Click here to go to the corresponding page for the latest version of DIALS
Source code for dials.algorithms.indexing.max_cell
from __future__ import absolute_import, division, print_function
import logging
from scitbx.array_family import flex
from dials.algorithms.spot_finding.per_image_analysis import ice_rings_selection
from dials.algorithms.indexing.nearest_neighbor import NeighborAnalysis
from dials.algorithms.indexing import DialsIndexError
logger = logging.getLogger(__name__)
[docs]def find_max_cell(
reflections,
max_cell_multiplier=1.3,
step_size=45,
nearest_neighbor_percentile=None,
histogram_binning="linear",
nn_per_bin=5,
max_height_fraction=0.25,
filter_ice=True,
filter_overlaps=True,
overlaps_border=0,
):
logger.debug("Finding suitable max_cell based on %i reflections" % len(reflections))
# Exclude potential ice-ring spots from nearest neighbour analysis if needed
if filter_ice:
ice_sel = ice_rings_selection(reflections)
reflections = reflections.select(~ice_sel)
logger.debug(
"Rejecting %i reflections at ice ring resolution" % ice_sel.count(True)
)
# need bounding box in reflections to find overlaps; this is not there if
# spots are from XDS (for example)
if filter_overlaps and "bbox" in reflections:
overlap_sel = flex.bool(len(reflections), False)
overlaps = reflections.find_overlaps(border=overlaps_border)
for item in overlaps.edges():
i0 = overlaps.source(item)
i1 = overlaps.target(item)
overlap_sel[i0] = True
overlap_sel[i1] = True
logger.debug(
"Rejecting %i overlapping bounding boxes" % overlap_sel.count(True)
)
reflections = reflections.select(~overlap_sel)
logger.debug("%i reflections remain for max_cell identification" % len(reflections))
if not len(reflections):
raise DialsIndexError(
"Too few spots remaining for nearest neighbour analysis (%d)"
% len(reflections)
)
NN = NeighborAnalysis(
reflections,
step_size=step_size,
max_height_fraction=max_height_fraction,
tolerance=max_cell_multiplier,
percentile=nearest_neighbor_percentile,
histogram_binning=histogram_binning,
nn_per_bin=nn_per_bin,
)
return NN
