Rearrange quaternion declarations so that gtk-doc can cope

The utils file contains two gtk-doc sections, "utils" and "quaternion",
with a change of section halfway through.  It seems that gtk-doc doesn't
like it if the declarations are all mixed together.

3 files changed, 221 insertions, 202 deletions

diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index d58c5725..3968dd5d 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -8,6 +8,8 @@ reflist_new
 reflist_free
 reflection_new
 reflection_free
+reflist_add_notes
+reflist_get_notes
 <SUBSECTION>
 add_refl
 add_refl_to_list
@@ -18,7 +20,6 @@ next_refl
 find_refl
 next_found_refl
 <SUBSECTION>
-get_excitation_error
 get_detector_pos
 get_panel
 get_partiality
@@ -77,6 +78,7 @@ copy_reflist
 find_equiv_in_list
 resolution_limits
 max_intensity
+reflist_add_command_and_version
 </SECTION>
 
 <SECTION>
@@ -151,32 +153,32 @@ solve_svd
 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
 poisson_noise
 notrail
+random_flat
+flat_noise
+show_matrix
+STATUS
+ERROR
+J_to_eV
+eV_to_J
+biggest
 smallest
+check_prefix
+safe_basename
+deg2rad
+rad2deg
+is_odd
 ph_en_to_lambda
 ph_lambda_to_en
 ph_eV_to_lambda
 ph_lambda_to_eV
-random_flat
-flat_noise
-show_matrix
 likely
 unlikely
 UNUSED
@@ -218,6 +220,20 @@ ImageFeatureList
 SpectrumType
 sample
 <SUBSECTION>
+imagefile
+imagefile_close
+imagefile_copy_fields
+imagefile_field_list
+imagefile_get_hdfile
+imagefile_get_type
+imagefile_open
+imagefile_read
+imagefile_read_simple
+<SUBSECTION>
+new_imagefile_field_list
+add_imagefile_field
+free_imagefile_field_list
+<SUBSECTION>
 image_add_feature
 image_feature_closest
 image_reflection_closest
@@ -268,10 +284,11 @@ INDEXING_DEFAULTS_ASDF
 INDEXING_DEFAULTS_FELIX
 INDEXING_METHOD_MASK
 INDEXING_CONTROL_FLAGS
-build_indexer_list
+setup_indexing
 cleanup_indexing
-prepare_indexing
+get_indm_from_string
 index_pattern
+index_pattern_2
 indexer_str
 dirax_prepare
 run_dirax
@@ -314,6 +331,7 @@ describe_symmetry
 symmetry_name
 set_symmetry_name
 get_matrix_name
+pointgroup_warning
 is_centrosymmetric
 is_centric
 </SECTION>
@@ -351,15 +369,14 @@ rigid_group
 rg_collection
 <SUBSECTION>
 copy_geom
-fill_in_values
+fill_in_adu
 free_detector_geometry
 get_detector_geometry
 get_detector_geometry_2
 write_detector_geometry
 write_detector_geometry_2
-find_panel
+panel_number
 find_panel_by_name
-find_panel_number
 simple_geometry
 record_image
 get_pixel_extents
@@ -378,6 +395,7 @@ rigid_group_is_in_collection
 single_panel_data_source
 find_rigid_group_collection_by_name
 detector_has_clen_references
+adjust_centering_for_rail
 </SECTION>
 
 <SECTION>
@@ -466,6 +484,7 @@ crystal_get_resolution_limit
 crystal_get_user_flag
 crystal_get_num_implausible_reflections
 crystal_get_notes
+crystal_get_det_shift
 crystal_set_cell
 crystal_set_image
 crystal_set_mosaicity
@@ -479,6 +498,7 @@ crystal_set_user_flag
 crystal_set_num_implausible_reflections
 crystal_set_notes
 crystal_add_notes
+crystal_set_det_shift
 </SECTION>
 
 <SECTION>
@@ -500,7 +520,9 @@ y_gradient
 <FILE>peaks</FILE>
 peak_sanity_check
 search_peaks
+search_peaks_peakfinder8
 make_BgMask
+peakfinder8
 validate_peaks
 sort_peaks
 </SECTION>
@@ -557,6 +579,7 @@ close_stream
 read_chunk
 read_chunk_2
 write_chunk
+write_chunk_2
 rewind_stream
 is_stream
 write_command
diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c
index 461da0cd..90d81a71 100644
--- a/libcrystfel/src/utils.c
+++ b/libcrystfel/src/utils.c
@@ -387,144 +387,6 @@ int poisson_noise(gsl_rng *rng, double expected)
 }
 
 
-/**
- * SECTION:quaternion
- * @short_description: Simple quaternion handling
- * @title: Quaternion
- * @section_id:
- * @see_also:
- * @include: "utils.h"
- * @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
- * orient the unit cell.
- */
-
-/**
- * quaternion_modulus:
- * @q: A %quaternion
- *
- * If a quaternion represents a pure rotation, its modulus should be unity.
- *
- * Returns: the modulus of the given quaternion.
- **/
-double quaternion_modulus(struct quaternion q)
-{
-	return sqrt(q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z);
-}
-
-
-/**
- * normalise_quaternion:
- * @q: A %quaternion
- *
- * Rescales the quaternion such that its modulus is unity.
- *
- * Returns: the normalised version of @q
- **/
-struct quaternion normalise_quaternion(struct quaternion q)
-{
-	double mod;
-	struct quaternion r;
-
-	mod = quaternion_modulus(q);
-
-	r.w = q.w / mod;
-	r.x = q.x / mod;
-	r.y = q.y / mod;
-	r.z = q.z / mod;
-
-	return r;
-}
-
-
-/**
- * random_quaternion:
- * @rng: A GSL random number generator to use
- *
- * Returns: a randomly generated, normalised, quaternion.
- **/
-struct quaternion random_quaternion(gsl_rng *rng)
-{
-	struct quaternion q;
-
-	q.w = 2.0*gsl_rng_uniform(rng) - 1.0;
-	q.x = 2.0*gsl_rng_uniform(rng) - 1.0;
-	q.y = 2.0*gsl_rng_uniform(rng) - 1.0;
-	q.z = 2.0*gsl_rng_uniform(rng) - 1.0;
-	q = normalise_quaternion(q);
-
-	return q;
-}
-
-
-/**
- * quaternion_valid:
- * @q: A %quaternion
- *
- * Checks if the given quaternion is normalised.
- *
- * This function performs a nasty floating point comparison of the form
- * <code>(modulus > 0.999) && (modulus < 1.001)</code>, and so should not be
- * relied upon to spot anything other than the most obvious input error.
- *
- * Returns: 1 if the quaternion is normalised, 0 if not.
- **/
-int quaternion_valid(struct quaternion q)
-{
-	double qmod;
-
-	qmod = quaternion_modulus(q);
-
-	/* Modulus = 1 to within some tolerance?
-	 * Nasty allowance for floating-point accuracy follows... */
-	if ( (qmod > 0.999) && (qmod < 1.001) ) return 1;
-
-	return 0;
-}
-
-
-/**
- * quat_rot
- * @q: A vector (in the form of a "struct rvec")
- * @z: A %quaternion
- *
- * Rotates a vector according to a quaternion.
- *
- * Returns: A rotated version of @p.
- **/
-struct rvec quat_rot(struct rvec q, struct quaternion z)
-{
-	struct rvec res;
-	double t01, t02, t03, t11, t12, t13, t22, t23, t33;
-
-	t01 = z.w*z.x;
-	t02 = z.w*z.y;
-	t03 = z.w*z.z;
-	t11 = z.x*z.x;
-	t12 = z.x*z.y;
-	t13 = z.x*z.z;
-	t22 = z.y*z.y;
-	t23 = z.y*z.z;
-	t33 = z.z*z.z;
-
-	res.u = (1.0 - 2.0 * (t22 + t33)) * q.u
-	            + (2.0 * (t12 + t03)) * q.v
-	            + (2.0 * (t13 - t02)) * q.w;
-
-	res.v =       (2.0 * (t12 - t03)) * q.u
-	      + (1.0 - 2.0 * (t11 + t33)) * q.v
-	            + (2.0 * (t01 + t23)) * q.w;
-
-	res.w =       (2.0 * (t02 + t13)) * q.u
-	            + (2.0 * (t23 - t01)) * q.v
-	      + (1.0 - 2.0 * (t11 + t22)) * q.w;
-
-	return res;
-}
-
-
 /* Return non-zero if c is in delims */
 static int assplode_isdelim(const char c, const char *delims)
 {
@@ -691,3 +553,141 @@ void utils_fudge_gslcblas()
 {
         STATUS("%p\n", cblas_sgemm);
 }
+
+
+/**
+ * SECTION:quaternion
+ * @short_description: Simple quaternion handling
+ * @title: Quaternion
+ * @section_id:
+ * @see_also:
+ * @include: "utils.h"
+ * @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
+ * orient the unit cell.
+ */
+
+/**
+ * quaternion_modulus:
+ * @q: A %quaternion
+ *
+ * If a quaternion represents a pure rotation, its modulus should be unity.
+ *
+ * Returns: the modulus of the given quaternion.
+ **/
+double quaternion_modulus(struct quaternion q)
+{
+	return sqrt(q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z);
+}
+
+
+/**
+ * normalise_quaternion:
+ * @q: A %quaternion
+ *
+ * Rescales the quaternion such that its modulus is unity.
+ *
+ * Returns: the normalised version of @q
+ **/
+struct quaternion normalise_quaternion(struct quaternion q)
+{
+	double mod;
+	struct quaternion r;
+
+	mod = quaternion_modulus(q);
+
+	r.w = q.w / mod;
+	r.x = q.x / mod;
+	r.y = q.y / mod;
+	r.z = q.z / mod;
+
+	return r;
+}
+
+
+/**
+ * random_quaternion:
+ * @rng: A GSL random number generator to use
+ *
+ * Returns: a randomly generated, normalised, quaternion.
+ **/
+struct quaternion random_quaternion(gsl_rng *rng)
+{
+	struct quaternion q;
+
+	q.w = 2.0*gsl_rng_uniform(rng) - 1.0;
+	q.x = 2.0*gsl_rng_uniform(rng) - 1.0;
+	q.y = 2.0*gsl_rng_uniform(rng) - 1.0;
+	q.z = 2.0*gsl_rng_uniform(rng) - 1.0;
+	q = normalise_quaternion(q);
+
+	return q;
+}
+
+
+/**
+ * quaternion_valid:
+ * @q: A %quaternion
+ *
+ * Checks if the given quaternion is normalised.
+ *
+ * This function performs a nasty floating point comparison of the form
+ * <code>(modulus > 0.999) && (modulus < 1.001)</code>, and so should not be
+ * relied upon to spot anything other than the most obvious input error.
+ *
+ * Returns: 1 if the quaternion is normalised, 0 if not.
+ **/
+int quaternion_valid(struct quaternion q)
+{
+	double qmod;
+
+	qmod = quaternion_modulus(q);
+
+	/* Modulus = 1 to within some tolerance?
+	 * Nasty allowance for floating-point accuracy follows... */
+	if ( (qmod > 0.999) && (qmod < 1.001) ) return 1;
+
+	return 0;
+}
+
+
+/**
+ * quat_rot
+ * @q: A vector (in the form of a "struct rvec")
+ * @z: A %quaternion
+ *
+ * Rotates a vector according to a quaternion.
+ *
+ * Returns: A rotated version of @p.
+ **/
+struct rvec quat_rot(struct rvec q, struct quaternion z)
+{
+	struct rvec res;
+	double t01, t02, t03, t11, t12, t13, t22, t23, t33;
+
+	t01 = z.w*z.x;
+	t02 = z.w*z.y;
+	t03 = z.w*z.z;
+	t11 = z.x*z.x;
+	t12 = z.x*z.y;
+	t13 = z.x*z.z;
+	t22 = z.y*z.y;
+	t23 = z.y*z.z;
+	t33 = z.z*z.z;
+
+	res.u = (1.0 - 2.0 * (t22 + t33)) * q.u
+	            + (2.0 * (t12 + t03)) * q.v
+	            + (2.0 * (t13 - t02)) * q.w;
+
+	res.v =       (2.0 * (t12 - t03)) * q.u
+	      + (1.0 - 2.0 * (t11 + t33)) * q.v
+	            + (2.0 * (t01 + t23)) * q.w;
+
+	res.w =       (2.0 * (t02 + t13)) * q.u
+	            + (2.0 * (t23 - t01)) * q.v
+	      + (1.0 - 2.0 * (t11 + t22)) * q.w;
+
+	return res;
+}
diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h
index 4955f875..a759ff15 100644
--- a/libcrystfel/src/utils.h
+++ b/libcrystfel/src/utils.h
@@ -61,44 +61,10 @@
 #define THOMSON_LENGTH (2.81794e-15)
 
 
-/* ------------------------------ Quaternions ------------------------------- */
-
-/**
- * quaternion:
- *
- * <programlisting>
- * struct quaternion
- * {
- *    double w
- *    double x
- *    double y
- *    double z
- * };
- * </programlisting>
- *
- * A structure representing a quaternion.
- *
- **/
-struct quaternion;
-
-struct quaternion {
-	double w;
-	double x;
-	double y;
-	double z;
-};
-
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-extern struct quaternion normalise_quaternion(struct quaternion q);
-extern double quaternion_modulus(struct quaternion q);
-extern struct quaternion random_quaternion(gsl_rng *rng);
-extern int quaternion_valid(struct quaternion q);
-extern struct rvec quat_rot(struct rvec q, struct quaternion z);
-
-
 /* --------------------------- Useful functions ----------------------------- */
 
 extern void show_matrix_eqn(gsl_matrix *M, gsl_vector *v);
@@ -126,17 +92,6 @@ extern double flat_noise(gsl_rng *rng, double expected, double width);
 extern double gaussian_noise(gsl_rng *rng, double expected, double stddev);
 extern int poisson_noise(gsl_rng *rng, double expected);
 
-/* Keep these ones inline, to avoid function call overhead */
-static inline struct quaternion invalid_quaternion(void)
-{
-	struct quaternion quat;
-	quat.w = 0.0;
-	quat.x = 0.0;
-	quat.y = 0.0;
-	quat.z = 0.0;
-	return quat;
-}
-
 static inline double distance(double x1, double y1, double x2, double y2)
 {
 	return sqrt((x2-x1)*(x2-x1) + (y2-y1)*(y2-y1));
@@ -275,6 +230,47 @@ extern char *safe_basename(const char *in);
 #define unlikely(x) (x)
 #endif
 
+
+/* ------------------------------ Quaternions ------------------------------- */
+
+/**
+ * quaternion:
+ *  @w: component
+ *  @x: component
+ *  @y: component
+ *  @z: component
+ *
+ * A structure representing a quaternion.
+ *
+ **/
+struct quaternion;
+
+struct quaternion {
+	double w;
+	double x;
+	double y;
+	double z;
+};
+
+extern struct quaternion normalise_quaternion(struct quaternion q);
+extern double quaternion_modulus(struct quaternion q);
+extern struct quaternion random_quaternion(gsl_rng *rng);
+extern int quaternion_valid(struct quaternion q);
+extern struct rvec quat_rot(struct rvec q, struct quaternion z);
+
+/* Keep these ones inline, to avoid function call overhead */
+static inline struct quaternion invalid_quaternion(void)
+{
+	struct quaternion quat;
+	quat.w = 0.0;
+	quat.x = 0.0;
+	quat.y = 0.0;
+	quat.z = 0.0;
+	return quat;
+}
+
+
+
 #ifdef __cplusplus
 }
 #endif