Make indexing "retry" and "multi" optional

7 files changed, 98 insertions, 27 deletions

diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/asdf.c
index e5d3466f..87f00716 100644
--- a/libcrystfel/src/asdf.c
+++ b/libcrystfel/src/asdf.c
@@ -1178,7 +1178,8 @@ IndexingPrivate *asdf_prepare(IndexingMethod *indm, UnitCell *cell,
 
 	/* Flags that asdf knows about */
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
-	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS;
+	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
+	       | INDEXING_RETRY | INDEXING_MULTI;
 
 	dp = malloc(sizeof(struct asdf_private));
 	if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index fb69cece..014a4790 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -654,7 +654,8 @@ IndexingPrivate *dirax_prepare(IndexingMethod *indm, UnitCell *cell,
 
 	/* Flags that DirAx knows about */
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
-	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS;
+	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
+	       | INDEXING_RETRY | INDEXING_MULTI;
 
 	dp = malloc(sizeof(struct dirax_private));
 	if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
index f5bae88a..2a6a0e44 100644
--- a/libcrystfel/src/felix.c
+++ b/libcrystfel/src/felix.c
@@ -676,7 +676,8 @@ IndexingPrivate *felix_prepare(IndexingMethod *indm, UnitCell *cell,
 
 	/* Flags that Felix knows about */
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS
-	       | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS;
+	       | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS
+	       | INDEXING_RETRY | INDEXING_MULTI;
 
 	gp->cell = cell;
 	gp->indm = *indm;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 2e54859d..af5b81c7 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -346,6 +346,46 @@ static int delete_explained_peaks(struct image *image, Crystal *cr)
 }
 
 
+/* indm = the current indexing method
+ * r = the result from try_indexer() on this method just now
+ * image = the image structure
+ *
+ * Returns false for "try again", true for "no, stop now"
+ */
+static int finished_retry(IndexingMethod indm, int r, struct image *image)
+{
+	if ( r == 0 ) {
+
+		/* Indexing failed on the previous attempt.  Maybe try again
+		 * after poking the peak list a bit */
+
+		if ( indm & INDEXING_RETRY ) {
+			/* Retry with fewer peaks */
+			return delete_weakest_peaks(image->features);
+		} else {
+			/* Indexing failed, opted not to try again */
+			return 1;
+		}
+
+	} else {
+
+		/* Indexing succeeded on previous attempt.  Maybe try again
+		 * after deleting the explained peaks */
+
+		if ( indm & INDEXING_MULTI ) {
+			/* Remove "used" spots and try for
+			 * another lattice */
+			Crystal *cr;
+			cr = image->crystals[image->n_crystals-1];
+			return delete_explained_peaks(image, cr);
+		} else {
+			return 1;
+		}
+
+	}
+}
+
+
 void index_pattern(struct image *image,
                    IndexingMethod *indms, IndexingPrivate **iprivs)
 {
@@ -373,18 +413,7 @@ void index_pattern(struct image *image,
 
 			r = try_indexer(image, indms[n], iprivs[n]);
 			ntry++;
-
-			if ( r == 0 ) {
-				/* Retry with fewer peaks */
-				done = delete_weakest_peaks(image->features);
-			} else {
-				/* Remove "used" spots and try for
-				 * another lattice */
-				Crystal *cr;
-				cr = image->crystals[image->n_crystals-1];
-				done = delete_explained_peaks(image, cr);
-			}
-
+			done = finished_retry(indms[n], r, image);
 			if ( ntry > 5 ) done = 1;
 
 		} while ( !done );
@@ -459,11 +488,12 @@ static IndexingMethod set_cellparams(IndexingMethod a)
 	return a | INDEXING_USE_CELL_PARAMETERS;
 }
 
+
 char *indexer_str(IndexingMethod indm)
 {
 	char *str;
 
-	str = malloc(32);
+	str = malloc(256);
 	if ( str == NULL ) {
 		ERROR("Failed to allocate string.\n");
 		return NULL;
@@ -538,6 +568,18 @@ char *indexer_str(IndexingMethod indm)
 		strcat(str, "-nocell");
 	}
 
+	if ( indm & INDEXING_RETRY ) {
+		strcat(str, "-retry");
+	} else {
+		strcat(str, "-noretry");
+	}
+
+	if ( indm & INDEXING_MULTI ) {
+		strcat(str, "-multi");
+	} else {
+		strcat(str, "-nomulti");
+	}
+
 	return str;
 }
 
@@ -605,6 +647,18 @@ IndexingMethod *build_indexer_list(const char *str)
 		} else if ( strcmp(methods[i], "nocell") == 0) {
 			list[nmeth] = set_nocellparams(list[nmeth]);
 
+		} else if ( strcmp(methods[i], "retry") == 0) {
+			list[nmeth] |= INDEXING_RETRY;
+
+		} else if ( strcmp(methods[i], "noretry") == 0) {
+			list[nmeth] &= ~INDEXING_RETRY;
+
+		} else if ( strcmp(methods[i], "multi") == 0) {
+			list[nmeth] |= INDEXING_MULTI;
+
+		} else if ( strcmp(methods[i], "nomulti") == 0) {
+			list[nmeth] &= ~INDEXING_MULTI;
+
 		} else {
 			ERROR("Bad list of indexing methods: '%s'\n", str);
 			return NULL;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 0ce74e37..855af70d 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -3,13 +3,13 @@
  *
  * Perform indexing (somehow)
  *
- * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2015 Thomas White <taw@physics.org>
+ *   2010-2016 Thomas White <taw@physics.org>
  *   2010      Richard Kirian
  *   2012      Lorenzo Galli
  *   2015      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
@@ -40,25 +40,31 @@
 
 
 #define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS         \
-                                     | INDEXING_CHECK_CELL_COMBINATIONS)
+                                     | INDEXING_CHECK_CELL_COMBINATIONS        \
+                                     | INDEXING_RETRY | INDEXING_MULTI)
 
-#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS         \
-                                     | INDEXING_CHECK_CELL_COMBINATIONS)
+#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS           \
+                                     | INDEXING_CHECK_CELL_COMBINATIONS        \
+                                     | INDEXING_RETRY | INDEXING_MULTI)
 
 #define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS       \
                                      | INDEXING_CHECK_CELL_COMBINATIONS        \
                                      | INDEXING_USE_LATTICE_TYPE               \
-                                     | INDEXING_USE_CELL_PARAMETERS)
+                                     | INDEXING_USE_CELL_PARAMETERS            \
+                                     | INDEXING_RETRY | INDEXING_MULTI)
 
-#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX                  \
+/* Note: no INDEXING_MULTI because Felix is already multi-crystal */
+#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX                                \
                                      | INDEXING_USE_LATTICE_TYPE               \
-                                     | INDEXING_USE_CELL_PARAMETERS)
+                                     | INDEXING_USE_CELL_PARAMETERS            \
+                                     | INDEXING_RETRY)
 
 /* Axis check is needed for XDS, because it likes to permute the axes */
 #define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE        \
                                      | INDEXING_USE_CELL_PARAMETERS            \
                                      | INDEXING_CHECK_CELL_AXES                \
-                                     | INDEXING_CHECK_PEAKS)
+                                     | INDEXING_CHECK_PEAKS                    \
+                                     | INDEXING_RETRY | INDEXING_MULTI)
 
 /**
  * IndexingMethod:
@@ -80,6 +86,10 @@
  *   guide the indexing process.
  * @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
  *   indexingprocess.
+ * @INDEXING_RETRY: If the indexer doesn't succeed, delete the weakest peaks
+ *   and try again.
+ * @INDEXING_MULTI: If the indexer succeeds, delete the peaks explained by the
+ *   lattice and try again in the hope of finding another crystal.
  *
  * An enumeration of all the available indexing methods.  The dummy value
  * @INDEXING_SIMULATION is used by partial_sim to indicate that no indexing was
@@ -105,6 +115,8 @@ typedef enum {
 	INDEXING_CHECK_PEAKS             = 1024,
 	INDEXING_USE_LATTICE_TYPE        = 2048,
 	INDEXING_USE_CELL_PARAMETERS     = 4096,
+	INDEXING_RETRY                   = 8192,
+	INDEXING_MULTI                   = 16384
 
 } IndexingMethod;
 
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index fe917d27..5b4b623f 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -871,7 +871,8 @@ IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
 	/* Flags that MOSFLM knows about */
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
 	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
-	       | INDEXING_USE_LATTICE_TYPE| INDEXING_USE_CELL_PARAMETERS;
+	       | INDEXING_USE_LATTICE_TYPE| INDEXING_USE_CELL_PARAMETERS
+	       | INDEXING_RETRY | INDEXING_MULTI;
 
 	if ( (*indm & INDEXING_USE_LATTICE_TYPE)
 	   && !((*indm & INDEXING_CHECK_CELL_COMBINATIONS)
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 36898949..ea0fc836 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -676,7 +676,8 @@ IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell,
 	/* Flags that XDS knows about */
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
 	          | INDEXING_CHECK_CELL_AXES | INDEXING_USE_LATTICE_TYPE
-	          | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS;
+	          | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS
+	          | INDEXING_RETRY | INDEXING_MULTI;
 
 	xp->ltl = ltl;
 	xp->cell = cell;