README.md
__init__.py
conftest.py
libtbx_refresh.py
run_tests.py
setup.py
algorithms/__init__.py
algorithms/background/__init__.py
algorithms/background/modeller.py
algorithms/background/glm/__init__.py
algorithms/background/glm/algorithm.py
algorithms/background/gmodel/__init__.py
algorithms/background/gmodel/algorithm.py
algorithms/background/gmodel/modeller.py
algorithms/background/median/__init__.py
algorithms/background/median/algorithm.py
algorithms/background/simple/__init__.py
algorithms/background/simple/algorithm.py
algorithms/background_lookup/__init__.py
algorithms/background_lookup/background_and_gain.py
algorithms/background_lookup/detector_noise.py
algorithms/centroid/__init__.py
algorithms/centroid/centroid_px_to_mm.py
algorithms/centroid/simple/__init__.py
algorithms/centroid/simple/algorithm.py
algorithms/clustering/__init__.py
algorithms/clustering/observers.py
algorithms/clustering/plots.py
algorithms/clustering/test_observers.py
algorithms/clustering/test_plots.py
algorithms/clustering/test_unit_cell.py
algorithms/clustering/unit_cell.py
algorithms/filtering/__init__.py
algorithms/image/__init__.py
algorithms/image/centroid/__init__.py
algorithms/image/connected_components/__init__.py
algorithms/image/fill_holes/__init__.py
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algorithms/image/threshold/__init__.py
algorithms/indexing/__init__.py
algorithms/indexing/compare_orientation_matrices.py
algorithms/indexing/fft1d.py
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algorithms/indexing/indexer.py
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algorithms/indexing/max_cell.py
algorithms/indexing/nave_parameters.py
algorithms/indexing/nearest_neighbor.py
algorithms/indexing/real_space_grid_search.py
algorithms/indexing/refinement.py
algorithms/indexing/stills_indexer.py
algorithms/indexing/symmetry.py
algorithms/indexing/test_max_cell.py
algorithms/integration/__init__.py
algorithms/integration/filtering.py
algorithms/integration/image_integrator.py
algorithms/integration/integrator.py
algorithms/integration/integrator_stills.py
algorithms/integration/kapton_2019_correction.py
algorithms/integration/kapton_correction.py
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algorithms/integration/parallel_integrator.py
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algorithms/integration/report.py
algorithms/integration/stills_significance_filter.py
algorithms/integration/validation.py
algorithms/integration/bayes/__init__.py
algorithms/integration/bayes/algorithm.py
algorithms/integration/fit/__init__.py
algorithms/integration/sum/__init__.py
algorithms/integration/sum/algorithm.py
algorithms/polygon/__init__.py
algorithms/polygon/spatial_interpolation.py
algorithms/polygon/clip/__init__.py
algorithms/profile_model/__init__.py
algorithms/profile_model/factory.py
algorithms/profile_model/gaussian_rs/__init__.py
algorithms/profile_model/gaussian_rs/algorithm.py
algorithms/profile_model/gaussian_rs/calculator.py
algorithms/profile_model/gaussian_rs/model.py
algorithms/profile_model/gaussian_rs/transform/__init__.py
algorithms/profile_model/modeller/__init__.py
algorithms/refinement/__init__.py
algorithms/refinement/constraints.py
algorithms/refinement/engine.py
algorithms/refinement/refinement_helpers.py
algorithms/refinement/refiner.py
algorithms/refinement/reflection_manager.py
algorithms/refinement/rotation_decomposition.py
algorithms/refinement/sparse_engine.py
algorithms/refinement/stills_detector_metrology.py
algorithms/refinement/target.py
algorithms/refinement/target_stills.py
algorithms/refinement/two_theta_refiner.py
algorithms/refinement/weighting_strategies.py
algorithms/refinement/analysis/__init__.py
algorithms/refinement/analysis/centroid_analysis.py
algorithms/refinement/outlier_detection/__init__.py
algorithms/refinement/outlier_detection/mcd.py
algorithms/refinement/outlier_detection/outlier_base.py
algorithms/refinement/outlier_detection/sauter_poon.py
algorithms/refinement/outlier_detection/tukey.py
algorithms/refinement/parameterisation/__init__.py
algorithms/refinement/parameterisation/autoreduce.py
algorithms/refinement/parameterisation/beam_parameters.py
algorithms/refinement/parameterisation/configure.py
algorithms/refinement/parameterisation/crystal_parameters.py
algorithms/refinement/parameterisation/detector_parameters.py
algorithms/refinement/parameterisation/goniometer_parameters.py
algorithms/refinement/parameterisation/model_parameters.py
algorithms/refinement/parameterisation/parameter_report.py
algorithms/refinement/parameterisation/prediction_parameters.py
algorithms/refinement/parameterisation/prediction_parameters_stills.py
algorithms/refinement/parameterisation/scan_varying_beam_parameters.py
algorithms/refinement/parameterisation/scan_varying_crystal_parameters.py
algorithms/refinement/parameterisation/scan_varying_detector_parameters.py
algorithms/refinement/parameterisation/scan_varying_goniometer_parameters.py
algorithms/refinement/parameterisation/scan_varying_model_parameters.py
algorithms/refinement/parameterisation/scan_varying_prediction_parameters.py
algorithms/refinement/prediction/__init__.py
algorithms/refinement/prediction/managed_predictors.py
algorithms/refinement/restraints/__init__.py
algorithms/refinement/restraints/restraints.py
algorithms/refinement/restraints/restraints_parameterisation.py
algorithms/rs_mapper/__init__.py
algorithms/scaling/Ih_table.py
algorithms/scaling/__init__.py
algorithms/scaling/active_parameter_managers.py
algorithms/scaling/algorithm.py
algorithms/scaling/basis_functions.py
algorithms/scaling/combine_intensities.py
algorithms/scaling/observers.py
algorithms/scaling/outlier_rejection.py
algorithms/scaling/parameter_handler.py
algorithms/scaling/plots.py
algorithms/scaling/reflection_selection.py
algorithms/scaling/scaler.py
algorithms/scaling/scaler_factory.py
algorithms/scaling/scaling_library.py
algorithms/scaling/scaling_options.py
algorithms/scaling/scaling_refiner.py
algorithms/scaling/scaling_restraints.py
algorithms/scaling/scaling_utilities.py
algorithms/scaling/target_function.py
algorithms/scaling/test_Ih_table.py
algorithms/scaling/test_basis_function.py
algorithms/scaling/test_combine_intensities.py
algorithms/scaling/test_error_model.py
algorithms/scaling/test_gaussian_smoother.py
algorithms/scaling/test_model.py
algorithms/scaling/test_model_factory.py
algorithms/scaling/test_observers.py
algorithms/scaling/test_outlier_rejection.py
algorithms/scaling/test_param_manager.py
algorithms/scaling/test_plots.py
algorithms/scaling/test_reflection_selection.py
algorithms/scaling/test_scale.py
algorithms/scaling/test_scale_and_filter.py
algorithms/scaling/test_scale_components.py
algorithms/scaling/test_scaler.py
algorithms/scaling/test_scaler_factory.py
algorithms/scaling/test_scaling_library.py
algorithms/scaling/test_scaling_restaints.py
algorithms/scaling/test_scaling_utilities.py
algorithms/scaling/test_target_function.py
algorithms/scaling/test_targetscaler.py
algorithms/scaling/test_weighting.py
algorithms/scaling/weighting.py
algorithms/scaling/cross_validation/__init__.py
algorithms/scaling/cross_validation/cross_validate.py
algorithms/scaling/cross_validation/crossvalidator.py
algorithms/scaling/cross_validation/test_crossvalidation.py
algorithms/scaling/error_model/__init__.py
algorithms/scaling/error_model/error_model.py
algorithms/scaling/error_model/error_model_target.py
algorithms/scaling/model/__init__.py
algorithms/scaling/model/model.py
algorithms/scaling/model/scaling_model_ext.py
algorithms/scaling/model/scaling_model_factory.py
algorithms/scaling/model/components/__init__.py
algorithms/scaling/model/components/scale_components.py
algorithms/scaling/model/components/smooth_scale_components.py
algorithms/shadowing/__init__.py
algorithms/shadowing/filter.py
algorithms/shoebox/__init__.py
algorithms/shoebox/masker.py
algorithms/simulation/__init__.py
algorithms/simulation/generate_test_reflections.py
algorithms/simulation/reciprocal_space.py
algorithms/simulation/utils.py
algorithms/spatial_indexing/__init__.py
algorithms/spot_finding/__init__.py
algorithms/spot_finding/factory.py
algorithms/spot_finding/finder.py
algorithms/spot_finding/per_image_analysis.py
algorithms/spot_finding/spot_matcher.py
algorithms/spot_finding/threshold.py
algorithms/spot_finding/helen/__init__.py
algorithms/spot_prediction/__init__.py
algorithms/spot_prediction/reeke.py
algorithms/spot_prediction/reflection_predictor.py
algorithms/statistics/__init__.py
algorithms/statistics/delta_cchalf.py
algorithms/statistics/fast_mcd.py
algorithms/statistics/ks_test.py
algorithms/statistics/temp.py
algorithms/symmetry/__init__.py
algorithms/symmetry/determine_space_group.py
algorithms/symmetry/origin.py
algorithms/symmetry/reindex_to_reference.py
algorithms/symmetry/test_correlation_coefficient_accumulator.py
algorithms/symmetry/test_determine_space_group.py
algorithms/symmetry/test_reindex_to_reference.py
algorithms/symmetry/test_score_symmetry_element_subgroup.py
algorithms/symmetry/cosym/__init__.py
algorithms/symmetry/cosym/_generate_test_data.py
algorithms/symmetry/cosym/engine.py
algorithms/symmetry/cosym/observers.py
algorithms/symmetry/cosym/plots.py
algorithms/symmetry/cosym/seed_clustering.py
algorithms/symmetry/cosym/target.py
algorithms/symmetry/cosym/test_cosym_analyse_datasets.py
algorithms/symmetry/cosym/test_cosym_symmetry_analysis.py
algorithms/symmetry/cosym/test_cosym_target.py
algorithms/symmetry/cosym/test_observers.py
algorithms/symmetry/cosym/test_plots.py
array_family/__init__.py
array_family/flex.py
array_family/shared.py
command_line/__init__.py
command_line/align_crystal.py
command_line/analyse_background.py
command_line/analyse_output.py
command_line/apply_mask.py
command_line/assign_experiment_identifiers.py
command_line/augment_spots.py
command_line/background.py
command_line/bad_pixels.py
command_line/batch_analysis.py
command_line/calc_rmsds.py
command_line/check_indexing_symmetry.py
command_line/check_strategy.py
command_line/cluster_exec.py
command_line/cluster_unit_cell.py
command_line/combine_experiments.py
command_line/combine_found_spots.py
command_line/compare_beam_spindle_angles.py
command_line/compare_mosflm_dials.py
command_line/compare_mosflm_xds.py
command_line/compare_orientation_matrices.py
command_line/compare_reflections.py
command_line/compare_xds_dials.py
command_line/compare_xds_dials2.py
command_line/complete_full_sphere.py
command_line/compute_delta_cchalf.py
command_line/convert_to_cbf.py
command_line/cosym.py
command_line/create_profile_model.py
command_line/detect_blanks.py
command_line/dials_import.py
command_line/diffraction_geometry_viewer.py
command_line/display_reference_profiles.py
command_line/duelling_profiles.py
command_line/dump_mtz_orientation.py
command_line/estimate_gain.py
command_line/estimate_resolution_limit.py
command_line/export.py
command_line/export_bitmaps.py
command_line/export_nxmx_to_mtz.py
command_line/export_stills_process_integration_pickle.py
command_line/export_text.py
command_line/extract_background_signal.py
command_line/extract_shoeboxes.py
command_line/filter_reflections.py
command_line/find_hot_pixels.py
command_line/find_shared_models.py
command_line/find_spots.py
command_line/find_spots_client.py
command_line/find_spots_server.py
command_line/frame_orientations.py
command_line/generate_bias_lookup_table.py
command_line/generate_distortion_maps.py
command_line/generate_mask.py
command_line/generate_process_test_reflections.py
command_line/generate_test_reflections.py
command_line/generate_tutorial_text.py
command_line/geometry_viewer.py
command_line/goniometer_calibration.py
command_line/griddex.py
command_line/hot_pixel_mask_to_xy.py
command_line/image_correlation.py
command_line/image_viewer.py
command_line/import_stream.py
command_line/import_xds.py
command_line/index.py
command_line/integrate.py
command_line/make_polar_background_image.py
command_line/make_radial_average.py
command_line/make_sphinx_html.py
command_line/merge_cbf.py
command_line/merge_reflection_lists.py
command_line/model_background.py
command_line/modify_geometry.py
command_line/plot_Fo_vs_Fc.py
command_line/plot_centroid_analysis.py
command_line/plot_detector_shifts.py
command_line/plot_find_spots_client.py
command_line/plot_reflections.py
command_line/plot_scan_varying_model.py
command_line/plugins.py
command_line/precommitbx.py
command_line/predict.py
command_line/print_test_reflections.py
command_line/pseudo_event_data.py
command_line/rebin_images.py
command_line/reciprocal_lattice_viewer.py
command_line/refine.py
command_line/refine_bravais_settings.py
command_line/reflection_viewer.py
command_line/reindex.py
command_line/remove_absent_reflections.py
command_line/report.py
command_line/rfactor.py
command_line/rl_csv.py
command_line/rl_png.py
command_line/rs_mapper.py
command_line/saturation_analysis.py
command_line/scale.py
command_line/scale_and_filter.py
command_line/scale_down_image.py
command_line/scale_down_images.py
command_line/search_beam_position.py
command_line/semisynthetic_variance_analysis.py
command_line/shadow_plot.py
command_line/show.py
command_line/show_extensions.py
command_line/show_indexed_strong.py
command_line/show_integration_memory_info.py
command_line/show_mask.py
command_line/show_profiles.py
command_line/show_spots.py
command_line/simple_strategy.py
command_line/simulate.py
command_line/simulate_rs.py
command_line/slice_sweep.py
command_line/sort_reflections.py
command_line/split_experiments.py
command_line/spot_box_plot.py
command_line/spot_counts_per_image.py
command_line/spot_resolution_shells.py
command_line/stereographic_projection.py
command_line/stills_detector_hybrid_refine.py
command_line/stills_process.py
command_line/stills_process_mpi.py
command_line/sum_images.py
command_line/symmetry.py
command_line/two_theta_offset.py
command_line/two_theta_refine.py
command_line/unify_setting.py
command_line/unit_cell_histogram.py
command_line/version.py
data/__init__.py
data/lookup.py
data/multiprocessing.py
dials.egg-info/PKG-INFO
dials.egg-info/SOURCES.txt
dials.egg-info/dependency_links.txt
dials.egg-info/not-zip-safe
dials.egg-info/requires.txt
dials.egg-info/top_level.txt
extensions/__init__.py
extensions/dispersion_spotfinder_threshold_ext.py
extensions/gaussian_rs_profile_model_ext.py
extensions/glm_background_ext.py
extensions/global_spotfinder_threshold_ext.py
extensions/gmodel_background_ext.py
extensions/helen_spotfinder_threshold_ext.py
extensions/median_background_ext.py
extensions/null_background_ext.py
extensions/simple_background_ext.py
extensions/simple_centroid_ext.py
model/__init__.py
model/data/__init__.py
model/experiment/__init__.py
model/experiment/profile.py
model/serialize/__init__.py
model/serialize/dump.py
model/serialize/imageset.py
model/serialize/load.py
nexus/__init__.py
precommitbx/__init__.py
precommitbx/installer.py
precommitbx/nagger.py
precommitbx/setup.py
precommitbx/_precommitbx/__init__.py
precommitbx/_precommitbx/main.py
pychef/__init__.py
pychef/test_pychef.py
report/__init__.py
report/analysis.py
report/html_report.py
report/plots.py
report/test_analysis.py
report/test_plots.py
test/__init__.py
test/test_cpp_components.py
test/test_phil.py
test/test_plot_reflections.py
test/test_python3_regression.py
test/test_scan_varying_integration_bug.py
test/algorithms/__init__.py
test/algorithms/generate_test_reflections/__init__.py
test/algorithms/generate_test_reflections/test_generate_test_refl.py
test/algorithms/indexing/__init__.py
test/algorithms/indexing/test_assign_indices.py
test/algorithms/indexing/test_compare_orientation_matrices.py
test/algorithms/indexing/test_index.py
test/algorithms/indexing/test_phi_scan.py
test/algorithms/indexing/test_symmetry.py
test/algorithms/integration/__init__.py
test/algorithms/integration/test_corrections.py
test/algorithms/integration/test_filter_overlaps.py
test/algorithms/integration/test_integration_summation_2d.py
test/algorithms/integration/test_interface.py
test/algorithms/integration/test_kapton.py
test/algorithms/integration/test_parallel_integrator.py
test/algorithms/integration/profile/__init__.py
test/algorithms/integration/profile/test_circle_sampler.py
test/algorithms/integration/profile/test_empirical_modeller.py
test/algorithms/integration/profile/test_grid_sampler.py
test/algorithms/integration/profile/test_multi_experiment_modeller.py
test/algorithms/integration/profile/test_profile_fitting.py
test/algorithms/integration/profile/test_single_sampler.py
test/algorithms/refinement/__init__.py
test/algorithms/refinement/params.py
test/algorithms/refinement/setup_geometry.py
test/algorithms/refinement/setup_minimiser.py
test/algorithms/refinement/test_angle_derivatives_wrt_vector_elts.py
test/algorithms/refinement/test_beam_parameters.py
test/algorithms/refinement/test_constraints.py
test/algorithms/refinement/test_crystal_parameters.py
test/algorithms/refinement/test_cspad_refinement.py
test/algorithms/refinement/test_detector_parameters.py
test/algorithms/refinement/test_dials-423.py
test/algorithms/refinement/test_finite_diffs.py
test/algorithms/refinement/test_goniometer_parameters.py
test/algorithms/refinement/test_hierarchical_detector_refinement.py
test/algorithms/refinement/test_multi_experiment_refinement.py
test/algorithms/refinement/test_multi_panel_detector_parameterisation.py
test/algorithms/refinement/test_orientation_refinement.py
test/algorithms/refinement/test_parameter_auto_reduction.py
test/algorithms/refinement/test_prediction_parameters.py
test/algorithms/refinement/test_ref_passage_categorisation.py
test/algorithms/refinement/test_refine_multi_stills.py
test/algorithms/refinement/test_refine_multi_wedges.py
test/algorithms/refinement/test_refinement_regression.py
test/algorithms/refinement/test_refiner_units.py
test/algorithms/refinement/test_restraints_gradients.py
test/algorithms/refinement/test_restraints_parameterisation.py
test/algorithms/refinement/test_rotation_decomposition.py
test/algorithms/refinement/test_scan_varying_beam_refinement.py
test/algorithms/refinement/test_scan_varying_block_calculation.py
test/algorithms/refinement/test_scan_varying_model_parameters.py
test/algorithms/refinement/test_scan_varying_prediction_parameters.py
test/algorithms/refinement/test_stills_prediction_parameters.py
test/algorithms/refinement/test_stills_refinement.py
test/algorithms/refinement/test_stills_spherical_relp_derivatives.py
test/algorithms/refinement/test_sv_multi_panel_refinement.py
test/algorithms/refinement/test_two_theta_refinement.py
test/algorithms/refinement/test_xfel_metrology.py
test/algorithms/spot_prediction/__init__.py
test/algorithms/spot_prediction/test_index_generator.py
test/algorithms/spot_prediction/test_pixel_to_miller_index.py
test/algorithms/spot_prediction/test_ray_predictor.py
test/algorithms/spot_prediction/test_reeke.py
test/algorithms/spot_prediction/test_reeke_index_generator.py
test/algorithms/spot_prediction/test_rotation_angles.py
test/algorithms/spot_prediction/test_scan_static_reflection_predictor.py
test/algorithms/spot_prediction/test_scan_varying_predictor.py
test/algorithms/spot_prediction/test_scan_varying_reflection_predictor.py
test/algorithms/spot_prediction/test_spot_prediction.py
test/algorithms/spot_prediction/test_stills_reflection_predictor.py
test/model/__init__.py
test/model/data/__init__.py
test/model/data/all_foreground_valid_data.py
test/model/data/test_observation.py
test/model/data/test_pixel_list.py
test/model/data/test_prediction.py
test/model/data/test_shoebox.py
util/Resolutionizer.py
util/__init__.py
util/_progress.py
util/add_hash.py
util/ascii_art.py
util/banner.py
util/batch_handling.py
util/best.py
util/cluster_map.py
util/command_line.py
util/exclude_images.py
util/export_json.py
util/export_mmcif.py
util/export_mtz.py
util/export_sadabs.py
util/export_text.py
util/export_xds_ascii.py
util/ext.py
util/filter_reflections.py
util/image.py
util/installer.py
util/intensity_explorer.py
util/ioutil.py
util/log.py
util/masking.py
util/mosflm.py
util/mp.py
util/multi_dataset_handling.py
util/nexus_old.py
util/observer.py
util/options.py
util/phil.py
util/pprint.py
util/pycbf_extra.py
util/rebin_images.py
util/report.py
util/scale_down_image.py
util/show_version.py
util/slice.py
util/stream.py
util/test_slice.py
util/version.py
util/wx_viewer.py
util/xds.py
util/image_viewer/__init__.py
util/image_viewer/mask_frame.py
util/image_viewer/rstbx_frame.py
util/image_viewer/spotfinder_frame.py
util/image_viewer/spotfinder_wrap.py
util/image_viewer/viewer_tools.py
util/image_viewer/slip_viewer/__init__.py
util/image_viewer/slip_viewer/calibration_frame.py
util/image_viewer/slip_viewer/example_frame_plugin_hidden.py
util/image_viewer/slip_viewer/frame.py
util/image_viewer/slip_viewer/pyslip.py
util/image_viewer/slip_viewer/ring_frame.py
util/image_viewer/slip_viewer/score_frame.py
util/image_viewer/slip_viewer/slip_display.py
util/image_viewer/slip_viewer/slip_viewer_image_factory.py
util/image_viewer/slip_viewer/tile_generation.py
util/image_viewer/slip_viewer/uc_frame.py
util/nexus/__init__.py
util/nexus/nx_mx.py
util/nexus/nx_reflections.py
viewer/__init__.py
viewer/bitmap_from_array.py
viewer/flex_3d_array_viewer_tests.py
viewer/from_flex_to_wxbitmap.py
viewer/slice_viewer.py
viewer/viewer_interface.py
viewer/viewer_low_level_util.py