reflist RefList Reflection RefListIterator reflist_new reflist_free reflection_new reflection_free reflist_add_notes reflist_get_notes add_refl add_refl_to_list first_refl next_refl find_refl next_found_refl get_detector_pos get_panel get_partiality get_lorentz get_partial get_indices get_symmetric_indices get_intensity get_redundancy get_esd_intensity get_phase get_mean_bg get_peak get_temp1 get_temp2 get_flag set_detector_pos set_panel set_partiality set_lorentz set_partial set_intensity set_redundancy set_esd_intensity set_phase set_mean_bg set_peak set_symmetric_indices set_temp1 set_temp2 set_flag copy_data num_reflections tree_depth lock_reflection unlock_reflection GET_H GET_K GET_L SERIAL

reflist-utils write_reflist write_reflist_2 write_reflections_to_file read_reflections read_reflections_from_file asymmetric_indices res_cutoff check_list_symmetry copy_reflist find_equiv_in_list resolution_limits max_intensity reflist_add_command_and_version

unitcell UnitCell LatticeType UnitCellTransformation rvec cell_new cell_new_from_cell cell_new_from_direct_axes cell_new_from_parameters cell_new_from_reciprocal_axes cell_free cell_get_cartesian cell_get_parameters cell_get_reciprocal cell_get_centering cell_get_lattice_type cell_get_unique_axis cell_has_parameters cell_set_cartesian cell_set_parameters cell_set_reciprocal cell_set_centering cell_set_lattice_type cell_set_unique_axis cell_transform cell_transform_inverse tfn_combine tfn_identity tfn_from_intmat tfn_inverse tfn_print tfn_vector tfn_free cell_rep

cell-utils cell_rotate rotate_cell cell_print resolution match_cell match_cell_ab cell_is_sensible validate_cell uncenter_cell bravais_lattice right_handed str_lattice forbidden_reflection load_cell_from_pdb load_cell_from_file write_cell lattice_from_str cell_get_volume

utils show_matrix_eqn solve_svd AssplodeFlag C_VACUO ELECTRON_CHARGE PLANCK THOMSON_LENGTH assplode chomp gaussian_noise progress_bar poisson_noise notrail random_flat flat_noise show_matrix STATUS ERROR J_to_eV eV_to_J biggest smallest check_prefix safe_basename deg2rad rad2deg is_odd ph_en_to_lambda ph_lambda_to_en ph_eV_to_lambda ph_lambda_to_eV likely unlikely UNUSED

quaternion quaternion quaternion_modulus normalise_quaternion random_quaternion quaternion_valid quat_rot

histogram Histogram histogram_init histogram_free histogram_add_value histogram_show histogram_get_data histogram_get_max histogram_get_min histogram_get_num_bins histogram_set_max histogram_set_min histogram_set_num_bins

image image beam_params imagefeature ImageFeatureList SpectrumType sample imagefile imagefile_close imagefile_copy_fields imagefile_field_list imagefile_get_hdfile imagefile_get_type imagefile_open imagefile_read imagefile_read_simple new_imagefile_field_list add_imagefile_field free_imagefile_field_list image_add_feature image_feature_closest image_reflection_closest image_feature_count image_feature_list_free image_feature_list_new image_get_feature image_add_crystal image_remove_feature free_all_crystals remove_flagged_crystals

thread-pool TPGetTaskFunc TPWorkFunc TPFinalFunc run_threads stderr_lock get_status_label

statistics stat_pearson_f_ignore stat_pearson_f_zero stat_pearson_i stat_r1_i stat_r1_ignore stat_r1_zero stat_r2 stat_rdiff_ignore stat_rdiff_intensity stat_rdiff_zero stat_scale_intensity

indexing IndexingMethod IndexingPrivate INDEXING_DEFAULTS_DIRAX INDEXING_DEFAULTS_MOSFLM INDEXING_DEFAULTS_XDS INDEXING_DEFAULTS_ASDF INDEXING_DEFAULTS_FELIX INDEXING_METHOD_MASK INDEXING_CONTROL_FLAGS setup_indexing cleanup_indexing get_indm_from_string index_pattern index_pattern_2 indexer_str dirax_prepare run_dirax dirax_cleanup mosflm_prepare run_mosflm mosflm_cleanup xds_prepare run_xds xds_cleanup asdf_prepare run_asdf asdf_cleanup felix_prepare felix_index felix_cleanup

symmetry SymOpList SymOpMask free_symoplist num_equivs get_pointgroup parse_symmetry_operations add_symop get_equiv get_symop special_position get_asymm get_ambiguities is_subgroup new_symopmask free_symopmask describe_symmetry symmetry_name set_symmetry_name get_matrix_name pointgroup_warning is_centrosymmetric is_centric

integer_matrix IntegerMatrix intmat_new intmat_copy intmat_identity intmat_free intmat_get intmat_set intmat_intmat_mult intmat_intvec_mult intmat_det intmat_inverse intmat_equals intmat_is_identity intmat_is_inversion intmat_print

detector detector panel badregion rigid_group rg_collection copy_geom fill_in_adu free_detector_geometry get_detector_geometry get_detector_geometry_2 write_detector_geometry write_detector_geometry_2 panel_number find_panel_by_name simple_geometry record_image get_pixel_extents get_q_for_panel get_tt smallest_q reverse_2d_mapping largest_q in_bad_region mark_resolution_range_as_bad find_orig_panel find_orig_panel_number panel_is_in_rigid_group rigid_group_is_in_collection single_panel_data_source find_rigid_group_collection_by_name detector_has_clen_references adjust_centering_for_rail

events event event_list dim_structure filename_plus_event initialize_event push_path_entry_to_event pop_path_entry_from_event push_dim_entry_to_event pop_dim_entry_from_event copy_event free_event find_event get_event_string get_event_from_event_string event_path_placeholder_subst retrieve_full_path initialize_filename_plus_event free_filename_plus_event initialize_event_list append_event_to_event_list add_non_existing_event_to_event_list copy_event_list free_event_list initialize_dim_structure default_dim_structure set_dim_structure_entry free_dim_structure_entry free_dim_structure

crystal

hdf5-file hdf5_read hdf5_read2 hdf5_write hdf5_write_image hdfile hdfile_close hdfile_get_image_binned hdfile_get_string_value hdfile_open hdfile_read_group hdfile_set_first_image hdfile_set_image hdfile_get_value copy_hdf5_field copy_hdf5_fields add_copy_hdf5_field new_copy_hdf5_field_list free_copy_hdf5_field_list get_peaks get_peaks_2 get_peaks_cxi get_peaks_cxi_2 hdfile_is_scalar check_path_existence fill_event_list

crystal Crystal crystal_new crystal_copy crystal_free crystal_get_cell crystal_get_image crystal_get_mosaicity crystal_get_num_saturated_reflections crystal_get_osf crystal_get_Bfac crystal_get_profile_radius crystal_get_reflections crystal_get_resolution_limit crystal_get_user_flag crystal_get_num_implausible_reflections crystal_get_notes crystal_get_det_shift crystal_set_cell crystal_set_image crystal_set_mosaicity crystal_set_num_saturated_reflections crystal_set_osf crystal_set_Bfac crystal_set_profile_radius crystal_set_reflections crystal_set_resolution_limit crystal_set_user_flag crystal_set_num_implausible_reflections crystal_set_notes crystal_add_notes crystal_set_det_shift

geometry PartialityModel gparam find_intersections find_intersections_to_res update_partialities polarisation_correction sphere_fraction gaussian_fraction r_gradient x_gradient y_gradient

peaks peak_sanity_check search_peaks search_peaks_peakfinder8 make_BgMask peakfinder8 validate_peaks sort_peaks

render render_scale

filter filter_cm filter_noise filter_median

integration INTEGRATION_DEFAULTS_PROF2D INTEGRATION_DEFAULTS_RINGS INTEGRATION_METHOD_MASK IntegrationMethod IntDiag integrate_all integrate_all_2 integrate_all_3 integrate_all_4 integration_method

stream Stream StreamReadFlags CHUNK_START_MARKER CHUNK_END_MARKER CRYSTAL_START_MARKER CRYSTAL_END_MARKER PEAK_LIST_START_MARKER PEAK_LIST_END_MARKER REFLECTION_START_MARKER REFLECTION_END_MARKER GEOM_START_MARKER GEOM_END_MARKER CELL_START_MARKER CELL_END_MARKER open_stream_fd_for_write open_stream_for_read open_stream_for_write open_stream_for_write_2 open_stream_for_write_3 get_stream_fd close_stream read_chunk read_chunk_2 write_chunk write_chunk_2 rewind_stream is_stream write_command write_geometry_file stuff_from_stream

predict-refine refine_prediction refine_radius