Source code for dials.algorithms.indexing.max_cell

import logging

from scitbx.array_family import flex

from dials.algorithms.indexing import DialsIndexError
from dials.algorithms.indexing.nearest_neighbor import NeighborAnalysis
from dials.algorithms.spot_finding.per_image_analysis import ice_rings_selection

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