From a1e0854a972a988a7153df04f74dcee3ff9e75b9 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 10 Jan 2013 13:49:11 +0100
Subject: indexamajig: Add --integrate-found

---
 src/im-sandbox.c  | 13 +++++++++++--
 src/im-sandbox.h  |  1 +
 src/indexamajig.c |  6 ++++++
 3 files changed, 18 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 32bcba15..c8cceb2b 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -301,9 +301,17 @@ static void process_image(const struct index_args *iargs,
 	              iargs->config_insane, iargs->tols);
 
 	if ( image.indexed_cell != NULL ) {
+
 		pargs->indexable = 1;
-		image.reflections = find_intersections(&image,
-				image.indexed_cell);
+
+		if ( iargs->integrate_found ) {
+			image.reflections = select_intersections(&image,
+			                                    image.indexed_cell);
+		} else {
+			image.reflections = find_intersections(&image,
+			                                    image.indexed_cell);
+		}
+
 		if (image.reflections != NULL) {
 			integrate_reflections(&image,
 			                      iargs->config_closer,
@@ -314,6 +322,7 @@ static void process_image(const struct index_args *iargs,
 			                      iargs->ir_out,
 			                      iargs->integrate_saturated);
 		}
+
 	} else {
 		image.reflections = NULL;
 	}
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 3851fb40..872f84ad 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -69,6 +69,7 @@ struct index_args
 	int integrate_saturated;
 	int use_saturated;
 	int no_revalidate;
+	int integrate_found;
 };
 
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index ae03986c..b132331c 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -167,6 +167,9 @@ static void show_help(const char *s)
 "                           peaks which contain pixels above max_adu.\n"
 "     --no-revalidate      Don't re-integrate and check HDF5 peaks for\n"
 "                           validity.\n"
+"     --integrate-found    Skip the spot prediction step, and just integrate\n"
+"                           the intensities of the spots found by the initial\n"
+"                           peak search.\n"
 );
 }
 
@@ -251,6 +254,7 @@ int main(int argc, char *argv[])
 	int integrate_saturated = 0;
 	int use_saturated = 0;
 	int no_revalidate = 0;
+	int integrate_found = 0;
 
 	copyme = new_copy_hdf5_field_list();
 	if ( copyme == NULL ) {
@@ -300,6 +304,7 @@ int main(int argc, char *argv[])
 		{"integrate-saturated",0, &integrate_saturated,1},
 		{"use-saturated",0, &use_saturated,            1},
 		{"no-revalidate",      0, &no_revalidate,      1},
+		{"integrate-found",    0, &integrate_found,    1},
 		{0, 0, NULL, 0}
 	};
 
@@ -649,6 +654,7 @@ int main(int argc, char *argv[])
 	iargs.use_saturated = use_saturated;
 	iargs.integrate_saturated = integrate_saturated;
 	iargs.no_revalidate = no_revalidate;
+	iargs.integrate_found = integrate_found;
 
 	create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
 	                    use_this_one_instead, ofh);
-- 
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