Fixed bounds of calculcated bounding boxes and allowed size of boundi…

…ng box to be set at the Python level.

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

@@ -442,6 +442,7 @@ namespace dials {
 
  /// Calculate the rotation angles at the following XDS
  // e3 coordinates: -delta_m, +delta_m
+ /*
  double wavelength1 = xcs.to_wavelength(-delta_m, s1);
  double wavelength2 = xcs.to_wavelength(+delta_m, s1);
  double tof1 = beam_.get_tof_from_wavelength(wavelength1, L1);
@@ -451,8 +452,18 @@ namespace dials {
  double z1 = sequence_.get_frame_from_tof(tof1);
  double z2 = sequence_.get_frame_from_tof(tof2);
  double2 z(z1, z2);
+ */
+ double z0 = frame - delta_m;
+ if (z0 < 0) {
+ z0 = 0;
+ }
+ double max_z = sequence_.get_array_range()[1];
+ double z1 = frame + delta_m;
+ if (z1 > max_z) {
+ z1 = max_z;
+ }
 
- int6 bbox(x0, x1, y0, y1, frame - 30, frame + 30);
+ int6 bbox(x0, x1, y0, y1, z0, z1);
  DIALS_ASSERT(bbox[1] > bbox[0]);
  DIALS_ASSERT(bbox[3] > bbox[2]);
  DIALS_ASSERT(bbox[5] > bbox[4]);

src/dials/command_line/simple_tof_integrate.py

@@ -581,7 +581,7 @@ def run_simple_integrate(params, experiments, reflections):
  model_reflections = reflections.select(used_in_ref)
 
  # sigma_m in 3.1 of Kabsch 2010
- sigma_m = 0.01
+ sigma_m = 3
  sigma_b = 0.01
  # The Gaussian model given in 2.3 of Kabsch 2010
  experiment.profile = GaussianRSProfileModel(