From 155ca0064e5605a345d141202d6cbf7dce9a220b Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Fri, 4 Feb 2011 15:26:48 +0100
Subject: indexamajig: Allow the user to switch off the sanity check if they
 want

---
 src/index.c       | 6 ++++--
 src/index.h       | 2 +-
 src/indexamajig.c | 9 ++++++++-
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/index.c b/src/index.c
index 57399c61..5675eb0f 100644
--- a/src/index.c
+++ b/src/index.c
@@ -129,7 +129,8 @@ void map_all_peaks(struct image *image)
 
 
 void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
-                   int cellr, int verbose, IndexingPrivate **ipriv)
+                   int cellr, int verbose, IndexingPrivate **ipriv,
+                   int config_insane)
 {
 	int i;
 	int n = 0;
@@ -207,7 +208,8 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 			if ( new_cell == NULL ) continue;
 
 			/* Sanity check */
-			if ( !peak_sanity_check(image, new_cell, 0, 0.1) ) {
+			if ( !config_insane &&
+			     !peak_sanity_check(image, new_cell, 0, 0.1) ) {
 				STATUS("Failed peak sanity check.\n");
 				cell_free(new_cell);
 				continue;
diff --git a/src/index.h b/src/index.h
index b58c9b53..8f3e0ab7 100644
--- a/src/index.h
+++ b/src/index.h
@@ -51,7 +51,7 @@ extern void map_all_peaks(struct image *image);
 
 extern void index_pattern(struct image *image, UnitCell *cell,
                           IndexingMethod *indm, int cellr, int verbose,
-                          IndexingPrivate **priv);
+                          IndexingPrivate **priv, int config_insane);
 
 extern void cleanup_indexing(IndexingPrivate **priv);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index c997ed12..6c01f95e 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -62,6 +62,7 @@ struct static_index_args
 	int config_polar;
 	int config_satcorr;
 	int config_closer;
+	int config_insane;
 	float threshold;
 	float min_gradient;
 	struct detector *det;
@@ -197,6 +198,8 @@ static void show_help(const char *s)
 "     --no-closer-peak     Don't integrate from the location of a nearby peak\n"
 "                           instead of the position closest to the reciprocal\n"
 "                           lattice point.\n"
+"     --insane             Don't check that the reduced cell accounts for at\n"
+"                           least 10%% of the located peaks.\n"
 );
 }
 
@@ -387,7 +390,8 @@ static void process_image(void *pp, int cookie)
 
 	/* Calculate orientation matrix (by magic) */
 	index_pattern(&image, cell, indm, pargs->static_args.cellr,
-		      config_verbose, pargs->static_args.ipriv);
+		      config_verbose, pargs->static_args.ipriv,
+		      pargs->static_args.config_insane);
 
 	/* No cell at this point?  Then we're done. */
 	if ( image.indexed_cell == NULL ) goto done;
@@ -510,6 +514,7 @@ int main(int argc, char *argv[])
 	int config_satcorr = 1;
 	int config_checkprefix = 1;
 	int config_closer = 1;
+	int config_insane = 0;
 	float threshold = 800.0;
 	float min_gradient = 100000.0;
 	struct detector *det;
@@ -572,6 +577,7 @@ int main(int argc, char *argv[])
 		{"no-check-prefix",    0, &config_checkprefix, 0},
 		{"no-closer-peak",     0, &config_closer,      0},
 		{"gpu-dev",            1, NULL,                5},
+		{"insane",             1, &config_insane,      1},
 		{0, 0, NULL, 0}
 	};
 
@@ -862,6 +868,7 @@ int main(int argc, char *argv[])
 	qargs.static_args.config_polar = config_polar;
 	qargs.static_args.config_satcorr = config_satcorr;
 	qargs.static_args.config_closer = config_closer;
+	qargs.static_args.config_insane = config_insane;
 	qargs.static_args.cellr = cellr;
 	qargs.static_args.threshold = threshold;
 	qargs.static_args.min_gradient = min_gradient;
-- 
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