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-rw-r--r--libcrystfel/src/cell-utils.c2
-rw-r--r--libcrystfel/src/datatemplate.c2
-rw-r--r--libcrystfel/src/filters.c5
-rw-r--r--libcrystfel/src/image.c2
-rw-r--r--libcrystfel/src/index.c3
-rw-r--r--libcrystfel/src/indexers/asdf.c21
-rw-r--r--libcrystfel/src/indexers/felix.c2
-rw-r--r--libcrystfel/src/indexers/fromfile.c3
-rw-r--r--libcrystfel/src/indexers/mosflm.c5
-rw-r--r--libcrystfel/src/indexers/xds.c2
-rw-r--r--libcrystfel/src/integration.c3
-rw-r--r--libcrystfel/src/peaks.c4
-rw-r--r--libcrystfel/src/reflist-utils.c2
-rw-r--r--libcrystfel/src/stream.c6
14 files changed, 37 insertions, 25 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");
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 18:07:17 +0000