def process(self, _edObject = None): EDPluginControl.process(self) self.DEBUG("EDPluginControlRunXds.process") # First run is vanilla without any modification params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file self.first_run.dataInput = params self.first_run.executeSynchronous() EDVerbose.DEBUG('first run completed...') if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.first_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # second run w/ JOB set to DEFPIX INTEGRATE CORRECT self.second_run = self.loadPlugin(self.controlled_plugin_name) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.jobs = 'DEFPIX INTEGRATE CORRECT' self.second_run.dataInput = params self.second_run.executeSynchronous() EDVerbose.DEBUG('second run completed') if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.second_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # third run with JOB set to ALL and mxaprocs = 4 and maxjobs = 1 self.third_run = self.loadPlugin(self.controlled_plugin_name) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.jobs = 'ALL' params.maxprocs = 4 params.maxjobs = 1 self.third_run.dataInput = params self.third_run.executeSynchronous() EDVerbose.DEBUG('third run completed') if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.third_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # final run with parallelism like 3 but JOB like 2 self.final_run = self.loadPlugin(self.controlled_plugin_name) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.jobs = 'DEFPIX INTEGRATE CORRECT' params.maxprocs = 4 params.maxjobs = 1 self.final_run.dataInput = params self.final_run.executeSynchronous() EDVerbose.DEBUG('final run completed') if self.final_run.dataOutput is not None and self.final_run.dataOutput.succeeded: EDVerbose.DEBUG('... and it worked') self.successful_run = self.final_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # all runs failed so bail out ... self.setFailure() else: # use the xds parser plugin to parse the xds output file... parser = self.loadPlugin("EDPluginParseXdsOutput") wd = self.successful_run.getWorkingDirectory() parser_input = XSDataXdsOutputFile() correct_lp_path = XSDataFile() correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP')) parser_input.correct_lp = correct_lp_path gxparm_path = os.path.join(wd, 'GXPARM.XDS') if os.path.isfile(gxparm_path): gxparm = XSDataFile() gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS')) parser_input.gxparm = gxparm parser.dataInput = parser_input parser.executeSynchronous() if parser.isFailure(): # that should not happen self.setFailure() return self.dataOutput = parser.dataOutput
def process(self, _edObject = None): EDPluginControl.process(self) self.DEBUG("EDPluginControlRunXdsFastProc.process") # First run is vanilla without any modification params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.spacegroup = self.dataInput.spacegroup params.unit_cell = self.dataInput.unit_cell self.first_run.dataInput = params self.first_run.executeSynchronous() EDVerbose.DEBUG('first run completed...') if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.first_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: self.second_run = self.loadPlugin(self.controlled_plugin_name) self.DEBUG('retrying with increased SPOT_RANGE') self.DEBUG('copying previously generated files to the new plugin dir') copy_xds_files(self.first_run.getWorkingDirectory(), self.second_run.getWorkingDirectory()) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.job = XSDataString('DEFPIX INTEGRATE CORRECT') params.spacegroup = self.dataInput.spacegroup params.unit_cell = self.dataInput.unit_cell # increase all the spot ranges end by 20, constrained to # the data range upper limit spot_range = list() for srange in self.spot_range: range_begin = srange[0] range_end = srange[1] + 20 if range_end > self.end_image_no: self.DEBUG('End of range {0} would be past the last image {1}'.format(range_end, self.end_image_no)) range_end = self.end_image_no self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(srange, range_begin, range_end)) r = XSDataRange(begin=range_begin, end=range_end) spot_range.append(r) params.spot_range = spot_range self.second_run.dataInput = params self.second_run.executeSynchronous() EDVerbose.DEBUG('second run completed') if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.second_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: self.third_run = self.loadPlugin(self.controlled_plugin_name) self.DEBUG('retrying with increased SPOT_RANGE') self.DEBUG('copying previously generated files to the new plugin dir') copy_xds_files(self.second_run.getWorkingDirectory(), self.third_run.getWorkingDirectory()) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.job = XSDataString('DEFPIX INTEGRATE CORRECT') params.spacegroup = self.dataInput.spacegroup params.unit_cell = self.dataInput.unit_cell spot_range = list() for srange in self.spot_range: range_begin = srange[0] range_end = srange[1] + 40 if range_end > self.end_image_no: self.DEBUG('End of range {0} would be past the last image {1}'.format(range_end, self.end_image_no)) range_end = self.end_image_no self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(srange, range_begin, range_end)) r = XSDataRange(begin=range_begin, end=range_end) spot_range.append(r) params.spot_range = spot_range self.third_run.dataInput = params self.third_run.executeSynchronous() EDVerbose.DEBUG('third run completed') if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.third_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # all runs failed so bail out ... self.setFailure() else: # use the xds parser plugin to parse the xds output file... parser = self.loadPlugin("EDPluginParseXdsOutput") wd = self.successful_run.getWorkingDirectory() parser_input = XSDataXdsOutputFile() correct_lp_path = XSDataFile() correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP')) parser_input.correct_lp = correct_lp_path gxparm_path = os.path.join(wd, 'GXPARM.XDS') if os.path.isfile(gxparm_path): gxparm = XSDataFile() gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS')) parser_input.gxparm = gxparm parser.dataInput = parser_input parser.executeSynchronous() if parser.isFailure(): # that should not happen self.setFailure() return self.dataOutput = parser.dataOutput
def process(self, _edObject=None): EDPluginControl.process(self) self.DEBUG("EDPluginControlRunXdsFastProc.process") # First run is vanilla without any modification params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.spacegroup = self.dataInput.spacegroup params.unit_cell = self.dataInput.unit_cell self.first_run.dataInput = params self.first_run.executeSynchronous() EDVerbose.DEBUG('first run completed...') if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.first_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: self.second_run = self.loadPlugin(self.controlled_plugin_name) self.DEBUG('retrying with increased SPOT_RANGE') self.DEBUG( 'copying previously generated files to the new plugin dir') copy_xds_files(self.first_run.getWorkingDirectory(), self.second_run.getWorkingDirectory()) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.job = XSDataString('DEFPIX INTEGRATE CORRECT') params.spacegroup = self.dataInput.spacegroup params.unit_cell = self.dataInput.unit_cell # increase all the spot ranges end by 20, constrained to # the data range upper limit spot_range = list() for srange in self.spot_range: range_begin = srange[0] range_end = srange[1] + 20 if range_end > self.end_image_no: self.DEBUG( 'End of range {0} would be past the last image {1}'. format(range_end, self.end_image_no)) range_end = self.end_image_no self.DEBUG('Changing spot range {0} to [{1} {2}]'.format( srange, range_begin, range_end)) r = XSDataRange(begin=range_begin, end=range_end) spot_range.append(r) params.spot_range = spot_range self.second_run.dataInput = params self.second_run.executeSynchronous() EDVerbose.DEBUG('second run completed') if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.second_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: self.third_run = self.loadPlugin(self.controlled_plugin_name) self.DEBUG('retrying with increased SPOT_RANGE') self.DEBUG( 'copying previously generated files to the new plugin dir') copy_xds_files(self.second_run.getWorkingDirectory(), self.third_run.getWorkingDirectory()) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.job = XSDataString('DEFPIX INTEGRATE CORRECT') params.spacegroup = self.dataInput.spacegroup params.unit_cell = self.dataInput.unit_cell spot_range = list() for srange in self.spot_range: range_begin = srange[0] range_end = srange[1] + 40 if range_end > self.end_image_no: self.DEBUG( 'End of range {0} would be past the last image {1}'. format(range_end, self.end_image_no)) range_end = self.end_image_no self.DEBUG('Changing spot range {0} to [{1} {2}]'.format( srange, range_begin, range_end)) r = XSDataRange(begin=range_begin, end=range_end) spot_range.append(r) params.spot_range = spot_range self.third_run.dataInput = params self.third_run.executeSynchronous() EDVerbose.DEBUG('third run completed') if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value: EDVerbose.DEBUG('... and it worked') self.successful_run = self.third_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # all runs failed so bail out ... self.setFailure() else: # use the xds parser plugin to parse the xds output file... parser = self.loadPlugin("EDPluginParseXdsOutput") wd = self.successful_run.getWorkingDirectory() parser_input = XSDataXdsOutputFile() correct_lp_path = XSDataFile() correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP')) parser_input.correct_lp = correct_lp_path gxparm_path = os.path.join(wd, 'GXPARM.XDS') if os.path.isfile(gxparm_path): gxparm = XSDataFile() gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS')) parser_input.gxparm = gxparm parser.dataInput = parser_input parser.executeSynchronous() if parser.isFailure(): # that should not happen self.setFailure() return self.dataOutput = parser.dataOutput
def process(self, _edObject=None): EDPluginControl.process(self) self.DEBUG("EDPluginControlRunXds.process") # First run is vanilla without any modification params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file self.first_run.dataInput = params self.first_run.executeSynchronous() EDVerbose.DEBUG('first run completed...') if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded: EDVerbose.DEBUG('... and it worked') self.successful_run = self.first_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # second run w/ JOB set to DEFPIX INTEGRATE CORRECT self.second_run = self.loadPlugin(self.controlled_plugin_name) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.jobs = 'DEFPIX INTEGRATE CORRECT' self.second_run.dataInput = params self.second_run.executeSynchronous() EDVerbose.DEBUG('second run completed') if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded: EDVerbose.DEBUG('... and it worked') self.successful_run = self.second_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # third run with JOB set to ALL and mxaprocs = 4 and maxjobs = 1 self.third_run = self.loadPlugin(self.controlled_plugin_name) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.jobs = 'ALL' params.maxprocs = 4 params.maxjobs = 1 self.third_run.dataInput = params self.third_run.executeSynchronous() EDVerbose.DEBUG('third run completed') if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded: EDVerbose.DEBUG('... and it worked') self.successful_run = self.third_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # final run with parallelism like 3 but JOB like 2 self.final_run = self.loadPlugin(self.controlled_plugin_name) params = XSDataMinimalXdsIn() params.input_file = self.dataInput.input_file params.jobs = 'DEFPIX INTEGRATE CORRECT' params.maxprocs = 4 params.maxjobs = 1 self.final_run.dataInput = params self.final_run.executeSynchronous() EDVerbose.DEBUG('final run completed') if self.final_run.dataOutput is not None and self.final_run.dataOutput.succeeded: EDVerbose.DEBUG('... and it worked') self.successful_run = self.final_run else: EDVerbose.DEBUG('... and it failed') if not self.successful_run: # all runs failed so bail out ... self.setFailure() else: # use the xds parser plugin to parse the xds output file... parser = self.loadPlugin("EDPluginParseXdsOutput") wd = self.successful_run.getWorkingDirectory() parser_input = XSDataXdsOutputFile() correct_lp_path = XSDataFile() correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP')) parser_input.correct_lp = correct_lp_path gxparm_path = os.path.join(wd, 'GXPARM.XDS') if os.path.isfile(gxparm_path): gxparm = XSDataFile() gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS')) parser_input.gxparm = gxparm parser.dataInput = parser_input parser.executeSynchronous() if parser.isFailure(): # that should not happen self.setFailure() return self.dataOutput = parser.dataOutput
log_to_ispyb([self.integration_id_anom, self.integration_id_noanom], 'Scaling', 'Successful', 'anom/noanom generation finished in {0}s'.format(self.stats['anom/noanom_generation'])) # we can now use the xds output parser on the two correct.lp # files, w/ and w/out anom parse_anom_input = XSDataXdsOutputFile() parse_anom_input.correct_lp = XSDataFile() parse_anom_input.correct_lp.path = self.generate.dataOutput.correct_lp_anom # this one is the same as the first XDS run since they share # the same directory gxparm_file_anom = XSDataFile() gxparm_file_anom.path = self.generate.dataOutput.gxparm parse_anom_input.gxparm = gxparm_file_anom self.parse_xds_anom.dataInput = parse_anom_input self.parse_xds_anom.executeSynchronous() if self.parse_xds_anom.isFailure(): EDVerbose.ERROR('parsing the xds generated w/ anom failed') self.setFailure() return # now the other one w/out anom parse_noanom_input = XSDataXdsOutputFile() parse_noanom_input.correct_lp = XSDataFile() parse_noanom_input.correct_lp.path = self.generate.dataOutput.correct_lp_no_anom
[self.integration_id_anom, self.integration_id_noanom], 'Scaling', 'Successful', 'anom/noanom generation finished in {0}s'.format( self.stats['anom/noanom_generation'])) # we can now use the xds output parser on the two correct.lp # files, w/ and w/out anom parse_anom_input = XSDataXdsOutputFile() parse_anom_input.correct_lp = XSDataFile() parse_anom_input.correct_lp.path = self.generate.dataOutput.correct_lp_anom # this one is the same as the first XDS run since they share # the same directory gxparm_file_anom = XSDataFile() gxparm_file_anom.path = self.generate.dataOutput.gxparm parse_anom_input.gxparm = gxparm_file_anom self.parse_xds_anom.dataInput = parse_anom_input self.parse_xds_anom.executeSynchronous() if self.parse_xds_anom.isFailure(): EDVerbose.ERROR('parsing the xds generated w/ anom failed') self.setFailure() return # now the other one w/out anom parse_noanom_input = XSDataXdsOutputFile() parse_noanom_input.correct_lp = XSDataFile() parse_noanom_input.correct_lp.path = self.generate.dataOutput.correct_lp_no_anom