From 483e3d5883461f0572a181211b6aa306fd2bfdc0 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 28 Nov 2012 16:31:19 +0100
Subject: indexamajig: Add --integrate-saturated

---
 libcrystfel/src/peaks.c | 14 ++++++++------
 libcrystfel/src/peaks.h |  3 ++-
 src/im-sandbox.c        |  3 ++-
 src/im-sandbox.h        |  1 +
 src/indexamajig.c       |  5 +++++
 5 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index bf6a92f0..f13c7245 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -293,10 +293,9 @@ static int integrate_peak(struct image *image, int cfs, int css,
 
 		val = image->data[idx];
 
-		/* Veto peak if it contains saturation in bg region */
+		/* Check if peak contains saturation in bg region */
 		if ( use_max_adu && (val > p->max_adu) ) {
 			if ( saturated != NULL ) *saturated = 1;
-			return 1;
 		}
 
 		bg_tot += val;
@@ -353,10 +352,9 @@ static int integrate_peak(struct image *image, int cfs, int css,
 
 		val = image->data[idx] - bg_mean;
 
-		/* Veto peak if it contains saturation */
+		/* Check if peak contains saturation */
 		if ( use_max_adu && (val > p->max_adu) ) {
 			if ( saturated != NULL ) *saturated = 1;
-			return 1;
 		}
 
 		pk_counts++;
@@ -697,7 +695,8 @@ static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
 /* Integrate the list of predicted reflections in "image" */
 void integrate_reflections(struct image *image, int use_closer, int bgsub,
                            double min_snr,
-                           double ir_inn, double ir_mid, double ir_out)
+                           double ir_inn, double ir_mid, double ir_out,
+                           int integrate_saturated)
 {
 	struct integr_ind *il;
 	int n, i;
@@ -794,7 +793,10 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
 		                   &intensity, &sigma, ir_inn, ir_mid, ir_out,
 		                   1, bgMasks[pnum], &saturated);
 
-		if ( saturated ) image->n_saturated++;
+		if ( saturated ) {
+			image->n_saturated++;
+			if ( !integrate_saturated ) r = 1;
+		}
 
 		/* I/sigma(I) cutoff */
 		if ( intensity/sigma < min_snr ) r = 1;
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 39fdf54c..ec76fd3b 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -43,7 +43,8 @@ extern void search_peaks(struct image *image, float threshold,
 
 extern void integrate_reflections(struct image *image,
                                   int use_closer, int bgsub, double min_snr,
-                                  double ir_inn, double ir_mid, double ir_out);
+                                  double ir_inn, double ir_mid, double ir_out,
+                                  int integrate_saturated);
 
 extern double peak_lattice_agreement(struct image *image, UnitCell *cell,
                                      double *pst);
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 70839f21..80bb78e0 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -328,7 +328,8 @@ static void process_image(const struct index_args *iargs,
 			                      iargs->min_int_snr,
 			                      iargs->ir_inn,
 			                      iargs->ir_mid,
-			                      iargs->ir_out);
+			                      iargs->ir_out,
+			                      iargs->integrate_saturated);
 		}
 	} else {
 		image.reflections = NULL;
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 8ad9fd90..9f23f88b 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -66,6 +66,7 @@ struct index_args
 	double ir_mid;
 	double ir_out;
 	struct copy_hdf5_field *copyme;
+	int integrate_saturated;
 };
 
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f628eb29..2e5c8904 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -161,6 +161,8 @@ static void show_help(const char *s)
 "                           least 10%% of the located peaks.\n"
 "     --no-bg-sub          Don't subtract local background estimates from\n"
 "                           integrated intensities.\n"
+"     --integrate-saturated  During the final integration stage, don't reject\n"
+"                            peaks which contain pixels above max_adu.\n"
 );
 }
 
@@ -242,6 +244,7 @@ int main(int argc, char *argv[])
 	float ir_inn = 4.0;
 	float ir_mid = 5.0;
 	float ir_out = 7.0;
+	int integrate_saturated = 0;
 
 	copyme = new_copy_hdf5_field_list();
 	if ( copyme == NULL ) {
@@ -288,6 +291,7 @@ int main(int argc, char *argv[])
 		{"min-integration-snr",1, NULL,               12},
 		{"tolerance",          1, NULL,               13},
 		{"int-radius",         1, NULL,               14},
+		{"integrate-saturated",0, &integrate_saturated,1},
 		{0, 0, NULL, 0}
 	};
 
@@ -634,6 +638,7 @@ int main(int argc, char *argv[])
 	iargs.ir_inn = ir_inn;
 	iargs.ir_mid = ir_mid;
 	iargs.ir_out = ir_out;
+	iargs.integrate_saturated = integrate_saturated;
 
 	create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
 	                    use_this_one_instead, ofh);
-- 
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