def crystal_parameters():
from dxtbx.model.experiment.experiment_list import ExperimentListFactory
from dials.array_family import flex
from scitbx import matrix
experiments = ExperimentListFactory.from_json_file("experiments.json")
reflections = flex.reflection_table.from_pickle("reflections.pickle")
beam = experiments[0].beam
detector = experiments[0].detector
goniometer = experiments[0].goniometer
scan = experiments[0].scan
crystal = experiments[0].crystal
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalUnitCellParameterisation, )
parameters = CrystalUnitCellParameterisation(crystal)
print("")
print("Parameters")
for param in parameters.get_params():
print(param.name, param.value)
print("")
print("db/dp")
for db_dp in parameters.get_ds_dp():
print(db_dp.round(5))
print("")
print("B matrix")
B = crystal.get_B().round(7)
print(B)
print(B.transpose() * B)
# from rstbx.symmetry.constraints.parameter_reduction import symmetrize_reduce_enlarge
# temp = symmetrize_reduce_enlarge(crystal.get_space_group())
# temp.set_orientation(crystal.get_B())
# independent = temp.forward_independent_parameters()
# print independent
# new_mm = temp.enlarge(independent)
# temp.Bconverter.validate_and_setG(new_mm)
# B = temp.Bconverter.back_as_orientation()
# print matrix.sqr(B.reciprocal_matrix()).round(5)
# from cctbx import sgtbx
# from rstbx.symmetry.constraints import AGconvert
# constraints = sgtbx.tensor_rank_2_constraints(space_group=crystal.get_space_group(), reciprocal_space=True)
# params = constraints.all_params(independent_params=tuple(p.value for p in
# parameters.get_params()))
# from cctbx.crystal_orientation import crystal_orientation
# converter = AGconvert()
# converter.forward(crystal_orientation(crystal.get_B(), False))
# converter.validate_and_setG(params)
# orientation = converter.back_as_orientation()
# print orientation
# print ""
print("SUM(p * dp/dp)")
MAT = [
p.value * db_dp
for p, db_dp in zip(parameters.get_params(), parameters.get_ds_dp())
]
COV = sum(MAT[1:], MAT[0])
print(2 * COV.round(7))
print((2 * COV - crystal.get_B()).round(7))
