def __init__(self, image_number, *args):
ScanVaryingCrystalOrientationParameterisation.__init__(self, *args)
# set overloads now, after construction of the base class
self.compose = self._compose
self.get_state = self._get_state
self.set_time_point(image_number)
def __init__(self, image_number, *args):
ScanVaryingCrystalOrientationParameterisation.__init__(self, *args)
# set overloads now, after construction of the base class
self.compose = self._compose
self.get_state = self._get_state
self.set_time_point(image_number)
def create_models(self, cmdline_overrides=None):
from dxtbx.model import ScanFactory
from libtbx.phil import parse
from dials.test.algorithms.refinement.setup_geometry import Extract
if cmdline_overrides is None:
cmdline_overrides = []
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.test.algorithms.refinement.geometry_phil
""",
process_includes=True,
)
# Extract models
models = Extract(master_phil,
overrides,
cmdline_args=cmdline_overrides)
self.detector = models.detector
self.goniometer = models.goniometer
self.crystal = models.crystal
self.beam = models.beam
# Make a scan of 1-20 * 0.5 deg images
sf = ScanFactory()
self.scan = sf.make_scan((1, 20), 0.5, (0, 0.5), list(range(20)))
# Generate an ExperimentList
self.experiments = ExperimentList()
self.experiments.append(
Experiment(
beam=self.beam,
detector=self.detector,
goniometer=self.goniometer,
scan=self.scan,
crystal=self.crystal,
imageset=None,
))
# Create a reflection predictor for the experiments
self.ref_predictor = ScansExperimentsPredictor(self.experiments)
# Create scan-varying parameterisations of these models, with 3 samples
self.det_param = ScanVaryingDetectorParameterisationSinglePanel(
self.detector, self.scan.get_array_range(), 3)
self.s0_param = ScanVaryingBeamParameterisation(
self.beam, self.scan.get_array_range(), 3, self.goniometer)
self.xlo_param = ScanVaryingCrystalOrientationParameterisation(
self.crystal, self.scan.get_array_range(), 3)
self.xluc_param = ScanVaryingCrystalUnitCellParameterisation(
self.crystal, self.scan.get_array_range(), 3)
self.gon_param = ScanVaryingGoniometerParameterisation(
self.goniometer, self.scan.get_array_range(), 3, self.beam)
def _get_state(self):
"""override for get_state to do so only at the requested t"""
# ensure the state is updated by re-composing
self.compose()
return ScanVaryingCrystalOrientationParameterisation.get_state(self)
def _compose(self):
"""override for compose to pass in the requested t"""
ScanVaryingCrystalOrientationParameterisation.compose(self,
self.image_number)
def _get_state(self):
"""override for get_state to do so only at the requested t"""
# ensure the state is updated by re-composing
self.compose()
return ScanVaryingCrystalOrientationParameterisation.get_state(self)
def _compose(self):
"""override for compose to pass in the requested t"""
ScanVaryingCrystalOrientationParameterisation.compose(
self, self.image_number)
def __init__(self, image_number, *args):
ScanVaryingCrystalOrientationParameterisation.__init__(self, *args)
self.set_time_point(image_number)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
# Make a scan of 1-360 * 0.5 deg images
sf = scan_factory()
myscan = sf.make_scan((1,360), 0.5, (0, 0.5), range(360))
# Create parameterisations of these models, with 5 samples for the
# scan-varying crystal parameterisations
det_param = DetectorParameterisationSinglePanel(mydetector)
s0_param = BeamParameterisation(mybeam, mygonio)
xlo_param = ScanVaryingCrystalOrientationParameterisation(
mycrystal, myscan.get_array_range(), 5)
xluc_param = ScanVaryingCrystalUnitCellParameterisation(
mycrystal, myscan.get_array_range(), 5)
#### Cause the crystal U and B to vary over the scan
# Vary orientation angles by ~1.0 mrad each checkpoint
p_vals = xlo_param.get_param_vals()
sigmas = [1.0] * len(p_vals)
new_vals = random_param_shift(p_vals, sigmas)
xlo_param.set_param_vals(new_vals)
# Vary unit cell parameters, on order of 1% of the initial metrical
# matrix parameters
p_vals = xluc_param.get_param_vals()
sigmas = [0.01 * p for p in p_vals]
