#!/usr/bin/env python # XScale.py # Copyright (C) 2006 CCLRC, Graeme Winter # # This code is distributed under the BSD license, a copy of which is # included in the root directory of this package. # # A wrapper for XSCALE, the XDS Scaling program. # import os import sys import copy import math import time import shutil if not os.environ.has_key('XIA2CORE_ROOT'): raise RuntimeError, 'XIA2CORE_ROOT not defined' if not os.environ.has_key('XIA2_ROOT'): raise RuntimeError, 'XIA2_ROOT not defined' if not os.path.join(os.environ['XIA2CORE_ROOT'], 'Python') in sys.path: sys.path.append(os.path.join(os.environ['XIA2CORE_ROOT'], 'Python')) if not os.environ['XIA2_ROOT'] in sys.path: sys.path.append(os.environ['XIA2_ROOT']) from Driver.DriverFactory import DriverFactory from XDS import xds_check_error from Handlers.Flags import Flags from Handlers.Streams import Debug from Handlers.Phil import PhilIndex from XScaleHelpers import get_correlation_coefficients_and_group def XScaleR(DriverType = None, correct_decay = True, correct_absorption = True, correct_modulation = True): DriverInstance = DriverFactory.Driver(DriverType) class XScaleWrapper(DriverInstance.__class__): '''A wrapper for wrapping XSCALE.''' def __init__(self): # set up the object ancestors... DriverInstance.__class__.__init__(self) # now set myself up... self._parallel = Flags.get_parallel() if self._parallel <= 1: self.set_executable('xscale') else: self.set_executable('xscale_par') self._version = 'new' # overall information self._resolution_shells = '' self._cell = None self._spacegroup_number = None self._reindex_matrix = None # corrections to apply - N.B. default values come from the # factory function default arguments... self._correct_decay = correct_decay self._correct_absorption = correct_absorption self._correct_modulation = correct_modulation # input reflections information - including grouping information # in the same way as the .xinfo files - through the wavelength # names, which will be used for the output files. self._input_reflection_files = [] self._input_reflection_wavelength_names = [] self._input_resolution_ranges = [] # these are generated at the run time self._transposed_input = { } self._transposed_input_keys = [] # output self._output_reflection_files = { } self._remove = [] # decisions about the scaling self._crystal = None self._zero_dose = False self._anomalous = True self._merge = False # scale factor output self._scale_factor = 1.0 # Rmerge values - for the scale model analysis - N.B. get # one for each data set, obviously... self._rmerges = { } return def add_reflection_file(self, reflections, wavelength, resolution): self._input_reflection_files.append(reflections) self._input_reflection_wavelength_names.append(wavelength) self._input_resolution_ranges.append(resolution) return def get_remove(self): return self._remove def set_crystal(self, crystal): self._crystal = crystal return def set_zero_dose(self, zero_dose = True): self._zero_dose = zero_dose return def set_anomalous(self, anomalous = True): self._anomalous = anomalous return def set_correct_decay(self, correct_decay): self._correct_decay = correct_decay return def set_correct_absorption(self, correct_absorption): self._correct_absorption = correct_absorption return def set_correct_modulation(self, correct_modulation): self._correct_modulation = correct_modulation return def get_output_reflection_files(self): '''Get a dictionary of output reflection files keyed by wavelength name.''' return copy.deepcopy(self._output_reflection_files) def _transform_input_files(self): '''Transform the input files to an order we can manage.''' for j in range(len(self._input_reflection_files)): hkl = self._input_reflection_files[j] wave = self._input_reflection_wavelength_names[j] resol = self._input_resolution_ranges[j] if not self._transposed_input.has_key(wave): self._transposed_input[wave] = {'hkl':[], 'resol':[]} self._transposed_input_keys.append(wave) self._transposed_input[wave]['hkl'].append(hkl) self._transposed_input[wave]['resol'].append(resol) return def set_spacegroup_number(self, spacegroup_number): self._spacegroup_number = spacegroup_number return def set_cell(self, cell): self._cell = cell return def set_reindex_matrix(self, reindex_matrix): if not len(reindex_matrix) == 12: raise RuntimeError, 'reindex matrix must be 12 numbers' self._reindex_matrix = reindex_matrix return def _write_xscale_inp(self): '''Write xscale.inp.''' self._transform_input_files() xscale_inp = open(os.path.join(self.get_working_directory(), 'XSCALE.INP'), 'w') # header information xscale_inp.write('MAXIMUM_NUMBER_OF_PROCESSORS=%d\n' % \ self._parallel) xscale_inp.write('SPACE_GROUP_NUMBER=%d\n' % \ self._spacegroup_number) xscale_inp.write('UNIT_CELL_CONSTANTS=') xscale_inp.write('%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f\n' % \ tuple(self._cell)) xscale_inp.write( 'MINIMUM_I/SIGMA=%.1f\n' %PhilIndex.params.xds.xscale.min_isigma) if self._reindex_matrix: xscale_inp.write( 'REIDX=%d %d %d %d %d %d %d %d %d %d %d %d\n' % \ tuple(map(int, self._reindex_matrix))) # now information about the wavelengths for wave in self._transposed_input_keys: self._output_reflection_files[wave] = os.path.join( self.get_working_directory(), '%s.HKL' % wave) xscale_inp.write( 'OUTPUT_FILE=%s.HKL ' % wave) if self._version == 'new': xscale_inp.write('\n') if self._anomalous: xscale_inp.write('FRIEDEL\'S_LAW=FALSE MERGE=FALSE\n') xscale_inp.write('STRICT_ABSORPTION_CORRECTION=TRUE\n') else: xscale_inp.write('FRIEDEL\'S_LAW=TRUE MERGE=FALSE\n') if self._version == 'new': xscale_inp.write('\n') for j in range(len(self._transposed_input[wave]['hkl'])): # FIXME note to self, this should now be a local # file which has been placed in here by XDSScaler - # should check that the files exists though... resolution = self._transposed_input[wave]['resol'][j] if resolution[0]: xscale_inp.write( 'INPUT_FILE=%s XDS_ASCII\n' % \ self._transposed_input[wave]['hkl'][j]) xscale_inp.write( 'INCLUDE_RESOLUTION_RANGE= %.2f %.2f\n' % \ (resolution[1], resolution[0])) else: xscale_inp.write( 'INPUT_FILE=%s XDS_ASCII\n' % \ self._transposed_input[wave]['hkl'][j]) # FIXME this needs to be removed before being used again # in anger! # xscale_inp.write('CORRECTIONS=DECAY ABSORPTION\n') corrections = 'CORRECTIONS=' if self._correct_decay: corrections += ' DECAY' if self._correct_modulation: corrections += ' MODULATION' if self._correct_absorption: corrections += ' ABSORPTION' corrections += '\n' xscale_inp.write(corrections) if self._crystal and self._zero_dose: xscale_inp.write('CRYSTAL_NAME=%s\n' % self._crystal) xscale_inp.close() return def run(self): '''Actually run XSCALE.''' self._write_xscale_inp() # copy the input file... shutil.copyfile(os.path.join(self.get_working_directory(), 'XSCALE.INP'), os.path.join(self.get_working_directory(), '%d_XSCALE.INP' % self.get_xpid())) self.start() self.close_wait() # copy the LP file shutil.copyfile(os.path.join(self.get_working_directory(), 'XSCALE.LP'), os.path.join(self.get_working_directory(), '%d_XSCALE.LP' % self.get_xpid())) # now look at XSCALE.LP xds_check_error(self.get_all_output()) dname = None # get the outlier reflections... and the overall scale factor for line in open(os.path.join( self.get_working_directory(), 'XSCALE.LP'), 'r').readlines(): if '"alien"' in line: h, k, l = tuple(map(int, line.split()[:3])) z = float(line.split()[4]) if not (h, k, l, z) in self._remove: self._remove.append((h, k, l, z)) if 'FACTOR TO PLACE ALL DATA SETS TO ' in line: self._scale_factor = float(line.split()[-1]) if 'STATISTICS OF SCALED OUTPUT DATA SET' in line: dname = line.split()[-1].replace('.HKL', '') if 'total' in line and not dname in self._rmerges: if len(line.split()) > 5: self._rmerges[dname] = float( line.replace('%', '').split()[5]) # trac #419 - if the data sets are not correctly indexed, # throw an exception. N.B. this will only work if the # data sets are moderately complete (i.e. there are more # than a handful of common reflections) - which may not be # the case in MULTICRYSTAL mode. if ' !!! WARNING !!! ' in line and \ 'CORRELATION FACTORS ARE DANGEROUSLY SMALL' in line: groups = get_correlation_coefficients_and_group( os.path.join(self.get_working_directory(), 'XSCALE.LP')) Debug.write('Low correlations - check data sets') for j, name in enumerate(groups): Debug.write('Group %d' % j) for file_name in groups[name]: Debug.write(file_name) if not Flags.get_microcrystal(): raise RuntimeError, 'reindexing error: %s' % \ os.path.join(self.get_working_directory(), 'XSCALE.LP') return def get_scale_factor(self): return self._scale_factor def get_rmerges(self): return self._rmerges return XScaleWrapper()