Fix imageviewer for tof data when including integrated reflections. F…

…ilter out reflections with bounding boxes outside of detectors rather than truncating them. Allow for user defined sigma_b and sigma_m in tof integration. Integrate all predicted spots by default rather than just those observed.

src/dials/algorithms/profile_model/gaussian_rs/bbox_calculator.h

@@ -462,6 +462,10 @@ namespace dials {
  if (z1 > max_z) {
  z1 = max_z;
  }
+ if (z0 > z1) {
+ z0 = -1;
+ z1 = 0;
+ }
 
  int6 bbox(x0, x1, y0, y1, z0, z1);
  DIALS_ASSERT(bbox[1] > bbox[0]);

src/dials/command_line/simple_tof_integrate.py

@@ -23,6 +23,9 @@
 from dials.algorithms.integration.report import IntegrationReport, ProfileModelReport
 from dials.algorithms.profile_model.gaussian_rs import GaussianRSProfileModeller
 from dials.algorithms.profile_model.gaussian_rs import Model as GaussianRSProfileModel
+from dials.algorithms.profile_model.gaussian_rs.calculator import (
+ ComputeEsdBeamDivergence,
+)
 from dials.algorithms.shoebox import MaskCode
 from dials.array_family import flex
 from dials.command_line.integrate import process_reference
@@ -64,6 +67,12 @@
  .help = "Use integration by profile fitting using a Gaussian"
  "convoluted with back-to-back exponential functions"
 }
+sigma_b = 0.01
+ .type = float
+ .help = "Used to calculate xy bounding box of predicted reflections"
+sigma_m = 3
+ .type = float
+ .help = "Used to calculate z bounding box of predicted reflections"
 keep_shoeboxes = False
  .type = bool
  .help = "Retain shoeboxes in output reflection table"
@@ -592,10 +601,9 @@ def run_simple_integrate(params, experiments, reflections):
  matched, reflections, unmatched = predicted_reflections.match_with_reference(
  reflections
  )
- sel = predicted_reflections.get_flags(predicted_reflections.flags.reference_spot)
- predicted_reflections = predicted_reflections.select(sel)
- if "idx" in reflections:
- predicted_reflections["idx"] = reflections["idx"]
+ # if "idx" in reflections:
+ # predicted_reflections["idx"] = reflections["idx"]
+ # sel = predicted_reflections.get_flags(predicted_reflections.flags.reference_spot)
 
  """
  Create profile model and add it to experiment.
@@ -606,9 +614,13 @@ def run_simple_integrate(params, experiments, reflections):
  used_in_ref = reflections.get_flags(reflections.flags.used_in_refinement)
  model_reflections = reflections.select(used_in_ref)
 
+ sigma_b = ComputeEsdBeamDivergence(
+ experiment.detector, model_reflections, centroid_definition="s1"
+ ).sigma()
+
  # sigma_m in 3.1 of Kabsch 2010
- sigma_m = 3
- sigma_b = 0.01
+ sigma_m = params.sigma_m
+ sigma_b = 0.001
  # The Gaussian model given in 2.3 of Kabsch 2010
  for idx, experiment in enumerate(experiments):
  experiments[idx].profile = GaussianRSProfileModel(
@@ -625,9 +637,12 @@ def run_simple_integrate(params, experiments, reflections):
 
  predicted_reflections.compute_bbox(experiments)
  x1, x2, y1, y2, t1, t2 = predicted_reflections["bbox"].parts()
+ predicted_reflections = predicted_reflections.select(t1 > 0)
+ x1, x2, y1, y2, t1, t2 = predicted_reflections["bbox"].parts()
  predicted_reflections = predicted_reflections.select(
  t2 < experiments[0].sequence.get_image_range()[1]
  )
+
  predicted_reflections.compute_d(experiments)
  predicted_reflections.compute_partiality(experiments)
 

src/dials/util/image_viewer/spotfinder_frame.py

@@ -14,6 +14,7 @@
 from cctbx import crystal, uctbx
 from cctbx.miller import index_generator
 from dxtbx.imageset import ImageSet
+from dxtbx.model import Scan
 from dxtbx.model.detector_helpers import get_detector_projection_2d_axes
 from dxtbx.model.experiment_list import ExperimentList, ExperimentListFactory
 from libtbx.utils import flat_list
@@ -2005,7 +2006,7 @@ def _basis_vector_overlay_data(self, i_expt, i_frame, experiment):
  beam = imageset.get_beam()
  gonio = imageset.get_goniometer()
  still = scan is None or gonio is None
- if not still:
+ if not still and isinstance(scan, Scan):
  phi = scan.get_angle_from_array_index(
  i_frame - imageset.get_array_range()[0], deg=True
  )
@@ -2029,7 +2030,7 @@ def _basis_vector_overlay_data(self, i_expt, i_frame, experiment):
  for i, h in enumerate(((1, 0, 0), (0, 1, 0), (0, 0, 1))):
  r = A * matrix.col(h) * self.settings.basis_vector_scale
 
- if still:
+ if still or not isinstance(scan, Scan):
  s1 = matrix.col(beam.get_unit_s0()) + r
  else:
  r_phi = r.rotate_around_origin(axis, phi, deg=True)