indexamajig: Write target unit cell into stream

5 files changed, 106 insertions, 1 deletions

diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 3b3c5fe3..69d4174a 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -1230,6 +1230,38 @@ static int get_angle_rad(char **bits, int nbits, double *pl)
 	return 0;
 }
 
+/**
+ * write_cell:
+ * @cell: a %UnitCell
+ * @fh: a file handle
+ *
+ * Writes @cell to @fh, in CrystFEL unit cell file format
+ *
+ */
+void write_cell(UnitCell *cell, FILE *fh)
+{
+	double a, b, c, al, be, ga;
+	LatticeType lt;
+
+	fprintf(fh, "CrystFEL unit cell file version 1.0\n\n");
+	lt = cell_get_lattice_type(cell);
+	fprintf(fh, "lattice_type = %s\n", str_lattice(lt));
+	if ( (lt == L_MONOCLINIC)
+	  || (lt == L_TETRAGONAL)
+	  || (lt == L_HEXAGONAL) )
+	{
+		fprintf(fh, "unique_axis = %c\n", cell_get_unique_axis(cell));
+	}
+	fprintf(fh, "centering = %c\n", cell_get_centering(cell));
+	cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
+	fprintf(fh, "a = %.2f A\n", a*1e10);
+	fprintf(fh, "b = %.2f A\n", b*1e10);
+	fprintf(fh, "c = %.2f A\n", c*1e10);
+	fprintf(fh, "al = %.2f deg\n", rad2deg(al));
+	fprintf(fh, "be = %.2f deg\n", rad2deg(be));
+	fprintf(fh, "ga = %.2f deg\n", rad2deg(ga));
+}
+
 
 /**
  * load_cell_from_file:
diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h
index 98bc667c..000c863a 100644
--- a/libcrystfel/src/cell-utils.h
+++ b/libcrystfel/src/cell-utils.h
@@ -57,6 +57,7 @@ extern UnitCell *match_cell_ab(UnitCell *cell, UnitCell *tempcell);
 
 extern UnitCell *load_cell_from_pdb(const char *filename);
 extern UnitCell *load_cell_from_file(const char *filename);
+extern void write_cell(UnitCell *cell, FILE *fh);
 
 extern int cell_is_sensible(UnitCell *cell);
 
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index c5ab6626..43fd273c 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1390,6 +1390,71 @@ Stream *open_stream_fd_for_write(int fd)
 }
 
 
+static void write_cell_to_stream(Stream *st, UnitCell *cell)
+{
+	fprintf(st->fh, CELL_START_MARKER"\n");
+	write_cell(cell, st->fh);
+	fprintf(st->fh, "; Please note: this is the target unit cell.\n");
+	fprintf(st->fh, "; The actual unit cells produced by indexing "
+	                "depend on many other factors.\n");
+	fprintf(st->fh, CELL_END_MARKER"\n");
+	fflush(st->fh);
+}
+
+
+/**
+ * open_stream_for_write_3
+ * @filename: Filename of new stream
+ * @geom_filename: The geometry filename to copy
+ * @cell: A %UnitCell to write into the stream
+ * @argc: The number of arguments to the program
+ * @argv: The arguments to the program
+ *
+ * Creates a new stream with name @filename, and adds the stream format
+ * and version header, plus a verbatim copy of the geometry file and the unit
+ * cell in CrystFEL format.
+ *
+ * Returns: a %Stream, or NULL on failure.
+ */
+Stream *open_stream_for_write_3(const char *filename,
+                                const char *geom_filename, UnitCell *cell,
+                                int argc, char *argv[])
+
+{
+	Stream *st;
+
+	st = malloc(sizeof(struct _stream));
+	if ( st == NULL ) return NULL;
+
+	st->fh = fopen(filename, "w");
+	if ( st->fh == NULL ) {
+		ERROR("Failed to open stream.\n");
+		free(st);
+		return NULL;
+	}
+
+	st->major_version = LATEST_MAJOR_VERSION;
+	st->minor_version = LATEST_MINOR_VERSION;
+
+	fprintf(st->fh, "CrystFEL stream format %i.%i\n",
+	        st->major_version, st->minor_version);
+	fprintf(st->fh, "Generated by CrystFEL "CRYSTFEL_VERSIONSTRING"\n");
+	fflush(st->fh);
+
+	if ( (argc > 0) && (argv != NULL) ) {
+		write_command(st, argc, argv);
+	}
+	if ( geom_filename != NULL ) {
+		write_geometry_file(st, geom_filename);
+	}
+	if ( cell != NULL ) {
+		write_cell_to_stream(st, cell);
+	}
+
+	return st;
+}
+
+
 /**
  * open_stream_for_write_2
  * @filename: Filename of new stream
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index a8cf4639..ff8628c0 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -39,9 +39,12 @@
 struct image;
 struct hdfile;
 struct event;
+#include "cell.h"
 
 #define GEOM_START_MARKER "----- Begin geometry file -----"
 #define GEOM_END_MARKER "----- End geometry file -----"
+#define CELL_START_MARKER "----- Begin unit cell -----"
+#define CELL_END_MARKER "----- End unit cell -----"
 #define CHUNK_START_MARKER "----- Begin chunk -----"
 #define CHUNK_END_MARKER "----- End chunk -----"
 #define PEAK_LIST_START_MARKER "Peaks from peak search"
@@ -92,6 +95,9 @@ extern Stream *open_stream_for_write(const char *filename);
 extern Stream *open_stream_for_write_2(const char *filename,
                                 const char* geom_filename, int argc,
                                 char *argv[]);
+extern Stream *open_stream_for_write_3(const char *filename,
+                                const char* geom_filename, UnitCell *cell,
+                                int argc, char *argv[]);
 extern Stream *open_stream_fd_for_write(int fd);
 extern int get_stream_fd(Stream *st);
 extern void close_stream(Stream *st);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 94ce6a42..a726c1b2 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -724,7 +724,8 @@ int main(int argc, char *argv[])
 	}
 
 	/* Open output stream */
-	st = open_stream_for_write_2(outfile, geom_filename, argc, argv);
+	st = open_stream_for_write_3(outfile, geom_filename, iargs.cell,
+	                             argc, argv);
 	if ( st == NULL ) {
 		ERROR("Failed to open stream '%s'\n", outfile);
 		return 1;