xfel package

Subpackages

• xfel.cftbx package
  • Subpackages
    • xfel.cftbx.detector package
      • Submodules
      • xfel.cftbx.detector.cspad_cbf_tbx module
        • add_tiles_to_cbf()
        • cbf_file_to_basis_dict()
        • copy_cbf_header()
        • env_dxtbx_from_slac_metrology()
        • format_object_from_data()
        • get_calib_file_path()
        • get_cspad_cbf_handle()
        • map_detector_to_basis_dict()
        • metro_phil_to_basis_dict()
        • read_optical_metrology_from_flat_file()
        • write_cspad_cbf()
      • xfel.cftbx.detector.cspad_detector module
      • xfel.cftbx.detector.generic_detector module
      • xfel.cftbx.detector.metrology module
      • xfel.cftbx.detector.metrology2phil module
        • metrology2phil()
        • sections2phil()
      • Module contents
  • Module contents
• xfel.clustering package
  • xfel.clustering.cluster module
    • cluster.Cluster
      • Cluster
        • Cluster.__dict__
        • Cluster.__init__()
        • Cluster.__len__()
        • Cluster.__module__
        • Cluster.__weakref__
        • Cluster.ab_cluster()
        • Cluster.all_frames_intensity_stats()
        • Cluster.best_by_CC()
        • Cluster.dump_as_mtz()
        • Cluster.dump_file_list()
        • Cluster.from_crystal_symmetries()
        • Cluster.from_directories()
        • Cluster.from_expts()
        • Cluster.from_files()
        • Cluster.from_iterable()
        • Cluster.from_list()
        • Cluster.intensity_statistics()
        • Cluster.make_sub_cluster()
        • Cluster.merge_dict()
        • Cluster.point_group_filter()
        • Cluster.prime_postrefine()
        • Cluster.print_ucs()
        • Cluster.to_pandas()
        • Cluster.total_intensity_filter()
        • Cluster.uc_feature_vector()
        • Cluster.visualise_orientational_distribution()
  • xfel.clustering.cluster_groups module
    • unit_cell_info()
  • xfel.clustering.singleframe module
    • singleframe.SingleFrame
      • SingleFrame
        • SingleFrame.ANGSTROMS_TO_EV
        • SingleFrame.__init__()
        • SingleFrame.__module__
        • SingleFrame.distance_from()
        • SingleFrame.filter_negative_intensities()
        • SingleFrame.init_calc_wilson()
        • SingleFrame.make_g6()
        • SingleFrame.n_reflections_by_sigi()
        • SingleFrame.plot_wilson()
        • SingleFrame.polarization_correction()
        • SingleFrame.to_panda()
        • SingleFrame.trim_res_limit()
• xfel.command_line package
  • Submodules
  • xfel.command_line.auto_submit module
    • match_runs()
    • run()
  • xfel.command_line.brehm_diederichs module
    • run()
  • xfel.command_line.cbf_average module
    • run()
  • xfel.command_line.cluster_42 module
  • xfel.command_line.cluster_intensity_statistics module
  • xfel.command_line.cluster_per_frame_wilson module
  • xfel.command_line.cluster_unit_cell module
  • xfel.command_line.cluster_visualise_orientations module
  • xfel.command_line.convert_gain_map module
    • convert_2x2()
    • convert_detector()
    • fake_config
      • fake_config.quadMask()
      • fake_config.roiMask()
      • fake_config.sections()
    • fake_cspad_ElementV2
      • fake_cspad_ElementV2.data()
      • fake_cspad_ElementV2.quad()
    • fake_env
      • fake_env.getConfig()
    • fake_evt
      • fake_evt.getCsPadQuads()
      • fake_evt.getTime()
    • fake_get_config()
    • run()
  • xfel.command_line.convert_gain_map_cbf module
    • convert_detector()
    • run()
  • xfel.command_line.cxi_apply_metrology module
  • xfel.command_line.cxi_cspad_pinwheel module
    • run()
  • xfel.command_line.cxi_diff module
    • run()
  • xfel.command_line.cxi_display_metrology module
  • xfel.command_line.cxi_generate_circular_gain_mask module
  • xfel.command_line.cxi_image2pickle module
  • xfel.command_line.cxi_index module
  • xfel.command_line.cxi_lsf module
    • run()
  • xfel.command_line.cxi_merge module
    • OutlierCellError
    • WrongBravaisError
    • consistent_set_and_model()
    • get_boundaries_from_sensor_ID()
    • get_observations()
    • load_result()
    • plot_overall_completeness()
    • plot_statistics
      • plot_statistics.plot_statistics_histograms()
      • plot_statistics.plot_unit_cell_histograms()
      • plot_statistics.show_all_pyplot()
    • resolution_bin
    • run()
    • scaling_manager
      • scaling_manager.add_frame()
      • scaling_manager.finalize_and_save_data()
      • scaling_manager.get_overall_correlation()
      • scaling_manager.get_plot_statistics()
      • scaling_manager.reset()
      • scaling_manager.scale_all()
      • scaling_manager.scale_frame()
      • scaling_manager.scale_frame_detail()
      • scaling_manager.show_unit_cell_histograms()
      • scaling_manager.single_reflection_histograms()
      • scaling_manager.sum_intensities()
    • scaling_result
    • show_overall_observations()
    • unit_cell_distribution
      • unit_cell_distribution.add_cell()
      • unit_cell_distribution.add_cells()
      • unit_cell_distribution.get_average_cell_dimensions()
      • unit_cell_distribution.show_histograms()
  • xfel.command_line.cxi_optical2cbfheader module
  • xfel.command_line.cxi_pbs module
    • run()
  • xfel.command_line.cxi_pickle2cbf module
  • xfel.command_line.cxi_plotcv module
    • run()
  • xfel.command_line.cxi_psana module
    • run()
  • xfel.command_line.cxi_pyana module
    • run()
  • xfel.command_line.cxi_spots module
  • xfel.command_line.cxi_stream_to_pickle module
    • check_image()
    • crystfel_to_cctbx_coord_system()
    • image_template()
    • make_int_pickle()
    • unit_cell_to_symetry_object()
  • xfel.command_line.cxi_view module
  • xfel.command_line.cxi_xmerge module
    • run()
    • xscaling_manager
      • xscaling_manager.read_all_mysql()
      • xscaling_manager.scale_all()
  • xfel.command_line.get_next_trial_id module
  • xfel.command_line.grid_index module
  • xfel.command_line.histogram_finalise module
  • xfel.command_line.list_db_metadata module
    • run()
  • xfel.command_line.make_mask module
    • point_in_polygon()
    • point_inside_circle()
    • run()
  • xfel.command_line.metrology module
    • get_phil()
    • run()
    • validate_phil()
  • xfel.command_line.monitor_detectors module
  • xfel.command_line.monitor_trials module
  • xfel.command_line.overlay_spectra module
    • estimate_signal_to_noise()
    • full_width_half_max()
    • run()
  • xfel.command_line.plot_to_subpixel module
    • run()
  • xfel.command_line.postrefine module
    • determine_mean_I_mproc()
    • postrefine_by_frame_mproc()
    • read_input()
    • scale_frame_by_mean_I_mproc()
  • xfel.command_line.print_pickle module
    • generate_data_from_streams()
    • generate_streams_from_path()
    • keywise_printout()
  • xfel.command_line.quadrants module
    • view_raw_image()
  • xfel.command_line.radial_average module
    • apply_sub_pixel_metrology()
    • distance()
    • get_tile_center()
    • get_tile_coords()
    • get_tile_id()
    • run()
    • show_tiles()
  • xfel.command_line.smooth_spectrum module
    • estimate_signal_to_noise()
    • fourier_filter()
    • interpolate()
    • pyplot_label_axes()
    • run()
  • xfel.command_line.subtract_background module
    • run()
    • signal_to_noise_statistical()
    • subtract_background()
  • xfel.command_line.trial_stats module
    • run()
  • xfel.command_line.view_pixel_histograms module
    • PixelFitError
    • check_pixel_histogram_fit()
    • hist_outline()
    • pixel_histograms
      • pixel_histograms.fit_one_histogram()
      • pixel_histograms.pixels()
      • pixel_histograms.plot()
      • pixel_histograms.plot_gaussians()
      • pixel_histograms.plot_one_histogram()
      • pixel_histograms.single_peak_fit()
    • run()
    • sliding_average()
  • xfel.command_line.xes_finalise module
  • xfel.command_line.xes_histograms module
  • Module contents
• xfel.cxi package
  • Subpackages
    • xfel.cxi.cspad_ana package
      • Submodules
      • xfel.cxi.cspad_ana.average_tbx module
        • average_mixin
          • average_mixin.beginjob()
          • average_mixin.endjob()
          • average_mixin.event()
      • xfel.cxi.cspad_ana.common_mode module
        • common_mode_correction
          • common_mode_correction.beginjob()
          • common_mode_correction.chebyshev_common_mode()
          • common_mode_correction.chebyshev_fit()
          • common_mode_correction.common_mode()
          • common_mode_correction.do_photon_counting()
          • common_mode_correction.do_sigma_scaling()
          • common_mode_correction.endjob()
          • common_mode_correction.event()
      • xfel.cxi.cspad_ana.cspad_tbx module
        • CsPad2x2Image()
        • CsPadDetector()
        • CsPadElement()
        • cbcaa()
        • dpack()
        • dwritef()
        • dwritef2()
        • env_distance()
        • env_injector_xyz()
        • env_laser_status()
        • env_sifoil()
        • env_wavelength_sxr()
        • evt_beam_charge()
        • evt_get_quads()
        • evt_pulse_energy()
        • evt_pulse_length()
        • evt_repetition_rate()
        • evt_seqno()
        • evt_time()
        • evt_timestamp()
        • evt_wavelength()
        • getOptBool()
        • getOptEvalOrString()
        • getOptFloat()
        • getOptInteger()
        • getOptROI()
        • getOptString()
        • getOptStrings()
        • hdf5pack()
        • image()
        • image_xpp()
        • iplace()
        • pathsubst()
        • rplace()
        • write_tiff()
      • xfel.cxi.cspad_ana.display_calib module
        • display_calib()
      • xfel.cxi.cspad_ana.histogram_finalise module
        • finalise_one_run
        • histogram_finalise
        • update_histograms()
      • xfel.cxi.cspad_ana.hitfinder_tbx module
        • distl_hitfinder
          • distl_hitfinder.distl_filter()
          • distl_hitfinder.get_active_data()
          • distl_hitfinder.set_up_hitfinder()
      • xfel.cxi.cspad_ana.mod_average module
        • mod_average
          • mod_average.beginjob()
          • mod_average.endjob()
          • mod_average.event()
      • xfel.cxi.cspad_ana.mod_average_cbf module
      • xfel.cxi.cspad_ana.mod_cbf_hitfind module
      • xfel.cxi.cspad_ana.mod_cbf_index module
      • xfel.cxi.cspad_ana.mod_cspad_cbf module
      • xfel.cxi.cspad_ana.mod_cspad_cbf_dump module
      • xfel.cxi.cspad_ana.mod_daq_status module
        • StatusFrame_thread
          • StatusFrame_thread.run()
          • StatusFrame_thread.start_local()
        • mod_daq_status
          • mod_daq_status.beginjob()
          • mod_daq_status.endjob()
          • mod_daq_status.event()
          • mod_daq_status.initialize()
          • mod_daq_status.update_plot()
      • xfel.cxi.cspad_ana.mod_dump module
        • mod_dump
          • mod_dump.event()
      • xfel.cxi.cspad_ana.mod_dump_bitmap module
        • mod_dump_bitmap
          • mod_dump_bitmap.event()
      • xfel.cxi.cspad_ana.mod_event_info module
        • laser_status
          • laser_status.ms_since_last_status_change()
          • laser_status.set_status()
          • laser_status.status
          • laser_status.status_change_timestamp
        • mod_event_info
          • mod_event_info.beginjob()
          • mod_event_info.endjob()
          • mod_event_info.event()
      • xfel.cxi.cspad_ana.mod_filter module
        • mod_filter
          • mod_filter.beginjob()
          • mod_filter.endjob()
          • mod_filter.event()
      • xfel.cxi.cspad_ana.mod_hdf5 module
        • mod_hdf5
          • mod_hdf5.event()
      • xfel.cxi.cspad_ana.mod_hitfind module
        • mod_hitfind
          • mod_hitfind.beginjob()
          • mod_hitfind.commit_entries()
          • mod_hitfind.commit_progress_entries()
          • mod_hitfind.endjob()
          • mod_hitfind.event()
          • mod_hitfind.queue_entry()
          • mod_hitfind.queue_progress_entry()
      • xfel.cxi.cspad_ana.mod_illumination_filter module
        • mod_illumination_filter
          • mod_illumination_filter.beginjob()
          • mod_illumination_filter.endjob()
          • mod_illumination_filter.event()
      • xfel.cxi.cspad_ana.mod_ledge module
      • xfel.cxi.cspad_ana.mod_mar module
        • mod_mar
          • mod_mar.begincalibcycle()
          • mod_mar.beginjob()
          • mod_mar.endjob()
          • mod_mar.event()
      • xfel.cxi.cspad_ana.mod_param module
        • mod_param
          • mod_param.beginjob()
          • mod_param.endjob()
          • mod_param.event()
      • xfel.cxi.cspad_ana.mod_pickle2cbf_dump module
      • xfel.cxi.cspad_ana.mod_pulnix_dump module
        • mod_pulnix_dump
          • mod_pulnix_dump.beginjob()
          • mod_pulnix_dump.endjob()
          • mod_pulnix_dump.event()
      • xfel.cxi.cspad_ana.mod_radial_average module
        • mod_radial_average
          • mod_radial_average.beginjob()
          • mod_radial_average.endjob()
          • mod_radial_average.event()
      • xfel.cxi.cspad_ana.mod_spectra module
      • xfel.cxi.cspad_ana.mod_spectra_view module
      • xfel.cxi.cspad_ana.mod_view module
      • xfel.cxi.cspad_ana.mod_xes module
        • mod_xes
          • mod_xes.endjob()
          • mod_xes.event()
      • xfel.cxi.cspad_ana.parse_calib module
        • Section
          • Section.corners()
          • Section.corners_asic()
          • Section.q_size
          • Section.qrotate()
          • Section.srotate()
          • Section.translate()
        • calib2sections()
        • calib2tensor3()
        • fread_matrix()
        • fread_tensor3()
        • fread_vector()
        • v2calib2sections()
      • xfel.cxi.cspad_ana.pixel_histograms module
        • pixel_histograms
          • pixel_histograms.beginjob()
          • pixel_histograms.endjob()
          • pixel_histograms.event()
      • xfel.cxi.cspad_ana.xes_finalise module
        • cspad2x2_bad_pixel_mask_cxi_run7()
        • cspad_unbound_pixel_mask()
        • filter_outlying_pixels()
        • finalise_one_run
        • first_moment_analysis
          • first_moment_analysis.as_trace()
          • first_moment_analysis.calculate()
        • get_spectrum()
        • output_image()
        • output_matlab_form()
        • output_spectrum()
        • plot_energy()
        • spec_plot()
        • xes_finalise
      • xfel.cxi.cspad_ana.xes_histograms module
        • run()
        • xes_from_histograms
      • Module contents
        • skip_event_flag()
    • xfel.cxi.gfx package
      • Submodules
      • xfel.cxi.gfx.status_plot module
        • RunNumberEvent
        • SaveImageEvent
        • StatusFrame
          • StatusFrame.OnSaveImage()
          • StatusFrame.OnSetRunNumber()
          • StatusFrame.OnUpdate()
          • StatusFrame.create_plot_panel()
          • StatusFrame.show_controls_default
        • StatusPlot
          • StatusPlot.show_plot()
        • UpdateEvent
        • draw_plot()
        • draw_plot_to_file()
        • format_time()
      • xfel.cxi.gfx.trials_plot module
        • Run
          • Run.cull_braggs()
          • Run.max()
          • Run.min()
          • Run.recalc_hits()
          • Run.width()
        • TrialsPlot
          • TrialsPlot.show_plot()
        • TrialsPlotFrame
          • TrialsPlotFrame.OnPan()
          • TrialsPlotFrame.OnTimeLockCheck()
          • TrialsPlotFrame.OnTimer()
          • TrialsPlotFrame.OnZoom()
          • TrialsPlotFrame.create_plot_panel()
          • TrialsPlotFrame.cull_braggs()
          • TrialsPlotFrame.load_data()
          • TrialsPlotFrame.set_params()
          • TrialsPlotFrame.show_controls_default
          • TrialsPlotFrame.show_plot()
        • run()
      • xfel.cxi.gfx.wx_detectors module
        • DetectorPlot
          • DetectorPlot.save_png()
          • DetectorPlot.set_run_id()
          • DetectorPlot.show_plot()
        • DetectorPlotFrame
          • DetectorPlotFrame.OnSave()
          • DetectorPlotFrame.OnTimer()
          • DetectorPlotFrame.create_plot_panel()
          • DetectorPlotFrame.find_logs()
          • DetectorPlotFrame.set_run_id()
          • DetectorPlotFrame.set_watch_dir()
          • DetectorPlotFrame.show_controls_default
          • DetectorPlotFrame.update_from_logs()
          • DetectorPlotFrame.update_hit_rate()
        • run()
      • Module contents
    • xfel.cxi.merging package
      • Submodules
      • xfel.cxi.merging.general_fcalc module
      • xfel.cxi.merging.phil_validation module
      • xfel.cxi.merging.refine module
      • Module contents
    • xfel.cxi.postrefine package
      • Submodules
      • xfel.cxi.postrefine.justsum module
      • xfel.cxi.postrefine.mod_energy module
      • xfel.cxi.postrefine.mod_graddesc module
      • xfel.cxi.postrefine.mod_leastsqr module
      • xfel.cxi.postrefine.mod_normal_eqns module
      • xfel.cxi.postrefine.mod_partiality module
      • xfel.cxi.postrefine.mod_pdb module
      • xfel.cxi.postrefine.mod_polar module
      • xfel.cxi.postrefine.mod_results module
      • xfel.cxi.postrefine.mod_util module
      • xfel.cxi.postrefine.postrefine module
      • xfel.cxi.postrefine.probe module
      • xfel.cxi.postrefine.probe_best module
      • xfel.cxi.postrefine.read_serial_and_img module
      • xfel.cxi.postrefine.test_energy_model module
      • xfel.cxi.postrefine.test_rs module
      • Module contents
  • Submodules
  • xfel.cxi.average_spots module
    • ImageFactory()
    • img_add()
    • main()
    • spot_add()
  • xfel.cxi.completeness_plot module
  • xfel.cxi.correction_vector_plot module
    • lines
      • lines.literals()
      • lines.vectors()
    • manage_sql
      • manage_sql.get_cursor()
      • manage_sql.get_frame_dictionary()
      • manage_sql.initialize_tables_and_insert_command()
      • manage_sql.insert()
      • manage_sql.send_insert_command()
    • run_correction_vector_plot()
  • xfel.cxi.cxi_cc module
    • binned_correlation()
    • correlation()
    • load_cc_data()
    • r1_factor()
    • r_split()
    • run_cc()
    • scale_factor()
    • split_sigma_test()
  • xfel.cxi.display_powder_arcs module
    • apply_gaussian_noise()
    • get_mmtbx_icalc()
    • is_pinwheel_region()
    • superimpose_powder_arcs()
  • xfel.cxi.display_spots module
    • ImageFactory()
    • empty
    • run_one()
    • run_one_index()
    • run_one_index_core()
    • view_raw_image()
    • wrapper_of_callback
      • wrapper_of_callback.display()
      • wrapper_of_callback.display_with_callback()
      • wrapper_of_callback.user_callback()
  • xfel.cxi.integrate_image_api module
    • integrate_one_image()
  • xfel.cxi.merging_database module
  • xfel.cxi.merging_database_fs module
  • xfel.cxi.merging_database_sqlite3 module
  • xfel.cxi.strong_zulu module
    • integrate_one_image()
  • xfel.cxi.util module
    • is_odd_numbered()
  • Module contents
• xfel.metrology package
  • Subpackages
    • xfel.metrology.legacy_scale package
      • Module contents
  • Submodules
  • xfel.metrology.flatfile module
    • optimise_rectangle
      • optimise_rectangle.compute_functional_and_gradients()
    • optimise_rectangle_2
      • optimise_rectangle_2.compute_functional_and_gradients()
    • optimise_rectangle_3
      • optimise_rectangle_3.compute_functional_and_gradients()
    • parse_metrology()
  • xfel.metrology.mark0 module
    • consistency_controls()
    • correction_vectors
      • correction_vectors.DETECTOR_NORMAL
      • correction_vectors.INCIDENT_BEAM
      • correction_vectors.delrsq_functional()
      • correction_vectors.get_frames_from_mysql()
      • correction_vectors.get_obs_from_mysql()
      • correction_vectors.print_table()
      • correction_vectors.read_data()
      • correction_vectors.standalone_check()
      • correction_vectors.tile_weight()
    • get_phil()
    • run()
  • xfel.metrology.mark1 module
    • fit_translation
      • fit_translation.compute_functional_and_gradients()
      • fit_translation.curvatures()
      • fit_translation.post_min_recalc()
      • fit_translation.print_table()
    • run()
  • xfel.metrology.mark10 module
    • fit_translation4
      • fit_translation4.compute_finite_difference_gradients_if_requested()
      • fit_translation4.compute_functional_and_gradients()
      • fit_translation4.detector_origin_analysis()
      • fit_translation4.jacobian_frame_rotx
      • fit_translation4.parameter_based_model()
      • fit_translation4.parameter_based_model_one_frame_detail()
      • fit_translation4.print_table()
      • fit_translation4.print_table_2()
      • fit_translation4.print_unit_translations()
      • fit_translation4.radial_transverse_analysis()
      • fit_translation4.run_cycle_a()
      • fit_translation4.run_cycle_b()
      • fit_translation4.same_sensor_table()
  • xfel.metrology.mark3 module
    • fit_translation2
      • fit_translation2.compute_functional_and_gradients()
      • fit_translation2.curvatures()
      • fit_translation2.nominal_tile_centers()
      • fit_translation2.parameter_based_model()
      • fit_translation2.post_min_recalc()
      • fit_translation2.print_table()
      • fit_translation2.same_sensor_table()
    • run()
  • xfel.metrology.quadrant module
    • one_panel
      • one_panel.CC()
    • one_sensor
      • one_sensor.CC()
  • Module contents
• xfel.mono_simulation package
  • Submodules
  • xfel.mono_simulation.max_like module
  • xfel.mono_simulation.mono_treatment module
    • post_outlier_rejection()
    • pre_get_predictions()
    • refinement
      • refinement.contour_plot_DEPRECATED_DOES_NOT_APPLY_SUBPIXEL_METROLOGY()
      • refinement.grid
      • refinement.per_frame_helper_factory()
      • refinement.refine_rotx_roty2()
      • refinement.show_plot()
    • refinement2
      • refinement2.grid
      • refinement2.refine_all()
    • refinement_base
  • Module contents

Submodules

xfel.detector_formats module

xfel.phil_preferences module

xfel.phil_preferences.load_cxi_phil(path, args=[])

Module contents