Read/write lattice type, centering and unique axis information from/to stream

3 files changed, 78 insertions, 14 deletions

diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index b1604815..8b881178 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -113,6 +113,21 @@ const char *str_lattice(LatticeType l)
 }
 
 
+LatticeType lattice_from_str(const char *s)
+{
+	if ( strcmp(s, "triclinic") == 0 ) return L_TRICLINIC;
+	if ( strcmp(s, "monoclinic") == 0 ) return L_MONOCLINIC;
+	if ( strcmp(s, "orthorhombic") == 0 ) return L_ORTHORHOMBIC;
+	if ( strcmp(s, "tetragonal") == 0 ) return L_TETRAGONAL;
+	if ( strcmp(s, "rhombohedral") == 0 ) return L_RHOMBOHEDRAL;
+	if ( strcmp(s, "hexagonal") == 0 ) return L_HEXAGONAL;
+	if ( strcmp(s, "cubic") == 0 ) return L_CUBIC;
+
+	ERROR("Unrecognised lattice type '%s'\n", s);
+	return L_TRICLINIC;
+}
+
+
 int right_handed(UnitCell *cell)
 {
 	double asx, asy, asz;
diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h
index 8eb08ca7..e816e2b2 100644
--- a/libcrystfel/src/cell-utils.h
+++ b/libcrystfel/src/cell-utils.h
@@ -62,6 +62,7 @@ extern int bravais_lattice(UnitCell *cell);
 extern int right_handed(UnitCell *cell);
 
 extern const char *str_lattice(LatticeType l);
+extern LatticeType lattice_from_str(const char *s);
 
 extern int forbidden_reflection(UnitCell *cell,
                                 signed int h, signed int k, signed int l);
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index c6d88629..03f969f8 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -43,6 +43,7 @@
 #include <fcntl.h>
 
 #include "cell.h"
+#include "cell-utils.h"
 #include "utils.h"
 #include "image.h"
 #include "stream.h"
@@ -159,6 +160,11 @@ static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
 	fprintf(st->fh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
 	        csx/1e9, csy/1e9, csz/1e9);
 
+	fprintf(st->fh, "lattice_type = %s\n",
+	        str_lattice(cell_get_lattice_type(cell)));
+	fprintf(st->fh, "centering = %c\n", cell_get_centering(cell));
+	fprintf(st->fh, "unique_axis = %c\n", cell_get_unique_axis(cell));
+
 	reflist = crystal_get_reflections(cr);
 	if ( reflist != NULL ) {
 
@@ -261,6 +267,12 @@ void read_crystal(Stream *st, struct image *image)
 	int have_as = 0;
 	int have_bs = 0;
 	int have_cs = 0;
+	int have_latt = 0;
+	int have_cen = 0;
+	int have_ua = 0;
+	char centering = 'P';
+	char unique_axis = '*';
+	LatticeType lattice_type = L_TRICLINIC;
 	Crystal *cr;
 	int n;
 	Crystal **crystals_new;
@@ -274,6 +286,7 @@ void read_crystal(Stream *st, struct image *image)
 	do {
 
 		float u, v, w;
+		char c;
 
 		rval = fgets(line, 1023, st->fh);
 
@@ -296,23 +309,31 @@ void read_crystal(Stream *st, struct image *image)
 			have_cs = 1;
 		}
 
-		if ( have_as && have_bs && have_cs ) {
-
-			UnitCell *cell;
-
-			cell = crystal_get_cell(cr);
-
-			if ( cell != NULL ) {
-				ERROR("Duplicate cell found in stream!\n");
-				ERROR("I'll use the most recent one.\n");
-				cell_free(cell);
+		if ( sscanf(line, "centering = %c", &c) == 1 ) {
+			if ( !have_cen ) {
+				centering = c;
+				have_cen = 1;
+			} else {
+				ERROR("Duplicate centering ignored.\n");
 			}
+		}
 
-			cell = cell_new_from_reciprocal_axes(as, bs, cs);
-			crystal_set_cell(cr, cell);
-
-			have_as = 0;  have_bs = 0;  have_cs = 0;
+		if ( sscanf(line, "unique_axis = %c", &c) == 1 ) {
+			if ( !have_ua ) {
+				unique_axis = c;
+				have_ua = 1;
+			} else {
+				ERROR("Duplicate unique axis ignored.\n");
+			}
+		}
 
+		if ( strncmp(line, "lattice_type = ", 15) == 0 ) {
+			if ( !have_latt ) {
+				lattice_type = lattice_from_str(line+15);
+				have_latt = 1;
+			} else {
+				ERROR("Duplicate lattice type ignored.\n");
+			}
 		}
 
 		if ( strncmp(line, "num_saturated_reflections = ", 28) == 0 ) {
@@ -339,6 +360,33 @@ void read_crystal(Stream *st, struct image *image)
 
 	} while ( 1 );
 
+	if ( have_as && have_bs && have_cs ) {
+
+		UnitCell *cell;
+
+		cell = crystal_get_cell(cr);
+
+		if ( cell != NULL ) {
+			ERROR("Duplicate cell found in stream!\n");
+			ERROR("I'll use the most recent one.\n");
+			cell_free(cell);
+		}
+
+		cell = cell_new_from_reciprocal_axes(as, bs, cs);
+
+		if ( have_cen && have_ua && have_latt ) {
+			cell_set_centering(cell, centering);
+			cell_set_unique_axis(cell, unique_axis);
+			cell_set_lattice_type(cell, lattice_type);
+		} /* else keep default triclinic P */
+
+		crystal_set_cell(cr, cell);
+
+		have_as = 0;  have_bs = 0;  have_cs = 0;
+		have_latt = 0;  have_ua = 0;  have_cen = 0;
+
+	}
+
 	/* Add crystal to the list for this image */
 	n = image->n_crystals+1;
 	crystals_new = realloc(image->crystals, n*sizeof(Crystal *));