Push output stream mutex down, and improve output of --near-bragg and --dump-peaks

4 files changed, 37 insertions, 12 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 47d9a971..d61e6af5 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -189,6 +189,7 @@ static struct image *get_simage(struct image *template, int alternate)
 	image->lambda = ph_en_to_lambda(eV_to_J(1.8e3));
 	image->features = template->features;
 	image->filename = template->filename;
+	image->indexed_cell = template->indexed_cell;
 
 	return image;
 }
@@ -296,7 +297,7 @@ static void *process_image(void *pargsv)
 	search_peaks(&image);
 	if ( image_feature_count(image.features) < 5 ) goto done;
 
-	if ( config_dumpfound ) dump_peaks(&image);
+	if ( config_dumpfound ) dump_peaks(&image, pargs->output_mutex);
 
 	/* Not indexing nor writing xfel.drx?
 	 * Then there's nothing left to do. */
@@ -319,9 +320,8 @@ static void *process_image(void *pargsv)
 	if ( config_nearbragg ) {
 		/* Use original data (temporarily) */
 		simage->data = data_for_measurement;
-		pthread_mutex_lock(pargs->output_mutex);
-		output_intensities(simage, image.indexed_cell);
-		pthread_mutex_unlock(pargs->output_mutex);
+		output_intensities(simage, image.indexed_cell,
+		                   pargs->output_mutex);
 		simage->data = NULL;
 	}
 
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 7bf9143c..ab223288 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -308,7 +308,7 @@ int main(int argc, char *argv[])
 		record_image(&image, !config_nonoise);
 
 		if ( config_nearbragg ) {
-			output_intensities(&image, cell);
+			output_intensities(&image, cell, NULL);
 		}
 
 		if ( config_powder ) {
diff --git a/src/peaks.c b/src/peaks.c
index 104cf170..c0e9e270 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -20,6 +20,7 @@
 #include <string.h>
 #include <assert.h>
 #include <gsl/gsl_statistics_int.h>
+#include <pthread.h>
 
 #include "image.h"
 #include "utils.h"
@@ -329,11 +330,15 @@ void search_peaks(struct image *image)
 }
 
 
-void dump_peaks(struct image *image)
+void dump_peaks(struct image *image, pthread_mutex_t *mutex)
 {
 	int i;
 
-	printf("x/px\ty/px\t(1/d)/nm^-1\n");
+	/* Get exclusive access to the output stream if necessary */
+	if ( mutex != NULL ) pthread_mutex_lock(mutex);
+
+	printf("Peaks from peak search in %s\n", image->filename);
+	printf("  x/px     y/px   (1/d)/nm^-1    Intensity\n");
 
 	for ( i=0; i<image_feature_count(image->features); i++ ) {
 
@@ -346,18 +351,25 @@ void dump_peaks(struct image *image)
 		map_position(image, f->x, f->y, &rx, &ry, &rz);
 		q = modulus(rx, ry, rz);
 
-		printf("%7.3f\t%7.3f\t%7.3f\t%7.3f\n", f->x, f->y, q/1.0e9, 1.0);
+		printf("%8.3f %8.3f %8.3f    %12.3f\n",
+		       f->x, f->y, q/1.0e9, f->intensity);
 
 	}
+
+	printf("\n");
+
+	if ( mutex != NULL ) pthread_mutex_unlock(mutex);
 }
 
 
-void output_intensities(struct image *image, UnitCell *cell)
+void output_intensities(struct image *image, UnitCell *cell,
+                        pthread_mutex_t *mutex)
 {
 	int x, y;
 	double ax, ay, az;
 	double bx, by, bz;
 	double cx, cy, cz;
+	double a, b, c, al, be, ga;
 	struct reflhit hits[MAX_HITS];
 	int n_hits = 0;
 	int i;
@@ -422,11 +434,19 @@ void output_intensities(struct image *image, UnitCell *cell)
 
 	STATUS("Found %i reflections\n", n_hits);
 
+	/* Get exclusive access to the output stream if necessary */
+	if ( mutex != NULL ) pthread_mutex_lock(mutex);
+
 	/* Explicit printf() used here (not normally allowed) because
 	 * we really want to output to stdout */
-	printf("New pattern: %s %7.5f %7.5f %7.5f %7.5f\n", image->filename,
+	printf("Reflections from indexing in %s\n", image->filename);
+	printf("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(image->indexed_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",
+	       a*1.0e9, b*1.0e9, c*1.0e9,
+	       rad2deg(al), rad2deg(be), rad2deg(ga));
 	for ( i=0; i<n_hits; i++ ) {
 
 		float x, y, intensity;
@@ -456,4 +476,6 @@ void output_intensities(struct image *image, UnitCell *cell)
 
 	/* Blank line at end */
 	printf("\n");
+
+	if ( mutex != NULL ) pthread_mutex_unlock(mutex);
 }
diff --git a/src/peaks.h b/src/peaks.h
index 510282f8..a5c771b7 100644
--- a/src/peaks.h
+++ b/src/peaks.h
@@ -17,8 +17,11 @@
 #include <config.h>
 #endif
 
+#include <pthread.h>
+
 extern void search_peaks(struct image *image);
-extern void dump_peaks(struct image *image);
-extern void output_intensities(struct image *image, UnitCell *cell);
+extern void dump_peaks(struct image *image, pthread_mutex_t *mutex);
+extern void output_intensities(struct image *image, UnitCell *cell,
+                               pthread_mutex_t *mutex);
 
 #endif	/* PEAKS_H */