def refine_subgroup(args):
assert len(args) == 5
from dials.command_line.check_indexing_symmetry \
import get_symop_correlation_coefficients, normalise_intensities
params, subgroup, used_reflections, experiments, refiner_verbosity = args
used_reflections = copy.deepcopy(used_reflections)
triclinic_miller = used_reflections['miller_index']
cb_op = subgroup['cb_op_inp_best']
higher_symmetry_miller = cb_op.apply(triclinic_miller)
used_reflections['miller_index'] = higher_symmetry_miller
unrefined_crystal = copy.deepcopy(subgroup.unrefined_crystal)
for expt in experiments:
expt.crystal = unrefined_crystal
from dials.algorithms.indexing.refinement import refine
subgroup.max_cc = None
subgroup.min_cc = None
subgroup.correlation_coefficients = []
subgroup.cc_nrefs = []
try:
logger = logging.getLogger()
disabled = logger.disabled
logger.disabled = True
iqr_multiplier = params.refinement.reflections.outlier.tukey.iqr_multiplier
params.refinement.reflections.outlier.tukey.iqr_multiplier = 2 * iqr_multiplier
refinery, refined, outliers = refine(params,
used_reflections,
experiments,
verbosity=refiner_verbosity)
params.refinement.reflections.outlier.tukey.iqr_multiplier = iqr_multiplier
refinery, refined, outliers = refine(params,
used_reflections,
refinery.get_experiments(),
verbosity=refiner_verbosity)
except RuntimeError as e:
if (str(e) == "scitbx Error: g0 - astry*astry -astrz*astrz <= 0."
or str(e) == "scitbx Error: g1-bstrz*bstrz <= 0."):
subgroup.refined_experiments = None
subgroup.rmsd = None
subgroup.Nmatches = None
else:
raise
else:
dall = refinery.rmsds()
dx = dall[0]
dy = dall[1]
subgroup.rmsd = math.sqrt(dx * dx + dy * dy)
subgroup.Nmatches = len(refinery.get_matches())
subgroup.refined_experiments = refinery.get_experiments()
assert len(subgroup.refined_experiments.crystals()) == 1
subgroup.refined_crystal = subgroup.refined_experiments.crystals()[0]
cs = crystal.symmetry(
unit_cell=subgroup.refined_crystal.get_unit_cell(),
space_group=subgroup.refined_crystal.get_space_group())
if 'intensity.sum.value' in used_reflections:
# remove refl with -ve variance
sel = used_reflections['intensity.sum.variance'] > 0
good_reflections = used_reflections.select(sel)
from cctbx import miller
ms = miller.set(cs, good_reflections['miller_index'])
ms = ms.array(
good_reflections['intensity.sum.value'] /
flex.sqrt(good_reflections['intensity.sum.variance']))
if params.normalise:
if params.normalise_bins:
ms = normalise_intensities(ms,
n_bins=params.normalise_bins)
else:
ms = normalise_intensities(ms)
if params.cc_n_bins is not None:
ms.setup_binner(n_bins=params.cc_n_bins)
ccs, nrefs = get_symop_correlation_coefficients(
ms, use_binning=(params.cc_n_bins is not None))
subgroup.correlation_coefficients = ccs
subgroup.cc_nrefs = nrefs
ccs = ccs.select(nrefs > 10)
if len(ccs) > 1:
subgroup.max_cc = flex.max(ccs[1:])
subgroup.min_cc = flex.min(ccs[1:])
finally:
logger.disabled = disabled
return subgroup
cs = crystal.symmetry(
unit_cell=subgroup.refined_crystal.get_unit_cell(),
space_group=subgroup.refined_crystal.get_space_group())
if 'intensity.sum.value' in used_reflections:
from cctbx import miller
ms = miller.set(cs, used_reflections['miller_index'])
ms = ms.array(used_reflections['intensity.sum.value'] /
flex.sqrt(used_reflections['intensity.sum.variance']))
if params.normalise:
if params.normalise_bins:
ms = normalise_intensities(ms, n_bins=params.normalise_bins)
else:
ms = normalise_intensities(ms)
if params.cc_n_bins is not None:
ms.setup_binner(n_bins=params.cc_n_bins)
ccs, nrefs = get_symop_correlation_coefficients(
ms, use_binning=(params.cc_n_bins is not None))
subgroup.correlation_coefficients = ccs
subgroup.cc_nrefs = nrefs
ccs = ccs.select(nrefs > 10)
if len(ccs) > 1:
subgroup.max_cc = flex.max(ccs[1:])
subgroup.min_cc = flex.min(ccs[1:])
finally:
logger.disabled = disabled
return subgroup
from cctbx.sgtbx import subgroups
from cctbx.sgtbx import bravais_types
from cctbx.sgtbx import change_of_basis_op
find_max_delta = sgtbx.lattice_symmetry_find_max_delta
def refine_subgroup(args):
assert len(args) == 4
from dials.command_line.check_indexing_symmetry import (
get_symop_correlation_coefficients,
normalise_intensities,
)
params, subgroup, used_reflections, experiments = args
used_reflections = copy.deepcopy(used_reflections)
triclinic_miller = used_reflections["miller_index"]
cb_op = subgroup["cb_op_inp_best"]
higher_symmetry_miller = cb_op.apply(triclinic_miller)
used_reflections["miller_index"] = higher_symmetry_miller
unrefined_crystal = copy.deepcopy(subgroup.unrefined_crystal)
for expt in experiments:
expt.crystal = unrefined_crystal
from dials.algorithms.indexing.refinement import refine
subgroup.max_cc = None
subgroup.min_cc = None
subgroup.correlation_coefficients = []
subgroup.cc_nrefs = []
with LoggingContext("dials.algorithms.refinement", level=logging.ERROR):
try:
outlier_algorithm = params.refinement.reflections.outlier.algorithm
sel = used_reflections.get_flags(
used_reflections.flags.used_in_refinement)
if sel.all_eq(False):
# Soft outlier rejection if no used_in_refinement flag is set
params.refinement.reflections.outlier.algorithm = "tukey"
iqr_multiplier = (
params.refinement.reflections.outlier.tukey.iqr_multiplier)
params.refinement.reflections.outlier.tukey.iqr_multiplier = (
2 * iqr_multiplier)
sel = ~sel
else:
# Remove reflections not previously used in refinement
params.refinement.reflections.outlier.algorithm = "null"
refinery, refined, outliers = refine(params,
used_reflections.select(sel),
experiments)
params.refinement.reflections.outlier.algorithm = outlier_algorithm
refinery, refined, outliers = refine(params, used_reflections,
refinery.get_experiments())
except RuntimeError as e:
if (str(e) == "scitbx Error: g0 - astry*astry -astrz*astrz <= 0."
or str(e) == "scitbx Error: g1-bstrz*bstrz <= 0."):
subgroup.refined_experiments = None
subgroup.rmsd = None
subgroup.Nmatches = None
else:
raise
else:
dall = refinery.rmsds()
dx = dall[0]
dy = dall[1]
subgroup.rmsd = math.sqrt(dx * dx + dy * dy)
subgroup.Nmatches = len(refinery.get_matches())
subgroup.refined_experiments = refinery.get_experiments()
assert len(subgroup.refined_experiments.crystals()) == 1
subgroup.refined_crystal = subgroup.refined_experiments.crystals(
)[0]
cs = crystal.symmetry(
unit_cell=subgroup.refined_crystal.get_unit_cell(),
space_group=subgroup.refined_crystal.get_space_group(),
)
if "intensity.sum.value" in used_reflections:
# remove refl with -ve variance
sel = used_reflections["intensity.sum.variance"] > 0
good_reflections = used_reflections.select(sel)
from cctbx import miller
ms = miller.set(cs, good_reflections["miller_index"])
ms = ms.array(
good_reflections["intensity.sum.value"] /
flex.sqrt(good_reflections["intensity.sum.variance"]))
if params.normalise:
if params.normalise_bins:
ms = normalise_intensities(
ms, n_bins=params.normalise_bins)
else:
ms = normalise_intensities(ms)
if params.cc_n_bins is not None:
ms.setup_binner(n_bins=params.cc_n_bins)
ccs, nrefs = get_symop_correlation_coefficients(
ms, use_binning=(params.cc_n_bins is not None))
subgroup.correlation_coefficients = ccs
subgroup.cc_nrefs = nrefs
ccs = ccs.select(nrefs > 10)
if len(ccs) > 1:
subgroup.max_cc = flex.max(ccs[1:])
subgroup.min_cc = flex.min(ccs[1:])
return subgroup
sel = used_reflections['intensity.sum.variance'] > 0
good_reflections = used_reflections.select(sel)
from cctbx import miller
ms = miller.set(cs, good_reflections['miller_index'])
ms = ms.array(
good_reflections['intensity.sum.value'] /
flex.sqrt(good_reflections['intensity.sum.variance']))
if params.normalise:
if params.normalise_bins:
ms = normalise_intensities(ms,
n_bins=params.normalise_bins)
else:
ms = normalise_intensities(ms)
if params.cc_n_bins is not None:
ms.setup_binner(n_bins=params.cc_n_bins)
ccs, nrefs = get_symop_correlation_coefficients(
ms, use_binning=(params.cc_n_bins is not None))
subgroup.correlation_coefficients = ccs
subgroup.cc_nrefs = nrefs
ccs = ccs.select(nrefs > 10)
if len(ccs) > 1:
subgroup.max_cc = flex.max(ccs[1:])
subgroup.min_cc = flex.min(ccs[1:])
finally:
logger.disabled = disabled
return subgroup
from cctbx.sgtbx import subgroups
from cctbx.sgtbx import bravais_types
from cctbx.sgtbx import change_of_basis_op
find_max_delta = sgtbx.lattice_symmetry_find_max_delta
