Clean up shadowed variables

9 files changed, 52 insertions, 54 deletions

diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index cdd4156b..5131fb20 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -982,7 +982,6 @@ UnitCell *load_cell_from_file(const char *filename)
 
 	do {
 
-		char line[1024];
 		int n1;
 		int i;
 		char **bits;
diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index a2b974a7..48fe4cfa 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -1122,10 +1122,10 @@ DataTemplate *data_template_new_from_string(const char *string_in)
 		/* Copy the next line from the big string */
 		const char *nl = strchr(string, '\n');
 		if ( nl != NULL ) {
-			size_t len = nl - string;
-			line = strndup(string, nl-string);
-			line[len] = '\0';
-			string += len+1;
+			size_t nlen = nl - string;
+			line = strndup(string, nlen);
+			line[nlen] = '\0';
+			string += nlen+1;
 		} else {
 			line = strdup(string);
 			done = 1;
@@ -1437,7 +1437,7 @@ DataTemplate *data_template_new_from_string(const char *string_in)
 
 	for ( rgci=0; rgci<n_rgc_definitions; rgci++ ) {
 
-		int rgi, n2;
+		int n2;
 		struct rg_collection *rgcollection = NULL;
 
 		rgcollection = find_or_add_rg_coll(dt, rgc_defl[rgci]->name);
diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c
index 494254cc..ec8fc36f 100644
--- a/libcrystfel/src/image-hdf5.c
+++ b/libcrystfel/src/image-hdf5.c
@@ -814,13 +814,13 @@ int image_hdf5_read_header_to_cache(struct image *image, const char *name)
 		} else if ( class == H5T_STRING ) {
 
 			htri_t v;
-			hid_t type;
+			hid_t stype;
 			char *val;
-			int r;
+			int rv;
 
-			type = H5Dget_type(dh);
-			v = H5Tis_variable_str(type);
-			H5Tclose(type);
+			stype = H5Dget_type(dh);
+			v = H5Tis_variable_str(stype);
+			H5Tclose(stype);
 
 			if ( v == 0 ) {
 				val = read_single_fixed_string(dh);
@@ -835,16 +835,16 @@ int image_hdf5_read_header_to_cache(struct image *image, const char *name)
 			if ( val != NULL ) {
 				image_cache_header_str(image, name, val);
 				free(val);
-				r = 0;
+				rv = 0;
 			} else {
 				ERROR("Failed to read string '%s'\n",
 				      subst_name);
-				r = 1;
+				rv = 1;
 			}
 
 			free(subst_name);
 			close_hdf5(fh);
-			return r;
+			return rv;
 
 		} else {
 			/* Should never be reached */
@@ -956,18 +956,18 @@ int image_hdf5_read_header_to_cache(struct image *image, const char *name)
 
 	} else if ( class == H5T_STRING ) {
 
-		hid_t type;
+		hid_t stype;
 
-		type = H5Dget_type(dh);
-		if ( H5Tis_variable_str(type) ) {
+		stype = H5Dget_type(dh);
+		if ( H5Tis_variable_str(stype) ) {
 
 			/* Vlen string from array */
 
-			herr_t r;
+			herr_t rv;
 			char *val;
 
-			r = H5Dread(dh, type, ms, sh, H5P_DEFAULT, &val);
-			if ( r < 0 ) {
+			rv = H5Dread(dh, stype, ms, sh, H5P_DEFAULT, &val);
+			if ( rv < 0 ) {
 				ERROR("Can't read HDF5 vlen string from array - %s\n",
 				      subst_name);
 				free(subst_name);
@@ -988,20 +988,20 @@ int image_hdf5_read_header_to_cache(struct image *image, const char *name)
 
 			/* Fixed-length string from array */
 
-			herr_t r;
+			herr_t rv;
 			char *val;
-			size_t size;
+			size_t ssize;
 
-			size = H5Tget_size(type);
-			val = malloc(size);
+			ssize = H5Tget_size(stype);
+			val = malloc(ssize);
 			if ( val == NULL ) {
 				close_hdf5(fh);
 				free(subst_name);
 				return 1;
 			}
-			r = H5Dread(dh, type, ms, sh, H5P_DEFAULT, val);
-			H5Tclose(type);
-			if ( r < 0 ) {
+			rv = H5Dread(dh, stype, ms, sh, H5P_DEFAULT, val);
+			H5Tclose(stype);
+			if ( rv < 0 ) {
 				ERROR("Couldn't read HDF5 fixed string from array - %s\n",
 				      subst_name);
 				close_hdf5(fh);
@@ -1009,7 +1009,7 @@ int image_hdf5_read_header_to_cache(struct image *image, const char *name)
 				return 1;
 			} else {
 
-				val[size] = '\0';
+				val[ssize] = '\0';
 				chomp(val);
 				image_cache_header_str(image, name, val);
 				free(val);
diff --git a/libcrystfel/src/indexers/dirax.c b/libcrystfel/src/indexers/dirax.c
index ef90a3f7..d1be9e7c 100644
--- a/libcrystfel/src/indexers/dirax.c
+++ b/libcrystfel/src/indexers/dirax.c
@@ -228,10 +228,10 @@ static void dirax_parseline(const char *line, struct image *image,
 	                               &d, &d, &d, &d, &d, &d, &di) == 9 ) {
 		if ( acl_nh > dirax->best_acl_nh ) {
 
-			int i, found = 0;
+			int i_acl, found = 0;
 
-			for ( i=0; i<dirax->n_acls_tried; i++ ) {
-				if ( dirax->acls_tried[i] == acl ) found = 1;
+			for ( i_acl=0; i_acl<dirax->n_acls_tried; i_acl++ ) {
+				if ( dirax->acls_tried[i_acl] == acl ) found = 1;
 			}
 
 			if ( !found ) {
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 72aa0bad..29598a01 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -1538,15 +1538,15 @@ static int find_seeds(struct TakeTwoCell *cell, struct taketwo_private *tp)
 
 			cell->seeds = tmp;
 
-			int i;
-			for ( i = 0; i < seed_num; i++)
+			int seed_i;
+			for ( seed_i = 0; seed_i < seed_num; seed_i++)
 			{
-				if (seeds[i].idx1 < 0 || seeds[i].idx2 < 0)
+				if (seeds[seed_i].idx1 < 0 || seeds[seed_i].idx2 < 0)
 				{
 					continue;
 				}
 
-				cell->seeds[cell->seed_count] = seeds[i];
+				cell->seeds[cell->seed_count] = seeds[seed_i];
 				cell->seed_count++;
 			}
 
diff --git a/libcrystfel/src/rational.c b/libcrystfel/src/rational.c
index 76aa7014..db02ee93 100644
--- a/libcrystfel/src/rational.c
+++ b/libcrystfel/src/rational.c
@@ -460,16 +460,16 @@ int transform_fractional_coords_rtnl(const RationalMatrix *P,
 			                rtnl_mtx_get(cm, h, k));
 
 			for ( j=0; j<cm->cols; j++ ) {
-				Rational t = rtnl_mtx_get(cm, i, j);
+				Rational tcol = rtnl_mtx_get(cm, i, j);
 				Rational p = rtnl_mul(dval, rtnl_mtx_get(cm, h, j));
-				t = rtnl_sub(t, p);
-				rtnl_mtx_set(cm, i, j, t);
+				tcol = rtnl_sub(tcol, p);
+				rtnl_mtx_set(cm, i, j, tcol);
 			}
 
 			/* Divide the right hand side as well */
-			Rational t = vec[i];
+			Rational trhs = vec[i];
 			Rational p = rtnl_mul(dval, vec[h]);
-			vec[i] = rtnl_sub(t, p);
+			vec[i] = rtnl_sub(trhs, p);
 		}
 
 		h++;
diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index 4a284c07..52cf5e61 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -411,7 +411,6 @@ static RefList *read_reflections_from_file(FILE *fh, char **sym)
 
 	/* We are now in the notes region */
 	do {
-		char line[1024];
 		rval = fgets(line, 1023, fh);
 		if ( rval == NULL ) continue;
 		chomp(line);
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 6c716fda..3dc8abcd 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -240,7 +240,7 @@ static RefList *read_stream_reflections_2_3(Stream *st)
 		char line[1024];
 		signed int h, k, l;
 		float intensity, sigma, fs, ss, pk, bg;
-		char pn[32];
+		char pname[32];
 		int r;
 
 		rval = fgets(line, 1023, st->fh);
@@ -252,7 +252,7 @@ static RefList *read_stream_reflections_2_3(Stream *st)
 
 		r = sscanf(line, "%i %i %i %f %f %f %f %f %f %s",
 		           &h, &k, &l, &intensity, &sigma, &pk, &bg,
-			   &fs, &ss, pn);
+			   &fs, &ss, pname);
 
 		if ( (r != 10) && (!first) ) {
 			reflist_free(out);
@@ -664,12 +664,12 @@ int stream_write_chunk(Stream *st, const struct image *i,
 
 	if ( i->detgeom != NULL ) {
 
-		int j;
+		int pn;
 		double tclen = 0.0;
 
-		for ( j=0; j<i->detgeom->n_panels; j++ ) {
-			tclen += i->detgeom->panels[j].cnz
-				* i->detgeom->panels[j].pixel_pitch;
+		for ( pn=0; pn<i->detgeom->n_panels; pn++ ) {
+			tclen += i->detgeom->panels[pn].cnz
+				* i->detgeom->panels[pn].pixel_pitch;
 		}
 		fprintf(st->fh, "average_camera_length = %f m\n",
 		        tclen / i->detgeom->n_panels);
@@ -814,8 +814,8 @@ static void read_crystal(Stream *st, struct image *image,
 		}
 
 		if ( strncmp(line, "num_saturated_reflections = ", 28) == 0 ) {
-			int n = atoi(line+28);
-			crystal_set_num_saturated_reflections(cr, n);
+			int nsat = atoi(line+28);
+			crystal_set_num_saturated_reflections(cr, nsat);
 		}
 
 		if ( sscanf(line, "diffraction_resolution_limit = %f nm^-1",
diff --git a/libcrystfel/src/thread-pool.c b/libcrystfel/src/thread-pool.c
index 7860d698..0951fcc6 100644
--- a/libcrystfel/src/thread-pool.c
+++ b/libcrystfel/src/thread-pool.c
@@ -86,11 +86,11 @@ static void *task_worker(void *pargsv)
 {
 	struct worker_args *w = pargsv;
 	struct task_queue *q = w->tq;
-	int *cookie;
+	int *cookie_slot;
 
-	cookie = malloc(sizeof(int));
-	*cookie = w->id;
-	pthread_setspecific(status_label_key, cookie);
+	cookie_slot = malloc(sizeof(int));
+	*cookie_slot = w->id;
+	pthread_setspecific(status_label_key, cookie_slot);
 
 	free(w);
 
@@ -129,7 +129,7 @@ static void *task_worker(void *pargsv)
 
 	} while ( 1 );
 
-	free(cookie);
+	free(cookie_slot);
 
 	return NULL;
 }