Perform prediction refinement straight after indexing

This allows indexing to be attempted again (either a new method or with
"retry") if the prediction refinement fails, increasing overall indexing
rate.

Side-effect: there are some hoops which would need to be jumped through
to store the profile radius before refinement and hence enable
scripts/plot-predict-refine to work.  For now, we'll ignore this as it's
clear that the prediction refinement is working.

3 files changed, 55 insertions, 8 deletions

diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index cd7047dd..82ad8f7e 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -280,6 +280,26 @@ void image_add_crystal(struct image *image, Crystal *cryst)
 }
 
 
+void remove_flagged_crystals(struct image *image)
+{
+	int i;
+
+	for ( i=0; i<image->n_crystals; i++ ) {
+		if ( crystal_get_user_flag(image->crystals[i]) ) {
+			int j;
+			Crystal *deleteme = image->crystals[i];
+			cell_free(crystal_get_cell(deleteme));
+			crystal_free(deleteme);
+			for ( j=i; j<image->n_crystals-1; j++ ) {
+				image->crystals[j] = image->crystals[j+1];
+			}
+			image->n_crystals--;
+		}
+	}
+
+}
+
+
 /* Free all crystals, including their RefLists and UnitCells */
 void free_all_crystals(struct image *image)
 {
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index e9cd76fc..ddbfc9dc 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -227,6 +227,7 @@ extern struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx);
 extern ImageFeatureList *sort_peaks(ImageFeatureList *flist);
 
 extern void image_add_crystal(struct image *image, Crystal *cryst);
+extern void remove_flagged_crystals(struct image *image);
 extern void free_all_crystals(struct image *image);
 
 #ifdef __cplusplus
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 2b84a621..6a74a958 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -55,6 +55,7 @@
 #include "geometry.h"
 #include "cell-utils.h"
 #include "felix.h"
+#include "predict-refine.h"
 
 
 static int debug_index(struct image *image)
@@ -234,36 +235,61 @@ void map_all_peaks(struct image *image)
 static int try_indexer(struct image *image, IndexingMethod indm,
                        IndexingPrivate *ipriv)
 {
+	int i, r, n_bad;
+
 	switch ( indm & INDEXING_METHOD_MASK ) {
 
 		case INDEXING_NONE :
 		return 0;
 
 		case INDEXING_DIRAX :
-		return run_dirax(image, ipriv);
+		r = run_dirax(image, ipriv);
+		break;
 
 		case INDEXING_ASDF :
-		return run_asdf(image, ipriv);
+		r = run_asdf(image, ipriv);
+		break;
 
 		case INDEXING_MOSFLM :
-		return run_mosflm(image, ipriv);
+		r = run_mosflm(image, ipriv);
+		break;
 
 		case INDEXING_XDS :
-		return run_xds(image, ipriv);
+		r = run_xds(image, ipriv);
+		break;
 
 		case INDEXING_DEBUG :
-		return debug_index(image);
+		r = debug_index(image);
+		break;
 
 		case INDEXING_FELIX :
-		return felix_index(image, ipriv);
+		r = felix_index(image, ipriv);
+		break;
 
 		default :
 		ERROR("Unrecognised indexing method: %i\n", indm);
-		break;
+		return 0;
 
 	}
 
-	return 0;
+	/* 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++;
+		}
+	}
+
+	remove_flagged_crystals(image);
+
+	if ( n_bad == r ) return 0;
+	return r;
 }