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authorHelen Ginn <helen@strubi.ox.ac.uk>2018-04-27 22:24:10 +0200
committerThomas White <taw@physics.org>2018-05-02 09:46:14 +0200
commitf06de02c7350ebf41c91cac7309751317c4c0943 (patch)
treeb163338f559cc84e113f59fba0d637d10f653fb0
parent8ee6527f2eea3e87970b7a8d7c2df1c4c0389afa (diff)
Taketwo private structure takes care of duplicate solutions
-rw-r--r--libcrystfel/src/taketwo.c165
1 files changed, 122 insertions, 43 deletions
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
index 5acc99d9..0dc1ed51 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/taketwo.c
@@ -156,6 +156,12 @@ struct taketwo_private
{
IndexingMethod indm;
UnitCell *cell;
+ int serial_num; /* -1 if unassigned */
+ unsigned int attempts;
+
+ gsl_matrix **prevSols; /**< Previous solutions to be ignored */
+ unsigned int numPrevs; /**< Previous solution count */
+
};
/**
@@ -167,9 +173,6 @@ struct TakeTwoCell
gsl_matrix **rotSymOps;
unsigned int numOps;
- gsl_matrix **prevSols; /**< Previous solutions to be ignored */
- unsigned int numPrevs; /**< Previous solution count */
-
struct SpotVec *obs_vecs;
struct Seed *seeds;
int seed_count;
@@ -861,39 +864,8 @@ static int weed_duplicate_matches(struct Seed **seeds,
}
signed int i, j;
- int duplicates = 0;
-
- /* First we weed out duplicates with previous solutions */
-
- for (i = *match_count - 1; i >= 0; i--) {
- int her_match = (*seeds)[i].idx1;
- int his_match = (*seeds)[i].idx2;
-
- gsl_matrix *mat;
- mat = rot_mat_from_indices((*seeds)[i].obs1, (*seeds)[i].obs2,
- her_match, his_match, cell);
-
- if (mat == NULL)
- {
- continue;
- }
-
- for (j = 0; j < cell->numPrevs; j++)
- {
- int sim = symm_rot_mats_are_similar(cell->prevSols[j],
- mat, cell);
- /* Found a duplicate with a previous solution */
- if (sim)
- {
- (*seeds)[i].idx1 = -1;
- (*seeds)[i].idx2 = -1;
- break;
- }
- }
-
- gsl_matrix_free(mat);
- }
+ int duplicates = 0;
/* Now we weed out the self-duplicates from the remaining batch */
@@ -1196,8 +1168,51 @@ static int sort_seed_by_score(const void *av, const void *bv)
return a->score > b->score;
}
+static void remove_old_solutions(struct TakeTwoCell *cell,
+ struct taketwo_private *tp)
+{
+ int duplicates = 0;
+ struct Seed *seeds = cell->seeds;
+ unsigned int total = cell->seed_count;
+
+ /* First we remove duplicates with previous solutions */
+
+ int i, j;
+ for (i = total - 1; i >= 0; i--) {
+ int her_match = seeds[i].idx1;
+ int his_match = seeds[i].idx2;
+
+ gsl_matrix *mat;
+ mat = rot_mat_from_indices(seeds[i].obs1, seeds[i].obs2,
+ her_match, his_match, cell);
+
+ if (mat == NULL)
+ {
+ continue;
+ }
+
+ for (j = 0; j < tp->numPrevs; j++)
+ {
+ int sim = symm_rot_mats_are_similar(tp->prevSols[j],
+ mat, cell);
+
+ /* Found a duplicate with a previous solution */
+ if (sim)
+ {
+ seeds[i].idx1 = -1;
+ seeds[i].idx2 = -1;
+ duplicates++;
+ break;
+ }
+ }
-static int find_seeds(struct TakeTwoCell *cell)
+ gsl_matrix_free(mat);
+ }
+
+ STATUS("Removing %i duplicates due to prev solutions.\n", duplicates);
+}
+
+static int find_seeds(struct TakeTwoCell *cell, struct taketwo_private *tp)
{
struct SpotVec *obs_vecs = cell->obs_vecs;
int obs_vec_count = cell->obs_vec_count;
@@ -1663,7 +1678,8 @@ static void cleanup_taketwo_cell(struct TakeTwoCell *ttCell)
* successful.
**/
static UnitCell *run_taketwo(UnitCell *cell, const struct taketwo_options *opts,
- struct rvec *rlps, int rlp_count)
+ struct rvec *rlps, int rlp_count,
+ struct taketwo_private *tp)
{
int cell_vec_count = 0;
struct TheoryVec *theory_vecs = NULL;
@@ -1678,13 +1694,11 @@ static UnitCell *run_taketwo(UnitCell *cell, const struct taketwo_options *opts,
ttCell.seed_count = 0;
ttCell.rotSymOps = NULL;
ttCell.obs_vecs = NULL;
- ttCell.prevSols = NULL;
ttCell.twiz1Tmp = gsl_matrix_calloc(3, 3);
ttCell.twiz2Tmp = gsl_matrix_calloc(3, 3);
ttCell.vec1Tmp = gsl_vector_calloc(3);
ttCell.vec2Tmp = gsl_vector_calloc(3);
ttCell.numOps = 0;
- ttCell.numPrevs = 0;
ttCell.obs_vec_count = 0;
success = generate_rotation_sym_ops(&ttCell);
@@ -1726,20 +1740,62 @@ static UnitCell *run_taketwo(UnitCell *cell, const struct taketwo_options *opts,
if ( !success ) return NULL;
- find_seeds(&ttCell);
+ find_seeds(&ttCell, tp);
+// remove_old_solutions(&ttCell, tp);
start_seeds(&solution, &ttCell);
if ( solution == NULL ) {
return NULL;
}
+ for (int i = 0; i < tp->numPrevs; i++)
+ {
+ gsl_matrix *sol = tp->prevSols[i];
+
+ int sim = symm_rot_mats_are_similar(sol, solution, &ttCell);
+ if (sim)
+ {
+// STATUS("Warning! Returning previous solution.\n");
+ }
+ }
+
+ int new_size = (tp->numPrevs + 1) * sizeof(gsl_matrix *);
+ gsl_matrix **tmp = realloc(tp->prevSols, new_size);
+
+ if (!tmp) {
+ apologise();
+ }
+
+ tp->prevSols = tmp;
+
+ tp->prevSols[tp->numPrevs] = solution;
+ tp->numPrevs++;
+
result = transform_cell_gsl(cell, solution);
- gsl_matrix_free(solution);
cleanup_taketwo_cell(&ttCell);
return result;
}
+/* Cleans up the per-image information for taketwo */
+
+static void partial_taketwo_cleanup(struct taketwo_private *tp)
+{
+ if (tp->prevSols != NULL)
+ {
+ for (int i = 0; i < tp->numPrevs; i++)
+ {
+ gsl_matrix_free(tp->prevSols[i]);
+ }
+
+ free(tp->prevSols);
+ }
+
+ tp->attempts = 0;
+ tp->numPrevs = 0;
+ tp->prevSols = NULL;
+
+}
/* CrystFEL interface hooks */
@@ -1753,6 +1809,24 @@ int taketwo_index(struct image *image, const struct taketwo_options *opts,
int i;
struct taketwo_private *tp = (struct taketwo_private *)priv;
+ /* Check serial number against previous for solution tracking */
+ int this_serial = image->serial;
+
+ if (tp->serial_num == this_serial)
+ {
+ tp->attempts++;
+ }
+ else
+ {
+ partial_taketwo_cleanup(tp);
+ tp->serial_num = this_serial;
+ }
+
+ /*
+ STATUS("Indexing %i with %i attempts, %i crystals\n", this_serial, tp->attempts,
+ image->n_crystals);
+ */
+
rlps = malloc((image_feature_count(image->features)+1)*sizeof(struct rvec));
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *pk = image_get_feature(image->features, i);
@@ -1766,7 +1840,7 @@ int taketwo_index(struct image *image, const struct taketwo_options *opts,
rlps[n_rlps].v = 0.0;
rlps[n_rlps++].w = 0.0;
- cell = run_taketwo(tp->cell, opts, rlps, n_rlps);
+ cell = run_taketwo(tp->cell, opts, rlps, n_rlps, tp);
free(rlps);
if ( cell == NULL ) return 0;
@@ -1829,14 +1903,19 @@ void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell)
tp->cell = cell;
tp->indm = *indm;
+ tp->serial_num = -1;
+ tp->attempts = 0;
+ tp->prevSols = NULL;
+ tp->numPrevs = 0;
return tp;
}
-
void taketwo_cleanup(IndexingPrivate *pp)
{
struct taketwo_private *tp = (struct taketwo_private *)pp;
+
+ partial_taketwo_cleanup(tp);
free(tp);
}