Merge branch 'master' of git.bitwiz.org.uk:crystfel

4 files changed, 25 insertions, 4 deletions

diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index 4272cbe6..a5fc7d26 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -45,6 +45,9 @@ struct hdfile *hdfile_open(const char *filename)
 	f = malloc(sizeof(struct hdfile));
 	if ( f == NULL ) return NULL;
 
+	/* Please stop spamming my terminal */
+	H5Eset_auto(H5E_DEFAULT, NULL, NULL);
+
 	f->fh = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
 	if ( f->fh < 0 ) {
 		ERROR("Couldn't open file: %s\n", filename);
@@ -239,6 +242,11 @@ static void debodge_saturation(struct hdfile *f, struct image *image)
 	dh = H5Dopen(f->fh, "/processing/hitfinder/peakinfo_saturated",
 	             H5P_DEFAULT);
 
+	if ( dh < 0 ) {
+		ERROR("Couldn't open saturation table.\n");
+		return;
+	}
+
 	sh = H5Dget_space(dh);
 	if ( sh < 0 ) {
 		H5Dclose(dh);
@@ -341,6 +349,7 @@ int hdf5_read(struct hdfile *f, struct image *image)
 	mask_dh = H5Dopen(f->fh, "/processing/hitfinder/masks", H5P_DEFAULT);
 	if ( mask_dh <= 0 ) {
 		ERROR("Couldn't open flags\n");
+		image->flags = NULL;
 	} else {
 		flags = malloc(sizeof(uint16_t)*f->nx*f->ny);
 		r = H5Dread(mask_dh, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL,
@@ -351,8 +360,8 @@ int hdf5_read(struct hdfile *f, struct image *image)
 		} else {
 			image->flags = flags;
 		}
+		H5Dclose(mask_dh);
 	}
-	H5Dclose(mask_dh);
 
 	/* Read wavelength from file */
 	image->lambda = get_wavelength(f);
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 130b6681..39931bdb 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -320,6 +320,8 @@ int main(int argc, char *argv[])
 	image.lambda = ph_en_to_lambda(eV_to_J(PHOTON_ENERGY)); /* Wavelength */
 	cell = load_cell_from_pdb(filename);
 	image.filename = NULL;
+	image.features = NULL;
+	image.flags = NULL;
 
 	#include "geometry-lcls.tmp"
 
@@ -382,6 +384,7 @@ int main(int argc, char *argv[])
 		record_image(&image, !config_nonoise);
 
 		if ( config_nearbragg ) {
+			find_projected_peaks(&image, cell);
 			output_intensities(&image, cell, NULL, 1);
 		}
 
diff --git a/src/peaks.c b/src/peaks.c
index c6b79d25..68482e94 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -167,6 +167,9 @@ static int integrate_peak(struct image *image, int xp, int yp,
 		}
 
 		p = find_panel(&image->det, x+xp, y+yp);
+		if ( p == NULL ) {
+			return 1;
+		}
 
 		/* Area of one pixel */
 		pix_area = pow(1.0/p->res, 2.0);
@@ -396,7 +399,7 @@ void dump_peaks(struct image *image, pthread_mutex_t *mutex)
 }
 
 
-static int find_projected_peaks(struct image *image, UnitCell *cell)
+int find_projected_peaks(struct image *image, UnitCell *cell)
 {
 	int x, y;
 	double ax, ay, az;
@@ -561,8 +564,13 @@ void output_intensities(struct image *image, UnitCell *cell,
 		struct imagefeature *f;
 
 		/* Wait.. is there a really close feature which was detected? */
-		f = image_feature_closest(image->features, hits[i].x, hits[i].y,
-		                          &d, &idx);
+		if ( image->features != NULL ) {
+			f = image_feature_closest(image->features,
+			                          hits[i].x, hits[i].y,
+			                          &d, &idx);
+		} else {
+			f = NULL;
+		}
 		if ( (f != NULL) && (d < PEAK_REALLY_CLOSE) ) {
 
 			int r;
diff --git a/src/peaks.h b/src/peaks.h
index 10cf5b0a..3335761c 100644
--- a/src/peaks.h
+++ b/src/peaks.h
@@ -24,5 +24,6 @@ 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 unpolar);
 extern int peak_sanity_check(struct image *image, UnitCell *cell);
+extern int find_projected_peaks(struct image *image, UnitCell *cell);
 
 #endif	/* PEAKS_H */