diff options
Diffstat (limited to 'libcrystfel/src/indexers/taketwo.c')
-rw-r--r-- | libcrystfel/src/indexers/taketwo.c | 86 |
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; |