def test_scan_margin(dials_data):
# Use 4 scan data for this test
data_dir = dials_data("l_cysteine_dials_output")
experiments = ExperimentListFactory.from_json_file(
(data_dir / "indexed.expt").strpath, check_format=False)
reflections = flex.reflection_table.from_file(
(data_dir / "indexed.refl").strpath)
orig_phi = reflections["xyzobs.mm.value"].parts()[2]
# Reflection Manager works on predictions, but this dataset has none, so
# need to set the predictions flag
reflections.set_flags(flex.bool(len(reflections), True),
reflections.flags.predicted)
# Create a reflection manager without trimming scan margins
refman = ReflectionManager(reflections, experiments)
refman.finalise()
refs1 = refman.get_matches()
phi1 = refs1["xyzobs.mm.value"].parts()[2]
# Create a reflection manager with 1 degree width scan margins
margin = 1.0
refman2 = ReflectionManager(reflections, experiments, scan_margin=margin)
refman2.finalise()
refs2 = refman2.get_matches()
phi2 = refs2["xyzobs.mm.value"].parts()[2]
# Check zero scan margins do not trim
assert min(orig_phi) == min(phi1)
assert max(orig_phi) == max(phi1)
# Check 1 degree scan margin trims approximately 1 degree
assert min(phi2) == pytest.approx(min(phi1) + math.radians(margin),
abs=1e-3)
assert max(phi2) == pytest.approx(max(phi1) - math.radians(margin),
abs=1e-3)
###############################
# 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 '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.
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.)**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)
# Redefine the reflection predictor to use the type expected by the Target class
ref_predictor = ExperimentsPredictor(experiments)
# make a target to ensure reflections are predicted and refman is finalised
from dials.algorithms.refinement.target import \
LeastSquaresPositionalResidualWithRmsdCutoff
target = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments,
ref_predictor,
refman,
pred_param,
restraints_parameterisation=None)
def test(cmdline_overrides=[]):
tc = _Test()
tc.create_models(cmdline_overrides)
reflections = tc.generate_reflections()
# use a ReflectionManager to exclude reflections too close to the spindle,
# plus set the frame numbers
from dials.algorithms.refinement.reflection_manager import ReflectionManager
refman = ReflectionManager(reflections, tc.experiments, outlier_detector=None)
refman.finalise()
# create prediction parameterisation of the requested type
pred_param = ScanVaryingPredictionParameterisation(
tc.experiments,
[tc.det_param],
[tc.s0_param],
[tc.xlo_param],
[tc.xluc_param],
[tc.gon_param],
)
# keep only those reflections that pass inclusion criteria and have predictions
reflections = refman.get_matches()
# get analytical gradients
pred_param.compose(reflections)
an_grads = pred_param.get_gradients(reflections)
# get finite difference gradients
p_vals = pred_param.get_param_vals()
p_names = pred_param.get_param_names()
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)
pred_param.compose(reflections)
tc.ref_predictor(reflections)
rev_state = reflections["xyzcal.mm"].deep_copy()
p_vals[i] += delta
pred_param.set_param_vals(p_vals)
pred_param.compose(reflections)
tc.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
try:
for (a, b) in zip(x_grads, an_grads[i]["dX_dp"]):
assert a == pytest.approx(b, abs=1e-5)
for (a, b) in zip(y_grads, an_grads[i]["dY_dp"]):
assert a == pytest.approx(b, abs=1e-5)
for (a, b) in zip(phi_grads, an_grads[i]["dphi_dp"]):
assert a == pytest.approx(b, abs=1e-5)
except AssertionError:
print("Failure for {}".format(p_names[i]))
raise
# return to the initial state
pred_param.set_param_vals(p_vals)
pred_param.compose(reflections)
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.
px_size = mydetector[0].get_pixel_size()
var_x = flex.double(len(obs_refs), (px_size[0] / 2.)**2)
var_y = flex.double(len(obs_refs), (px_size[1] / 2.)**2)
var_phi = flex.double(len(obs_refs), (im_width / 2.)**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)
# Redefine the reflection predictor to use the type expected by the Target class
ref_predictor = ExperimentsPredictor(experiments)
# make a target to ensure reflections are predicted and refman is finalised
from dials.algorithms.refinement.target import \
LeastSquaresPositionalResidualWithRmsdCutoff
target = LeastSquaresPositionalResidualWithRmsdCutoff(experiments,
ref_predictor, refman, pred_param, restraints_parameterisation=None)
# 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)
def test1():
dials_regression = libtbx.env.find_in_repositories(
relative_path="dials_regression", test=os.path.isdir)
# use a datablock that contains a CS-PAD detector description
data_dir = os.path.join(dials_regression, "refinement_test_data",
"hierarchy_test")
datablock_path = os.path.join(data_dir, "datablock.json")
assert os.path.exists(datablock_path)
# load models
from dxtbx.datablock import DataBlockFactory
datablock = DataBlockFactory.from_serialized_format(datablock_path,
check_format=False)
im_set = datablock[0].extract_imagesets()[0]
from copy import deepcopy
detector = 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., 40., 0.), (0., 0., 40.),
space_group_symbol="P1")
from dxtbx.model import GoniometerFactory
goniometer = GoniometerFactory.known_axis((1., 0., 0.))
# Build a mock scan for a 180 degree sweep
from dxtbx.model import ScanFactory
sf = ScanFactory()
scan = sf.make_scan(image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=range(1800),
deg=True)
sweep_range = scan.get_oscillation_range(deg=False)
im_width = scan.get_oscillation(deg=False)[1]
assert sweep_range == (0., pi)
assert approx_equal(im_width, 0.1 * pi / 180.)
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 \
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,
verbosity=0,
max_iterations=20)
# Refiner
from dials.algorithms.refinement.refiner import Refiner
refiner = Refiner(reflections=refs,
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
verbosity=0)
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
import math
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 approx_equal(math.fabs(o1.length() - o2.length()) / o1.length(),
0,
eps=1e-5)
# ...the angle between them
assert approx_equal(o1.accute_angle(o2), 0, eps=1e-5)
print "OK"
return
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))
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)
def test(init_test):
single_panel_detector = init_test.experiments_single_panel.detectors()[0]
multi_panel_detector = init_test.experiments_multi_panel.detectors()[0]
beam = init_test.experiments_single_panel.beams()[0]
gonio = init_test.experiments_single_panel.goniometers()[0]
crystal = init_test.experiments_single_panel.crystals()[0]
# Parameterise the models
det_param = DetectorParameterisationSinglePanel(single_panel_detector)
s0_param = BeamParameterisation(beam, gonio)
xlo_param = CrystalOrientationParameterisation(crystal)
xluc_param = CrystalUnitCellParameterisation(crystal)
multi_det_param = DetectorParameterisationMultiPanel(multi_panel_detector, beam)
# 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, first for the single panel detector
pred_param = XYPhiPredictionParameterisation(
init_test.experiments_single_panel,
[det_param],
[s0_param],
[xlo_param],
[xluc_param],
)
# ... and now for the multi-panel detector
pred_param2 = XYPhiPredictionParameterisation(
init_test.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 = crystal.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(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)
###############################
# 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(
init_test.observations_single_panel, init_test.experiments_single_panel
)
refman2 = ReflectionManager(
init_test.observations_multi_panel, init_test.experiments_multi_panel
)
###############################
# Set up the target functions #
###############################
target = LeastSquaresPositionalResidualWithRmsdCutoff(
init_test.experiments_single_panel,
ScansExperimentsPredictor(init_test.experiments_single_panel),
refman,
pred_param,
restraints_parameterisation=None,
)
target2 = LeastSquaresPositionalResidualWithRmsdCutoff(
init_test.experiments_multi_panel,
ScansExperimentsPredictor(init_test.experiments_multi_panel),
refman2,
pred_param2,
restraints_parameterisation=None,
)
#################################
# Set up the refinement engines #
#################################
refiner = setup_minimiser.Extract(master_phil, target, pred_param).refiner
refiner2 = setup_minimiser.Extract(master_phil, target2, pred_param2).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)
###############################
# 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, ExperimentsPredictor(experiments_single_panel),
refman, pred_param, restraints_parameterisation=None)
mytarget2 = LeastSquaresPositionalResidualWithRmsdCutoff(
experiments_multi_panel, ExperimentsPredictor(experiments_multi_panel),
refman2, pred_param2, restraints_parameterisation=None)
#################################
# Set up the refinement engines #
def __call__(self, cmdline_overrides):
self.create_models(cmdline_overrides)
reflections = self.generate_reflections()
# use a ReflectionManager to exclude reflections too close to the spindle,
# plus set the frame numbers
from dials.algorithms.refinement.reflection_manager import ReflectionManager
refman = ReflectionManager(reflections, self.experiments,
outlier_detector=None)
# create prediction parameterisation of the requested type
pred_param = self._pred_param_type(self.experiments, [self.det_param],
[self.s0_param], [self.xlo_param], [self.xluc_param])
# make a target to ensure reflections are predicted and refman is finalised
from dials.algorithms.refinement.target import \
LeastSquaresPositionalResidualWithRmsdCutoff
target = LeastSquaresPositionalResidualWithRmsdCutoff(self.experiments,
self.ref_predictor, refman, pred_param, restraints_parameterisation=None)
# keep only those reflections that pass inclusion criteria and have predictions
reflections = refman.get_matches()
# get analytical gradients
pred_param.compose(reflections)
an_grads = pred_param.get_gradients(reflections)
# get finite difference gradients
p_vals = pred_param.get_param_vals()
p_names = pred_param.get_param_names()
deltas = [1.e-7] * len(p_vals)
for i in range(len(deltas)):
val = p_vals[i]
p_vals[i] -= deltas[i] / 2.
pred_param.set_param_vals(p_vals)
pred_param.compose(reflections)
self.ref_predictor(reflections)
rev_state = reflections['xyzcal.mm'].deep_copy()
p_vals[i] += deltas[i]
pred_param.set_param_vals(p_vals)
pred_param.compose(reflections)
self.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 /= deltas[i]
y_grads /= deltas[i]
phi_grads /= deltas[i]
try:
for n, (a,b) in enumerate(zip(x_grads, an_grads[i]["dX_dp"])):
assert approx_equal(a, b, eps=1.e-6)
for n, (a,b) in enumerate(zip(y_grads, an_grads[i]["dY_dp"])):
assert approx_equal(a, b, eps=1.e-6)
for n, (a,b) in enumerate(zip(phi_grads, an_grads[i]["dphi_dp"])):
assert approx_equal(a, b, eps=1.e-6)
except AssertionError:
print "Failure for {0}".format(p_names[i])
# return to the initial state
pred_param.set_param_vals(p_vals)
pred_param.compose(reflections)
print "OK"
return
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)
