Work on documentation

2 files changed, 178 insertions, 2 deletions

diff --git a/doc/reference/CrystFEL-docs.sgml b/doc/reference/CrystFEL-docs.sgml
index 607afbff..88e03fd5 100644
--- a/doc/reference/CrystFEL-docs.sgml
+++ b/doc/reference/CrystFEL-docs.sgml
@@ -38,6 +38,33 @@
   </chapter>
 
   <chapter>
+    <title>Statistics and R-factors</title>
+        <xi:include href="xml/statistics.xml"><xi:fallback /></xi:include>
+  </chapter>
+
+  <chapter>
+    <title>Symmetry</title>
+        <xi:include href="xml/symmetry.xml"><xi:fallback /></xi:include>
+  </chapter>
+
+  <chapter>
+    <title>Simulation</title>
+        <xi:include href="xml/simulation.xml"><xi:fallback /></xi:include>
+  </chapter>
+
+  <chapter>
+    <title>Indexing</title>
+        <xi:include href="xml/indexing.xml"><xi:fallback /></xi:include>
+  </chapter>
+
+  <chapter>
+    <title>Detector</title>
+        <xi:include href="xml/detector.xml"><xi:fallback /></xi:include>
+  </chapter>
+
+
+
+  <chapter>
     <title>Parallel programming</title>
         <xi:include href="xml/thread-pool.xml"><xi:fallback /></xi:include>
   </chapter>
diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt
index 8cd2ed6a..aff52a00 100644
--- a/doc/reference/CrystFEL-sections.txt
+++ b/doc/reference/CrystFEL-sections.txt
@@ -2,18 +2,24 @@
 <FILE>reflist</FILE>
 RefList
 Reflection
+RefListIterator
 <SUBSECTION>
 reflist_new
 reflist_free
 <SUBSECTION>
+add_refl
+<SUBSECTION>
+first_refl
+next_refl
+<SUBSECTION>
 find_refl
 next_found_refl
-optimise_reflist
 <SUBSECTION>
 get_excitation_error
 get_detector_pos
-get_indices
 get_partiality
+get_indices
+get_symmetric_indices
 get_intensity
 get_partial
 get_scalable
@@ -22,7 +28,19 @@ get_sum_squared_dev
 get_esd_intensity
 get_phase
 <SUBSECTION>
+set_detector_pos
+set_partial
+set_int
+set_scalable
+set_redundancy
+set_sum_squared_dev
+set_esd_intensity
+set_ph
+set_symmetric_indices
+<SUBSECTION>
 copy_data
+num_reflections
+tree_depth
 </SECTION>
 
 <SECTION>
@@ -31,6 +49,7 @@ write_reflist
 write_reflections_to_file
 read_reflections
 read_reflections_from_file
+asymmetric_indices
 </SECTION>
 
 <SECTION>
@@ -38,6 +57,16 @@ read_reflections_from_file
 ReflItemList
 <SUBSECTION>
 new_items
+add_item
+add_item_with_op
+clear_items
+delete_items
+find_item
+num_items
+union_items
+union_op_items
+intersection_items
+get_item
 </SECTION>
 
 <SECTION>
@@ -45,11 +74,61 @@ new_items
 UnitCell
 <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_spacegroup
+<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_spacegroup
+<SUBSECTION>
+cell_rotate
+rotate_cell
+cell_print
+resolution
+match_cell
+match_cell_ab
 </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
+modulus
+poisson_noise
+notrail
+smallest
 </SECTION>
 
 <SECTION>
@@ -66,9 +145,79 @@ quat_rot
 <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_remove_feature
 </SECTION>
 
 <SECTION>
 <FILE>thread-pool</FILE>
+TPGetTaskFunc
+TPWorkFunc
+TPFinalFunc
+<SUBSECTION>
 run_threads
 </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>simulation</FILE>
+clError
+cleanup_gpu
+GradientMethod
+get_cl_dev
+get_diffraction
+get_diffraction_gpu
+setup_gpu
+</SECTION>
+
+<SECTION>
+<FILE>indexing</FILE>
+IndexingMethod
+IndexingPrivate
+MAX_CELL_CANDIDATES
+build_indexer_list
+cleanup_indexing
+prepare_indexing
+index_pattern
+</SECTION>
+
+<SECTION>
+<FILE>symmetry</FILE>
+check_list_symmetry
+check_symmetry
+has_bisecting_mirror_or_diad
+has_perpendicular_mirror
+is_polyhedral
+rotational_order
+</SECTION>
+
+<SECTION>
+<FILE>detector</FILE>
+copy_geom
+fill_in_values
+free_detector_geometry
+get_detector_geometry
+find_panel
+find_panel_by_name
+find_panel_number
+</SECTION>