Work on documentation

8 files changed, 407 insertions, 22 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>
diff --git a/src/cell.c b/src/cell.c
index 36eae721..caeab3c7 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -110,6 +110,13 @@ UnitCell *cell_new()
 }
 
 
+/**
+ * cell_free:
+ * @cell: A %UnitCell to free.
+ *
+ * Frees a %UnitCell, and all internal resources concerning that cell.
+ *
+ */
 void cell_free(UnitCell *cell)
 {
 	if ( cell == NULL ) return;
@@ -553,6 +560,16 @@ static const char *cell_rep(UnitCell *cell)
 }
 
 
+/**
+ * cell_rotate:
+ * @in: A %UnitCell to rotate
+ * @quat: A %quaternion
+ *
+ * Rotate a %UnitCell using a %quaternion.
+ *
+ * Returns: a newly allocated rotated copy of @in.
+ *
+ */
 UnitCell *cell_rotate(UnitCell *in, struct quaternion quat)
 {
 	struct rvec a, b, c;
diff --git a/src/reflist.c b/src/reflist.c
index a88ce2c9..2db76914 100644
--- a/src/reflist.c
+++ b/src/reflist.c
@@ -299,9 +299,9 @@ void get_indices(const Reflection *refl,
 /**
  * get_symmetric_indices:
  * @refl: A %Reflection
- * @h: Location at which to store the 'h' index of the reflection
- * @k: Location at which to store the 'k' index of the reflection
- * @l: Location at which to store the 'l' index of the reflection
+ * @hs: Location at which to store the 'h' index of the reflection
+ * @ks: Location at which to store the 'k' index of the reflection
+ * @ls: Location at which to store the 'l' index of the reflection
  *
  * This function gives the symmetric indices, that is, the "real" indices before
  * squashing down to the asymmetric reciprocal unit.  This may be useful if the
@@ -466,6 +466,14 @@ void copy_data(Reflection *to, const Reflection *from)
 }
 
 
+/**
+ * set_detector_pos:
+ * @refl: A %Reflection
+ * @exerr: The excitation error for this reflection
+ * @fs: The fast scan offset of the reflection
+ * @ss: The slow scan offset of the reflection
+ *
+ **/
 void set_detector_pos(Reflection *refl, double exerr, double fs, double ss)
 {
 	refl->data.excitation_error = exerr;
@@ -474,6 +482,19 @@ void set_detector_pos(Reflection *refl, double exerr, double fs, double ss)
 }
 
 
+/**
+ * set_partial:
+ * @refl: A %Reflection
+ * @r1: The first excitation error
+ * @r2: The second excitation error
+ * @p: The partiality
+ * @clamp_low: The first clamp status
+ * @clamp_high: The second clamp status
+ *
+ * This function is used during post refinement (in conjunction with
+ * get_partial()) to get access to the details of the partiality calculation.
+ *
+ **/
 void set_partial(Reflection *refl, double r1, double r2, double p,
                  double clamp_low, double clamp_high)
 {
@@ -485,42 +506,107 @@ void set_partial(Reflection *refl, double r1, double r2, double p,
 }
 
 
+/**
+ * set_int:
+ * @refl: A %Reflection
+ * @intensity: The intensity for the reflection.
+ *
+ * Set the intensity for the reflection.  Note that retrieval is done with
+ * get_intensity().
+ **/
 void set_int(Reflection *refl, double intensity)
 {
 	refl->data.intensity = intensity;
 }
 
 
+/**
+ * set_scalable:
+ * @refl: A %Reflection
+ * @scalable: Non-zero if this reflection was marked as useful for scaling and
+ * post refinement.
+ *
+ **/
 void set_scalable(Reflection *refl, int scalable)
 {
 	refl->data.scalable = scalable;
 }
 
 
+/**
+ * set_redundancy:
+ * @refl: A %Reflection
+ * @red: New redundancy for the reflection
+ *
+ * The redundancy of the reflection is the number of measurements that have been
+ * made of it.  Note that a redundancy of zero may have a special meaning, such
+ * as that the reflection was impossible to integrate.  Note further that each
+ * reflection in the list has its own redundancy, even if there are multiple
+ * copies of the reflection in the list.  The total number of reflection
+ * measurements should always be the sum of the redundancies in the entire list.
+ *
+ **/
 void set_redundancy(Reflection *refl, int red)
 {
 	refl->data.redundancy = red;
 }
 
 
+/**
+ * set_sum_squared_dev:
+ * @refl: A %Reflection
+ * @dev: New sum squared deviation for the reflection
+ *
+ * The sum squared deviation is used to estimate the standard errors on the
+ * intensities during 'Monte Carlo' merging.  It is defined as the sum of the
+ * squared deviations between the intensities and the mean intensity from all
+ * measurements of the reflection (and probably its symmetry equivalents
+ * according to some point group).
+ *
+ **/
 void set_sum_squared_dev(Reflection *refl, double dev)
 {
 	refl->data.sum_squared_dev = dev;
 }
 
 
+/**
+ * set_esd_intensity:
+ * @refl: A %Reflection
+ * @esd: New standard error for this reflection's intensity measurement
+ *
+ **/
 void set_esd_intensity(Reflection *refl, double esd)
 {
 	refl->data.esd_i = esd;
 }
 
 
+/**
+ * set_ph:
+ * @refl: A %Reflection
+ * @phase: New phase for the reflection
+ *
+ **/
 void set_ph(Reflection *refl, double phase)
 {
 	refl->data.phase = phase;
 }
 
 
+/**
+ * set_symmetric_indices:
+ * @refl: A %Reflection
+ * @hs: The 'h' index of the reflection
+ * @ks: The 'k' index of the reflection
+ * @ls: The 'l' index of the reflection
+ *
+ * This function gives the symmetric indices, that is, the "real" indices before
+ * squashing down to the asymmetric reciprocal unit.  This may be useful if the
+ * list is indexed according to the asymmetric indices, but you still need
+ * access to the symmetric version.  This happens during post-refinement.
+ *
+ **/
 void set_symmetric_indices(Reflection *refl,
                            signed int hs, signed int ks, signed int ls)
 {
@@ -600,6 +686,20 @@ static Reflection *insert_node(Reflection *refl, Reflection *new)
 }
 
 
+/**
+ * add_refl
+ * @list: A %RefList
+ * @h: The 'h' index of the reflection
+ * @k: The 'k' index of the reflection
+ * @l: The 'l' index of the reflection
+ *
+ * Adds a new reflection to @list.  Note that the implementation allows there to
+ * be multiple reflections with the same indices in the list, so this function
+ * should succeed even if the given indices already feature in the list.
+ *
+ * Returns: The newly created reflection, or NULL on failure.
+ *
+ **/
 Reflection *add_refl(RefList *list, signed int h, signed int k, signed int l)
 {
 	Reflection *new;
@@ -642,6 +742,18 @@ struct _reflistiterator {
 };
 
 
+/**
+ * first_refl:
+ * @list: A %RefList to iterate over
+ * @piter: Address at which to store a %RefListIterator
+ *
+ * This function sets up the state required for iteration over the entire list,
+ * and then returns the first reflection in the list.  An iterator object will
+ * be created and its address stored at the location given in piter.
+ *
+ * Returns: the first reflection in the list.
+ *
+ **/
 Reflection *first_refl(RefList *list, RefListIterator **piter)
 {
 	RefListIterator *iter;
@@ -681,6 +793,17 @@ Reflection *first_refl(RefList *list, RefListIterator **piter)
 }
 
 
+/**
+ * next_refl:
+ * @refl: A reflection
+ * @iter: A %RefListIterator
+ *
+ * This function looks up the next reflection in the list that was given earlier
+ * to first_refl().
+ *
+ * Returns: the next reflection in the list, or NULL if no more.
+ *
+ **/
 Reflection *next_refl(Reflection *refl, RefListIterator *iter)
 {
 	int returned = 1;
@@ -742,12 +865,29 @@ static int recursive_count(Reflection *refl)
 }
 
 
+/**
+ * num_reflections:
+ * @list: A %RefList
+ *
+ * Returns: the number of reflections in @list.
+ *
+ **/
 int num_reflections(RefList *list)
 {
 	return recursive_count(list->head);
 }
 
 
+/**
+ * tree_depth:
+ * @list: A %RefList
+ *
+ * If the depth of the tree is more than about 20, access to the list will be
+ * slow.  This should never happen.
+ *
+ * Returns: the depth of the RB-tree used internally to represent @list.
+ *
+ **/
 int tree_depth(RefList *list)
 {
 	return recursive_depth(list->head);
diff --git a/src/reflist.h b/src/reflist.h
index 83a0de90..ffdef55a 100644
--- a/src/reflist.h
+++ b/src/reflist.h
@@ -19,18 +19,32 @@
 /**
  * RefList:
  *
+ * A %RefList represents a list of Bragg reflections.
+ *
  * This data structure is opaque.  You must use the available accessor functions
  * to read and write its contents.
- */
+ *
+ **/
 typedef struct _reflist RefList;
 
 /**
  * Reflection:
  *
+ * A %Reflection represents a single Bragg reflection.
+ *
  * This data structure is opaque.  You must use the available accessor functions
  * to read and write its contents.
- */
+ *
+ **/
 typedef struct _reflection Reflection;
+
+/**
+ * RefListIterator:
+ *
+ * A %RefListIterator is an opaque data type used when iterating over a
+ * %RefList.
+ *
+ **/
 typedef struct _reflistiterator RefListIterator;
 
 /* Creation/deletion */
@@ -79,7 +93,7 @@ extern Reflection *add_refl(RefList *list,
                             signed int h, signed int k, signed int l);
 
 /* Iteration */
-extern Reflection *first_refl(RefList *list, RefListIterator **iterator);
+extern Reflection *first_refl(RefList *list, RefListIterator **piter);
 extern Reflection *next_refl(Reflection *refl, RefListIterator *iter);
 
 /* Misc */
diff --git a/src/thread-pool.c b/src/thread-pool.c
index e8ca4d6a..0ae26e17 100644
--- a/src/thread-pool.c
+++ b/src/thread-pool.c
@@ -124,8 +124,6 @@ signed int get_status_label()
 }
 
 
-/* ---------------------------- Custom get_task() --------------------------- */
-
 struct task_queue
 {
 	pthread_mutex_t  lock;
@@ -203,28 +201,29 @@ static void *task_worker(void *pargsv)
  * @get_task: The function which will determine the next unassigned task
  * @final: The function which will be called to clean up after a task
  * @queue_args: A pointer to any data required to determine the next task
- * @max: Stop calling get_task() after starting this number of jobs
+ * @max: Stop calling get_task after starting this number of jobs
  * @cpu_num: The number of CPUs in the system
  * @cpu_groupsize: The group size into which the CPUs are grouped
  * @cpu_offset: The CPU group number at which to start pinning threads
  *
- * get_task() will be called every time a worker is idle.  It returns either
+ * 'get_task' will be called every time a worker is idle.  It returns either
  * NULL, indicating that no further work is available, or a pointer which will
- * be passed to work().
+ * be passed to 'work'.
  *
- * final() will be called once per image, and will be given both queue_args
+ * 'final' will be called once per image, and will be given both queue_args
  * and the last task pointer.
  *
- * get_task() and final() will be called only under lock, and so do NOT need to
- * be re-entrant or otherwise thread safe.
+ * 'get_task' and 'final' will be called only under lock, and so do NOT need to
+ * be re-entrant or otherwise thread safe.  'work', of course, needs to be
+ * thread safe.
  *
- * Work will stop after 'max' tasks have been processed whether get_task()
+ * Work will stop after 'max' tasks have been processed whether get_task
  * returned NULL or not.  If "max" is zero, all tasks will be processed.
  *
  * Returns: The number of tasks completed.
  **/
-int run_threads(int n_threads, void (*work)(void *, int),
-                void *(*get_task)(void *), void (*final)(void *, void *),
+int run_threads(int n_threads, TPWorkFunc work,
+                TPGetTaskFunc get_task, TPFinalFunc final,
                 void *queue_args, int max,
                 int cpu_num, int cpu_groupsize, int cpu_offset)
 {
diff --git a/src/thread-pool.h b/src/thread-pool.h
index eb7fb99c..a99a7ade 100644
--- a/src/thread-pool.h
+++ b/src/thread-pool.h
@@ -23,8 +23,47 @@
 extern pthread_mutex_t stderr_lock;
 extern signed int get_status_label(void);
 
-extern int run_threads(int n_threads, void (*work)(void *, int),
-                       void *(*get_task)(void *), void (*final)(void *, void *),
+
+/**
+ * TPGetTaskFunc:
+ * @qargs: The queue_args pointer which was given to run_threads().
+ * Returns: A pointer which will be passed to the worker function.
+ *
+ * This function is called, non-reentrantly, to get a new work item to give to
+ * your work function.  The stuff you need to generate the new work item should
+ * have been stored in @qargs which was passed to run_threads().
+ *
+ **/
+typedef void *(*TPGetTaskFunc)(void *qargs);
+
+
+/**
+ * TPWorkFunc:
+ * @work: The queue_args pointer which was given to run_threads().
+ * @cookie: A small integral number which is guaranteed to be unique among all
+ * currently running threads.
+ *
+ * This function is called, reentrantly, for each work item.
+ *
+ **/
+typedef void (*TPWorkFunc)(void *work, int cookie);
+
+
+/**
+ * TPFinalFunc:
+ * @qargs: The queue_args pointer which was given to run_threads().
+ * @work: The pointer which was returned by your get_task function.
+ *
+ * This function is called, non-reentrantly, after each work item has been
+ * completed.  A typical use might be to update some counters inside @qargs
+ * according to fields withing @work which were filled by your 'work' function.
+ *
+ **/
+typedef void (*TPFinalFunc)(void *qargs, void *work);
+
+
+extern int run_threads(int n_threads, TPWorkFunc work,
+                       TPGetTaskFunc get_task, TPFinalFunc final,
                        void *queue_args, int max,
                        int cpu_num, int cpu_groupsize, int cpu_offset);
 
diff --git a/src/utils.c b/src/utils.c
index 3d96263e..d10f0f42 100644
--- a/src/utils.c
+++ b/src/utils.c
@@ -178,7 +178,7 @@ int poisson_noise(double expected)
  * @Image:
  *
  * There is a simple quaternion structure in CrystFEL.  At the moment, it is
- * only used when simulating patterns, as an argument to %cell_rotate to
+ * only used when simulating patterns, as an argument to cell_rotate() to
  * orient the unit cell.
  */