Update API docs

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
@@ -83,6 +83,11 @@
   </chapter>
 
   <chapter>
+    <title>Prediction refinement</title>
+        <xi:include href="xml/predict-refine.xml"><xi:fallback /></xi:include>
+  </chapter>
+
+  <chapter>
     <title>Integration</title>
         <xi:include href="xml/integration.xml"><xi:fallback /></xi:include>
   </chapter>
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
 <SUBSECTION>
 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
 <SUBSECTION>
 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
 <SUBSECTION>
 copy_data
 num_reflections
@@ -80,6 +84,7 @@ max_intensity
 UnitCell
 LatticeType
 UnitCellTransformation
+rvec
 <SUBSECTION>
 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
 </SECTION>
 
 <SECTION>
 <FILE>utils</FILE>
 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
 </SECTION>
 
 <SECTION>
@@ -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
 </SECTION>
 
 <SECTION>
 <FILE>events</FILE>
 event
 event_list
+dim_structure
+filename_plus_event
 <SUBSECTION>
 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
 </SECTION>
 
 <SECTION>
 <FILE>geometry</FILE>
 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
 </SECTION>
 
 <SECTION>
@@ -534,5 +546,11 @@ rewind_stream
 is_stream
 write_command
 write_geometry_file
-extract_f_from_stuff
+stuff_from_stream
+</SECTION>
+
+<SECTION>
+<FILE>predict-refine</FILE>
+refine_prediction
+refine_radius
 </SECTION>
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.