Fixes for indexing pipeline

5 files changed, 23 insertions, 25 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 821be39a..cd6628e9 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -68,7 +68,6 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 	IndexingPrivate **iprivs;
 
 	while ( indm[nm] != INDEXING_NONE ) nm++;
-	STATUS("Preparing %i indexing method%s.\n", nm, maybes(nm));
 	iprivs = malloc((nm+1) * sizeof(IndexingPrivate *));
 
 	for ( n=0; n<nm; n++ ) {
@@ -76,12 +75,13 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 		switch ( indm[n] & INDEXING_METHOD_MASK ) {
 
 			case INDEXING_DIRAX :
-			iprivs[n] = dirax_prepare(indm[nm], cell, filename, det,
+			iprivs[n] = dirax_prepare(indm[n], cell, filename, det,
 			                          beam, ltl);
 			break;
 
 			case INDEXING_MOSFLM :
-			iprivs[n] = NULL;
+			iprivs[n] = mosflm_prepare(indm[n], cell, filename, det,
+			                          beam, ltl);
 			break;
 
 			case INDEXING_REAX :
diff --git a/libcrystfel/src/mosflm.h b/libcrystfel/src/mosflm.h
index 1d296cb7..65aeb631 100644
--- a/libcrystfel/src/mosflm.h
+++ b/libcrystfel/src/mosflm.h
@@ -40,5 +40,9 @@
 
 extern int run_mosflm(struct image *image, IndexingPrivate *ipriv);
 
+extern IndexingPrivate *mosflm_prepare(IndexingMethod indm, UnitCell *cell,
+                                       const char *filename,
+                                       struct detector *det,
+                                       struct beam_params *beam, float *ltl);
 
 #endif	/* MOSFLM_H */
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 08595ef5..54ba6468 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -148,7 +148,7 @@ static int cull_peaks(struct image *image)
 
 
 static void add_crystal_to_mask(struct image *image, struct panel *p,
-                                double ir_out, double ir_inn, int w, int h,
+                                double ir_inn, int w, int h,
                                 int *mask, Crystal *cr)
 {
 	Reflection *refl;
@@ -200,8 +200,7 @@ static void add_crystal_to_mask(struct image *image, struct panel *p,
 
 
 /* cfs, css relative to panel origin */
-static int *make_BgMask(struct image *image, struct panel *p,
-                        double ir_out, double ir_inn)
+static int *make_BgMask(struct image *image, struct panel *p, double ir_inn)
 {
 	int *mask;
 	int w, h;
@@ -215,7 +214,7 @@ static int *make_BgMask(struct image *image, struct panel *p,
 	if ( image->crystals == NULL ) return mask;
 
 	for ( i=0; i<image->n_crystals; i++ ) {
-		add_crystal_to_mask(image, p, ir_inn, ir_out,
+		add_crystal_to_mask(image, p, ir_inn,
 		                    w, h, mask, image->crystals[i]);
 	}
 
@@ -860,8 +859,7 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
 	}
 	for ( i=0; i<image->det->n_panels; i++ ) {
 		int *mask;
-		mask = make_BgMask(image, &image->det->panels[i],
-		                   ir_out, ir_inn);
+		mask = make_BgMask(image, &image->det->panels[i], ir_inn);
 		if ( mask == NULL ) {
 			ERROR("Couldn't create background mask.\n");
 			return;
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 113dc359..fbcbaf2e 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -52,16 +52,6 @@
 #define LATEST_MAJOR_VERSION (2)
 #define LATEST_MINOR_VERSION (1)
 
-#define CHUNK_START_MARKER "----- Begin chunk -----"
-#define CHUNK_END_MARKER "----- End chunk -----"
-#define PEAK_LIST_START_MARKER "Peaks from peak search"
-#define PEAK_LIST_END_MARKER "End of peak list"
-#define CRYSTAL_START_MARKER "--- Begin crystal"
-#define CRYSTAL_END_MARKER "--- End crystal"
-#define REFLECTION_START_MARKER "Reflections measured after indexing"
-/* REFLECTION_END_MARKER is over in reflist-utils.h because it is also
- * used to terminate a standalone list of reflections */
-
 
 struct _stream
 {
@@ -184,8 +174,6 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
 
 	if ( include_reflections ) {
 
-		fprintf(st->fh, "\n");
-
 		if ( reflist != NULL ) {
 
 			fprintf(st->fh, REFLECTION_START_MARKER"\n");
@@ -199,7 +187,7 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
 		}
 	}
 
-	fprintf(st->fh, CRYSTAL_START_MARKER"\n\n");
+	fprintf(st->fh, CRYSTAL_END_MARKER"\n");
 }
 
 
@@ -226,19 +214,17 @@ void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
 	copy_hdf5_fields(hdfile, i->copyme, st->fh);
 
 	if ( include_peaks ) {
-		fprintf(st->fh, "\n");
 		write_peaks(i, st->fh);
 	}
 
 	fprintf(st->fh, "photon_energy_eV = %f\n",
 	        J_to_eV(ph_lambda_to_en(i->lambda)));
 
-	fprintf(st->fh, "\n");
 	for ( j=0; j<i->n_crystals; j++ ) {
 		write_crystal(st, i->crystals[j], include_reflections);
 	}
 
-	fprintf(st->fh, CHUNK_END_MARKER"\n\n");
+	fprintf(st->fh, CHUNK_END_MARKER"\n");
 
 	fflush(st->fh);
 }
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index 4d561cd2..cdce0ea2 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -38,6 +38,16 @@
 struct image;
 struct hdfile;
 
+#define CHUNK_START_MARKER "----- Begin chunk -----"
+#define CHUNK_END_MARKER "----- End chunk -----"
+#define PEAK_LIST_START_MARKER "Peaks from peak search"
+#define PEAK_LIST_END_MARKER "End of peak list"
+#define CRYSTAL_START_MARKER "--- Begin crystal"
+#define CRYSTAL_END_MARKER "--- End crystal"
+#define REFLECTION_START_MARKER "Reflections measured after indexing"
+/* REFLECTION_END_MARKER is over in reflist-utils.h because it is also
+ * used to terminate a standalone list of reflections */
+
 typedef struct _stream Stream;
 
 extern Stream *open_stream_for_read(const char *filename);