├── .gitignore ├── INSTALL.md ├── LICENSE ├── README.md ├── beamline ├── cheetah_daemon │ ├── shika_cheetah_daemon │ ├── shika_daemon.py │ └── start_shika.sh └── eiger │ ├── backup_gui.py │ ├── download_eiger.py │ ├── hit_extract_online.py │ └── qsub_hit_extract_online.sh ├── cctbx_progs ├── aniso_cutoff.py ├── apply_b_factor.py ├── apply_sigma_cutoff_for_merged.py ├── calc_DF_over_F.py ├── check_freeR_flag_consistency.py ├── check_scattering_factor.py ├── compare_model_r_factors.py ├── copy_free_R_flag.py ├── create_free_R_flag.py ├── dano_noise.py ├── dano_vs_d.py ├── diff_hkls.py ├── dump_anomalous_differences.py ├── emma_shelxd_lst.py ├── eval_Rfree_CCfree_from_refine_mtz.py ├── eval_Rfree_factors_with_common_reflections.py ├── exclude_resolution_range.py ├── get_cc_mtz_mtz.py ├── get_ccano_calc_obs.py ├── get_ccano_mtz_mtz.py ├── get_mean_for_hkl.py ├── plot_anomalous.py ├── prepare_phaser.py ├── prepare_refmac.py ├── read_x_and_dano.py ├── sca_reso_cut.py └── trans_cell.py ├── doc ├── eiger-en.md ├── eiger-ja.md ├── kamo-en.md ├── kamo-ja.md ├── shika-ja.md └── shika_figs │ ├── html1.png │ ├── main1.png │ ├── plot1.png │ └── tokuma1.png ├── dxtbx_formats ├── FormatEMD.py └── FormatSEReBIC.py └── yamtbx ├── SConscript ├── __init__.py ├── boost_python └── utils_ext.cpp ├── command_line ├── __init__.py ├── adxv_eiger.py ├── beam_direction_plot.py ├── cif_converter.py ├── easy_anode.py ├── eiger_binning.py ├── eiger_bslz4_after.py ├── eiger_reduce_master.py ├── eiger_splitdata_after.py ├── kamo.py ├── kamo_auto_multi_merge.py ├── kamo_auto_multi_merge_report.py ├── kamo_decide_resolution_cutoff.py ├── kamo_merge_single_images_integrated.py ├── kamo_multi_determine_symmetry.py ├── kamo_multi_merge.py ├── kamo_multi_prep_merging.py ├── kamo_resolve_indexing_ambiguity.py ├── kamo_single_images_integration.py ├── kamo_test_installation.py ├── resolution_shells.py ├── run_xscale.py ├── shika.py ├── xds_aniso_analysis.py └── yamtbx_ipython.py ├── dataproc ├── SConscript ├── XIO │ ├── NOTE │ ├── XIO.py │ ├── XIO_collect_info.py │ ├── XIO_info.py │ ├── __init__.py │ ├── oxford2adsc.py │ ├── oxford2raw32.py │ └── plugins │ │ ├── __init__.py │ │ ├── adp_export.py │ │ ├── adsc_interpreter.py │ │ ├── diffdump_export.py │ │ ├── eiger_hdf5_interpreter.py │ │ ├── mar345_interpreter.py │ │ ├── mar555_interpreter.py │ │ ├── mar_interpreter.py │ │ ├── marccd_interpreter.py │ │ ├── minicbf_interpreter.py │ │ ├── mosflm_export.py │ │ ├── mscccd_interpreter.py │ │ ├── oxford_interpreter.py │ │ ├── pycgtypes │ │ ├── README.txt │ │ ├── __init__.py │ │ ├── license.txt │ │ ├── mat3.py │ │ ├── mat4.py │ │ ├── quat.py │ │ ├── vec3.py │ │ └── vec4.py │ │ ├── raxis_interpreter.py │ │ └── xds_export.py ├── __init__.py ├── adxv.py ├── aimless.py ├── anisotropic_analysis.py ├── auto │ ├── __init__.py │ ├── blend.py │ ├── cc_clustering.py │ ├── command_line │ │ ├── __init__.py │ │ ├── auto_data_proc_gui.py │ │ ├── auto_multi_merge.py │ │ ├── auto_multi_merge_report.py │ │ ├── decide_resolution_cutoff.py │ │ ├── evaluate_single_images_integrated.py │ │ ├── evaluate_xds_runs.py │ │ ├── find_datasets.py │ │ ├── merge_single_images_integrated.py │ │ ├── multi_check_cell_consistency.py │ │ ├── multi_determine_symmetry.py │ │ ├── multi_merge.py │ │ ├── multi_prep_merging.py │ │ ├── prep_xds_runs.py │ │ ├── run_all_xds_simple.py │ │ └── single_images_integration.py │ ├── gui_config.py │ ├── gui_logger.py │ ├── html_report.py │ ├── js │ │ └── d3-3.5.10 │ │ │ ├── LICENSE │ │ │ ├── d3.js │ │ │ ├── d3.min.js │ │ │ └── index.js │ ├── multi_merging │ │ ├── __init__.py │ │ ├── aimless.py │ │ ├── command_line │ │ │ ├── resolve_index_by_brehm_diederichs.py │ │ │ └── resolve_index_by_reference.py │ │ ├── html_report.py │ │ ├── resolve_reindex.py │ │ └── xscale.py │ └── resolution_cutoff.py ├── bl_logfiles.py ├── blend_lcv.py ├── boost_python │ └── byteoffset_h5_ext.cpp ├── cbf.py ├── command_line │ ├── __init__.py │ ├── adxv_eiger.py │ ├── beam_direction_plot.py │ ├── calc_lcv.py │ ├── cbf2bin.py │ ├── cbf_replace_negatives.py │ ├── check_diffscan_time.py │ ├── cheetahh5tocbf.py │ ├── cmos_for_crystfel.py │ ├── convert_emd.py │ ├── copy_free_R_flag.py │ ├── create_free_R_flag.py │ ├── dataset_timestamps.py │ ├── dump_marccd_header.py │ ├── dump_shika_pickle.py │ ├── easy_anode.py │ ├── easy_ctruncate.py │ ├── eiger2bin.py │ ├── eiger_apply_flatfield_correction.py │ ├── eiger_binning.py │ ├── eiger_bslz4_after.py │ ├── eiger_check_deadmodules.py │ ├── eiger_reduce_master.py │ ├── eiger_splitdata_after.py │ ├── eval_refine_R_by_scaling_B.py │ ├── img_for_crystfel.py │ ├── mrc2cbf.py │ ├── nexush52cbf.py │ ├── pilatus_for_crystfel.py │ ├── plot_I_d.py │ ├── pointless_show_batch_assign.py │ ├── sort_by_timestamps.py │ └── tst_byteoffset_and_lz4.py ├── crystfel │ ├── __init__.py │ ├── boost_python │ │ ├── SConscript │ │ ├── crystfel_ext.cpp │ │ └── merge_equivalents.cpp │ ├── command_line │ │ ├── __init__.py │ │ ├── compare_hkl.py │ │ ├── geom_for_xds.py │ │ ├── get_cells.py │ │ ├── hkl2various.py │ │ ├── prep_geom_for_pilatus.py │ │ ├── prep_sort_stream.py │ │ ├── sort_stream.py │ │ ├── stats_mmcif.py │ │ ├── stats_stream_savememory.py │ │ └── test_indexing_mode_with_reference.py │ ├── geom.py │ ├── hkl.py │ ├── merge_equivalents.h │ └── stream.py ├── dataset.py ├── dials │ ├── __init__.py │ └── command_line │ │ ├── __init__.py │ │ ├── import_xds_for_refine.py │ │ ├── import_xds_for_refine_stills.py │ │ └── run_dials_auto.py ├── eiger.py ├── hkl2000 │ ├── __init__.py │ ├── command_line │ │ └── calc_scales_for_xfiles.py │ └── xfile.py ├── marccd.py ├── myspotfinder │ ├── __init__.py │ ├── command_line │ │ ├── __init__.py │ │ ├── dump_shikadb.py │ │ ├── make_html_report.py │ │ ├── make_summary_dat_from_shikadb.py │ │ ├── spot_finder_backend.py │ │ └── spot_finder_gui.py │ ├── config_manager.py │ └── shikalog.py ├── pointless.py ├── scale_data.py ├── spotfinder_info.py ├── xds │ ├── __init__.py │ ├── colspot.py │ ├── command_line │ │ ├── __init__.py │ │ ├── add_saturation_info_to_mtz.py │ │ ├── analyze_xscale_lp.py │ │ ├── bkg_by_d_from_bkgpix.py │ │ ├── check_segment_definition.py │ │ ├── clustering_by_cc.py │ │ ├── decay_as_b.py │ │ ├── estimate_resolution_by_spotxds.py │ │ ├── eval_resolution_hkl_files.py │ │ ├── get_cc_with_multiple_targets.py │ │ ├── make_plot_to_compare_correctlp.py │ │ ├── my_patch_shutter_problem.py │ │ ├── prepare_xds_runs.py │ │ ├── run_xscale.py │ │ ├── xds2labelit.py │ │ ├── xds2mtz.py │ │ ├── xds2shelx.py │ │ ├── xds_analyze_overlaps.py │ │ ├── xds_aniso_analysis.py │ │ ├── xds_beamcenter_search.py │ │ ├── xds_check_predictions.py │ │ ├── xds_check_spots_with_image.py │ │ ├── xds_create_dummy_xparm.py │ │ ├── xds_dump_CORRECT.LP.py │ │ ├── xds_inp_for_multisegment_pilatus.py │ │ ├── xds_integrate_lp_to_xparm.py │ │ ├── xds_merge_framecbf.py │ │ ├── xds_pairwise_cc.py │ │ ├── xds_plot_integrate.py │ │ ├── xds_predict_mitai.py │ │ ├── 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