Added method to predict spots for asymmetric unit.

src/dials/algorithms/indexing/model_evaluation.py

@@ -36,7 +36,7 @@ def filter_doubled_cell(solutions):
  accepted_solutions = []
  for i1, s1 in enumerate(solutions):
  doubled_cell = False
- for (m1, m2, m3) in (
+ for m1, m2, m3 in (
  (2, 1, 1),
  (1, 2, 1),
  (1, 1, 2),

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

@@ -184,7 +184,10 @@ namespace dials { namespace algorithms { namespace boost_python {
  .def("__call__", predict_observed_with_panel)
  .def("__call__", predict_observed_with_panel_list)
  .def("for_reflection_table", &Predictor::for_reflection_table)
- .def("for_reflection_table", &Predictor::for_reflection_table_with_individual_ub);
+ .def("for_reflection_table", &Predictor::for_reflection_table_with_individual_ub)
+ .def("all_reflections_for_asu",
+ &Predictor::all_reflections_for_asu,
+ (arg("goniometer"), arg("phi")));
  }
  void export_reflection_predictor() {
  export_scan_static_reflection_predictor();

src/dials/algorithms/spot_prediction/reflection_predictor.h

@@ -28,6 +28,7 @@
 #include <dials/algorithms/spot_prediction/stills_ray_predictor.h>
 #include <dials/algorithms/spot_prediction/ray_intersection.h>
 #include <iostream>
+#include <cctbx/miller/index_generator.h>
 
 namespace dials { namespace algorithms {
 
@@ -1356,6 +1357,70 @@ namespace dials { namespace algorithms {
  return af::reflection_table();
  }
 
+ af::reflection_table all_reflections_for_asu(Goniometer goniometer, double phi) {
+ mat3<double> fixed_rotation = goniometer.get_fixed_rotation();
+ mat3<double> setting_rotation = goniometer.get_setting_rotation();
+ vec3<double> rotation_axis = goniometer.get_rotation_axis();
+ mat3<double> rotation =
+ scitbx::math::r3_rotation::axis_and_angle_as_matrix(rotation_axis, phi);
+ vec3<double> unit_s0 = beam_.get_unit_s0();
+ vec2<double> wavelength_range = beam_.get_wavelength_range();
+
+ cctbx::miller::index_generator indices =
+ cctbx::miller::index_generator(unit_cell_, space_group_type_, false, dmin_);
+
+ af::shared<miller_index> indices_arr = indices.to_array();
+
+ af::reflection_table table;
+ af::shared<double> wavelength_column;
+ table["wavelength_cal"] = wavelength_column;
+ af::shared<vec3<double> > s0_column;
+ table["s0_cal"] = s0_column;
+ tof_prediction_data predictions(table);
+
+ for (std::size_t i = 0; i < indices_arr.size(); ++i) {
+ miller_index h = indices_arr[i];
+
+ vec3<double> q = setting_rotation * rotation * fixed_rotation * ub_ * h;
+
+ // Calculate the wavelength required to meet the diffraction condition
+ double wavelength = -2 * ((unit_s0 * q) / (q * q));
+ if (wavelength < wavelength_range[0] || wavelength > wavelength_range[1]) {
+ continue;
+ }
+ vec3<double> s0 = unit_s0 / wavelength;
+ DIALS_ASSERT(s0.length() > 0);
+
+ // Calculate the Ray (default zero angle and 'entering' as false)
+ vec3<double> s1 = s0 + q;
+
+ int panel = detector_.get_panel_intersection(s1);
+ if (panel == -1) {
+ continue;
+ }
+
+ Detector::coord_type coord;
+ coord.first = panel;
+ coord.second = detector_[panel].get_ray_intersection(s1);
+ vec2<double> mm = coord.second;
+ vec2<double> px = detector_[panel].millimeter_to_pixel(mm);
+
+ // Add the reflections to the table
+ predictions.hkl.push_back(h);
+ predictions.enter.push_back(false);
+ predictions.s1.push_back(s1);
+ predictions.xyz_mm.push_back(vec3<double>(mm[0], mm[1], 0.0));
+ predictions.xyz_px.push_back(vec3<double>(px[0], px[1], 0.0));
+ predictions.panel.push_back(panel);
+ predictions.flags.push_back(af::Predicted);
+ predictions.wavelength_cal.push_back(wavelength);
+ predictions.s0_cal.push_back(s0);
+ }
+
+ // Return the reflection table
+ return table;
+ }
+
  /**
  * Predict reflections for UB. Also filters based on ewald sphere proximity.
  * @param ub The UB matrix
@@ -1514,14 +1579,6 @@ namespace dials { namespace algorithms {
  append_for_ray(p, h, ray, panel, wavelength, s0);
  }
 
- /**
- * Predict for the given Miller index, ray, panel number and delta psi
- * @param p The reflection data
- * @param h The miller index
- * @param ray The ray data
- * @param panel The panel number
- * @param delpsi The calculated minimum rotation to Ewald sphere
- */
  void append_for_ray(tof_prediction_data &p,
  const miller_index &h,
  const Ray &ray,

src/dials/command_line/dials_import.py

@@ -209,7 +209,6 @@ def _extract_or_read_imagesets(params):
 
  # Check we have some filenames
  if len(experiments) == 0:
-
  # FIXME Should probably make this smarter since it requires editing here
  # and in dials.import phil scope
  try:
@@ -223,7 +222,6 @@ def _extract_or_read_imagesets(params):
  # Check if a template has been set and print help if not, otherwise try to
  # import the images based on the template input
  if len(params.input.template) > 0:
-
  experiments = ExperimentListFactory.from_templates(
  params.input.template,
  image_range=params.geometry.scan.image_range,
@@ -530,7 +528,6 @@ def __call__(self, imageset_list):
 
  # Loop through imagesets
  for imageset in imageset_list:
-
  # Set the external lookups
  imageset = self.update_lookup(imageset, lookup)
 
@@ -794,7 +791,6 @@ def assert_single_sequence(experiments, params):
  ]
 
  if len(sequences) > 1:
-
  # Print some info about multiple sequences
  diagnose_multiple_sequences(sequences, params)
 
@@ -914,7 +910,6 @@ def do_import(
 
  # Print out info for all experiments
  for experiment in experiments:
-
  # Print some experiment info - override the output of image range
  # if appropriate
  image_range = params.geometry.scan.image_range