indexamajig: Restore --no-refine

Adds yet another indexing option...

7 files changed, 48 insertions, 26 deletions

diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/asdf.c
index 39a574ae..c52b04ff 100644
--- a/libcrystfel/src/asdf.c
+++ b/libcrystfel/src/asdf.c
@@ -1181,7 +1181,7 @@ 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_RETRY | INDEXING_MULTI;
+	       | INDEXING_CONTROL_FLAGS;
 
 	dp = malloc(sizeof(struct asdf_private));
 	if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index 014a4790..79b6d1ac 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -655,7 +655,7 @@ 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_RETRY | INDEXING_MULTI;
+	       | INDEXING_CONTROL_FLAGS;
 
 	dp = malloc(sizeof(struct dirax_private));
 	if ( dp == NULL ) return NULL;
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
index 18f60345..8a978957 100644
--- a/libcrystfel/src/felix.c
+++ b/libcrystfel/src/felix.c
@@ -679,7 +679,7 @@ 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_RETRY | INDEXING_MULTI;
+	       | INDEXING_CONTROL_FLAGS;
 
 	gp->cell = cell;
 	gp->indm = *indm;
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 6a74a958..11931b01 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -235,7 +235,7 @@ void map_all_peaks(struct image *image)
 static int try_indexer(struct image *image, IndexingMethod indm,
                        IndexingPrivate *ipriv)
 {
-	int i, r, n_bad;
+	int i, r;
 
 	switch ( indm & INDEXING_METHOD_MASK ) {
 
@@ -272,23 +272,28 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 
 	}
 
-	/* Attempt prediction refinement */
-	n_bad = 0;
-	for ( i=0; i<r; i++ ) {
-		Crystal *cr = image->crystals[image->n_crystals-i-1];
-		crystal_set_image(cr, image);
-		crystal_set_user_flag(cr, 0);
-		crystal_set_profile_radius(cr, 0.02e9);
-		crystal_set_mosaicity(cr, 0.0);
-		if ( refine_prediction(image, cr) != 0 ) {
-			crystal_set_user_flag(cr, 1);
-			n_bad++;
+	if ( indm & INDEXING_REFINE ) {
+
+		/* Attempt prediction refinement */
+		int n_bad = 0;
+		for ( i=0; i<r; i++ ) {
+			Crystal *cr = image->crystals[image->n_crystals-i-1];
+			crystal_set_image(cr, image);
+			crystal_set_user_flag(cr, 0);
+			crystal_set_profile_radius(cr, 0.02e9);
+			crystal_set_mosaicity(cr, 0.0);
+			if ( refine_prediction(image, cr) != 0 ) {
+				crystal_set_user_flag(cr, 1);
+				n_bad++;
+			}
 		}
-	}
 
-	remove_flagged_crystals(image);
+		remove_flagged_crystals(image);
+
+		if ( n_bad == r ) return 0;
+
+	}
 
-	if ( n_bad == r ) return 0;
 	return r;
 }
 
@@ -614,6 +619,12 @@ char *indexer_str(IndexingMethod indm)
 		strcat(str, "-nomulti");
 	}
 
+	if ( indm & INDEXING_REFINE ) {
+		strcat(str, "-refine");
+	} else {
+		strcat(str, "-norefine");
+	}
+
 	return str;
 }
 
@@ -693,6 +704,12 @@ IndexingMethod *build_indexer_list(const char *str)
 		} else if ( strcmp(methods[i], "nomulti") == 0) {
 			list[nmeth] &= ~INDEXING_MULTI;
 
+		} else if ( strcmp(methods[i], "refine") == 0) {
+			list[nmeth] |= INDEXING_REFINE;
+
+		} else if ( strcmp(methods[i], "norefine") == 0) {
+			list[nmeth] &= ~INDEXING_REFINE;
+
 		} 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 fc2477da..2fb5a13d 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -41,29 +41,29 @@
 
 #define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS         \
                                      | INDEXING_CHECK_CELL_COMBINATIONS        \
-                                     | INDEXING_RETRY)
+                                     | INDEXING_RETRY | INDEXING_REFINE)
 
 #define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS           \
                                      | INDEXING_CHECK_CELL_COMBINATIONS        \
-                                     | INDEXING_RETRY)
+                                     | INDEXING_RETRY | INDEXING_REFINE)
 
 #define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS       \
                                      | INDEXING_CHECK_CELL_COMBINATIONS        \
                                      | INDEXING_USE_LATTICE_TYPE               \
                                      | INDEXING_USE_CELL_PARAMETERS            \
-                                     | INDEXING_RETRY)
+                                     | INDEXING_RETRY | INDEXING_REFINE)
 
 #define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX                                \
                                      | INDEXING_USE_LATTICE_TYPE               \
                                      | INDEXING_USE_CELL_PARAMETERS            \
-                                     | INDEXING_RETRY)
+                                     | INDEXING_RETRY | INDEXING_REFINE)
 
 /* 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_RETRY)
+                                     | INDEXING_RETRY | INDEXING_REFINE)
 
 /**
  * IndexingMethod:
@@ -89,6 +89,7 @@
  *   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.
+ * @INDEXING_REFINE: Perform "prediction refinement" after indexing.
  *
  * An enumeration of all the available indexing methods.  The dummy value
  * @INDEXING_SIMULATION is used by partial_sim to indicate that no indexing was
@@ -115,7 +116,8 @@ typedef enum {
 	INDEXING_USE_LATTICE_TYPE        = 2048,
 	INDEXING_USE_CELL_PARAMETERS     = 4096,
 	INDEXING_RETRY                   = 8192,
-	INDEXING_MULTI                   = 16384
+	INDEXING_MULTI                   = 16384,
+	INDEXING_REFINE                  = 32768,
 
 } IndexingMethod;
 
@@ -123,6 +125,9 @@ typedef enum {
  * core of the indexing method */
 #define INDEXING_METHOD_MASK (0xff)
 
+/* Indexing flags which the indexing method does not need to know about */
+#define INDEXING_CONTROL_FLAGS (INDEXING_RETRY | INDEXING_MULTI | INDEXING_REFINE)
+
 #ifdef __cplusplus
 extern "C" {
 #endif
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 5b4b623f..8a546630 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -872,7 +872,7 @@ IndexingPrivate *mosflm_prepare(IndexingMethod *indm, UnitCell *cell,
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
 	       | INDEXING_CHECK_CELL_AXES | INDEXING_CHECK_PEAKS
 	       | INDEXING_USE_LATTICE_TYPE| INDEXING_USE_CELL_PARAMETERS
-	       | INDEXING_RETRY | INDEXING_MULTI;
+	       | INDEXING_CONTROL_FLAGS;
 
 	if ( (*indm & INDEXING_USE_LATTICE_TYPE)
 	   && !((*indm & INDEXING_CHECK_CELL_COMBINATIONS)
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index ea0fc836..bda60d89 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -677,7 +677,7 @@ IndexingPrivate *xds_prepare(IndexingMethod *indm, UnitCell *cell,
 	*indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_CELL_COMBINATIONS
 	          | INDEXING_CHECK_CELL_AXES | INDEXING_USE_LATTICE_TYPE
 	          | INDEXING_CHECK_PEAKS | INDEXING_USE_CELL_PARAMETERS
-	          | INDEXING_RETRY | INDEXING_MULTI;
+		  | INDEXING_CONTROL_FLAGS;
 
 	xp->ltl = ltl;
 	xp->cell = cell;