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authorThomas White <taw@bitwiz.org.uk>2011-03-29 10:37:01 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:22 +0100
commit1c13a85b311f7029f87413b4472412546eabd3af (patch)
treeb75e185eb67853223a73bb621a62407934d7a87b /src
parent176b63b62ec8e9ee1cc782d25399f3abf25c85f2 (diff)
More documentation
Diffstat (limited to 'src')
-rw-r--r--src/image.h8
-rw-r--r--src/reflist-utils.c13
-rw-r--r--src/reflist.c65
3 files changed, 84 insertions, 2 deletions
diff --git a/src/image.h b/src/image.h
index 92047aa1..d6e22aee 100644
--- a/src/image.h
+++ b/src/image.h
@@ -103,6 +103,14 @@ typedef struct _imagefeaturelist ImageFeatureList;
* by-product of the scattering vector calculation and can be used later for
* calculating intensities from differential scattering cross sections.
*
+ * <structfield>candidate_cells</structfield> is an array of unit cells directly
+ * returned by the low-level indexing system. <structfield>ncells</structfield>
+ * is the number of candidate unit cells which were found. The maximum number
+ * of cells which may be returned is <function>MAX_CELL_CANDIDATES</function>.
+ * <structfield>indexed_cell</structfield> contains the "correct" unit cell
+ * after cell reduction or matching has been performed. The job of the cell
+ * reduction is to convert the list of candidate cells into a single indexed
+ * cell, or <function>NULL</function> on failure.
**/
struct image;
diff --git a/src/reflist-utils.c b/src/reflist-utils.c
index 510dfa42..19ce0ee8 100644
--- a/src/reflist-utils.c
+++ b/src/reflist-utils.c
@@ -20,6 +20,19 @@
#include "symmetry.h"
+/**
+ * SECTION:reflist-utils
+ * @short_description: Reflection list utilities
+ * @title: RefList utilities
+ * @section_id:
+ * @see_also:
+ * @include: "reflist-utils.h"
+ * @Image:
+ *
+ * There are some utility functions associated with the core %RefList.
+ **/
+
+
double *intensities_from_list(RefList *list)
{
Reflection *refl;
diff --git a/src/reflist.c b/src/reflist.c
index beee7f2e..bf94367f 100644
--- a/src/reflist.c
+++ b/src/reflist.c
@@ -322,8 +322,8 @@ double get_intensity(const Reflection *refl)
* @clamp_low: Location at which to store the first clamp status
* @clamp_high: Location at which to store the second clamp status
*
- * This function is used during post refinement to get access to the details of
- * the partiality calculation.
+ * This function is used during post refinement (in conjunction with
+ * set_partial()) to get access to the details of the partiality calculation.
*
**/
void get_partial(const Reflection *refl, double *r1, double *r2, double *p,
@@ -337,30 +337,79 @@ void get_partial(const Reflection *refl, double *r1, double *r2, double *p,
}
+/**
+ * get_scalable:
+ * @refl: A %Reflection
+ *
+ * Returns: non-zero if this reflection was marked as useful for scaling and
+ * post refinement.
+ *
+ **/
int get_scalable(const Reflection *refl)
{
return refl->data.scalable;
}
+/**
+ * get_redundancy:
+ * @refl: A %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.
+ *
+ * Returns: the number of measurements of this reflection.
+ *
+ **/
int get_redundancy(const Reflection *refl)
{
return refl->data.redundancy;
}
+/**
+ * get_sum_squared_dev:
+ * @refl: A %Reflection
+ *
+ * The sum squared deviation is used to estimate the standard errors on the
+ * intensities during 'Monte Carlo' merging.
+ *
+ * Returns: 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).
+ *
+ **/
double get_sum_squared_dev(const Reflection *refl)
{
return refl->data.sum_squared_dev;
}
+/**
+ * get_esd_intensity:
+ * @refl: A %Reflection
+ *
+ * Returns: the standard error in the intensity measurement (as returned by
+ * get_intensity()) for this reflection.
+ *
+ **/
double get_esd_intensity(const Reflection *refl)
{
return refl->data.esd_i;
}
+/**
+ * get_phase:
+ * @refl: A %Reflection
+ *
+ * Returns: the phase for this reflection.
+ *
+ **/
double get_phase(const Reflection *refl)
{
return refl->data.phase;
@@ -369,6 +418,18 @@ double get_phase(const Reflection *refl)
/********************************** Setters ***********************************/
+/**
+ * copy_data:
+ * @to: %Reflection to copy data into
+ * @from: %Reflection to copy data from
+ *
+ * This function is used to copy the data (which is everything listed above in
+ * the list of getters and setters, apart from the indices themselves) from one
+ * reflection to another. This might be used when creating a new list from an
+ * old one, perhaps using the asymmetric indices instead of the raw indices for
+ * the new list.
+ *
+ **/
void copy_data(Reflection *to, const Reflection *from)
{
memcpy(&to->data, &from->data, sizeof(struct _refldata));