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-rw-r--r--src/calibrate_detector.c1
-rw-r--r--src/cubeit.c1
-rw-r--r--src/image.h5
-rw-r--r--src/indexamajig.c21
-rw-r--r--src/pattern_sim.c15
-rw-r--r--src/peaks.c21
-rw-r--r--src/peaks.h10
-rw-r--r--src/reintegrate.c16
8 files changed, 54 insertions, 36 deletions
diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index 9aeae803..417ee36e 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -168,7 +168,6 @@ static void add_image(void *args, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = pargs->filename;
- image.reflections = NULL;
image.det = NULL;
STATUS("%3i: Processing '%s'\n", cookie, pargs->filename);
diff --git a/src/cubeit.c b/src/cubeit.c
index 30deb724..d5a0a539 100644
--- a/src/cubeit.c
+++ b/src/cubeit.c
@@ -218,7 +218,6 @@ static void sum_image(void *pg, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = apargs->filename;
- image.reflections = NULL;
image.det = pargs->det;
STATUS("Processing '%s'\n", apargs->filename);
diff --git a/src/image.h b/src/image.h
index ce0e7343..e0c190f2 100644
--- a/src/image.h
+++ b/src/image.h
@@ -65,7 +65,6 @@ struct image {
struct detector *det;
struct beam_params *beam; /* The nominal beam parameters */
char *filename;
- RefList *reflections;
int id; /* ID number of the thread
* handling this image */
@@ -86,6 +85,10 @@ struct image {
int width;
int height;
+ /* Reflections (used for scaling ONLY) */
+ RefList *reflections;
+
+ /* Detected peaks */
ImageFeatureList *features;
};
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 40d7cbd8..b3008232 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -38,6 +38,7 @@
#include "thread-pool.h"
#include "beam-parameters.h"
#include "symmetry.h"
+#include "geometry.h"
enum {
@@ -262,9 +263,6 @@ static struct image *get_simage(struct image *template, int alternate)
image->indexed_cell = template->indexed_cell;
image->f0 = template->f0;
- /* Prevent muppetry */
- image->reflections = NULL;
-
return image;
}
@@ -325,7 +323,6 @@ static void process_image(void *pp, int cookie)
image.indexed_cell = NULL;
image.id = cookie;
image.filename = filename;
- image.reflections = NULL;
image.det = pargs->static_args.det;
STATUS("Processing '%s'\n", image.filename);
@@ -397,11 +394,22 @@ static void process_image(void *pp, int cookie)
/* Measure intensities if requested */
if ( config_nearbragg ) {
- output_intensities(&image, image.indexed_cell,
+
+ RefList *reflections;
+
+ //reflections = find_intersections(&image, image.indexed_cell,
+ // 0);
+ reflections = find_projected_peaks(&image, image.indexed_cell,
+ 0, 0.1);
+
+ output_intensities(&image, image.indexed_cell, reflections,
pargs->static_args.output_mutex,
config_polar,
pargs->static_args.config_closer,
- pargs->static_args.ofh, 0, 0.1);
+ pargs->static_args.ofh);
+
+ reflist_free(reflections);
+
}
simage = get_simage(&image, config_alternate);
@@ -432,7 +440,6 @@ done:
free(image.data);
free(image.flags);
image_feature_list_free(image.features);
- reflist_free(image.reflections);
hdfile_close(hdfile);
}
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 90425328..326ce362 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -564,10 +564,17 @@ int main(int argc, char *argv[])
record_image(&image, !config_nonoise);
if ( config_nearbragg ) {
- find_projected_peaks(&image, cell, 0, 0.1);
- output_intensities(&image, cell, NULL, 0, 0, stdout,
- 0, 0.1);
- reflist_free(image.reflections);
+
+ RefList *reflections;
+
+ reflections = find_projected_peaks(&image, cell,
+ 0, 0.1);
+
+ output_intensities(&image, cell, reflections, NULL,
+ 0, 0, stdout);
+
+ reflist_free(reflections);
+
}
if ( powder_fn != NULL ) {
diff --git a/src/peaks.c b/src/peaks.c
index fa0d2843..c9dbe8e0 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -473,8 +473,8 @@ void dump_peaks(struct image *image, FILE *ofh, pthread_mutex_t *mutex)
}
-int find_projected_peaks(struct image *image, UnitCell *cell,
- int circular_domain, double domain_r)
+RefList *find_projected_peaks(struct image *image, UnitCell *cell,
+ int circular_domain, double domain_r)
{
int x, y;
double ax, ay, az;
@@ -550,9 +550,7 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
optimise_reflist(reflections);
STATUS("Found %i reflections\n", n_reflections);
- image->reflections = reflections;
-
- return n_reflections;
+ return reflections;
}
@@ -664,9 +662,8 @@ static void output_header(FILE *ofh, UnitCell *cell, struct image *image)
void output_intensities(struct image *image, UnitCell *cell,
- pthread_mutex_t *mutex, int polar,
- int use_closer, FILE *ofh,
- int circular_domain, double domain_r)
+ RefList *reflections, pthread_mutex_t *mutex, int polar,
+ int use_closer, FILE *ofh)
{
double asx, asy, asz;
double bsx, bsy, bsz;
@@ -674,10 +671,6 @@ void output_intensities(struct image *image, UnitCell *cell,
Reflection *refl;
RefListIterator *iter;
- if ( image->reflections == NULL ) {
- find_projected_peaks(image, cell, circular_domain, domain_r);
- }
-
/* Get exclusive access to the output stream if necessary */
if ( mutex != NULL ) pthread_mutex_lock(mutex);
@@ -687,7 +680,7 @@ void output_intensities(struct image *image, UnitCell *cell,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
- for ( refl = first_refl(image->reflections, &iter);
+ for ( refl = first_refl(reflections, &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
@@ -768,7 +761,7 @@ void output_intensities(struct image *image, UnitCell *cell,
/* Write h,k,l, integrated intensity and centroid coordinates */
get_indices(refl, &h, &k, &l);
fprintf(ofh, "%3i %3i %3i %6f (at %5.2f,%5.2f) max=%6f bg=%6f\n",
- h, l, l, intensity, x, y, max, bg);
+ h, k, l, intensity, x, y, max, bg);
}
diff --git a/src/peaks.h b/src/peaks.h
index 8b506e42..2801153d 100644
--- a/src/peaks.h
+++ b/src/peaks.h
@@ -19,14 +19,16 @@
#include <pthread.h>
+#include "reflist.h"
+
extern void search_peaks(struct image *image, float threshold,
float min_gradient);
extern void dump_peaks(struct image *image, FILE *ofh, pthread_mutex_t *mutex);
extern void output_intensities(struct image *image, UnitCell *cell,
+ RefList *reflections,
pthread_mutex_t *mutex, int polar,
- int use_closer, FILE *ofh, int circular_domain,
- double domain_r);
+ int use_closer, FILE *ofh);
extern void output_pixels(struct image *image, UnitCell *cell,
pthread_mutex_t *mutex, int do_polar,
@@ -34,8 +36,8 @@ extern void output_pixels(struct image *image, UnitCell *cell,
extern int peak_sanity_check(struct image *image, UnitCell *cell,
int circular_domain, double domain_r);
-extern int find_projected_peaks(struct image *image, UnitCell *cell,
- int circular_domain, double domain_r);
+extern RefList *find_projected_peaks(struct image *image, UnitCell *cell,
+ int circular_domain, double domain_r);
extern int integrate_peak(struct image *image, int xp, int yp,
float *xc, float *yc, float *intensity,
double *pbg, double *pmax,
diff --git a/src/reintegrate.c b/src/reintegrate.c
index a3ee85c9..8450eaab 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -110,7 +110,6 @@ static void process_image(void *pg, int cookie)
image.flags = NULL;
image.indexed_cell = NULL;
image.filename = apargs->filename;
- image.reflections = NULL;
image.det = pargs->det;
STATUS("Processing '%s'\n", apargs->filename);
@@ -137,9 +136,18 @@ static void process_image(void *pg, int cookie)
} else {
- output_intensities(&image, apargs->cell,
- pargs->output_mutex, pargs->config_polar,
- pargs->config_closer, pargs->ofh, 0, 0.1);
+ RefList *reflections;
+
+ reflections = find_projected_peaks(&image, image.indexed_cell,
+ 0, 0.1);
+
+ output_intensities(&image, image.indexed_cell, reflections,
+ pargs->output_mutex,
+ pargs->config_polar,
+ pargs->config_closer,
+ pargs->ofh);
+
+ reflist_free(reflections);
}
free(image.data);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-17 04:31:33 +0000