def __init__(self, parameters_dict, configdict, is_scaled=False):
"""Create the phyiscal scaling model components."""
super(PhysicalScalingModel, self).__init__(configdict, is_scaled)
if "scale" in configdict["corrections"]:
scale_setup = parameters_dict["scale"]
self._components["scale"] = SmoothScaleComponent1D(
scale_setup["parameters"], scale_setup["parameter_esds"])
if "decay" in configdict["corrections"]:
decay_setup = parameters_dict["decay"]
self._components["decay"] = SmoothBScaleComponent1D(
decay_setup["parameters"], decay_setup["parameter_esds"])
if "absorption" in configdict["corrections"]:
absorption_setup = parameters_dict["absorption"]
self._components["absorption"] = SHScaleComponent(
absorption_setup["parameters"],
absorption_setup["parameter_esds"])
def test_SHScalefactor():
"""Test the spherical harmonic absorption component."""
initial_param = 0.1
initial_val = 0.2
SF = SHScaleComponent(flex.double([initial_param] * 3))
assert SF.n_params == 3
assert list(SF.parameters) == [initial_param] * 3
# Test functionality just by setting sph_harm_table directly and calling
# update_reflection_data to initialise the harmonic values.
harmonic_values = sparse.matrix(3, 1)
harmonic_values[0, 0] = initial_val
harmonic_values[1, 0] = initial_val
harmonic_values[2, 0] = initial_val
SF.data = {"sph_harm_table": harmonic_values}
SF.update_reflection_data()
print(SF.harmonic_values)
assert SF.harmonic_values[0][0, 0] == initial_val
assert SF.harmonic_values[0][0, 1] == initial_val
assert SF.harmonic_values[0][0, 2] == initial_val
s, d = SF.calculate_scales_and_derivatives()
assert list(s) == [1.0 + (3.0 * initial_val * initial_param)]
assert d[0, 0] == initial_val
assert d[0, 1] == initial_val
assert d[0, 2] == initial_val
s, d = SF.calculate_scales_and_derivatives()
# Test functionality of passing in a selection
harmonic_values = sparse.matrix(3, 2)
harmonic_values[0, 0] = initial_val
harmonic_values[0, 1] = initial_val
harmonic_values[2, 0] = initial_val
SF.data = {"sph_harm_table": harmonic_values}
SF.update_reflection_data(flex.bool([False, True]))
assert SF.harmonic_values[0].n_rows == 1
assert SF.harmonic_values[0].n_cols == 3
assert SF.n_refl[0] == 1
# Test setting of restraints and that restraints are calculated.
# Not testing actual calculation as may want to change the form.
SF.parameter_restraints = flex.double([0.1, 0.2, 0.3])
assert SF.parameter_restraints == flex.double([0.1, 0.2, 0.3])
restraints = SF.calculate_restraints()
assert restraints[0] is not None
assert restraints[1] is not None
jacobian_restraints = SF.calculate_jacobian_restraints()
assert jacobian_restraints[0] is not None
assert jacobian_restraints[1] is not None