def ref_gen_static(experiments):
"""Generate some reflections using the static predictor"""
beam = experiments[0].beam
crystal = experiments[0].crystal
detector = experiments[0].detector
scan = experiments[0].scan
# All indices to the detector max resolution
dmin = detector.get_max_resolution(beam.get_s0())
index_generator = IndexGenerator(
crystal.get_unit_cell(), space_group(space_group_symbols(1).hall()).type(), dmin
)
indices = index_generator.to_array()
# Predict rays within the sequence range
sequence_range = scan.get_oscillation_range(deg=False)
ray_predictor = ScansRayPredictor(experiments, sequence_range)
refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(detector, refs)
refs = refs.select(intersects)
# Make a reflection predictor and re-predict for these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
refs["id"] = flex.int(len(refs), 0)
refs = ref_predictor(refs)
return refs
def generate_reflections(self):
from cctbx.sgtbx import space_group, space_group_symbols
from dials.algorithms.spot_prediction import IndexGenerator, ray_intersection
sequence_range = self.scan.get_oscillation_range(deg=False)
resolution = 2.0
index_generator = IndexGenerator(
self.crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Predict rays within the sequence range
ray_predictor = ScansRayPredictor(self.experiments, sequence_range)
obs_refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(self.detector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Re-predict using the Experiments predictor for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = self.ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = self.detector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0)**2)
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(
var_x, var_y, var_phi)
# set the flex random seed to an 'uninteresting' number
flex.set_random_seed(12407)
# take 10 random reflections for speed
reflections = obs_refs.select(flex.random_selection(len(obs_refs), 10))
# use a BlockCalculator to calculate the blocks per image
from dials.algorithms.refinement.reflection_manager import BlockCalculator
block_calculator = BlockCalculator(self.experiments, reflections)
reflections = block_calculator.per_image()
return reflections
def generate_reflections(experiments):
from dials.algorithms.spot_prediction import IndexGenerator
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansRayPredictor,
ScansExperimentsPredictor,
)
from dials.algorithms.spot_prediction import ray_intersection
from cctbx.sgtbx import space_group, space_group_symbols
from scitbx.array_family import flex
detector = experiments[0].detector
crystal = experiments[0].crystal
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Predict rays within the sequence range
scan = experiments[0].scan
sequence_range = scan.get_oscillation_range(deg=False)
ray_predictor = ScansRayPredictor(experiments, sequence_range)
obs_refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(detector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = detector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0)**2)
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
return obs_refs, ref_predictor
def generate_reflections(self):
# Build a mock scan for a 3 degree sequence
sf = ScanFactory()
self.scan = sf.make_scan(
image_range=(1, 1),
exposure_times=0.1,
oscillation=(0, 3.0),
epochs=list(range(1)),
deg=True,
)
sequence_range = self.scan.get_oscillation_range(deg=False)
# Create a scans ExperimentList, only for generating reflections
experiments = ExperimentList()
experiments.append(
Experiment(
beam=self.beam,
detector=self.detector,
goniometer=self.gonio,
scan=self.scan,
crystal=self.crystal,
imageset=None,
))
# Create a ScansRayPredictor
ray_predictor = ScansRayPredictor(experiments, sequence_range)
# Generate rays - only to work out which hkls are predicted
resolution = 2.0
index_generator = IndexGenerator(
self.crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
rays = ray_predictor(indices)
# Make a standard reflection_table and copy in the ray data
self.reflections = flex.reflection_table.empty_standard(len(rays))
self.reflections.update(rays)
# Set dummy observed variances to allow statistical weights to be set
self.reflections["xyzobs.mm.variance"] += (1e-3, 1e-3, 1e-6)
def generate_reflections(experiments):
from cctbx.sgtbx import space_group, space_group_symbols
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansExperimentsPredictor,
ScansRayPredictor,
)
from dials.algorithms.spot_prediction import IndexGenerator, ray_intersection
detector = experiments[0].detector
crystal = experiments[0].crystal
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Predict rays within the sequence range
scan = experiments[0].scan
sequence_range = scan.get_oscillation_range(deg=False)
ray_predictor = ScansRayPredictor(experiments, sequence_range)
obs_refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(detector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
return obs_refs
def test():
from cctbx.sgtbx import space_group, space_group_symbols
# We will set up a mock scan
from dxtbx.model import ScanFactory
from dxtbx.model.experiment_list import Experiment, ExperimentList
from libtbx.phil import parse
from scitbx import matrix
from scitbx.array_family import flex
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansExperimentsPredictor,
ScansRayPredictor,
)
# Reflection prediction
from dials.algorithms.spot_prediction import IndexGenerator
# Building experimental models
from dials.test.algorithms.refinement.setup_geometry import Extract
master_phil = parse(
"""
include scope dials.test.algorithms.refinement.geometry_phil
include scope dials.test.algorithms.refinement.minimiser_phil
""",
process_includes=True,
)
overrides = """geometry.parameters.crystal.a.length.range = 10 50
geometry.parameters.crystal.b.length.range = 10 50
geometry.parameters.crystal.c.length.range = 10 50"""
models = Extract(master_phil, local_overrides=overrides)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
#############################
# Generate some reflections #
#############################
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Build a mock scan for a 30 degree sequence
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 300),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(300)),
deg=True,
)
sequence_range = myscan.get_oscillation_range(deg=False)
assert sequence_range == pytest.approx((0.0, math.pi / 6.0))
im_width = myscan.get_oscillation(deg=False)[1]
assert im_width == pytest.approx(0.1 * math.pi / 180.0)
# Create an ExperimentList for ScansRayPredictor
experiments = ExperimentList()
experiments.append(
Experiment(
beam=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
))
# Select those that are excited in a 30 degree sequence and get angles
ray_predictor = ScansRayPredictor(experiments, sequence_range)
obs_refs = ray_predictor(indices)
# Set the experiment number
obs_refs["id"] = flex.int(len(obs_refs), 0)
# Calculate intersections
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs = ref_predictor(obs_refs)
print("Total number of observations made", len(obs_refs))
s0 = matrix.col(mybeam.get_s0())
spindle = matrix.col(mygonio.get_rotation_axis())
for ref in obs_refs.rows():
# get the s1 vector of this reflection
s1 = matrix.col(ref["s1"])
r = s1 - s0
r_orig = r.rotate_around_origin(spindle, -1.0, deg=True)
# is it outside the Ewald sphere (i.e. entering)?
test = (s0 + r_orig).length() > s0.length()
assert ref["entering"] == test
def test():
# Build models, with a larger crystal than default in order to get plenty of
# reflections on the 'still' image
overrides = """
geometry.parameters.crystal.a.length.range=40 50;
geometry.parameters.crystal.b.length.range=40 50;
geometry.parameters.crystal.c.length.range=40 50;
geometry.parameters.random_seed = 42"""
master_phil = parse(
"""
include scope dials.test.algorithms.refinement.geometry_phil
""",
process_includes=True,
)
models = Extract(master_phil, overrides)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
# Build a mock scan for a 3 degree sweep
from dxtbx.model import ScanFactory
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1),
exposure_times=0.1,
oscillation=(0, 3.0),
epochs=list(range(1)),
deg=True,
)
sweep_range = myscan.get_oscillation_range(deg=False)
# Create parameterisations of these models
det_param = DetectorParameterisationSinglePanel(mydetector)
s0_param = BeamParameterisation(mybeam, mygonio)
xlo_param = CrystalOrientationParameterisation(mycrystal)
xluc_param = CrystalUnitCellParameterisation(mycrystal)
# Create a scans ExperimentList, only for generating reflections
experiments = ExperimentList()
experiments.append(
Experiment(
beam=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
))
# Create a stills ExperimentList
stills_experiments = ExperimentList()
stills_experiments.append(
Experiment(beam=mybeam,
detector=mydetector,
crystal=mycrystal,
imageset=None))
# Generate rays - only to work out which hkls are predicted
ray_predictor = ScansRayPredictor(experiments, sweep_range)
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
rays = ray_predictor(indices)
# Make a standard reflection_table and copy in the ray data
reflections = flex.reflection_table.empty_standard(len(rays))
reflections.update(rays)
# Build a standard prediction parameterisation for the stills experiment to do
# FD calculation (not used for its analytical gradients)
pred_param = StillsPredictionParameterisation(
stills_experiments,
detector_parameterisations=[det_param],
beam_parameterisations=[s0_param],
xl_orientation_parameterisations=[xlo_param],
xl_unit_cell_parameterisations=[xluc_param],
)
# Make a managed SphericalRelpStillsReflectionPredictor reflection predictor
# for the first (only) experiment
ref_predictor = Predictor(stills_experiments)
# Predict these reflections in place. Must do this ahead of calculating
# the analytical gradients so quantities like s1 are correct
ref_predictor.update()
ref_predictor.predict(reflections)
# calculate analytical gradients
ag = AnalyticalGradients(
stills_experiments,
detector_parameterisation=det_param,
beam_parameterisation=s0_param,
xl_orientation_parameterisation=xlo_param,
xl_unit_cell_parameterisation=xluc_param,
)
an_grads = ag.get_beam_gradients(reflections)
an_grads.update(ag.get_crystal_orientation_gradients(reflections))
an_grads.update(ag.get_crystal_unit_cell_gradients(reflections))
# get finite difference gradients
p_vals = pred_param.get_param_vals()
deltas = [1.0e-7] * len(p_vals)
fd_grads = []
p_names = pred_param.get_param_names()
for i, delta in enumerate(deltas):
# save parameter value
val = p_vals[i]
# calc reverse state
p_vals[i] -= delta / 2.0
pred_param.set_param_vals(p_vals)
ref_predictor.update()
ref_predictor.predict(reflections)
x, y, _ = reflections["xyzcal.mm"].deep_copy().parts()
s1 = reflections["s1"].deep_copy()
rev_state = s1
# calc forward state
p_vals[i] += delta
pred_param.set_param_vals(p_vals)
ref_predictor.update()
ref_predictor.predict(reflections)
x, y, _ = reflections["xyzcal.mm"].deep_copy().parts()
s1 = reflections["s1"].deep_copy()
fwd_state = s1
# reset parameter to saved value
p_vals[i] = val
# finite difference - currently for s1 only
fd = fwd_state - rev_state
inv_delta = 1.0 / delta
s1_grads = fd * inv_delta
# store gradients
fd_grads.append({"name": p_names[i], "ds1": s1_grads})
# return to the initial state
pred_param.set_param_vals(p_vals)
for i, fd_grad in enumerate(fd_grads):
## compare FD with analytical calculations
print("\n\nParameter {0}: {1}".format(i, fd_grad["name"]))
print("d[s1]/dp for the first reflection")
print("finite diff", fd_grad["ds1"][0])
try:
an_grad = an_grads[fd_grad["name"]]
except KeyError:
continue
print("checking analytical vs finite difference gradients for s1")
for a, b in zip(fd_grad["ds1"], an_grad["ds1"]):
assert a == pytest.approx(b, abs=1e-7)
def test(args=[]):
#############################
# Setup experimental models #
#############################
master_phil = parse(
"""
include scope dials.test.algorithms.refinement.geometry_phil
include scope dials.test.algorithms.refinement.minimiser_phil
""",
process_includes=True,
)
models = setup_geometry.Extract(master_phil, cmdline_args=args)
single_panel_detector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
# Make a 3x3 multi panel detector filling the same space as the existing
# single panel detector. Each panel of the multi-panel detector has pixels with
# 1/3 the length dimensions of the single panel.
multi_panel_detector = Detector()
for x in range(3):
for y in range(3):
new_panel = make_panel_in_array((x, y), single_panel_detector[0])
multi_panel_detector.add_panel(new_panel)
# Build a mock scan for a 180 degree sweep
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(1800)),
deg=True,
)
sweep_range = myscan.get_oscillation_range(deg=False)
im_width = myscan.get_oscillation(deg=False)[1]
assert sweep_range == (0.0, pi)
assert approx_equal(im_width, 0.1 * pi / 180.0)
# Build ExperimentLists
experiments_single_panel = ExperimentList()
experiments_multi_panel = ExperimentList()
experiments_single_panel.append(
Experiment(
beam=mybeam,
detector=single_panel_detector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
))
experiments_multi_panel.append(
Experiment(
beam=mybeam,
detector=multi_panel_detector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
))
###########################
# Parameterise the models #
###########################
det_param = DetectorParameterisationSinglePanel(single_panel_detector)
s0_param = BeamParameterisation(mybeam, mygonio)
xlo_param = CrystalOrientationParameterisation(mycrystal)
xluc_param = CrystalUnitCellParameterisation(mycrystal)
multi_det_param = DetectorParameterisationMultiPanel(
multi_panel_detector, mybeam)
# Fix beam to the X-Z plane (imgCIF geometry), fix wavelength
s0_param.set_fixed([True, False, True])
# Fix crystal parameters
# xluc_param.set_fixed([True, True, True, True, True, True])
########################################################################
# Link model parameterisations together into a parameterisation of the #
# prediction equation #
########################################################################
pred_param = XYPhiPredictionParameterisation(experiments_single_panel,
[det_param], [s0_param],
[xlo_param], [xluc_param])
pred_param2 = XYPhiPredictionParameterisation(
experiments_multi_panel,
[multi_det_param],
[s0_param],
[xlo_param],
[xluc_param],
)
################################
# Apply known parameter shifts #
################################
# shift detectors by 1.0 mm each translation and 2 mrad each rotation
det_p_vals = det_param.get_param_vals()
p_vals = [
a + b for a, b in zip(det_p_vals, [1.0, 1.0, 1.0, 2.0, 2.0, 2.0])
]
det_param.set_param_vals(p_vals)
multi_det_p_vals = multi_det_param.get_param_vals()
p_vals = [
a + b for a, b in zip(multi_det_p_vals, [1.0, 1.0, 1.0, 2.0, 2.0, 2.0])
]
multi_det_param.set_param_vals(p_vals)
# shift beam by 2 mrad in free axis
s0_p_vals = s0_param.get_param_vals()
p_vals = list(s0_p_vals)
p_vals[0] += 2.0
s0_param.set_param_vals(p_vals)
# rotate crystal a bit (=2 mrad each rotation)
xlo_p_vals = xlo_param.get_param_vals()
p_vals = [a + b for a, b in zip(xlo_p_vals, [2.0, 2.0, 2.0])]
xlo_param.set_param_vals(p_vals)
# change unit cell a bit (=0.1 Angstrom length upsets, 0.1 degree of
# gamma angle)
xluc_p_vals = xluc_param.get_param_vals()
cell_params = mycrystal.get_unit_cell().parameters()
cell_params = [
a + b for a, b in zip(cell_params, [0.1, 0.1, 0.1, 0.0, 0.0, 0.1])
]
new_uc = unit_cell(cell_params)
newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
S = symmetrize_reduce_enlarge(mycrystal.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)
#############################
# Generate some reflections #
#############################
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# for the reflection predictor, it doesn't matter which experiment list is
# passed, as the detector is not used
ref_predictor = ScansRayPredictor(experiments_single_panel, sweep_range)
# get two sets of identical reflections
obs_refs = ref_predictor(indices)
obs_refs2 = ref_predictor(indices)
for r1, r2 in zip(obs_refs, obs_refs2):
assert r1["s1"] == r2["s1"]
# get the panel intersections
sel = ray_intersection(single_panel_detector, obs_refs)
obs_refs = obs_refs.select(sel)
sel = ray_intersection(multi_panel_detector, obs_refs2)
obs_refs2 = obs_refs2.select(sel)
assert len(obs_refs) == len(obs_refs2)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
obs_refs2["xyzobs.mm.value"] = obs_refs2["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = single_panel_detector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0)**2)
# set the variances and frame numbers
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
obs_refs2["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
# Add in flags and ID columns by copying into standard reflection tables
tmp = flex.reflection_table.empty_standard(len(obs_refs))
tmp.update(obs_refs)
obs_refs = tmp
tmp = flex.reflection_table.empty_standard(len(obs_refs2))
tmp.update(obs_refs2)
obs_refs2 = tmp
###############################
# Undo known parameter shifts #
###############################
s0_param.set_param_vals(s0_p_vals)
det_param.set_param_vals(det_p_vals)
multi_det_param.set_param_vals(det_p_vals)
xlo_param.set_param_vals(xlo_p_vals)
xluc_param.set_param_vals(xluc_p_vals)
#####################################
# Select reflections for refinement #
#####################################
refman = ReflectionManager(obs_refs, experiments_single_panel)
refman2 = ReflectionManager(obs_refs, experiments_multi_panel)
###############################
# Set up the target functions #
###############################
mytarget = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments_single_panel,
ScansExperimentsPredictor(experiments_single_panel),
refman,
pred_param,
restraints_parameterisation=None,
)
mytarget2 = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments_multi_panel,
ScansExperimentsPredictor(experiments_multi_panel),
refman2,
pred_param2,
restraints_parameterisation=None,
)
#################################
# Set up the refinement engines #
#################################
refiner = setup_minimiser.Extract(master_phil,
mytarget,
pred_param,
cmdline_args=args).refiner
refiner2 = setup_minimiser.Extract(master_phil,
mytarget2,
pred_param2,
cmdline_args=args).refiner
refiner.run()
# reset parameters and run refinement with the multi panel detector
s0_param.set_param_vals(s0_p_vals)
multi_det_param.set_param_vals(det_p_vals)
xlo_param.set_param_vals(xlo_p_vals)
xluc_param.set_param_vals(xluc_p_vals)
refiner2.run()
# same number of steps
assert refiner.get_num_steps() == refiner2.get_num_steps()
# same rmsds
for rmsd, rmsd2 in zip(refiner.history["rmsd"], refiner2.history["rmsd"]):
assert approx_equal(rmsd, rmsd2)
# same parameter values each step
for params, params2 in zip(refiner.history["parameter_vector"],
refiner.history["parameter_vector"]):
assert approx_equal(params, params2)
def test():
# Python and cctbx imports
from math import pi
from scitbx import matrix
from scitbx.array_family import flex
from libtbx.phil import parse
from libtbx.test_utils import approx_equal
# Get modules to build models and minimiser using PHIL
import dials.test.algorithms.refinement.setup_geometry as setup_geometry
import dials.test.algorithms.refinement.setup_minimiser as setup_minimiser
# We will set up a mock scan and a mock experiment list
from dxtbx.model import ScanFactory
from dxtbx.model.experiment_list import ExperimentList, Experiment
# Model parameterisations
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationSinglePanel, )
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation, )
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationParameterisation,
CrystalUnitCellParameterisation,
)
# Symmetry constrained parameterisation for the unit cell
from cctbx.uctbx import unit_cell
from rstbx.symmetry.constraints.parameter_reduction import symmetrize_reduce_enlarge
# Reflection prediction
from dials.algorithms.spot_prediction import IndexGenerator, ray_intersection
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansRayPredictor,
ScansExperimentsPredictor,
)
from cctbx.sgtbx import space_group, space_group_symbols
# Parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.prediction_parameters import (
XYPhiPredictionParameterisation, )
# Imports for the target function
from dials.algorithms.refinement.target import (
LeastSquaresPositionalResidualWithRmsdCutoff, )
from dials.algorithms.refinement.reflection_manager import ReflectionManager
#############################
# Setup experimental models #
#############################
override = """geometry.parameters
{
beam.wavelength.random=False
beam.wavelength.value=1.0
beam.direction.inclination.random=False
crystal.a.length.random=False
crystal.a.length.value=12.0
crystal.a.direction.method=exactly
crystal.a.direction.exactly.direction=1.0 0.002 -0.004
crystal.b.length.random=False
crystal.b.length.value=14.0
crystal.b.direction.method=exactly
crystal.b.direction.exactly.direction=-0.002 1.0 0.002
crystal.c.length.random=False
crystal.c.length.value=13.0
crystal.c.direction.method=exactly
crystal.c.direction.exactly.direction=0.002 -0.004 1.0
detector.directions.method=exactly
detector.directions.exactly.dir1=0.99 0.002 -0.004
detector.directions.exactly.norm=0.002 -0.001 0.99
detector.centre.method=exactly
detector.centre.exactly.value=1.0 -0.5 199.0
}"""
master_phil = parse(
"""
include scope dials.test.algorithms.refinement.geometry_phil
include scope dials.test.algorithms.refinement.minimiser_phil
""",
process_includes=True,
)
models = setup_geometry.Extract(master_phil,
local_overrides=override,
verbose=False)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
###########################
# Parameterise the models #
###########################
det_param = DetectorParameterisationSinglePanel(mydetector)
s0_param = BeamParameterisation(mybeam, mygonio)
xlo_param = CrystalOrientationParameterisation(mycrystal)
xluc_param = CrystalUnitCellParameterisation(mycrystal)
# Fix beam to the X-Z plane (imgCIF geometry), fix wavelength
s0_param.set_fixed([True, False, True])
########################################################################
# Link model parameterisations together into a parameterisation of the #
# prediction equation #
########################################################################
# Build a mock scan for a 180 degree sweep
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(1800)),
deg=True,
)
# Build an ExperimentList
experiments = ExperimentList()
experiments.append(
Experiment(
beam=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
))
# Create the PredictionParameterisation
pred_param = XYPhiPredictionParameterisation(experiments, [det_param],
[s0_param], [xlo_param],
[xluc_param])
################################
# Apply known parameter shifts #
################################
# shift detector by 1.0 mm each translation and 4 mrad each rotation
det_p_vals = det_param.get_param_vals()
p_vals = [
a + b for a, b in zip(det_p_vals, [1.0, 1.0, 1.0, 4.0, 4.0, 4.0])
]
det_param.set_param_vals(p_vals)
# shift beam by 4 mrad in free axis
s0_p_vals = s0_param.get_param_vals()
p_vals = list(s0_p_vals)
p_vals[0] += 4.0
s0_param.set_param_vals(p_vals)
# rotate crystal a bit (=3 mrad each rotation)
xlo_p_vals = xlo_param.get_param_vals()
p_vals = [a + b for a, b in zip(xlo_p_vals, [3.0, 3.0, 3.0])]
xlo_param.set_param_vals(p_vals)
# change unit cell a bit (=0.1 Angstrom length upsets, 0.1 degree of
# alpha and beta angles)
xluc_p_vals = xluc_param.get_param_vals()
cell_params = mycrystal.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])
]
new_uc = unit_cell(cell_params)
newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
S = symmetrize_reduce_enlarge(mycrystal.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)
#############################
# Generate some reflections #
#############################
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
sweep_range = myscan.get_oscillation_range(deg=False)
im_width = myscan.get_oscillation(deg=False)[1]
assert sweep_range == (0.0, pi)
assert approx_equal(im_width, 0.1 * pi / 180.0)
# Predict rays within the sweep range
ray_predictor = ScansRayPredictor(experiments, sweep_range)
obs_refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(mydetector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0)**2)
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
# The total number of observations should be 1128
assert len(obs_refs) == 1128
###############################
# Undo known parameter shifts #
###############################
s0_param.set_param_vals(s0_p_vals)
det_param.set_param_vals(det_p_vals)
xlo_param.set_param_vals(xlo_p_vals)
xluc_param.set_param_vals(xluc_p_vals)
#####################################
# Select reflections for refinement #
#####################################
refman = ReflectionManager(obs_refs,
experiments,
outlier_detector=None,
close_to_spindle_cutoff=0.1)
##############################
# Set up the target function #
##############################
# The current 'achieved' criterion compares RMSD against 1/3 the pixel size and
# 1/3 the image width in radians. For the simulated data, these are just made up
mytarget = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments,
ref_predictor,
refman,
pred_param,
restraints_parameterisation=None)
######################################
# Set up the LSTBX refinement engine #
######################################
overrides = """minimiser.parameters.engine=GaussNewton
minimiser.parameters.logfile=None"""
refiner = setup_minimiser.Extract(master_phil,
mytarget,
pred_param,
local_overrides=overrides).refiner
refiner.run()
assert mytarget.achieved()
assert refiner.get_num_steps() == 1
assert approx_equal(
mytarget.rmsds(),
(0.00508252354876, 0.00420954552156, 8.97303428289e-05))
###############################
# Undo known parameter shifts #
###############################
s0_param.set_param_vals(s0_p_vals)
det_param.set_param_vals(det_p_vals)
xlo_param.set_param_vals(xlo_p_vals)
xluc_param.set_param_vals(xluc_p_vals)
######################################################
# Set up the LBFGS with curvatures refinement engine #
######################################################
overrides = """minimiser.parameters.engine=LBFGScurvs
minimiser.parameters.logfile=None"""
refiner = setup_minimiser.Extract(master_phil,
mytarget,
pred_param,
local_overrides=overrides).refiner
refiner.run()
assert mytarget.achieved()
assert refiner.get_num_steps() == 9
assert approx_equal(mytarget.rmsds(),
(0.0558857700305, 0.0333446685335, 0.000347402754278))
def test(args=[]):
# Python and cctbx imports
from math import pi
from scitbx import matrix
from libtbx.phil import parse
from libtbx.test_utils import approx_equal
# Import for surgery on reflection_tables
from dials.array_family import flex
# Get module to build models using PHIL
import dials.test.algorithms.refinement.setup_geometry as setup_geometry
# We will set up a mock scan and a mock experiment list
from dxtbx.model import ScanFactory
from dxtbx.model.experiment_list import ExperimentList, Experiment
# Crystal parameterisations
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationParameterisation,
CrystalUnitCellParameterisation,
)
# Symmetry constrained parameterisation for the unit cell
from cctbx.uctbx import unit_cell
from rstbx.symmetry.constraints.parameter_reduction import symmetrize_reduce_enlarge
# Reflection prediction
from dials.algorithms.spot_prediction import IndexGenerator
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansRayPredictor,
StillsExperimentsPredictor,
)
from dials.algorithms.spot_prediction import ray_intersection
from cctbx.sgtbx import space_group, space_group_symbols
#############################
# Setup experimental models #
#############################
master_phil = parse(
"""
include scope dials.test.algorithms.refinement.geometry_phil
include scope dials.test.algorithms.refinement.minimiser_phil
""",
process_includes=True,
)
# build models, with a larger crystal than default in order to get enough
# reflections on the 'still' image
param = """
geometry.parameters.crystal.a.length.range=40 50;
geometry.parameters.crystal.b.length.range=40 50;
geometry.parameters.crystal.c.length.range=40 50;
geometry.parameters.random_seed = 42"""
models = setup_geometry.Extract(master_phil,
cmdline_args=args,
local_overrides=param)
crystal = models.crystal
mydetector = models.detector
mygonio = models.goniometer
mybeam = models.beam
# Build a mock scan for a 1.5 degree wedge. Only used for generating indices near
# the Ewald sphere
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1),
exposure_times=0.1,
oscillation=(0, 1.5),
epochs=list(range(1)),
deg=True,
)
sweep_range = myscan.get_oscillation_range(deg=False)
im_width = myscan.get_oscillation(deg=False)[1]
assert approx_equal(im_width, 1.5 * pi / 180.0)
# Build experiment lists
stills_experiments = ExperimentList()
stills_experiments.append(
Experiment(beam=mybeam,
detector=mydetector,
crystal=crystal,
imageset=None))
scans_experiments = ExperimentList()
scans_experiments.append(
Experiment(
beam=mybeam,
detector=mydetector,
crystal=crystal,
goniometer=mygonio,
scan=myscan,
imageset=None,
))
##########################################################
# Parameterise the models (only for perturbing geometry) #
##########################################################
xlo_param = CrystalOrientationParameterisation(crystal)
xluc_param = CrystalUnitCellParameterisation(crystal)
################################
# Apply known parameter shifts #
################################
# rotate crystal (=5 mrad each rotation)
xlo_p_vals = []
p_vals = xlo_param.get_param_vals()
xlo_p_vals.append(p_vals)
new_p_vals = [a + b for a, b in zip(p_vals, [5.0, 5.0, 5.0])]
xlo_param.set_param_vals(new_p_vals)
# change unit cell (=1.0 Angstrom length upsets, 0.5 degree of
# gamma angle)
xluc_p_vals = []
p_vals = xluc_param.get_param_vals()
xluc_p_vals.append(p_vals)
cell_params = crystal.get_unit_cell().parameters()
cell_params = [
a + b for a, b in zip(cell_params, [1.0, 1.0, -1.0, 0.0, 0.0, 0.5])
]
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)
# keep track of the target crystal model to compare with refined
from copy import deepcopy
target_crystal = deepcopy(crystal)
#############################
# Generate some reflections #
#############################
# All indices in a 2.0 Angstrom sphere for crystal
resolution = 2.0
index_generator = IndexGenerator(
crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Build a ray predictor and predict rays close to the Ewald sphere by using
# the narrow rotation scan
ref_predictor = ScansRayPredictor(scans_experiments, sweep_range)
obs_refs = ref_predictor(indices, experiment_id=0)
# Take only those rays that intersect the detector
intersects = ray_intersection(mydetector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Add in flags and ID columns by copying into standard reflection table
tmp = flex.reflection_table.empty_standard(len(obs_refs))
tmp.update(obs_refs)
obs_refs = tmp
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0)**2)
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
# Re-predict using the stills reflection predictor
stills_ref_predictor = StillsExperimentsPredictor(stills_experiments)
obs_refs_stills = stills_ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs_stills["xyzobs.mm.value"] = obs_refs_stills["xyzcal.mm"]
###############################
# Undo known parameter shifts #
###############################
xlo_param.set_param_vals(xlo_p_vals[0])
xluc_param.set_param_vals(xluc_p_vals[0])
# make a refiner
from dials.algorithms.refinement.refiner import phil_scope
params = phil_scope.fetch(source=parse("")).extract()
# Change this to get a plot
do_plot = False
if do_plot:
params.refinement.refinery.journal.track_parameter_correlation = True
from dials.algorithms.refinement.refiner import RefinerFactory
# decrease bin_size_fraction to terminate on RMSD convergence
params.refinement.target.bin_size_fraction = 0.01
params.refinement.parameterisation.beam.fix = "all"
params.refinement.parameterisation.detector.fix = "all"
refiner = RefinerFactory.from_parameters_data_experiments(
params, obs_refs_stills, stills_experiments)
# run refinement
history = refiner.run()
# regression tests
assert len(history["rmsd"]) == 9
refined_crystal = refiner.get_experiments()[0].crystal
uc1 = refined_crystal.get_unit_cell()
uc2 = target_crystal.get_unit_cell()
assert uc1.is_similar_to(uc2)
if do_plot:
plt = refiner.parameter_correlation_plot(
len(history["parameter_correlation"]) - 1)
plt.show()
print("Target values of parameters are")
msg = "Parameters: " + "%.5f " * len(pred_param)
print(msg % tuple(pred_param.get_param_vals()))
print()
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Predict rays within the sweep range
ray_predictor = ScansRayPredictor(experiments, sweep_range)
obs_refs = ray_predictor(indices)
print("Total number of reflections excited", len(obs_refs))
# Take only those rays that intersect the detector
intersects = ray_intersection(mydetector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
def test(args=[]):
# Python and cctbx imports
from math import pi
from cctbx.sgtbx import space_group, space_group_symbols
# Symmetry constrained parameterisation for the unit cell
from cctbx.uctbx import unit_cell
# We will set up a mock scan and a mock experiment list
from dxtbx.model import ScanFactory
from dxtbx.model.experiment_list import Experiment, ExperimentList
from libtbx.phil import parse
from libtbx.test_utils import approx_equal
from rstbx.symmetry.constraints.parameter_reduction import symmetrize_reduce_enlarge
from scitbx import matrix
from scitbx.array_family import flex
# Get module to build models using PHIL
import dials.test.algorithms.refinement.setup_geometry as setup_geometry
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation, )
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationParameterisation,
CrystalUnitCellParameterisation,
)
# Model parameterisations
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationSinglePanel, )
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansExperimentsPredictor,
ScansRayPredictor,
)
# Reflection prediction
from dials.algorithms.spot_prediction import IndexGenerator, ray_intersection
#############################
# Setup experimental models #
#############################
master_phil = parse(
"""
include scope dials.test.algorithms.refinement.geometry_phil
include scope dials.test.algorithms.refinement.minimiser_phil
""",
process_includes=True,
)
models = setup_geometry.Extract(
master_phil,
cmdline_args=args,
local_overrides="geometry.parameters.random_seed = 1",
)
crystal1 = models.crystal
models = setup_geometry.Extract(
master_phil,
cmdline_args=args,
local_overrides="geometry.parameters.random_seed = 2",
)
mydetector = models.detector
mygonio = models.goniometer
crystal2 = models.crystal
mybeam = models.beam
# Build a mock scan for a 180 degree sequence
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(1800)),
deg=True,
)
sequence_range = myscan.get_oscillation_range(deg=False)
im_width = myscan.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=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=crystal1,
imageset=None,
))
experiments.append(
Experiment(
beam=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=crystal2,
imageset=None,
))
assert len(experiments.detectors()) == 1
##########################################################
# Parameterise the models (only for perturbing geometry) #
##########################################################
det_param = DetectorParameterisationSinglePanel(mydetector)
s0_param = BeamParameterisation(mybeam, mygonio)
xl1o_param = CrystalOrientationParameterisation(crystal1)
xl1uc_param = CrystalUnitCellParameterisation(crystal1)
xl2o_param = CrystalOrientationParameterisation(crystal2)
xl2uc_param = CrystalUnitCellParameterisation(crystal2)
# Fix beam to the X-Z plane (imgCIF geometry), fix wavelength
s0_param.set_fixed([True, False, True])
# Fix crystal parameters
# xluc_param.set_fixed([True, True, True, True, True, True])
########################################################################
# Link model parameterisations together into a parameterisation of the #
# prediction equation #
########################################################################
# pred_param = XYPhiPredictionParameterisation(experiments,
# [det_param], [s0_param], [xlo_param], [xluc_param])
################################
# Apply known parameter shifts #
################################
# shift detector by 1.0 mm each translation and 2 mrad each rotation
det_p_vals = det_param.get_param_vals()
p_vals = [
a + b for a, b in zip(det_p_vals, [1.0, 1.0, 1.0, 2.0, 2.0, 2.0])
]
det_param.set_param_vals(p_vals)
# shift beam by 2 mrad in free axis
s0_p_vals = s0_param.get_param_vals()
p_vals = list(s0_p_vals)
p_vals[0] += 2.0
s0_param.set_param_vals(p_vals)
# rotate crystal a bit (=2 mrad each rotation)
xlo_p_vals = []
for xlo in (xl1o_param, xl2o_param):
p_vals = xlo.get_param_vals()
xlo_p_vals.append(p_vals)
new_p_vals = [a + b for a, b in zip(p_vals, [2.0, 2.0, 2.0])]
xlo.set_param_vals(new_p_vals)
# change unit cell a bit (=0.1 Angstrom length upsets, 0.1 degree of
# gamma angle)
xluc_p_vals = []
for xluc, xl in ((xl1uc_param, crystal1), ((xl2uc_param, crystal2))):
p_vals = xluc.get_param_vals()
xluc_p_vals.append(p_vals)
cell_params = xl.get_unit_cell().parameters()
cell_params = [
a + b for a, b in zip(cell_params, [0.1, 0.1, 0.1, 0.0, 0.0, 0.1])
]
new_uc = unit_cell(cell_params)
newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
S = symmetrize_reduce_enlarge(xl.get_space_group())
S.set_orientation(orientation=newB)
X = tuple([e * 1.0e5 for e in S.forward_independent_parameters()])
xluc.set_param_vals(X)
#############################
# Generate some reflections #
#############################
# print "Reflections will be generated with the following geometry:"
# print mybeam
# print mydetector
# print crystal1
# print crystal2
# All indices in a 2.0 Angstrom sphere for crystal1
resolution = 2.0
index_generator = IndexGenerator(
crystal1.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices1 = index_generator.to_array()
# All indices in a 2.0 Angstrom sphere for crystal2
resolution = 2.0
index_generator = IndexGenerator(
crystal2.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices2 = index_generator.to_array()
# Predict rays within the sequence range. Set experiment IDs
ray_predictor = ScansRayPredictor(experiments, sequence_range)
obs_refs1 = ray_predictor(indices1, experiment_id=0)
obs_refs1["id"] = flex.int(len(obs_refs1), 0)
obs_refs2 = ray_predictor(indices2, experiment_id=1)
obs_refs2["id"] = flex.int(len(obs_refs2), 1)
# Take only those rays that intersect the detector
intersects = ray_intersection(mydetector, obs_refs1)
obs_refs1 = obs_refs1.select(intersects)
intersects = ray_intersection(mydetector, obs_refs2)
obs_refs2 = obs_refs2.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs1 = ref_predictor(obs_refs1)
obs_refs2 = ref_predictor(obs_refs2)
# Set 'observed' centroids from the predicted ones
obs_refs1["xyzobs.mm.value"] = obs_refs1["xyzcal.mm"]
obs_refs2["xyzobs.mm.value"] = obs_refs2["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs1), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs1), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs1), (im_width / 2.0)**2)
obs_refs1["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
var_x = flex.double(len(obs_refs2), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs2), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs2), (im_width / 2.0)**2)
obs_refs2["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
# print "Total number of reflections excited for crystal1", len(obs_refs1)
# print "Total number of reflections excited for crystal2", len(obs_refs2)
# concatenate reflection lists
obs_refs1.extend(obs_refs2)
obs_refs = obs_refs1
###############################
# Undo known parameter shifts #
###############################
s0_param.set_param_vals(s0_p_vals)
det_param.set_param_vals(det_p_vals)
xl1o_param.set_param_vals(xlo_p_vals[0])
xl2o_param.set_param_vals(xlo_p_vals[1])
xl1uc_param.set_param_vals(xluc_p_vals[0])
xl2uc_param.set_param_vals(xluc_p_vals[1])
# print "Initial values of parameters are"
# msg = "Parameters: " + "%.5f " * len(pred_param)
# print msg % tuple(pred_param.get_param_vals())
# print
# make a refiner
from dials.algorithms.refinement.refiner import phil_scope
params = phil_scope.fetch(source=parse("")).extract()
# in case we want a plot
params.refinement.refinery.journal.track_parameter_correlation = True
# scan static first
from dials.algorithms.refinement.refiner import RefinerFactory
refiner = RefinerFactory.from_parameters_data_experiments(
params, obs_refs, experiments)
refiner.run()
# scan varying
params.refinement.parameterisation.scan_varying = True
refiner = RefinerFactory.from_parameters_data_experiments(
params, obs_refs, experiments)
refiner.run()
# Ensure all models have scan-varying state set
# (https://github.com/dials/dials/issues/798)
refined_experiments = refiner.get_experiments()
sp = [xl.get_num_scan_points() for xl in refined_experiments.crystals()]
assert sp.count(1801) == 2
def init_test():
models = setup_geometry.Extract(master_phil)
single_panel_detector = models.detector
gonio = models.goniometer
crystal = models.crystal
beam = models.beam
# Make a 3x3 multi panel detector filling the same space as the existing
# single panel detector. Each panel of the multi-panel detector has pixels
# with 1/3 the length dimensions of the single panel.
multi_panel_detector = Detector()
for x in range(3):
for y in range(3):
new_panel = make_panel_in_array((x, y), single_panel_detector[0])
multi_panel_detector.add_panel(new_panel)
# Build a mock scan for a 180 degree sequence
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 ExperimentLists
experiments_single_panel = ExperimentList()
experiments_multi_panel = ExperimentList()
experiments_single_panel.append(
Experiment(
beam=beam,
detector=single_panel_detector,
goniometer=gonio,
scan=scan,
crystal=crystal,
imageset=None,
)
)
experiments_multi_panel.append(
Experiment(
beam=beam,
detector=multi_panel_detector,
goniometer=gonio,
scan=scan,
crystal=crystal,
imageset=None,
)
)
# Generate some reflections
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
crystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# for the reflection predictor, it doesn't matter which experiment list is
# passed, as the detector is not used
ref_predictor = ScansRayPredictor(
experiments_single_panel, scan.get_oscillation_range(deg=False)
)
# get two sets of identical reflections
obs_refs_single = ref_predictor(indices)
obs_refs_multi = ref_predictor(indices)
for r1, r2 in zip(obs_refs_single.rows(), obs_refs_multi.rows()):
assert r1["s1"] == r2["s1"]
# get the panel intersections
sel = ray_intersection(single_panel_detector, obs_refs_single)
obs_refs_single = obs_refs_single.select(sel)
sel = ray_intersection(multi_panel_detector, obs_refs_multi)
obs_refs_multi = obs_refs_multi.select(sel)
assert len(obs_refs_single) == len(obs_refs_multi)
# Set 'observed' centroids from the predicted ones
obs_refs_single["xyzobs.mm.value"] = obs_refs_single["xyzcal.mm"]
obs_refs_multi["xyzobs.mm.value"] = obs_refs_multi["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = single_panel_detector[0].get_pixel_size()
var_x = flex.double(len(obs_refs_single), (px_size[0] / 2.0) ** 2)
var_y = flex.double(len(obs_refs_single), (px_size[1] / 2.0) ** 2)
var_phi = flex.double(len(obs_refs_single), (im_width / 2.0) ** 2)
# set the variances and frame numbers
obs_refs_single["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
obs_refs_multi["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
# Add in flags and ID columns by copying into standard reflection tables
tmp = flex.reflection_table.empty_standard(len(obs_refs_single))
tmp.update(obs_refs_single)
obs_refs_single = tmp
tmp = flex.reflection_table.empty_standard(len(obs_refs_multi))
tmp.update(obs_refs_multi)
obs_refs_multi = tmp
test_data = namedtuple(
"test_data",
[
"experiments_single_panel",
"experiments_multi_panel",
"observations_single_panel",
"observations_multi_panel",
],
)
return test_data(
experiments_single_panel,
experiments_multi_panel,
obs_refs_single,
obs_refs_multi,
)
def test(args=[]):
# Python and cctbx imports
from math import pi
import random
from scitbx import matrix
from scitbx.array_family import flex
from libtbx.phil import parse
from libtbx.test_utils import approx_equal
# Experimental model builder
from dials.test.algorithms.refinement.setup_geometry import Extract
# We will set up a mock scan and a mock experiment list
from dxtbx.model import ScanFactory
from dxtbx.model.experiment_list import ExperimentList, Experiment
# Model parameterisations
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationSinglePanel, )
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation, )
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationParameterisation,
CrystalUnitCellParameterisation,
)
# Reflection prediction
from dials.algorithms.spot_prediction import IndexGenerator, ray_intersection
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansRayPredictor,
ScansExperimentsPredictor,
)
from cctbx.sgtbx import space_group, space_group_symbols
# Parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.prediction_parameters import (
XYPhiPredictionParameterisation, )
# Imports for the target function
from dials.algorithms.refinement.target import (
LeastSquaresPositionalResidualWithRmsdCutoff, )
from dials.algorithms.refinement.reflection_manager import ReflectionManager
# Local functions
def random_direction_close_to(vector, sd=0.5):
return vector.rotate_around_origin(
matrix.col((random.random(), random.random(),
random.random())).normalize(),
random.gauss(0, sd),
deg=True,
)
#############################
# Setup experimental models #
#############################
# make a small cell to speed up calculations
overrides = """geometry.parameters.crystal.a.length.range = 10 15
geometry.parameters.crystal.b.length.range = 10 15
geometry.parameters.crystal.c.length.range = 10 15"""
master_phil = parse(
"""
include scope dials.test.algorithms.refinement.geometry_phil
""",
process_includes=True,
)
models = Extract(master_phil, overrides, cmdline_args=args)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
# Build a mock scan for a 180 degree sweep of 0.1 degree images
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(1800)),
deg=True,
)
sweep_range = myscan.get_oscillation_range(deg=False)
im_width = myscan.get_oscillation(deg=False)[1]
assert sweep_range == (0.0, pi)
assert approx_equal(im_width, 0.1 * pi / 180.0)
experiments = ExperimentList()
experiments.append(
Experiment(
beam=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
))
###########################
# Parameterise the models #
###########################
det_param = DetectorParameterisationSinglePanel(mydetector)
s0_param = BeamParameterisation(mybeam, mygonio)
xlo_param = CrystalOrientationParameterisation(mycrystal)
xluc_param = CrystalUnitCellParameterisation(mycrystal)
########################################################################
# Link model parameterisations together into a parameterisation of the #
# prediction equation #
########################################################################
pred_param = XYPhiPredictionParameterisation(experiments, [det_param],
[s0_param], [xlo_param],
[xluc_param])
################################
# Apply known parameter shifts #
################################
# shift detector by 0.2 mm each translation and 2 mrad each rotation
det_p_vals = det_param.get_param_vals()
p_vals = [
a + b for a, b in zip(det_p_vals, [2.0, 2.0, 2.0, 2.0, 2.0, 2.0])
]
det_param.set_param_vals(p_vals)
# shift beam by 2 mrad in one axis
s0_p_vals = s0_param.get_param_vals()
p_vals = list(s0_p_vals)
p_vals[1] += 2.0
s0_param.set_param_vals(p_vals)
# rotate crystal a bit (=2 mrad each rotation)
xlo_p_vals = xlo_param.get_param_vals()
p_vals = [a + b for a, b in zip(xlo_p_vals, [2.0, 2.0, 2.0])]
xlo_param.set_param_vals(p_vals)
#############################
# Generate some reflections #
#############################
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Predict rays within the sweep range
ray_predictor = ScansRayPredictor(experiments, sweep_range)
obs_refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(mydetector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0)**2)
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
###############################
# Undo known parameter shifts #
###############################
s0_param.set_param_vals(s0_p_vals)
det_param.set_param_vals(det_p_vals)
xlo_param.set_param_vals(xlo_p_vals)
#####################################
# Select reflections for refinement #
#####################################
refman = ReflectionManager(obs_refs, experiments)
##############################
# Set up the target function #
##############################
# Redefine the reflection predictor to use the type expected by the Target class
ref_predictor = ScansExperimentsPredictor(experiments)
mytarget = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments,
ref_predictor,
refman,
pred_param,
restraints_parameterisation=None)
# get the functional and gradients
mytarget.predict()
L, dL_dp, curvs = mytarget.compute_functional_gradients_and_curvatures()
####################################
# Do FD calculation for comparison #
####################################
# function for calculating finite difference gradients of the target function
def get_fd_gradients(target, pred_param, deltas):
"""Calculate centered finite difference gradients for each of the
parameters of the target function.
"deltas" must be a sequence of the same length as the parameter list, and
contains the step size for the difference calculations for each parameter.
"""
p_vals = pred_param.get_param_vals()
assert len(deltas) == len(p_vals)
fd_grad = []
fd_curvs = []
for i in range(len(deltas)):
val = p_vals[i]
p_vals[i] -= deltas[i] / 2.0
pred_param.set_param_vals(p_vals)
target.predict()
rev_state = target.compute_functional_gradients_and_curvatures()
p_vals[i] += deltas[i]
pred_param.set_param_vals(p_vals)
target.predict()
fwd_state = target.compute_functional_gradients_and_curvatures()
# finite difference estimation of first derivatives
fd_grad.append((fwd_state[0] - rev_state[0]) / deltas[i])
# finite difference estimation of curvatures, using the analytical
# first derivatives
fd_curvs.append((fwd_state[1][i] - rev_state[1][i]) / deltas[i])
# set parameter back to centred value
p_vals[i] = val
# return to the initial state
pred_param.set_param_vals(p_vals)
return fd_grad, fd_curvs
# test normalised differences between FD and analytical calculations
fdgrads = get_fd_gradients(mytarget, pred_param,
[1.0e-7] * len(pred_param))
diffs = [a - b for a, b in zip(dL_dp, fdgrads[0])]
norm_diffs = tuple([a / b for a, b in zip(diffs, fdgrads[0])])
for e in norm_diffs:
assert abs(e) < 0.001 # check differences less than 0.1%
# test normalised differences between FD curvatures and analytical least
# squares approximation. We don't expect this to be especially close
if curvs:
diffs = [a - b for a, b in zip(curvs, fdgrads[1])]
norm_diffs = tuple([a / b for a, b in zip(diffs, fdgrads[1])])
for e in norm_diffs:
assert abs(e) < 0.1 # check differences less than 10%
def test():
from cctbx.sgtbx import space_group, space_group_symbols
from dxtbx.model.experiment_list import Experiment, ExperimentList
from libtbx.phil import parse
from scitbx.array_family import flex
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation, )
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationParameterisation,
CrystalUnitCellParameterisation,
)
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationSinglePanel, )
from dials.algorithms.refinement.parameterisation.goniometer_parameters import (
GoniometerParameterisation, )
#### Import model parameterisations
from dials.algorithms.refinement.parameterisation.prediction_parameters import (
XYPhiPredictionParameterisation, )
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansExperimentsPredictor,
ScansRayPredictor,
)
##### Imports for reflection prediction
from dials.algorithms.spot_prediction import IndexGenerator, ray_intersection
##### Import model builder
from dials.tests.algorithms.refinement.setup_geometry import Extract
#### Create models
overrides = """geometry.parameters.crystal.a.length.range = 10 50
geometry.parameters.crystal.b.length.range = 10 50
geometry.parameters.crystal.c.length.range = 10 50"""
master_phil = parse(
"""
include scope dials.tests.algorithms.refinement.geometry_phil
""",
process_includes=True,
)
models = Extract(master_phil, overrides)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
# Build a mock scan for a 72 degree sequence
sequence_range = (0.0, math.pi / 5.0)
from dxtbx.model import ScanFactory
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 720),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(720)),
deg=True,
)
#### Create parameterisations of these models
det_param = DetectorParameterisationSinglePanel(mydetector)
s0_param = BeamParameterisation(mybeam, mygonio)
xlo_param = CrystalOrientationParameterisation(mycrystal)
xluc_param = CrystalUnitCellParameterisation(mycrystal)
gon_param = GoniometerParameterisation(mygonio, mybeam)
# Create an ExperimentList
experiments = ExperimentList()
experiments.append(
Experiment(
beam=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
))
#### Unit tests
# Build a prediction parameterisation
pred_param = XYPhiPredictionParameterisation(
experiments,
detector_parameterisations=[det_param],
beam_parameterisations=[s0_param],
xl_orientation_parameterisations=[xlo_param],
xl_unit_cell_parameterisations=[xluc_param],
goniometer_parameterisations=[gon_param],
)
# Generate reflections
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Predict rays within the sequence range
ray_predictor = ScansRayPredictor(experiments, sequence_range)
obs_refs = ray_predictor(indices)
# Take only those rays that intersect the detector
intersects = ray_intersection(mydetector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * math.pi / 180.0
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0)**2)
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
# use a ReflectionManager to exclude reflections too close to the spindle
from dials.algorithms.refinement.reflection_manager import ReflectionManager
refman = ReflectionManager(obs_refs, experiments, outlier_detector=None)
refman.finalise()
# Redefine the reflection predictor to use the type expected by the Target class
ref_predictor = ScansExperimentsPredictor(experiments)
# keep only those reflections that pass inclusion criteria and have predictions
reflections = refman.get_matches()
# get analytical gradients
an_grads = pred_param.get_gradients(reflections)
# get finite difference gradients
p_vals = pred_param.get_param_vals()
deltas = [1.0e-7] * len(p_vals)
for i, delta in enumerate(deltas):
val = p_vals[i]
p_vals[i] -= delta / 2.0
pred_param.set_param_vals(p_vals)
ref_predictor(reflections)
rev_state = reflections["xyzcal.mm"].deep_copy()
p_vals[i] += delta
pred_param.set_param_vals(p_vals)
ref_predictor(reflections)
fwd_state = reflections["xyzcal.mm"].deep_copy()
p_vals[i] = val
fd = fwd_state - rev_state
x_grads, y_grads, phi_grads = fd.parts()
x_grads /= delta
y_grads /= delta
phi_grads /= delta
# compare with analytical calculation
assert x_grads == pytest.approx(an_grads[i]["dX_dp"], abs=5.0e-6)
assert y_grads == pytest.approx(an_grads[i]["dY_dp"], abs=5.5e-6)
assert phi_grads == pytest.approx(an_grads[i]["dphi_dp"], abs=5.0e-6)
# return to the initial state
pred_param.set_param_vals(p_vals)
def test(args=[]):
from math import pi
from cctbx.sgtbx import space_group, space_group_symbols
# Symmetry constrained parameterisation for the unit cell
from cctbx.uctbx import unit_cell
# We will set up a mock scan and a mock experiment list
from dxtbx.model import ScanFactory
from dxtbx.model.experiment_list import Experiment, ExperimentList
from libtbx.phil import parse
from libtbx.test_utils import approx_equal
from rstbx.symmetry.constraints.parameter_reduction import symmetrize_reduce_enlarge
from scitbx import matrix
from scitbx.array_family import flex
# Get modules to build models and minimiser using PHIL
import dials.tests.algorithms.refinement.setup_geometry as setup_geometry
import dials.tests.algorithms.refinement.setup_minimiser as setup_minimiser
from dials.algorithms.refinement.parameterisation.beam_parameters import (
BeamParameterisation,
)
from dials.algorithms.refinement.parameterisation.crystal_parameters import (
CrystalOrientationParameterisation,
CrystalUnitCellParameterisation,
)
# Model parameterisations
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationSinglePanel,
)
# Parameterisation of the prediction equation
from dials.algorithms.refinement.parameterisation.prediction_parameters import (
XYPhiPredictionParameterisation,
)
from dials.algorithms.refinement.prediction.managed_predictors import (
ScansExperimentsPredictor,
ScansRayPredictor,
)
from dials.algorithms.refinement.reflection_manager import ReflectionManager
# Imports for the target function
from dials.algorithms.refinement.target import (
LeastSquaresPositionalResidualWithRmsdCutoff,
)
# Reflection prediction
from dials.algorithms.spot_prediction import IndexGenerator, ray_intersection
#############################
# Setup experimental models #
#############################
master_phil = parse(
"""
include scope dials.tests.algorithms.refinement.geometry_phil
include scope dials.tests.algorithms.refinement.minimiser_phil
""",
process_includes=True,
)
models = setup_geometry.Extract(master_phil, cmdline_args=args)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
# Build a mock scan for a 180 degree sequence
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=list(range(1800)),
deg=True,
)
sequence_range = myscan.get_oscillation_range(deg=False)
im_width = myscan.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=mybeam,
detector=mydetector,
goniometer=mygonio,
scan=myscan,
crystal=mycrystal,
imageset=None,
)
)
###########################
# Parameterise the models #
###########################
det_param = DetectorParameterisationSinglePanel(mydetector)
s0_param = BeamParameterisation(mybeam, mygonio)
xlo_param = CrystalOrientationParameterisation(mycrystal)
xluc_param = CrystalUnitCellParameterisation(mycrystal)
# Fix beam to the X-Z plane (imgCIF geometry), fix wavelength
s0_param.set_fixed([True, False, True])
# Fix crystal parameters
# xluc_param.set_fixed([True, True, True, True, True, True])
########################################################################
# Link model parameterisations together into a parameterisation of the #
# prediction equation #
########################################################################
pred_param = XYPhiPredictionParameterisation(
experiments, [det_param], [s0_param], [xlo_param], [xluc_param]
)
################################
# Apply known parameter shifts #
################################
# shift detector by 1.0 mm each translation and 2 mrad each rotation
det_p_vals = det_param.get_param_vals()
p_vals = [a + b for a, b in zip(det_p_vals, [1.0, 1.0, 1.0, 2.0, 2.0, 2.0])]
det_param.set_param_vals(p_vals)
# shift beam by 2 mrad in free axis
s0_p_vals = s0_param.get_param_vals()
p_vals = list(s0_p_vals)
p_vals[0] += 2.0
s0_param.set_param_vals(p_vals)
# rotate crystal a bit (=2 mrad each rotation)
xlo_p_vals = xlo_param.get_param_vals()
p_vals = [a + b for a, b in zip(xlo_p_vals, [2.0, 2.0, 2.0])]
xlo_param.set_param_vals(p_vals)
# change unit cell a bit (=0.1 Angstrom length upsets, 0.1 degree of
# gamma angle)
xluc_p_vals = xluc_param.get_param_vals()
cell_params = mycrystal.get_unit_cell().parameters()
cell_params = [a + b for a, b in zip(cell_params, [0.1, 0.1, 0.1, 0.0, 0.0, 0.1])]
new_uc = unit_cell(cell_params)
newB = matrix.sqr(new_uc.fractionalization_matrix()).transpose()
S = symmetrize_reduce_enlarge(mycrystal.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)
#############################
# Generate some reflections #
#############################
print("Reflections will be generated with the following geometry:")
print(mybeam)
print(mydetector)
print(mycrystal)
print("Target values of parameters are")
msg = "Parameters: " + "%.5f " * len(pred_param)
print(msg % tuple(pred_param.get_param_vals()))
print()
# All indices in a 2.0 Angstrom sphere
resolution = 2.0
index_generator = IndexGenerator(
mycrystal.get_unit_cell(),
space_group(space_group_symbols(1).hall()).type(),
resolution,
)
indices = index_generator.to_array()
# Predict rays within the sequence range
ray_predictor = ScansRayPredictor(experiments, sequence_range)
obs_refs = ray_predictor(indices)
print("Total number of reflections excited", len(obs_refs))
# Take only those rays that intersect the detector
intersects = ray_intersection(mydetector, obs_refs)
obs_refs = obs_refs.select(intersects)
# Make a reflection predictor and re-predict for all these reflections. The
# result is the same, but we gain also the flags and xyzcal.px columns
ref_predictor = ScansExperimentsPredictor(experiments)
obs_refs["id"] = flex.int(len(obs_refs), 0)
obs_refs = ref_predictor(obs_refs)
# Set 'observed' centroids from the predicted ones
obs_refs["xyzobs.mm.value"] = obs_refs["xyzcal.mm"]
# Invent some variances for the centroid positions of the simulated data
im_width = 0.1 * pi / 180.0
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.0) ** 2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.0) ** 2)
var_phi = flex.double(len(obs_refs), (im_width / 2.0) ** 2)
obs_refs["xyzobs.mm.variance"] = flex.vec3_double(var_x, var_y, var_phi)
print("Total number of observations made", len(obs_refs))
###############################
# Undo known parameter shifts #
###############################
s0_param.set_param_vals(s0_p_vals)
det_param.set_param_vals(det_p_vals)
xlo_param.set_param_vals(xlo_p_vals)
xluc_param.set_param_vals(xluc_p_vals)
print("Initial values of parameters are")
msg = "Parameters: " + "%.5f " * len(pred_param)
print(msg % tuple(pred_param.get_param_vals()))
print()
#####################################
# Select reflections for refinement #
#####################################
refman = ReflectionManager(obs_refs, experiments)
##############################
# Set up the target function #
##############################
# The current 'achieved' criterion compares RMSD against 1/3 the pixel size and
# 1/3 the image width in radians. For the simulated data, these are just made up
mytarget = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments, ref_predictor, refman, pred_param, restraints_parameterisation=None
)
################################
# Set up the refinement engine #
################################
refiner = setup_minimiser.Extract(
master_phil, mytarget, pred_param, cmdline_args=args
).refiner
print("Prior to refinement the experimental model is:")
print(mybeam)
print(mydetector)
print(mycrystal)
refiner.run()
print()
print("Refinement has completed with the following geometry:")
print(mybeam)
print(mydetector)
print(mycrystal)
