Merge pull request #29 from toastisme/add_wavelength_cal_to_refl

Add wavelength_cal to reflection table.

src/dials/algorithms/indexing/bravais_settings.py

@@ -111,6 +111,7 @@ def as_dict(self):
  "rmsd": item.rmsd,
  "nspots": item.Nmatches,
  "bravais": item["bravais"],
+ "volume": uc.volume(),
  "unit_cell": uc.parameters(),
  "cb_op": str(item["cb_op_inp_best"] * self.cb_op_to_primitive),
  "max_cc": item.max_cc,

src/dials/algorithms/indexing/indexer.py

@@ -907,6 +907,8 @@ def refine(self, experiments, reflections):
  predicted = refiner.predict_for_indexed()
  reflections["xyzcal.mm"] = predicted["xyzcal.mm"]
  reflections["entering"] = predicted["entering"]
+ if "wavelength_cal" in predicted:
+ reflections["wavelength_cal"] = predicted["wavelength_cal"]
  reflections.unset_flags(
  flex.bool(len(reflections), True), reflections.flags.centroid_outlier
  )

src/dials/algorithms/refinement/refiner.py

@@ -247,6 +247,7 @@ def _filter_reflections(reflections):
  "shoebox",
  "delpsical.weights",
  "wavelength",
+ "wavelength_cal",
  "tof",
  "s0",
  ]

src/dials/array_family/flex_ext.py

@@ -1065,8 +1065,7 @@ def contains_tof_data(self):
 
  def get_pixel_bbox_centroid_positions(
  self, panel: int, pixel_pos: Tuple[int, int]
- ) -> Tuple[list, list, list]:
-
+ ) -> Tuple[list, list, list, list]:
  """
  Finds any bounding boxes within px and py on panel
  and returns their pz positions along with
@@ -1080,11 +1079,16 @@ def get_pixel_bbox_centroid_positions(
  centroids = self["xyzobs.px.value"].select(sel)
  else:
  centroids = None
+ if "miller_index" in self:
+ miller_indices = self["miller_index"].select(sel)
+ else:
+ miller_indices = None
  py = int(pixel_pos[0])
  px = int(pixel_pos[1])
  bbox_pos = []
  centroid_pos = []
  refl_ids = []
+ selected_miller_indices = []
  for i in range(len(x0)):
  if px >= x0[i] and px <= x1[i]:
  if py >= y0[i] and py <= y1[i]:
@@ -1095,7 +1099,12 @@ def get_pixel_bbox_centroid_positions(
  ci = centroids[i][2]
  x, y = z0[i], z1[i]
  assert ci >= x and ci <= y, f"{ci} {x} {y}"
- return bbox_pos, centroid_pos, refl_ids
+ if miller_indices:
+ selected_miller_indices.append(miller_indices[i])
+ else:
+ selected_miller_indices.append((0, 0, 0))
+
+ return bbox_pos, centroid_pos, refl_ids, selected_miller_indices
 
  def find_overlaps(self, experiments=None, border=0):
  """
@@ -1337,7 +1346,6 @@ def centroid_px_to_mm(self, experiments):
  self["xyzobs.mm.variance"].set_selected(sel, centroid_variance)
 
  def add_beam_data(self, experiments):
-
  """
  Adds wavelength, tof, s0, and unit_s0 columns to self.
  All experiments with a TOFSequence have values set from their time-of-flight.
@@ -1519,10 +1527,7 @@ def map_centroids_to_reciprocal_space(
  if self.contains_beam_data():
  import numpy as np
 
- if calculated:
- wavelengths = self["wavelength_cal"].select(sel)
- else:
- wavelengths = self["wavelength"].select(sel)
+ wavelengths = self["wavelength"].select(sel)
  S = cctbx.array_family.flex.vec3_double(len(s1))
  s1 = s1 / s1.norms()
  for s1_idx in range(len(s1)):

src/dials/command_line/simple_tof_integrate.py

@@ -531,6 +531,8 @@ def run_simple_integrate(params, experiments, 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"]
 
  """
  Create profile model and add it to erperiment.