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-rw-r--r--libcrystfel/src/integration.c106
1 files changed, 53 insertions, 53 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 8b05efe7..d2c06db7 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -393,7 +393,7 @@ static int alloc_boxes(struct intcontext *ic, int new_max_boxes)
{
struct peak_box *boxes_new;
- boxes_new = realloc(ic->boxes, sizeof(struct peak_box)*new_max_boxes);
+ boxes_new = cfrealloc(ic->boxes, sizeof(struct peak_box)*new_max_boxes);
if ( boxes_new == NULL ) return 1;
ic->boxes = boxes_new;
@@ -467,7 +467,7 @@ struct intcontext *intcontext_new(struct image *image,
int i;
struct intcontext *ic;
- ic = malloc(sizeof(struct intcontext));
+ ic = cfmalloc(sizeof(struct intcontext));
if ( ic == NULL ) return NULL;
ic->halfw = ir_out;
@@ -481,36 +481,36 @@ struct intcontext *intcontext_new(struct image *image,
ic->int_diag = INTDIAG_NONE;
ic->w = 2*ic->halfw + 1;
- ic->bm = malloc(ic->w * ic->w * sizeof(enum boxmask_val));
+ ic->bm = cfmalloc(ic->w * ic->w * sizeof(enum boxmask_val));
if ( ic->bm == NULL ) {
ERROR("Failed to allocate box mask.\n");
- free(ic);
+ cffree(ic);
return NULL;
}
/* How many reference profiles? */
ic->n_reference_profiles = 1;
- ic->reference_profiles = calloc(ic->n_reference_profiles,
- sizeof(double *));
+ ic->reference_profiles = cfcalloc(ic->n_reference_profiles,
+ sizeof(double *));
if ( ic->reference_profiles == NULL ) {
- free(ic);
+ cffree(ic);
return NULL;
}
- ic->reference_den = calloc(ic->n_reference_profiles, sizeof(double *));
+ ic->reference_den = cfcalloc(ic->n_reference_profiles, sizeof(double *));
if ( ic->reference_den == NULL ) {
- free(ic);
+ cffree(ic);
return NULL;
}
- ic->n_profiles_in_reference = calloc(ic->n_reference_profiles,
- sizeof(int));
+ ic->n_profiles_in_reference = cfcalloc(ic->n_reference_profiles,
+ sizeof(int));
if ( ic->n_profiles_in_reference == NULL ) {
- free(ic);
+ cffree(ic);
return NULL;
}
for ( i=0; i<ic->n_reference_profiles; i++ ) {
- ic->reference_profiles[i] = malloc(ic->w*ic->w*sizeof(double));
+ ic->reference_profiles[i] = cfmalloc(ic->w*ic->w*sizeof(double));
if ( ic->reference_profiles[i] == NULL ) return NULL;
- ic->reference_den[i] = malloc(ic->w*ic->w*sizeof(double));
+ ic->reference_den[i] = cfmalloc(ic->w*ic->w*sizeof(double));
if ( ic->reference_den[i] == NULL ) return NULL;
}
zero_profiles(ic);
@@ -519,7 +519,7 @@ struct intcontext *intcontext_new(struct image *image,
ic->n_boxes = 0;
ic->max_boxes = 0;
if ( alloc_boxes(ic, 32) ) {
- free(ic);
+ cffree(ic);
return NULL;
}
@@ -534,20 +534,20 @@ void intcontext_free(struct intcontext *ic)
int i;
for ( i=0; i<ic->n_boxes; i++ ) {
- free(ic->boxes[i].bm);
+ cffree(ic->boxes[i].bm);
gsl_matrix_free(ic->boxes[i].bgm);
}
- free(ic->boxes);
+ cffree(ic->boxes);
for ( i=0; i<ic->n_reference_profiles; i++ ) {
- free(ic->reference_profiles[i]);
- free(ic->reference_den[i]);
- }
- free(ic->reference_profiles);
- free(ic->reference_den);
- free(ic->n_profiles_in_reference);
- free(ic->bm);
- free(ic);
+ cffree(ic->reference_profiles[i]);
+ cffree(ic->reference_den[i]);
+ }
+ cffree(ic->reference_profiles);
+ cffree(ic->reference_den);
+ cffree(ic->n_profiles_in_reference);
+ cffree(ic->bm);
+ cffree(ic);
}
@@ -604,7 +604,7 @@ static void delete_box(struct intcontext *ic, struct peak_box *bx)
return;
}
- free(bx->bm);
+ cffree(bx->bm);
gsl_matrix_free(bx->bgm);
memmove(&ic->boxes[i], &ic->boxes[i+1],
@@ -803,7 +803,7 @@ static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
if ( sat != NULL ) *sat = 0;
- bx->bm = malloc(ic->w*ic->w*sizeof(enum boxmask_val));
+ bx->bm = cfmalloc(ic->w*ic->w*sizeof(enum boxmask_val));
if ( bx->bm == NULL ) {
ERROR("Failed to allocate box mask\n");
return 1;
@@ -980,7 +980,7 @@ static int center_and_check_box(struct intcontext *ic, struct peak_box *bx,
t_offs_fs += ifs;
t_offs_ss += iss;
- free(bx->bm);
+ cffree(bx->bm);
if ( check_box(ic, bx, sat) ) {
return 1;
}
@@ -1342,17 +1342,16 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list)
void integrate_prof2d(IntegrationMethod meth,
- Crystal *cr, struct image *image, IntDiag int_diag,
+ Crystal *cr, RefList *list,
+ struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out,
pthread_mutex_t *term_lock, int **masks)
{
- RefList *list;
UnitCell *cell;
struct intcontext *ic;
int i;
- list = crystal_get_reflections(cr);
cell = crystal_get_cell(cr);
ic = intcontext_new(image, cell, meth,
@@ -1515,7 +1514,7 @@ static double estimate_resolution(Crystal *cr, struct image *image)
UnitCell *cell;
- acc = malloc(max_acc*sizeof(double));
+ acc = cfmalloc(max_acc*sizeof(double));
if ( acc == NULL ) {
ERROR("Allocation failed during estimate_resolution!\n");
return INFINITY;
@@ -1577,7 +1576,7 @@ static double estimate_resolution(Crystal *cr, struct image *image)
if ( n_acc < 3 ) {
STATUS("WARNING: Too few peaks to estimate resolution.\n");
- free(acc);
+ cffree(acc);
return 0.0;
}
@@ -1587,18 +1586,18 @@ static double estimate_resolution(Crystal *cr, struct image *image)
if ( n < 2 ) n = 2;
max_res = acc[(n_acc-1)-n];
- free(acc);
+ cffree(acc);
return max_res;
}
static void integrate_rings(IntegrationMethod meth,
- Crystal *cr, struct image *image, IntDiag int_diag,
+ Crystal *cr, RefList *list,
+ struct image *image, IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
double ir_inn, double ir_mid, double ir_out,
pthread_mutex_t *term_lock, int **masks)
{
- RefList *list;
Reflection *refl;
RefListIterator *iter;
UnitCell *cell;
@@ -1606,7 +1605,6 @@ static void integrate_rings(IntegrationMethod meth,
int n_rej = 0;
int n_refl = 0;
- list = crystal_get_reflections(cr);
cell = crystal_get_cell(cr);
ic = intcontext_new(image, cell, meth,
@@ -1653,23 +1651,21 @@ void integrate_all_5(struct image *image, IntegrationMethod meth,
/* Predict all reflections */
for ( i=0; i<image->n_crystals; i++ ) {
- RefList *list;
double res;
- double saved_R = crystal_get_profile_radius(image->crystals[i]);
+ double saved_R = crystal_get_profile_radius(image->crystals[i].cr);
if ( overpredict ) {
- crystal_set_profile_radius(image->crystals[i],
+ crystal_set_profile_radius(image->crystals[i].cr,
saved_R * 5);
}
- res = estimate_resolution(image->crystals[i], image);
- crystal_set_resolution_limit(image->crystals[i], res);
+ res = estimate_resolution(image->crystals[i].cr, image);
+ crystal_set_resolution_limit(image->crystals[i].cr, res);
- list = predict_to_res(image->crystals[i], res+push_res);
- crystal_set_reflections(image->crystals[i], list);
+ image->crystals[i].refls = predict_to_res(image->crystals[i].cr, image, res+push_res);
if ( overpredict ) {
- crystal_set_profile_radius(image->crystals[i], saved_R);
+ crystal_set_profile_radius(image->crystals[i].cr, saved_R);
}
}
@@ -1681,22 +1677,26 @@ void integrate_all_5(struct image *image, IntegrationMethod meth,
for ( i=0; i<image->n_crystals; i++ ) {
- Crystal *cr = image->crystals[i];
-
switch ( meth & INTEGRATION_METHOD_MASK ) {
case INTEGRATION_NONE :
break;
case INTEGRATION_RINGS :
- integrate_rings(meth, cr, image,
+ integrate_rings(meth,
+ image->crystals[i].cr,
+ image->crystals[i].refls,
+ image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out,
term_lock, masks);
break;
case INTEGRATION_PROF2D :
- integrate_prof2d(meth, cr, image,
+ integrate_prof2d(meth,
+ image->crystals[i].cr,
+ image->crystals[i].refls,
+ image,
int_diag, idh, idk, idl,
ir_inn, ir_mid, ir_out,
term_lock, masks);
@@ -1711,7 +1711,7 @@ void integrate_all_5(struct image *image, IntegrationMethod meth,
}
for ( i=0; i<image->detgeom->n_panels; i++ ) {
- free(masks[i]);
+ cffree(masks[i]);
}
}
@@ -1794,7 +1794,7 @@ char *str_integration_method(IntegrationMethod m)
strcat(tmp, "-grad");
}
- return strdup(tmp);
+ return cfstrdup(tmp);
}
@@ -1854,10 +1854,10 @@ IntegrationMethod integration_method(const char *str, int *err)
return INTEGRATION_NONE;
}
- free(methods[i]);
+ cffree(methods[i]);
}
- free(methods);
+ cffree(methods);
return meth;
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-17 06:53:43 +0000