Indexing pipeline - "done"!

4 files changed, 26 insertions, 7 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 2370e26e..821be39a 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -241,7 +241,7 @@ static IndexingMethod set_axes(IndexingMethod a)
 }
 
 
-IndexingMethod *build_indexer_list(const char *str, int *need_cell)
+IndexingMethod *build_indexer_list(const char *str)
 {
 	int n, i;
 	char **methods;
@@ -249,9 +249,6 @@ IndexingMethod *build_indexer_list(const char *str, int *need_cell)
 	int tmp;
 	int nmeth = 0;
 
-	if ( need_cell == NULL ) need_cell = &tmp;
-	*need_cell = 0;
-
 	n = assplode(str, ",-", &methods, ASSPLODE_NONE);
 	list = malloc((n+1)*sizeof(IndexingMethod));
 
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index e0dcb8e0..093e4ad6 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -82,7 +82,7 @@ typedef enum {
  **/
 typedef void *IndexingPrivate;
 
-extern IndexingMethod *build_indexer_list(const char *str, int *need_cell);
+extern IndexingMethod *build_indexer_list(const char *str);
 
 extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
                                           const char *filename,
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 31fb8527..113dc359 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -38,6 +38,9 @@
 #include <stdio.h>
 #include <string.h>
 #include <assert.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
 
 #include "cell.h"
 #include "utils.h"
@@ -236,6 +239,8 @@ void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
 	}
 
 	fprintf(st->fh, CHUNK_END_MARKER"\n\n");
+
+	fflush(st->fh);
 }
 
 
@@ -497,14 +502,14 @@ Stream *open_stream_for_read(const char *filename)
 }
 
 
-Stream *open_stream_for_write(const char *filename)
+Stream *open_stream_fd_for_write(int fd)
 {
 	Stream *st;
 
 	st = malloc(sizeof(struct _stream));
 	if ( st == NULL ) return NULL;
 
-	st->fh = fopen(filename, "w");
+	st->fh = fdopen(fd, "w");
 	if ( st->fh == NULL ) {
 		free(st);
 		return NULL;
@@ -520,6 +525,21 @@ Stream *open_stream_for_write(const char *filename)
 }
 
 
+
+Stream *open_stream_for_write(const char *filename)
+{
+	int fd;
+
+	fd = open(filename, O_CREAT | O_TRUNC | O_WRONLY, S_IRUSR | S_IWUSR);
+	if ( fd == -1 ) {
+		ERROR("Failed to open stream.\n");
+		return NULL;
+	}
+
+	return open_stream_fd_for_write(fd);
+}
+
+
 void close_stream(Stream *st)
 {
 	fclose(st->fh);
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index 9340ca0d..4d561cd2 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -42,6 +42,8 @@ typedef struct _stream Stream;
 
 extern Stream *open_stream_for_read(const char *filename);
 extern Stream *open_stream_for_write(const char *filename);
+extern Stream *open_stream_fd_for_write(int fd);
+
 extern void close_stream(Stream *st);
 
 extern void write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,