Changed predicted reflections calculation during tof_integrate.

src/dials/algorithms/spot_prediction/__init__.py

@@ -234,6 +234,40 @@ def post_prediction(self, reflections):
 
  return reflections
 
+ def indices_for_ub(self, indices):
+ reflection_table = self.predictor(indices)
+ reflection_table = self.post_prediction(reflection_table)
+
+ interpolation_tof = self.experiment.scan.get_property("time_of_flight")
+ interpolation_frames = list(range(len(interpolation_tof)))
+ tof_to_frame = tof_helpers.tof_to_frame_interpolator(
+ interpolation_tof, interpolation_frames
+ )
+ L0 = self.experiment.beam.get_sample_to_source_distance() * 10**-3 # (m)
+
+ reflection_tof = (
+ tof_helpers.tof_from_wavelength(
+ reflection_table["wavelength_cal"],
+ L0 + reflection_table["L1"] * 10**-3,
+ )
+ * 10**6
+ )
+
+ reflection_table = reflection_table.select(
+ (reflection_tof > min(interpolation_tof))
+ & (reflection_tof < max(interpolation_tof))
+ )
+
+ reflection_tof = reflection_tof.select(
+ (reflection_tof > min(interpolation_tof))
+ & (reflection_tof < max(interpolation_tof))
+ )
+ reflection_frames = flumpy.from_numpy(tof_to_frame(reflection_tof))
+ x, y, _ = reflection_table["xyzcal.px"].parts()
+ reflection_table["xyzcal.px"] = flex.vec3_double(x, y, reflection_frames)
+
+ return reflection_table
+
  def for_ub(self, ub):
 
  reflection_table = self.predictor.for_ub(ub)

src/dials/command_line/tof_integrate.py

@@ -19,6 +19,7 @@
  ComputeEsdBeamDivergence,
 )
 from dials.algorithms.shoebox import MaskCode
+from dials.algorithms.spot_prediction import TOFReflectionPredictor
 from dials.array_family import flex
 from dials.command_line.integrate import process_reference
 from dials.extensions.simple_background_ext import SimpleBackgroundExt
@@ -330,22 +331,20 @@ def run_integrate(params, experiments, reflections):
  dmin = expt_dmin
 
  predicted_reflections = None
+ miller_indices = reflections["miller_index"]
  for idx, experiment in enumerate(experiments):
 
+ predictor = TOFReflectionPredictor(experiment, dmin)
  if predicted_reflections is None:
- predicted_reflections = flex.reflection_table.from_predictions(
- experiment, padding=1.0, dmin=dmin
- )
+ predicted_reflections = predictor.indices_for_ub(miller_indices)
  predicted_reflections["id"] = cctbx.array_family.flex.int(
  len(predicted_reflections), idx
  )
  predicted_reflections["imageset_id"] = cctbx.array_family.flex.int(
  len(predicted_reflections), idx
  )
  else:
- r = flex.reflection_table.from_predictions(
- experiment, padding=1.0, dmin=dmin
- )
+ r = predictor.indices_for_ub(miller_indices)
  r["id"] = cctbx.array_family.flex.int(len(r), idx)
  r["imageset_id"] = cctbx.array_family.flex.int(len(r), idx)
  predicted_reflections.extend(r)
@@ -497,7 +496,7 @@ def run_integrate(params, experiments, reflections):
  expt_reflections.compute_summed_intensity()
 
  if params.method.line_profile_fitting:
- print("Calculating line profile fitted intensities")
+ print(f"Calculating line profile fitted intensities for expt {idx}")
  expt_reflections = compute_line_profile_intensity(expt_reflections)
  predicted_reflections.set_selected(sel, expt_reflections)
  else:
@@ -539,7 +538,7 @@ def run_integrate(params, experiments, reflections):
  expt_reflections.compute_summed_intensity()
 
  if params.method.line_profile_fitting:
- print("Calculating line profile fitted intensities")
+ print(f"Calculating line profile fitted intensities for expt {idx}")
  expt_reflections = compute_line_profile_intensity(expt_reflections)
  predicted_reflections.set_selected(sel, expt_reflections)
  else:
@@ -581,7 +580,7 @@ def run_integrate(params, experiments, reflections):
  expt_reflections.compute_summed_intensity()
 
  if params.method.line_profile_fitting:
- print("Calculating line profile fitted intensities")
+ print(f"Calculating line profile fitted intensities for expt {idx}")
  expt_reflections = compute_line_profile_intensity(expt_reflections)
  predicted_reflections.set_selected(sel, expt_reflections)