ewoksmx.tasks.mx_pipelines.autoproc_pipeline.AutoPROC_pipeline#

class ewoksmx.tasks.mx_pipelines.autoproc_pipeline.AutoPROC_pipeline(inputs=None, varinfo=None, node_id=None, node_attrs=None, execinfo=None, profile_directory=None)[source]#

Bases: PrepareEdnaPipeline

Prepare the AutoPROC pipeline.

https://www.globalphasing.com/autoproc/

Parameters:

inputs (Optional[Mapping])
varinfo (Optional[dict])
node_id (Union[str, int, tuple, None])
node_attrs (Optional[dict])
execinfo (Optional[dict])
profile_directory (Optional[dict])

CFG = InstrumentConfigRegistry(default=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number=None, detector=None), bm07=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='60-0128', detector=Detector(serial_number='60-0128', description='Dectris PILATUS3 Si 6M', xds_name='PILATUS', nx=2463, ny=2527, pixel_size_x=0.172, pixel_size_y=0.172, sensor_material='Si', sensor_thickness=1.0, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[487, 495, 0, 2528], [981, 989, 0, 2528], [1475, 1483, 0, 2528], [1969, 1977, 0, 2528], [0, 2464, 195, 213], [0, 2464, 407, 425], [0, 2464, 619, 637], [0, 2464, 831, 849], [0, 2464, 1043, 1061], [0, 2464, 1255, 1273], [0, 2464, 1467, 1485], [0, 2464, 1679, 1697], [0, 2464, 1891, 1909], [0, 2464, 2103, 2121], [0, 2464, 2315, 2333]])), id23eh1=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='E-32-0126', detector=Detector(serial_number='E-32-0126', description='Dectris EIGER2 CdTe 16M', xds_name='PILATUS', nx=4148, ny=4362, pixel_size_x=0.075, pixel_size_y=0.075, sensor_material='CdTe', sensor_thickness=0.75, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[0, 4149, 512, 549], [0, 4149, 1062, 1099], [0, 4149, 1612, 1649], [0, 4149, 2162, 2199], [0, 4149, 2712, 2749], [0, 4149, 3262, 3299], [0, 4149, 3812, 3849], [513, 514, 0, 4362], [1028, 1039, 0, 4362], [1553, 1554, 0, 4362], [2068, 2079, 0, 4362], [2593, 2594, 0, 4362], [3108, 3119, 0, 4362], [3633, 3634, 0, 4362]])), id23eh2=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='E-18-0133', detector=Detector(serial_number='E-18-0133', description='Dectris EIGER2 Si 9M', xds_name='PILATUS', nx=3262, ny=3108, pixel_size_x=0.075, pixel_size_y=0.075, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[1029, 1040, 0, 3269], [2069, 2082, 0, 3269], [0, 3110, 513, 553], [0, 3110, 1064, 1104], [0, 3110, 1615, 1655], [0, 3110, 2166, 2206], [0, 3110, 2717, 2757]])), id23eh2sim1=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='E-18-0133', detector=Detector(serial_number='E-18-0133', description='Dectris EIGER2 Si 9M', xds_name='PILATUS', nx=3262, ny=3108, pixel_size_x=0.075, pixel_size_y=0.075, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[1029, 1040, 0, 3269], [2069, 2082, 0, 3269], [0, 3110, 513, 553], [0, 3110, 1064, 1104], [0, 3110, 1615, 1655], [0, 3110, 2166, 2206], [0, 3110, 2717, 2757]])), id30a1=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='D029099', detector=Detector(serial_number='D029099', description='Dectris PILATUS4 Si 4M', xds_name='PILATUS', nx=2073, ny=2180, pixel_size_x=0.15, pixel_size_y=0.15, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[0, 2072, 255, 274], [0, 2072, 530, 549], [0, 2072, 805, 824], [0, 2072, 1080, 1099], [0, 2072, 1355, 1374], [0, 2072, 1630, 1649], [0, 2072, 1905, 1924], [513, 519, 0, 2179], [1033, 1039, 0, 2179], [1553, 1559, 0, 2179]])), id30a1sim1=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='D029099', detector=Detector(serial_number='D029099', description='Dectris PILATUS4 Si 4M', xds_name='PILATUS', nx=2073, ny=2180, pixel_size_x=0.15, pixel_size_y=0.15, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[0, 2072, 255, 274], [0, 2072, 530, 549], [0, 2072, 805, 824], [0, 2072, 1080, 1099], [0, 2072, 1355, 1374], [0, 2072, 1630, 1649], [0, 2072, 1905, 1924], [513, 519, 0, 2179], [1033, 1039, 0, 2179], [1553, 1559, 0, 2179]])), id30a1sim2=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='D029099', detector=Detector(serial_number='D029099', description='Dectris PILATUS4 Si 4M', xds_name='PILATUS', nx=2073, ny=2180, pixel_size_x=0.15, pixel_size_y=0.15, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[0, 2072, 255, 274], [0, 2072, 530, 549], [0, 2072, 805, 824], [0, 2072, 1080, 1099], [0, 2072, 1355, 1374], [0, 2072, 1630, 1649], [0, 2072, 1905, 1924], [513, 519, 0, 2179], [1033, 1039, 0, 2179], [1553, 1559, 0, 2179]])), id30a1sim3=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='D029099', detector=Detector(serial_number='D029099', description='Dectris PILATUS4 Si 4M', xds_name='PILATUS', nx=2073, ny=2180, pixel_size_x=0.15, pixel_size_y=0.15, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[0, 2072, 255, 274], [0, 2072, 530, 549], [0, 2072, 805, 824], [0, 2072, 1080, 1099], [0, 2072, 1355, 1374], [0, 2072, 1630, 1649], [0, 2072, 1905, 1924], [513, 519, 0, 2179], [1033, 1039, 0, 2179], [1553, 1559, 0, 2179]])), id30a2=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='D029099', detector=Detector(serial_number='D029099', description='Dectris PILATUS4 Si 4M', xds_name='PILATUS', nx=2073, ny=2180, pixel_size_x=0.15, pixel_size_y=0.15, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[0, 2072, 255, 274], [0, 2072, 530, 549], [0, 2072, 805, 824], [0, 2072, 1080, 1099], [0, 2072, 1355, 1374], [0, 2072, 1630, 1649], [0, 2072, 1905, 1924], [513, 519, 0, 2179], [1033, 1039, 0, 2179], [1553, 1559, 0, 2179]])), id30a3=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='E-08-0104', detector=Detector(serial_number='E-08-0104', description='Dectris EIGER1 Si 4M', xds_name='PILATUS', nx=2070, ny=2167, pixel_size_x=0.075, pixel_size_y=0.075, sensor_material='Si', sensor_thickness=0.45, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[1029, 1040, 0, 2167], [0, 2070, 512, 550], [0, 2070, 1063, 1103], [0, 2070, 1614, 1654]])), id30b=InstrumentConfig(slurm_parameters=SlurmParameters(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800), grenades_fastproc=GrenadesFastprocPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', hdf5_lib_path=PosixPath('/cvmfs/sb.esrf.fr/software/packages/ubuntu20.04/x86_64/neggia/1.2.0/dectris-neggia.so'), calc_cell_cmd='cell_from_space_group.pl', xds_config_filename='XDS.INP', xds_config_fields_with_path={'NAME_TEMPLATE_OF_DATA_FRAMES': False, 'X-GEO_CORR': True, 'Y-GEO_CORR': True}, xds_config_fields_to_modify_add={'space_group_number': 'SPACE_GROUP_NUMBER', 'cell_params': 'UNIT_CELL_CONSTANTS', 'library': 'LIB', 'frames_path': 'NAME_TEMPLATE_OF_DATA_FRAMES', 'exclude_range': 'EXCLUDE_DATA_RANGE'}, cell_refinement_dir_name='cell_params', stdout_latice_keyword='LATTICE', grenades_script_filename='grenades_fastproc.sh', grenades_script_filename_high_res='grenades_fastproc_res.sh', dcloid_file_name='DCOLID.txt'), XIA2_DIALS=Xia2DialPipeline(slurm_mem=96000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), prepare_slurm_pipeline=PrepareSlurmPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup'), prepare_edna_pipeline=PrepareEdnaPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_pipeline=TestPipeline(slurm_mem=7000, slurm_queue='dummy_mx', slurm_nodes=7, slurm_core=7, slurm_time=700, process_working_dirname='nobackup'), grenades_parallel_proc_pipeline=GrenadesParallelProcPipeline(icat_dir_name='grenades_parallelproc', xds_config_filename='XDS.INP', xds_command='xdsproc.pl', xds_command_txt_filename='command_line.txt'), mx_pipeline_input=MXPipelineInput(raw_data_foldername='RAW_DATA', processed_data_foldername='PROCESSED_DATA', metadata_filename='metadata.json', reprocess_folder_prefix_name='reprocess', xds_config_filename='XDS.INP', dcloid_file_name='DCOLID.txt'), EDNA_proc=EdnaProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), Dummy_EDNA_pipeline=TestEdnaPipeline(slurm_mem=8000, slurm_queue='dummy_edna_mx', slurm_nodes=8, slurm_core=8, slurm_time=800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), autoPROC=AutoProcPipeline(slurm_mem=16000, slurm_queue='mx', slurm_nodes=1, slurm_core=20, slurm_time=1800, process_working_dirname='nobackup', ispyb_xml_file_name=PosixPath('ispyb.xml')), geometry=GeometryParameters(detector_x_axis='1.0 0.0 0.0', detector_y_axis='0.0 1.0 0.0', rotation_axis='1.0 0.0 0.0', incident_beam_direction='0.0 0.0 1.0'), detector_serial_number='D033638', detector=Detector(serial_number='D033638', description='Dectris PILATUS4 CdTe 4M', xds_name='PILATUS', nx=2073, ny=2180, pixel_size_x=0.15, pixel_size_y=0.15, sensor_material='CdTe', sensor_thickness=1.0, minimum_valid_pixel_value=0, overload=1048500, trusted_region=[0.0, 1.41], trusted_pixel=[7000, 30000], untrusted_rectangle=[[0, 2072, 255, 274], [0, 2072, 530, 549], [0, 2072, 805, 824], [0, 2072, 1080, 1099], [0, 2072, 1355, 1374], [0, 2072, 1630, 1649], [0, 2072, 1905, 1924], [513, 519, 0, 2179], [1033, 1039, 0, 2179], [1553, 1559, 0, 2179]])))#

DATA_MODEL#: alias of XSDataInputControlAutoPROC

EDNA_PLUGIN_NAME: str = 'EDPluginControlAutoPROCv1_0'#

MISSING_DATA = <MISSING_DATA>#

PIPELINE_NAME: str = 'autoPROC'#

assert_ready_to_execute()#

cancel()#: Function called when a task is cancelled. To be implemented by the derived classes

property cancelled: bool#: Return True if the task has been cancelled by the user

classmethod class_nonce()#

classmethod class_nonce_data()#

classmethod class_registry_name()#

Return type:: Optional[str]

cleanup_references()#: Removes all references to the inputs. Side effect: fixes the uhash of the task and outputs

property done: bool#: Completed (with or without exception)

property exception: Exception | None#

execute(force_rerun=False, raise_on_error=True, cleanup_references=False)#

Parameters:

force_rerun (Optional[bool])
raise_on_error (Optional[bool])
cleanup_references (Optional[bool])

property failed: bool#: Completed with exception

fix_uhash()#: Fix the uhash when it is derived from the uhash data.

get_icat_jobs()#

Return type:: List[dict]

get_input_uhashes()#

get_input_value(key, default=<MISSING_DATA>)#

Parameters:: default (Any)
Return type:: Any

get_input_values()#

get_named_input_values()#

get_output_transfer_data()#: The values are either DataUri or Variable

get_output_uhashes()#

get_output_value(key, default=<MISSING_DATA>)#

Parameters:: default (Any)
Return type:: Any

get_output_values()#

get_positional_input_values()#

classmethod get_subclass(registry_name, _second_attempt=False)#: Retrieving a derived class

classmethod get_subclass_names()#

Return type:: List[str]

classmethod get_subclasses()#

get_uhash_init(serialize=False)#

property icat_dir: Path#

property input_file_path: Path#

classmethod input_model()#

Return type:: Optional[Type[BaseInputModel]]

classmethod input_names()#

Return type:: Set[str]

property input_uhashes#

property input_values#: DEPRECATED

property input_variables: VariableContainer#

property inputs: ReadOnlyVariableContainerNamespace#

instance_nonce()#

classmethod instantiate(registry_name, **kw)#

Factory method for instantiating a derived class.

Parameters:

registry_name (str) – for example “tasklib.tasks.MyTask” or “MyTask”
**kw – Task constructor arguments
registry_name

Returns Task:

property is_ready_to_execute#

property job_id: str | None#

property label: str#

property metadata: dict#

property missing_inputs: VariableContainerMissingNamespace#

property missing_outputs: VariableContainerMissingNamespace#

property n_positional_inputs: int#

classmethod n_required_positional_inputs()#

Return type:: int

property named_input_values#: DEPRECATED

property node_id: str | int | tuple#

notify_icat(data)#

Parameters:: data (dict)
Return type:: None

property npositional_inputs#: DEPRECATED

classmethod optional_input_names()#

Return type:: Set[str]

property output_metadata: dict | None#

classmethod output_model()#

Return type:: Optional[Type[BaseOutputModel]]

classmethod output_names()#

Return type:: Set[str]

property output_transfer_data#: DEPRECATED

property output_uhashes#: DEPRECATED

property output_values#: DEPRECATED

property output_variables: VariableContainer#

property outputs: VariableContainerNamespace#

property positional_input_values#: DEPRECATED

prepare_pipeline()#

Return type:: None

property processing_base_dir: Path#

property reprocess_path: Path#

classmethod required_input_names()#

Return type:: Set[str]

reset_state()#

run()#: To be implemented by the derived classes

property script_file_path: Path#

script_template_variables()#

Return type:: dict

set_uhash_init(pre_uhash=None, instance_nonce=None)#

Parameters:

pre_uhash (Union[str, bytes, UniversalHash, HasUhash, None])
instance_nonce (Optional[Any])

slurm_parameters()#

Return type:: dict

property succeeded: bool#: Completed without exception and with output values

property task_identifier: str#

property uhash: UniversalHash | None#

uhash_randomize()#

undo_fix_uhash()#

undo_randomize()#

property workflow_id: str | None#

ewoksmx.tasks.mx_pipelines.autoproc_pipeline.AutoPROC_pipeline#

This Page