def superpower_postrefine(idx, CB_OP_C_P, old_Amat):
Amat = old_Amat
from LS49.work_pre_experiment.post5_ang_misset import get_item
from LS49.ML_push.exploratory_missetting import metric
R = get_item(idx)
print("get ersatz_postrefined with index", idx)
C = crystal_orientation.crystal_orientation(
Amat, crystal_orientation.basis_type.direct)
C.show(legend="ground truth, P1")
C2 = C.change_basis(CB_OP_C_P.inverse())
C2.show(legend="ground truth, C2")
direct_A = R["integrated_crystal_model"].get_A_inverse_as_sqr(
) # from dials model, integration step
permute = sqr((0, 0, 1, 0, 1, 0, -1, 0, 0))
sim_compatible = direct_A * permute # permute columns when post multiplying
P = crystal_orientation.crystal_orientation(
sim_compatible, crystal_orientation.basis_type.direct)
P.show(legend="dials_integrated, C2")
PR = P.change_basis(CB_OP_C_P)
PR.show(legend="dials_integrated, primitive setting")
PRC2 = PR.change_basis(CB_OP_C_P.inverse()) # dials integrated, C2
cb_op_align = PR.best_similarity_transformation(C, 200, 1)
align_PR = PR.change_basis(sqr(cb_op_align))
align_PR.show(legend="dials_integrated, P1, aligned")
print("alignment matrix", cb_op_align)
metric_val = metric(align_PR, C)
print("Key %d aligned angular offset is %12.9f deg." % (idx, metric_val))
print("Key %d alignC2 angular offset is %12.9f deg." %
(idx, metric(align_PR.change_basis(CB_OP_C_P.inverse()), C2)))
minimum = 1000. # metric_val
ixm = 0
iym = 0
best_Ori_C2 = None
for ix in range(-10, 11, 2):
xrotated_Ori = PRC2.rotate_thru((0, 0, 1), ix * 0.01 * math.pi / 180.)
for iy in range(-10, 11, 2):
yrotated_Ori = xrotated_Ori.rotate_thru((0, 1, 0),
iy * 0.01 * math.pi / 180.)
new_aligned_Ori = yrotated_Ori.change_basis(
CB_OP_C_P).change_basis(sqr(cb_op_align)).change_basis(
CB_OP_C_P.inverse())
grid_metric_val = metric(new_aligned_Ori, C2)
if grid_metric_val < minimum:
ixm = ix
iym = iy
best_Ori_C2 = new_aligned_Ori
#print("ix %4d"%ix,"iy %4d"%iy,"grid search angular offset is %12.9f deg."%(grid_metric_val))
minimum = min(minimum, grid_metric_val)
print("Key %d minimC2 angular offset is %12.9f deg." % (idx, minimum),
"with ix=%d iy=%d" % (ixm, iym))
best_Ori = best_Ori_C2.change_basis(CB_OP_C_P)
print(
"Key %d minimum angular offset is %12.9f deg." %
(idx, metric(best_Ori, C)), "with ix=%d iy=%d" % (ixm, iym))
best_Ori.show(legend="superpower, aligned")
return dict(superpower_postrefine=best_Ori.direct_matrix(),
dials_refine=align_PR.direct_matrix(),
coarse_ground_truth=C.direct_matrix())
def get_current_angular_offsets(self,rotxyz): # pass in the x,y,z rotations in units of 0.01 degree
from LS49.ML_push.exploratory_missetting import metric
updated_mat = self.dials_integrated_P1_aligned.rotate_thru((1.0,0.0,0.0), rotxyz[0] * math.pi* 0.01/180.
).rotate_thru((0.0,1.0,0.0), rotxyz[1] * math.pi* 0.01/180.
).rotate_thru((0.0,0.0,1.0), rotxyz[2] * math.pi* 0.01/180.)
metric_P1 = metric(updated_mat,self.ground_truth_P1)
metric_C2 = metric(updated_mat.change_basis(self.CB_OP_C_P.inverse()) ,self.ground_truth_C2)
return metric_P1,metric_C2
def get_idx_rotation_models(self, idx):
rotation = sqr(ersatz_all_orientations()[idx])
Amat = (rotation *
sqr(self.sfall_main.unit_cell().orthogonalization_matrix())
).transpose()
from LS49.work_pre_experiment.post5_ang_misset import get_item
from LS49.ML_push.exploratory_missetting import metric
R = get_item(idx)
print("coarse ground truth with index", idx)
C = crystal_orientation.crystal_orientation(
Amat, crystal_orientation.basis_type.direct)
C.show(legend="ground truth, P1")
C2 = C.change_basis(self.CB_OP_C_P.inverse())
C2.show(legend="ground truth, C2")
direct_A = R["integrated_crystal_model"].get_A_inverse_as_sqr(
) # from dials model, integration step
permute = sqr((0, 0, 1, 0, 1, 0, -1, 0, 0))
sim_compatible = direct_A * permute # permute columns when post multiplying
P = crystal_orientation.crystal_orientation(
sim_compatible, crystal_orientation.basis_type.direct)
P.show(legend="dials_integrated, C2")
PR = P.change_basis(self.CB_OP_C_P)
PR.show(legend="dials_integrated, primitive setting")
PRC2 = PR.change_basis(
self.CB_OP_C_P.inverse()) # dials integrated, C2
cb_op_align = PR.best_similarity_transformation(C, 200, 1)
align_PR = PR.change_basis(sqr(cb_op_align))
align_PR.show(legend="dials_integrated, P1, aligned")
print("alignment matrix", cb_op_align)
metric_val = metric(align_PR, C)
print("Key %d aligned angular offset is %12.9f deg." %
(idx, metric_val))
print(
"Key %d alignC2 angular offset is %12.9f deg." %
(idx, metric(align_PR.change_basis(self.CB_OP_C_P.inverse()), C2)))
# coarse, dials crystal orientation models = C, align_PR
# apply Rotx:
align_PR_dx = align_PR.rotate_thru((1.0, 0.0, 0.0),
math.pi * 0.01 / 180.)
align_PR_dy = align_PR.rotate_thru((0.0, 1.0, 0.0),
math.pi * 0.01 / 180.)
align_PR_dz = align_PR.rotate_thru((0.0, 0.0, 1.0),
math.pi * 0.01 / 180.)
self.dials_integrated_P1_aligned = align_PR
self.ground_truth_P1 = C
self.ground_truth_C2 = C2
return (dict(Amat=align_PR.direct_matrix(),
Amat_dx=align_PR_dx.direct_matrix(),
Amat_dy=align_PR_dy.direct_matrix(),
Amat_dz=align_PR_dz.direct_matrix()))
def get_incremented_rotation_models(self,rotxyz): # pass in the x,y,z rotations in units of 0.01 degree
from LS49.ML_push.exploratory_missetting import metric
updated_mat = self.dials_integrated_P1_aligned.rotate_thru((1.0,0.0,0.0), rotxyz[0] * math.pi* 0.01/180.
).rotate_thru((0.0,1.0,0.0), rotxyz[1] * math.pi* 0.01/180.
).rotate_thru((0.0,0.0,1.0), rotxyz[2] * math.pi* 0.01/180.)
metric_val = metric(updated_mat,self.ground_truth_P1)
print("minimization step, aligned angular offset is %12.9f deg."%(metric_val))
new_dx = updated_mat.rotate_thru((1.0,0.0,0.0), math.pi* 0.01/180.)
new_dy = updated_mat.rotate_thru((0.0,1.0,0.0), math.pi* 0.01/180.)
new_dz = updated_mat.rotate_thru((0.0,0.0,1.0), math.pi* 0.01/180.)
return (dict(Amat=updated_mat.direct_matrix(),Amat_dx=new_dx.direct_matrix(),
Amat_dy=new_dy.direct_matrix(), Amat_dz=new_dz.direct_matrix()))