aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel
diff options
context:
space:
mode:
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/cell-utils.c6
-rw-r--r--libcrystfel/src/taketwo.c191
2 files changed, 72 insertions, 125 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 841d88f9..8fa3b894 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -1454,14 +1454,8 @@ UnitCell *transform_cell_gsl(UnitCell *in, gsl_matrix *m)
gsl_matrix_set(c, 1, 2, csy);
gsl_matrix_set(c, 2, 2, csz);
- STATUS("---\n");
- show_matrix(m);
- STATUS("\n");
- show_matrix(c);
- STATUS("\n");
res = gsl_matrix_calloc(3, 3);
gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, m, c, 0.0, res);
- show_matrix(res);
out = cell_new_from_cell(in);
cell_set_reciprocal(out, gsl_matrix_get(res, 0, 0),
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
index b5604d1a..b7f117ea 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/taketwo.c
@@ -310,11 +310,9 @@ static int rot_mats_are_similar(gsl_matrix *rot1, gsl_matrix *rot2)
tr = matrix_trace(mul);
gsl_matrix_free(mul);
- double max = sqrt(4.0*(1.0-cos(TRACE_TOLERANCE)));
+ double max = sqrt(4.0*(1.0-cos(TRACE_TOLERANCE)));
- // STATUS("Trace is %.3f (max %.3f)\n", tr, max);
-
- return (tr < max);
+ return (tr < max);
}
@@ -456,30 +454,30 @@ static int obs_vecs_match_angles(struct SpotVec *her_obs,
double angle_diff = fabs(theory_angle - obs_angle);
- if ( angle_diff < ANGLE_TOLERANCE ) {
- size_t new_size = (*match_count + 1) *
- sizeof(int);
- if (her_match_idxs && his_match_idxs)
- {
- /* Reallocate the array to fit in another match */
- int *temp_hers;
- temp_hers = realloc(*her_match_idxs, new_size);
- int *temp_his;
- temp_his = realloc(*his_match_idxs, new_size);
+ if ( angle_diff < ANGLE_TOLERANCE ) {
+ size_t new_size = (*match_count + 1) *
+ sizeof(int);
+ if (her_match_idxs && his_match_idxs)
+ {
+ /* Reallocate the array to fit in another match */
+ int *temp_hers;
+ temp_hers = realloc(*her_match_idxs, new_size);
+ int *temp_his;
+ temp_his = realloc(*his_match_idxs, new_size);
- if ( temp_hers == NULL || temp_his == NULL ) {
- apologise();
- }
+ if ( temp_hers == NULL || temp_his == NULL ) {
+ apologise();
+ }
- (*her_match_idxs) = temp_hers;
- (*his_match_idxs) = temp_his;
+ (*her_match_idxs) = temp_hers;
+ (*his_match_idxs) = temp_his;
- (*her_match_idxs)[*match_count] = i;
- (*his_match_idxs)[*match_count] = j;
- }
+ (*her_match_idxs)[*match_count] = i;
+ (*his_match_idxs)[*match_count] = j;
+ }
- (*match_count)++;
- }
+ (*match_count)++;
+ }
}
}
@@ -503,16 +501,12 @@ static int obs_angles_match_array(struct SpotVec *obs_vecs, int test_idx,
struct SpotVec *his_obs = &obs_vecs[obs_members[i]];
/* placeholders, but results are ignored */
- int match_count = 0;
+ int match_count = 0;
/* check our test vector matches existing network member */
obs_vecs_match_angles(her_obs, his_obs,
NULL, NULL, &match_count);
- /* FIXME: this is going to be broken */
- // if (idx2 != match_members[i]) return 0;
- //STATUS("match %i %i %i %i\n", idx1, idx2, test_idx,
- // match_members[i]);
}
return 1;
@@ -529,8 +523,7 @@ static signed int find_next_index(gsl_matrix *rot, struct SpotVec *obs_vecs,
int *match_found)
{
int i;
- // STATUS("Checking for next index from start=%i, max %i\n", start, obs_vec_count);
-
+
for ( i=start; i<obs_vec_count; i++ ) {
/* first we check for a shared spot - harshest condition */
@@ -561,8 +554,6 @@ static signed int find_next_index(gsl_matrix *rot, struct SpotVec *obs_vecs,
obs_vecs_match_angles(&obs_vecs[obs_members[0]], &obs_vecs[i],
&member_idx, &test_idx, &match_num);
- // STATUS("There are %i matches for next obs vector %i\n", match_num, i)
-
/* if ok is set to 0, give up on this vector before
* checking the next value of j */
int j;
@@ -575,9 +566,6 @@ static signed int find_next_index(gsl_matrix *rot, struct SpotVec *obs_vecs,
/* First observed vector and matching theoretical */
member_match = obs_vecs[idx0].matches[match_members[0]];
-// STATUS("]]]]] %i %i %i %i\n",
-// idx0, i, match_members[0], test_idx);
-
/* Potential match with another vector */
struct rvec a_match = obs_vecs[i].matches[test_idx[j]];
@@ -624,70 +612,58 @@ static int grow_network(gsl_matrix *rot, struct SpotVec *obs_vecs,
/* we can start from after the 2nd observed vector in the seed */
int start = obs_idx2 + 1;
- STATUS("obs_vec_count = %i\n", obs_vec_count);
-
+
while ( 1 ) {
- if (start > obs_vec_count) {
- STATUS("Reached end of observed vectors.\n");
- return -1;
- }
+ if (start > obs_vec_count) {
+ return -1;
+ }
- int match_found = -1;
-
- signed int next_index = find_next_index(rot, obs_vecs,
- obs_vec_count, obs_members,
- match_members,
- start, member_num,
- &match_found);
- // STATUS("Next index is %i, match is %i\n", next_index, match_found);
-
- if ( member_num < 2 ) {
- STATUS("giving up on seed..\n");
- return 0;
- }
+ int match_found = -1;
+
+ signed int next_index = find_next_index(rot, obs_vecs,
+ obs_vec_count, obs_members,
+ match_members,
+ start, member_num,
+ &match_found);
- if ( next_index < 0 ) {
- /* If there have been too many dead ends, give up
- * on indexing altogether.
- **/
- if ( dead_ends > MAX_DEAD_ENDS ) {
- dead_ends = 0;
- continue;
- }
+ if ( member_num < 2 ) {
+ return 0;
+ }
- /* We have not had too many dead ends. Try removing
- the last member and continue. */
- start++;
- member_num--;
- dead_ends++;
+ if ( next_index < 0 ) {
+ /* If there have been too many dead ends, give up
+ * on indexing altogether.
+ **/
+ if ( dead_ends > MAX_DEAD_ENDS ) {
+ dead_ends = 0;
+ continue;
+ }
- continue;
- }
+ /* We have not had too many dead ends. Try removing
+ the last member and continue. */
+ start++;
+ member_num--;
+ dead_ends++;
- /* we have elongated membership - so reset dead_ends counter */
- // dead_ends = 0;
+ continue;
+ }
- obs_members[member_num] = next_index;
- match_members[member_num] = match_found;
+ /* we have elongated membership - so reset dead_ends counter */
+ // dead_ends = 0;
- start = next_index + 1;
- member_num++;
-
- if (member_num > *max_members) {
- *max_members = member_num;
- }
-
- STATUS("elongating seed, now %i members. They are: ", member_num);
- int c;
- for (c = 0; c < member_num; c++) {
- STATUS("%i, ", obs_members[c]);
- }
+ obs_members[member_num] = next_index;
+ match_members[member_num] = match_found;
+
+ start = next_index + 1;
+ member_num++;
- STATUS("\n");
-
- /* If member_num is high enough, we want to return a yes */
- if ( member_num > NETWORK_MEMBER_THRESHOLD ) break;
+ if (member_num > *max_members) {
+ *max_members = member_num;
+ }
+
+ /* If member_num is high enough, we want to return a yes */
+ if ( member_num > NETWORK_MEMBER_THRESHOLD ) break;
}
/* Deal with this shit after coffee */
@@ -710,8 +686,7 @@ static int start_seed(struct SpotVec *obs_vecs, int obs_vec_count, int i,
int j, int i_match, int j_match, gsl_matrix **rotation,
int *max_members, int accept_anything)
{
- STATUS("starting new seed for obsvs %i and %i..\n", i, j);
- gsl_matrix *rot_mat = gsl_matrix_calloc(3, 3);
+ gsl_matrix *rot_mat = gsl_matrix_calloc(3, 3);
// FIXME: go through ALL matches, not jsut first
rot_mat = generate_rot_mat(obs_vecs[i].obsvec,
@@ -720,14 +695,7 @@ static int start_seed(struct SpotVec *obs_vecs, int obs_vec_count, int i,
obs_vecs[j].matches[j_match]);
/* Try to expand this rotation matrix to a larger network */
- STATUS("idx: %i %i %i %i spots %i %i and %i %i\n",
- i_match, j_match, i, j,
- spot_idx(obs_vecs[i].her_rlp),
- spot_idx(obs_vecs[i].his_rlp),
- spot_idx(obs_vecs[j].her_rlp),
- spot_idx(obs_vecs[j].his_rlp));
- show_matrix(rot_mat);
-
+
int success = grow_network(rot_mat, obs_vecs, obs_vec_count,
i, j, i_match, j_match, max_members,
accept_anything);
@@ -762,8 +730,7 @@ static int find_seed(struct SpotVec *obs_vecs, int obs_vec_count,
* by spot instead of by vector.
*/
int shared = obs_vecs_share_spot(&obs_vecs[i], &obs_vecs[j]);
- //STATUS("checking %i %i\n", i, j);
-
+
if ( !shared ) continue;
/* cell vector "matches" index for i, j respectively */
@@ -775,8 +742,7 @@ static int find_seed(struct SpotVec *obs_vecs, int obs_vec_count,
obs_vecs_match_angles(&obs_vecs[i], &obs_vecs[j],
&i_idx, &j_idx, &matches);
if ( matches == 0 ) continue;
- STATUS("...ok, %i matches\n", matches);
-
+
/* We have seeds! Pass each of them through the seed-starter */
/* If a seed has the highest achieved membership, make note...*/
int k;
@@ -843,11 +809,6 @@ static int match_obs_to_cell_vecs(struct rvec *cell_vecs, int cell_vec_count,
int count = 0;
struct sortme *for_sort = NULL;
- if ( (i==0) || (i==1) || (i==2) ) {
- STATUS("length of %i = %f\n", i,
- obs_vecs[i].distance/1e10);
- }
-
for ( j=0; j<cell_vec_count; j++ ) {
/* get distance for unit cell vector */
@@ -871,9 +832,6 @@ static int match_obs_to_cell_vecs(struct rvec *cell_vecs, int cell_vec_count,
count++;
}
- if ( (i==0) || (i==1) || (i==2) ) {
- STATUS("%i matches for %i\n", count, i);
- }
qsort(for_sort, count, sizeof(struct sortme), sort_func);
obs_vecs[i].matches = malloc(count*sizeof(struct rvec));
obs_vecs[i].match_num = count;
@@ -900,8 +858,7 @@ static int gen_observed_vecs(struct rvec *rlps, int rlp_count,
for ( i=0; i<rlp_count-1; i++ ) {
for ( j=i+1; j<rlp_count; j++ ) {
- //STATUS("%i %i %i %i\n", i, j, rlp_count, count);
-
+
/* calculate difference vector between rlps */
struct rvec diff = diff_vec(rlps[i], rlps[j]);
@@ -909,7 +866,6 @@ static int gen_observed_vecs(struct rvec *rlps, int rlp_count,
double sqlength = sq_length(diff);
if ( sqlength > max_sq_length ) continue;
-// STATUS("obs %i (spots %i and %i)", count, i, j);
count++;
@@ -1047,16 +1003,13 @@ static UnitCell *run_taketwo(UnitCell *cell, struct rvec *rlps, int rlp_count)
success = gen_theoretical_vecs(cell, &cell_vecs, &cell_vec_count);
if ( !success ) return NULL;
- STATUS("cell_vec_count = %i\n", cell_vec_count);
global_rlps = rlps;
global_nrlps = rlp_count;
success = gen_observed_vecs(rlps, rlp_count, &obs_vecs, &obs_vec_count);
if ( !success ) return NULL;
- STATUS("obs_vec_count = %i\n", obs_vec_count);
- STATUS("rlp_count = %i\n", rlp_count);
-
+
success = match_obs_to_cell_vecs(cell_vecs, cell_vec_count,
obs_vecs, obs_vec_count);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-06 00:50:17 +0000