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Source code for dials.algorithms.refinement.target_stills
#
# Copyright (C) (2014) STFC Rutherford Appleton Laboratory, UK.
#
# Author: David Waterman.
#
# This code is distributed under the BSD license, a copy of which is
# included in the root directory of this package.
#
# python and cctbx imports
from __future__ import absolute_import, division
from __future__ import print_function
from math import pi, sqrt
from cctbx.array_family import flex
# dials imports
from dials.algorithms.refinement.target import Target, SparseGradientsMixin
# constants
TWO_PI = 2.0 * pi
[docs]class LeastSquaresStillsResidualWithRmsdCutoff(Target):
"""An implementation of the target class providing a least squares residual
in terms of detector impact position X, Y and minimum rotation to the Ewald
sphere, DeltaPsi. Terminates refinement on achieved rmsd (or on intrisic
convergence of the chosen minimiser)"""
_grad_names = ["dX_dp", "dY_dp", "dDeltaPsi_dp"]
rmsd_names = ["RMSD_X", "RMSD_Y", "RMSD_DeltaPsi"]
rmsd_units = ["mm", "mm", "rad"]
def __init__(
self,
experiments,
predictor,
reflection_manager,
prediction_parameterisation,
restraints_parameterisation,
frac_binsize_cutoff=0.33333,
absolute_cutoffs=None,
gradient_calculation_blocksize=None,
):
Target.__init__(
self,
experiments,
predictor,
reflection_manager,
prediction_parameterisation,
restraints_parameterisation,
gradient_calculation_blocksize,
)
# Set up the RMSD achieved criterion. For simplicity, we take models from
# the first Experiment only. If this is not appropriate for refinement over
# all experiments then absolute cutoffs should be used instead.
detector = experiments[0].detector
if not absolute_cutoffs:
pixel_sizes = [p.get_pixel_size() for p in detector]
min_px_size_x = min(e[0] for e in pixel_sizes)
min_px_size_y = min(e[1] for e in pixel_sizes)
self._binsize_cutoffs = [
min_px_size_x * frac_binsize_cutoff,
min_px_size_y * frac_binsize_cutoff,
]
else:
self._binsize_cutoffs = absolute_cutoffs[:2]
return
def _predict_core(self, reflections):
"""perform prediction for the specified reflections"""
# do prediction (updates reflection table in situ).
self._reflection_predictor(reflections)
x_obs, y_obs, _ = reflections["xyzobs.mm.value"].parts()
delpsi = reflections["delpsical.rad"]
x_calc, y_calc, _ = reflections["xyzcal.mm"].parts()
# calculate residuals and assign columns
reflections["x_resid"] = x_calc - x_obs
reflections["x_resid2"] = reflections["x_resid"] ** 2
reflections["y_resid"] = y_calc - y_obs
reflections["y_resid2"] = reflections["y_resid"] ** 2
reflections["delpsical2"] = reflections["delpsical.rad"] ** 2
return reflections
[docs] def predict_for_reflection_table(self, reflections, skip_derivatives=False):
"""perform prediction for all reflections in the supplied table"""
# Just predict. The other preparation is irrelevant for stills, as is
# skip_derivatives
return self._predict_core(reflections)
@staticmethod
def _extract_residuals_and_weights(matches):
# return residuals and weights as 1d flex.double vectors
residuals = flex.double.concatenate(matches["x_resid"], matches["y_resid"])
residuals.extend(matches["delpsical.rad"])
weights, w_y, _ = matches["xyzobs.mm.weights"].parts()
w_delpsi = matches["delpsical.weights"]
weights.extend(w_y)
weights.extend(w_delpsi)
return residuals, weights
@staticmethod
def _extract_squared_residuals(matches):
residuals2 = flex.double.concatenate(matches["x_resid2"], matches["y_resid2"])
residuals2.extend(matches["delpsical2"])
return residuals2
def _rmsds_core(self, reflections):
"""calculate unweighted RMSDs"""
resid_x = flex.sum(reflections["x_resid2"])
resid_y = flex.sum(reflections["y_resid2"])
resid_z = flex.sum(reflections["delpsical2"])
n = len(reflections)
rmsds = (sqrt(resid_x / n), sqrt(resid_y / n), sqrt(resid_z / n))
return rmsds
[docs] def achieved(self):
"""RMSD criterion for target achieved """
r = self._rmsds if self._rmsds else self.rmsds()
# reset cached rmsds to avoid getting out of step
self._rmsds = None
# only use RMSD_X and RMSD_Y
if r[0] < self._binsize_cutoffs[0] and r[1] < self._binsize_cutoffs[1]:
return True
return False
[docs]class LeastSquaresStillsResidualWithRmsdCutoffSparse(
SparseGradientsMixin, LeastSquaresStillsResidualWithRmsdCutoff
):
"""A version of the LeastSquaresStillsResidualWithRmsdCutoff Target that
uses a sparse matrix data structure for memory efficiency when there are a
large number of Experiments"""
pass
