Convert indexamajig to new Stream API

5 files changed, 25 insertions, 17 deletions

diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h
index 9607708f..d90ae461 100644
--- a/libcrystfel/src/utils.h
+++ b/libcrystfel/src/utils.h
@@ -80,6 +80,8 @@ extern gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M, int *n_filt,
 extern size_t notrail(char *s);
 extern void chomp(char *s);
 
+#define CLEAR_BIT(val, bit) (((val) | (bit)) ^ (bit))
+
 /**
  * Controls the behaviour of \ref assplode.
  **/
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 83594585..8c40fa91 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -444,7 +444,7 @@ static int pump_chunk(FILE *fh, int ofd)
 				if ( chunk_started ) {
 					ERROR("EOF during chunk!\n");
 					lwrite(ofd, "Unfinished chunk!\n");
-					lwrite(ofd, CHUNK_END_MARKER"\n");
+					lwrite(ofd, STREAM_CHUNK_END_MARKER"\n");
 				} /* else normal end of output */
 				return 1;
 			}
@@ -457,7 +457,7 @@ static int pump_chunk(FILE *fh, int ofd)
 		if ( strcmp(line, "FLUSH\n") == 0 ) break;
 		lwrite(ofd, line);
 
-		if ( strcmp(line, CHUNK_END_MARKER"\n") == 0 ) break;
+		if ( strcmp(line, STREAM_CHUNK_END_MARKER"\n") == 0 ) break;
 
 	} while ( 1 );
 	return 0;
@@ -524,7 +524,7 @@ static void try_read(struct sandbox *sb, TimeAccounts *taccs)
 	struct timeval tv;
 	fd_set fds;
 	int fdmax;
-	const int ofd = get_stream_fd(sb->stream);
+	const int ofd = stream_get_fd(sb->stream);
 
 	time_accounts_set(taccs, TACC_SELECT);
 
@@ -659,9 +659,9 @@ static void start_worker_process(struct sandbox *sb, int slot)
 		 *               prefix
 		 */
 
-		st = open_stream_fd_for_write(stream_pipe[1]);
+		st = stream_open_fd_for_write(stream_pipe[1]);
 		r = run_work(sb->iargs, st, slot, tmp, sb);
-		close_stream(st);
+		stream_close(st);
 
 		free(tmp);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 2081580b..c074e801 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -544,11 +544,13 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		break;
 
 		case 603 :
-		args->iargs.stream_peaks = 0;
+		args->iargs.stream_flags = CLEAR_BIT(args->iargs.stream_flags,
+		                                     STREAM_PEAKS);
 		break;
 
 		case 604 :
-		args->iargs.stream_refls = 0;
+		args->iargs.stream_flags = CLEAR_BIT(args->iargs.stream_flags,
+		                                     STREAM_REFLECTIONS);
 		break;
 
 		case 605 :
@@ -643,8 +645,8 @@ 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_peaks = 1;
-	args.iargs.stream_refls = 1;
+	args.iargs.stream_flags = STREAM_PEAKS | STREAM_REFLECTIONS
+	                        | STREAM_CRYSTALS | STREAM_UNITCELL;
 	args.iargs.stream_nonhits = 1;
 	args.iargs.int_diag = INTDIAG_NONE;
 	args.iargs.min_peaks = 0;
@@ -996,13 +998,18 @@ int main(int argc, char *argv[])
 	free(rn);
 
 	/* Open output stream */
-	st = open_stream_for_write_4(args.outfile, args.geom_filename,
-	                             args.iargs.cell, argc, argv,
-	                             args.indm_str);
+	st = stream_open_for_write(args.outfile);
 	if ( st == NULL ) {
 		ERROR("Failed to open stream '%s'\n", args.outfile);
 		return 1;
 	}
+
+	/* Write audit info */
+	stream_write_commandline_args(st, argc, argv);
+	stream_write_geometry_file(st, args.geom_filename);
+	stream_write_target_cell(st, args.iargs.cell);
+	stream_write_indexing_methods(st, args.indm_str);
+
 	free(args.outfile);
 	free(args.indm_str);
 
@@ -1031,7 +1038,7 @@ int main(int argc, char *argv[])
 	free(args.temp_location);
 	free(tmpdir);
 	data_template_free(args.iargs.dtempl);
-	close_stream(st);
+	stream_close(st);
 	cleanup_indexing(args.iargs.ipriv);
 
 	return r;
diff --git a/src/process_image.c b/src/process_image.c
index 5cc89d1b..24a93ce1 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -407,8 +407,8 @@ streamwrite:
 	time_accounts_set(taccs, TACC_WRITESTREAM);
 	set_last_task(last_task, "stream write");
 	sb_shared->pings[cookie]++;
-	ret = write_chunk(st, image, iargs->dtempl,
-	                  iargs->stream_peaks, iargs->stream_refls);
+	ret = stream_write_chunk(st, image, iargs->dtempl,
+	                         iargs->stream_flags);
 	if ( ret != 0 ) {
 		ERROR("Error writing stream file.\n");
 	}
diff --git a/src/process_image.h b/src/process_image.h
index 354641c3..6e86f923 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -83,8 +83,7 @@ struct index_args
 	int integrate_saturated;
 	int use_saturated;
 	int no_revalidate;
-	int stream_peaks;
-	int stream_refls;
+	int stream_flags;
 	int stream_nonhits;
 	IntegrationMethod int_meth;
 	IntDiag int_diag;