From e2335528269bf688d724248d3771cd3cee6558de Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 14 Aug 2014 11:10:18 +0200
Subject: Factorise reflection prediction and do it before creating the mask

---
 libcrystfel/src/integration.c | 29 ++++++++++++++---------------
 tests/prof2d_check.c          |  5 ++---
 2 files changed, 16 insertions(+), 18 deletions(-)

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 07a3e393..ec8bf05d 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1487,7 +1487,7 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list)
 }
 
 
-static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
+static void integrate_prof2d(IntegrationMethod meth,
                              Crystal *cr, struct image *image, IntDiag int_diag,
                              signed int idh, signed int idk, signed int idl,
                              double ir_inn, double ir_mid, double ir_out,
@@ -1499,11 +1499,9 @@ static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
 	int i;
 	int n_saturated = 0;
 
+	list = crystal_get_reflections(cr);
 	cell = crystal_get_cell(cr);
 
-	/* Create initial list of reflections with nominal parameters */
-	list = find_intersections(image, cr, pmodel);
-
 	ic.halfw = ir_out;
 	ic.image = image;
 	ic.k = 1.0/image->lambda;
@@ -1545,8 +1543,6 @@ static void integrate_prof2d(IntegrationMethod meth, PartialityModel pmodel,
 	free_intcontext(&ic);
 
 	image->num_saturated_peaks = n_saturated;
-
-	crystal_set_reflections(cr, list);
 }
 
 
@@ -1745,7 +1741,7 @@ static double estimate_resolution(UnitCell *cell, ImageFeatureList *flist)
 }
 
 
-static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
+static void integrate_rings(IntegrationMethod meth,
                             Crystal *cr, struct image *image, IntDiag int_diag,
                             signed int idh, signed int idk, signed int idl,
                             double ir_inn, double ir_mid, double ir_out,
@@ -1757,11 +1753,7 @@ static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
 	UnitCell *cell;
 	struct intcontext ic;
 
-	list = find_intersections(image, cr, pmodel);
-	if ( list == NULL ) return;
-
-	if ( num_reflections(list) == 0 ) return;
-
+	list = crystal_get_reflections(cr);
 	cell = crystal_get_cell(cr);
 
 	ic.halfw = ir_out;
@@ -1797,7 +1789,6 @@ static void integrate_rings(IntegrationMethod meth, PartialityModel pmodel,
 	free_intcontext(&ic);
 
 	crystal_set_num_saturated_reflections(cr, ic.n_saturated);
-	crystal_set_reflections(cr, list);
 
 	if ( ic.n_implausible ) {
 		STATUS("Warning: %i implausibly negative reflection%s.\n",
@@ -1837,6 +1828,14 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
 	int i;
 	int *masks[image->det->n_panels];
 
+	/* Predict all reflections */
+	for ( i=0; i<image->n_crystals; i++ ) {
+		RefList *list;
+		list = find_intersections(image, image->crystals[i],
+		                          PMODEL_SCSPHERE);
+		crystal_set_reflections(image->crystals[i], list);
+	}
+
 	for ( i=0; i<image->det->n_panels; i++ ) {
 		masks[i] = make_BgMask(image, &image->det->panels[i], ir_inn);
 	}
@@ -1852,7 +1851,7 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
 			break;
 
 			case INTEGRATION_RINGS :
-			integrate_rings(meth, pmodel, cr, image,
+			integrate_rings(meth, cr, image,
 			                int_diag, idh, idk, idl,
 			                ir_inn, ir_mid, ir_out,
 			                results_pipe, masks);
@@ -1861,7 +1860,7 @@ void integrate_all_4(struct image *image, IntegrationMethod meth,
 			break;
 
 			case INTEGRATION_PROF2D :
-			integrate_prof2d(meth, pmodel, cr, image,
+			integrate_prof2d(meth, cr, image,
 			                 int_diag, idh, idk, idl,
 			                 ir_inn, ir_mid, ir_out,
 			                 results_pipe, masks);
diff --git a/tests/prof2d_check.c b/tests/prof2d_check.c
index 3352db49..38abe6f3 100644
--- a/tests/prof2d_check.c
+++ b/tests/prof2d_check.c
@@ -140,6 +140,7 @@ int main(int argc, char *argv[])
 	image.crystals = &cr;
 
 	list = find_intersections(&image, cr, PMODEL_SPHERE);
+	crystal_set_reflections(cr, list);
 
 	for ( fs=0; fs<w; fs++ ) {
 	for ( ss=0; ss<h; ss++ ) {
@@ -175,11 +176,9 @@ int main(int argc, char *argv[])
 
 	STATUS("%i strong, %i weak\n", n_strong, n_weak);
 
-	reflist_free(list);  /* integrate_prof2d() will predict again */
-	integrate_prof2d(INTEGRATION_PROF2D, PMODEL_SPHERE, cr, &image,
+	integrate_prof2d(INTEGRATION_PROF2D, cr, &image,
 	                 INTDIAG_NONE, 0, 0, 0, ir_inn, ir_mid, ir_out, 0,
 	                 NULL);
-	list = crystal_get_reflections(cr);
 
 	printf("Weak reflections:\n");
 	hi = histogram_init();
-- 
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