diff --git a/src/dials/algorithms/indexing/indexer.py b/src/dials/algorithms/indexing/indexer.py index 3b3c1c4bb0..30463afc6e 100644 --- a/src/dials/algorithms/indexing/indexer.py +++ b/src/dials/algorithms/indexing/indexer.py @@ -941,6 +941,25 @@ def find_max_cell(self): self.params.max_cell = params.multiplier * max(uc_params[:3]) logger.info("Using max_cell: %.1f Angstrom", self.params.max_cell) else: + + convert_reflections_z_to_deg = True + all_tof_experiments = False + for expt in self.experiments: + if expt.scan is not None and expt.scan.has_property( + "time_of_flight" + ): + all_tof_experiments = True + elif all_tof_experiments: + raise ValueError( + "Cannot find max cell for ToF and non-ToF experiments at the same time" + ) + + if all_tof_experiments: + if params.step_size < 100: + logger.info("Setting default ToF step size to 500 usec") + params.step_size = 500 + convert_reflections_z_to_deg = False + self.params.max_cell = find_max_cell( self.reflections, max_cell_multiplier=params.multiplier, @@ -952,6 +971,7 @@ def find_max_cell(self): filter_ice=params.filter_ice, filter_overlaps=params.filter_overlaps, overlaps_border=params.overlaps_border, + convert_reflections_z_to_deg=convert_reflections_z_to_deg, ).max_cell logger.info("Found max_cell: %.1f Angstrom", self.params.max_cell) diff --git a/src/dials/algorithms/indexing/max_cell.py b/src/dials/algorithms/indexing/max_cell.py index 7c45cc6d5d..dccb542abf 100644 --- a/src/dials/algorithms/indexing/max_cell.py +++ b/src/dials/algorithms/indexing/max_cell.py @@ -22,6 +22,7 @@ def find_max_cell( filter_ice=True, filter_overlaps=True, overlaps_border=0, + convert_reflections_z_to_deg=True, ): logger.debug("Finding suitable max_cell based on %i reflections", len(reflections)) # Exclude potential ice-ring spots from nearest neighbour analysis if needed @@ -63,6 +64,7 @@ def find_max_cell( percentile=nearest_neighbor_percentile, histogram_binning=histogram_binning, nn_per_bin=nn_per_bin, + convert_reflections_z_to_deg=convert_reflections_z_to_deg, ) except AssertionError as e: raise DialsIndexError("Failure in nearest neighbour analysis:\n" + str(e)) diff --git a/src/dials/algorithms/indexing/nearest_neighbor.py b/src/dials/algorithms/indexing/nearest_neighbor.py index 4d5de82d88..2e5c0af2e1 100644 --- a/src/dials/algorithms/indexing/nearest_neighbor.py +++ b/src/dials/algorithms/indexing/nearest_neighbor.py @@ -13,6 +13,7 @@ def __init__( percentile=None, histogram_binning="linear", nn_per_bin=5, + convert_reflections_z_to_deg=True, ): self.tolerance = tolerance # Margin of error for max unit cell estimate from scitbx.array_family import flex @@ -28,7 +29,10 @@ def __init__( else: entering_flags = flex.bool(reflections.size(), True) rs_vectors = reflections["rlp"] - phi_deg = reflections["xyzobs.mm.value"].parts()[2] * (180 / math.pi) + + z = reflections["xyzobs.mm.value"].parts()[2] + if convert_reflections_z_to_deg: + z = z * (180 / math.pi) d_spacings = flex.double() # nearest neighbor analysis @@ -38,16 +42,16 @@ def __init__( sel_imageset = reflections["imageset_id"] == imageset_id if sel_imageset.count(True) == 0: continue - phi_min = flex.min(phi_deg.select(sel_imageset)) - phi_max = flex.max(phi_deg.select(sel_imageset)) - d_phi = phi_max - phi_min - n_steps = max(int(math.ceil(d_phi / step_size)), 1) + z_min = flex.min(z.select(sel_imageset)) + z_max = flex.max(z.select(sel_imageset)) + d_z = z_max - z_min + n_steps = max(int(math.ceil(d_z / step_size)), 1) for n in range(n_steps): sel_step = ( sel_imageset - & (phi_deg >= (phi_min + n * step_size)) - & (phi_deg < (phi_min + (n + 1) * step_size)) + & (z >= (z_min + n * step_size)) + & (z < (z_min + (n + 1) * step_size)) ) for entering in (True, False):