Merge pull request #37 from toastisme/enable_multiple_tof_orientations

Added goniometer rotations to ToF workflow.

src/dials/algorithms/integration/processor.py

@@ -930,7 +930,7 @@ def summary(self):
  Get a summary of the processing
  """
  # Compute the task table
- if self.experiments.all_stills() or self.experiments.is_single_tof_experiment():
+ if self.experiments.all_stills() or self.experiments.all_tof_experiments():
  rows = [["#", "Group", "Frame From", "Frame To", "# Reflections"]]
  for i in range(len(self)):
  job = self.manager.job(i)

src/dials/algorithms/refinement/parameterisation/configure.py

@@ -395,7 +395,7 @@ def _set_n_intervals(smoother_params, analysis, scan, exp_ids):
 def _parameterise_beams(options, experiments, analysis):
  beam_params = []
 
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  return beam_params
 
  sv_beam = options.scan_varying and not options.beam.force_static
@@ -810,7 +810,7 @@ def build_prediction_parameterisation(
 
  # Build the prediction equation parameterisation
  if do_stills: # doing stills
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  PredParam = TOFPredictionParameterisation
  elif options.sparse:
  if options.spherical_relp_model:

src/dials/algorithms/refinement/prediction/managed_predictors.py

@@ -235,7 +235,7 @@ class ExperimentsPredictorFactory:
  @staticmethod
  def from_experiments(experiments, force_stills=False, spherical_relp=False):
 
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  return TOFExperimentsPredictor(experiments)
 
  # Determine whether or not to use a stills predictor

src/dials/algorithms/refinement/refiner.py

@@ -373,7 +373,7 @@ def _build_components(cls, params, reflections, experiments):
  obs["x_resid"] = x_calc - x_obs
  obs["y_resid"] = y_calc - y_obs
 
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
 
  obs["wavelength_resid"] = obs["wavelength_cal"] - obs["wavelength"]
  obs["wavelength_resid2"] = (obs["wavelength_cal"] - obs["wavelength"]) ** 2

src/dials/algorithms/refinement/reflection_manager.py

@@ -229,7 +229,7 @@ def from_parameters_reflections_experiments(
  flex.set_random_seed(params.random_seed)
  logger.debug("Random seed set to %d", params.random_seed)
 
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  refman = TOFReflectionManager
 
  # check whether we deal with stills or scans
@@ -269,7 +269,7 @@ def from_parameters_reflections_experiments(
  if params.outlier.algorithm in ("null", None):
  outlier_detector = None
  else:
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  colnames = ["x_resid", "y_resid", "wavelength_resid"]
  elif do_stills:
  colnames = ["x_resid", "y_resid"]
@@ -362,7 +362,7 @@ def __init__(
  self._axes = [
  matrix.col(g.get_rotation_axis()) if g else None for g in goniometers
  ]
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  self._s0vecs = [None]
  else:
  self._s0vecs = [matrix.col(e.beam.get_s0()) for e in self._experiments]

src/dials/algorithms/refinement/target.py

@@ -80,7 +80,7 @@ def from_parameters_and_experiments(
 
  # Determine whether the target is in X, Y, Phi space or just X, Y to choose
  # the right Target to instantiate
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  targ = TOFLeastSquaresPositionalResidualWithRmsdCutoff
  elif do_stills:
  if do_sparse:

src/dials/algorithms/spot_prediction/__init__.py

@@ -115,6 +115,7 @@ def __init__(self, experiment, dmin):
  self.predictor = TOFReflectionPredictor(
  experiment.beam,
  experiment.detector,
+ experiment.goniometer,
  experiment.crystal.get_A(),
  experiment.crystal.get_unit_cell(),
  experiment.crystal.get_space_group().type(),

src/dials/algorithms/spot_prediction/boost_python/ray_predictor.cc

@@ -62,9 +62,9 @@ namespace dials { namespace algorithms { namespace boost_python {
  void export_tof_ray_predictor() {
  // Create and return the wrapper for the spot predictor object
  class_<TOFRayPredictor>("TOFRayPredictor", no_init)
- .def(init<vec3<double> >((arg("unit_s0"))))
- .def(
-  "__call__", &TOFRayPredictor::operator(), (arg("miller_index"), arg("UB")));
+ .def(init<vec3<double>, mat3<double>, mat3<double> >(
+  (arg("unit_s0"), arg("fixed_rotation"), arg("setting_rotation"))))
+ .def("__call__", &TOFRayPredictor::operator(), (arg("miller_index"), arg("UB")));
  }
 
 }}} // namespace dials::algorithms::boost_python

src/dials/algorithms/spot_prediction/boost_python/reflection_predictor.cc

@@ -174,6 +174,7 @@ namespace dials { namespace algorithms { namespace boost_python {
  class_<Predictor>("TOFReflectionPredictor", no_init)
  .def(init<const PolyBeam&,
  const Detector&,
+ const Goniometer&,
  mat3<double>,
  const cctbx::uctbx::unit_cell&,
  const cctbx::sgtbx::space_group_type&,

src/dials/algorithms/spot_prediction/ray_predictor.h

@@ -88,7 +88,7 @@ namespace dials { namespace algorithms {
  vec2<double> phi;
  try {
  phi = calculate_rotation_angles_(pstar0);
- } catch (error const&) {
+ } catch (error const &) {
  return rays;
  }
 
@@ -124,7 +124,7 @@ namespace dials { namespace algorithms {
  vec2<double> phi;
  try {
  phi = calculate_rotation_angles_(pstar0);
- } catch (error const&) {
+ } catch (error const &) {
  return rays;
  }
 
@@ -251,52 +251,59 @@ namespace dials { namespace algorithms {
  };
 
  /**
- * Class to predict s1 rays for ToF data 
+ * Class to predict s1 rays for ToF data
  */
- class TOFRayPredictor{
-  public:
-  typedef cctbx::miller::index<> miller_index;
+ class TOFRayPredictor {
+ public:
+ typedef cctbx::miller::index<> miller_index;
 
- TOFRayPredictor(const vec3<double> unit_s0) : unit_s0_(unit_s0){
- DIALS_ASSERT(unit_s0_.length() > 0.0);
- }
+ TOFRayPredictor(const vec3<double> unit_s0,
+ mat3<double> fixed_rotation,
+ mat3<double> setting_rotation)
+ : unit_s0_(unit_s0),
+ fixed_rotation_(fixed_rotation),
+ setting_rotation_(setting_rotation)
 
- /**
- * For a given miller index and UB matrix, calculates the predicted s1 ray. 
- * The TOFRayPredictor wavelength and s0 variables are updated during the calculation,
- * so that they can be monitored for convergence.
- * @param h The miller index
- * @param ub The UB matrix
- * @returns Ray
- */
- Ray operator()(const miller_index &h, 
- const mat3<double> &ub){
-
- // Calculate the reciprocal lattice vector
- vec3<double> q = ub * h;
-
- // Calculate the wavelength required to meet the diffraction condition
- wavelength_ = -2*((unit_s0_ * q)/(q *q));
- s0_ = unit_s0_ / wavelength_;
- DIALS_ASSERT(s0_.length() > 0);
-
- // Calculate the Ray (default zero angle and 'entering' as false)
- vec3<double> s1 = s0_ + q;
- return Ray(s1, 0.0, false);
- }
+ {
+ DIALS_ASSERT(unit_s0_.length() > 0.0);
+ }
 
- double get_wavelength() const{
- return wavelength_;
- }
+ /**
+ * For a given miller index and UB matrix, calculates the predicted s1 ray.
+ * The TOFRayPredictor wavelength and s0 variables are updated during the
+ * calculation, so that they can be monitored for convergence.
+ * @param h The miller index
+ * @param ub The UB matrix
+ * @returns Ray
+ */
+ Ray operator()(const miller_index &h, const mat3<double> &ub) {
+ // Calculate the reciprocal lattice vector
+ vec3<double> q = setting_rotation_ * fixed_rotation_ * ub * h;
+
+ // Calculate the wavelength required to meet the diffraction condition
+ wavelength_ = -2 * ((unit_s0_ * q) / (q * q));
+ s0_ = unit_s0_ / wavelength_;
+ DIALS_ASSERT(s0_.length() > 0);
+
+ // Calculate the Ray (default zero angle and 'entering' as false)
+ vec3<double> s1 = s0_ + q;
+ return Ray(s1, 0.0, false);
+ }
 
- vec3<double> get_s0() const{
- return s0_;
- }
+ double get_wavelength() const {
+ return wavelength_;
+ }
+
+ vec3<double> get_s0() const {
+ return s0_;
+ }
 
- private:
- const vec3<double> unit_s0_;
- double wavelength_;
- vec3<double> s0_;
+ private:
+ const vec3<double> unit_s0_;
+ double wavelength_;
+ vec3<double> s0_;
+ mat3<double> fixed_rotation_;
+ mat3<double> setting_rotation_;
  };
 
 }} // namespace dials::algorithms

src/dials/algorithms/spot_prediction/reflection_predictor.h

@@ -1336,17 +1336,21 @@ namespace dials { namespace algorithms {
  */
  TOFReflectionPredictor(const PolyBeam &beam,
  const Detector &detector,
+ const Goniometer &goniometer,
  mat3<double> ub,
  const cctbx::uctbx::unit_cell &unit_cell,
  const cctbx::sgtbx::space_group_type &space_group_type,
  const double &dmin)
  : beam_(beam),
  detector_(detector),
+ goniometer_(goniometer),
  ub_(ub),
  unit_cell_(unit_cell),
  space_group_type_(space_group_type),
  dmin_(dmin),
- predict_ray_(beam.get_unit_s0()) {}
+ predict_ray_(beam.get_unit_s0(),
+ goniometer.get_fixed_rotation(),
+ goniometer.get_setting_rotation()) {}
 
  /**
  * Predict all reflection.
@@ -1626,6 +1630,7 @@ namespace dials { namespace algorithms {
  protected:
  PolyBeam beam_;
  Detector detector_;
+ Goniometer goniometer_;
  mat3<double> ub_;
  cctbx::uctbx::unit_cell unit_cell_;
  cctbx::sgtbx::space_group_type space_group_type_;

src/dials/command_line/integrate.py

@@ -486,7 +486,7 @@ def run_integration(params, experiments, reference=None):
  logger.info("\n".join(("", "=" * 80, "")))
  logger.info(heading("Predicting reflections"))
 
- if experiments.is_single_tof_experiment() and not params.prediction.d_min:
+ if experiments.all_tof_experiments() and not params.prediction.d_min:
 
  min_s0_idx = min(
  range(len(reference["wavelength"])), key=reference["wavelength"].__getitem__

src/dials/command_line/symmetry.py

@@ -269,7 +269,7 @@ def eliminate_sys_absent(experiments, reflections):
 def get_subset_for_symmetry(experiments, reflection_tables, exclude_images=None):
  """Select an image range for symmetry analysis, or just select
  the first 360 degrees of data."""
- if experiments.is_single_tof_experiment():
+ if experiments.all_tof_experiments():
  return reflection_tables
  refls_for_sym = []
  if exclude_images: