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, e:
if (str(e) == "scitbx Error: g0 - astry*astry -astrz*astrz <= 0."
or str(e) == "scitbx Error: g1-bstrz*bstrz <= 0."):
subgroup.refined_crystal = None
subgroup.rmsd = None
subgroup.Nmatches = None
subgroup.scan = None
subgroup.goniometer = None
subgroup.beam = None
subgroup.detector = None
else:
raise
def refine(self, experiments, reflections):
from dials.algorithms.indexing.refinement import refine
refiner, refined, outliers = refine(
self.all_params,
reflections,
experiments,
verbosity=self.params.refinement_protocol.verbosity,
)
if outliers is not None:
reflections["id"].set_selected(outliers, -1)
predicted = refiner.predict_for_indexed()
reflections["xyzcal.mm"] = predicted["xyzcal.mm"]
reflections["entering"] = predicted["entering"]
reflections.unset_flags(flex.bool(len(reflections), True),
reflections.flags.centroid_outlier)
assert (reflections.get_flags(
reflections.flags.centroid_outlier).count(True) == 0)
reflections.set_flags(
predicted.get_flags(predicted.flags.centroid_outlier),
reflections.flags.centroid_outlier,
)
reflections.set_flags(
refiner.selection_used_for_refinement(),
reflections.flags.used_in_refinement,
)
return refiner.get_experiments(), reflections
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, e:
if (str(e) == "scitbx Error: g0 - astry*astry -astrz*astrz <= 0." or
str(e) == "scitbx Error: g1-bstrz*bstrz <= 0."):
subgroup.refined_crystal = None
subgroup.rmsd = None
subgroup.Nmatches = None
subgroup.scan = None
subgroup.goniometer = None
subgroup.beam = None
subgroup.detector = None
else: raise
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
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
def run():
random_seed = 35
flex.set_random_seed(random_seed)
random.seed(random_seed)
data = merge_close_spots.merge_close_spots()
# unit cell and space group for lysozyme
known_symmetry = crystal.symmetry("78,78,37,90,90,90", "P43212")
sim = data.two_color_sim
merged_spot_info = data.spot_proximity(sim)
merged_refl = merged_spot_info[0]
detector = data.detector
beams = data.beams
# to make sure input crystal and indexed crystal model are the same
# orientation before using the refiner
A = sim['input_orientation']
A_inv = A.inverse()
a = A_inv[:3]
b = A_inv[3:6]
c = A_inv[6:]
crystinp = Crystal(a, b, c, space_group=known_symmetry.space_group())
result = index(merged_refl, detector, known_symmetry, beams)
print("RESULTS ARE IN")
cm = result.refined_experiments.crystals()[0]
R, best_axis, best_angle, change_of_basis = difference_rotation_matrix_axis_angle(
crystal_a=cm, crystal_b=crystinp)
euler_angles = euler.xyz_angles(R)
print "input crystal: %s" % crystinp
print "Indexed crystal: %s" % cm
print "rotation of: %s" % R
print "euler angles:", euler_angles
print "change of basis:", change_of_basis.as_hkl()
# cmd_line = command_line.argument_interpreter(master_params=master_phil_scope)
# working_phil = cmd_line.process_and_fetch(args=[])
params = master_phil_scope.extract()
params.refinement.parameterisation.beam.fix = "all"
params.refinement.parameterisation.detector.fix = "all"
params.indexing.known_symmetry.space_group = known_symmetry.space_group_info(
)
params.refinement.verbosity = 3
params.indexing.refinement_protocol.d_min_start = 3
params.indexing.refinement_protocol.n_macro_cycles = 1
params.indexing.known_symmetry.unit_cell = known_symmetry.unit_cell()
params.indexing.multiple_lattice_search.max_lattices = 1
params.indexing.debug = True
params.indexing.known_symmetry.absolute_angle_tolerance = 5.0
params.indexing.known_symmetry.relative_length_tolerance = 0.3
expts = copy.deepcopy(result.refined_experiments)
expts.crystals()[0].change_basis(change_of_basis)
print(expts.crystals()[0])
refined = refine(params, result.reflections, expts, verbosity=1)
print(refined[0].get_experiments().crystals()[0])
# from annlib_ext import AnnAdaptor
# ann = AnnAdaptor(merged_refl['xyzobs.px.value'].as_double(), dim=3, k=1)
# ann.query(result.reflections['xyzobs.px.value'].as_double()+1e-6)
indices_sim = change_of_basis.apply(merged_refl['set_miller_index'])
id_sim = merged_refl['set_id']
# only get those that refined:
idx = align_merged_and_refined_refl(merged_refl,
result.refined_reflections)
indices_sim = flex.miller_index([indices_sim[i] for i in idx])
id_sim = flex.int([id_sim[i] for i in idx])
indices_result = result.refined_reflections['miller_index']
id_result = result.refined_reflections['id']
correct_ind = (indices_sim == indices_result)
wrong_wavelength = (id_sim != id_result) & (id_sim != 2)
wrong_index = (indices_sim != indices_result)
correct_wavelength = (id_sim == id_result) | (id_sim == 2)
correct = correct_ind & correct_wavelength
print "Correct index and wavelength: %i/%i" % (correct.count(True),
len(correct))
print "Correct index but wrong wavelength: %i/%i" % (
wrong_wavelength.count(True), len(wrong_wavelength))
print "Wrong index but correct wavelength: %i/%i" % (
wrong_index.count(True), len(correct_wavelength))
