Remove STREAM_UNITCELL and STREAM_CRYSTALS

These flags weren't orthogonal at all, which was turning some routines
into spaghetti-code.

It's still possible to avoid read/write of peak lists, reflection data
or image data.  But that's it.

11 files changed, 26 insertions, 58 deletions

diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 5b4b777b..2df1bb72 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -619,9 +619,6 @@ int stream_write_chunk(Stream *st, const struct image *i,
 	char *indexer;
 	int ret = 0;
 
-	if ( srf & STREAM_REFLECTIONS ) srf |= STREAM_CRYSTALS;
-	if ( srf & STREAM_UNITCELL ) srf |= STREAM_CRYSTALS;
-
 	fprintf(st->fh, STREAM_CHUNK_START_MARKER"\n");
 
 	fprintf(st->fh, "Image filename: %s\n", i->filename);
@@ -666,14 +663,12 @@ int stream_write_chunk(Stream *st, const struct image *i,
 		ret = write_peaks(i, st->dtempl, st->fh);
 	}
 
-	if ( srf & STREAM_CRYSTALS ) {
-		for ( j=0; j<i->n_crystals; j++ ) {
-			if ( crystal_get_user_flag(i->crystals[j]) ) {
-				continue;
-			}
-			ret = write_crystal(st, i->crystals[j],
-			                    srf & STREAM_REFLECTIONS);
+	for ( j=0; j<i->n_crystals; j++ ) {
+		if ( crystal_get_user_flag(i->crystals[j]) ) {
+			continue;
 		}
+		ret = write_crystal(st, i->crystals[j],
+		                    srf & STREAM_REFLECTIONS);
 	}
 
 	fprintf(st->fh, STREAM_CHUNK_END_MARKER"\n");
@@ -755,29 +750,25 @@ static void read_crystal(Stream *st, struct image *image,
 		if ( rval == NULL ) break;
 
 		chomp(line);
-		if ( (srf & STREAM_UNITCELL)
-		  && (sscanf(line, "astar = %f %f %f", &u, &v, &w) == 3) )
+		if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) == 3 )
 		{
 			as.u = u*1e9;  as.v = v*1e9;  as.w = w*1e9;
 			have_as = 1;
 		}
 
-		if ( (srf & STREAM_UNITCELL)
-		  && (sscanf(line, "bstar = %f %f %f", &u, &v, &w) == 3) )
+		if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) == 3 )
 		{
 			bs.u = u*1e9;  bs.v = v*1e9;  bs.w = w*1e9;
 			have_bs = 1;
 		}
 
-		if ( (srf & STREAM_UNITCELL)
-		  && (sscanf(line, "cstar = %f %f %f", &u, &v, &w) == 3) )
+		if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) == 3 )
 		{
 			cs.u = u*1e9;  cs.v = v*1e9;  cs.w = w*1e9;
 			have_cs = 1;
 		}
 
-		if ( (srf & STREAM_UNITCELL)
-		  && (sscanf(line, "centering = %c", &c) == 1) )
+		if ( sscanf(line, "centering = %c", &c) == 1 )
 		{
 			if ( !have_cen ) {
 				centering = c;
@@ -788,8 +779,7 @@ static void read_crystal(Stream *st, struct image *image,
 			}
 		}
 
-		if ( (srf & STREAM_UNITCELL)
-		  && (sscanf(line, "unique_axis = %c", &c) == 1) )
+		if ( sscanf(line, "unique_axis = %c", &c) == 1 )
 		{
 			if ( !have_ua ) {
 				unique_axis = c;
@@ -800,8 +790,7 @@ static void read_crystal(Stream *st, struct image *image,
 			}
 		}
 
-		if ( (srf & STREAM_UNITCELL)
-		  && (strncmp(line, "lattice_type = ", 15) == 0) )
+		if ( strncmp(line, "lattice_type = ", 15) == 0 )
 		{
 			if ( !have_latt ) {
 				lattice_type = lattice_from_str(line+15);
@@ -926,10 +915,6 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
 	image = image_new();
 	if ( image == NULL ) return NULL;
 
-	if ( (srf & STREAM_REFLECTIONS) || (srf & STREAM_UNITCELL) ) {
-		srf |= STREAM_CRYSTALS;
-	}
-
 	do {
 		int ser;
 		float div, bw;
@@ -997,8 +982,7 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
 
 		}
 
-		if ( (srf & STREAM_CRYSTALS)
-		  && (strcmp(line, STREAM_CRYSTAL_START_MARKER) == 0) ) {
+		if ( strcmp(line, STREAM_CRYSTAL_START_MARKER) == 0 ) {
 			read_crystal(st, image, srf);
 		}
 
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index 9e92b35a..7bb1b6ab 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -61,26 +61,20 @@ typedef struct _stream Stream;
 
 /**
  * A bitfield of things that can be read from or written to a stream.
- * Use this (and \ref read_chunk) to read the stream faster if you
- * don't need the entire contents of the stream.
+ * Use this together with stream_{read,write}_chunk to read/write the
+ * stream faster if you don't need all the information.
  *
- * Using either of \p STREAM_REFLECTIONS or * \p STREAM_UNITCELL
- * implies \p STREAM_CRYSTALS.
+ * General information about crystals (including unit cell parameters)
+ * is always read and written.
  **/
 typedef enum {
 
-	/** Read the unit cell */
-	STREAM_UNITCELL = 1,
-
 	/** Read the integrated reflections */
 	STREAM_REFLECTIONS = 2,
 
 	/** Read the peak search results */
 	STREAM_PEAKS = 4,
 
-	/** Read the general information about crystals */
-	STREAM_CRYSTALS = 8,
-
 	/** Read the image data */
 	STREAM_IMAGE_DATA = 16,
 
diff --git a/src/ambigator.c b/src/ambigator.c
index c3afd6c1..c14b1051 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -1259,8 +1259,7 @@ int main(int argc, char *argv[])
 		struct image *image;
 		int i;
 
-		image = stream_read_chunk(st, STREAM_UNITCELL
-		                          | STREAM_REFLECTIONS);
+		image = stream_read_chunk(st, STREAM_REFLECTIONS);
 		if ( image == NULL ) break;
 
 		image_feature_list_free(image->features);
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index 84a8aa16..9d4cdeec 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -2002,7 +2002,7 @@ int main(int argc, char *argv[])
 		struct image *image;
 		int i;
 
-		image = stream_read_chunk(st, STREAM_UNITCELL);
+		image = stream_read_chunk(st, 0);
 		if ( image == NULL ) break;
 
 		for ( i=0; i<image->n_crystals; i++ ) {
diff --git a/src/crystfel_gui.c b/src/crystfel_gui.c
index 7f4f29f0..3d07f35b 100644
--- a/src/crystfel_gui.c
+++ b/src/crystfel_gui.c
@@ -145,10 +145,8 @@ static void update_imageview(struct crystfelproject *proj)
 		}
 
 		image = stream_read_chunk(proj->stream,
-		                          STREAM_UNITCELL
-		                        | STREAM_REFLECTIONS
+		                          STREAM_REFLECTIONS
 		                        | STREAM_PEAKS
-		                        | STREAM_CRYSTALS
 		                        | STREAM_IMAGE_DATA);
 
 		if ( image == NULL ) {
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 15315952..774a7ffc 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -650,8 +650,7 @@ int main(int argc, char *argv[])
 	args.iargs.ir_out = -1.0;
 	args.iargs.use_saturated = 1;
 	args.iargs.no_revalidate = 0;
-	args.iargs.stream_flags = STREAM_PEAKS | STREAM_REFLECTIONS
-	                        | STREAM_CRYSTALS | STREAM_UNITCELL;
+	args.iargs.stream_flags = STREAM_PEAKS | STREAM_REFLECTIONS;
 	args.iargs.stream_nonhits = 1;
 	args.iargs.int_diag = INTDIAG_NONE;
 	args.iargs.min_peaks = 0;
diff --git a/src/partial_sim.c b/src/partial_sim.c
index a0f60e1e..85222dd2 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -346,7 +346,7 @@ static void *create_job(void *vqargs)
 		struct image *image;
 
 		image = stream_read_chunk(qargs->template_stream,
-		                          STREAM_UNITCELL | STREAM_REFLECTIONS);
+		                          STREAM_REFLECTIONS);
 		if ( image == NULL ) {
 			ERROR("Failed to read template chunk!\n");
 			return NULL;
@@ -473,9 +473,7 @@ static void finalise_job(void *vqargs, void *vwargs)
 	int ret;
 
 	ret = stream_write_chunk(qargs->stream, wargs->image,
-	                         STREAM_UNITCELL
-	                                      | STREAM_REFLECTIONS
-	                                      | STREAM_CRYSTALS);
+	                         STREAM_REFLECTIONS);
 	if ( ret != 0 ) {
 		ERROR("WARNING: error writing stream file.\n");
 	}
diff --git a/src/partialator.c b/src/partialator.c
index 1a28e3f3..40c7c4eb 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1405,8 +1405,7 @@ int main(int argc, char *argv[])
 		RefList *as;
 		int i;
 
-		image = stream_read_chunk(st, STREAM_REFLECTIONS
-		                                    | STREAM_UNITCELL);
+		image = stream_read_chunk(st, STREAM_REFLECTIONS);
 		if ( image == NULL ) break;
 
 		if ( isnan(image->div) || isnan(image->bw) ) {
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index b83677b7..b6988dea 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -1049,8 +1049,7 @@ int main(int argc, char *argv[])
 			Crystal *cr;
 
 			/* Get data from next chunk */
-			templ_image = stream_read_chunk(st,
-			                                STREAM_CRYSTALS);
+			templ_image = stream_read_chunk(st, 0);
 			if ( templ_image == NULL ) break;
 			if ( templ_image->n_crystals == 0 ) continue;
 
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 812903a2..440ad3ee 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -432,8 +432,7 @@ static int merge_all(Stream *st,
 
 		/* Get data from next chunk */
 		image = stream_read_chunk(st,
-		                          STREAM_REFLECTIONS
-		                        | STREAM_UNITCELL);
+		                          STREAM_REFLECTIONS);
 		if ( image == NULL ) break;
 
 		n_images++;
diff --git a/src/whirligig.c b/src/whirligig.c
index 0d5a2f0d..cac51902 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -720,8 +720,7 @@ int main(int argc, char *argv[])
 
 		struct image *image;
 
-		image = stream_read_chunk(st, STREAM_REFLECTIONS
-		                                  | STREAM_UNITCELL);
+		image = stream_read_chunk(st, STREAM_REFLECTIONS);
 
 		if ( image == NULL ) break;