From fcba20a4c51793701c5946cca8fc264aa2e72450 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 28 Nov 2012 17:41:46 +0100
Subject: indexamajig: Add --use-saturated

---
 src/im-sandbox.c  | 6 ++++--
 src/im-sandbox.h  | 1 +
 src/indexamajig.c | 5 +++++
 3 files changed, 10 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 80bb78e0..aed0b04b 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -292,13 +292,15 @@ static void process_image(const struct index_args *iargs,
 			ERROR("Failed to get peaks from HDF5 file.\n");
 		}
 		validate_peaks(&image, iargs->min_int_snr,
-		               iargs->ir_inn, iargs->ir_mid, iargs->ir_out);
+		               iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
+		               iargs->use_saturated);
 		break;
 
 		case PEAK_ZAEF:
 		search_peaks(&image, iargs->threshold,
 		             iargs->min_gradient, iargs->min_snr,
-		             iargs->ir_inn, iargs->ir_mid, iargs->ir_out);
+		             iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
+		             iargs->use_saturated);
 		break;
 
 	}
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 9f23f88b..50dc599b 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -67,6 +67,7 @@ struct index_args
 	double ir_out;
 	struct copy_hdf5_field *copyme;
 	int integrate_saturated;
+	int use_saturated;
 };
 
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 2e5c8904..57c16932 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"
+"     --use-saturated       During the initial peak search, don't reject\n"
+"                            peaks which contain pixels above max_adu.\n"
 "     --integrate-saturated  During the final integration stage, don't reject\n"
 "                            peaks which contain pixels above max_adu.\n"
 );
@@ -245,6 +247,7 @@ int main(int argc, char *argv[])
 	float ir_mid = 5.0;
 	float ir_out = 7.0;
 	int integrate_saturated = 0;
+	int use_saturated = 0;
 
 	copyme = new_copy_hdf5_field_list();
 	if ( copyme == NULL ) {
@@ -292,6 +295,7 @@ int main(int argc, char *argv[])
 		{"tolerance",          1, NULL,               13},
 		{"int-radius",         1, NULL,               14},
 		{"integrate-saturated",0, &integrate_saturated,1},
+		{"use-saturated",0, &use_saturated,            1},
 		{0, 0, NULL, 0}
 	};
 
@@ -638,6 +642,7 @@ int main(int argc, char *argv[])
 	iargs.ir_inn = ir_inn;
 	iargs.ir_mid = ir_mid;
 	iargs.ir_out = ir_out;
+	iargs.use_saturated = use_saturated;
 	iargs.integrate_saturated = integrate_saturated;
 
 	create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
-- 
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