#!/usr/bin/env python # Index.py # # Copyright (C) 2014 Diamond Light Source, Richard Gildea, Graeme Winter # # This code is distributed under the BSD license, a copy of which is # included in the root directory of this package. # # Autoindex using the DIALS code: assumes spots found from same. from __future__ import division import os import shutil from __init__ import _setup_xia2_environ _setup_xia2_environ() from Handlers.Flags import Flags def Index(DriverType = None): '''A factory for IndexWrapper classes.''' from Driver.DriverFactory import DriverFactory DriverInstance = DriverFactory.Driver(DriverType) class IndexWrapper(DriverInstance.__class__): def __init__(self): DriverInstance.__class__.__init__(self) self.set_executable('dials.index') self._sweep_filename = None self._spot_filename = None self._unit_cell = None self._space_group = None self._maximum_spot_error = 3.0 self._detector_fix = None self._beam_fix = None self._indexing_method = "fft3d" self._p1_cell = None self._indxr_input_cell = None self._indxr_input_lattice = None self._experiment_filename = None self._indexed_filename = None self._nref = None self._rmsd_x = None self._rmsd_y = None self._rmsd_z = None self._max_cell = None self._phil_file = None return def set_sweep_filename(self, sweep_filename): if sweep_filename == 'datablock.json': raise RuntimeError, 'chosen sweep name will be overwritten' self._sweep_filename = sweep_filename return def set_spot_filename(self, spot_filename): self._spot_filename = spot_filename return def set_indexer_input_lattice(self, lattice): self._indxr_input_lattice = lattice return def set_indexer_user_input_lattice(self, user): self._indxr_user_input_lattice = user return def set_indexer_input_cell(self, cell): if not type(cell) == type(()): raise RuntimeError, 'cell must be a 6-tuple de floats' if len(cell) != 6: raise RuntimeError, 'cell must be a 6-tuple de floats' self._indxr_input_cell = tuple(map(float, cell)) return def set_maximum_spot_error(self, maximum_spot_error): self._maximum_spot_error = maximum_spot_error return def set_detector_fix(self, detector_fix): self._detector_fix = detector_fix return def set_beam_fix(self, beam_fix): self._beam_fix = beam_fix return def set_indexing_method(self, method): self._indexing_method = method return def set_indexing_method(self): return self._indexing_method def get_sweep_filename(self): return os.path.join(self.get_working_directory(), 'datablock.json') def get_experiments_filename(self): return self._experiment_filename def get_indexed_filename(self): return self._indexed_filename def get_p1_cell(self): return self._p1_cell def set_phil_file(self, phil_file): self._phil_file = phil_file return def get_nref_rmsds(self): return self._nref, (self._rmsd_x, self._rmsd_y, self._rmsd_z) def set_max_cell(self, max_cell): self._max_cell = max_cell return def run(self, method): from Handlers.Streams import Debug Debug.write('Running dials.index') self.clear_command_line() self.add_command_line(self._sweep_filename) self.add_command_line(self._spot_filename) self.add_command_line('method=%s' % method) self.add_command_line('use_all_reflections=False') self.add_command_line('close_to_spindle_cutoff=0.02') if self._max_cell: self.add_command_line('max_cell=%d' % self._max_cell) if self._indxr_input_lattice is not None: from Experts.SymmetryExpert import lattice_to_spacegroup_number self._symm = lattice_to_spacegroup_number( self._indxr_input_lattice) self.add_command_line('space_group=%s' % self._symm) if self._indxr_input_cell is not None: self.add_command_line( 'unit_cell="%s,%s,%s,%s,%s,%s"' %self._indxr_input_cell) if self._maximum_spot_error: self.add_command_line('maximum_spot_error=%.f' % self._maximum_spot_error) if self._detector_fix: self.add_command_line('detector.fix=%s' % self._detector_fix) if self._beam_fix: self.add_command_line('beam.fix=%s' % self._beam_fix) if self._phil_file is not None: self.add_command_line("%s" %self._phil_file) self.start() self.close_wait() self.check_for_errors() self._experiment_filename = os.path.join( self.get_working_directory(), '%d_experiments.json' %self.get_xpid()) shutil.copyfile( os.path.join(self.get_working_directory(), 'experiments.json'), self._experiment_filename) self._indexed_filename = os.path.join( self.get_working_directory(), '%d_indexed.pickle' %self.get_xpid()) shutil.copyfile( os.path.join(self.get_working_directory(), 'indexed.pickle'), self._indexed_filename) records = self.get_all_output() for i, record in enumerate(records): if 'Unit cell:' in record: self._p1_cell = map(float, record.replace('(', '').replace( ')', '').replace(',', '').split()[-6:]) if 'Final RMSDs by experiment' in record: values = records[i+6].strip().strip('|').split('|') if len(values): values = [float(v) for v in values] if values[0] == 0: self._nref = int(values[1]) self._rmsd_x = values[2] self._rmsd_y = values[3] self._rmsd_z = values[4] return return IndexWrapper() if __name__ == '__main__': import sys image_file = sys.argv[1] scan_ranges = [(int(token.split(',')[0]), int(token.split(',')[1])) for token in sys.argv[2:]] from Wrappers.Dials.Import import Import from Wrappers.Dials.Spotfinder import Spotfinder from Wrappers.Dials.RefineBravaisSettings import RefineBravaisSettings print "Begin importing" importer = Import() importer.setup_from_image(image_file) importer.set_image_range(scan_ranges[0]) importer.run() print ''.join(importer.get_all_output()) print "Done importing" print "Begin spotfinding" spotfinder = Spotfinder() spotfinder.set_sweep_filename(importer.get_sweep_filename()) spotfinder.set_scan_ranges(scan_ranges) spotfinder.run() print ''.join(spotfinder.get_all_output()) print "Done spotfinding" print "Begin indexing" indexer = Index() indexer.set_spot_filename(spotfinder.get_spot_filename()) indexer.set_sweep_filename(importer.get_sweep_filename()) indexer.run('fft3d') print ''.join(indexer.get_all_output()) print "Done indexing" print "Begin refining" rbs = RefineBravaisSettings() rbs.set_experiments_filename(indexer.get_experiments_filename()) rbs.set_indexed_filename(indexer.get_indexed_filename()) rbs.run() print ''.join(rbs.get_all_output()) print "Done refining"