From 0ce14ba49cd6150e09a9dd32ea3451e3e47f16bf Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 21 Jun 2012 12:20:11 +0200
Subject: More fussiness

---
 libcrystfel/src/peaks.c   | 36 +++++++++++++++++-------------------
 libcrystfel/src/reflist.c |  5 ++++-
 src/indexamajig.c         |  1 +
 3 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 3ae7de8e..99a12ae5 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -146,14 +146,18 @@ static int cull_peaks(struct image *image)
 	return nelim;
 }
 
+
 static unsigned char *make_BgMask(struct image *image, struct panel *p,
                                   double ir_out, int cfs, int css, double ir_in)
 {
 	Reflection *refl;
 	RefListIterator *iter;
 	unsigned char *mask;
+	int w, h;
 
-	mask = calloc(4*ir_out*ir_out, sizeof(unsigned char));
+	w = p->max_fs - p->min_fs + 1;
+	h = p->max_ss - p->min_ss + 1;
+	mask = calloc(w*h, sizeof(unsigned char));
 	if ( mask == NULL ) return NULL;
 
 	/* Loop over all reflections */
@@ -163,6 +167,7 @@ static unsigned char *make_BgMask(struct image *image, struct panel *p,
 	{
 		struct panel *p2;
 		double pk2_fs, pk2_ss;
+		signed int fs, ss;
 
 		get_detector_pos(refl, &pk2_fs, &pk2_ss);
 
@@ -170,31 +175,25 @@ static unsigned char *make_BgMask(struct image *image, struct panel *p,
 		p2 = find_panel(image->det, pk2_fs, pk2_ss);
 		if ( p2 != p ) continue;
 
-		/* If other peak area overlaps larger bg area, set mask */
-		if ( (fabs(pk2_fs-cfs)<ir_out+ir_in)
-		  && (fabs(pk2_ss-css)<ir_out+ir_in) ) {
-
-			signed int fs, ss;
+		for ( fs=-ir_in; fs<=ir_in; fs++ ) {
+		for ( ss=-ir_in; ss<=ir_in; ss++ ) {
 
-			for ( fs=-ir_out; fs<=ir_out; fs++ ) {
-			for ( ss=-ir_out; ss<=ir_out; ss++ ) {
+			double d_fs, d_ss, distSq;
 
-				double d_fs, d_ss, distSq;
+			d_fs = cfs + fs;
+			d_ss = css + ss;
+			distSq = d_fs*d_fs + d_ss*d_ss;
 
-				d_fs = cfs + fs - pk2_fs;
-				d_ss = css + ss - pk2_ss;
-				distSq = d_fs*d_fs + d_ss*d_ss;
+			if ( distSq < ir_in*ir_in ) {
 
-				if ( distSq < ir_in*ir_in ) {
+				int idx;
+				idx = fs+ir_out+2*ir_out*(ss+ir_out);
+				mask[idx] = 1;
 
-					int idx;
-					idx = fs+ir_out+2*ir_out*(ss+ir_out);
-					mask[idx] = 1;
-				}
-			}
 			}
 
 		}
+		}
 
 	}
 
@@ -224,7 +223,6 @@ static int integrate_peak(struct image *image, int cfs, int css,
 	double aduph;
 	unsigned char *bgPkMask;
 
-
 	p = find_panel(image->det, cfs, css);
 	if ( p == NULL ) return 1;
 	if ( p->no_index ) return 1;
diff --git a/libcrystfel/src/reflist.c b/libcrystfel/src/reflist.c
index cea25bf3..64154774 100644
--- a/libcrystfel/src/reflist.c
+++ b/libcrystfel/src/reflist.c
@@ -900,6 +900,7 @@ struct _reflistiterator {
  **/
 Reflection *first_refl(RefList *list, RefListIterator **piter)
 {
+	Reflection *refl;
 	RefListIterator *iter;
 
 	iter = malloc(sizeof(struct _reflistiterator));
@@ -908,7 +909,9 @@ Reflection *first_refl(RefList *list, RefListIterator **piter)
 	iter->stack_ptr = 0;
 	*piter = iter;
 
-	Reflection *refl = list->head;
+	if ( list == NULL ) return NULL;
+
+	refl = list->head;
 
 	do {
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 8c073e2c..c3e1bedf 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -264,6 +264,7 @@ static void process_image(void *pp, int cookie)
 	image.data = NULL;
 	image.flags = NULL;
 	image.indexed_cell = NULL;
+	image.reflections = NULL;
 	image.id = cookie;
 	image.filename = filename;
 	image.det = copy_geom(pargs->static_args.det);
-- 
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