From 90063123279d99825f76d0bb06feb7471e200bea Mon Sep 17 00:00:00 2001
From: Thomas White <taw@bitwiz.org.uk>
Date: Thu, 30 May 2013 06:42:15 -0700
Subject: Tidy up

---
 libcrystfel/src/integration.c | 37 ++++++++++++++++++++++++++++++++++++-
 src/process_image.c           |  7 +++++++
 2 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 0acd060a..315c8a33 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -49,7 +49,8 @@
 #include "integration.h"
 
 
-#define VERBOSITY ((h==0) && (k==13) && (l==13))
+#define VERBOSITY (0)
+// ((h==-6) && (k==0) && (l==-8))
 
 
 static void check_eigen(gsl_vector *e_val)
@@ -549,6 +550,23 @@ static int init_intcontext(struct intcontext *ic)
 }
 
 
+static void free_intcontext(struct intcontext *ic)
+{
+	int i;
+
+	free(ic->boxes);
+	for ( i=0; i<ic->n_reference_profiles; i++ ) {
+		free(ic->reference_profiles[i]);
+		free(ic->reference_den[i]);
+	}
+	free(ic->reference_profiles);
+	free(ic->reference_den);
+	free(ic->n_profiles_in_reference);
+	free(ic->bm);
+	gsl_matrix_free(ic->bgm);
+}
+
+
 static void setup_ring_masks(struct intcontext *ic,
                              double ir_inn, double ir_mid, double ir_out)
 {
@@ -602,6 +620,19 @@ static struct peak_box *add_box(struct intcontext *ic)
 
 	idx = ic->n_boxes++;
 
+	ic->boxes[idx].cfs = 0;
+	ic->boxes[idx].css = 0;
+	ic->boxes[idx].bm = NULL;
+	ic->boxes[idx].pn = -1;
+	ic->boxes[idx].p = NULL;
+	ic->boxes[idx].a = 0.0;
+	ic->boxes[idx].b = 0.0;
+	ic->boxes[idx].c = 0.0;
+	ic->boxes[idx].intensity = 0.0;
+	ic->boxes[idx].sigma = 0.0;
+	ic->boxes[idx].J = 0.0;
+	ic->boxes[idx].rp = -1;
+	ic->boxes[idx].refl = NULL;
 	ic->boxes[idx].verbose = 0;
 
 	return &ic->boxes[idx];
@@ -1184,6 +1215,8 @@ static void measure_all_intensities(IntegrationMethod meth, RefList *list,
 		}
 	}
 
+	free_intcontext(&ic);
+
 	image->num_saturated_peaks = n_saturated;
 }
 
@@ -1581,6 +1614,8 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
 
 	}
 
+	free_intcontext(&ic);
+
 	crystal_set_num_saturated_reflections(cr, n_saturated);
 	crystal_set_resolution_limit(cr, limit);
 	crystal_set_reflections(cr, list);
diff --git a/src/process_image.c b/src/process_image.c
index 65deace5..7e91de2d 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -183,9 +183,16 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	            iargs->stream_peaks, iargs->stream_refls);
 
 	for ( i=0; i<image.n_crystals; i++ ) {
+		cell_free(crystal_get_cell(image.crystals[i]));
+		reflist_free(crystal_get_reflections(image.crystals[i]));
 		crystal_free(image.crystals[i]);
 	}
 
+	for ( i=0; i<image.det->n_panels; i++ ) {
+		free(image.dp[i]);
+		free(image.bad[i]);
+	}
+
 	free(image.data);
 	if ( image.flags != NULL ) free(image.flags);
 	image_feature_list_free(image.features);
-- 
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