Added "--tolerance" option in indexamajig

5 files changed, 33 insertions, 10 deletions

diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index c31697bc..a6df931b 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -669,7 +669,7 @@ static int same_vector(struct cvec a, struct cvec b)
 
 /* Attempt to make 'cell' fit into 'template' somehow */
 UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose,
-                     int reduce)
+                     float *tols, int reduce)
 {
 	signed int n1l, n2l, n3l;
 	double asx, asy, asz;
@@ -683,8 +683,7 @@ UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose,
 	float best_fom = +999999999.9; /* Large number.. */
 	int ncand[3] = {0,0,0};
 	signed int ilow, ihigh;
-	float ltl = 5.0;     /* percent */
-	float angtol = deg2rad(1.5);
+	float angtol = deg2rad(tols[3]);
 
 	if ( cell_get_reciprocal(template, &asx, &asy, &asz,
 	                         &bsx, &bsy, &bsz,
@@ -753,7 +752,7 @@ UnitCell *match_cell(UnitCell *cell, UnitCell *template, int verbose,
 			/* Test modulus for agreement with moduli of template */
 			for ( i=0; i<3; i++ ) {
 
-				if ( !within_tolerance(lengths[i], tlen, ltl) )
+				if ( !within_tolerance(lengths[i], tlen, tols[i]) )
 					continue;
 
 				cand[i][ncand[i]].vec.u = tx;
diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h
index 72c0b6df..e69ce721 100644
--- a/libcrystfel/src/cell.h
+++ b/libcrystfel/src/cell.h
@@ -96,7 +96,7 @@ extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
 extern void cell_print(UnitCell *cell);
 
 extern UnitCell *match_cell(UnitCell *cell, UnitCell *tempcell, int verbose,
-                            int reduce);
+                            float *ltl, int reduce);
 
 extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell);
 
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 34a5dda3..56b34baa 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -139,7 +139,7 @@ void map_all_peaks(struct image *image)
 
 void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
                    int cellr, int verbose, IndexingPrivate **ipriv,
-                   int config_insane)
+                   int config_insane, float *ltl)
 {
 	int i;
 	int n = 0;
@@ -191,10 +191,10 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 				new_cell = cell_new_from_cell(cand);
 				break;
 			case CELLR_REDUCE :
-				new_cell = match_cell(cand, cell, verbose, 1);
+				new_cell = match_cell(cand, cell, verbose, ltl, 1);
 				break;
 			case CELLR_COMPARE :
-				new_cell = match_cell(cand, cell, verbose, 0);
+				new_cell = match_cell(cand, cell, verbose, ltl, 0);
 				break;
 			case CELLR_COMPARE_AB :
 				new_cell = match_cell_ab(cand, cell);
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 9d4b69bd..1457e93f 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -54,7 +54,7 @@ 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, int config_insane);
+                          IndexingPrivate **priv, int config_insane, float *ltl);
 
 extern void cleanup_indexing(IndexingPrivate **priv);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 7feb3968..6f3704bc 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -75,6 +75,7 @@ struct static_index_args
 	IndexingPrivate **ipriv;
 	int peaks;                /* Peak detection method */
 	int cellr;
+	float tols[4];
 	struct beam_params *beam;
 	const char *element;
 	const char *hdf5_peak_path;
@@ -171,6 +172,9 @@ static void show_help(const char *s)
 "                           compare : match by at most changing the order of\n"
 "                                     the indices.\n"
 "                           compare_ab : compare 'a' and 'b' lengths only.\n"
+"     --tolerance=<a,b,c,angl>  Set the tolerance for a,b,c axis (in %%)\n"
+"                                and for the angles (in deg) when reducing\n"
+"                                or comparing (default is 5%% and 1.5deg)\n"
 "     --filter-cm          Perform common-mode noise subtraction on images\n"
 "                           before proceeding.  Intensities will be extracted\n"
 "                           from the image as it is after this processing.\n"
@@ -354,7 +358,7 @@ static void process_image(void *pp, int cookie)
 	image.profile_radius = 0.0001e9;
 	index_pattern(&image, cell, indm, pargs->static_args.cellr,
 		      config_verbose, pargs->static_args.ipriv,
-		      pargs->static_args.config_insane);
+		      pargs->static_args.config_insane, pargs->static_args.tols);
 
 	if ( image.indexed_cell != NULL ) {
 
@@ -555,6 +559,8 @@ int main(int argc, char *argv[])
 	char *prefix = NULL;
 	char *speaks = NULL;
 	char *scellr = NULL;
+	char *toler = NULL;
+	float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* for a,b,c in % and for the angles in deg */
 	int cellr;
 	int peaks;
 	int nthreads = 1;
@@ -587,6 +593,7 @@ int main(int argc, char *argv[])
 		{"no-index",           0, &config_noindex,     1},
 		{"peaks",              1, NULL,                2},
 		{"cell-reduction",     1, NULL,                3},
+		{"tolerance",          1, NULL,               13},
 		{"indexing",           1, NULL,               'z'},
 		{"geometry",           1, NULL,               'g'},
 		{"beam",               1, NULL,               'b'},
@@ -676,6 +683,10 @@ int main(int argc, char *argv[])
 			scellr = strdup(optarg);
 			break;
 
+		case 13 :
+			toler = strdup(optarg);
+			break;
+
 		case 4 :
 			min_gradient = strtof(optarg, NULL);
 			break;
@@ -868,6 +879,15 @@ int main(int argc, char *argv[])
 	/* No indexing -> no reduction */
 	if ( indm == NULL ) reduction_needs_cell = 0;
 
+	if ( toler != NULL ) {
+		int ttt;
+		ttt = sscanf(toler, "%f,%f,%f,%f", &tols[0], &tols[1], &tols[2], &tols[3] );
+		if ( ttt != 4 ) {
+			ERROR("Invalid parameters for '--tolerance'\n");
+			return 1;
+		}
+	}
+
 	if ( geometry == NULL ) {
 		ERROR("You need to specify a geometry file with --geometry\n");
 		return 1;
@@ -944,6 +964,10 @@ int main(int argc, char *argv[])
 	qargs.static_args.config_insane = config_insane;
 	qargs.static_args.config_bgsub = config_bgsub;
 	qargs.static_args.cellr = cellr;
+	qargs.static_args.tols[0] = tols[0];
+	qargs.static_args.tols[1] = tols[1];
+	qargs.static_args.tols[2] = tols[2];
+	qargs.static_args.tols[3] = tols[3];
 	qargs.static_args.threshold = threshold;
 	qargs.static_args.min_gradient = min_gradient;
 	qargs.static_args.min_snr = min_snr;