From ceae2d277c9add4731cb24cf33570e988bb57c3e Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 16 Feb 2015 16:40:50 +0100 Subject: Update API docs --- doc/reference/libcrystfel/CrystFEL-docs.sgml | 5 ++++ doc/reference/libcrystfel/CrystFEL-sections.txt | 36 ++++++++++++++++++++++++- libcrystfel/src/cell-utils.c | 10 ++++--- libcrystfel/src/detector.h | 1 + 4 files changed, 47 insertions(+), 5 deletions(-) diff --git a/doc/reference/libcrystfel/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml index 1aef3ddb..e9027306 100644 --- a/doc/reference/libcrystfel/CrystFEL-docs.sgml +++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml @@ -42,6 +42,11 @@ + + Events + + + Geometry of diffraction diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index f3b5dc59..7b06c2cd 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -94,6 +94,7 @@ cell_get_reciprocal cell_get_centering cell_get_lattice_type cell_get_unique_axis +cell_has_parameters cell_set_cartesian cell_set_parameters @@ -132,6 +133,7 @@ right_handed str_lattice forbidden_reflection load_cell_from_pdb +load_cell_from_file lattice_from_str @@ -202,10 +204,15 @@ histogram_set_num_bins
image image +beam_params +imagefeature ImageFeatureList SpectrumType +sample + image_add_feature image_feature_closest +image_reflection_closest image_feature_count image_feature_list_free image_feature_list_new @@ -327,11 +334,18 @@ intmat_print
detector +detector +panel +badregion +rigid_group +rg_collection + copy_geom fill_in_values free_detector_geometry get_detector_geometry write_detector_geometry +write_detector_geometry_2 find_panel find_panel_by_name find_panel_number @@ -342,15 +356,22 @@ get_q get_q_for_panel get_tt smallest_q -twod_mapping reverse_2d_mapping largest_q in_bad_region mark_resolution_range_as_bad +find_orig_panel +panel_is_in_rigid_group +rigid_group_is_in_collection +single_panel_data_source +find_rigid_group_collection_by_name
events +event +event_list + initialize_event push_path_entry_to_event pop_path_entry_from_event @@ -358,6 +379,7 @@ 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 @@ -374,6 +396,7 @@ initialize_dim_structure default_dim_structure set_dim_structure_entry free_dim_structure_entry +free_dim_structure
@@ -383,6 +406,7 @@ free_dim_structure_entry
hdf5-file hdf5_read +hdf5_read2 hdf5_write hdf5_write_image hdfile @@ -394,13 +418,17 @@ hdfile_read_group hdfile_set_first_image hdfile_set_image get_value +get_ev_based_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_cxi hdfile_is_scalar +check_path_existence +fill_event_list
@@ -419,6 +447,7 @@ crystal_get_profile_radius crystal_get_reflections crystal_get_resolution_limit crystal_get_user_flag +crystal_get_num_implausible_reflections crystal_set_cell crystal_set_image crystal_set_mosaicity @@ -428,16 +457,20 @@ crystal_set_profile_radius crystal_set_reflections crystal_set_resolution_limit crystal_set_user_flag +crystal_set_num_implausible_reflections
geometry PartialityModel find_intersections +find_intersections_to_res select_intersections update_partialities update_partialities_2 polarisation_correction +sphere_fraction +gaussian_fraction
@@ -501,4 +534,5 @@ rewind_stream is_stream write_command write_geometry_file +extract_f_from_stuff
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index 95e7353e..7c7a58a6 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -3,13 +3,13 @@ * * Unit Cell utility functions * - * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Lorenzo Galli * * Authors: - * 2009-2012,2014 Thomas White - * 2012 Lorenzo Galli + * 2009-2012,2014-2015 Thomas White + * 2012 Lorenzo Galli * * This file is part of CrystFEL. * @@ -1090,8 +1090,9 @@ static void determine_lattice(UnitCell *cell, /** * load_cell_from_pdb: + * @filename: The filename from which to load the cell * - * Loads a unit cell from a PDB file. + * Loads a unit cell from the CRYST1 line of a PDB file. * * Returns: a newly allocated %UnitCell. * @@ -1225,6 +1226,7 @@ static int get_angle_rad(char **bits, int nbits, double *pl) /** * load_cell_from_file: + * @filename: The filename from which to load the cell * * Loads a unit cell from a file of any type (PDB or CrystFEL format) * diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h index 8f4d009c..a5a7b98a 100644 --- a/libcrystfel/src/detector.h +++ b/libcrystfel/src/detector.h @@ -38,6 +38,7 @@ #define DETECTOR_H struct rigid_group; +struct rg_collection; struct detector; struct panel; struct badregion; -- cgit v1.2.3