indexamajig: Take output stream as a command line parameter

src/indexamajig.c

@@ -44,7 +44,6 @@ struct process_args
 	/* Input */
 	char *filename;
 	int id;
-	pthread_mutex_t *output_mutex;  /* Protects stdout */
 	pthread_mutex_t *gpu_mutex;     /* Protects "gctx" */
 	UnitCell *cell;
 	int config_cmfilter;
@@ -76,6 +75,10 @@ struct process_args
 	int done;
 	int indexable;
 	int sane;
+
+	/* Output stream */
+	pthread_mutex_t *output_mutex;  /* Protects the output stream */
+	FILE *ofh;
 };
 
 
@@ -365,7 +368,7 @@ static void process_image(struct process_args *pargs)
 		output_intensities(&image, image.indexed_cell,
 		                   pargs->output_mutex, config_polar,
 		                   pargs->config_sa, pargs->config_closer,
-		                   0, 0.1);
+		                   pargs->ofh, 0, 0.1);
 	}
 
 	simage = get_simage(&image, config_alternate);
@@ -439,7 +442,9 @@ int main(int argc, char *argv[])
 	int c;
 	struct gpu_context *gctx = NULL;
 	char *filename = NULL;
+	char *outfile = NULL;
 	FILE *fh;
+	FILE *ofh;
 	char *rval = NULL;
 	int n_images;
 	int n_indexable;
@@ -486,6 +491,7 @@ int main(int argc, char *argv[])
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
 		{"input",              1, NULL,               'i'},
+		{"output",             1, NULL,               'o'},
 		{"gpu",                0, &config_gpu,         1},
 		{"no-index",           0, &config_noindex,     1},
 		{"dump-peaks",         0, &config_dumpfound,   1},
@@ -514,7 +520,7 @@ int main(int argc, char *argv[])
 	};
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:",
+	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:",
 	                        longopts, NULL)) != -1) {
 
 		switch (c) {
@@ -526,6 +532,10 @@ int main(int argc, char *argv[])
 			filename = strdup(optarg);
 			break;
 
+		case 'o' :
+			outfile = strdup(optarg);
+			break;
+
 		case 'z' :
 			indm_str = strdup(optarg);
 			break;
@@ -584,6 +594,20 @@ int main(int argc, char *argv[])
 	}
 	free(filename);
 
+	if ( outfile == NULL ) {
+		outfile = strdup("-");
+	}
+	if ( strcmp(outfile, "-") == 0 ) {
+		ofh = stdout;
+	} else {
+		ofh = fopen(outfile, "w");
+	}
+	if ( ofh == NULL ) {
+		ERROR("Failed to open output file '%s'\n", outfile);
+		return 1;
+	}
+	free(outfile);
+
 	if ( intfile != NULL ) {
 		ReflItemList *items;
 		items = read_reflections(intfile, intensities,
@@ -674,6 +698,7 @@ int main(int argc, char *argv[])
 	for ( i=0; i<nthreads; i++ ) {
 		worker_args[i] = malloc(sizeof(struct process_args));
 		worker_args[i]->filename = malloc(1024);
+		worker_args[i]->ofh = ofh;
 		worker_active[i] = 0;
 	}
 

src/pattern_sim.c

@@ -419,7 +419,8 @@ int main(int argc, char *argv[])
 
 		if ( config_nearbragg ) {
 			find_projected_peaks(&image, cell, 0, 0.1);
-			output_intensities(&image, cell, NULL, 0, 1, 0, 0, 0.1);
+			output_intensities(&image, cell, NULL, 0, 1, 0, stdout,
+			                   0, 0.1);
 		}
 
 		if ( powder_fn != NULL ) {

src/peaks.c

@@ -618,7 +618,8 @@ int peak_sanity_check(struct image *image, UnitCell *cell,
 
 void output_intensities(struct image *image, UnitCell *cell,
                         pthread_mutex_t *mutex, int polar, int sa,
-                        int use_closer, int circular_domain, double domain_r)
+                        int use_closer, FILE *ofh,
+                        int circular_domain, double domain_r)
 {
 	int i;
 	int n_found;
@@ -641,22 +642,22 @@ void output_intensities(struct image *image, UnitCell *cell,
 
 	/* Explicit printf() used here (not normally allowed) because
 	 * we really want to output to stdout */
-	printf("Reflections from indexing in %s\n", image->filename);
-	printf("Orientation (wxyz): %7.5f %7.5f %7.5f %7.5f\n",
+	fprintf(ofh, "Reflections from indexing in %s\n", image->filename);
+	fprintf(ofh, "Orientation (wxyz): %7.5f %7.5f %7.5f %7.5f\n",
 	       image->orientation.w, image->orientation.x,
 	       image->orientation.y, image->orientation.z);
 	cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
-	printf("Cell parameters %7.5f %7.5f %7.5f nm, %7.5f %7.5f %7.5f deg\n",
+	fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm, %7.5f %7.5f %7.5f deg\n",
 	       a*1.0e9, b*1.0e9, c*1.0e9,
 	       rad2deg(al), rad2deg(be), rad2deg(ga));
 	cell_get_reciprocal(cell, &asx, &asy, &asz,
 	                          &bsx, &bsy, &bsz,
 	                          &csx, &csy, &csz);
-	printf("astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+	fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
 	       asx/1e9, asy/1e9, asz/1e9);
-	printf("bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+	fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
 	       bsx/1e9, bsy/1e9, bsz/1e9);
-	printf("cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+	fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
 	       csx/1e9, csy/1e9, csz/1e9);
 
 	if ( image->f0_available ) {
@@ -747,7 +748,7 @@ void output_intensities(struct image *image, UnitCell *cell,
 		}
 
 		/* Write h,k,l, integrated intensity and centroid coordinates */
-		printf("%3i %3i %3i %6f (at %5.2f,%5.2f)\n",
+		fprintf(ofh, "%3i %3i %3i %6f (at %5.2f,%5.2f)\n",
 		       image->hits[i].h, image->hits[i].k, image->hits[i].l,
 		       intensity, x, y);
 
@@ -779,16 +780,16 @@ void output_intensities(struct image *image, UnitCell *cell,
 
 	}
 
-	printf("Peak statistics: %i peaks found by the peak search out of "
+	fprintf(ofh, "Peak statistics: %i peaks found by the peak search out of "
 	       "%i were close to indexed positions. "
 	       "%i indexed positions out of %i were close to detected peaks.\n",
 	       n_foundclose, n_found, n_indclose, image->n_hits);
-	printf("%i integrations using indexed locations were aborted because "
+	fprintf(ofh, "%i integrations using indexed locations were aborted because "
 	       "they hit one or more bad pixels.\n", n_veto);
-	printf("%i integrations using peak search locations were aborted "
+	fprintf(ofh, "%i integrations using peak search locations were aborted "
 	       "because they hit one or more bad pixels.\n", n_veto_second);
 	/* Blank line at end */
-	printf("\n");
+	fprintf(ofh, "\n");
 
 	if ( mutex != NULL ) pthread_mutex_unlock(mutex);
 }

src/peaks.h

@@ -23,7 +23,7 @@ extern void search_peaks(struct image *image, float threshold);
 extern void dump_peaks(struct image *image, pthread_mutex_t *mutex);
 extern void output_intensities(struct image *image, UnitCell *cell,
                                pthread_mutex_t *mutex, int polar, int sa,
-                               int use_closer, int circular_domain,
+                               int use_closer, FILE *ofh, int circular_domain,
                                double domain_r);
 extern int peak_sanity_check(struct image *image, UnitCell *cell,
                              int circular_domain, double domain_r);

src/reintegrate.c

@@ -135,7 +135,7 @@ static void process_image(struct process_args *pargs)
 		output_intensities(&image, pargs->cell,
 		                   pargs->output_mutex, pargs->config_polar,
 		                   pargs->config_sa, pargs->config_closer,
-		                   0, 0.1);
+		                   stdout, 0, 0.1);
 	}
 
 	free(image.data);