Formatting

4 files changed, 62 insertions, 35 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 1e160f7d..f5f6bb57 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -496,7 +496,8 @@ void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev)
 
 
 			if (det->path_dim !=0 || det->dim_dim !=0 ){
-				p->clen = get_ev_based_value(f, p->clen_from, ev) * 1.0e-3;
+				p->clen = get_ev_based_value(f, p->clen_from,
+				                             ev) * 1.0e-3;
 			} else {
 				p->clen = get_value(f, p->clen_from) * 1.0e-3;
 			}
@@ -1031,6 +1032,7 @@ struct detector *get_detector_geometry(const char *filename,
 
 		n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE);
 		if ( n2 < 2 ) {
+
 			/* This was a top-level option, not handled above. */
 			parse_toplevel(det, beam, bits[0], bits[2]);
 			for ( i=0; i<n1; i++ ) free(bits[i]);
@@ -1134,8 +1136,8 @@ struct detector *get_detector_geometry(const char *filename,
 	}
 
 	if ( dim_reject ==  1) {
-		ERROR("All panels' data and mask entries must have the same number "\
-			"of placeholders\n");
+		ERROR("All panels' data and mask entries must have the same "
+		      "number of placeholders\n");
 		reject = 1;
 	}
 
@@ -1157,16 +1159,20 @@ struct detector *get_detector_geometry(const char *filename,
 
 		for ( di=0; di<det->panels[i].dim_structure->num_dims; di++ ) {
 
-			if ( det->panels[i].dim_structure->dims[di] == HYSL_UNDEFINED  ) {
+			if ( det->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_UNDEFINED  ) {
 				dim_dim_reject = 1;
 			}
-			if ( det->panels[i].dim_structure->dims[di] == HYSL_PLACEHOLDER  ) {
+			if ( det->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_PLACEHOLDER  ) {
 				panel_dim_dim += 1;
 			}
-			if ( det->panels[i].dim_structure->dims[di] == HYSL_SS  ) {
+			if ( det->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_SS  ) {
 				found_ss += 1;
 			}
-			if ( det->panels[i].dim_structure->dims[di] == HYSL_FS  ) {
+			if ( det->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_FS  ) {
 				found_fs += 1;
 			}
 
@@ -1183,7 +1189,8 @@ struct detector *get_detector_geometry(const char *filename,
 		}
 
 		if ( panel_dim_dim > 1 ) {
-			ERROR("Maximum one placeholder dim coordinate is allowed\n");
+			ERROR("Maximum one placeholder dim coordinate is "
+			      "allowed\n");
 			dim_dim_reject = 1;
 		}
 
@@ -1269,8 +1276,10 @@ struct detector *get_detector_geometry(const char *filename,
 		det->panels[i].orig_max_ss = det->panels[i].max_ss;
 		det->panels[i].orig_min_ss = det->panels[i].min_ss;
 
-		det->panels[i].w = det->panels[i].max_fs-det->panels[i].min_fs+1;
-		det->panels[i].h = det->panels[i].max_ss-det->panels[i].min_ss+1;
+		det->panels[i].w =
+		                 det->panels[i].max_fs-det->panels[i].min_fs+1;
+		det->panels[i].h =
+		                 det->panels[i].max_ss-det->panels[i].min_ss+1;
 
 		det->panels[i].min_fs = 0;
 		det->panels[i].max_fs = det->panels[i].w-1;
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 41fbc17c..e38ae67b 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -530,7 +530,8 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p,
 			fs = fs - p->orig_min_fs + p->min_fs;
 			ss = ss - p->orig_min_ss + p->min_ss;
 
-			image_add_feature(image->features, fs, ss, image, val, NULL);
+			image_add_feature(image->features, fs, ss, image, val,
+			                  NULL);
 
 		}
 
@@ -807,12 +808,13 @@ static void write_location(hid_t fh, struct image *image,
 		m_offset[1] = p.min_fs;
 		m_count[0] = p.max_ss - p.min_ss +1;
 		m_count[1] = p.max_fs - p.min_fs +1;
+
 		dimsm[0] = image->height;
 		dimsm[1] = image->width;
 		memspace = H5Screate_simple(2, dimsm, NULL);
+
 		r = H5Sselect_hyperslab(memspace, H5S_SELECT_SET,
 		                        m_offset, NULL, m_count, NULL);
-
 		r = H5Dwrite(dh, H5T_NATIVE_FLOAT, memspace,
 		             dh_dataspace, H5P_DEFAULT, image->data);
 		if ( r < 0 ) {
@@ -978,15 +980,18 @@ int hdf5_write_image(const char *filename, struct image *image, char *element)
 		write_location(fh, image, &locations[li]);
 	}
 
-	if ( image->beam->photon_energy_from == NULL ) {
+	if ( image->beam == NULL || image->beam->photon_energy_from == NULL ) {
 		ph_en_loc = "photon_energy_eV";
 	} else {
 		ph_en_loc = image->beam->photon_energy_from;
 	}
+
 	write_photon_energy(fh, ph_lambda_to_eV(image->lambda), ph_en_loc);
-	if ( image->spectrum_size > 0 ) {
+
+	if ( image->spectrum != NULL && image->spectrum_size > 0 ) {
+
 		write_spectrum(fh, image->spectrum, image->spectrum_size,
-		               image->nsamples);
+		              image->nsamples);
 	}
 
 	H5Fclose(fh);
@@ -994,8 +999,8 @@ int hdf5_write_image(const char *filename, struct image *image, char *element)
 	for ( li=0; li<num_locations; li ++ ) {
 		free(locations[li].panel_idxs);
 	}
-	free(locations);
 
+	free(locations);
 	return 0;
 }
 
@@ -2334,7 +2339,8 @@ struct event_list *fill_event_list(struct hdfile *hdfile, struct detector *det)
 
 				int fail_add;
 
-				fail_add = add_non_existing_event_to_event_list(master_el,
+				fail_add = add_non_existing_event_to_event_list(
+				                     master_el,
 				                     panel_ev_list->events[ei]);
 				if ( fail_add ) {
 
@@ -2380,19 +2386,23 @@ struct event_list *fill_event_list(struct hdfile *hdfile, struct detector *det)
 				int hsdi;
 				int panel_path_dim = 0;
 
-				full_panel_path = retrieve_full_path(master_el->events[evi],
-				                                     det->panels[pai].data);
+				full_panel_path = retrieve_full_path(
+				                  master_el->events[evi],
+				                  det->panels[pai].data);
 
-				dh = H5Dopen2(hdfile->fh, full_panel_path, H5P_DEFAULT);
+				dh = H5Dopen2(hdfile->fh, full_panel_path,
+				              H5P_DEFAULT);
 				sh = H5Dget_space(dh);
 				dims = H5Sget_simple_extent_ndims(sh);
 
 				size = malloc(dims*sizeof(hsize_t));
 				max_size = malloc(dims*sizeof(hsize_t));
 
-				dims = H5Sget_simple_extent_dims(sh, size, max_size);
+				dims = H5Sget_simple_extent_dims(sh, size,
+				                                 max_size);
 
-				for ( hsdi=0; hsdi<det->panels[pai].dim_structure->num_dims;
+				for ( hsdi=0;
+				      hsdi<det->panels[pai].dim_structure->num_dims;
 				      hsdi++ ) {
 					if (det->panels[pai].dim_structure->dims[hsdi] ==
 				    HYSL_PLACEHOLDER ) {
@@ -2408,8 +2418,8 @@ struct event_list *fill_event_list(struct hdfile *hdfile, struct detector *det)
 
 				} else if ( panel_path_dim != global_path_dim ) {
 
-					ERROR("Data blocks paths for panels must have the same "
-					      "number of placeholders");
+					ERROR("Data blocks paths for panels must "
+					      "have the same number of placeholders");
 					free(size);
 					free(max_size);
 					return NULL;
@@ -2424,7 +2434,7 @@ struct event_list *fill_event_list(struct hdfile *hdfile, struct detector *det)
 				mlwd_ev = copy_event(master_el->events[evi]);
 				push_dim_entry_to_event(mlwd_ev, mlwd);
 				append_event_to_event_list(master_el_with_dims,
-										mlwd_ev);
+				                           mlwd_ev);
 				free(mlwd_ev);
 			}
 
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 3cabef96..3dfccea3 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -121,7 +121,8 @@ struct imagefeature *image_feature_closest(ImageFeatureList *flist,
 		double ds;
 		struct panel *p2;
 
-		p2 = find_panel(det, flist->features[i].fs, flist->features[i].ss);
+		p2 = find_panel(det, flist->features[i].fs,
+		                flist->features[i].ss);
 
 		if ( p1 != p2 ) {
 			continue;
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 6d741d9d..17c0619a 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -59,7 +59,6 @@
 #define AT_LEAST_VERSION(st, a, b) ((st->major_version>=(a)) \
                                     && (st->minor_version>=(b)))
 
-
 struct _stream
 {
 	FILE *fh;
@@ -211,8 +210,8 @@ static int write_peaks(struct image *image, FILE *ofh)
 				return 1;
 			}
 
-			/* Convert coordinates to match arrangement of panels in HDF5
-			 * file */
+			/* Convert coordinates to match arrangement of panels in
+			 * HDF5 file */
 			write_fs = f->fs - p->min_fs + p->orig_min_fs;
 			write_ss = f->ss - p->min_ss + p->orig_min_ss;
 
@@ -588,7 +587,8 @@ static int write_stream_reflections_2_2(FILE *fh, RefList *list,
 
 			fprintf(fh, "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f"
 			            " %6.1f %6.1f\n",
-			        h, k, l, intensity, esd_i, pk, bg, write_fs, write_ss);
+			        h, k, l, intensity, esd_i, pk, bg, write_fs,
+			        write_ss);
 
 		} else {
 
@@ -735,14 +735,19 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
 
 			fprintf(st->fh, REFLECTION_START_MARKER"\n");
 			if ( AT_LEAST_VERSION(st, 2, 3) ) {
-				ret = write_stream_reflections_2_3(st->fh, reflist,
+				ret = write_stream_reflections_2_3(st->fh,
+				                                   reflist,
 				                                   image);
 			} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
-				ret = write_stream_reflections_2_2(st->fh, reflist, image);
+				ret = write_stream_reflections_2_2(st->fh,
+			                                           reflist,
+			                                           image);
 			} else {
 				/* This function writes like a normal reflection
 				 * list was written in stream 2.1 */
-				ret = write_stream_reflections_2_1(st->fh, reflist, image);
+				ret = write_stream_reflections_2_1(st->fh,
+				                                   reflist,
+				                                   image);
 			}
 			fprintf(st->fh, REFLECTION_END_MARKER"\n");
 
@@ -983,9 +988,11 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 				reflist = read_stream_reflections_2_3(st->fh,
                                                       image->det);
 			} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
-				reflist = read_stream_reflections_2_2(st->fh, image->det);
+				reflist = read_stream_reflections_2_2(st->fh,
+				          image->det);
 			} else {
-				reflist = read_stream_reflections_2_1(st->fh, image->det);
+				reflist = read_stream_reflections_2_1(st->fh,
+				          image->det);
 			}
 			if ( reflist == NULL ) {
 				ERROR("Failed while reading reflections\n");