def test_resolution_speed_comparator(self):
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)
dx = dataset.x_err
structure = si | sio2_l | polymer_l | polymer_l | d2o(0, 3)
model = ReflectModel(structure, bkg=2e-6, dq_type="constant")
objective = Objective(model,
dataset,
use_weights=False,
transform=Transform("logY"))
# check that choose_resolution_approach doesn't change state
# of model
fastest_method = choose_dq_type(objective)
assert model.dq_type == "constant"
assert_equal(dx, objective.data.x_err)
# check that the comparison worked
const_time = time.time()
for i in range(1000):
objective.generative()
const_time = time.time() - const_time
model.dq_type = "pointwise"
point_time = time.time()
for i in range(1000):
objective.generative()
point_time = time.time() - point_time
if fastest_method == "pointwise":
assert point_time < const_time
elif fastest_method == "constant":
assert const_time < point_time
# check that we could use the function to setup a reflectmodel
ReflectModel(structure, bkg=2e-6, dq_type=choose_dq_type(objective))
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 test_multidimensionality(self):
# Check that ND data can be used with an objective/model/data
# (or at least it doesn't stand in the way)
rng = np.random.default_rng()
x = rng.uniform(size=100).reshape(50, 2)
desired = line_ND(x, self.p)
assert desired.shape == (50, 2)
data = Data1D((x, desired))
model = Model(self.p, fitfunc=line_ND)
y = model(x)
assert_allclose(y, desired)
objective = Objective(model, data)
assert_allclose(objective.chisqr(), 0)
assert_allclose(objective.generative(), desired)
assert_allclose(objective.residuals(), 0)
assert objective.residuals().shape == (50, 2)
objective.logl()
objective.logpost()
covar = objective.covar()
assert covar.shape == (2, 2)
class Model():
"""The Model class represents a refnx model using predictions made by the classifier and regressors.
Class Attributes:
roughness (int): the default roughness between each layer in Angstrom.
rough_bounds (tuple): the range of values to fit for roughness.
si_sld (float): the substrate SLD (silicon).
dq (float): the instrument resolution parameter.
scale (float): the instrument scale parameter.
bkg (float): value for the background parameter.
"""
roughness = 8
rough_bounds = CurveGenerator.rough_bounds
si_sld = NeutronGenerator.substrate_sld
dq = CurveGenerator.dq
scale = CurveGenerator.scale
bkg = 2e-7
def __init__(self, file_path, layers, predicted_slds, predicted_depths, xray):
"""Initialises the Model class by creating a refnx model with given predicted values.
Args:
file_path (string): a path to the file with the data to construct the model for.
layers (int): the number of layers for the model predicted by the classifier.
predicted_slds (ndarray): an array of predicted SLDs for each layer.
predicted_depths (ndarray): an array of predicted depths for each layer.
xray (Boolean): whether the model should use a neutron or x-ray probe.
"""
self.structure = SLD(0, name='Air') #Model starts with air.
if xray: #Use x-ray probe
for i in range(layers):
density = predicted_slds[i] / XRayGenerator.density_constant
SLD_layer = MaterialSLD(XRayGenerator.material, density, probe='x-ray', wavelength=XRayGenerator.wavelength, name='Layer {}'.format(i+1))
layer = SLD_layer(thick=predicted_depths[i], rough=Model.roughness)
layer.density.setp(bounds=XRayGenerator.density_bounds, vary=True)
layer.thick.setp(bounds=ImageGenerator.depth_bounds, vary=True)
layer.rough.setp(bounds=Model.rough_bounds, vary=True)
self.structure = self.structure | layer #Next comes each layer.
#Then substrate
si_substrate = MaterialSLD(XRayGenerator.material, XRayGenerator.substrate_density, probe='x-ray', name='Si Substrate')(thick=0, rough=Model.roughness)
else: #Use neutron probe
for i in range(layers):
layer = SLD(predicted_slds[i], name='Layer {}'.format(i+1))(thick=predicted_depths[i], rough=Model.roughness)
layer.sld.real.setp(bounds=ImageGenerator.sld_neutron_bounds, vary=True)
layer.thick.setp(bounds=ImageGenerator.depth_bounds, vary=True)
layer.rough.setp(bounds=Model.rough_bounds, vary=True)
self.structure = self.structure | layer #Next comes each layer.
#Then substrate
si_substrate = SLD(Model.si_sld, name='Si Substrate')(thick=0, rough=Model.roughness)
si_substrate.rough.setp(bounds=Model.rough_bounds, vary=True)
self.structure = self.structure | si_substrate
data = self.__load_data(file_path) #Pre-process and load given dataset.
self.model = ReflectModel(self.structure, scale=Model.scale, dq=Model.dq, bkg=Model.bkg)
self.objective = Objective(self.model, data)
def __load_data(self, file_path):
"""Loads a reflectivity dataset from a given file path and applies scaling.
Args:
file_path (string): a path to the file with the data to construct the model for.
"""
data = ReflectDataset(file_path) #Load the data for which the model is designed for.
self.filename = os.path.basename(data.filename)
data.scale(np.max(data.data[1])) #Normalise Y and Error by dividing by max R point.
x, y, y_err = data.x.tolist(), data.y.tolist(), data.y_err.tolist()
removed = [] #Remove any points containing 0 values as these cause NaNs when fitting.
for i in range(len(x)):
if x[i] == 0 or y[i] == 0 or y_err[i] == 0:
removed.append(i)
#Remove the identified points and return the processed dataset.
x = np.delete(np.array(x), removed)
y = np.delete(np.array(y), removed)
y_err = np.delete(np.array(y_err), removed)
data_new = np.array([x, y, y_err])
return ReflectDataset(data_new)
def fit(self):
"""Fits the model to the data using differential evolution."""
fitter = CurveFitter(self.objective)
fitter.fit('differential_evolution', verbose=False)
def plot_objective(self, prediction=True):
"""Plots the current objective for the model against given dataset.
Args:
prediction (Boolean): whether the plot is a prediction or fit.
"""
if prediction:
title='Reflectivity Plot using Predicted Values'
label="Predicted"
else:
title='Reflectivity Plot using Fitted Values'
label="Fitted"
fig = plt.figure(figsize=[9,7], dpi=600)
ax = fig.add_subplot(111)
y, y_err, model = self.objective._data_transform(model=self.objective.generative())
# Add the data in a transformed fashion.
ax.errorbar(self.objective.data.x, y, y_err, label=self.filename,
color="blue", marker="o", ms=3, lw=0, elinewidth=1, capsize=1.5)
#Add the prediction/fit
ax.plot(self.objective.data.x, model, color="red", label=label, zorder=20)
plt.xlabel("$\mathregular{Q\ (Å^{-1})}$", fontsize=11, weight='bold')
plt.ylabel('Reflectivity (arb.)', fontsize=11, weight='bold')
plt.yscale('log')
plt.legend()
if title:
plt.title(title, fontsize=15, pad=15)