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-rw-r--r--libcrystfel/src/utils.h2
-rw-r--r--src/im-sandbox.c10
-rw-r--r--src/indexamajig.c23
-rw-r--r--src/process_image.c4
-rw-r--r--src/process_image.h3
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;