indexamajig: Get peak threshold on command line

4 files changed, 16 insertions, 6 deletions

diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index 0759ff6b..e5945015 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -103,7 +103,8 @@ static void sum_peaks(struct image *image, double *sum)
 	int w = image->width;
 	const int lim = INTEGRATION_RADIUS * INTEGRATION_RADIUS;
 
-	search_peaks(image);
+	/* FIXME: Get threshold value from command line */
+	search_peaks(image, 800.0);
 
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index b8d3df88..b118593e 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -61,6 +61,7 @@ struct process_args
 	int config_sanity;
 	int config_satcorr;
 	int config_sa;
+	float threshold;
 	struct detector *det;
 	IndexingMethod indm;
 	IndexingPrivate *ipriv;
@@ -145,6 +146,7 @@ static void show_help(const char *s)
 "                           included in the HDF5 file.\n"
 "      --no-sa             Don't correct for the differing solid angles of\n"
 "                           the pixels.\n"
+"      --threshold=<n>     Only accept peaks above <n> ADU.  Default: 800.\n"
 "\n"
 "\nOptions for greater performance or verbosity:\n\n"
 "      --verbose           Be verbose about indexing.\n"
@@ -325,7 +327,7 @@ static struct process_result process_image(struct process_args *pargs)
 	}
 
 	/* Perform 'fine' peak search */
-	search_peaks(&image);
+	search_peaks(&image, pargs->threshold);
 
 	/* Get rid of noise-filtered version at this point
 	 * - it was strictly for the purposes of peak detection. */
@@ -468,6 +470,7 @@ int main(int argc, char *argv[])
 	int config_sanity = 0;
 	int config_satcorr = 0;
 	int config_sa = 1;
+	float threshold = 800.0;
 	struct detector *det;
 	char *geometry = NULL;
 	IndexingMethod indm;
@@ -512,11 +515,12 @@ int main(int argc, char *argv[])
 		{"check-sanity",       0, &config_sanity,      1},
 		{"sat-corr",           0, &config_satcorr,     1},
 		{"no-sa",              0, &config_sa,          0},
+		{"threshold",          1, NULL,               't'},
 		{0, 0, NULL, 0}
 	};
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:",
+	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:",
 	                        longopts, NULL)) != -1) {
 
 		switch (c) {
@@ -552,6 +556,10 @@ int main(int argc, char *argv[])
 			geometry = strdup(optarg);
 			break;
 
+		case 't' :
+			threshold = strtof(optarg, NULL);
+			break;
+
 		case 0 :
 			break;
 
@@ -707,6 +715,7 @@ int main(int argc, char *argv[])
 		pargs->indm = indm;
 		pargs->intensities = intensities;
 		pargs->gctx = gctx;
+		pargs->threshold = threshold;
 		pargs->id = i;
 		pthread_mutex_lock(&pargs->control_mutex);
 		pargs->done = 0;
diff --git a/src/peaks.c b/src/peaks.c
index 56a79a05..7630f965 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -266,7 +266,7 @@ int integrate_peak(struct image *image, int xp, int yp,
 }
 
 
-void search_peaks(struct image *image)
+void search_peaks(struct image *image, float threshold)
 {
 	int x, y, width, height;
 	float *data;
@@ -305,7 +305,7 @@ void search_peaks(struct image *image)
 		int r;
 
 		/* Overall threshold */
-		if ( data[x+width*y] < 50 ) continue;
+		if ( data[x+width*y] < threshold ) continue;
 
 		/* Get gradients */
 		dx1 = data[x+width*y] - data[(x+1)+width*y];
diff --git a/src/peaks.h b/src/peaks.h
index f262a54e..c5d1fb57 100644
--- a/src/peaks.h
+++ b/src/peaks.h
@@ -19,7 +19,7 @@
 
 #include <pthread.h>
 
-extern void search_peaks(struct image *image);
+extern void search_peaks(struct image *image, float threshold);
 extern void dump_peaks(struct image *image, pthread_mutex_t *mutex);
 extern void output_intensities(struct image *image, UnitCell *cell,
                                pthread_mutex_t *mutex, int polar, int sa);