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Diffstat (limited to 'libcrystfel/src/indexers/taketwo.c')
-rw-r--r--libcrystfel/src/indexers/taketwo.c86
1 files changed, 43 insertions, 43 deletions
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 0b652b9f..c87d6b3d 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -524,7 +524,7 @@ static double matrix_trace(gsl_matrix *a)
static char *add_unique_axis(const char *inp, char ua)
{
- char *pg = malloc(64);
+ char *pg = cfmalloc(64);
if ( pg == NULL ) return NULL;
snprintf(pg, 63, "%s_ua%c", inp, ua);
return pg;
@@ -584,7 +584,7 @@ static char *get_chiral_holohedry(UnitCell *cell)
if ( add_ua ) {
return add_unique_axis(pg, cell_get_unique_axis(cell));
} else {
- return strdup(pg);
+ return cfstrdup(pg);
}
}
@@ -595,7 +595,7 @@ static SymOpList *sym_ops_for_cell(UnitCell *cell)
char *pg = get_chiral_holohedry(cell);
rawList = get_pointgroup(pg);
- free(pg);
+ cffree(pg);
return rawList;
}
@@ -845,7 +845,7 @@ static int obs_vecs_match_angles(int her, int his,
new_size *= sizeof(struct Seed);
/* Reallocate the array to fit in another match */
- struct Seed *tmp_seeds = realloc(*seeds, new_size);
+ struct Seed *tmp_seeds = cfrealloc(*seeds, new_size);
if ( tmp_seeds == NULL ) {
apologise();
@@ -878,8 +878,8 @@ static signed int finish_solution(gsl_matrix *rot, struct SpotVec *obs_vecs,
gsl_matrix *sub = gsl_matrix_calloc(3, 3);
gsl_matrix *mul = gsl_matrix_calloc(3, 3);
- gsl_matrix **rotations = malloc(sizeof(*rotations)* pow(member_num, 2)
- - member_num);
+ gsl_matrix **rotations = cfmalloc(sizeof(*rotations)* pow(member_num, 2)
+ - member_num);
int i, j, count;
@@ -929,7 +929,7 @@ static signed int finish_solution(gsl_matrix *rot, struct SpotVec *obs_vecs,
gsl_matrix_free(rotations[i]);
}
- free(rotations);
+ cffree(rotations);
gsl_matrix_free(sub);
gsl_matrix_free(mul);
@@ -1011,7 +1011,7 @@ static int weed_duplicate_matches(struct Seed **seeds,
}
}
- free(old_mats);
+ cffree(old_mats);
return 1;
}
@@ -1310,8 +1310,8 @@ static unsigned int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
}
/* indices of members of the self-consistent network of vectors */
- obs_members = malloc((cell->member_thresh+3)*sizeof(int));
- match_members = malloc((cell->member_thresh+3)*sizeof(int));
+ obs_members = cfmalloc((cell->member_thresh+3)*sizeof(int));
+ match_members = cfmalloc((cell->member_thresh+3)*sizeof(int));
if ( (obs_members == NULL) || (match_members == NULL) ) {
apologise();
return 0;
@@ -1334,8 +1334,8 @@ static unsigned int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
while ( 1 ) {
if (start > obs_vec_count) {
- free(obs_members);
- free(match_members);
+ cffree(obs_members);
+ cffree(match_members);
return 0;
}
@@ -1347,8 +1347,8 @@ static unsigned int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
&match_found, cell);
if ( member_num < 2 ) {
- free(obs_members);
- free(match_members);
+ cffree(obs_members);
+ cffree(match_members);
return 0;
}
@@ -1383,8 +1383,8 @@ static unsigned int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
finish_solution(rot, obs_vecs, obs_members,
match_members, member_num, cell);
- free(obs_members);
- free(match_members);
+ cffree(obs_members);
+ cffree(match_members);
return ( member_num );
}
@@ -1519,7 +1519,7 @@ static int find_seeds(struct TakeTwoCell *cell, struct taketwo_private *tp)
size_t new_size = cell->seed_count + seed_num;
new_size *= sizeof(struct Seed);
- struct Seed *tmp = realloc(cell->seeds, new_size);
+ struct Seed *tmp = cfrealloc(cell->seeds, new_size);
if (tmp == NULL) {
apologise();
@@ -1539,7 +1539,7 @@ static int find_seeds(struct TakeTwoCell *cell, struct taketwo_private *tp)
cell->seed_count++;
}
- free(seeds);
+ cffree(seeds);
}
}
@@ -1590,12 +1590,12 @@ static unsigned int start_seeds(gsl_matrix **rotation, struct TakeTwoCell *cell)
}
if (member_num >= NETWORK_MEMBER_THRESHOLD) {
- free(seeds);
+ cffree(seeds);
return max_members;
}
}
- free(seeds);
+ cffree(seeds);
return max_members;
}
@@ -1652,7 +1652,7 @@ static int generate_rotation_sym_ops(struct TakeTwoCell *ttCell)
int i, j, k;
int numOps = num_equivs(rawList, NULL);
- ttCell->rotSymOps = malloc(numOps * sizeof(gsl_matrix *));
+ ttCell->rotSymOps = cfmalloc(numOps * sizeof(gsl_matrix *));
ttCell->numOps = numOps;
if (ttCell->rotSymOps == NULL) {
@@ -1764,13 +1764,13 @@ static int match_obs_to_cell_vecs(struct TheoryVec *cell_vecs, int cell_vec_coun
/* Sort in order to get most agreeable matches first */
qsort(for_sort, count, sizeof(struct sortme), sort_theory_distances);
- *match_array = malloc(count*sizeof(struct TheoryVec));
+ *match_array = cfmalloc(count*sizeof(struct TheoryVec));
*match_count = count;
for ( j=0; j<count; j++ ) {
(*match_array)[j] = for_sort[j].v;
}
- free(for_sort);
+ cffree(for_sort);
}
return 1;
@@ -1806,8 +1806,8 @@ static int gen_observed_vecs(struct rvec *rlps, int rlp_count,
count++;
struct SpotVec *temp_obs_vecs;
- temp_obs_vecs = realloc(cell->obs_vecs,
- count*sizeof(struct SpotVec));
+ temp_obs_vecs = cfrealloc(cell->obs_vecs,
+ count*sizeof(struct SpotVec));
if ( temp_obs_vecs == NULL ) {
return 0;
@@ -1899,8 +1899,8 @@ static int gen_theoretical_vecs(UnitCell *cell, struct TheoryVec **cell_vecs,
count++;
struct TheoryVec *temp_cell_vecs;
- temp_cell_vecs = realloc(*cell_vecs,
- count*sizeof(struct TheoryVec));
+ temp_cell_vecs = cfrealloc(*cell_vecs,
+ count*sizeof(struct TheoryVec));
if ( temp_cell_vecs == NULL ) {
return 0;
@@ -1929,10 +1929,10 @@ static void cleanup_taketwo_obs_vecs(struct SpotVec *obs_vecs,
{
int i;
for ( i=0; i<obs_vec_count; i++ ) {
- free(obs_vecs[i].matches);
+ cffree(obs_vecs[i].matches);
}
- free(obs_vecs);
+ cffree(obs_vecs);
}
static void cleanup_taketwo_cell(struct TakeTwoCell *ttCell)
@@ -1943,7 +1943,7 @@ static void cleanup_taketwo_cell(struct TakeTwoCell *ttCell)
for ( i=0; i<ttCell->numOps; i++ ) {
gsl_matrix_free(ttCell->rotSymOps[i]);
}
- free(ttCell->rotSymOps);
+ cffree(ttCell->rotSymOps);
cleanup_taketwo_obs_vecs(ttCell->obs_vecs,
ttCell->obs_vec_count);
@@ -2056,12 +2056,12 @@ static UnitCell *run_taketwo(UnitCell *cell, const struct taketwo_options *opts,
/* Add the current solution to the previous solutions list */
int new_size = (tp->numPrevs + 1) * sizeof(gsl_matrix *);
- gsl_matrix **tmp = realloc(tp->prevSols, new_size);
- double *tmpScores = realloc(tp->prevScores,
+ gsl_matrix **tmp = cfrealloc(tp->prevSols, new_size);
+ double *tmpScores = cfrealloc(tp->prevScores,
(tp->numPrevs + 1) * sizeof(double));
unsigned int *tmpSuccesses;
- tmpSuccesses = realloc(tp->membership,
- (tp->numPrevs + 1) * sizeof(unsigned int));
+ tmpSuccesses = cfrealloc(tp->membership,
+ (tp->numPrevs + 1) * sizeof(unsigned int));
if (!tmp) {
apologise();
@@ -2096,11 +2096,11 @@ static void partial_taketwo_cleanup(struct taketwo_private *tp)
gsl_matrix_free(tp->prevSols[i]);
}
- free(tp->prevSols);
+ cffree(tp->prevSols);
}
- free(tp->prevScores);
- free(tp->membership);
+ cffree(tp->prevScores);
+ cffree(tp->membership);
tp->prevScores = NULL;
tp->membership = NULL;
tp->xtal_num = 0;
@@ -2143,7 +2143,7 @@ int taketwo_index(struct image *image, void *priv)
tp->xtal_num = image->n_crystals;
}
- rlps = malloc((image_feature_count(image->features)+1)*sizeof(struct rvec));
+ rlps = cfmalloc((image_feature_count(image->features)+1)*sizeof(struct rvec));
for ( i=0; i<image_feature_count(image->features); i++ ) {
double r[3];
@@ -2164,7 +2164,7 @@ int taketwo_index(struct image *image, void *priv)
rlps[n_rlps++].w = 0.0;
cell = run_taketwo(tp->cell, tp->opts, rlps, n_rlps, tp);
- free(rlps);
+ cffree(rlps);
if ( cell == NULL ) return 0;
cr = crystal_new();
@@ -2222,7 +2222,7 @@ void *taketwo_prepare(IndexingMethod *indm, struct taketwo_options *opts,
STATUS("\n");
- tp = malloc(sizeof(struct taketwo_private));
+ tp = cfmalloc(sizeof(struct taketwo_private));
if ( tp == NULL ) return NULL;
tp->cell = cell;
@@ -2248,9 +2248,9 @@ void taketwo_cleanup(IndexingPrivate *pp)
struct taketwo_private *tp = (struct taketwo_private *)pp;
partial_taketwo_cleanup(tp);
- free(tp->theory_vecs);
+ cffree(tp->theory_vecs);
- free(tp);
+ cffree(tp);
}
@@ -2280,7 +2280,7 @@ int taketwo_default_options(struct taketwo_options **opts_ptr)
{
struct taketwo_options *opts;
- opts = malloc(sizeof(struct taketwo_options));
+ opts = cfmalloc(sizeof(struct taketwo_options));
if ( opts == NULL ) return ENOMEM;
opts->member_thresh = -1.0;
opts->len_tol = -1.0;
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-17 06:04:48 +0000