From ecce96b99c98c2b5efadbf186d2085115dbc142a Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Sun, 9 Nov 2014 06:23:27 +0100
Subject: Record number of implausibly negative reflections in stream

---
 libcrystfel/src/crystal.c     | 15 +++++++++++++++
 libcrystfel/src/crystal.h     |  3 +++
 libcrystfel/src/integration.c |  1 +
 libcrystfel/src/stream.c      |  2 ++
 4 files changed, 21 insertions(+)

diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index 02255110..c6e0a9dd 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -63,6 +63,8 @@ struct _crystal
 	/* Integrated (or about-to-be-integrated) reflections */
 	RefList                 *reflections;
 	long long int           n_saturated;  /* Number of overloads */
+	long long int           n_implausible;  /* Number of implausibly
+	                                         * negative reflectionss */
 
 	/* User flag, e.g. for "this is a bad crystal". */
 	int                     user_flag;
@@ -91,6 +93,7 @@ Crystal *crystal_new()
 	cryst->reflections = NULL;
 	cryst->resolution_limit = 0.0;
 	cryst->n_saturated = 0;
+	cryst->n_implausible = 0;
 
 	return cryst;
 }
@@ -167,6 +170,12 @@ long long int crystal_get_num_saturated_reflections(Crystal *cryst)
 }
 
 
+long long int crystal_get_num_implausible_reflections(Crystal *cryst)
+{
+	return cryst->n_implausible;
+}
+
+
 struct image *crystal_get_image(Crystal *cryst)
 {
 	return cryst->image;
@@ -224,6 +233,12 @@ void crystal_set_num_saturated_reflections(Crystal *cryst, long long int n)
 }
 
 
+void crystal_set_num_implausible_reflections(Crystal *cryst, long long int n)
+{
+	cryst->n_implausible = n;
+}
+
+
 void crystal_set_image(Crystal *cryst, struct image *image)
 {
 	cryst->image = image;
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
index 11b85e35..987cabbf 100644
--- a/libcrystfel/src/crystal.h
+++ b/libcrystfel/src/crystal.h
@@ -59,6 +59,7 @@ extern double crystal_get_profile_radius(Crystal *cryst);
 extern RefList *crystal_get_reflections(Crystal *cryst);
 extern double crystal_get_resolution_limit(Crystal *cryst);
 extern long long int crystal_get_num_saturated_reflections(Crystal *cryst);
+extern long long int crystal_get_num_implausible_reflections(Crystal *cryst);
 extern int crystal_get_user_flag(Crystal *cryst);
 extern double crystal_get_osf(Crystal *cryst);
 extern struct image *crystal_get_image(Crystal *cryst);
@@ -70,6 +71,8 @@ extern void crystal_set_reflections(Crystal *cryst, RefList *reflist);
 extern void crystal_set_resolution_limit(Crystal *cryst, double res);
 extern void crystal_set_num_saturated_reflections(Crystal *cryst,
                                                   long long int n);
+extern void crystal_set_num_implausible_reflections(Crystal *cryst,
+                                                    long long int n);
 extern void crystal_set_user_flag(Crystal *cryst, int flag);
 extern void crystal_set_osf(Crystal *cryst, double osf);
 extern void crystal_set_image(Crystal *cryst, struct image *image);
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 8e175f5b..f352c0c6 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1801,6 +1801,7 @@ static void integrate_rings(IntegrationMethod meth,
 	free_intcontext(&ic);
 
 	crystal_set_num_saturated_reflections(cr, ic.n_saturated);
+	crystal_set_num_implausible_reflections(cr, ic.n_implausible);
 
 	if ( ic.n_implausible ) {
 		STATUS("Warning: %i implausibly negative reflection%s in %s.\n",
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index e4ed4caf..07568024 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -585,6 +585,8 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
 		                num_integrated_reflections(reflist));
 		fprintf(st->fh, "num_saturated_reflections = %lli\n",
 				crystal_get_num_saturated_reflections(cr));
+		fprintf(st->fh, "num_implausible_reflections = %lli\n",
+				crystal_get_num_implausible_reflections(cr));
 
 	}
 
-- 
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