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Diffstat (limited to 'doc/reference/libcrystfel/CrystFEL-sections.txt')
-rw-r--r-- | doc/reference/libcrystfel/CrystFEL-sections.txt | 427 |
1 files changed, 427 insertions, 0 deletions
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt new file mode 100644 index 00000000..b14f4adc --- /dev/null +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -0,0 +1,427 @@ +<SECTION> +<FILE>reflist</FILE> +RefList +Reflection +RefListIterator +<SUBSECTION> +reflist_new +reflist_free +reflection_new +reflection_free +<SUBSECTION> +add_refl +add_refl_to_list +<SUBSECTION> +first_refl +next_refl +<SUBSECTION> +find_refl +next_found_refl +<SUBSECTION> +get_excitation_error +get_detector_pos +get_partiality +get_indices +get_symmetric_indices +get_intensity +get_partial +get_scalable +get_refinable +get_redundancy +get_esd_intensity +get_phase +get_temp1 +get_temp2 +<SUBSECTION> +set_detector_pos +set_partial +set_intensity +set_scalable +set_refinable +set_redundancy +set_esd_intensity +set_phase +set_symmetric_indices +set_temp1 +set_temp2 +<SUBSECTION> +copy_data +num_reflections +tree_depth +lock_reflection +unlock_reflection +</SECTION> + +<SECTION> +<FILE>reflist-utils</FILE> +write_reflist +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 +</SECTION> + +<SECTION> +<FILE>unitcell</FILE> +UnitCell +LatticeType +UnitCellTransformation +<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_pointgroup +cell_get_reciprocal +cell_get_centering +cell_get_lattice_type +cell_get_unique_axis +<SUBSECTION> +cell_set_cartesian +cell_set_cartesian_a +cell_set_cartesian_b +cell_set_cartesian_c +cell_set_parameters +cell_set_pointgroup +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 +match_cell_ab +cell_is_sensible +validate_cell +uncenter_cell +bravais_lattice +right_handed +str_lattice +forbidden_reflection +load_cell_from_pdb +</SECTION> + +<SECTION> +<FILE>utils</FILE> +show_matrix_eqn +AssplodeFlag +C_VACUO +ELECTRON_CHARGE +ERROR +J_to_eV +PLANCK +STATUS +THOMSON_LENGTH +assplode +biggest +check_prefix +chomp +deg2rad +eV_to_J +gaussian_noise +safe_basename +progress_bar +rad2deg +is_odd +poisson_noise +notrail +smallest +ph_en_to_lambda +ph_lambda_to_en +ph_eV_to_lambda +ph_lambda_to_eV +random_flat +flat_noise +</SECTION> + +<SECTION> +<FILE>quaternion</FILE> +quaternion +<SUBSECTION> +quaternion_modulus +normalise_quaternion +random_quaternion +quaternion_valid +quat_rot +</SECTION> + +<SECTION> +<FILE>image</FILE> +image +ImageFeatureList +image_add_feature +image_feature_closest +image_feature_count +image_feature_list_free +image_feature_list_new +image_get_feature +image_add_crystal +image_remove_feature +free_all_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 +INDEXING_DEFAULTS_DIRAX +INDEXING_DEFAULTS_GRAINSPOTTER +INDEXING_DEFAULTS_MOSFLM +INDEXING_DEFAULTS_REAX +INDEXING_DEFAULTS_XDS +INDEXING_METHOD_MASK +build_indexer_list +cleanup_indexing +prepare_indexing +index_pattern +indexer_str +dirax_prepare +run_dirax +dirax_cleanup +mosflm_prepare +run_mosflm +mosflm_cleanup +xds_prepare +run_xds +xds_cleanup +reax_prepare +reax_index +reax_cleanup +grainspotter_prepare +grainspotter_index +grainspotter_cleanup +</SECTION> + +<SECTION> +<FILE>symmetry</FILE> +SymOpList +SymOpMask +<SUBSECTION> +free_symoplist +num_equivs +get_pointgroup +add_symop +get_equiv +special_position +get_asymm +get_ambiguities +is_subgroup +<SUBSECTION> +new_symopmask +free_symopmask +<SUBSECTION> +describe_symmetry +symmetry_name +is_centrosymmetric +</SECTION> + +<SECTION> +<FILE>integer_matrix</FILE> +IntegerMatrix +<SUBSECTION> +intmat_new +intmat_copy +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> +copy_geom +fill_in_values +free_detector_geometry +get_detector_geometry +write_detector_geometry +find_panel +find_panel_by_name +find_panel_number +simple_geometry +record_image +get_pixel_extents +get_q +get_q_for_panel +get_tt +smallest_q +reverse_2d_mapping +largest_q +in_bad_region +</SECTION> + +<SECTION> +<FILE>beam-params</FILE> +beam_params +get_beam_parameters +fill_in_beam_parameters +free_beam_parameters +</SECTION> + +<SECTION> +<FILE>crystal</FILE> +</SECTION> + +<SECTION> +<FILE>hdf5-file</FILE> +hdf5_read +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 +get_value +copy_hdf5_field +copy_hdf5_fields +add_copy_hdf5_field +new_copy_hdf5_field_list +free_copy_hdf5_field_list +get_peaks +</SECTION> + +<SECTION> +<FILE>crystal</FILE> +Crystal +crystal_new +crystal_copy +crystal_free +<SUBSECTION> +crystal_get_cell +crystal_get_image +crystal_get_mosaicity +crystal_get_num_saturated_reflections +crystal_get_osf +crystal_get_profile_radius +crystal_get_reflections +crystal_get_resolution_limit +crystal_get_user_flag +crystal_set_cell +crystal_set_image +crystal_set_mosaicity +crystal_set_num_saturated_reflections +crystal_set_osf +crystal_set_profile_radius +crystal_set_reflections +crystal_set_resolution_limit +crystal_set_user_flag +</SECTION> + +<SECTION> +<FILE>geometry</FILE> +find_intersections +select_intersections +update_partialities +</SECTION> + +<SECTION> +<FILE>peaks</FILE> +peak_sanity_check +search_peaks +integrate_reflections +validate_peaks +</SECTION> + +<SECTION> +<FILE>render</FILE> +render_scale +</SECTION> + +<SECTION> +<FILE>filter</FILE> +filter_cm +filter_noise +</SECTION> + +<SECTION> +<FILE>stream</FILE> +Stream +CHUNK_END_MARKER +CHUNK_START_MARKER +CRYSTAL_END_MARKER +CRYSTAL_START_MARKER +PEAK_LIST_END_MARKER +PEAK_LIST_START_MARKER +REFLECTION_END_MARKER +REFLECTION_START_MARKER +open_stream_fd_for_write +open_stream_for_read +open_stream_for_write +close_stream +read_chunk +write_chunk +rewind_stream +is_stream +write_command +write_line +</SECTION> |