Copy geometry file into stream

4 files changed, 72 insertions, 10 deletions

diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 13b9065d..fcb3bb21 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -875,18 +875,21 @@ Stream *open_stream_fd_for_write(int fd)
 
 
 /**
- * open_stream_for_write
+ * open_stream_for_write_2
  * @filename: Filename of new stream
  *
  * Creates a new stream with name @filename, and adds the stream format
- * and version headers.
+ * and version header, plus a verbatim copy of the geometry file
  *
  * You may want to follow this with a call to write_command() to record the
  * command line.
  *
  * Returns: a %Stream, or NULL on failure.
  */
-Stream *open_stream_for_write(const char *filename)
+Stream *open_stream_for_write_2(const char *filename,
+                                const char* geom_filename, int argc,
+                                char *argv[])
+
 {
 	Stream *st;
 
@@ -908,11 +911,36 @@ Stream *open_stream_for_write(const char *filename)
 	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);
+	}
+
 	return st;
 }
 
 
 /**
+ * open_stream_for_write
+ * @filename: Filename of new stream
+ *
+ * Creates a new stream with name @filename, and adds the stream format
+ * and version headers.
+ *
+ * You may want to follow this with a call to write_command() to record the
+ * command line.
+ *
+ * Returns: a %Stream, or NULL on failure.
+ */
+Stream *open_stream_for_write(const char *filename)
+{
+	return open_stream_for_write_2(filename, NULL, 0, NULL);
+}
+
+
+/**
  * get_stream_fd
  * @st: A %Stream
  *
@@ -985,6 +1013,37 @@ void write_command(Stream *st, int argc, char *argv[])
 
 
 /**
+ * write_geometry_file
+ * @st: A %Stream
+ * @geom_filename: geomtry file name
+ *
+ * Writes the content of the geometry file to @st. This should usually be
+ * called immediately after write_command().
+ */
+void write_geometry_file(Stream *st, const char *geom_filename) {
+
+	char line[2014];
+	FILE *geom_fh;
+	char *rval;
+
+	geom_fh = fopen(geom_filename, "r");
+	if ( geom_fh == NULL ) {
+		ERROR("Failed to read detector geometry from "
+		      "'%s'\n", geom_filename);
+		return;
+	}
+	fprintf(st->fh, GEOM_START_MARKER"\n");
+
+	do {
+		rval = fgets(line, 1023, geom_fh);
+		fprintf(st->fh, line);
+	} while ( rval != NULL );
+	fprintf(st->fh, GEOM_END_MARKER"\n");
+	fflush(st->fh);
+}
+
+
+/**
  * rewind_stream:
  * @st: A %Stream
  *
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index d7108439..1c2e57c6 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -38,6 +38,8 @@
 struct image;
 struct hdfile;
 
+#define GEOM_START_MARKER "----- Begin geometry file -----"
+#define GEOM_END_MARKER "----- End geometry file -----"
 #define CHUNK_START_MARKER "----- Begin chunk -----"
 #define CHUNK_END_MARKER "----- End chunk -----"
 #define PEAK_LIST_START_MARKER "Peaks from peak search"
@@ -79,6 +81,9 @@ extern "C" {
 
 extern Stream *open_stream_for_read(const char *filename);
 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_fd_for_write(int fd);
 extern int get_stream_fd(Stream *st);
 extern void close_stream(Stream *st);
@@ -89,7 +94,7 @@ extern void write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,
                         int include_peaks, int include_reflections);
 
 extern void write_command(Stream *st, int argc, char *argv[]);
-
+extern void write_geometry_file(Stream *st, const char *geom_filename);
 extern int rewind_stream(Stream *st);
 extern int is_stream(const char *filename);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index d75e24be..fcf97dd4 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -197,6 +197,7 @@ int main(int argc, char *argv[])
 	char *int_str = NULL;
 	char *tempdir = NULL;
 	char *int_diag = NULL;
+	char *geom_filename = NULL;
 
 	/* Defaults */
 	iargs.cell = NULL;
@@ -335,6 +336,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'g' :
+			geom_filename = optarg;
 			iargs.det = get_detector_geometry(optarg);
 			if ( iargs.det == NULL ) {
 				ERROR("Failed to read detector geometry from "
@@ -654,15 +656,13 @@ int main(int argc, char *argv[])
 
 	}
 
-	st = open_stream_for_write(outfile);
+	st = open_stream_for_write_2(outfile, geom_filename, argc, argv);
 	if ( st == NULL ) {
 		ERROR("Failed to open stream '%s'\n", outfile);
 		return 1;
 	}
 	free(outfile);
 
-	write_command(st, argc, argv);
-
 	/* Prepare the indexer */
 	if ( indm != NULL ) {
 		ipriv = prepare_indexing(indm, iargs.cell, iargs.det,
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 862eadef..a113532b 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -689,15 +689,13 @@ int main(int argc, char *argv[])
 		ERROR("You must give a filename for the output.\n");
 		return 1;
 	}
-	stream = open_stream_for_write(output_file);
+	stream = open_stream_for_write_2(output_file, geomfile, argc, argv);
 	if ( stream == NULL ) {
 		ERROR("Couldn't open output file '%s'\n", output_file);
 		return 1;
 	}
 	free(output_file);
 
-	write_command(stream, argc, argv);
-
 	image.det = det;
 	image.width = det->max_fs + 1;
 	image.height = det->max_ss + 1;