Make find_projected_peaks() behave like find_intersections()

Also make sure output_intensities() deals only with integration

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);