5 * np.random.rand(N)
y = self.m_true * x + self.b_true
y += np.abs(self.f_true * y) * np.random.randn(N)
y += y_err * np.random.randn(N)
self.data = Data1D(data=(x, y, y_err))
self.p = Parameter(self.b_ls, "b", vary=True, bounds=(-100, 100))
self.p |= Parameter(self.m_ls, "m", vary=True, bounds=(-100, 100))
self.model = Model(self.p, fitfunc=line)
self.objective = Objective(self.model, self.data)
assert_(len(self.objective.varying_parameters()) == 2)
mod = np.array([
4.78166609,
4.42364699,
4.16404064,
3.50343504,
3.4257084,
2.93594347,
2.92035638,
2.67533842,
2.28136038,
2.19772983,
1.99295496,
1.93748334,
1.87484436,
1.65161016,
1.44613461,
1.11128101,
1.04584535,
0.86055984,
0.76913963,
0.73906649,
0.73331407,
0.68350418,
0.65216599,
0.59838566,
0.13070299,
0.10749131,
-0.01010195,
-0.10010155,
-0.29495372,
-0.42817431,
-0.43122391,
-0.64637715,
-1.30560686,
-1.32626428,
-1.44835768,
-1.52589881,
-1.56371158,
-2.12048349,
-2.24899179,
-2.50292682,
-2.53576659,
-2.55797996,
-2.60870542,
-2.7074727,
-3.93781479,
-4.12415366,
-4.42313742,
-4.98368609,
-5.38782395,
-5.44077086,
])
self.mod = mod
self.mcfitter = CurveFitter(self.objective)
def test_bounds_list(self):
bnds = bounds_list(self.p)
assert_allclose(bnds, [(-100, 100), (-100, 100)])
# try making a Parameter bound a normal distribution, then get an
# approximation to box bounds
self.p[0].bounds = PDF(norm(0, 1))
assert_allclose(bounds_list(self.p),
[norm(0, 1).ppf([0.005, 0.995]), (-100, 100)])
def test_constraints(self):
# constraints should work during fitting
self.p[0].value = 5.4
self.p[1].constraint = -0.203 * self.p[0]
assert_equal(self.p[1].value, self.p[0].value * -0.203)
res = self.mcfitter.fit()
assert_(res.success)
assert_equal(len(self.objective.varying_parameters()), 1)
# lnsigma is parameters[0]
assert_(self.p[0] is self.objective.parameters.flattened()[0])
assert_(self.p[1] is self.objective.parameters.flattened()[1])
assert_almost_equal(self.p[0].value, res.x[0])
assert_almost_equal(self.p[1].value, self.p[0].value * -0.203)
# check that constraints work during sampling
# the CurveFitter has to be set up again if you change how the
# parameters are being fitted.
mcfitter = CurveFitter(self.objective)
assert_(mcfitter.nvary == 1)
mcfitter.sample(5)
assert_equal(self.p[1].value, self.p[0].value * -0.203)
# the constrained parameters should have a chain
assert_(self.p[0].chain is not None)
assert_(self.p[1].chain is not None)
assert_allclose(self.p[1].chain, self.p[0].chain * -0.203)
def test_mcmc(self):
self.mcfitter.sample(steps=50, nthin=1, verbose=False)
assert_equal(self.mcfitter.nvary, 2)
# smoke test for corner plot
self.mcfitter.objective.corner()
# we're not doing Parallel Tempering here.
assert_(self.mcfitter._ntemps == -1)
assert_(isinstance(self.mcfitter.sampler, emcee.EnsembleSampler))
# should be able to multithread
mcfitter = CurveFitter(self.objective, nwalkers=50)
res = mcfitter.sample(steps=33, nthin=2, verbose=False, pool=2)
# check that the autocorrelation function at least runs
acfs = mcfitter.acf(nburn=10)
assert_equal(acfs.shape[-1], mcfitter.nvary)
# check the standalone autocorrelation calculator
acfs2 = autocorrelation_chain(mcfitter.chain, nburn=10)
assert_equal(acfs, acfs2)
# check integrated_time
integrated_time(acfs2, tol=5)
# check chain shape
assert_equal(mcfitter.chain.shape, (33, 50, 2))
# assert_equal(mcfitter._lastpos, mcfitter.chain[:, -1, :])
assert_equal(res[0].chain.shape, (33, 50))
# if the number of parameters changes there should be an Exception
# raised
from pytest import raises
with raises(RuntimeError):
self.p[0].vary = False
self.mcfitter.sample(1)
# can fix by making the sampler again
self.mcfitter.make_sampler()
self.mcfitter.sample(1)
def test_random_seed(self):
# check that MCMC sampling is reproducible
self.mcfitter.sample(steps=2, random_state=1)
# get a starting pos
starting_pos = self.mcfitter._state.coords
# is sampling reproducible
self.mcfitter.reset()
self.mcfitter.initialise(pos=starting_pos)
self.mcfitter.sample(3, random_state=1, pool=1)
chain1 = np.copy(self.mcfitter.chain)
self.mcfitter.reset()
self.mcfitter.initialise(pos=starting_pos)
self.mcfitter.sample(3, random_state=1, pool=1)
chain2 = np.copy(self.mcfitter.chain)
assert_equal(chain1, chain2)
def test_mcmc_pt(self):
# smoke test for parallel tempering
x = np.array(self.objective.parameters)
mcfitter = CurveFitter(self.objective, ntemps=10, nwalkers=50)
assert_equal(mcfitter.sampler.ntemps, 10)
# check that the parallel sampling works
# and that chain shape is correct
res = mcfitter.sample(steps=5, nthin=2, verbose=False, pool=-1)
assert_equal(mcfitter.chain.shape, (5, 10, 50, 2))
assert_equal(res[0].chain.shape, (5, 50))
assert_equal(mcfitter.chain[:, 0, :, 0], res[0].chain)
assert_equal(mcfitter.chain[:, 0, :, 1], res[1].chain)
chain = np.copy(mcfitter.chain)
# the sampler should store the probability
assert_equal(mcfitter.logpost.shape, (5, 10, 50))
assert_allclose(mcfitter.logpost, mcfitter.sampler._ptchain.logP)
logprobs = mcfitter.logpost
highest_prob_loc = np.argmax(logprobs[:, 0])
idx = np.unravel_index(highest_prob_loc, logprobs[:, 0].shape)
idx = list(idx)
idx.insert(1, 0)
idx = tuple(idx)
assert_equal(idx, mcfitter.index_max_prob)
pvals = mcfitter.chain[idx]
assert_allclose(logprobs[idx], self.objective.logpost(pvals))
# try resetting the chain
mcfitter.reset()
# test for reproducible operation
self.objective.setp(x)
mcfitter = CurveFitter(self.objective, ntemps=10, nwalkers=50)
mcfitter.initialise("jitter", random_state=1)
mcfitter.sample(steps=5, nthin=2, verbose=False, random_state=2)
chain = np.copy(mcfitter.chain)
self.objective.setp(x)
mcfitter = CurveFitter(self.objective, ntemps=10, nwalkers=50)
mcfitter.initialise("jitter", random_state=1)
mcfitter.sample(steps=5, nthin=2, verbose=False, random_state=2)
chain2 = np.copy(mcfitter.chain)
assert_allclose(chain2, chain)
def test_mcmc_init(self):
# smoke test for sampler initialisation
# TODO check that the initialisation worked.
# reproducible initialisation with random_state dependents
self.mcfitter.initialise("prior", random_state=1)
starting_pos = np.copy(self.mcfitter._state.coords)
self.mcfitter.initialise("prior", random_state=1)
starting_pos2 = self.mcfitter._state.coords
assert_equal(starting_pos, starting_pos2)
self.mcfitter.initialise("jitter", random_state=1)
starting_pos = np.copy(self.mcfitter._state.coords)
self.mcfitter.initialise("jitter", random_state=1)
starting_pos2 = self.mcfitter._state.coords
assert_equal(starting_pos, starting_pos2)
mcfitter = CurveFitter(self.objective, nwalkers=100)
mcfitter.initialise("covar")
assert_equal(mcfitter._state.coords.shape, (100, 2))
mcfitter.initialise("prior")
assert_equal(mcfitter._state.coords.shape, (100, 2))
mcfitter.initialise("jitter")
assert_equal(mcfitter._state.coords.shape, (100, 2))
# initialise with last position
mcfitter.sample(steps=1)
chain = mcfitter.chain
mcfitter.initialise(pos=chain[-1])
assert_equal(mcfitter._state.coords.shape, (100, 2))
# initialise with chain
mcfitter.sample(steps=2)
chain = mcfitter.chain
mcfitter.initialise(pos=chain)
assert_equal(mcfitter._state.coords, chain[-1])
# initialise with chain if it's never been run before
mcfitter = CurveFitter(self.objective, nwalkers=100)
mcfitter.initialise(chain)
# initialise for Parallel tempering
mcfitter = CurveFitter(self.objective, ntemps=20, nwalkers=100)
mcfitter.initialise("covar")
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
mcfitter.initialise("prior")
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
mcfitter.initialise("jitter")
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
# initialise with last position
mcfitter.sample(steps=1)
chain = mcfitter.chain
mcfitter.initialise(pos=chain[-1])
assert_equal(mcfitter._state.coords.shape, (20, 100, 2))
# initialise with chain
mcfitter.sample(steps=2)
chain = mcfitter.chain
mcfitter.initialise(pos=np.copy(chain))
assert_equal(mcfitter._state.coords, chain[-1])
# initialise with chain if it's never been run before
mcfitter = CurveFitter(self.objective, nwalkers=100, ntemps=20)
mcfitter.initialise(chain)
def test_fit_smoke(self):
# smoke tests to check that fit runs
def callback(xk):
return
def callback2(xk, **kws):
return
# L-BFGS-B
res0 = self.mcfitter.fit(callback=callback)
assert_almost_equal(res0.x, [self.b_ls, self.m_ls], 6)
res0 = self.mcfitter.fit()
res0 = self.mcfitter.fit(verbose=False)
res0 = self.mcfitter.fit(verbose=False, callback=callback)
# least_squares
res1 = self.mcfitter.fit(method="least_squares")
assert_almost_equal(res1.x, [self.b_ls, self.m_ls], 6)
# least_squares doesn't accept a callback. As well as testing that
# least_squares works, it checks that providing a callback doesn't
# trip the fitter up.
res1 = self.mcfitter.fit(method="least_squares", callback=callback)
assert_almost_equal(res1.x, [self.b_ls, self.m_ls], 6)
# need full bounds for differential_evolution
self.p[0].range(3, 7)
self.p[1].range(-2, 0)
res2 = self.mcfitter.fit(
method="differential_evolution",
seed=1,
popsize=10,
maxiter=100,
callback=callback2,
)
assert_almost_equal(res2.x, [self.b_ls, self.m_ls], 6)
# check that the res object has covar and stderr
assert_("covar" in res0)
assert_("stderr" in res0)
def test_NIST(self):
# Run all the NIST standard tests with leastsq
for model in NIST_Models:
try:
NIST_runner(model)
except Exception:
print(model)
raise
