From 466402c6a1b2804c168aa0da40a54842243ca60a Mon Sep 17 00:00:00 2001 From: Thomas White Date: Mon, 20 Jul 2015 15:52:38 +0200 Subject: Update API docs --- doc/reference/libcrystfel/CrystFEL-docs.sgml | 5 +++ doc/reference/libcrystfel/CrystFEL-sections.txt | 44 +++++++++++++++++-------- libcrystfel/src/geometry.c | 9 ++++- libcrystfel/src/index.h | 1 + libcrystfel/src/reflist.c | 2 +- libcrystfel/src/utils.c | 8 ++--- 6 files changed, 50 insertions(+), 19 deletions(-) diff --git a/doc/reference/libcrystfel/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml index ae0a115a..6c7baa74 100644 --- a/doc/reference/libcrystfel/CrystFEL-docs.sgml +++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml @@ -82,6 +82,11 @@ + + Prediction refinement + + + Integration diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt index 7b06c2cd..f423ee82 100644 --- a/doc/reference/libcrystfel/CrystFEL-sections.txt +++ b/doc/reference/libcrystfel/CrystFEL-sections.txt @@ -20,6 +20,7 @@ next_found_refl get_excitation_error get_detector_pos +get_panel get_partiality get_lorentz get_partial @@ -33,8 +34,10 @@ get_mean_bg get_peak get_temp1 get_temp2 +get_flag set_detector_pos +set_panel set_partiality set_lorentz set_partial @@ -47,6 +50,7 @@ set_peak set_symmetric_indices set_temp1 set_temp2 +set_flag copy_data num_reflections @@ -80,6 +84,7 @@ max_intensity UnitCell LatticeType UnitCellTransformation +rvec cell_new cell_new_from_cell @@ -135,11 +140,13 @@ forbidden_reflection load_cell_from_pdb load_cell_from_file lattice_from_str +cell_get_volume
utils show_matrix_eqn +solve_svd AssplodeFlag C_VACUO ELECTRON_CHARGE @@ -253,10 +260,9 @@ stat_scale_intensity IndexingMethod IndexingPrivate INDEXING_DEFAULTS_DIRAX -INDEXING_DEFAULTS_GRAINSPOTTER INDEXING_DEFAULTS_MOSFLM -INDEXING_DEFAULTS_REAX INDEXING_DEFAULTS_XDS +INDEXING_DEFAULTS_ASDF INDEXING_METHOD_MASK build_indexer_list cleanup_indexing @@ -272,12 +278,9 @@ mosflm_cleanup xds_prepare run_xds xds_cleanup -reax_prepare -reax_index -reax_cleanup -grainspotter_prepare -grainspotter_index -grainspotter_cleanup +asdf_prepare +run_asdf +asdf_cleanup
@@ -365,12 +368,15 @@ panel_is_in_rigid_group rigid_group_is_in_collection single_panel_data_source find_rigid_group_collection_by_name +detector_has_clen_references
events event event_list +dim_structure +filename_plus_event initialize_event push_path_entry_to_event @@ -417,8 +423,7 @@ hdfile_open hdfile_read_group hdfile_set_first_image hdfile_set_image -get_value -get_ev_based_value +hdfile_get_value copy_hdf5_field copy_hdf5_fields add_copy_hdf5_field @@ -443,34 +448,41 @@ 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_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
geometry PartialityModel +gparam find_intersections find_intersections_to_res -select_intersections update_partialities -update_partialities_2 polarisation_correction sphere_fraction gaussian_fraction +r_gradient +x_gradient +y_gradient
@@ -534,5 +546,11 @@ rewind_stream is_stream write_command write_geometry_file -extract_f_from_stuff +stuff_from_stream +
+ +
+predict-refine +refine_prediction +refine_radius
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c index 3325923c..d8b40a16 100644 --- a/libcrystfel/src/geometry.c +++ b/libcrystfel/src/geometry.c @@ -495,7 +495,14 @@ static void set_unity_partialities(Crystal *cryst) } -/* Calculate partialities and apply them to the image's reflections */ +/** + * update_partialities: + * @cryst: A %Crystal + * @pmodel: A %PartialityModel + * + * Updates the partialities of @cryst's reflections according to @pmodel and + * the current state of the crystal (e.g. its unit cell parameters). + */ void update_partialities(Crystal *cryst, PartialityModel pmodel) { Reflection *refl; diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h index 8d5964e4..d835d003 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -63,6 +63,7 @@ * @INDEXING_XDS: Invoke XDS * @INDEXING_SIMULATION: Dummy value * @INDEXING_DEBUG: Results injector for debugging + * @INDEXING_ASDF: Use in-built "asdf" indexer * @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell * axes for agreement with given cell. * @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given diff --git a/libcrystfel/src/reflist.c b/libcrystfel/src/reflist.c index ccc421f3..2906dc01 100644 --- a/libcrystfel/src/reflist.c +++ b/libcrystfel/src/reflist.c @@ -600,7 +600,7 @@ void set_detector_pos(Reflection *refl, double fs, double ss) /** * set_panel: * @refl: A %Reflection - * @panel: Pointer to the panel structure on which the reflection appears + * @p: Pointer to the panel structure on which the reflection appears * * Note that the pointer will be stored, not the contents of the structure. * diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c index af0abedc..461da0cd 100644 --- a/libcrystfel/src/utils.c +++ b/libcrystfel/src/utils.c @@ -156,10 +156,10 @@ static int check_eigen(gsl_vector *e_val, int verbose) /** * solve_svd: - * v: a gsl_vector - * M: a gsl_matrix - * n_filt: pointer to store the number of filtered eigenvalues - * verbose: flag for verbosity on the terminal + * @v: a gsl_vector + * @M: a gsl_matrix + * @n_filt: pointer to store the number of filtered eigenvalues + * @verbose: flag for verbosity on the terminal * * Solves the matrix equation M.x = v, returning x. * Performs rescaling and eigenvalue filtering. -- cgit v1.2.3