def get_hkl_offset_correlation_coefficients(
dials_reflections,
dials_crystal,
map_to_asu=False,
grid_h=0,
grid_k=0,
grid_l=0,
reference=None,
):
# N.B. deliberately ignoring d_min, d_max as these are inconsistent with
# changing the miller indices
from cctbx import sgtbx
from cctbx.miller import set as miller_set
from dials.array_family import flex
cs = cctbx_crystal_from_dials(dials_crystal)
ms = cctbx_i_over_sigi_ms_from_dials_data(dials_reflections, cs)
if reference:
reference_ms = cctbx_i_over_sigi_ms_from_dials_data(reference, cs)
else:
reference_ms = None
ccs = flex.double()
offsets = flex.vec3_int()
nref = flex.size_t()
if reference:
cb_op = sgtbx.change_of_basis_op("x,y,z")
else:
cb_op = sgtbx.change_of_basis_op("-x,-y,-z")
hkl_test = [
(h, k, l)
for h in range(-grid_h, grid_h + 1)
for k in range(-grid_k, grid_k + 1)
for l in range(-grid_l, grid_l + 1)
]
for hkl in hkl_test:
indices = offset_miller_indices(ms.indices(), hkl)
reindexed_indices = cb_op.apply(indices)
rms = miller_set(cs, reindexed_indices).array(ms.data())
if reference_ms:
_ms = reference_ms
else:
_ms = miller_set(cs, indices).array(ms.data())
n, cc = compute_miller_set_correlation(_ms, rms, map_to_asu=map_to_asu)
ccs.append(cc)
offsets.append(hkl)
nref.append(n)
return offsets, ccs, nref
def get_hkl_offset_correlation_coefficients(
dials_reflections, dials_crystal, map_to_asu=False,
grid_h=0, grid_k=0, grid_l=0, reference=None):
# N.B. deliberately ignoring d_min, d_max as these are inconsistent with
# changing the miller indices
from dials.array_family import flex
from cctbx.miller import set as miller_set
from cctbx import sgtbx
cs = cctbx_crystal_from_dials(dials_crystal)
ms = cctbx_i_over_sigi_ms_from_dials_data(dials_reflections, cs)
if reference:
reference_ms = cctbx_i_over_sigi_ms_from_dials_data(reference, cs)
else:
reference_ms = None
ccs = flex.double()
offsets = flex.vec3_int()
nref = flex.size_t()
if reference:
cb_op = sgtbx.change_of_basis_op('x,y,z')
else:
cb_op = sgtbx.change_of_basis_op('-x,-y,-z')
hkl_test = [(h, k, l) for h in range(-grid_h, grid_h + 1) \
for k in range(-grid_k, grid_k + 1) \
for l in range(-grid_l, grid_l + 1)]
for hkl in hkl_test:
indices = offset_miller_indices(ms.indices(), hkl)
reindexed_indices = cb_op.apply(indices)
rms = miller_set(cs, reindexed_indices).array(ms.data())
if reference_ms:
_ms = reference_ms
else:
_ms = miller_set(cs, indices).array(ms.data())
n, cc = compute_miller_set_correlation(_ms, rms, map_to_asu=map_to_asu)
ccs.append(cc)
offsets.append(hkl)
nref.append(n)
return offsets, ccs, nref
def refls_to_hkl(refls,
detector,
beam,
crystal,
update_table=False,
returnQ=False):
"""
convert pixel panel reflections to miller index data
:param refls: reflecton table for a panel or a tuple of (x,y)
:param detector: dxtbx detector model
:param beam: dxtbx beam model
:param crystal: dxtbx crystal model
:param update_table: whether to update the refltable
:param returnQ: whether to return intermediately computed q vectors
:return: if as_numpy two Nx3 numpy arrays are returned
(one for fractional and one for whole HKL)
else dictionary of hkl_i (nearest) and hkl (fractional)
"""
if 'rlp' not in list(refls.keys()):
q_vecs = refls_to_q(refls, detector, beam, update_table=update_table)
else:
q_vecs = np.vstack([r['rlp'] for r in refls])
Ai = sqr(crystal.get_A()).inverse()
Ai = Ai.as_numpy_array()
HKL = np.dot(Ai, q_vecs.T)
HKLi = map(lambda h: np.ceil(h - 0.5).astype(int), HKL)
if update_table:
refls['miller_index'] = flex.miller_index(len(refls), (0, 0, 0))
mil_idx = flex.vec3_int(tuple(map(tuple, np.vstack(HKLi).T)))
for i in range(len(refls)):
refls['miller_index'][i] = mil_idx[i]
if returnQ:
return np.vstack(HKL).T, np.vstack(HKLi).T, q_vecs
else:
return np.vstack(HKL).T, np.vstack(HKLi).T