From 13d65b9785d1557e29f5f06871d01bad8e76e44c Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 21 Jul 2021 15:22:12 +0200
Subject: Clean up shadowed variables

---
 libcrystfel/src/cell-utils.c       |  1 -
 libcrystfel/src/datatemplate.c     | 10 ++++-----
 libcrystfel/src/image-hdf5.c       | 44 +++++++++++++++++++-------------------
 libcrystfel/src/indexers/dirax.c   |  6 +++---
 libcrystfel/src/indexers/taketwo.c |  8 +++----
 libcrystfel/src/rational.c         | 10 ++++-----
 libcrystfel/src/reflist-utils.c    |  1 -
 libcrystfel/src/stream.c           | 16 +++++++-------
 libcrystfel/src/thread-pool.c      | 10 ++++-----
 src/ambigator.c                    | 27 ++++++++++++-----------
 src/cell_tool.c                    | 22 +++++++++----------
 src/crystfel_gui.c                 | 18 ++++++++--------
 src/diffraction-gpu.c              | 13 +++++++----
 src/gui_backend_slurm.c            |  6 +++---
 src/gui_project.c                  | 42 ++++++++++++++++++------------------
 src/partialator.c                  | 37 ++++++++++++++++----------------
 src/pattern_sim.c                  | 26 +++++++++++-----------
 src/process_hkl.c                  | 14 ++++++------
 src/render_hkl.c                   |  3 +--
 src/whirligig.c                    | 26 ++++++++++++----------
 20 files changed, 175 insertions(+), 165 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;
 }
diff --git a/src/ambigator.c b/src/ambigator.c
index 02252cd7..a7ec0eae 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -1056,7 +1056,7 @@ int main(int argc, char *argv[])
 	int n_dif;
 	struct flist **crystals;
 	Stream *st;
-	int i;
+	int j;
 	int *assignments;
 	int *orig_assignments;
 	gsl_rng *rng;
@@ -1362,6 +1362,7 @@ int main(int argc, char *argv[])
 	if ( start_ass_fn != NULL ) {
 
 		FILE *fh;
+		int i;
 		fh = fopen(start_ass_fn, "r");
 		if ( fh == NULL ) {
 			ERROR("Failed to open '%s'\n", start_ass_fn);
@@ -1387,13 +1388,14 @@ int main(int argc, char *argv[])
 		free(start_ass_fn);
 
 	} else {
+		int i;
 		for ( i=0; i<n_crystals; i++ ) {
 			assignments[i] = (random_flat(rng, 1.0) > 0.5);
 		}
 	}
 
-	for ( i=0; i<n_crystals; i++ ) {
-		orig_assignments[i] = assignments[i];
+	for ( j=0; j<n_crystals; j++ ) {
+		orig_assignments[j] = assignments[j];
 	}
 
 	if ( fg_graph_fn != NULL ) {
@@ -1415,16 +1417,16 @@ int main(int argc, char *argv[])
 	}
 	STATUS("Mean number of correlations per crystal: %.1f\n", mean_nac);
 
-	for ( i=0; i<n_crystals; i++ ) {
-		free(crystals[i]->s);
-		free(crystals[i]->i);
-		free(crystals[i]->s_reidx);
-		free(crystals[i]->i_reidx);
-		free(crystals[i]);
+	for ( j=0; j<n_crystals; j++ ) {
+		free(crystals[j]->s);
+		free(crystals[j]->i);
+		free(crystals[j]->s_reidx);
+		free(crystals[j]->i_reidx);
+		free(crystals[j]);
 	}
 	free(crystals);
 
-	for ( i=0; i<n_iter; i++ ) {
+	for ( j=0; j<n_iter; j++ ) {
 		detwin(ccs, n_crystals, assignments, fgfh, crystals);
 	}
 
@@ -1442,6 +1444,7 @@ int main(int argc, char *argv[])
 		if ( fh == NULL ) {
 			ERROR("Failed to open '%s'\n", end_ass_fn);
 		} else {
+			int i;
 			for ( i=0; i<n_crystals; i++ ) {
 				fprintf(fh, "%i\n", assignments[i]);
 			}
@@ -1450,8 +1453,8 @@ int main(int argc, char *argv[])
 	}
 
 	n_dif = 0;
-	for ( i=0; i<n_crystals; i++ ) {
-		if ( orig_assignments[i] != assignments[i] ) n_dif++;
+	for ( j=0; j<n_crystals; j++ ) {
+		if ( orig_assignments[j] != assignments[j] ) n_dif++;
 	}
 	STATUS("%i assignments are different from their starting values.\n",
 	       n_dif);
diff --git a/src/cell_tool.c b/src/cell_tool.c
index 8ed674f9..dbd3544c 100644
--- a/src/cell_tool.c
+++ b/src/cell_tool.c
@@ -191,7 +191,7 @@ static int all_rings(UnitCell *cell, SymOpList *sym, double mres)
 	RefList *list;
 	int i, n;
 	RefListIterator *iter;
-	Reflection *refl;
+	Reflection *ring;
 	struct sortmerefl *sortus;
 
 	cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
@@ -235,19 +235,19 @@ static int all_rings(UnitCell *cell, SymOpList *sym, double mres)
 	sortus = malloc(n*sizeof(struct sortmerefl));
 
 	i = 0;
-	for ( refl = first_refl(list, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) )
+	for ( ring = first_refl(list, &iter);
+	      ring != NULL;
+	      ring = next_refl(ring, iter) )
 	{
-		signed int h, k, l;
+		signed int rh, rk, rl;
 
-		get_indices(refl, &h, &k, &l);
+		get_indices(ring, &rh, &rk, &rl);
 
-		sortus[i].h = h;
-		sortus[i].k = k;
-		sortus[i].l = l;
-		sortus[i].resolution = 2.0*resolution(cell, h, k, l);  /* one over d */
-		sortus[i].multi = get_redundancy(refl);
+		sortus[i].h = rh;
+		sortus[i].k = rk;
+		sortus[i].l = rl;
+		sortus[i].resolution = 2.0*resolution(cell, rh, rk, rl);  /* one over d */
+		sortus[i].multi = get_redundancy(ring);
 		i++;
 
 	}
diff --git a/src/crystfel_gui.c b/src/crystfel_gui.c
index 159d1bc2..dbf949cd 100644
--- a/src/crystfel_gui.c
+++ b/src/crystfel_gui.c
@@ -1081,7 +1081,7 @@ int main(int argc, char *argv[])
 
 	if ( load_result == 0 ) {
 		DataTemplate *dtempl;
-		GtkAction *w;
+		GtkAction *act;
 		proj.cur_frame = 0;
 
 		if ( proj.geom_filename != NULL ) {
@@ -1103,20 +1103,20 @@ int main(int argc, char *argv[])
 			stream_close(st);
 		}
 
-		w = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/centre");
-		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(w),
+		act = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/centre");
+		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(act),
 		                             proj.show_centre);
 
-		w = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/peaks");
-		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(w),
+		act = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/peaks");
+		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(act),
 		                             proj.show_peaks);
 
-		w = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/refls");
-		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(w),
+		act = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/refls");
+		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(act),
 		                             proj.show_refls);
 
-		w = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/labelrefls");
-		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(w),
+		act = gtk_ui_manager_get_action(proj.ui, "/mainwindow/view/labelrefls");
+		gtk_toggle_action_set_active(GTK_TOGGLE_ACTION(act),
 		                             proj.label_refls);
 
 		update_imageview(&proj);
diff --git a/src/diffraction-gpu.c b/src/diffraction-gpu.c
index 7829d9da..97badc36 100644
--- a/src/diffraction-gpu.c
+++ b/src/diffraction-gpu.c
@@ -391,7 +391,7 @@ struct gpu_context *setup_gpu(int no_sfac,
 	size_t flags_size;
 	float *flags_ptr;
 	size_t maxwgsize;
-	int i;
+	int iplat;
 	int have_ctx = 0;
 	char cflags[512] = "";
 	char *insert_stuff = NULL;
@@ -409,10 +409,10 @@ struct gpu_context *setup_gpu(int no_sfac,
 	}
 
 	/* Find a GPU platform in the list */
-	for ( i=0; i<nplat; i++ ) {
+	for ( iplat=0; iplat<nplat; iplat++ ) {
 
 		prop[0] = CL_CONTEXT_PLATFORM;
-		prop[1] = (cl_context_properties)platforms[i];
+		prop[1] = (cl_context_properties)platforms[iplat];
 		prop[2] = 0;
 
 		gctx = malloc(sizeof(*gctx));
@@ -430,7 +430,8 @@ struct gpu_context *setup_gpu(int no_sfac,
 				return NULL;
 			}
 		} else {
-			STATUS("Using OpenCL platform %i (%i total)\n", i, nplat);
+			STATUS("Using OpenCL platform %i (%i total)\n",
+			       iplat, nplat);
 			have_ctx = 1;
 			break;
 		}
@@ -454,10 +455,12 @@ struct gpu_context *setup_gpu(int no_sfac,
 	intensities_size = IDIM*IDIM*IDIM*sizeof(cl_float);
 	intensities_ptr = malloc(intensities_size);
 	if ( intensities != NULL ) {
+		int i;
 		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
 			intensities_ptr[i] = intensities[i];
 		}
 	} else {
+		int i;
 		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
 			intensities_ptr[i] = 100.0;  /* Does nothing */
 		}
@@ -522,10 +525,12 @@ struct gpu_context *setup_gpu(int no_sfac,
 	flags_size = IDIM*IDIM*IDIM*sizeof(cl_float);
 	flags_ptr = malloc(flags_size);
 	if ( flags != NULL ) {
+		int i;
 		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
 			flags_ptr[i] = flags[i];
 		}
 	} else {
+		int i;
 		for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
 			flags_ptr[i] = 1.0;
 		}
diff --git a/src/gui_backend_slurm.c b/src/gui_backend_slurm.c
index 801921ea..aeabad3d 100644
--- a/src/gui_backend_slurm.c
+++ b/src/gui_backend_slurm.c
@@ -166,15 +166,15 @@ static double indexing_progress(struct slurm_job *job, int *running)
 
 	} else {
 
-		int i;
+		int ijob;
 		int n_proc = 0;
 
-		for ( i=0; i<job->n_blocks; i++ ) {
+		for ( ijob=0; ijob<job->n_blocks; ijob++ ) {
 
 			char tmp[128];
 			char *stderr_filename;
 
-			snprintf(tmp, 127, "stderr-%i.log", i);
+			snprintf(tmp, 127, "stderr-%i.log", ijob);
 			stderr_filename = relative_to_cwd(job->workdir, tmp);
 
 			n_proc += read_number_processed(stderr_filename);
diff --git a/src/gui_project.c b/src/gui_project.c
index 7141fcb8..952bbbe6 100644
--- a/src/gui_project.c
+++ b/src/gui_project.c
@@ -891,7 +891,7 @@ int load_project(struct crystfelproject *proj)
 
 int save_project(struct crystfelproject *proj)
 {
-	int i;
+	int ibackend, iresult, iframe;
 	FILE *fh;
 
 	fh = fopen("crystfel.project", "w");
@@ -986,9 +986,9 @@ int save_project(struct crystfelproject *proj)
 
 	fprintf(fh, "indexing.backend %s\n",
 	        proj->backends[proj->indexing_backend_selected].name);
-	for ( i=0; i<proj->n_backends; i++ ) {
+	for ( ibackend=0; ibackend<proj->n_backends; ibackend++ ) {
 		struct crystfel_backend *be;
-		be = &proj->backends[i];
+		be = &proj->backends[ibackend];
 		be->write_indexing_opts(be->indexing_opts_priv, fh);
 	}
 
@@ -1064,9 +1064,9 @@ int save_project(struct crystfelproject *proj)
 	}
 	fprintf(fh, "ambi.backend %s\n",
 	        proj->backends[proj->ambi_backend_selected].name);
-	for ( i=0; i<proj->n_backends; i++ ) {
+	for ( ibackend=0; ibackend<proj->n_backends; ibackend++ ) {
 		struct crystfel_backend *be;
-		be = &proj->backends[i];
+		be = &proj->backends[ibackend];
 		be->write_ambi_opts(be->ambi_opts_priv, fh);
 	}
 	if ( proj->ambi_new_job_title != NULL ) {
@@ -1109,9 +1109,9 @@ int save_project(struct crystfelproject *proj)
 
 	fprintf(fh, "merging.backend %s\n",
 	        proj->backends[proj->merging_backend_selected].name);
-	for ( i=0; i<proj->n_backends; i++ ) {
+	for ( ibackend=0; ibackend<proj->n_backends; ibackend++ ) {
 		struct crystfel_backend *be;
-		be = &proj->backends[i];
+		be = &proj->backends[ibackend];
 		be->write_merging_opts(be->merging_opts_priv, fh);
 	}
 	if ( proj->merging_new_job_title != NULL ) {
@@ -1134,33 +1134,33 @@ int save_project(struct crystfelproject *proj)
 	fprintf(fh, "label_refls %i\n", proj->label_refls);
 
 	fprintf(fh, "-----\n");
-	for ( i=0; i<proj->n_results; i++ ) {
+	for ( iresult=0; iresult<proj->n_results; iresult++ ) {
 		int j;
-		fprintf(fh, "Result %s\n", proj->results[i].name);
-		for ( j=0; j<proj->results[i].n_streams; j++ ) {
+		fprintf(fh, "Result %s\n", proj->results[iresult].name);
+		for ( j=0; j<proj->results[iresult].n_streams; j++ ) {
 			fprintf(fh, "   Stream %s\n",
-			        proj->results[i].streams[j]);
+			        proj->results[iresult].streams[j]);
 		}
 		if ( strcmp(selected_result(proj),
-		            proj->results[i].name) == 0 )
+		            proj->results[iresult].name) == 0 )
 		{
 			fprintf(fh, "   Selected\n");
 		}
 	}
-	for ( i=0; i<proj->n_merge_results; i++ ) {
-		fprintf(fh, "Result %s\n", proj->merge_results[i].name);
-		fprintf(fh, "   HKL %s\n", proj->merge_results[i].hkl);
-		fprintf(fh, "   HKL1 %s\n", proj->merge_results[i].hkl1);
-		fprintf(fh, "   HKL2 %s\n", proj->merge_results[i].hkl2);
+	for ( iresult=0; iresult<proj->n_merge_results; iresult++ ) {
+		fprintf(fh, "Result %s\n", proj->merge_results[iresult].name);
+		fprintf(fh, "   HKL %s\n", proj->merge_results[iresult].hkl);
+		fprintf(fh, "   HKL1 %s\n", proj->merge_results[iresult].hkl1);
+		fprintf(fh, "   HKL2 %s\n", proj->merge_results[iresult].hkl2);
 	}
 
 	fprintf(fh, "-----\n");
-	for ( i=0; i<proj->n_frames; i++ ) {
-		if ( proj->events[i] != NULL ) {
+	for ( iframe=0; iframe<proj->n_frames; iframe++ ) {
+		if ( proj->events[iframe] != NULL ) {
 			fprintf(fh, "%s %s\n",
-			        proj->filenames[i], proj->events[i]);
+			        proj->filenames[iframe], proj->events[iframe]);
 		} else {
-			fprintf(fh, "%s\n", proj->filenames[i]);
+			fprintf(fh, "%s\n", proj->filenames[iframe]);
 		}
 	}
 
diff --git a/src/partialator.c b/src/partialator.c
index 249eda93..ca0249ce 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1014,7 +1014,7 @@ int main(int argc, char *argv[])
 	SymOpList *amb;
 	SymOpList *w_sym;
 	int nthreads = 1;
-	int i;
+	int istream, icmd, icryst, itn;
 	int n_iter = 10;
 	RefList *full;
 	int n_images = 0;
@@ -1104,8 +1104,8 @@ int main(int argc, char *argv[])
 	};
 
 	cmdline[0] = '\0';
-	for ( i=1; i<argc; i++ ) {
-		strncat(cmdline, argv[i], 1023-strlen(cmdline));
+	for ( icmd=1; icmd<argc; icmd++ ) {
+		strncat(cmdline, argv[icmd], 1023-strlen(cmdline));
 		strncat(cmdline, " ", 1023-strlen(cmdline));
 	}
 
@@ -1471,11 +1471,11 @@ int main(int argc, char *argv[])
 	}
 
 	audit_info = NULL;
-	for ( i=0; i<stream_list.n; i++ ) {
+	for ( istream=0; istream<stream_list.n; istream++ ) {
 
-		Stream *st = stream_open_for_read(stream_list.filenames[i]);
+		Stream *st = stream_open_for_read(stream_list.filenames[istream]);
 		if ( st == NULL ) {
-			ERROR("Couldn't open %s\n", stream_list.filenames[i]);
+			ERROR("Couldn't open %s\n", stream_list.filenames[istream]);
 			return 1;
 		}
 
@@ -1605,9 +1605,9 @@ int main(int argc, char *argv[])
 	if ( sparams_fh != NULL ) fclose(sparams_fh);
 
 	STATUS("Initial partiality calculation...\n");
-	for ( i=0; i<n_crystals; i++ ) {
+	for ( icryst=0; icryst<n_crystals; icryst++ ) {
 
-		Crystal *cr = crystals[i];
+		Crystal *cr = crystals[icryst];
 		update_predictions(cr);
 
 		/* Polarisation correction requires kpred values */
@@ -1647,13 +1647,13 @@ int main(int argc, char *argv[])
 	}
 
 	/* Iterate */
-	for ( i=0; i<n_iter; i++ ) {
+	for ( itn=0; itn<n_iter; itn++ ) {
 
-		STATUS("Scaling and refinement cycle %i of %i\n", i+1, n_iter);
+		STATUS("Scaling and refinement cycle %i of %i\n", itn+1, n_iter);
 
 		if ( !no_pr ) {
 			refine_all(crystals, n_crystals, full, nthreads, pmodel,
-			           i+1, no_logs, sym, amb, scaleflags);
+			           itn+1, no_logs, sym, amb, scaleflags);
 		}
 
 		/* Create new reference if needed */
@@ -1674,13 +1674,13 @@ int main(int argc, char *argv[])
 		show_all_residuals(crystals, n_crystals, full, no_free);
 
 		if ( do_write_logs ) {
-			write_pgraph(full, crystals, n_crystals, i+1, "");
+			write_pgraph(full, crystals, n_crystals, itn+1, "");
 		}
 
 		if ( output_everycycle ) {
 
 			char tmp[1024];
-			snprintf(tmp, 1024, "iter%.2d_%s", i+1, outfile);
+			snprintf(tmp, 1024, "iter%.2d_%s", itn+1, outfile);
 
 			/* Output results */
 			STATUS("Writing overall results to %s\n", tmp);
@@ -1745,6 +1745,7 @@ int main(int argc, char *argv[])
 
 	/* Output custom split results */
 	if ( csplit != NULL ) {
+		int i;
 		for ( i=0; i<csplit->n_datasets; i++ ) {
 			write_custom_split(csplit, i, crystals, n_crystals,
 			                   pmodel, min_measurements, push_res,
@@ -1754,15 +1755,15 @@ int main(int argc, char *argv[])
 
 	/* Clean up */
 	gsl_rng_free(rng);
-	for ( i=0; i<n_crystals; i++ ) {
-		struct image *image = crystal_get_image(crystals[i]);
+	for ( icryst=0; icryst<n_crystals; icryst++ ) {
+		struct image *image = crystal_get_image(crystals[icryst]);
 		spectrum_free(image->spectrum);
-		reflist_free(crystal_get_reflections(crystals[i]));
+		reflist_free(crystal_get_reflections(crystals[icryst]));
 		free(image->filename);
 		free(image->ev);
 		free(image);
-		cell_free(crystal_get_cell(crystals[i]));
-		crystal_free(crystals[i]);
+		cell_free(crystal_get_cell(crystals[icryst]));
+		crystal_free(crystals[icryst]);
 	}
 	free_contribs(full);
 	reflist_free(full);
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 7098869d..b6414aa1 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -481,7 +481,7 @@ int main(int argc, char *argv[])
 	int config_gpu = 0;
 	int config_random = 0;
 	char *powder_fn = NULL;
-	char *filename = NULL;
+	char *cell_filename = NULL;
 	char *grad_str = NULL;
 	char *outfile = NULL;
 	char *geometry = NULL;
@@ -599,7 +599,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'p' :
-			filename = strdup(optarg);
+			cell_filename = strdup(optarg);
 			break;
 
 			case 'o' :
@@ -761,8 +761,8 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
-	if ( filename == NULL ) {
-		filename = strdup("molecule.pdb");
+	if ( cell_filename == NULL ) {
+		cell_filename = strdup("molecule.pdb");
 	}
 
 	if ( outfile == NULL ) {
@@ -844,7 +844,7 @@ int main(int argc, char *argv[])
 	free(spectrum_str);
 
 	/* Load unit cell */
-	input_cell = load_cell_from_file(filename);
+	input_cell = load_cell_from_file(cell_filename);
 	if ( input_cell == NULL ) {
 		exit(1);
 	}
@@ -988,7 +988,7 @@ int main(int argc, char *argv[])
 	do {
 
 		int na, nb, nc;
-		double a, b, c, d;
+		double a, b, c, dis;
 		UnitCell *cell;
 		int err = 0;
 		int pi;
@@ -1094,7 +1094,7 @@ int main(int argc, char *argv[])
 
 		}
 
-		cell_get_parameters(cell, &a, &b, &c, &d, &d, &d);
+		cell_get_parameters(cell, &a, &b, &c, &dis, &dis, &dis);
 		STATUS("Particle size = %i x %i x %i"
 		       " ( = %5.2f x %5.2f x %5.2f nm)\n",
 	               na, nb, nc, na*a/1.0e-9, nb*b/1.0e-9, nc*c/1.0e-9);
@@ -1148,22 +1148,22 @@ int main(int argc, char *argv[])
 
 		if ( !config_noimages ) {
 
-			char filename[1024];
+			char h5filename[1024];
 
 			if ( n_images != 1 ) {
-				snprintf(filename, 1023, "%s-%i.h5",
+				snprintf(h5filename, 1023, "%s-%i.h5",
 				         outfile, number);
 			} else {
-				strncpy(filename, outfile, 1023);
+				strncpy(h5filename, outfile, 1023);
 			}
 
 			number++;
 
 			/* Write the output file */
-			image_write(image, dtempl, filename);
+			image_write(image, dtempl, h5filename);
 
 			/* Add some pattern_sim-specific metadata */
-			add_metadata(filename, orientation, cell);
+			add_metadata(h5filename, orientation, cell);
 
 		}
 
@@ -1190,7 +1190,7 @@ skip:
 	cell_free(input_cell);
 	free(intensities);
 	free(outfile);
-	free(filename);
+	free(cell_filename);
 	free(sym_str);
 	free_symoplist(sym);
 
diff --git a/src/process_hkl.c b/src/process_hkl.c
index b16146e3..be1c95d4 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -604,7 +604,7 @@ int main(int argc, char *argv[])
 	                                    .disable = 0};
 	char *rval;
 	int min_measurements = 2;
-	int r;
+	int merge_r;
 	int start_after = 0;
 	int stop_after = 0;
 	double min_snr = -INFINITY;
@@ -876,13 +876,13 @@ int main(int argc, char *argv[])
 	if ( config_scale ) twopass = 1;
 
 	hist_i = 0;
-	r = merge_all(&stream_list, model, NULL, sym,
-	              &hist_vals, hist_h, hist_k, hist_l,
-	              &hist_i, polarisation, min_measurements, min_snr,
-	              max_adu, start_after, stop_after, min_res, push_res,
-	              min_cc, config_scale, flag_even_odd, stat_output);
+	merge_r = merge_all(&stream_list, model, NULL, sym,
+	                    &hist_vals, hist_h, hist_k, hist_l,
+	                    &hist_i, polarisation, min_measurements, min_snr,
+	                    max_adu, start_after, stop_after, min_res, push_res,
+	                    min_cc, config_scale, flag_even_odd, stat_output);
 	fprintf(stderr, "\n");
-	if ( r ) {
+	if ( merge_r ) {
 		ERROR("Error while reading stream.\n");
 		return 1;
 	}
diff --git a/src/render_hkl.c b/src/render_hkl.c
index c47a2c4d..00992d71 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -758,7 +758,6 @@ int main(int argc, char *argv[])
 	int config_colkey = 0;
 	int config_zawhinge = 0;
 	char *cellfile = NULL;
-	int r = 0;
 	double boost = 1.0;
 	char *sym_str = NULL;
 	char *sym_str_fromfile = NULL;
@@ -1049,5 +1048,5 @@ int main(int argc, char *argv[])
 	reflist_free(list);
 	if ( outfile != NULL ) free(outfile);
 
-	return r;
+	return 0;
 }
diff --git a/src/whirligig.c b/src/whirligig.c
index 611825ba..20fcfa40 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -485,12 +485,14 @@ static void add_to_window(struct image *cur, struct window *win,
 
 	if ( pos >= win->ws ) {
 
-		int sf, i;
+		int sf, iwin;
 
 		sf = (pos - win->ws) + 1;
 
 		if ( series_fills_window(win) ) {
 
+			int i;
+
 			win->ws += sf;
 			win->img = realloc(win->img,
 			                   win->ws*sizeof(struct image));
@@ -513,6 +515,8 @@ static void add_to_window(struct image *cur, struct window *win,
 
 		} else {
 
+			int iser;
+
 			pos -= sf;
 			if ( sf > win->join_ptr ) {
 
@@ -534,29 +538,29 @@ static void add_to_window(struct image *cur, struct window *win,
 				sf = win->ws;
 			}
 
-			for ( i=0; i<sf; i++ ) {
-				if ( win->img[i].serial != 0 ) {
-					free_all_crystals(&win->img[i]);
+			for ( iser=0; iser<sf; iser++ ) {
+				if ( win->img[iser].serial != 0 ) {
+					free_all_crystals(&win->img[iser]);
 				}
 			}
 
 			memmove(win->img, win->img+sf,
 			        (win->ws-sf)*sizeof(struct image));
 
-			for ( i=0; i<MAX_SER; i++ ) {
-				memmove(win->ser[i], win->ser[i]+sf,
+			for ( iser=0; iser<MAX_SER; iser++ ) {
+				memmove(win->ser[iser], win->ser[iser]+sf,
 					(win->ws-sf)*sizeof(signed int));
-				memmove(win->mat[i], win->mat[i]+sf,
+				memmove(win->mat[iser], win->mat[iser]+sf,
 					(win->ws-sf)*sizeof(IntegerMatrix *));
 			}
 		}
 
-		for ( i=0; i<sf; i++ ) {
+		for ( iwin=0; iwin<sf; iwin++ ) {
 			int j;
-			win->img[win->ws-sf+i].serial = 0;
+			win->img[win->ws-sf+iwin].serial = 0;
 			for ( j=0; j<MAX_SER; j++ ) {
-				win->ser[j][win->ws-sf+i] = -1;
-				win->mat[j][win->ws-sf+i] = NULL;
+				win->ser[j][win->ws-sf+iwin] = -1;
+				win->mat[j][win->ws-sf+iwin] = NULL;
 			}
 		}
 
-- 
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