Fixes for indexing pipeline

8 files changed, 55 insertions, 55 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);
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 825f2d6a..d476c72d 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -305,6 +305,8 @@ static void process_image(const struct index_args *iargs,
 	/* Index the pattern */
 	index_pattern(&image, indm, iargs->ipriv);
 
+	pargs->n_crystals = image.n_crystals;
+
 	/* Default beam parameters */
 	image.div = image.beam->divergence;
 	image.bw = image.beam->bandwidth;
@@ -328,22 +330,20 @@ static void process_image(const struct index_args *iargs,
 
 		crystal_set_reflections(image.crystals[i], reflections);
 
-		if ( reflections != NULL ) {
-
-			integrate_reflections(&image,
-			                      iargs->config_closer,
-			                      iargs->config_bgsub,
-			                      iargs->min_int_snr,
-			                      iargs->ir_inn,
-			                      iargs->ir_mid,
-			                      iargs->ir_out,
-			                      iargs->integrate_saturated);
-		}
-
 	}
 
-	write_chunk(st, &image, hdfile, iargs->include_peaks,
-	            iargs->include_reflections);
+	/* Integrate all the crystals at once - need all the crystals so that
+	 * overlaps can be detected. */
+	integrate_reflections(&image, iargs->config_closer,
+	                              iargs->config_bgsub,
+	                              iargs->min_int_snr,
+	                              iargs->ir_inn,
+	                              iargs->ir_mid,
+	                              iargs->ir_out,
+	                              iargs->integrate_saturated);
+
+	write_chunk(st, &image, hdfile,
+	            iargs->include_peaks, iargs->include_reflections);
 
 	for ( i=0; i<image.n_crystals; i++ ) {
 		crystal_free(image.crystals[i]);
@@ -485,15 +485,17 @@ static int pump_chunk(FILE *fh, FILE *ofh)
 
 		}
 
-		if ( strcmp(line, "END\n") == 0 ) {
+		fprintf(ofh, "%s", line);
+
+		if ( strcmp(line, CHUNK_END_MARKER"\n") == 0 ) {
 			chunk_finished = 1;
-		} else {
+		}
+		if ( strcmp(line, CHUNK_START_MARKER"\n") == 0 ) {
 			chunk_started = 1;
-			fprintf(ofh, "%s", line);
 		}
 
-	} while ( !chunk_finished );
 
+	} while ( !chunk_finished );
 	return 0;
 }
 
@@ -711,7 +713,7 @@ static void handle_zombie(struct sandbox *sb)
 
 void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
                     int config_basename, FILE *fh, char *use_this_one_instead,
-                    Stream *st)
+                    FILE *ofh)
 {
 	int i;
 	int allDone;
@@ -738,6 +740,7 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
 
 	pthread_mutex_init(&sb->lock, NULL);
 
+	sb->ofh = ofh;
 	sb->stream_pipe_read = calloc(n_proc, sizeof(int));
 	sb->stream_pipe_write = calloc(n_proc, sizeof(int));
 	if ( sb->stream_pipe_read == NULL ) {
@@ -950,15 +953,12 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
 		tNow = get_monotonic_seconds();
 		if ( tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS ) {
 
-			STATUS("Total so far: %i images processed, "
+			STATUS("%i images processed so far, "
 			       "%i had crystals, %i crystals overall.  "
-			       "Since the last message: %i images processed,"
-			       "%i had crystals, %i crystals overall.\n",
+			       "%i images processed since the last message\n",
 			       sb->n_processed, sb->n_hadcrystals,
 			       sb->n_crystals,
-			       sb->n_processed - sb->n_processed_last_stats,
-			       sb->n_hadcrystals - sb->n_hadcrystals_last_stats,
-			       sb->n_crystals - sb->n_crystals_last_stats);
+			       sb->n_processed - sb->n_processed_last_stats);
 
 			sb->n_processed_last_stats = sb->n_processed;
 			sb->n_hadcrystals_last_stats = sb->n_hadcrystals;
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index 176bfde0..96311056 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -76,4 +76,4 @@ struct index_args
 
 extern void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
                            int config_basename, FILE *fh,
-                           char *use_this_one_instead, Stream *st);
+                           char *use_this_one_instead, FILE *stream);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 3076ea86..5d57d336 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -180,7 +180,7 @@ int main(int argc, char *argv[])
 	char *filename = NULL;
 	char *outfile = NULL;
 	FILE *fh;
-	Stream *st;
+	FILE *ofh;
 	char *rval = NULL;
 	int config_noindex = 0;
 	int config_cmfilter = 0;
@@ -264,6 +264,7 @@ int main(int argc, char *argv[])
 		{"peaks",              1, NULL,                2},
 		{"cell-reduction",     1, NULL,                3},
 		{"min-gradient",       1, NULL,                4},
+		{"record",             1, NULL,                5},
 		{"cpus",               1, NULL,                6},
 		{"cpugroup",           1, NULL,                7},
 		{"cpuoffset",          1, NULL,                8},
@@ -352,6 +353,7 @@ int main(int argc, char *argv[])
 
 			case 5 :
 			ERROR("The option '--record' is no longer used.\n");
+			/* FIXME: Translate to new style */
 			break;
 
 			case 6 :
@@ -526,8 +528,8 @@ int main(int argc, char *argv[])
 		cell = NULL;
 	}
 
-	st = open_stream_for_write(outfile);
-	if ( st == NULL ) {
+	ofh = fopen(outfile, "w");
+	if ( ofh == NULL ) {
 		ERROR("Failed to open stream '%s'\n", outfile);
 		return 1;
 	}
@@ -600,7 +602,7 @@ int main(int argc, char *argv[])
 	iargs.include_reflections = 1;  /* FIXME! */
 
 	create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
-	                    use_this_one_instead, st);
+	                    use_this_one_instead, ofh);
 
 	free(prefix);