diff options
Diffstat (limited to 'doc/reference/libcrystfel/CrystFEL-sections.txt')
| -rw-r--r-- | doc/reference/libcrystfel/CrystFEL-sections.txt | 619 |
1 files changed, 0 insertions, 619 deletions
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt deleted file mode 100644 index 4a436e34..00000000 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ /dev/null @@ -1,619 +0,0 @@ -<SECTION> -<FILE>reflist</FILE> -RefList -Reflection -RefListIterator -<SUBSECTION> -reflist_new -reflist_free -reflection_new -reflection_free -reflist_add_notes -reflist_get_notes -<SUBSECTION> -add_refl -add_refl_to_list -<SUBSECTION> -first_refl -first_refl_const -next_refl -next_refl_const -<SUBSECTION> -find_refl -next_found_refl -<SUBSECTION> -get_detector_pos -get_panel -get_partiality -get_lorentz -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 -get_exerr -get_khalf -get_kpred -<SUBSECTION> -set_detector_pos -set_panel -set_partiality -set_lorentz -set_intensity -set_redundancy -set_esd_intensity -set_phase -set_mean_bg -set_peak -set_symmetric_indices -set_temp1 -set_temp2 -set_flag -set_exerr -set_khalf -set_kpred -<SUBSECTION> -copy_data -num_reflections -tree_depth -lock_reflection -unlock_reflection -GET_H -GET_K -GET_L -SERIAL -</SECTION> - -<SECTION> -<FILE>reflist-utils</FILE> -write_reflist -write_reflist_2 -read_reflections -read_reflections_2 -asymmetric_indices -res_cutoff -check_list_symmetry -copy_reflist -find_equiv_in_list -resolution_limits -max_intensity -reflist_add_command_and_version -</SECTION> - -<SECTION> -<FILE>unitcell</FILE> -UnitCell -LatticeType -UnitCellTransformation -rvec -<SUBSECTION> -cell_new -cell_new_from_cell -cell_new_from_direct_axes -cell_new_from_parameters -cell_new_from_reciprocal_axes -cell_free -<SUBSECTION> -cell_get_cartesian -cell_get_parameters -cell_get_reciprocal -cell_get_centering -cell_get_lattice_type -cell_get_unique_axis -cell_has_parameters -<SUBSECTION> -cell_set_cartesian -cell_set_parameters -cell_set_reciprocal -cell_set_centering -cell_set_lattice_type -cell_set_unique_axis -<SUBSECTION> -cell_transform -cell_transform_inverse -tfn_combine -tfn_identity -tfn_from_intmat -tfn_inverse -tfn_print -tfn_vector -tfn_free -<SUBSECTION> - -cell_rep -</SECTION> - -<SECTION> -<FILE>cell-utils</FILE> -cell_rotate -rotate_cell -cell_print -resolution -match_cell -compare_cells -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 -transform_cell_gsl -</SECTION> - -<SECTION> -<FILE>utils</FILE> -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 -</SECTION> - -<SECTION> -<FILE>quaternion</FILE> -quaternion -<SUBSECTION> -quaternion_modulus -normalise_quaternion -random_quaternion -quaternion_valid -quat_rot -</SECTION> - -<SECTION> -<FILE>histogram</FILE> -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 -</SECTION> - -<SECTION> -<FILE>image</FILE> -image -beam_params -imagefeature -ImageFeatureList -SpectrumType -sample -<SUBSECTION> -imagefile -imagefile_close -imagefile_copy_fields -imagefile_field_list -imagefile_get_hdfile -imagefile_get_type -imagefile_open -imagefile_read -imagefile_read_simple -is_cbf_file -<SUBSECTION> -new_imagefile_field_list -add_imagefile_field -free_imagefile_field_list -<SUBSECTION> -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 -</SECTION> - -<SECTION> -<FILE>thread-pool</FILE> -TPGetTaskFunc -TPWorkFunc -TPFinalFunc -<SUBSECTION> -run_threads -stderr_lock -get_status_label -</SECTION> - -<SECTION> -<FILE>statistics</FILE> -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 -</SECTION> - -<SECTION> -<FILE>indexing</FILE> -IndexingMethod -IndexingPrivate -IndexingFlags -INDEXING_DEFAULTS_DIRAX -INDEXING_DEFAULTS_MOSFLM -INDEXING_DEFAULTS_XDS -INDEXING_DEFAULTS_ASDF -INDEXING_DEFAULTS_FELIX -INDEXING_DEFAULTS_TAKETWO -INDEXING_METHOD_MASK -detect_indexing_methods -setup_indexing -cleanup_indexing -get_indm_from_string -get_indm_from_string_2 -index_pattern -index_pattern_2 -indexer_str -dirax_probe -dirax_prepare -run_dirax -dirax_cleanup -mosflm_probe -mosflm_prepare -run_mosflm -mosflm_cleanup -xds_probe -xds_prepare -run_xds -xds_cleanup -asdf_probe -asdf_prepare -run_asdf -asdf_cleanup -felix_options -felix_probe -felix_prepare -felix_index -felix_cleanup -taketwo_options -taketwo_probe -taketwo_prepare -taketwo_index -taketwo_cleanup -</SECTION> - -<SECTION> -<FILE>symmetry</FILE> -SymOpList -SymOpMask -<SUBSECTION> -free_symoplist -num_equivs -get_pointgroup -parse_symmetry_operations -add_symop -get_equiv -get_symop -special_position -get_asymm -get_ambiguities -is_subgroup -<SUBSECTION> -new_symopmask -free_symopmask -<SUBSECTION> -describe_symmetry -symmetry_name -set_symmetry_name -get_matrix_name -pointgroup_warning -is_centrosymmetric -is_centric -</SECTION> - -<SECTION> -<FILE>integer_matrix</FILE> -IntegerMatrix -<SUBSECTION> -intmat_new -intmat_copy -intmat_identity -intmat_free -<SUBSECTION> -intmat_get -intmat_set -<SUBSECTION> -intmat_intmat_mult -intmat_intvec_mult -intmat_det -intmat_inverse -<SUBSECTION> -intmat_equals -intmat_is_identity -intmat_is_inversion -<SUBSECTION> -intmat_print -</SECTION> - -<SECTION> -<FILE>detector</FILE> -detector -panel -badregion -rigid_group -rg_collection -<SUBSECTION> -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 -</SECTION> - -<SECTION> -<FILE>events</FILE> -event -event_list -dim_structure -filename_plus_event -<SUBSECTION> -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 -</SECTION> - -<SECTION> -<FILE>crystal</FILE> -</SECTION> - -<SECTION> -<FILE>hdf5-file</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 -</SECTION> - -<SECTION> -<FILE>crystal</FILE> -Crystal -crystal_new -crystal_copy -crystal_free -<SUBSECTION> -crystal_get_cell -crystal_get_cell_const -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 -</SECTION> - -<SECTION> -<FILE>geometry</FILE> -PartialityModel -gparam -predict_to_res -update_predictions -calculate_partialities -polarisation_correction -sphere_fraction -gaussian_fraction -r_gradient -x_gradient -y_gradient -</SECTION> - -<SECTION> -<FILE>peaks</FILE> -peak_sanity_check -search_peaks -search_peaks_peakfinder8 -make_BgMask -peakfinder8 -validate_peaks -sort_peaks -</SECTION> - -<SECTION> -<FILE>render</FILE> -render_scale -</SECTION> - -<SECTION> -<FILE>filter</FILE> -filter_cm -filter_noise -filter_median -</SECTION> - -<SECTION> -<FILE>integration</FILE> -INTEGRATION_DEFAULTS_PROF2D -INTEGRATION_DEFAULTS_RINGS -INTEGRATION_METHOD_MASK -IntegrationMethod -IntDiag -integrate_all -integrate_all_2 -integrate_all_3 -integrate_all_4 -integrate_all_5 -integration_method -</SECTION> - -<SECTION> -<FILE>stream</FILE> -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 -open_stream_for_write_4 -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 -stream_audit_info -stream_has_old_indexers -</SECTION> - -<SECTION> -<FILE>predict-refine</FILE> -refine_prediction -refine_radius -</SECTION> |