From 96046b5dbb09328b4dac40f363cd8157cf32b4fa Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 4 Feb 2010 19:18:16 +0100
Subject: Add --no-match option to skip the unit cell matching procedure

---
 src/index.c       | 12 +++++++-----
 src/index.h       |  3 ++-
 src/indexamajig.c |  7 ++++++-
 3 files changed, 15 insertions(+), 7 deletions(-)

(limited to 'src')

diff --git a/src/index.c b/src/index.c
index 4bc74b82..27d75554 100644
--- a/src/index.c
+++ b/src/index.c
@@ -102,7 +102,7 @@ static void write_drx(struct image *image)
 }
 
 
-void index_pattern(struct image *image, IndexingMethod indm)
+void index_pattern(struct image *image, IndexingMethod indm, int no_match)
 {
 	int i;
 	UnitCell *new_cell = NULL;
@@ -148,8 +148,10 @@ void index_pattern(struct image *image, IndexingMethod indm)
 		return;
 	}
 
-	new_cell = match_cell(image->indexed_cell,
-		              image->molecule->cell);
-	free(image->indexed_cell);
-	image->indexed_cell = new_cell;
+	if ( !no_match ) {
+		new_cell = match_cell(image->indexed_cell,
+			              image->molecule->cell);
+		free(image->indexed_cell);
+		image->indexed_cell = new_cell;
+	}
 }
diff --git a/src/index.h b/src/index.h
index a3dae020..08ffa2fc 100644
--- a/src/index.h
+++ b/src/index.h
@@ -25,7 +25,8 @@ typedef enum {
 } IndexingMethod;
 
 
-extern void index_pattern(struct image *image, IndexingMethod indm);
+extern void index_pattern(struct image *image, IndexingMethod indm,
+                          int no_match);
 /* x,y in pixels relative to central beam */
 extern int map_position(struct image *image, double x, double y,
                         double *rx, double *ry, double *rz);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 6b0ad3d9..3f75f8b0 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -56,6 +56,9 @@ static void show_help(const char *s)
 "                           unit cell.\n"
 "      --clean-image       Perform common-mode noise subtraction and\n"
 "                           background removal on images before proceeding.\n"
+"      --no-match          Don't attempt to match the indexed cell to the\n"
+"                           model, just proceed with the one generated by the\n"
+"                           auto-indexing procedure.\n"
 "\n");
 }
 
@@ -74,6 +77,7 @@ int main(int argc, char *argv[])
 	int config_writedrx = 0;
 	int config_simulate = 0;
 	int config_clean = 0;
+	int config_nomatch = 0;
 	IndexingMethod indm;
 	char *indm_str = NULL;
 
@@ -88,6 +92,7 @@ int main(int argc, char *argv[])
 		{"indexing",           1, NULL,               'z'},
 		{"simulate",           0, &config_simulate,    1},
 		{"clean-image",        0, &config_clean,       1},
+		{"no-match",           0, &config_nomatch,     1},
 		{0, 0, NULL, 0}
 	};
 
@@ -217,7 +222,7 @@ int main(int argc, char *argv[])
 
 			/* Calculate orientation matrix (by magic) */
 			if ( config_writedrx || (indm != INDEXING_NONE) ) {
-				index_pattern(&image, indm);
+				index_pattern(&image, indm, config_nomatch);
 			}
 
 			/* No cell at this point?  Then we're done. */
-- 
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