From a82278dbdd8311c46676b0921c423934208ec81a Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Mon, 11 Aug 2014 12:09:33 +0200
Subject: Take overlaps into account during integration

---
 libcrystfel/src/integration.c | 35 +++++++++++++++++++++++++++++++++++
 libcrystfel/src/integration.h |  2 ++
 libcrystfel/src/peaks.c       |  2 +-
 src/process_image.c           |  2 ++
 4 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index f42da36f..5e5ddd98 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1946,3 +1946,38 @@ IntegrationMethod integration_method(const char *str, int *err)
 	return meth;
 
 }
+
+
+/**
+ * flag_overlaps:
+ * @image: An image structure
+ * @ir_inn: The radius of the peak region to use
+ *
+ * Flags, in the bad pixel mask for @image, every pixel for which more than one
+ * reflection is predicted to have its peak region.
+ *
+ */
+void flag_overlaps(struct image *image, double ir_inn)
+{
+	int i;
+
+	for ( i=0; i<image->det->n_panels; i++ ) {
+
+		int *mask;
+		int fs, ss;
+		struct panel *p = &image->det->panels[i];
+
+		mask = make_BgMask(image, p, ir_inn);
+
+		for ( ss=0; ss<p->h; ss++ ) {
+		for ( fs=0; fs<p->w; fs++ ) {
+			if ( mask[fs+p->w*ss] > 1 ) {
+				image->bad[i][fs+p->w*ss] = 1;
+			}
+		}
+		}
+
+		free(mask);
+
+	}
+}
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 9e1c8ee1..6e80405c 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -112,6 +112,8 @@ extern void integrate_all_4(struct image *image, IntegrationMethod meth,
                             signed int idh, signed int idk, signed int idl,
                             int results_pipe);
 
+extern void flag_overlaps(struct image *image, double ir_inn);
+
 
 #ifdef __cplusplus
 }
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index a38e4d4d..ca5a6951 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -191,7 +191,7 @@ static void add_crystal_to_mask(struct image *image, struct panel *p,
 			if ( fs < 0 ) continue;
 			if ( ss < 0 ) continue;
 
-			mask[fs + ss*w] = 1;
+			mask[fs + ss*w]++;
 
 		}
 		}
diff --git a/src/process_image.c b/src/process_image.c
index 434ea984..1431a16e 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -179,6 +179,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		crystal_set_mosaicity(image.crystals[i], 0.0);  /* radians */
 	}
 
+	flag_overlaps(&image, iargs->ir_inn);
+
 	/* Integrate all the crystals at once - need all the crystals so that
 	 * overlaps can be detected. */
 	integrate_all_4(&image, iargs->int_meth, PMODEL_SPHERE, iargs->push_res,
-- 
cgit v1.2.3