Reduce variable scope where possible

29 files changed, 76 insertions, 61 deletions

diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 2f3dfc6b..cdd4156b 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -1220,7 +1220,6 @@ int cell_is_sensible(UnitCell *cell)
 int validate_cell(UnitCell *cell)
 {
 	int err = 0;
-	char cen, ua;
 
 	if ( cell_has_parameters(cell) && !cell_is_sensible(cell) ) {
 		ERROR("WARNING: Unit cell parameters are not sensible.\n");
@@ -1241,6 +1240,7 @@ int validate_cell(UnitCell *cell)
 	/* For monoclinic A, B or C centering, the unique axis must be something
 	 * other than the centering. */
 	if ( cell_get_lattice_type(cell) == L_MONOCLINIC ) {
+		char cen, ua;
 		cen = cell_get_centering(cell);
 		ua = cell_get_unique_axis(cell);
 		if ( ((cen == 'A') && (ua == 'a'))
diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index 9f8f102c..a2b974a7 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -646,9 +646,9 @@ static int parse_field_for_panel(struct panel_template *panel, const char *key,
 			reject = 1;
 		}
 	} else if ( strncmp(key, "dim", 3) == 0) {
-		int dim_entry;
 		char *endptr;
 		if ( key[3] != '\0' ) {
+			int dim_entry;
 			dim_entry = strtoul(key+3, &endptr, 10);
 			if ( endptr[0] != '\0' ) {
 				ERROR("Invalid dimension number %s\n",
diff --git a/libcrystfel/src/filters.c b/libcrystfel/src/filters.c
index a9c8737a..5f6a0b2d 100644
--- a/libcrystfel/src/filters.c
+++ b/libcrystfel/src/filters.c
@@ -99,13 +99,14 @@ void filters_fudge_gslcblas()
 #define SWAP(a,b) { float t=(a);(a)=(b);(b)=t; }
 static float kth_smallest(float *a, int n, int k)
 {
-	long i, j, l, m;
-	float x;
+	long l, m;
 
 	l = 0;
 	m = n-1;
 
 	while ( l < m ) {
+		long i, j;
+		float x;
 		x=a[k];
 		i=l;
 		j=m;
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 3c5af479..9fc647ab 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -1140,7 +1140,6 @@ static int create_satmap(struct image *image,
 			 * but it isn't this one.  Therefore make a fake
 			 * saturation map */
 
-			long int j;
 			int p_w, p_h;
 
 			p_w = p->orig_max_fs - p->orig_min_fs + 1;
@@ -1149,6 +1148,7 @@ static int create_satmap(struct image *image,
 			image->sat[i] = malloc(p_w*p_h*sizeof(float));
 
 			if ( image->sat[i] != NULL ) {
+				long int j;
 				for ( j=0; j<p_w*p_h; j++ ) {
 					image->sat[i][j] = INFINITY;
 				}
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index d8a135fc..e7b8b8cf 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -922,7 +922,6 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 	for ( n=0; n<ipriv->n_methods; n++ ) {
 
 		int done = 0;
-		int r;
 		int ntry = 0;
 		int success = 0;
 
@@ -932,6 +931,8 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 		do {
 
+			int r;
+
 			r = try_indexer(image, ipriv->methods[n],
 			                ipriv, ipriv->engine_private[n],
 			                last_task);
diff --git a/libcrystfel/src/indexers/asdf.c b/libcrystfel/src/indexers/asdf.c
index 7030a3e7..a1f8f50d 100644
--- a/libcrystfel/src/indexers/asdf.c
+++ b/libcrystfel/src/indexers/asdf.c
@@ -364,7 +364,7 @@ static float find_ds_fft(double *projections, int N_projections, double d_max,
 	memcpy(projections_sorted, projections, sizeof(double) * n);
 	qsort(projections_sorted, n, sizeof(double), compare_doubles);
 
-	int i, k;
+	int i;
 
 	int N = fftw.N; // number of points in fft calculation
 	double *in = fftw.in;
@@ -376,6 +376,7 @@ static float find_ds_fft(double *projections, int N_projections, double d_max,
 	}
 
 	for ( i=0; i<n; i++ ) {
+		int k;
 		k = (int)((projections_sorted[i] - projections_sorted[0]) /
 		          (projections_sorted[n - 1] - projections_sorted[0]) *
 		          (N - 1));
@@ -394,8 +395,8 @@ static float find_ds_fft(double *projections, int N_projections, double d_max,
 
 	int d = 1;
 	double max = 0;
-	double a;
 	for ( i=1; i<=i_max; i++ ) {
+		double a;
 		a = sqrt(out[i][0] * out[i][0] + out[i][1] * out[i][1]);
 		if (a > max) {
 			max = a;
@@ -581,8 +582,6 @@ static int refine_asdf_cell(struct asdf_cell *c, gsl_vector **reflections,
 
 static int reduce_asdf_cell(struct asdf_cell *cl)
 {
-	double a, b, c, alpha, beta, gamma, ab, bc, ca, bb, cc;
-
 	gsl_vector *va = gsl_vector_alloc(3);
 	gsl_vector *vb = gsl_vector_alloc(3);
 	gsl_vector *vc = gsl_vector_alloc(3);
@@ -591,6 +590,9 @@ static int reduce_asdf_cell(struct asdf_cell *cl)
 
 	int n = 0;
 	while ( changed ) {
+
+		double a, b, c, alpha, beta, gamma, ab, bc, ca;
+
 		n += 1;
 		changed = 0;
 
@@ -612,6 +614,8 @@ static int reduce_asdf_cell(struct asdf_cell *cl)
 
 		if ( changed == 0 ) {
 
+			double bb;
+
 			if ( gamma < 90 ) {
 				gsl_vector_scale(vb, -1);
 				gamma = 180 - gamma;
@@ -634,6 +638,8 @@ static int reduce_asdf_cell(struct asdf_cell *cl)
 
 		if ( changed == 0 ) {
 
+			double cc;
+
 			if ( beta < 90 ) {
 				gsl_vector_scale(vc, -1);
 				beta = 180 - beta;
@@ -659,6 +665,9 @@ static int reduce_asdf_cell(struct asdf_cell *cl)
 		}
 
 		if ( changed == 0 ) {
+
+			double cc;
+
 			if ( alpha < 90 ) {
 				gsl_vector_scale(vc, -1);
 				beta = 180 - beta;
@@ -901,10 +910,12 @@ static int **generate_triplets(int N_reflections, int N_triplets_max, int *N)
 		return 0;
 	}
 
-	int is_in_triplets;
 	n = 0;
 
 	while ( n < N_triplets ) {
+
+		int is_in_triplets;
+
 		/* Generate three different integer numbers < N_reflections */
 		i = rand() % N_reflections;
 		j = i;
diff --git a/libcrystfel/src/indexers/felix.c b/libcrystfel/src/indexers/felix.c
index b7d2a8a3..db7da8c4 100644
--- a/libcrystfel/src/indexers/felix.c
+++ b/libcrystfel/src/indexers/felix.c
@@ -131,7 +131,6 @@ static int read_felix(struct felix_private *gp, struct image *image,
 	float mean_ia;
 	int ngv;
 	char line[1024];
-	int r;
 	int n_crystals = 0;
 
 	fh = fopen(filename, "r");
@@ -151,6 +150,7 @@ static int read_felix(struct felix_private *gp, struct image *image,
 
 		Crystal *cr;
 		UnitCell *cell;
+		int r;
 
 		/* One line per grain */
 		if ( fgets( line, 1024, fh ) == NULL ) {
diff --git a/libcrystfel/src/indexers/fromfile.c b/libcrystfel/src/indexers/fromfile.c
index d7dfbd09..1716dd66 100644
--- a/libcrystfel/src/indexers/fromfile.c
+++ b/libcrystfel/src/indexers/fromfile.c
@@ -228,7 +228,6 @@ void *fromfile_prepare(IndexingMethod *indm, struct fromfile_options *opts)
 		float vals[11];
 		struct fromfile_key key;
 		Crystal *cr;
-		UnitCell *cell;
 		size_t len;
 		int n_sp;
 		struct fromfile_entry *item = NULL;
@@ -286,6 +285,8 @@ void *fromfile_prepare(IndexingMethod *indm, struct fromfile_options *opts)
 
 		} else {
 
+			UnitCell *cell;
+
 			cr = crystal_new();
 
 			/* mm -> m */
diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c
index 129e6859..e77f6384 100644
--- a/libcrystfel/src/indexers/mosflm.c
+++ b/libcrystfel/src/indexers/mosflm.c
@@ -481,7 +481,6 @@ static char *mosflm_spacegroup_for_lattice(UnitCell *cell)
 static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 {
 	char tmp[256];
-	char cen;
 	double wavelength;
 	double a = 0, b = 0, c = 0, alpha = 0, beta = 0, gamma = 0;
 
@@ -548,6 +547,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 
 		case 9 :
 		if ( mosflm->mp->indm & INDEXING_USE_CELL_PARAMETERS ) {
+			char cen;
 			cell_get_parameters(mosflm->mp->template,
 			                    &a, &b, &c, &alpha, &beta, &gamma);
 			cen = cell_get_centering(mosflm->mp->template);
@@ -886,9 +886,8 @@ const char *mosflm_probe(UnitCell *cell)
 	fh = fdopen(pty, "r");
 
 	for ( l=0; l<10; l++ ) {
-		char *pos;
 		if ( fgets(line, 1024, fh) != NULL ) {
-			pos = strstr(line, "Mosflm version ");
+			char *pos = strstr(line, "Mosflm version ");
 			if ( pos != NULL ) ok = 1;
 		}
 	}
diff --git a/libcrystfel/src/indexers/xds.c b/libcrystfel/src/indexers/xds.c
index 3936f791..8ef496cf 100644
--- a/libcrystfel/src/indexers/xds.c
+++ b/libcrystfel/src/indexers/xds.c
@@ -523,8 +523,8 @@ const char *xds_probe(UnitCell *cell)
 	fh = fdopen(pty, "r");
 
 	for ( l=0; l<10; l++ ) {
-		char *pos;
 		if ( fgets(line, 1024, fh) != NULL ) {
+			char *pos;
 			pos = strstr(line, "** XDS **");
 			if ( pos != NULL ) {
 				ok = 1;
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 2375388f..e797d26b 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -340,10 +340,9 @@ static void fit_gradient_bg(struct intcontext *ic, struct peak_box *bx)
 	for ( p=0; p<ic->w; p++ ) {
 	for ( q=0; q<ic->w; q++ ) {
 
-		double bi;
-
 		if ( bx->bm[p + ic->w*q] == BM_BG ) {
 
+			double bi;
 			bi = boxi(ic, bx, p, q);
 
 			addv(v, 0, bi*p);
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 689239e5..d260b66d 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -288,7 +288,6 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 		double grad;
 		int mask_fs, mask_ss;
 		int s_fs, s_ss;
-		double max;
 		unsigned int did_something;
 		int r;
 		int saturated;
@@ -321,6 +320,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 
 		do {
 
+			double max;
 			max = data[mask_fs+stride*mask_ss];
 			did_something = 0;
 
@@ -589,7 +589,6 @@ int indexing_peak_check(struct image *image, Crystal **crystals, int n_cryst,
 
 		struct imagefeature *f;
 		double q[3];
-		double h,k,l,hd,kd,ld;
 		int j;
 		int ok = 0;
 
@@ -604,6 +603,7 @@ int indexing_peak_check(struct image *image, Crystal **crystals, int n_cryst,
 			double bx, by, bz;
 			double cx, cy, cz;
 			double dx, dy;
+			double h,k,l,hd,kd,ld;
 
 			crystal_get_det_shift(crystals[j], &dx, &dy);
 
diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index 2b250eff..4a284c07 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -1099,13 +1099,13 @@ int write_to_mtz(RefList *reflist,
 	{
 		signed int h, k, l;
 		double one_over_d;
-		int isym;
 
 		get_indices(refl, &h, &k, &l);
 
 		one_over_d = 2.0*resolution(cell, h, k, l);
 		if ( (one_over_d > min_res) && (one_over_d < max_res) ) {
 
+			int isym;
 			float refldata[7];
 			signed int nh, nk, nl;
 			signed int fh, fk, fl;
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 8ffaed1a..6c716fda 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -242,7 +242,6 @@ static RefList *read_stream_reflections_2_3(Stream *st)
 		float intensity, sigma, fs, ss, pk, bg;
 		char pn[32];
 		int r;
-		Reflection *refl;
 
 		rval = fgets(line, 1023, st->fh);
 		st->ln++;
@@ -264,6 +263,7 @@ static RefList *read_stream_reflections_2_3(Stream *st)
 
 		if ( r == 10 ) {
 
+			Reflection *refl;
 			refl = add_refl(out, h, k, l);
 			if ( refl == NULL ) {
 				ERROR("Failed to add reflection\n");
@@ -313,7 +313,6 @@ static RefList *read_stream_reflections_2_1(Stream *st)
 		char phs[1024];
 		int cts;
 		int r;
-		Reflection *refl;
 
 		rval = fgets(line, 1023, st->fh);
 		st->ln++;
@@ -333,6 +332,7 @@ static RefList *read_stream_reflections_2_1(Stream *st)
 		first = 0;
 		if ( r == 9 ) {
 
+			Reflection *refl;
 			double ph;
 			char *v;
 
@@ -388,7 +388,6 @@ static RefList *read_stream_reflections_2_2(Stream *st)
 		signed int h, k, l;
 		float intensity, sigma, fs, ss, pk, bg;
 		int r;
-		Reflection *refl;
 
 		rval = fgets(line, 1023, st->fh);
 		st->ln++;
@@ -407,6 +406,7 @@ static RefList *read_stream_reflections_2_2(Stream *st)
 		first = 0;
 		if ( r == 9 ) {
 
+			Reflection *refl;
 			refl = add_refl(out, h, k, l);
 			if ( refl == NULL ) {
 				ERROR("Failed to add reflection\n");
diff --git a/src/ambigator.c b/src/ambigator.c
index 1657bfb6..02252cd7 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -119,7 +119,6 @@ static struct flist *asymm_and_merge(RefList *in, const SymOpList *sym,
 		signed int h, k, l;
 		signed int ha, ka, la;
 		Reflection *cr;
-		double res;
 		int group = 0;
 
 		get_indices(refl, &h, &k, &l);
@@ -127,7 +126,7 @@ static struct flist *asymm_and_merge(RefList *in, const SymOpList *sym,
 		if ( cell == NULL ) {
 			ERROR("Can't calculate resolution cutoff - no cell\n");
 		} else {
-			res = 2.0*resolution(cell, h, k, l);
+			double res = 2.0*resolution(cell, h, k, l);
 			if ( res < rmin ) continue;
 			if ( res > rmax ) continue;
 			if ( auto_res ) {
diff --git a/src/check_hkl.c b/src/check_hkl.c
index c4532f31..aa972a7f 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -350,12 +350,12 @@ static void wilson_plot(RefList *list, UnitCell *cell, const SymOpList *sym,
 	} else {
 		int bs = (pow(3.125e9/2.0, 2.0) - s2min)/s2step + 1;
 		double lnk, minus2B, cov00, cov01, cov11, sumsq;
-		double B;
 		if ( nbins - bs < 3 ) {
 			ERROR("Not enough bins to estimate B factor\n");
 			ERROR("Resolution of data, or number of bins, is too "
 			      "low.\n");
 		} else {
+			double B;
 			double *s2fit;
 			double *lnifit;
 			int nbfit = 0;
diff --git a/src/cl-utils.c b/src/cl-utils.c
index c2c1bf1d..1b6667c4 100644
--- a/src/cl-utils.c
+++ b/src/cl-utils.c
@@ -188,7 +188,7 @@ cl_device_id get_cl_dev(cl_context ctx, int n)
 	cl_device_id *dev;
 	cl_int r;
 	size_t size;
-	int i, num_devs;
+	int num_devs;
 
 	/* Get the required size of the array */
 	r = clGetContextInfo(ctx, CL_CONTEXT_DEVICES, 0, NULL, &size);
@@ -212,6 +212,8 @@ cl_device_id get_cl_dev(cl_context ctx, int n)
 
 	if ( n < 0 ) {
 
+		int i;
+
 		STATUS("Available devices:\n");
 		for ( i=0; i<num_devs; i++ ) {
 
@@ -267,7 +269,6 @@ cl_program load_program_from_string(const char *source_in, size_t len,
 	cl_int r;
 	char cflags[1024] = "";
 	char *insert_pos;
-	size_t il;
 	char *source;
 
 	/* Copy the code because we need to zero-terminate it */
@@ -282,6 +283,8 @@ cl_program load_program_from_string(const char *source_in, size_t len,
 		if ( insert_pos != NULL ) {
 
 			char *source2;
+			size_t il;
+
 			source2 = malloc(strlen(source)+strlen(insert_stuff)+1);
 			if ( source2 == NULL ) {
 				free(source);
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 4dd9e3fd..b6895f37 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -232,7 +232,6 @@ static RefList *twin_reflections(RefList *in, int need_all_parts,
 
 			signed int he, ke, le;
 			signed int hu, ku, lu;
-			Reflection *part;
 			int r;
 
 			get_equiv(holo, m, j, h, k, l, &he, &ke, &le);
@@ -262,6 +261,7 @@ static RefList *twin_reflections(RefList *in, int need_all_parts,
 
 				double i, sigi;
 				int mult;
+				Reflection *part;
 
 				part = find_refl(in, hu, ku, lu);
 
diff --git a/src/gui_project.c b/src/gui_project.c
index f72af893..7141fcb8 100644
--- a/src/gui_project.c
+++ b/src/gui_project.c
@@ -602,9 +602,8 @@ static void handle_var(const char *key, const char *val,
 
 void clear_project_files(struct crystfelproject *proj)
 {
-	int i;
-
 	if ( proj->filenames != NULL ) {
+		int i;
 		for ( i=0; i<proj->n_frames; i++ ) {
 			free(proj->filenames[i]);
 			free(proj->events[i]);
diff --git a/src/im-zmq.c b/src/im-zmq.c
index 4273b600..3fd04428 100644
--- a/src/im-zmq.c
+++ b/src/im-zmq.c
@@ -62,7 +62,6 @@ struct im_zmq *im_zmq_connect(const char *zmq_address,
                               const char *zmq_request)
 {
 	struct im_zmq *z;
-	int i;
 
 	z = malloc(sizeof(struct im_zmq));
 	if ( z == NULL ) return NULL;
@@ -93,6 +92,8 @@ struct im_zmq *im_zmq_connect(const char *zmq_address,
 
 	if ( zmq_request == NULL ) {
 
+		int i;
+
 		/* SUB mode */
 		if ( n_subscriptions == 0 ) {
 			ERROR("WARNING: No ZeroMQ subscriptions.  You should "
diff --git a/src/indexamajig.c b/src/indexamajig.c
index d9b0114d..9bbf7e5d 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -166,12 +166,11 @@ static void write_json_radii(FILE *fh, const char *name,
 
 static void write_methods(FILE *fh, const char *name, IndexingPrivate *ipriv)
 {
-	int i, n;
-	const IndexingMethod *methods;
-
 	fprintf(fh, "    \"%s\": [", name);
 
 	if ( ipriv != NULL ) {
+		const IndexingMethod *methods;
+		int i, n;
 		methods = indexing_methods(ipriv, &n);
 		for ( i=0; i<n; i++ ) {
 			fprintf(fh, " \"%s\"", indexer_str(methods[i]));
@@ -190,7 +189,6 @@ static void write_harvest_file(struct index_args *args,
                                int if_peaks, int if_checkcell)
 {
 	FILE *fh;
-	char *tmp;
 
 	fh = fopen(filename, "w");
 	if ( fh == NULL ) {
@@ -234,6 +232,9 @@ static void write_harvest_file(struct index_args *args,
 		fprintf(fh, "  \"indexing\": null\n");
 		fprintf(fh, "  \"integration\": null\n");
 	} else {
+
+		char *tmp;
+
 		fprintf(fh, "  \"indexing\": {\n");
 		write_methods(fh, "methods", args->ipriv);
 		write_json_cell(fh, "target_cell", args->cell);
diff --git a/src/list_events.c b/src/list_events.c
index 960c8929..67b27119 100644
--- a/src/list_events.c
+++ b/src/list_events.c
@@ -153,13 +153,13 @@ int main(int argc, char *argv[])
 	do {
 
 		char filename[1024];
-		int i;
 
 		rval = fgets(filename, 1024, ifh);
 		if ( rval != NULL ) {
 
 			char **evlist;
 			int num_events;
+			int i;
 
 			chomp(filename);
 
diff --git a/src/partial_sim.c b/src/partial_sim.c
index efba8ebd..ff9a73ac 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -98,7 +98,6 @@ static void calculate_partials(Crystal *cr,
 {
 	Reflection *refl;
 	RefListIterator *iter;
-	double res;
 
 	for ( refl = first_refl(crystal_get_reflections(cr), &iter);
 	      refl != NULL;
@@ -108,6 +107,7 @@ static void calculate_partials(Crystal *cr,
 		Reflection *rfull;
 		double L, p, Ip, If;
 		int bin;
+		double res;
 
 		get_indices(refl, &h, &k, &l);
 		get_asymm(sym, h, k, l, &h, &k, &l);
@@ -515,9 +515,7 @@ int main(int argc, char *argv[])
 	int n_threads = 1;
 	char *rval;
 	int i;
-	FILE *fh;
 	char *phist_file = NULL;
-	gsl_rng *rng_for_seeds;
 	int config_random = 0;
 	char *image_prefix = NULL;
 	Stream *template_stream = NULL;
@@ -969,6 +967,7 @@ int main(int argc, char *argv[])
 		fclose(fh);
 
 	} else {
+		gsl_rng *rng_for_seeds;
 		rng_for_seeds = gsl_rng_alloc(gsl_rng_mt19937);
 		for ( i=0; i<n_threads; i++ ) {
 			qargs.rngs[i] = gsl_rng_alloc(gsl_rng_mt19937);
@@ -993,14 +992,16 @@ int main(int argc, char *argv[])
 
 	if ( phist_file != NULL ) {
 
-		double overall_max = 0.0;
-		double overall_mean = 0.0;
-		long long int overall_total = 0;
+		FILE *fh;
 
 		fh = fopen(phist_file, "w");
 
 		if ( fh != NULL ) {
 
+			double overall_max = 0.0;
+			double overall_mean = 0.0;
+			long long int overall_total = 0;
+
 			for ( i=0; i<NBINS; i++ ) {
 
 				double rcen;
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 34d6c809..7098869d 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -131,7 +131,6 @@ static void record_panel(struct detgeom_panel *p, float *dp,
 	for ( fs=0; fs<p->w; fs++ ) {
 
 		double counts;
-		double cf;
 		double intensity, sa;
 		double pix_area, Lsq;
 		double xs, ys, rx, ry;
@@ -165,8 +164,7 @@ static void record_panel(struct detgeom_panel *p, float *dp,
 		if ( do_poisson ) {
 			counts = poisson_noise(rng, intensity * ph_per_e * sa);
 		} else {
-			cf = intensity * ph_per_e * sa;
-			counts = cf;
+			counts = intensity * ph_per_e * sa;
 		}
 
 		/* Number of photons in pixel */
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 27a8cd6a..c6ff3974 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -268,10 +268,8 @@ static void try_reindex(Crystal *crin, const RefList *full,
                         SymOpList *sym, SymOpList *amb, int scaleflags,
                         PartialityModel pmodel)
 {
-	RefList *list;
 	Crystal *cr;
-	UnitCell *cell;
-	double residual_original, residual_flipped;
+	double residual_original;
 	int idx, n;
 
 	if ( sym == NULL || amb == NULL ) return;
@@ -285,6 +283,10 @@ static void try_reindex(Crystal *crin, const RefList *full,
 
 	for ( idx=0; idx<n; idx++ ) {
 
+		RefList *list;
+		UnitCell *cell;
+		double residual_flipped;
+
 		cell = cell_new_from_cell(crystal_get_cell(crin));
 		if ( cell == NULL ) return;
 		reindex_cell(cell, amb, idx);
diff --git a/src/process_hkl.c b/src/process_hkl.c
index ed384a4a..b16146e3 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -131,9 +131,8 @@ static void plot_histogram(double *vals, int n, float hist_min, float hist_max,
 	step = (max-min)/nbins;
 
 	for ( i=0; i<n; i++ ) {
-		int bin;
 		if ( (vals[i] > min) && (vals[i] < max) ) {
-			bin = (vals[i]-min)/step;
+			int bin = (vals[i]-min)/step;
 			histo[bin]++;
 		}
 	}
@@ -282,7 +281,7 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr,
 	Reflection *refl;
 	RefListIterator *iter;
 	RefList *new_refl;
-	double scale, cc;
+	double scale;
 
 	new_refl = crystal_get_reflections(cr);
 
@@ -291,6 +290,7 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr,
 	polarisation_correction(new_refl, crystal_get_cell(cr), p);
 
 	if ( reference != NULL ) {
+		double cc;
 		if ( do_scale ) {
 			scale = scale_intensities(reference, new_refl, sym);
 		} else {
@@ -431,7 +431,6 @@ static int merge_stream(Stream *st,
 
 		for ( i=0; i<image->n_crystals; i++ ) {
 
-			int r;
 			Crystal *cr = image->crystals[i];
 
 			n_crystals_seen++;
@@ -439,6 +438,7 @@ static int merge_stream(Stream *st,
 			  && (crystal_get_resolution_limit(cr) >= min_res)
 			  && (flag_even_odd == 2 || n_crystals_seen%2 == flag_even_odd) )
 			{
+				int r;
 				n_crystals++;
 				r = merge_crystal(model, image, cr, reference,
 				                  sym, hist_vals,
@@ -889,8 +889,6 @@ int main(int argc, char *argv[])
 
 	if ( twopass ) {
 
-		RefList *reference;
-
 		if ( rewind_all_streams(&stream_list) ) {
 
 			ERROR("Couldn't rewind stream - scaling cannot be "
@@ -899,6 +897,7 @@ int main(int argc, char *argv[])
 		} else {
 
 			int r;
+			RefList *reference;
 
 			STATUS("Second pass for scaling and/or CCs...\n");
 
diff --git a/src/render_hkl.c b/src/render_hkl.c
index 94d6202a..c47a2c4d 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -421,7 +421,6 @@ static void render_za(UnitCell *cell, RefList *list,
 	double max_val;
 	double scale1, scale2, scale;
 	double sep_u, sep_v, max_r;
-	double u, v;
 	double as, bs, theta;
 	double asx, asy, asz;
 	double bsx, bsy, bsz;
@@ -562,6 +561,8 @@ static void render_za(UnitCell *cell, RefList *list,
 
 	if ( !noaxes ) {
 
+		double u, v;
+
 		/* Centre marker */
 		cairo_arc(dctx, (double)cx,
 				(double)cy, max_r, 0, 2*M_PI);
diff --git a/src/time-accounts.c b/src/time-accounts.c
index 679eb5f1..77ab9b5d 100644
--- a/src/time-accounts.c
+++ b/src/time-accounts.c
@@ -77,13 +77,13 @@ void time_accounts_free(TimeAccounts *accs)
 static int find_account(TimeAccounts *accs, enum timeaccount acc)
 {
 	int i;
-	static int warned_toomany = 0;
 
 	for ( i=0; i<accs->n_accs; i++ ) {
 		if ( accs->accs[i] == acc ) return i;
 	}
 
 	if ( i == MAX_ACCOUNTS ) {
+		static int warned_toomany = 0;
 		if ( !warned_toomany ) printf("Too many time accounts used!\n");
 		warned_toomany = 1;
 		return MAX_ACCOUNTS;
diff --git a/src/whirligig.c b/src/whirligig.c
index 546301ba..611825ba 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -403,8 +403,6 @@ static void connect_series(struct window *win)
 {
 	while ( win->join_ptr < win->ws ) {
 
-		int i;
-
 		if ( win->join_ptr == 0 ) {
 			win->join_ptr++;
 			continue;
@@ -415,6 +413,7 @@ static void connect_series(struct window *win)
 
 		/* Try to join this frame to each of the active series */
 		if ( win->join_ptr > 1 ) {
+			int i;
 			for ( i=0; i<MAX_SER; i++ ) {
 				if ( win->ser[i][win->join_ptr-1] != -1 ) {
 					try_join(win, i);