Eliminate duplicate symbols

This makes searching easier, and also permits Meson's unity build mode.

18 files changed, 112 insertions, 102 deletions

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index cc028025..2459f946 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -826,7 +826,7 @@ static int parse_toplevel(DataTemplate *dt,
 }
 
 
-static int num_path_placeholders(const char *str)
+static int dt_num_path_placeholders(const char *str)
 {
 	size_t i, len;
 	int n_pl;
@@ -1037,9 +1037,9 @@ DataTemplate *data_template_new_from_string(const char *string_in)
 		return NULL;
 	}
 
-	num_data_pl = num_path_placeholders(dt->panels[i].data);
-	num_mask_pl = num_path_placeholders(dt->panels[i].mask);
-	num_satmap_pl = num_path_placeholders(dt->panels[i].satmap);
+	num_data_pl = dt_num_path_placeholders(dt->panels[i].data);
+	num_mask_pl = dt_num_path_placeholders(dt->panels[i].mask);
+	num_satmap_pl = dt_num_path_placeholders(dt->panels[i].satmap);
 
 	/* This is because the "data" path will be used to expand
 	 * the path to generate the event list */
@@ -1122,19 +1122,19 @@ DataTemplate *data_template_new_from_string(const char *string_in)
 			reject = 1;
 		}
 
-		if ( num_path_placeholders(p->data) != num_data_pl ) {
+		if ( dt_num_path_placeholders(p->data) != num_data_pl ) {
 			ERROR("Data locations for all panels must "
 			      "have the same number of placeholders\n");
 			reject = 1;
 		}
 
-		if ( num_path_placeholders(p->mask) != num_mask_pl ) {
+		if ( dt_num_path_placeholders(p->mask) != num_mask_pl ) {
 			ERROR("Mask locations for all panels must "
 			      "have the same number of placeholders\n");
 			reject = 1;
 		}
 
-		if ( num_path_placeholders(p->satmap) != num_satmap_pl ) {
+		if ( dt_num_path_placeholders(p->satmap) != num_satmap_pl ) {
 			ERROR("Satmap locations for all panels must "
 			      "have the same number of placeholders\n");
 			reject = 1;
@@ -1392,7 +1392,7 @@ static double unit_string_to_unit(const char *str)
 }
 
 
-static double get_length(const char *from)
+static double dt_get_length(const char *from)
 {
 	double units;
 	char *sp;
@@ -1456,7 +1456,7 @@ struct detgeom *data_template_to_detgeom(const DataTemplate *dt)
 		/* NB cnx,cny are in pixels, cnz is in m */
 		detgeom->panels[i].cnx = dt->panels[i].cnx;
 		detgeom->panels[i].cny = dt->panels[i].cny;
-		detgeom->panels[i].cnz = get_length(dt->panels[i].cnz_from);
+		detgeom->panels[i].cnz = dt_get_length(dt->panels[i].cnz_from);
 
 		/* Apply offset (in m) and then convert cnz from
 		 * m to pixels */
@@ -1484,7 +1484,7 @@ struct detgeom *data_template_to_detgeom(const DataTemplate *dt)
 }
 
 
-static int num_placeholders(const struct panel_template *p)
+static int dt_num_placeholders(const struct panel_template *p)
 {
 	int i;
 	int n_pl = 0;
@@ -1514,7 +1514,7 @@ int data_template_get_slab_extents(const DataTemplate *dt,
 			return 1;
 		}
 
-		if ( num_placeholders(p) > 0 ) {
+		if ( dt_num_placeholders(p) > 0 ) {
 			/* Not slabby */
 			return 1;
 		}
diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c
index 4f6372f4..524e68a7 100644
--- a/libcrystfel/src/felix.c
+++ b/libcrystfel/src/felix.c
@@ -800,7 +800,7 @@ const char *felix_probe(UnitCell *cell)
 }
 
 
-static void show_help()
+static void felix_show_help()
 {
 	printf("Parameters for the Felix indexing algorithm:\n"
 "     --felix-domega        Degree range of omega (moscaicity) to consider.\n"
@@ -832,7 +832,8 @@ static void show_help()
 }
 
 
-static error_t parse_arg(int key, char *arg, struct argp_state *state)
+static error_t felix_parse_arg(int key, char *arg,
+                               struct argp_state *state)
 {
 	struct felix_options **opts_ptr = state->input;
 	float tmp;
@@ -855,7 +856,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		break;
 
 		case 1 :
-		show_help();
+		felix_show_help();
 		return EINVAL;
 
 		case 2 :
@@ -939,7 +940,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 }
 
 
-static struct argp_option options[] = {
+static struct argp_option felix_options[] = {
 
 	{"help-felix", 1, NULL, OPTION_NO_USAGE,
 	 "Show options for Felix indexing algorithm", 99},
@@ -958,4 +959,5 @@ static struct argp_option options[] = {
 };
 
 
-struct argp felix_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL };
+struct argp felix_argp = { felix_options, felix_parse_arg,
+                           NULL, NULL, NULL, NULL, NULL };
diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c
index fac79e99..c03bf2d2 100644
--- a/libcrystfel/src/image-hdf5.c
+++ b/libcrystfel/src/image-hdf5.c
@@ -204,7 +204,7 @@ int *read_dim_parts(const char *ev_orig, int *pn_dvals)
 }
 
 
-static int num_path_placeholders(const char *pattern)
+static int imh_num_path_placeholders(const char *pattern)
 {
 	size_t l, i;
 	int n_pl_exp = 0;
@@ -242,7 +242,7 @@ char *substitute_path(const char *ev, const char *pattern)
 	plvals = read_path_parts(ev, &n_plvals);
 	if ( plvals == NULL ) return NULL;
 
-	n_pl_exp = num_path_placeholders(pattern);
+	n_pl_exp = imh_num_path_placeholders(pattern);
 
 	if ( n_plvals != n_pl_exp ) {
 		ERROR("Wrong number of path placeholders: "
@@ -315,7 +315,7 @@ static void make_placeholder_skip(signed int *dt_dims,
 }
 
 
-static int num_placeholders(const struct panel_template *p)
+static int imh_num_placeholders(const struct panel_template *p)
 {
 	int i;
 	int n_pl = 0;
@@ -408,7 +408,7 @@ static int load_hdf5_hyperslab(struct panel_template *p,
 
 	/* Does the array have the expected number of dimensions? */
 	total_dt_dims = total_dimensions(p);
-	plh_dt_dims = num_placeholders(p);
+	plh_dt_dims = imh_num_placeholders(p);
 	if ( ndims != total_dt_dims ) {
 		/* If the dimensions match after excluding
 		 * placeholders, it's OK - probably a static mask
@@ -1230,7 +1230,7 @@ struct ev_list
 };
 
 
-static int add_to_list(struct ev_list *list, char *ev_str)
+static int add_ev_to_list(struct ev_list *list, char *ev_str)
 {
 	if ( list->n_events == list->max_events ) {
 		char **new_events = realloc(list->events,
@@ -1366,7 +1366,7 @@ static int rec_expand_paths(hid_t gh, struct ev_list *list,
 
 			addme = demunge_event(ev_str_new);
 			if ( addme != NULL ) {
-				add_to_list(list, addme);
+				add_ev_to_list(list, addme);
 				free(addme);
 			}
 			free(ev_str_new);
@@ -1448,7 +1448,7 @@ static int rec_expand_dims(struct ev_list *list,
 	if ( n_placeholder_dims == 1 ) {
 		for ( i=0; i<placeholder_sizes[0]; i++ ) {
 			snprintf(dim_ev, 16, "%s/%i", path_ev, i);
-			if ( add_to_list(list, dim_ev) ) return 1;
+			if ( add_ev_to_list(list, dim_ev) ) return 1;
 		}
 	} else {
 
@@ -1520,10 +1520,10 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
 
 	/* If the DataTemplate already says that one frame will be
 	 * found per file, short-circuit this whole affair */
-	if ( (num_placeholders(&dtempl->panels[0]) == 0)
-	  && (num_path_placeholders(dtempl->panels[0].data) == 0) )
+	if ( (imh_num_placeholders(&dtempl->panels[0]) == 0)
+	  && (imh_num_path_placeholders(dtempl->panels[0].data) == 0) )
 	{
-		add_to_list(&full_evs, "//");
+		add_ev_to_list(&full_evs, "//");
 		*pn_frames = full_evs.n_events;
 		return full_evs.events;
 	}
@@ -1632,7 +1632,7 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
 			                            &n_evs_this_path);
 
 			for ( j=0; j<n_evs_this_path; j++ ) {
-				add_to_list(&full_evs, evs_this_path[j]);
+				add_ev_to_list(&full_evs, evs_this_path[j]);
 				free(evs_this_path[j]);
 			}
 
@@ -1641,7 +1641,7 @@ char **image_hdf5_expand_frames(const DataTemplate *dtempl,
 		} else {
 
 			/* Easy case with no dims to expand */
-			add_to_list(&full_evs, path_evs[i]);
+			add_ev_to_list(&full_evs, path_evs[i]);
 
 		}
 
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 1780526b..68234a33 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -340,8 +340,8 @@ static char *get_value_and_units(struct image *image, const char *from,
 }
 
 
-static double get_length(struct image *image, const char *from,
-                         double default_scale)
+static double im_get_length(struct image *image, const char *from,
+                            double default_scale)
 {
 	char *units;
 	double value;
@@ -445,7 +445,9 @@ void create_detgeom(struct image *image, const DataTemplate *dtempl)
 		/* NB cnx,cny are in pixels, cnz is in m */
 		detgeom->panels[i].cnx = dtempl->panels[i].cnx;
 		detgeom->panels[i].cny = dtempl->panels[i].cny;
-		detgeom->panels[i].cnz = get_length(image, dtempl->panels[i].cnz_from, 1e-3);
+		detgeom->panels[i].cnz = im_get_length(image,
+		                                       dtempl->panels[i].cnz_from,
+		                                       1e-3);
 
 		/* Apply offset (in m) and then convert cnz from
 		 * m to pixels */
@@ -453,8 +455,8 @@ void create_detgeom(struct image *image, const DataTemplate *dtempl)
 		detgeom->panels[i].cnz /= detgeom->panels[i].pixel_pitch;
 
 		/* Apply overall shift (already in m) */
-		shift_x = get_length(image, dtempl->shift_x_from, 1.0);
-		shift_y = get_length(image, dtempl->shift_y_from, 1.0);
+		shift_x = im_get_length(image, dtempl->shift_x_from, 1.0);
+		shift_y = im_get_length(image, dtempl->shift_y_from, 1.0);
 
 		if ( !isnan(shift_x) ) {
 			detgeom->panels[i].cnx += shift_x;
diff --git a/libcrystfel/src/integer_matrix.c b/libcrystfel/src/integer_matrix.c
index 43f41eeb..f54acea5 100644
--- a/libcrystfel/src/integer_matrix.c
+++ b/libcrystfel/src/integer_matrix.c
@@ -253,8 +253,9 @@ void intmat_zero(IntegerMatrix *m)
 }
 
 
-static IntegerMatrix *delete_row_and_column(const IntegerMatrix *m,
-                                            unsigned int di, unsigned int dj)
+static IntegerMatrix *intmat_delete_row_and_column(const IntegerMatrix *m,
+                                                   unsigned int di,
+                                                   unsigned int dj)
 {
 	IntegerMatrix *n;
 	unsigned int i, j;
@@ -280,13 +281,13 @@ static IntegerMatrix *delete_row_and_column(const IntegerMatrix *m,
 }
 
 
-static signed int cofactor(const IntegerMatrix *m,
-                           unsigned int i, unsigned int j)
+static signed int intmat_cofactor(const IntegerMatrix *m,
+                                  unsigned int i, unsigned int j)
 {
 	IntegerMatrix *n;
 	signed int t, C;
 
-	n = delete_row_and_column(m, i, j);
+	n = intmat_delete_row_and_column(m, i, j);
 	if ( n == NULL ) {
 		fprintf(stderr, "Failed to allocate matrix.\n");
 		return 0;
@@ -324,7 +325,7 @@ signed int intmat_det(const IntegerMatrix *m)
 	i = 0;  /* Fixed */
 	for ( j=0; j<m->cols; j++ ) {
 
-		det += intmat_get(m, i, j) * cofactor(m, i, j);
+		det += intmat_get(m, i, j) * intmat_cofactor(m, i, j);
 
 	}
 
@@ -343,7 +344,7 @@ static IntegerMatrix *intmat_cofactors(const IntegerMatrix *m)
 	for ( i=0; i<n->rows; i++ ) {
 	for ( j=0; j<n->cols; j++ ) {
 
-		intmat_set(n, i, j, cofactor(m, i, j));
+		intmat_set(n, i, j, intmat_cofactor(m, i, j));
 
 	}
 	}
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 8f81dc10..4a66363b 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1533,16 +1533,6 @@ int integrate_rings_once(Reflection *refl,
 }
 
 
-static int compare_double(const void *av, const void *bv)
-{
-	double a = *(double *)av;
-	double b = *(double *)bv;
-	if ( a > b ) return 1;
-	if ( a < b ) return -1;
-	return 0;
-}
-
-
 static double estimate_resolution(UnitCell *cell, ImageFeatureList *flist)
 {
 	int i;
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index ef282cbe..bacd345f 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -201,10 +201,11 @@ static void mosflm_parseline(const char *line, struct image *image,
 }
 
 
-/* This is the opposite of spacegroup_for_lattice() below.
+/* This is the opposite of mosflm_spacegroup_for_lattice() below.
  * Note that this is not general, just a set of rules for interpreting MOSFLM's
  * output. */
-static LatticeType spacegroup_to_lattice(const char *sg, char *ua, char *cen)
+static LatticeType mosflm_spacegroup_to_lattice(const char *sg,
+                                                char *ua, char *cen)
 {
 	LatticeType latt;
 
@@ -298,7 +299,7 @@ static int read_newmat(struct mosflm_data *mosflm, const char *filename,
 		return 1;
 	}
 	//STATUS("MOSFLM says '%s'\n", symm);
-	latt = spacegroup_to_lattice(symm+5, &ua, &cen);
+	latt = mosflm_spacegroup_to_lattice(symm+5, &ua, &cen);
 
 	/* MOSFLM "A" matrix is multiplied by lambda, so fix this */
 	c = 1.0/image->lambda;
@@ -437,7 +438,7 @@ static void mosflm_sendline(const char *line, struct mosflm_data *mosflm)
 
 /* Turn what we know about the unit cell into something which we can give to
  * MOSFLM to make it give us only indexing results compatible with the cell. */
-static char *spacegroup_for_lattice(UnitCell *cell)
+static char *mosflm_spacegroup_for_lattice(UnitCell *cell)
 {
 	LatticeType latt;
 	char centering;
@@ -530,7 +531,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 				mosflm_sendline("CRYSTAL R\n", mosflm);
 			}
 
-			symm = spacegroup_for_lattice(mosflm->mp->template);
+			symm = mosflm_spacegroup_for_lattice(mosflm->mp->template);
 			snprintf(tmp, 255, "SYMM %s\n", symm);
 			//STATUS("Asking MOSFLM for '%s'\n", symm);
 			free(symm);
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 854eaf39..83239236 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -723,16 +723,6 @@ void validate_peaks(struct image *image, double min_snr,
 }
 
 
-static int compare_double(const void *av, const void *bv)
-{
-	double a = *(double *)av;
-	double b = *(double *)bv;
-	if ( a > b ) return 1;
-	if ( a < b ) return -1;
-	return 0;
-}
-
-
 double estimate_peak_resolution(ImageFeatureList *peaks, double lambda,
                                 struct detgeom *det)
 {
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c
index 39913284..b6a33148 100644
--- a/libcrystfel/src/pinkindexer.c
+++ b/libcrystfel/src/pinkindexer.c
@@ -396,7 +396,7 @@ const char *pinkIndexer_probe(UnitCell *cell)
 
 #endif /* HAVE_PINKINDEXER */
 
-static void show_help()
+static void pinkIndexer_show_help()
 {
 	printf(
 "Parameters for the PinkIndexer indexing algorithm:\n"
@@ -440,7 +440,8 @@ static void show_help()
 }
 
 
-static error_t parse_arg(int key, char *arg, struct argp_state *state)
+static error_t pinkindexer_parse_arg(int key, char *arg,
+                                     struct argp_state *state)
 {
 	float tmp, tmp2;
 	struct pinkIndexer_options **opts_ptr = state->input;
@@ -466,7 +467,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		break;
 
 		case 1 :
-		show_help();
+		pinkIndexer_show_help();
 		return EINVAL;
 
 		case 2 :
@@ -576,7 +577,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 }
 
 
-static struct argp_option options[] = {
+static struct argp_option pinkindexer_options[] = {
 
 	{"help-pinkindexer", 1, NULL, OPTION_NO_USAGE,
 	 "Show options for PinkIndexer indexing algorithm", 99},
@@ -617,4 +618,6 @@ static struct argp_option options[] = {
 };
 
 
-struct argp pinkIndexer_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL };
+struct argp pinkIndexer_argp = { pinkindexer_options,
+                                 pinkindexer_parse_arg,
+                                 NULL, NULL, NULL, NULL, NULL };
diff --git a/libcrystfel/src/rational.c b/libcrystfel/src/rational.c
index 05bca429..ee46a73b 100644
--- a/libcrystfel/src/rational.c
+++ b/libcrystfel/src/rational.c
@@ -640,8 +640,9 @@ void transform_fractional_coords_rtnl_inverse(const RationalMatrix *P,
 }
 
 
-static RationalMatrix *delete_row_and_column(const RationalMatrix *m,
-                                             unsigned int di, unsigned int dj)
+static RationalMatrix *rational_delete_row_and_column(const RationalMatrix *m,
+                                                      unsigned int di,
+                                                      unsigned int dj)
 {
 	RationalMatrix *n;
 	unsigned int i, j;
@@ -667,13 +668,13 @@ static RationalMatrix *delete_row_and_column(const RationalMatrix *m,
 }
 
 
-static Rational cofactor(const RationalMatrix *m,
-                         unsigned int i, unsigned int j)
+static Rational rational_cofactor(const RationalMatrix *m,
+                                  unsigned int i, unsigned int j)
 {
 	RationalMatrix *n;
 	Rational t, C;
 
-	n = delete_row_and_column(m, i, j);
+	n = rational_delete_row_and_column(m, i, j);
 	if ( n == NULL ) {
 		fprintf(stderr, "Failed to allocate matrix.\n");
 		return rtnl_zero();
@@ -708,7 +709,8 @@ Rational rtnl_mtx_det(const RationalMatrix *m)
 	det = rtnl_zero();
 	for ( j=0; j<m->cols; j++ ) {
 		Rational a;
-		a = rtnl_mul(rtnl_mtx_get(m, i, j), cofactor(m, i, j));
+		a = rtnl_mul(rtnl_mtx_get(m, i, j),
+		             rational_cofactor(m, i, j));
 		det = rtnl_add(det, a);
 	}
 
diff --git a/libcrystfel/src/reflist.c b/libcrystfel/src/reflist.c
index df8f24fc..d8741a2f 100644
--- a/libcrystfel/src/reflist.c
+++ b/libcrystfel/src/reflist.c
@@ -882,8 +882,11 @@ static Reflection *insert_node(Reflection *refl, Reflection *new)
 }
 
 
-static void add_to_list(RefList *list, Reflection *new,
-                        signed int h, signed int k, signed int l)
+static void add_refl_to_list_real(RefList *list,
+                                  Reflection *new,
+                                  signed int h,
+                                  signed int k,
+                                  signed int l)
 {
 	Reflection *f;
 
@@ -929,7 +932,7 @@ Reflection *add_refl(RefList *list, signed int h, signed int k, signed int l)
 	new = new_node(SERIAL(h, k, l));
 	if ( new == NULL ) return NULL;
 
-	add_to_list(list, new, h, k, l);
+	add_refl_to_list_real(list, new, h, k, l);
 
 	return new;
 }
@@ -948,7 +951,7 @@ void add_refl_to_list(Reflection *refl, RefList *list)
 
 	get_indices(refl, &h, &k, &l);
 
-	add_to_list(list, refl, h, k, l);
+	add_refl_to_list_real(list, refl, h, k, l);
 }
 
 
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
index a67d372c..5b5bff59 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/taketwo.c
@@ -2269,7 +2269,7 @@ const char *taketwo_probe(UnitCell *cell)
 }
 
 
-static void show_help()
+static void taketwo_show_help()
 {
 	printf("Parameters for the TakeTwo indexing algorithm:\n"
 "     --taketwo-member-threshold\n"
@@ -2284,7 +2284,8 @@ static void show_help()
 }
 
 
-static error_t parse_arg(int key, char *arg, struct argp_state *state)
+static error_t taketwo_parse_arg(int key, char *arg,
+                                 struct argp_state *state)
 {
 	struct taketwo_options **opts_ptr = state->input;
 	float tmp;
@@ -2301,7 +2302,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		break;
 
 		case 1 :
-		show_help();
+		taketwo_show_help();
 		return EINVAL;
 
 		case 2 :
@@ -2348,7 +2349,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 }
 
 
-static struct argp_option options[] = {
+static struct argp_option taketwo_options[] = {
 
 	{"help-taketwo", 1, NULL, OPTION_NO_USAGE,
 	 "Show options for TakeTwo indexing algorithm", 99},
@@ -2361,4 +2362,5 @@ static struct argp_option options[] = {
 };
 
 
-struct argp taketwo_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL };
+struct argp taketwo_argp = { taketwo_options, taketwo_parse_arg,
+                             NULL, NULL, NULL, NULL, NULL };
diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c
index 048180cf..8391fe95 100644
--- a/libcrystfel/src/utils.c
+++ b/libcrystfel/src/utils.c
@@ -803,6 +803,16 @@ char *load_entire_file(const char *filename)
 }
 
 
+int compare_double(const void *av, const void *bv)
+{
+	double a = *(double *)av;
+	double b = *(double *)bv;
+	if ( a > b ) return 1;
+	if ( a < b ) return -1;
+	return 0;
+}
+
+
 /* -------------------------- libcrystfel features  ------------------------ */
 
 int crystfel_has_peakfinder9()
diff --git a/libcrystfel/src/utils.h b/libcrystfel/src/utils.h
index be252672..51158e8b 100644
--- a/libcrystfel/src/utils.h
+++ b/libcrystfel/src/utils.h
@@ -267,6 +267,8 @@ extern struct quaternion random_quaternion(gsl_rng *rng);
 extern int quaternion_valid(struct quaternion q);
 extern struct rvec quat_rot(struct rvec q, struct quaternion z);
 
+extern int compare_double(const void *av, const void *bv);
+
 /* Keep these ones inline, to avoid function call overhead */
 static inline struct quaternion invalid_quaternion(void)
 {
diff --git a/libcrystfel/src/xds.c b/libcrystfel/src/xds.c
index 03e01179..02610d5e 100644
--- a/libcrystfel/src/xds.c
+++ b/libcrystfel/src/xds.c
@@ -73,7 +73,7 @@ struct xds_private
 };
 
 
-/* Essentially the reverse of spacegroup_for_lattice(), below */
+/* Essentially the reverse of xds_spacegroup_for_lattice(), below */
 static int convert_spacegroup_number(int spg, LatticeType *lt, char *cen,
                                      char *ua)
 {
@@ -240,7 +240,7 @@ static void write_spot(struct image *image)
 
 /* Turn what we know about the unit cell into something which we can give to
  * XDS to make it give us only indexing results compatible with the cell. */
-static const char *spacegroup_for_lattice(UnitCell *cell)
+static const char *xds_spacegroup_for_lattice(UnitCell *cell)
 {
 	LatticeType latt;
 	char centering;
@@ -335,7 +335,7 @@ static int write_inp(struct image *image, struct xds_private *xp)
 
 	if ( xp->indm & INDEXING_USE_LATTICE_TYPE ) {
 		fprintf(fh, "SPACE_GROUP_NUMBER= %s\n",
-			    spacegroup_for_lattice(xp->cell));
+			    xds_spacegroup_for_lattice(xp->cell));
 	} else {
 		fprintf(fh, "SPACE_GROUP_NUMBER= 0\n");
 	}
@@ -461,7 +461,7 @@ void *xds_prepare(IndexingMethod *indm, UnitCell *cell)
 		return NULL;
 	}
 
-	if ( (cell != NULL) && (spacegroup_for_lattice(cell) == NULL) ) {
+	if ( (cell != NULL) && (xds_spacegroup_for_lattice(cell) == NULL) ) {
 		ERROR("Don't know how to ask XDS for your cell.\n");
 		return NULL;
 	}
diff --git a/libcrystfel/src/xgandalf.c b/libcrystfel/src/xgandalf.c
index 9135c2f3..c66bff6c 100644
--- a/libcrystfel/src/xgandalf.c
+++ b/libcrystfel/src/xgandalf.c
@@ -346,7 +346,7 @@ const char *xgandalf_probe(UnitCell *cell)
 
 #endif // HAVE_XGANDALF
 
-static void show_help()
+static void xgandalf_show_help()
 {
 	printf("Parameters for the TakeTwo indexing algorithm:\n"
 "     --xgandalf-sampling-pitch\n"
@@ -378,7 +378,8 @@ static void show_help()
 }
 
 
-static error_t parse_arg(int key, char *arg, struct argp_state *state)
+static error_t xgandalf_parse_arg(int key, char *arg,
+                                  struct argp_state *state)
 {
 	struct xgandalf_options **opts_ptr = state->input;
 
@@ -397,7 +398,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		break;
 
 		case 1 :
-		show_help();
+		xgandalf_show_help();
 		return EINVAL;
 
 		case 2 :
@@ -457,7 +458,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 }
 
 
-static struct argp_option options[] = {
+static struct argp_option xgandalf_options[] = {
 
 	{"help-xgandalf", 1, NULL, OPTION_NO_USAGE,
 	 "Show options for XGANDALF indexing algorithm", 99},
@@ -488,4 +489,5 @@ static struct argp_option options[] = {
 };
 
 
-struct argp xgandalf_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL };
+struct argp xgandalf_argp = { xgandalf_options, xgandalf_parse_arg,
+                              NULL, NULL, NULL, NULL, NULL };
diff --git a/src/post-refinement.c b/src/post-refinement.c
index b3ce79c1..09438a82 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -753,7 +753,7 @@ struct refine_args
 };
 
 
-struct queue_args
+struct pr_queue_args
 {
 	int n_started;
 	int n_done;
@@ -780,7 +780,7 @@ static void refine_image(void *task, int id)
 static void *get_image(void *vqargs)
 {
 	struct refine_args *task;
-	struct queue_args *qargs = vqargs;
+	struct pr_queue_args *qargs = vqargs;
 
 	task = malloc(sizeof(struct refine_args));
 	memcpy(task, &qargs->task_defaults, sizeof(struct refine_args));
@@ -796,7 +796,7 @@ static void *get_image(void *vqargs)
 
 static void done_image(void *vqargs, void *task)
 {
-	struct queue_args *qa = vqargs;
+	struct pr_queue_args *qa = vqargs;
 
 	qa->n_done++;
 
@@ -811,7 +811,7 @@ void refine_all(Crystal **crystals, int n_crystals,
                 SymOpList *sym, SymOpList *amb, int scaleflags)
 {
 	struct refine_args task_defaults;
-	struct queue_args qargs;
+	struct pr_queue_args qargs;
 
 	task_defaults.full = full;
 	task_defaults.crystal = NULL;
diff --git a/src/scaling.c b/src/scaling.c
index 368c3ab5..864bab6f 100644
--- a/src/scaling.c
+++ b/src/scaling.c
@@ -57,7 +57,7 @@ struct scale_args
 };
 
 
-struct queue_args
+struct scale_queue_args
 {
 	int n_started;
 	int n_done;
@@ -77,7 +77,7 @@ static void scale_crystal(void *task, int id)
 static void *get_crystal(void *vqargs)
 {
 	struct scale_args *task;
-	struct queue_args *qargs = vqargs;
+	struct scale_queue_args *qargs = vqargs;
 
 	task = malloc(sizeof(struct scale_args));
 	memcpy(task, &qargs->task_defaults, sizeof(struct scale_args));
@@ -92,7 +92,7 @@ static void *get_crystal(void *vqargs)
 
 static void done_crystal(void *vqargs, void *task)
 {
-	struct queue_args *qa = vqargs;
+	struct scale_queue_args *qa = vqargs;
 	qa->n_done++;
 	progress_bar(qa->n_done, qa->n_crystals, "Scaling");
 	free(task);
@@ -124,7 +124,7 @@ static double total_log_r(Crystal **crystals, int n_crystals, RefList *full,
 void scale_all(Crystal **crystals, int n_crystals, int nthreads, int scaleflags)
 {
 	struct scale_args task_defaults;
-	struct queue_args qargs;
+	struct scale_queue_args qargs;
 	double old_res, new_res;
 	int niter = 0;