diff options
Diffstat (limited to 'doc/reference')
-rw-r--r-- | doc/reference/libcrystfel/CrystFEL-docs.sgml (renamed from doc/reference/CrystFEL-docs.sgml) | 25 | ||||
-rw-r--r-- | doc/reference/libcrystfel/CrystFEL-sections.txt (renamed from doc/reference/CrystFEL-sections.txt) | 135 | ||||
-rw-r--r-- | doc/reference/libcrystfel/Makefile.am (renamed from doc/reference/Makefile.am) | 2 | ||||
-rw-r--r-- | doc/reference/libcrystfel/xml/coding-standards.xml (renamed from doc/reference/xml/coding-standards.xml) | 0 |
4 files changed, 146 insertions, 16 deletions
diff --git a/doc/reference/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml index 34258a64..1c91e72f 100644 --- a/doc/reference/CrystFEL-docs.sgml +++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml @@ -38,6 +38,31 @@ </chapter> <chapter> + <title>Crystals</title> + <xi:include href="xml/crystal.xml"/> + </chapter> + + <chapter> + <title>Geometry of diffraction</title> + <xi:include href="xml/geometry.xml"/> + </chapter> + + <chapter> + <title>Beam parameters</title> + <xi:include href="xml/beam-params.xml"/> + </chapter> + + <chapter> + <title>Peaks</title> + <xi:include href="xml/peaks.xml"/> + </chapter> + + <chapter> + <title>Image filters</title> + <xi:include href="xml/filter.xml"/> + </chapter> + + <chapter> <title>Statistics and R-factors</title> <xi:include href="xml/statistics.xml"><xi:fallback /></xi:include> </chapter> diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index 18a20eb9..b14f4adc 100644 --- a/doc/reference/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -63,6 +63,8 @@ res_cutoff check_list_symmetry copy_reflist find_equiv_in_list +resolution_limits +max_intensity </SECTION> <SECTION> @@ -156,6 +158,10 @@ notrail smallest ph_en_to_lambda ph_lambda_to_en +ph_eV_to_lambda +ph_lambda_to_eV +random_flat +flat_noise </SECTION> <SECTION> @@ -179,7 +185,9 @@ 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> @@ -189,6 +197,8 @@ TPWorkFunc TPFinalFunc <SUBSECTION> run_threads +stderr_lock +get_status_label </SECTION> <SECTION> @@ -210,14 +220,32 @@ stat_scale_intensity <FILE>indexing</FILE> IndexingMethod IndexingPrivate -MAX_CELL_CANDIDATES +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 -map_all_peaks +mosflm_cleanup +xds_prepare +run_xds +xds_cleanup +reax_prepare +reax_index +reax_cleanup +grainspotter_prepare +grainspotter_index +grainspotter_cleanup </SECTION> <SECTION> @@ -228,6 +256,7 @@ SymOpMask free_symoplist num_equivs get_pointgroup +add_symop get_equiv special_position get_asymm @@ -284,12 +313,26 @@ 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 @@ -298,25 +341,87 @@ 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>stream</FILE> -parse_stream_flags -read_chunk -write_chunk -write_stream_header -skip_some_files -is_stream -get_value -count_patterns +<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_get_colour_scale -render_panels render_scale -render_tiff_fp -render_tiff_int16 +</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> diff --git a/doc/reference/Makefile.am b/doc/reference/libcrystfel/Makefile.am index 3b03513d..e4f49b03 100644 --- a/doc/reference/Makefile.am +++ b/doc/reference/libcrystfel/Makefile.am @@ -22,7 +22,7 @@ DOC_MAIN_SGML_FILE=$(DOC_MODULE)-docs.sgml # gtk-doc will search all .c and .h files beneath these paths # for inline comments documenting functions and macros. # e.g. DOC_SOURCE_DIR=../../../gtk ../../../gdk -DOC_SOURCE_DIR=../../libcrystfel/src ../../src +DOC_SOURCE_DIR=../../../libcrystfel/src # Extra options to pass to gtkdoc-scangobj. Not normally needed. SCANGOBJ_OPTIONS= diff --git a/doc/reference/xml/coding-standards.xml b/doc/reference/libcrystfel/xml/coding-standards.xml index d51ba293..d51ba293 100644 --- a/doc/reference/xml/coding-standards.xml +++ b/doc/reference/libcrystfel/xml/coding-standards.xml |