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Source code for dials.algorithms.refinement.target
"""Contains classes used to construct a target function for refinement,
principally Target and ReflectionManager."""
# python and cctbx imports
from __future__ import absolute_import, division, print_function
import abc
import math
from scitbx.array_family import flex
from scitbx import sparse
# PHIL
from libtbx.phil import parse
phil_str = """
rmsd_cutoff = *fraction_of_bin_size absolute
.help = "Method to choose rmsd cutoffs. This is currently either as a"
"fraction of the discrete units of the spot positional data, i.e."
"(pixel width, pixel height, image thickness in phi), or a tuple"
"of absolute values to use as the cutoffs"
.type = choice
bin_size_fraction = 0.0
.help = "Set this to a fractional value, say 0.2, to make a cut off in"
"the natural discrete units of positional data, viz.,"
"(pixel width, pixel height, image thickness in phi). This would"
"then determine when the RMSD target is achieved. Only used if"
"rmsd_cutoff = fraction_of_bin_size."
.type = float(value_min=0.)
absolute_cutoffs = None
.help = "Absolute Values for the RMSD target achieved cutoffs in X, Y and"
"Phi. The units are (mm, mm, rad)."
.type = floats(size=3, value_min=0.)
gradient_calculation_blocksize = None
.help = "Maximum number of reflections to use for gradient calculation."
"If there are more reflections than this in the manager then"
"the minimiser must do the full calculation in blocks."
.type = int(value_min=1)
"""
phil_scope = parse(phil_str)
# constants
RAD_TO_DEG = 180.0 / math.pi
[docs]class TargetFactory(object):
[docs] @staticmethod
def from_parameters_and_experiments(
params,
experiments,
reflection_manager,
predictor,
pred_param,
restraints_param,
do_stills=False,
do_sparse=False,
):
"""Given a set of parameters, configure a factory to build a
target function
Params:
params The input parameters
Returns:
The target factory instance
"""
if params.rmsd_cutoff == "fraction_of_bin_size":
absolute_cutoffs = None
elif params.rmsd_cutoff == "absolute":
absolute_cutoffs = params.absolute_cutoffs
else:
raise RuntimeError(
"Target function rmsd_cutoff option"
+ params.rmsd_cutoff
+ " not recognised"
)
# Determine whether the target is in X, Y, Phi space or just X, Y to choose
# the right Target to instantiate
if do_stills:
if do_sparse:
from dials.algorithms.refinement.target_stills import (
LeastSquaresStillsResidualWithRmsdCutoffSparse as targ,
)
else:
from dials.algorithms.refinement.target_stills import (
LeastSquaresStillsResidualWithRmsdCutoff as targ,
)
else:
if do_sparse:
targ = LeastSquaresPositionalResidualWithRmsdCutoffSparse
else:
targ = LeastSquaresPositionalResidualWithRmsdCutoff
# Here we pass in None for prediction_parameterisation and
# restraints_parameterisation, as these are not required for initialisation
# and will be linked to the object later
return targ(
experiments=experiments,
predictor=predictor,
reflection_manager=reflection_manager,
prediction_parameterisation=pred_param,
restraints_parameterisation=restraints_param,
frac_binsize_cutoff=params.bin_size_fraction,
absolute_cutoffs=absolute_cutoffs,
gradient_calculation_blocksize=params.gradient_calculation_blocksize,
)
[docs]class Target(object):
"""Abstract interface for a target function class
A Target object will be used by a Refinery. It will refer to a Reflection
Manager to get a list of observations. It will perform reflection prediction
on those observations and update the reflection manager with those
predictions. It will then query the reflection manager to get a list of
accepted reflections with observed and calculated positions. These are the
reflections for use in refinement. It obtains the gradients of reflection
positions from a relevant prediction parameterisation object. With all of
this information in place, it calculates the value of the target function,
the gradients of the target function and auxiliary information (e.g. RMSDs).
Concrete instances of this class implement the actual target function
calculation. The base class should not determine what type of target
function is used (e.g. least squares target), or limit whether the object
is used for a detector space & phi residual, or a reciprocal space residual.
This should all be set by a derived class.
"""
__metaclass__ = abc.ABCMeta
_grad_names = ["dX_dp", "dY_dp", "dphi_dp"]
rmsd_names = ["RMSD_X", "RMSD_Y", "RMSD_Phi"]
rmsd_units = ["mm", "mm", "rad"]
def __init__(
self,
experiments,
predictor,
reflection_manager,
prediction_parameterisation,
restraints_parameterisation=None,
gradient_calculation_blocksize=None,
):
self._experiments = experiments
self._reflection_predictor = predictor
self._reflection_manager = reflection_manager
self._prediction_parameterisation = prediction_parameterisation
self._restraints_parameterisation = restraints_parameterisation
# Quantities to cache each step
self._rmsds = None
self._matches = None
# Keep maximum number of reflections used for Jacobian calculation, if
# a cutoff is required
self._gradient_calculation_blocksize = gradient_calculation_blocksize
@property
def dim(self):
"""Get the number of dimensions of the target function"""
return len(self._grad_names)
def _predict_core(self, reflections, skip_derivatives=False):
"""perform prediction for the specified reflections"""
# If the prediction parameterisation has a compose method (true for the scan
# varying case) then call it. Prefer hasattr to try-except duck typing to
# avoid masking AttributeErrors that could be raised within the method.
if hasattr(self._prediction_parameterisation, "compose"):
self._prediction_parameterisation.compose(reflections, skip_derivatives)
# do prediction (updates reflection table in situ). Scan-varying prediction
# is done automatically if the crystal has scan-points (assuming reflections
# have ub_matrix set)
self._reflection_predictor(reflections)
x_obs, y_obs, phi_obs = reflections["xyzobs.mm.value"].parts()
x_calc, y_calc, phi_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["phi_resid"] = phi_calc - phi_obs
reflections["phi_resid2"] = reflections["phi_resid"] ** 2
return reflections
[docs] def predict(self):
"""perform reflection prediction for the working reflections and update the
reflection manager"""
# get the matches
reflections = self._reflection_manager.get_obs()
# reset the 'use' flag for all observations
self._reflection_manager.reset_accepted_reflections()
# predict
reflections = self._predict_core(reflections)
# set used_in_refinement flag to all those that had predictions
mask = reflections.get_flags(reflections.flags.predicted)
reflections.set_flags(mask, reflections.flags.used_in_refinement)
# collect the matches
self.update_matches(force=True)
[docs] def predict_for_free_reflections(self):
"""perform prediction for the reflections not used for refinement"""
refs = self._reflection_manager.get_free_reflections()
if len(refs) == 0:
return refs
return self._predict_core(refs)
[docs] def predict_for_reflection_table(self, reflections, skip_derivatives=False):
"""perform prediction for all reflections in the supplied table"""
if "entering" not in reflections:
reflections.calculate_entering_flags(self._experiments)
# can only predict for experiments that exist and within the scan range
# any other reflections will be left unchanged
inc = flex.size_t_range(len(reflections))
to_keep = flex.bool(len(inc), False)
for iexp, exp in enumerate(self._experiments):
sel = reflections["id"] == iexp
# keep all reflections if there is no rotation axis
if exp.goniometer is None:
to_keep.set_selected(sel, True)
continue
# trim reflections outside the scan range
phi = reflections["xyzobs.mm.value"].parts()[2]
phi_min, phi_max = exp.scan.get_oscillation_range(deg=False)
passed = (phi >= phi_min) & (phi <= phi_max)
to_keep.set_selected(sel, passed)
# determine indices to include and predict on the subset
inc = inc.select(to_keep)
sub_refl = reflections.select(inc)
preds = self._predict_core(sub_refl, skip_derivatives)
# set updated subset back into place
reflections.set_selected(inc, preds)
return reflections
[docs] def calculate_gradients(self, reflections=None, callback=None):
"""delegate to the prediction_parameterisation object to calculate
gradients for all the matched reflections, or just for those specified"""
self.update_matches()
if reflections:
gradients = self._prediction_parameterisation.get_gradients(
reflections, callback
)
else:
gradients = self._prediction_parameterisation.get_gradients(
self._matches, callback
)
return gradients
[docs] def get_num_matches(self):
"""return the number of reflections currently used in the calculation"""
self.update_matches()
return len(self._matches)
[docs] def get_num_matches_for_experiment(self, iexp=0):
"""return the number of reflections currently used in the calculation"""
self.update_matches()
sel = self._matches["id"] == iexp
return sel.count(True)
[docs] def get_num_matches_for_panel(self, ipanel=0):
"""return the number of reflections currently used in the calculation"""
self.update_matches()
sel = self._matches["panel"] == ipanel
return sel.count(True)
[docs] def update_matches(self, force=False):
"""ensure the observations matched to predictions are up to date"""
if not self._matches or force:
self._matches = self._reflection_manager.get_matches()
[docs] def compute_functional_gradients_and_curvatures(self, block=None):
"""calculate the value of the target function and its gradients. Set
approximate curvatures as a side-effect"""
self.update_matches()
if block is not None:
matches = block
else:
matches = self._matches
nref = len(matches)
# This is a hack for the case where nref=0. This should not be necessary
# if bounds are provided for parameters to stop the algorithm exploring
# unreasonable regions of parameter space where no predictions exist.
# Unfortunately the L-BFGS line search does make such extreme trials.
if nref == 0:
self._curv = [1.0] * len(self._prediction_parameterisation)
return 1.0e12, [1.0] * len(self._prediction_parameterisation)
residuals, weights = self._extract_residuals_and_weights(matches)
w_resid = weights * residuals
residuals2 = self._extract_squared_residuals(matches)
# calculate target function
L = 0.5 * flex.sum(weights * residuals2)
def process_one_gradient(result):
# copy gradients out of the result in the right order
grads = [result[key] for key in self._grad_names]
# reset result
for k in result:
result[k] = None
# add new keys
grads = self._concatenate_gradients(grads)
result["dL_dp"] = flex.sum(w_resid * grads)
result["curvature"] = flex.sum(weights * grads * grads)
return result
results = self.calculate_gradients(matches, callback=process_one_gradient)
dL_dp = [result["dL_dp"] for result in results]
curvs = [result["curvature"] for result in results]
return (L, dL_dp, curvs)
[docs] def compute_restraints_functional_gradients_and_curvatures(self):
"""use the restraints_parameterisation object, if present, to
calculate the least squares restraints objective plus gradients and
approximate curvatures"""
if not self._restraints_parameterisation:
return None
(
residuals,
jacobian,
weights,
) = self._restraints_parameterisation.get_residuals_gradients_and_weights()
w_resid = weights * residuals
residuals2 = residuals * residuals
# calculate target function
L = 0.5 * flex.sum(weights * residuals2)
# calculate gradients using the scalar product of sparse vector col with
# dense vector w_resid
dL_dp = [col * w_resid for col in jacobian.cols()]
# calculate lsq approximation to curvatures using weighted dot product
curvs = [sparse.weighted_dot(col, weights, col) for col in jacobian.cols()]
return (L, dL_dp, curvs)
[docs] def compute_residuals(self):
"""return the vector of residuals plus their weights"""
self.update_matches()
return self._extract_residuals_and_weights(self._matches)
[docs] def split_matches_into_blocks(self, nproc=1):
"""Return a list of the matches, split into blocks according to the
gradient_calculation_blocksize parameter and the number of processes (if relevant).
The number of blocks will be set such that the total number of reflections
being processed by concurrent processes does not exceed gradient_calculation_blocksize"""
self.update_matches()
# Need to be able to track the indices of the original matches table for
# scan-varying gradient calculations. A simple and robust (but slightly
# expensive) way to do this is to add an index column to the matches table
self._matches["imatch"] = flex.size_t_range(len(self._matches))
if self._gradient_calculation_blocksize:
nblocks = int(
math.floor(
len(self._matches) * nproc / self._gradient_calculation_blocksize
)
)
else:
nblocks = nproc
# ensure at least 100 reflections per block
nblocks = min(nblocks, int(len(self._matches) / 100))
nblocks = max(nblocks, 1)
blocksize = int(math.floor(len(self._matches) / nblocks))
blocks = []
for block_num in range(nblocks - 1):
start = block_num * blocksize
end = (block_num + 1) * blocksize
blocks.append(self._matches[start:end])
start = (nblocks - 1) * blocksize
end = len(self._matches)
blocks.append(self._matches[start:end])
return blocks
[docs] def compute_residuals_and_gradients(self, block=None):
"""return the vector of residuals plus their gradients and weights for
non-linear least squares methods"""
self.update_matches()
if block is not None:
matches = block
else:
matches = self._matches
# The gradients are provided as a list of dictionaries, where the
# dictionaries have keys corresponding to gradients of the different types
# of residual involved. For example, for scans the keys are 'dX_dp',
# 'dY_dp', 'dphi_dp'. Reshape this data structure so that all the gradients
# of a particular type of residual are kept together
gradients = self.calculate_gradients(matches)
reshaped = []
for key in self._grad_names:
reshaped.append([g[key] for g in gradients])
residuals, weights = self._extract_residuals_and_weights(matches)
nelem = len(matches) * len(self._grad_names)
nparam = len(self._prediction_parameterisation)
jacobian = self._build_jacobian(reshaped, nelem=nelem, nparam=nparam)
return (residuals, jacobian, weights)
[docs] def compute_restraints_residuals_and_gradients(self):
"""delegate to the restraints_parameterisation object, if present, to
calculate the vector of restraints residuals plus their gradients and
weights for non-linear least squares methods"""
if self._restraints_parameterisation:
(
residuals,
jacobian,
weights,
) = self._restraints_parameterisation.get_residuals_gradients_and_weights()
return (residuals, jacobian, weights)
else:
return None
@staticmethod
def _build_jacobian(grads_each_dim, nelem=None, nparam=None):
"""construct Jacobian from lists of gradient vectors. The elements of
grads_each_dim refer to the gradients of each dimension of the problem
(e.g. dX, dY, dZ). The elements for a single dimension give the arrays
of gradients of the associated residual for each parameter. This method
may be overridden for the case where these vectors use sparse storage"""
jacobian = flex.double(flex.grid(nelem, nparam))
# loop over parameters
for i in range(nparam):
col = grads_each_dim[0][i]
for g in grads_each_dim[1:]:
col.extend(g[i])
jacobian.matrix_paste_column_in_place(col, i)
return jacobian
@staticmethod
def _concatenate_gradients(grads):
"""concatenate gradient vectors and return a flex.double. This method
may be overriden for the case where these vectors use sparse storage"""
result = grads[0]
for g in grads[1:]:
result.extend(g)
return result
@staticmethod
@abc.abstractmethod
def _extract_residuals_and_weights(matches):
"""extract vector of residuals and corresponding weights. The space the
residuals are measured in (e.g. X, Y and Phi) and the order they are
returned is determined by a concrete implementation of a staticmethod"""
raise NotImplementedError()
@staticmethod
@abc.abstractmethod
def _extract_squared_residuals(matches):
"""extract vector of squared residuals. The space the residuals are measured
in (e.g. X, Y and Phi) and the order they are returned is determined by a
concrete implementation of a staticmethod"""
raise NotImplementedError()
[docs] def rmsds(self):
"""calculate unweighted RMSDs for the matches"""
self.update_matches()
# cache rmsd calculation for achieved test
self._rmsds = self._rmsds_core(self._matches)
return self._rmsds
[docs] def rmsds_for_reflection_table(self, reflections):
"""calculate unweighted RMSDs for the specified reflections. Caution: this
assumes that the table reflections has the keys expected by _rmsds_core"""
n = len(reflections)
if n == 0:
return None
return self._rmsds_core(reflections)
[docs] def rmsds_for_experiment(self, iexp=0):
"""calculate unweighted RMSDs for the selected experiment."""
self.update_matches()
sel = self._matches["id"] == iexp
n = sel.count(True)
if n == 0:
return None
rmsds = self._rmsds_core(self._matches.select(sel))
return rmsds
[docs] def rmsds_for_panel(self, ipanel=0):
"""calculate unweighted RMSDs for the selected panel."""
self.update_matches()
sel = self._matches["panel"] == ipanel
n = sel.count(True)
if n == 0:
return None
rmsds = self._rmsds_core(self._matches.select(sel))
return rmsds
[docs] @abc.abstractmethod
def achieved(self):
"""return True to terminate the refinement."""
raise NotImplementedError()
[docs]class LeastSquaresPositionalResidualWithRmsdCutoff(Target):
"""An implementation of the target class providing a least squares residual
in terms of detector impact position X, Y and phi, terminating on achieved
rmsd (or on intrisic convergence of the chosen minimiser)"""
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.
if experiments[0].scan:
image_width_rad = abs(experiments[0].scan.get_oscillation(deg=False)[1])
else:
image_width_rad = None
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,
image_width_rad * frac_binsize_cutoff,
]
else:
assert len(absolute_cutoffs) == 3
self._binsize_cutoffs = absolute_cutoffs
@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["phi_resid"])
weights, w_y, w_z = matches["xyzobs.mm.weights"].parts()
weights.extend(w_y)
weights.extend(w_z)
return residuals, weights
@staticmethod
def _extract_squared_residuals(matches):
residuals2 = flex.double.concatenate(matches["x_resid2"], matches["y_resid2"])
residuals2.extend(matches["phi_resid2"])
return residuals2
def _rmsds_core(self, reflections):
"""calculate unweighted RMSDs for the specified reflections"""
resid_x = flex.sum(reflections["x_resid2"])
resid_y = flex.sum(reflections["y_resid2"])
resid_phi = flex.sum(reflections["phi_resid2"])
n = len(reflections)
rmsds = (
math.sqrt(resid_x / n),
math.sqrt(resid_y / n),
math.sqrt(resid_phi / 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
if (
r[0] < self._binsize_cutoffs[0]
and r[1] < self._binsize_cutoffs[1]
and r[2] < self._binsize_cutoffs[2]
):
return True
return False
[docs]class SparseGradientsMixin:
"""Mixin class to build a sparse Jacobian from gradients of the prediction
formula stored as sparse vectors, and allow concatenation of gradient vectors
that employed sparse storage."""
@staticmethod
def _build_jacobian(grads_each_dim, nelem=None, nparam=None):
"""construct Jacobian from lists of sparse gradient vectors."""
nref = int(nelem / len(grads_each_dim))
blocks = [sparse.matrix(nref, nparam) for _ in grads_each_dim]
jacobian = sparse.matrix(nelem, nparam)
# loop over parameters, building full width blocks of the full Jacobian
for i in range(nparam):
for block, grad in zip(blocks, grads_each_dim):
block[:, i] = grad[i]
# set the blocks in the Jacobian
for i, block in enumerate(blocks):
jacobian.assign_block(block, (i * nref), 0)
return jacobian
@staticmethod
def _concatenate_gradients(grads):
"""concatenate sparse gradient vectors and return a flex.double."""
result = grads[0].as_dense_vector()
for g in grads[1:]:
result.extend(g.as_dense_vector())
return result
[docs]class LeastSquaresPositionalResidualWithRmsdCutoffSparse(
SparseGradientsMixin, LeastSquaresPositionalResidualWithRmsdCutoff
):
"""A version of the LeastSquaresPositionalResidualWithRmsdCutoff Target that
uses a sparse matrix data structure for memory efficiency when there are a
large number of Experiments"""
pass
