def __init__(self, parameters_dict, configdict, is_scaled=False):
"""Create the KB scaling model components."""
super(KBScalingModel, self).__init__(configdict, is_scaled)
if "scale" in configdict["corrections"]:
self._components["scale"] = SingleScaleFactor(
parameters_dict["scale"]["parameters"],
parameters_dict["scale"]["parameter_esds"],
)
if "decay" in configdict["corrections"]:
self._components["decay"] = SingleBScaleFactor(
parameters_dict["decay"]["parameters"],
parameters_dict["decay"]["parameter_esds"],
)
def test_SingleBScaleFactor():
"""Test forSingleBScaleFactor class."""
BSF = SingleBScaleFactor(flex.double([0.0]))
assert BSF.n_params == 1
assert list(BSF.parameters) == [0.0]
rt = flex.reflection_table()
rt["d"] = flex.double([1.0, 1.0])
# rt["id"] = flex.int([0, 0])
BSF.data = {"d": rt["d"]}
BSF.update_reflection_data()
assert BSF.n_refl == [2]
assert list(BSF.d_values[0]) == [1.0, 1.0]
s, d = BSF.calculate_scales_and_derivatives()
assert list(s) == [1.0, 1.0]
assert d[0, 0] == 0.5
assert d[1, 0] == 0.5
s, d = BSF.calculate_scales_and_derivatives()
BSF.update_reflection_data(flex.bool([True, False])) # Test selection.
assert BSF.n_refl[0] == 1
def test_RefinerCalculator(small_reflection_table):
"""Test for the RefinerCalculator class. This calculates scale factors and
derivatives for reflections based on the model components."""
# To test the basis function, need a scaling active parameter manager - to set
# this up we need a components dictionary with some reflection data.
# Let's use KB model components for simplicity - and have an extra fake 'abs'
# component.
rt = small_reflection_table
components = {
"scale": SingleScaleFactor(flex.double([1.0])),
"decay": SingleBScaleFactor(flex.double([0.0])),
"abs": SingleScaleFactor(flex.double([1.0])),
} # Create empty components.
components["scale"].data = {"id": rt["id"]}
components["decay"].data = {"d": rt["d"]}
components["abs"].data = {"id": rt["id"]}
for component in components.values():
component.update_reflection_data() # Add some data to components.
apm = scaling_active_parameter_manager(components, ["decay", "scale"])
# First test that scale factors can be successfully updated.
# Manually change the parameters in the apm.
decay = components["decay"] # Define alias
_ = components["scale"] # Define alias
# Note, order of params in apm.x depends on order in scaling model components.
new_B = 1.0
new_S = 2.0
apm.set_param_vals(flex.double([new_S, new_B]))
s, d = RefinerCalculator.calculate_scales_and_derivatives(apm, 0)
slist, dlist = RefinerCalculator._calc_component_scales_derivatives(apm, 0)
# Now test that the inverse scale factor is correctly calculated.
calculated_sfs = s
assert list(calculated_sfs) == pytest.approx(
list(new_S * flex.exp(new_B / (2.0 * flex.pow2(decay.d_values[0])))))
# Now check that the derivative matrix is correctly calculated.
calc_derivs = d
assert calc_derivs[0, 0] == dlist[0][0, 0] * slist[1][0]
assert calc_derivs[1, 0] == dlist[0][1, 0] * slist[1][1]
assert calc_derivs[2, 0] == dlist[0][2, 0] * slist[1][2]
assert calc_derivs[0, 1] == dlist[1][0, 0] * slist[0][0]
assert calc_derivs[1, 1] == dlist[1][1, 0] * slist[0][1]
assert calc_derivs[2, 1] == dlist[1][2, 0] * slist[0][2]
# Repeat the test when there is only one active parameter.
# First reset the parameters
components["decay"].parameters = flex.double([0.0])
components["scale"].parameters = flex.double([1.0])
components["abs"].parameters = flex.double([1.0])
components["decay"].calculate_scales_and_derivatives()
components["scale"].calculate_scales_and_derivatives()
components["abs"].calculate_scales_and_derivatives()
# Now generate a parameter manager for a single component.
apm = scaling_active_parameter_manager(components, ["scale"])
new_S = 2.0
apm.set_param_vals(flex.double(components["scale"].n_params, new_S))
s, d = RefinerCalculator.calculate_scales_and_derivatives(apm, 0)
slist, dlist = RefinerCalculator._calc_component_scales_derivatives(apm, 0)
# Test that the scales and derivatives were correctly calculated
assert list(s) == list([new_S] * slist[0].size())
assert d[0, 0] == dlist[0][0, 0]
assert d[1, 0] == dlist[0][1, 0]
assert d[2, 0] == dlist[0][2, 0]
# Test again for two components.
components["decay"].parameters = flex.double([0.0])
components["scale"].parameters = flex.double([1.0])
components["abs"].parameters = flex.double([1.0])
components["decay"].calculate_scales_and_derivatives()
components["scale"].calculate_scales_and_derivatives()
components["abs"].calculate_scales_and_derivatives()
apm = scaling_active_parameter_manager(components, ["scale", "decay"])
_, __ = RefinerCalculator.calculate_scales_and_derivatives(apm, 0)
# Test for no components
apm = scaling_active_parameter_manager(components, [])
_, d = RefinerCalculator.calculate_scales_and_derivatives(apm, 0)
assert d.n_cols == 0 and d.n_rows == 0