diff options
Diffstat (limited to 'libcrystfel/src/index.c')
| -rw-r--r-- | libcrystfel/src/index.c | 53 |
1 files changed, 25 insertions, 28 deletions
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index d93664b1..12cd9190 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -121,7 +121,7 @@ char *base_indexer_str(IndexingMethod indm) { char *str; - str = malloc(256); + str = cfmalloc(256); if ( str == NULL ) { ERROR("Failed to allocate string.\n"); return NULL; @@ -270,11 +270,11 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell, if ( priv == NULL ) { ERROR("Failed to prepare indexing method %s\n", str); - free(str); + cffree(str); return NULL; } - free(str); + cffree(str); if ( in != *m ) { ERROR("Note: flags were altered to take into account " @@ -296,7 +296,7 @@ IndexingMethod *parse_indexing_methods(const char *method_list, n = assplode(method_list, ",", &method_strings, ASSPLODE_NONE); - methods = malloc(n * sizeof(IndexingMethod)); + methods = cfmalloc(n * sizeof(IndexingMethod)); if ( methods == NULL ) { ERROR("Failed to allocate indexing method list\n"); return NULL; @@ -316,12 +316,12 @@ IndexingMethod *parse_indexing_methods(const char *method_list, ERROR("To disable indexing retry ('noretry'), use --no-retry.\n"); ERROR("To enable multi-lattice indexing by 'delete and retry', use --multi\n"); ERROR("------------------\n"); - free(methods); + cffree(methods); return NULL; } - free(method_strings[i]); + cffree(method_strings[i]); } - free(method_strings); + cffree(method_strings); *pn = n; return methods; @@ -393,13 +393,13 @@ IndexingPrivate *setup_indexing(const char *method_list, } - ipriv = malloc(sizeof(struct _indexingprivate)); + ipriv = cfmalloc(sizeof(struct _indexingprivate)); if ( ipriv == NULL ) { ERROR("Failed to allocate indexing data\n"); return NULL; } - ipriv->engine_private = malloc((n+1) * sizeof(void *)); + ipriv->engine_private = cfmalloc((n+1) * sizeof(void *)); for ( i=0; i<n; i++ ) { @@ -416,14 +416,14 @@ IndexingPrivate *setup_indexing(const char *method_list, asdf_opts); if ( ipriv->engine_private[i] == NULL ) { - free(ipriv->engine_private); + cffree(ipriv->engine_private); return NULL; } for ( j=0; j<i; j++ ) { if ( methods[i] == methods[j] ) { ERROR("Duplicate indexing method.\n"); - free(ipriv->engine_private); + cffree(ipriv->engine_private); return NULL; } } @@ -449,8 +449,8 @@ IndexingPrivate *setup_indexing(const char *method_list, char *str = indexer_str(methods[i]); char *tmp = friendly_indexer_name(methods[i]); STATUS(" %2i: %-25s (%s)\n", i, str, tmp); - free(str); - free(tmp); + cffree(str); + cffree(tmp); } show_indexing_flags(flags); @@ -523,10 +523,10 @@ void cleanup_indexing(IndexingPrivate *ipriv) } - free(ipriv->methods); - free(ipriv->engine_private); + cffree(ipriv->methods); + cffree(ipriv->engine_private); cell_free(ipriv->target_cell); - free(ipriv); + cffree(ipriv); } @@ -552,7 +552,6 @@ static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target, if ( out != NULL ) { /* Replace crystal's cell with new one */ - cell_free(crystal_get_cell(cr)); crystal_set_cell(cr, out); rtnl_mtx_free(rm); if ( !right_handed(out) ) STATUS("WARNING: left handed\n"); @@ -699,9 +698,8 @@ static int try_indexer(struct image *image, IndexingMethod indm, int this_crystal = image->n_crystals - i - 1; /* ... starting at the end of the (complete) list ... */ - Crystal *cr = image->crystals[this_crystal]; + Crystal *cr = image->crystals[this_crystal].cr; - crystal_set_image(cr, image); crystal_set_profile_radius(cr, 0.02e9); crystal_set_mosaicity(cr, 0.0); @@ -744,7 +742,7 @@ static int try_indexer(struct image *image, IndexingMethod indm, if ( ipriv->flags & INDEXING_CHECK_PEAKS ) { int mm = ipriv->flags & INDEXING_MULTI; - if ( !indexing_peak_check(image, &cr, 1, mm) ) { + if ( !indexing_peak_check(image, image->features, &cr, 1, mm) ) { crystal_set_user_flag(cr, 1); continue; } @@ -757,7 +755,7 @@ static int try_indexer(struct image *image, IndexingMethod indm, profile_start("cell-compare-to-others"); for ( j=0; j<this_crystal; j++ ) { - Crystal *that_cr = image->crystals[j]; + Crystal *that_cr = image->crystals[j].cr; /* 'tols' is in frac (not %) and radians */ const double tols[] = {0.1, 0.1, 0.1, deg2rad(5.0), @@ -909,7 +907,7 @@ static int finished_retry(IndexingMethod indm, IndexingFlags flags, if ( flags & INDEXING_MULTI ) { /* Remove "used" spots and try for another lattice */ Crystal *cr; - cr = image->crystals[image->n_crystals-1]; + cr = image->crystals[image->n_crystals-1].cr; return delete_explained_peaks(image, cr); } else { return 1; @@ -946,8 +944,7 @@ void index_pattern_4(struct image *image, IndexingPrivate *ipriv, int *ping, if ( ipriv == NULL ) return; - image->crystals = NULL; - image->n_crystals = 0; + free_all_crystals(image); /* No peaks? */ if ( image->features == NULL ) return; @@ -1195,10 +1192,10 @@ IndexingMethod get_indm_from_string_2(const char *str, int *err) return INDEXING_ERROR; } - free(bits[i]); + cffree(bits[i]); } - free(bits); + cffree(bits); if ( !have_method ) return warn_method(str); @@ -1230,7 +1227,7 @@ char *detect_indexing_methods(UnitCell *cell) { char *methods; - methods = malloc(1024); + methods = cfmalloc(1024); if ( methods == NULL ) return NULL; methods[0] = '\0'; @@ -1245,7 +1242,7 @@ char *detect_indexing_methods(UnitCell *cell) //do_probe(pinkIndexer_probe, cell, methods); if ( strlen(methods) == 0 ) { - free(methods); + cffree(methods); return NULL; } |