def test_translate(dials_regression, run_in_tmpdir):
"""Test as written in https://github.com/dials/dials/issues/471. This
is pretty slow!"""
# use the i04_weak_data for this test
data_dir = os.path.join(dials_regression, "image_examples", "DLS_I04")
image_path = os.path.join(data_dir, "grid_full_cbf_0005.cbf")
# Generate distortion maps
cmd = f"dials.generate_distortion_maps {image_path} dx=1 dy=2"
easy_run.fully_buffered(command=cmd).raise_if_errors()
# Import without correction
cmd = f"dials.import {image_path}"
easy_run.fully_buffered(command=cmd).raise_if_errors()
expt1 = ExperimentListFactory.from_serialized_format("imported.expt")[0]
# Should be no dx/dy lookup files
assert not expt1.imageset.external_lookup.dx.filename
assert not expt1.imageset.external_lookup.dy.filename
# Import with correction
cmd = f"dials.import {image_path} dx=dx.pickle dy=dy.pickle output.experiments=corrected.expt"
easy_run.fully_buffered(command=cmd).raise_if_errors()
expt2 = ExperimentListFactory.from_serialized_format("corrected.expt")[0]
# Check that dx/dy lookup files have been set
assert expt2.imageset.external_lookup.dx.filename
assert expt2.imageset.external_lookup.dy.filename
def experiment_list(infile, check_format=True):
""" Load an experiment list from a serialzied format. """
from dxtbx.model.experiment_list import ExperimentListFactory
return ExperimentListFactory.from_serialized_format(
infile, check_format=check_format
)
def experiment_list(infile, check_format=True):
"""Load an experiment list from a serialized format."""
# Resolve recursive import
from dxtbx.model.experiment_list import ExperimentListFactory
if infile and hasattr(infile, "__fspath__"):
infile = (infile.__fspath__()
) # Resolve file system path (PEP-519) object to string.
return ExperimentListFactory.from_serialized_format(
infile, check_format=check_format)
def test_filtered_arrays_from_experiments_reflections_with_batches(dials_data):
x4wide_dir = dials_data("x4wide_processed")
refl = flex.reflection_table.from_file(
x4wide_dir.join("AUTOMATIC_DEFAULT_scaled.refl").strpath)
expts = ExperimentListFactory.from_serialized_format(
x4wide_dir.join("AUTOMATIC_DEFAULT_scaled.expt").strpath,
check_format=False)
miller_arrays, batches = filtered_arrays_from_experiments_reflections(
expts, [refl], return_batches=True)
assert len(miller_arrays) == len(batches) == 1
assert miller_arrays[0].size() == batches[0].size() == 62920
assert len(set(batches[0].data())) == 88
assert flex.min(batches[0].data()) == 2
assert flex.max(batches[0].data()) == 89
def test_refinement(dials_regression):
"""Test a refinement run"""
# Get a beam and detector from a experiments. This one has a CS-PAD, but that
# is irrelevant
data_dir = os.path.join(dials_regression, "refinement_test_data",
"hierarchy_test")
experiments_path = os.path.join(data_dir, "datablock.json")
assert os.path.exists(experiments_path)
# load models
from dxtbx.model.experiment_list import ExperimentListFactory
experiments = ExperimentListFactory.from_serialized_format(
experiments_path, check_format=False)
im_set = experiments.imagesets()[0]
detector = deepcopy(im_set.get_detector())
beam = im_set.get_beam()
# Invent a crystal, goniometer and scan for this test
from dxtbx.model import Crystal
crystal = Crystal((40.0, 0.0, 0.0), (0.0, 40.0, 0.0), (0.0, 0.0, 40.0),
space_group_symbol="P1")
orig_xl = deepcopy(crystal)
from dxtbx.model import GoniometerFactory
goniometer = GoniometerFactory.known_axis((1.0, 0.0, 0.0))
# Build a mock scan for a 180 degree sequence
from dxtbx.model import ScanFactory
sf = ScanFactory()
scan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(1800)),
deg=True,
)
sequence_range = scan.get_oscillation_range(deg=False)
im_width = scan.get_oscillation(deg=False)[1]
assert sequence_range == (0.0, pi)
assert approx_equal(im_width, 0.1 * pi / 180.0)
# Build an experiment list
experiments = ExperimentList()
experiments.append(
Experiment(
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
crystal=crystal,
imageset=None,
))
# simulate some reflections
refs, _ = generate_reflections(experiments)
# change unit cell a bit (=0.1 Angstrom length upsets, 0.1 degree of
# alpha and beta angles)
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalUnitCellParameterisation, )
xluc_param = CrystalUnitCellParameterisation(crystal)
cell_params = crystal.get_unit_cell().parameters()
cell_params = [
a + b for a, b in zip(cell_params, [0.1, -0.1, 0.1, 0.1, -0.1, 0.0])
]
from cctbx.uctbx import unit_cell
from rstbx.symmetry.constraints.parameter_reduction import symmetrize_reduce_enlarge
from scitbx import matrix
new_uc = unit_cell(cell_params)
newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
S = symmetrize_reduce_enlarge(crystal.get_space_group())
S.set_orientation(orientation=newB)
X = tuple([e * 1.0e5 for e in S.forward_independent_parameters()])
xluc_param.set_param_vals(X)
# reparameterise the crystal at the perturbed geometry
xluc_param = CrystalUnitCellParameterisation(crystal)
# Dummy parameterisations for other models
beam_param = None
xlo_param = None
det_param = None
# parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.parameter_report import (
ParameterReporter, )
pred_param = TwoThetaPredictionParameterisation(experiments, det_param,
beam_param, xlo_param,
[xluc_param])
param_reporter = ParameterReporter(det_param, beam_param, xlo_param,
[xluc_param])
# reflection manager
refman = TwoThetaReflectionManager(refs, experiments, nref_per_degree=20)
# reflection predictor
ref_predictor = TwoThetaExperimentsPredictor(experiments)
# target function
target = TwoThetaTarget(experiments, ref_predictor, refman, pred_param)
# minimisation engine
from dials.algorithms.refinement.engine import (
LevenbergMarquardtIterations as Refinery, )
refinery = Refinery(
target=target,
prediction_parameterisation=pred_param,
log=None,
max_iterations=20,
)
# Refiner
from dials.algorithms.refinement.refiner import Refiner
refiner = Refiner(
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
)
refiner.run()
# compare crystal with original crystal
refined_xl = refiner.get_experiments()[0].crystal
# print refined_xl
assert refined_xl.is_similar_to(orig_xl,
uc_rel_length_tolerance=0.001,
uc_abs_angle_tolerance=0.01)
def test1(dials_regression):
# use a experiments that contains a CS-PAD detector description
data_dir = os.path.join(dials_regression, "refinement_test_data",
"hierarchy_test")
experiments_path = os.path.join(data_dir, "datablock.json")
assert os.path.exists(experiments_path)
# load models
from dxtbx.model.experiment_list import ExperimentListFactory
experiments = ExperimentListFactory.from_serialized_format(
experiments_path, check_format=False)
im_set = experiments.imagesets()[0]
detector = copy.deepcopy(im_set.get_detector())
beam = im_set.get_beam()
# we'll invent a crystal, goniometer and scan for this test
from dxtbx.model import Crystal
crystal = Crystal((40.0, 0.0, 0.0), (0.0, 40.0, 0.0), (0.0, 0.0, 40.0),
space_group_symbol="P1")
from dxtbx.model import GoniometerFactory
goniometer = GoniometerFactory.known_axis((1.0, 0.0, 0.0))
# Build a mock scan for a 180 degree sequence
from dxtbx.model import ScanFactory
sf = ScanFactory()
scan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(1800)),
deg=True,
)
sequence_range = scan.get_oscillation_range(deg=False)
im_width = scan.get_oscillation(deg=False)[1]
assert sequence_range == (0.0, math.pi)
assert im_width == pytest.approx(0.1 * math.pi / 180.0)
from dxtbx.model.experiment_list import ExperimentList, Experiment
# Build an experiment list
experiments = ExperimentList()
experiments.append(
Experiment(
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
crystal=crystal,
imageset=None,
))
# simulate some reflections
refs, ref_predictor = generate_reflections(experiments)
# move the detector quadrants apart by 2mm both horizontally and vertically
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationHierarchical, )
det_param = DetectorParameterisationHierarchical(detector, level=1)
det_p_vals = det_param.get_param_vals()
p_vals = list(det_p_vals)
p_vals[1] += 2
p_vals[2] -= 2
p_vals[7] += 2
p_vals[8] += 2
p_vals[13] -= 2
p_vals[14] += 2
p_vals[19] -= 2
p_vals[20] -= 2
det_param.set_param_vals(p_vals)
# reparameterise the detector at the new perturbed geometry
det_param = DetectorParameterisationHierarchical(detector, level=1)
# parameterise other models
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation, )
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationParameterisation,
CrystalUnitCellParameterisation,
)
beam_param = BeamParameterisation(beam, goniometer)
xlo_param = CrystalOrientationParameterisation(crystal)
xluc_param = CrystalUnitCellParameterisation(crystal)
# fix beam
beam_param.set_fixed([True] * 3)
# fix crystal
xluc_param.set_fixed([True] * 6)
xlo_param.set_fixed([True] * 3)
# parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.prediction_parameters import (
XYPhiPredictionParameterisation, )
from dials.algorithms.refinement.parameterisation.parameter_report import (
ParameterReporter, )
pred_param = XYPhiPredictionParameterisation(experiments, [det_param],
[beam_param], [xlo_param],
[xluc_param])
param_reporter = ParameterReporter([det_param], [beam_param], [xlo_param],
[xluc_param])
# reflection manager and target function
from dials.algorithms.refinement.target import (
LeastSquaresPositionalResidualWithRmsdCutoff, )
from dials.algorithms.refinement.reflection_manager import ReflectionManager
refman = ReflectionManager(refs, experiments, nref_per_degree=20)
# set a very tight rmsd target of 1/10000 of a pixel
target = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments,
ref_predictor,
refman,
pred_param,
restraints_parameterisation=None,
frac_binsize_cutoff=0.0001,
)
# minimisation engine
from dials.algorithms.refinement.engine import (
LevenbergMarquardtIterations as Refinery, )
refinery = Refinery(
target=target,
prediction_parameterisation=pred_param,
log=None,
max_iterations=20,
)
# Refiner
from dials.algorithms.refinement.refiner import Refiner
refiner = Refiner(
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
)
history = refiner.run()
assert history.reason_for_termination == "RMSD target achieved"
# compare detector with original detector
orig_det = im_set.get_detector()
refined_det = refiner.get_experiments()[0].detector
from scitbx import matrix
for op, rp in zip(orig_det, refined_det):
# compare the origin vectors by...
o1 = matrix.col(op.get_origin())
o2 = matrix.col(rp.get_origin())
# ...their relative lengths
assert math.fabs(o1.length() -
o2.length()) / o1.length() == pytest.approx(0,
abs=1e-5)
# ...the angle between them
assert o1.accute_angle(o2) == pytest.approx(0, abs=1e-5)
