Merge pull request #46 from toastisme/tof_integrate_remove_shoeboxes

Remove reflection shoeboxes by default after integrating.

src/dials/command_line/simple_tof_integrate.py

@@ -64,6 +64,9 @@
  .help = "Use integration by profile fitting using a Gaussian"
  "convoluted with back-to-back exponential functions"
 }
+keep_shoeboxes = False
+ .type = bool
+ .help = "Retain shoeboxes in output reflection table"
 """
 )
 
@@ -582,6 +585,9 @@ def run_simple_integrate(params, experiments, reflections):
  predicted_reflections.extend(r)
  predicted_reflections.calculate_entering_flags(experiments)
 
+ for i in range(len(experiments)):
+ predicted_reflections.experiment_identifiers()[i] = experiments[i].identifier
+
  # Updates flags to set which reflections to use in generating reference profiles
  matched, reflections, unmatched = predicted_reflections.match_with_reference(
  reflections
@@ -666,6 +672,7 @@ def run_simple_integrate(params, experiments, reflections):
 
  print("Calculating summed intensities")
  predicted_reflections.compute_summed_intensity()
+
  if params.method.line_profile_fitting:
  print("Calculating line profile fitted intensities")
  predicted_reflections = compute_line_profile_intensity(predicted_reflections)
@@ -690,11 +697,12 @@ def run_simple_integrate(params, experiments, reflections):
  )
  predicted_reflections["num_pixels.foreground"] = nvalfg
 
- predicted_reflections.experiment_identifiers()[0] = experiment.identifier
-
  integration_report = IntegrationReport(experiments, predicted_reflections)
  logger.info("")
  logger.info(integration_report.as_str(prefix=" "))
+
+ if not params.keep_shoeboxes:
+ del predicted_reflections["shoebox"]
  return predicted_reflections
 
  """
@@ -787,8 +795,8 @@ def run_simple_integrate(params, experiments, reflections):
  Remove shoeboxes
  """
 
- del predicted_reflections["shoebox"]
- predicted_reflections.experiment_identifiers()[0] = experiment.identifier
+ if not params.keep_shoeboxes:
+  del predicted_reflections["shoebox"]
  return predicted_reflections