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-rw-r--r--doc/reference/CrystFEL-sections.txt3
-rw-r--r--src/geometry.c29
-rw-r--r--src/geometry.h3
-rw-r--r--src/partialator.c11
-rw-r--r--src/post-refinement.c2
-rw-r--r--src/reflist.c59
-rw-r--r--src/reflist.h3
7 files changed, 80 insertions, 30 deletions
diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt
index 060ecf97..1d5b4016 100644
--- a/doc/reference/CrystFEL-sections.txt
+++ b/doc/reference/CrystFEL-sections.txt
@@ -6,8 +6,11 @@ RefListIterator
<SUBSECTION>
reflist_new
reflist_free
+reflection_new
+reflection_free
<SUBSECTION>
add_refl
+add_refl_to_list
<SUBSECTION>
first_refl
next_refl
diff --git a/src/geometry.c b/src/geometry.c
index bb946120..485abba3 100644
--- a/src/geometry.c
+++ b/src/geometry.c
@@ -122,7 +122,7 @@ static double partiality(double r1, double r2, double r)
}
-static Reflection *check_reflection(struct image *image, RefList *reflections,
+static Reflection *check_reflection(struct image *image,
signed int h, signed int k, signed int l,
double asx, double asy, double asz,
double bsx, double bsy, double bsz,
@@ -216,7 +216,7 @@ static Reflection *check_reflection(struct image *image, RefList *reflections,
if ( p == -1 ) return NULL;
/* Add peak to list */
- refl = add_refl(reflections, h, k, l);
+ refl = reflection_new(h, k, l);
set_detector_pos(refl, 0.0, xda, yda);
set_partial(refl, rlow, rhigh, part, clamp_low, clamp_high);
set_symmetric_indices(refl, h, k, l);
@@ -274,8 +274,16 @@ RefList *find_intersections(struct image *image, UnitCell *cell)
for ( h=-hmax; h<=hmax; h++ ) {
for ( k=-kmax; k<=kmax; k++ ) {
for ( l=-lmax; l<=lmax; l++ ) {
- check_reflection(image, reflections, h, k, l,
- asx,asy,asz,bsx,bsy,bsz,csx,csy,csz);
+
+ Reflection *refl;
+
+ refl = check_reflection(image, h, k, l,
+ asx,asy,asz,bsx,bsy,bsz,csx,csy,csz);
+
+ if ( refl != NULL ) {
+ refl = add_refl_to_list(refl, reflections);
+ }
+
}
}
}
@@ -285,8 +293,7 @@ RefList *find_intersections(struct image *image, UnitCell *cell)
/* Calculate partialities and apply them to the image's reflections */
-void update_partialities(struct image *image,
- int *n_expected, int *n_found, int *n_notfound)
+void update_partialities(struct image *image)
{
Reflection *refl;
RefListIterator *iter;
@@ -295,10 +302,6 @@ void update_partialities(struct image *image,
double bsx, bsy, bsz;
double csx, csy, csz;
- if ( n_expected != NULL ) *n_expected = 0;
- if ( n_found != NULL) *n_found = 0;
- if ( n_notfound != NULL) *n_notfound = 0;
-
cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz, &csx, &csy, &csz);
@@ -314,19 +317,15 @@ void update_partialities(struct image *image,
signed int h, k, l;
int clamp1, clamp2;
- if ( n_expected != NULL ) (*n_expected)++;
-
get_symmetric_indices(refl, &h, &k, &l);
- vals = check_reflection(image, predicted, h, k, l,
+ vals = check_reflection(image, h, k, l,
asx,asy,asz,bsx,bsy,bsz,csx,csy,csz);
if ( vals == NULL ) {
- if ( n_notfound != NULL) (*n_notfound)++;
set_redundancy(refl, 0);
continue;
}
- if ( n_found != NULL) (*n_found)++;
set_redundancy(refl, 1);
/* Transfer partiality stuff */
diff --git a/src/geometry.h b/src/geometry.h
index 486f1a60..ddf04b80 100644
--- a/src/geometry.h
+++ b/src/geometry.h
@@ -21,7 +21,6 @@
extern RefList *find_intersections(struct image *image, UnitCell *cell);
-extern void update_partialities(struct image *image,
- int *n_expected, int *n_found, int *n_notfound);
+extern void update_partialities(struct image *image);
#endif /* GEOMETRY_H */
diff --git a/src/partialator.c b/src/partialator.c
index 6b4719eb..4edf7bf4 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -269,9 +269,6 @@ int main(int argc, char *argv[])
int n_iter = 10;
struct beam_params *beam = NULL;
RefList *full;
- int n_found = 0;
- int n_expected = 0;
- int n_notfound = 0;
int n_usable_patterns = 0;
int nobs;
char *reference_file = NULL;
@@ -435,7 +432,6 @@ int main(int argc, char *argv[])
RefList *as;
struct image *cur;
- int nn_expected, nn_found, nn_notfound;
cur = &images[n_usable_patterns];
@@ -474,10 +470,7 @@ int main(int argc, char *argv[])
reflist_free(cur->reflections);
cur->reflections = as;
- update_partialities(cur, &nn_expected, &nn_found, &nn_notfound);
- n_expected += nn_expected;
- n_found += nn_found;
- n_notfound += nn_notfound;
+ update_partialities(cur);
nobs += select_scalable_reflections(cur->reflections,
reference);
@@ -487,8 +480,6 @@ int main(int argc, char *argv[])
}
fclose(fh);
- STATUS("Found %5.2f%% of the expected peaks (missed %i of %i).\n",
- 100.0 * (double)n_found / n_expected, n_notfound, n_expected);
/* Make initial estimates */
STATUS("Performing initial scaling.\n");
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 97957840..0f541ace 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -526,7 +526,7 @@ void pr_refine(struct image *image, const RefList *full)
max_shift = pr_iterate(image, full);
- update_partialities(image, NULL, NULL, NULL);
+ update_partialities(image);
if ( verbose ) {
dev = guide_dev(image, full);
diff --git a/src/reflist.c b/src/reflist.c
index 33a8d60e..18856c67 100644
--- a/src/reflist.c
+++ b/src/reflist.c
@@ -162,6 +162,34 @@ RefList *reflist_new()
}
+/**
+ * reflection_new:
+ * @h: The h index of the new reflection
+ * @k: The k index of the new reflection
+ * @l: The l index of the new reflection
+ *
+ * Creates a new individual reflection. You'll probably want to use
+ * add_refl_to_list() at some later point.
+ */
+Reflection *reflection_new(signed int h, signed int k, signed int l)
+{
+ return new_node(SERIAL(h, k, l));
+}
+
+
+/**
+ * reflection_free:
+ * @refl: The reflection to free.
+ *
+ * Destroys an individual reflection.
+ */
+void reflection_free(Reflection *refl)
+{
+ pthread_mutex_destroy(&refl->lock);
+ free(refl);
+}
+
+
static void recursive_free(Reflection *refl)
{
if ( refl->child[0] != NULL ) recursive_free(refl->child[0]);
@@ -169,8 +197,7 @@ static void recursive_free(Reflection *refl)
while ( refl != NULL ) {
Reflection *next = refl->next;
- pthread_mutex_destroy(&refl->lock);
- free(refl);
+ reflection_free(refl);
refl = next;
}
}
@@ -806,6 +833,34 @@ Reflection *add_refl(RefList *list, signed int h, signed int k, signed int l)
}
+/**
+ * add_refl_to_list
+ * @refl: A %Reflection
+ * @list: A %RefList
+ *
+ * Adds a reflection to @list. The reflection that actually gets added will be
+ * a newly created one, and all the data will be copied across. The original
+ * reflection will be destroyed and the new reflection returned.
+ *
+ * Returns: The newly created reflection, or NULL on failure.
+ *
+ **/
+Reflection *add_refl_to_list(Reflection *refl, RefList *list)
+{
+ signed int h, k, l;
+ Reflection *r_added;
+
+ get_indices(refl, &h, &k, &l);
+ r_added = add_refl(list, h, k, l);
+ if ( r_added == NULL ) return NULL;
+
+ copy_data(r_added, refl);
+ reflection_free(refl);
+
+ return r_added;
+}
+
+
/********************************* Iteration **********************************/
struct _reflistiterator {
diff --git a/src/reflist.h b/src/reflist.h
index 6d64498a..955db69b 100644
--- a/src/reflist.h
+++ b/src/reflist.h
@@ -50,6 +50,8 @@ typedef struct _reflistiterator RefListIterator;
/* Creation/deletion */
extern RefList *reflist_new(void);
extern void reflist_free(RefList *list);
+extern Reflection *reflection_new(signed int h, signed int k, signed int l);
+extern void reflection_free(Reflection *refl);
/* Search */
extern Reflection *find_refl(const RefList *list, signed int h, signed int k, signed int l);
@@ -95,6 +97,7 @@ extern void set_symmetric_indices(Reflection *refl,
/* Insertion */
extern Reflection *add_refl(RefList *list,
signed int h, signed int k, signed int l);
+extern Reflection *add_refl_to_list(Reflection *refl, RefList *list);
/* Iteration */
extern Reflection *first_refl(RefList *list, RefListIterator **piter);
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-28 11:09:03 +0000