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) raise RuntimeError('reindexing error: %s' % \ os.path.join(self.get_working_directory(), 'XSCALE.LP'))
def run(self, ignore_errors=False): """Run idxref.""" # image_header = self.get_header() ## crank through the header dictionary and replace incorrect ## information with updated values through the indexer ## interface if available... ## need to add distance, wavelength - that should be enough... # if self.get_distance(): # image_header['distance'] = self.get_distance() # if self.get_wavelength(): # image_header['wavelength'] = self.get_wavelength() # if self.get_two_theta(): # image_header['two_theta'] = self.get_two_theta() header = imageset_to_xds( self.get_imageset(), refined_beam_vector=self._refined_beam_vector, refined_rotation_axis=self._refined_rotation_axis, refined_distance=self._refined_distance, ) xds_inp = open(os.path.join(self.get_working_directory(), "XDS.INP"), "w") # what are we doing? xds_inp.write("JOB=IDXREF\n") xds_inp.write("MAXIMUM_NUMBER_OF_PROCESSORS=%d\n" % self._parallel) # FIXME this needs to be calculated from the beam centre... if self._refined_origin: xds_inp.write("ORGX=%f ORGY=%f\n" % tuple(self._refined_origin)) else: xds_inp.write("ORGX=%f ORGY=%f\n" % tuple(self._org)) # FIXME in here make sure sweep is wider than 5 degrees # before specifying AXIS: if <= 5 degrees replace AXIS with # nothing - base this on the maximum possible angular separation min_frame = self._spot_range[0][0] max_frame = self._spot_range[-1][1] refine_params = [p for p in self._params.refine] phi_width = self.get_phi_width() if "AXIS" in refine_params and (max_frame - min_frame) * phi_width < 5.0: refine_params.remove("AXIS") xds_inp.write("REFINE(IDXREF)=%s\n" % " ".join(refine_params)) if self._starting_frame and self._starting_angle: xds_inp.write("STARTING_FRAME=%d\n" % self._starting_frame) xds_inp.write("STARTING_ANGLE=%f\n" % self._starting_angle) # FIXME this looks like a potential bug - what will # happen if the input lattice has not been set?? if self._indxr_input_cell: self._cell = self._indxr_input_cell if self._indxr_input_lattice: self._symm = lattice_to_spacegroup_number(self._indxr_input_lattice) if self._cell: xds_inp.write("SPACE_GROUP_NUMBER=%d\n" % self._symm) cell_format = "%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f" xds_inp.write("UNIT_CELL_CONSTANTS=%s\n" % cell_format % self._cell) if self._a_axis: xds_inp.write("UNIT_CELL_A-AXIS=%.2f %.2f %.2f\n" % tuple(self._a_axis)) if self._b_axis: xds_inp.write("UNIT_CELL_B-AXIS=%.2f %.2f %.2f\n" % tuple(self._b_axis)) if self._c_axis: xds_inp.write("UNIT_CELL_C-AXIS=%.2f %.2f %.2f\n" % tuple(self._c_axis)) for record in header: xds_inp.write("%s\n" % record) name_template = template_to_xds( os.path.join(self.get_directory(), self.get_template()) ) record = "NAME_TEMPLATE_OF_DATA_FRAMES=%s\n" % name_template xds_inp.write(record) xds_inp.write("DATA_RANGE=%d %d\n" % self._data_range) for spot_range in self._spot_range: xds_inp.write("SPOT_RANGE=%d %d\n" % spot_range) xds_inp.write("BACKGROUND_RANGE=%d %d\n" % self._background_range) xds_inp.close() # copy the input file... shutil.copyfile( os.path.join(self.get_working_directory(), "XDS.INP"), os.path.join( self.get_working_directory(), "%d_IDXREF.INP" % self.get_xpid() ), ) # write the input data files... for file_name in self._input_data_files_list: src = self._input_data_files[file_name] dst = os.path.join(self.get_working_directory(), file_name) if src != dst: shutil.copyfile(src, dst) self.start() self.close_wait() xds_check_version_supported(self.get_all_output()) if not ignore_errors: xds_check_error(self.get_all_output()) # If xds_check_error detects any errors it will raise an exception # The caller can then continue using the run_continue_from_error() # function. If XDS does not throw any errors we just plow on. return self.continue_from_error()
def run(self): """Run xycorr.""" # image_header = self.get_header() # crank through the header dictionary and replace incorrect # information with updated values through the indexer # interface if available... # need to add distance, wavelength - that should be enough... # if self.get_distance(): # image_header['distance'] = self.get_distance() # if self.get_wavelength(): # image_header['wavelength'] = self.get_wavelength() # if self.get_two_theta(): # image_header['two_theta'] = self.get_two_theta() header = imageset_to_xds(self.get_imageset()) from xia2.Handlers.Phil import PhilIndex xds_params = PhilIndex.params.xia2.settings.xds xds_inp = open( os.path.join(self.get_working_directory(), "XDS.INP"), "w") # what are we doing? xds_inp.write("JOB=XYCORR\n") for record in header: xds_inp.write("%s\n" % record) if xds_params.geometry_x and xds_params.geometry_y: xds_inp.write("X-GEO_CORR=%s\n" % xds_params.geometry_x) xds_inp.write("Y-GEO_CORR=%s\n" % xds_params.geometry_y) name_template = template_to_xds( os.path.join(self.get_directory(), self.get_template())) record = "NAME_TEMPLATE_OF_DATA_FRAMES=%s\n" % name_template xds_inp.write(record) xds_inp.write("DATA_RANGE=%d %d\n" % self._data_range) for spot_range in self._spot_range: xds_inp.write("SPOT_RANGE=%d %d\n" % spot_range) xds_inp.write("BACKGROUND_RANGE=%d %d\n" % self._background_range) xds_inp.write("ORGX=%f ORGY=%f\n" % tuple(self._org)) xds_inp.close() # copy the input file... shutil.copyfile( os.path.join(self.get_working_directory(), "XDS.INP"), os.path.join(self.get_working_directory(), "%d_XYCORR.INP" % self.get_xpid()), ) # write the input data files... for file_name in self._input_data_files_list: src = self._input_data_files[file_name] dst = os.path.join(self.get_working_directory(), file_name) if src != dst: shutil.copyfile(src, dst) self.start() self.close_wait() xds_check_version_supported(self.get_all_output()) # check the status xds_check_error(self.get_all_output()) # copy the LP file shutil.copyfile( os.path.join(self.get_working_directory(), "XYCORR.LP"), os.path.join(self.get_working_directory(), "%d_XYCORR.LP" % self.get_xpid()), ) # gather the output files for file in self._output_data_files_list: self._output_data_files[file] = os.path.join( self.get_working_directory(), file) return
def run(self): '''Run correct.''' # this is ok... # if not self._cell: # raise RuntimeError('cell not set') # if not self._spacegroup_number: # raise RuntimeError('spacegroup not set') #image_header = self.get_header() ## crank through the header dictionary and replace incorrect ## information with updated values through the indexer ## interface if available... ## need to add distance, wavelength - that should be enough... #if self.get_distance(): #image_header['distance'] = self.get_distance() #if self.get_wavelength(): #image_header['wavelength'] = self.get_wavelength() #if self.get_two_theta(): #image_header['two_theta'] = self.get_two_theta() header = imageset_to_xds(self.get_imageset()) xds_inp = open( os.path.join(self.get_working_directory(), 'XDS.INP'), 'w') # what are we doing? xds_inp.write('JOB=CORRECT\n') xds_inp.write('MAXIMUM_NUMBER_OF_PROCESSORS=%d\n' % \ self._parallel) # check to see if we are excluding ice rings if self._ice != 0: Debug.write('Excluding ice rings') for record in open( os.path.abspath( os.path.join(os.path.dirname(__file__), '..', '..', 'Data', 'ice-rings.dat'))).readlines(): resol = tuple(map(float, record.split()[:2])) xds_inp.write('EXCLUDE_RESOLUTION_RANGE= %.2f %.2f\n' % \ resol) # exclude requested resolution ranges if self._excluded_regions: Debug.write('Excluding regions: %s' % repr(self._excluded_regions)) for upper, lower in self._excluded_regions: xds_inp.write('EXCLUDE_RESOLUTION_RANGE= %.2f %.2f\n' % \ (upper, lower)) # postrefine everything to give better values to the # next INTEGRATE run xds_inp.write('REFINE(CORRECT)=%s\n' % ' '.join(self._params.refine)) if self._polarization > 0.0: xds_inp.write('FRACTION_OF_POLARIZATION=%.2f\n' % \ self._polarization) if self._params.air is not None: xds_inp.write('AIR=%f' % self._params.air) for record in header: xds_inp.write('%s\n' % record) name_template = template_to_xds( os.path.join(self.get_directory(), self.get_template())) record = 'NAME_TEMPLATE_OF_DATA_FRAMES=%s\n' % \ name_template xds_inp.write(record) xds_inp.write('DATA_RANGE=%d %d\n' % self._data_range) # xds_inp.write('MINIMUM_ZETA=0.1\n') # include the resolution range, perhaps if self._resolution_high or self._resolution_low: xds_inp.write('INCLUDE_RESOLUTION_RANGE=%.2f %.2f\n' % \ (self._resolution_low, self._resolution_high)) if self._anomalous: xds_inp.write('FRIEDEL\'S_LAW=FALSE\n') xds_inp.write('STRICT_ABSORPTION_CORRECTION=TRUE\n') else: xds_inp.write('FRIEDEL\'S_LAW=TRUE\n') if self._spacegroup_number: if not self._cell: raise RuntimeError( 'cannot set spacegroup without unit cell') xds_inp.write('SPACE_GROUP_NUMBER=%d\n' % \ self._spacegroup_number) if self._cell: xds_inp.write('UNIT_CELL_CONSTANTS=') xds_inp.write('%6.2f %6.2f %6.2f %6.2f %6.2f %6.2f\n' % \ tuple(self._cell)) if self._reindex_matrix: xds_inp.write('REIDX=%d %d %d %d %d %d %d %d %d %d %d %d' % \ tuple(map(int, self._reindex_matrix))) xds_inp.close() # copy the input file... shutil.copyfile( os.path.join(self.get_working_directory(), 'XDS.INP'), os.path.join(self.get_working_directory(), '%d_CORRECT.INP' % self.get_xpid())) # write the input data files... for file_name in self._input_data_files_list: src = self._input_data_files[file_name] dst = os.path.join(self.get_working_directory(), file_name) if src != dst: shutil.copyfile(src, dst) self.start() self.close_wait() xds_check_version_supported(self.get_all_output()) xds_check_error(self.get_all_output()) # look for errors # like this perhaps # !!! ERROR !!! ILLEGAL SPACE GROUP NUMBER OR UNIT CELL # copy the LP file shutil.copyfile( os.path.join(self.get_working_directory(), 'CORRECT.LP'), os.path.join(self.get_working_directory(), '%d_CORRECT.LP' % self.get_xpid())) # gather the output files for file in self._output_data_files_list: self._output_data_files[file] = os.path.join( self.get_working_directory(), file) self._xds_ascii_hkl = os.path.join(self.get_working_directory(), 'XDS_ASCII.HKL') # do some parsing of the correct output... self._results = _parse_correct_lp( os.path.join(self.get_working_directory(), 'CORRECT.LP')) # check that the unit cell is comparable to what went in i.e. # the volume is the same to within a factor of 10 (which is # extremely generous and should only spot gross errors) original = unit_cell(self._cell) refined = unit_cell(self._results['cell']) if original.volume() / refined.volume() > 10: raise RuntimeError('catastrophic change in unit cell volume') if refined.volume() / original.volume() > 10: raise RuntimeError('catastrophic change in unit cell volume') # record reindex operation used for future reference... this # is to trap trac #419 if 'reindex_op' in self._results: format = 'XDS applied reindex:' + 12 * ' %d' Debug.write(format % tuple(self._results['reindex_op'])) self._reindex_used = self._results['reindex_op'] # get the reflections to remove... for line in open( os.path.join(self.get_working_directory(), 'CORRECT.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)) return
def run(self): """Run integrate.""" # image_header = self.get_header() ## crank through the header dictionary and replace incorrect ## information with updated values through the indexer ## interface if available... ## need to add distance, wavelength - that should be enough... # if self.get_distance(): # image_header['distance'] = self.get_distance() # if self.get_wavelength(): # image_header['wavelength'] = self.get_wavelength() # if self.get_two_theta(): # image_header['two_theta'] = self.get_two_theta() header = imageset_to_xds(self.get_imageset()) xds_inp = open(os.path.join(self.get_working_directory(), "XDS.INP"), "w") # what are we doing? xds_inp.write("JOB=INTEGRATE\n") xds_inp.write("MAXIMUM_NUMBER_OF_PROCESSORS=%d\n" % self._parallel) from xia2.Handlers.Phil import PhilIndex xds_params = PhilIndex.params.xds if xds_params.profile_grid_size: ab, c = xds_params.profile_grid_size assert ab > 0 and ab < 22 and (ab % 2) == 1 assert c > 0 and c < 22 and (c % 2) == 1 xds_inp.write( "NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA= %d\n" % ab ) xds_inp.write("NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= %d\n" % c) from libtbx import Auto mp_params = PhilIndex.params.xia2.settings.multiprocessing if mp_params.mode == "serial" and mp_params.njob > 1: xds_inp.write("MAXIMUM_NUMBER_OF_JOBS=%d\n" % mp_params.njob) elif mp_params.mode == "serial" and mp_params.njob == Auto: chunk_width = 30.0 phi_width = self.get_phi_width() nchunks = int( (self._data_range[1] - self._data_range[0] + 1) * phi_width / chunk_width ) Debug.write("Xparallel: -1 using %d chunks" % nchunks) xds_inp.write("MAXIMUM_NUMBER_OF_JOBS=%d\n" % nchunks) else: xds_inp.write("MAXIMUM_NUMBER_OF_JOBS=1\n") profile_fitting = PhilIndex.params.xia2.settings.integration.profile_fitting if not profile_fitting: xds_inp.write("PROFILE_FITTING=FALSE\n") # write out lots of output xds_inp.write("TEST=2\n") if self._params.delphi: xds_inp.write("DELPHI=%.1f\n" % self._params.delphi) elif PhilIndex.params.xia2.settings.small_molecule: xds_inp.write("DELPHI=%.1f\n" % xds_params.delphi_small) else: xds_inp.write("DELPHI=%.1f\n" % xds_params.delphi) if self._refined_xparm: xds_inp.write( "REFINE(INTEGRATE)=%s\n" % " ".join(self._params.refine_final) ) else: xds_inp.write("REFINE(INTEGRATE)=%s\n" % " ".join(self._params.refine)) if self._params.fix_scale: if _running_xds_version() >= 20130330: xds_inp.write( "DATA_RANGE_FIXED_SCALE_FACTOR= %d %d 1\n" % self._data_range ) else: xds_inp.write("FIXED_SCALE_FACTOR=TRUE\n") # check for updated input parameters or ones from phil if ( "BEAM_DIVERGENCE" in self._updates and "BEAM_DIVERGENCE_E.S.D." in self._updates ): xds_inp.write( "BEAM_DIVERGENCE=%f BEAM_DIVERGENCE_E.S.D.=%f\n" % ( self._updates["BEAM_DIVERGENCE"], self._updates["BEAM_DIVERGENCE_E.S.D."], ) ) elif self._params.beam_divergence and self._params.beam_divergence_esd: xds_inp.write( "BEAM_DIVERGENCE=%f BEAM_DIVERGENCE_E.S.D.=%f\n" % (self._params.beam_divergence, self._params.beam_divergence_esd) ) if ( "REFLECTING_RANGE" in self._updates and "REFLECTING_RANGE_E.S.D." in self._updates ): xds_inp.write( "REFLECTING_RANGE=%f REFLECTING_RANGE_E.S.D.=%f\n" % ( self._updates["REFLECTING_RANGE"], self._updates["REFLECTING_RANGE_E.S.D."], ) ) elif self._params.reflecting_range and self._params.reflecting_range_esd: xds_inp.write( "REFLECTING_RANGE=%f REFLECTING_RANGE_E.S.D.=%f\n" % (self._params.reflecting_range, self._params.reflecting_range_esd) ) for record in header: xds_inp.write("%s\n" % record) name_template = template_to_xds( os.path.join(self.get_directory(), self.get_template()) ) record = "NAME_TEMPLATE_OF_DATA_FRAMES=%s\n" % name_template xds_inp.write(record) lib_str = find_hdf5_lib( os.path.join(self.get_directory(), self.get_template()) ) if lib_str: xds_inp.write(lib_str) xds_inp.write("DATA_RANGE=%d %d\n" % self._data_range) xds_inp.close() # copy the input file... shutil.copyfile( os.path.join(self.get_working_directory(), "XDS.INP"), os.path.join( self.get_working_directory(), "%d_INTEGRATE.INP" % self.get_xpid() ), ) # write the input data files... for file_name in self._input_data_files_list: src = self._input_data_files[file_name] dst = os.path.join(self.get_working_directory(), file_name) if src != dst: shutil.copyfile(src, dst) self.start() self.close_wait() xds_check_version_supported(self.get_all_output()) xds_check_error(self.get_all_output()) # look for errors # like this perhaps - what the hell does this mean? # !!! ERROR !!! "STRONGHKL": ASSERT VIOLATION # copy the LP file shutil.copyfile( os.path.join(self.get_working_directory(), "INTEGRATE.LP"), os.path.join( self.get_working_directory(), "%d_INTEGRATE.LP" % self.get_xpid() ), ) # gather the output files for file in self._output_data_files_list: self._output_data_files[file] = os.path.join( self.get_working_directory(), file ) self._integrate_hkl = os.path.join( self.get_working_directory(), "INTEGRATE.HKL" ) # look through integrate.lp for some useful information # to help with the analysis space_group_number = 0 mosaics = [] for o in open( os.path.join(self.get_working_directory(), "INTEGRATE.LP") ).readlines(): if "SPACE_GROUP_NUMBER" in o: space_group_number = int(o.split()[-1]) if "CRYSTAL MOSAICITY (DEGREES)" in o: mosaic = float(o.split()[-1]) mosaics.append(mosaic) assert ( len(mosaics) > 0 ), "XDS refinement failed (no mosaic spread range reported)" self._min_mosaic = min(mosaics) self._max_mosaic = max(mosaics) self._mean_mosaic = sum(mosaics) / len(mosaics) Debug.write( "Mosaic spread range: %.3f %.3f %.3f" % (self._min_mosaic, self._mean_mosaic, self._max_mosaic) ) stats = _parse_integrate_lp( os.path.join(self.get_working_directory(), "INTEGRATE.LP") ) self._per_image_statistics = stats self._updates = _parse_integrate_lp_updates( os.path.join(self.get_working_directory(), "INTEGRATE.LP") ) 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 with open(os.path.join(self.get_working_directory(), "XSCALE.LP"), "r") as fh: lines = fh.readlines() for line in lines: 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 dname not 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")) logger.debug("Low correlations - check data sets") for j, name in enumerate(groups): logger.debug("Group %d" % j) for file_name in groups[name]: logger.debug(file_name) raise RuntimeError("reindexing error: %s" % os.path.join( self.get_working_directory(), "XSCALE.LP"))