def test_background_polynomial():
Rp.assemble_global_x()
Rp.bkgd[0] = 1
assert np.all(
np.isclose(Rp.background_polynomial(),
np.ones(len(Rp.two_theta), dtype=float)))
Rp.bkgd = np.array([1, 2, 3], dtype=float)
assert np.all(
np.isclose(Rp.background_polynomial(),
1.0 + 2.0 * Rp.two_theta + 3.0 * Rp.two_theta_powers[2, :]))
Rp.bkgd = np.array([0, 0, 0], dtype=float)
assert np.all(
np.isclose(Rp.background_polynomial(),
np.zeros(len(Rp.two_theta), dtype=float)))
def __init__(self, phase_list,
rietveld_plot=None,
bkgd_refine=False,
store_intermediate_state=False,
show_plots=False,
factr=DEFAULT_FACTR,
mask=None,
iprint=DEFAULT_IPRINT,
maxiter=DEFAULT_MAXITER,
m=DEFAULT_M,
pgtol=DEFAULT_PGTOL,
epsilon=DEFAULT_EPSILON,
method=DEFAULT_METHOD,
display=DEFAULT_DISPLAY,
# input_weights=None,
# composition_cutoff=default_composition_cutoff,
):
"""
Given some list of phases, an instance of the refinery is initialized
to readily run a refinement process.
"""
self.phase_list = phase_list
self.rietveld_plot = rietveld_plot
self.bkgd_refine = bkgd_refine
self.store_intermediate_state = store_intermediate_state
self.show_plots = show_plots
self.factr = factr
self.iprint = iprint
self.maxiter = maxiter
self.m = m
self.pgtol = pgtol
self.epsilon = epsilon
self.method = method
self.display = display
# self.composition_cutoff = composition_cutoff
self.weighted_sum_of_I_squared = np.sum(
RietveldPhases.I**2/RietveldPhases.sigma**2)
for key in refinement_parameters.keys:
if key in ("labels", "values", "uround", "l_limits", "u_limits"):
if len(self.phase_list) > 0:
# self.x = np.hstack((RietveldPhases.global_x,
# np.hstack((x.phase_x for x in self.phase_list))))
if key == "uround":
# print(RietveldPhases.global_parameters.x[key])
# print([phase.phase_parameters.x[key]
# for phase in self.phase_list])
tmp = np.concatenate((
RietveldPhases.global_parameters.x[key],
np.concatenate(
[phase.phase_parameters.x[key]
for phase in self.phase_list], axis=0))
, axis=0)
else:
tmp = np.hstack((RietveldPhases.global_parameters.x[key],
np.hstack((phase.phase_parameters.x[key] for phase in self.phase_list))))
else:
RietveldPhases.assemble_global_x()
tmp = RietveldPhases.global_parameters.x[key]
setattr(self, "x_" + key, tmp)
self.x = self.x_values
# for key in refinement_parameters.keys:
# setattr(self, key, RietveldPhases.global_parameters.x[key])
if self.bkgd_refine:
if len(self.phase_list) > 0:
self.raw_profile_state = np.sum(x.phase_profile() for x in
self.phase_list)
else:
self.raw_profile_state = np.zeros(len(RietveldPhases.two_theta))
self.global_mask = np.isin(np.array(xrange(len(self.x))),
np.array(xrange(len(RietveldPhases.global_x))))
self.bkgd_mask = self.make_mask(["bkgd"])
self.global_mask_no_bkgd = np.logical_xor(
self.global_mask, self.bkgd_mask)
self.scale_mask = self.make_mask(["sca"])
if mask is not None:
self.mask = mask
elif self.bkgd_refine:
self.mask = self.bkgd_mask
else:
self.mask = np.zeros(len(self.x),dtype=bool)
self.set_compositions()
# self.composition_by_volume = np.zeros(len(self.phase_list))
# if input_weights is not None:
# self.composition_by_weight = input_weights
# else: self.composition_by_weight = 100*np.ones(len(self.phase_list))
n=len(RietveldPhases.global_x)
self.phase_masks = []
self.global_and_phase_masks = []
for phase in self.phase_list:
self.phase_masks.append(np.isin(np.array(xrange(len(self.x))),
np.array(xrange(n,n+len(phase.phase_x)))))
self.global_and_phase_masks.append(np.logical_or(
self.global_mask_no_bkgd, self.phase_masks[-1]))
n+=len(phase.phase_x)
self.update_state()
if self.rietveld_plot is not None:
self.rietveld_plot.setplotdata()
self.rietveld_plot.updateplotprofile(self.total_profile_state,
wse=self.relative_differences_state)
def test_set_bkgd_order(test_phase):
Rp.global_parameters.set_bkgd_order(3)
Rp.assemble_global_x()
assert len(Rp.bkgd) == 3
assert len(test_phase.bkgd) == 3