diff options
| -rw-r--r-- | libcrystfel/src/stream.c | 65 | ||||
| -rw-r--r-- | libcrystfel/src/stream.h | 7 | ||||
| -rw-r--r-- | src/indexamajig.c | 6 | ||||
| -rw-r--r-- | src/partial_sim.c | 4 |
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; |