1 files changed, 77 insertions, 4 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 03bd6ae3..62f22c13 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -284,10 +284,13 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
 	}
 
 	for ( i=0; i<n; i++ ) {
-		methods[i] = get_indm_from_string(method_strings[i]);
-		if ( methods[i] == INDEXING_ERROR ) {
+		int err = 0;
+		methods[i] = get_indm_from_string_2(method_strings[i], &err);
+		if ( err ) {
 			ERROR("----- Notice -----\n");
-			ERROR("The way indexing options are used has changed in this CrystFEL version.\n");
+			ERROR("The way indexing options are given has changed in this CrystFEL version.\n");
+			ERROR("The indexing method should contain only the method itself and ");
+			ERROR("prior information modifiers ('cell' or 'latt')\n");
 			ERROR("To disable prediction refinement ('norefine'), use --no-refine.\n");
 			ERROR("To check cell axes only ('axes'), use --no-cell-combinations.\n");
 			ERROR("To disable all unit cell checks ('raw'), use --no-check-cell.\n");
@@ -298,6 +301,7 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
 			free(methods);
 			return NULL;
 		}
+
 	}
 
 	/* No cell parameters -> no cell checking, no prior cell */
@@ -878,13 +882,15 @@ static IndexingMethod warn_method(const char *str)
 }
 
 
-IndexingMethod get_indm_from_string(const char *str)
+IndexingMethod get_indm_from_string_2(const char *str, int *err)
 {
 	int n, i;
 	char **bits;
 	IndexingMethod method = INDEXING_NONE;
 	int have_method = 0;
 
+	if ( err != NULL ) *err = 0;
+
 	n = assplode(str, "-", &bits, ASSPLODE_NONE);
 
 	for ( i=0; i<n; i++ ) {
@@ -946,6 +952,28 @@ IndexingMethod get_indm_from_string(const char *str)
 		} else if ( strcmp(bits[i], "nocell") == 0) {
 			method = set_nocellparams(method);
 
+		/* Deprecated options */
+		} else if ( strcmp(bits[i], "retry") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "noretry") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "multi") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "nomulti") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "refine") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "norefine") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "raw") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "bad") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "comb") == 0) {
+			if ( err != NULL ) *err = 1;
+		} else if ( strcmp(bits[i], "axes") == 0) {
+			if ( err != NULL ) *err = 1;
+
 		} else {
 			ERROR("Bad list of indexing methods: '%s'\n", str);
 			return INDEXING_ERROR;
@@ -960,3 +988,48 @@ IndexingMethod get_indm_from_string(const char *str)
 
 	return method;
 }
+
+
+IndexingMethod get_indm_from_string(const char *str)
+{
+	return get_indm_from_string_2(str, NULL);
+}
+
+
+static void do_probe(const char *(*func)(UnitCell *cell),
+                     UnitCell *cell, char *methods)
+{
+	const char *probe;
+	probe = func(cell);
+	if ( probe != NULL ) {
+		if ( methods[0] != '\0' ) {
+			strcat(methods, ",");
+		}
+		strcat(methods, probe);
+	}
+}
+
+
+char *detect_indexing_methods(UnitCell *cell)
+{
+	char *methods;
+
+	methods = malloc(1024);
+	if ( methods == NULL ) return NULL;
+	methods[0] = '\0';
+
+	do_probe(mosflm_probe, cell, methods);
+	do_probe(dirax_probe, cell, methods);
+	do_probe(asdf_probe, cell, methods);
+	do_probe(xds_probe, cell, methods);
+	do_probe(taketwo_probe, cell, methods);
+	/* Don't automatically use Felix (yet) */
+	//do_probe(felix_probe, cell, methods);
+
+	if ( strlen(methods) == 0 ) {
+		free(methods);
+		return NULL;
+	}
+
+	return methods;
+}