def total_profile(self):
if self.bkgd_refine:
return RietveldPhases.background_polynomial() \
+ self.raw_profile_state
else:
return RietveldPhases.background_polynomial() \
+ np.sum( x.phase_profile() for x in self.phase_list)
def test_set_profile():
xyepath = os.path.join(os.path.dirname(__file__),
'..\\data\\profiles\\cement_15_03_11_0028.xye')
Rp.set_profile(xyepath, min_two_theta=50, max_two_theta=52)
assert Rp.two_theta is not None
print(repr(Rp.two_theta))
assert np.all(
np.isclose(
Rp.two_theta,
np.array([
50.0051, 50.0253, 50.0454, 50.0655, 50.0857, 50.1058, 50.1259,
50.1461, 50.1662, 50.1864, 50.2065, 50.2266, 50.2468, 50.2669,
50.2871, 50.3072, 50.3273, 50.3475, 50.3676, 50.3877, 50.4079,
50.428, 50.4482, 50.4683, 50.4884, 50.5086, 50.5287, 50.5489,
50.569, 50.5891, 50.6093, 50.6294, 50.6495, 50.6697, 50.6898,
50.71, 50.7301, 50.7502, 50.7704, 50.7905, 50.8107, 50.8308,
50.8509, 50.8711, 50.8912, 50.9113, 50.9315, 50.9516, 50.9718,
50.9919, 51.012, 51.0322, 51.0523, 51.0725, 51.0926, 51.1127,
51.1329, 51.153, 51.1731, 51.1933, 51.2134, 51.2336, 51.2537,
51.2738, 51.294, 51.3141, 51.3343, 51.3544, 51.3745, 51.3947,
51.4148, 51.4349, 51.4551, 51.4752, 51.4954, 51.5155, 51.5356,
51.5558, 51.5759, 51.5961, 51.6162, 51.6363, 51.6565, 51.6766,
51.6967, 51.7169, 51.737, 51.7572, 51.7773, 51.7974, 51.8176,
51.8377, 51.8579, 51.878, 51.8981, 51.9183, 51.9384, 51.9585,
51.9787, 51.9988
])))
def test_LP_intensity_scaling(set_profile):
assert len(Rp.two_theta) == len(Rp.LP_intensity_scaling())
two_theta = Rp.two_theta
assert np.all(np.isclose(Rp.LP_intensity_scaling(),
(1+np.cos(np.pi/180*two_theta)**2) \
/np.sin(np.pi/360*two_theta) \
/np.sin(np.pi/180*two_theta)))
def exercise_Rietveld_Refinery_SinglePhase():
RietveldPhases.global_params_from_string(global_input_string,
tst_two_theta, tst_y)
RR = RietveldRefinery(Rt,
minimizer_input_string,
store_intermediate_state=True)
RR.display(RR.minimize_Scale_Offset)
RR.display(RR.minimize_All)
RietveldPhases.empty_x()
def test_phase_list():
RietveldPhases.set_profile(r".//data//profiles//Jade-Al2O3-Sim.xye",
number_of_columns=2)
cifs = ["1000032.cif", "1507774.cif"]
test_phase_list = []
test_phase_list.append(
RietveldPhases(r".//data//cifs//" + cifs[0],
delta_theta=2.0,
intensity_cutoff=0.005))
return test_phase_list
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 exercise_Rietveld_Refinery_Multiphase():
RietveldPhases.global_params_from_string(global_input_string,
tst_two_theta, tst_y)
Rt = []
for cif, input_string in zip(cifs, input_strings):
Rt.append(
RietveldPhases(r"..//data//cifs//" + cif,
d_min,
d_max,
input_string_or_file_name=input_string,
delta_theta=2.0,
Intensity_Cutoff=0.005))
RR = RietveldRefinery(Rt,
minimizer_input_string,
store_intermediate_state=True)
RR.display(RR.minimize_Scale_Offset)
RR.display(RR.minimize_All)
RietveldPhases.empty_x()
def test_rietveld_phase_as_dict_with_cubic_crystal_system():
cub_phase = RietveldPhases('./data/cifs/Cement/1000039-AluminateCubic.cif')
assert len(cub_phase.phase_parameters.lattice_parameters) == 1
phase_dict = cub_phase.as_dict()
assert len(phase_dict['lattice_parameters']) == 6
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_phase():
RietveldPhases.set_profile('')
return RietveldPhases("./data/cifs/1000032.cif")
def rutile_phase():
return RietveldPhases("./data/cifs/9015662-rutile.cif")
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
def test_set_profile_empty_path():
Rp.set_profile('')
assert len(Rp.two_theta) == 1000
def set_profile():
return Rp.set_profile(r"./data/profiles/Jade-Al2O3-Sim.xye",
number_of_columns=2)