Fixed tof integrate error when using multiple orientations.

src/dials/algorithms/integration/fit/tof_line_profile.py

@@ -113,7 +113,7 @@ def compute_line_profile_data_for_reflection(
  l = BackToBackExponential(
  tof=tof,
  intensities=projected_intensity,
- A=A,
+ A=max(projected_intensity),
  alpha=alpha,
  beta=beta,
  sigma=sigma,
@@ -148,7 +148,7 @@ def compute_line_profile_data_for_reflection(
 
 def compute_line_profile_intensity(reflections):
 
- A = 200.0
+ # A = 200.0
  alpha = 0.4
  beta = 0.4
  sigma = 8.0
@@ -195,7 +195,7 @@ def compute_line_profile_intensity(reflections):
  l = BackToBackExponential(
  tof=tof,
  intensities=projected_intensity,
- A=A,
+ A=max(projected_intensity),
  alpha=alpha,
  beta=beta,
  sigma=sigma,

src/dials/command_line/tof_integrate.py

@@ -434,12 +434,15 @@ def run_integrate(params, experiments, reflections):
  incident_proton_charge = incident_fmt_class.get_proton_charge()
  empty_proton_charge = empty_fmt_class.get_proton_charge()
 
- for expt in experiments:
+ for idx, expt in enumerate(experiments):
  expt_data = expt.imageset
  expt_proton_charge = experiment_cls.get_instance(
  expt.imageset.paths()[0], **expt.imageset.data().get_params()
  ).get_proton_charge()
 
+ sel = predicted_reflections["id"] == idx
+ expt_reflections = predicted_reflections.select(sel)
+
  if applying_spherical_absorption_correction(params):
  logger.info(
  "Applying spherical absorption correction to target and Vanadium runs"
@@ -462,20 +465,47 @@ def run_integrate(params, experiments, reflections):
  )
 
  tof_extract_shoeboxes_to_reflection_table(
- predicted_reflections,
+ expt_reflections,
  expt,
  expt_data,
  incident_data,
  empty_data,
  corrections_data,
  params.corrections.lorentz,
  )
+ # tof_calculate_shoebox_mask(predicted_reflections, expt)
+ tof_calculate_shoebox_foreground(
+ expt_reflections, expt, params.foreground_radius
+ )
+ expt_reflections.is_overloaded(experiments)
+ expt_reflections.contains_invalid_pixels()
+ expt_reflections["partiality"] = flex.double(len(expt_reflections), 1.0)
+
+ # Background calculated explicitly to expose underlying algorithm
+ background_algorithm = SimpleBackgroundExt(
+ params=None, experiments=experiments
+ )
+ success = background_algorithm.compute_background(expt_reflections)
+ expt_reflections.set_flags(
+ ~success, expt_reflections.flags.failed_during_background_modelling
+ )
+
+ # Centroids calculated explicitly to expose underlying algorithm
+ # centroid_algorithm = SimpleCentroidExt(params=None, experiments=experiments)
+ # centroid_algorithm.compute_centroid(expt_reflections)
+
+ expt_reflections.compute_summed_intensity()
+
+ if params.method.line_profile_fitting:
+ print("Calculating line profile fitted intensities")
+ expt_reflections = compute_line_profile_intensity(expt_reflections)
+ predicted_reflections.set_selected(sel, expt_reflections)
  else:
  logger.info("Normalising target run with Vanadium run")
  if params.corrections.lorentz:
  logger.info("Applying Lorentz correction to target run")
  tof_extract_shoeboxes_to_reflection_table(
- predicted_reflections,
+ expt_reflections,
  expt,
  expt_data,
  incident_data,
@@ -485,43 +515,75 @@ def run_integrate(params, experiments, reflections):
  empty_proton_charge,
  params.corrections.lorentz,
  )
+ # tof_calculate_shoebox_mask(predicted_reflections, expt)
+ tof_calculate_shoebox_foreground(
+ expt_reflections, expt, params.foreground_radius
+ )
+ expt_reflections.is_overloaded(experiments)
+ expt_reflections.contains_invalid_pixels()
+ expt_reflections["partiality"] = flex.double(len(expt_reflections), 1.0)
+
+ # Background calculated explicitly to expose underlying algorithm
+ background_algorithm = SimpleBackgroundExt(
+ params=None, experiments=experiments
+ )
+ success = background_algorithm.compute_background(expt_reflections)
+ expt_reflections.set_flags(
+ ~success, expt_reflections.flags.failed_during_background_modelling
+ )
+
+ # Centroids calculated explicitly to expose underlying algorithm
+ # centroid_algorithm = SimpleCentroidExt(params=None, experiments=experiments)
+ # centroid_algorithm.compute_centroid(expt_reflections)
+
+ expt_reflections.compute_summed_intensity()
+
+ if params.method.line_profile_fitting:
+ print("Calculating line profile fitted intensities")
+ expt_reflections = compute_line_profile_intensity(expt_reflections)
+ predicted_reflections.set_selected(sel, expt_reflections)
  else:
  if params.corrections.lorentz:
  logger.info("Applying Lorentz correction to target run")
- for expt in experiments:
+ print("Calculating summed intensities")
+ for idx, expt in enumerate(experiments):
+ sel = predicted_reflections["id"] == idx
+ expt_reflections = predicted_reflections.select(sel)
  expt_data = expt.imageset
  tof_extract_shoeboxes_to_reflection_table(
- predicted_reflections,
+ expt_reflections,
  expt,
  expt_data,
  params.corrections.lorentz,
  )
 
- # tof_calculate_shoebox_mask(predicted_reflections, expt)
- tof_calculate_shoebox_foreground(
- predicted_reflections, expt, params.foreground_radius
- )
- predicted_reflections.is_overloaded(experiments)
- predicted_reflections.contains_invalid_pixels()
- predicted_reflections["partiality"] = flex.double(len(predicted_reflections), 1.0)
+  # tof_calculate_shoebox_mask(predicted_reflections, expt)
+  tof_calculate_shoebox_foreground(
+  expt_reflections, expt, params.foreground_radius
+  )
+  expt_reflections.is_overloaded(experiments)
+  expt_reflections.contains_invalid_pixels()
+  expt_reflections["partiality"] = flex.double(len(expt_reflections), 1.0)
 
- # Background calculated explicitly to expose underlying algorithm
- background_algorithm = SimpleBackgroundExt(params=None, experiments=experiments)
- success = background_algorithm.compute_background(predicted_reflections)
- predicted_reflections.set_flags(
- ~success, predicted_reflections.flags.failed_during_background_modelling
- )
+ # Background calculated explicitly to expose underlying algorithm
+ background_algorithm = SimpleBackgroundExt(
+ params=None, experiments=experiments
+ )
+ success = background_algorithm.compute_background(expt_reflections)
+ expt_reflections.set_flags(
+ ~success, expt_reflections.flags.failed_during_background_modelling
+ )
 
- # Centroids calculated explicitly to expose underlying algorithm
- # centroid_algorithm = SimpleCentroidExt(params=None, experiments=experiments)
- # centroid_algorithm.compute_centroid(predicted_reflections)
+  # Centroids calculated explicitly to expose underlying algorithm
+  # centroid_algorithm = SimpleCentroidExt(params=None, experiments=experiments)
+  # centroid_algorithm.compute_centroid(expt_reflections)
 
- print("Calculating summed intensities")
- predicted_reflections.compute_summed_intensity()
+ expt_reflections.compute_summed_intensity()
 
- if params.method.line_profile_fitting:
- print("Calculating line profile fitted intensities")
- predicted_reflections = compute_line_profile_intensity(predicted_reflections)
+ if params.method.line_profile_fitting:
+ print("Calculating line profile fitted intensities")
+ expt_reflections = compute_line_profile_intensity(expt_reflections)
+ predicted_reflections.set_selected(sel, expt_reflections)
 
  # Filter reflections with a high fraction of masked foreground
  valid_foreground_threshold = 1.0 # DIALS default