diff options
author | Helen Ginn <ginn@rescomp1.(none)> | 2017-01-17 13:30:47 +0000 |
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committer | Helen Ginn <ginn@rescomp1.(none)> | 2017-01-17 13:30:47 +0000 |
commit | 479077487c65a1e4264a28019c9079d00f00d8c6 (patch) | |
tree | dd9358937aa034b892e689eeb232f9ef9212cc46 /libcrystfel/src | |
parent | 0382b58398ab136c39d7f57cfef73dba2c0bb3a2 (diff) |
Add rlp retrieval from peak list and tidy up the output to the screen a tad
Diffstat (limited to 'libcrystfel/src')
-rw-r--r-- | libcrystfel/src/taketwo.c | 42 |
1 files changed, 26 insertions, 16 deletions
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c index ddad7cf7..2c6b4f06 100644 --- a/libcrystfel/src/taketwo.c +++ b/libcrystfel/src/taketwo.c @@ -86,13 +86,13 @@ int global_nrlps; #define MAX_NETWORK_MEMBERS (500) /* Maximum dead ends for a single branch extension during indexing */ -#define MAX_DEAD_ENDS (15) +#define MAX_DEAD_ENDS (10) /* Tolerance for two angles to be considered the same */ #define ANGLE_TOLERANCE (deg2rad(1.0)) /* Tolerance for rot_mats_are_similar */ -#define TRACE_TOLERANCE (deg2rad(7.0)) +#define TRACE_TOLERANCE (deg2rad(4.0)) /** TODO: * @@ -617,10 +617,10 @@ static signed int find_next_index(gsl_matrix *rot, struct SpotVec *obs_vecs, if (ok) { - generate_rot_mat(obs_vecs[idx0].obsvec, + /* generate_rot_mat(obs_vecs[idx0].obsvec, obs_vecs[i].obsvec, member_match, - a_match, 1); + a_match, 0);*/ *match_found = j; return i; } @@ -678,12 +678,10 @@ static int grow_network(gsl_matrix *rot, struct SpotVec *obs_vecs, } if ( next_index < 0 ) { - STATUS("dead end number %i..\n", dead_ends); - /* If there have been too many dead ends, give up + /* If there have been too many dead ends, give up * on indexing altogether. **/ if ( dead_ends > MAX_DEAD_ENDS ) { - STATUS("Too many dead ends!\n"); dead_ends = 0; continue; } @@ -693,7 +691,6 @@ static int grow_network(gsl_matrix *rot, struct SpotVec *obs_vecs, start++; member_num--; dead_ends++; - STATUS("Shaving back one.\n"); continue; } @@ -744,7 +741,7 @@ static int start_seed(struct SpotVec *obs_vecs, int obs_vec_count, int i, rot_mat = generate_rot_mat(obs_vecs[i].obsvec, obs_vecs[j].obsvec, obs_vecs[i].matches[i_match], - obs_vecs[j].matches[j_match], 1); + obs_vecs[j].matches[j_match], 0); /* Try to expand this rotation matrix to a larger network */ STATUS("idx: %i %i %i %i spots %i %i and %i %i\n", @@ -801,7 +798,7 @@ static int find_seed(struct SpotVec *obs_vecs, int obs_vec_count, /* We have seeds! Pass each of them through the seed-starter */ int k; - for ( k=0; k<matches; k++ ) { + for ( k=0; k<1; k++ ) { int success = start_seed(obs_vecs, obs_vec_count, i, j, i_idx[k], j_idx[k], rotation); @@ -912,11 +909,8 @@ 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); - struct rvec norm = new_rvec(diff.u, diff.v, diff.w); - normalise_rvec(&norm); - show_rvec(norm); - +// STATUS("obs %i (spots %i and %i)", count, i, j); + count++; struct SpotVec *temp_obs_vecs; @@ -1098,8 +1092,23 @@ int taketwo_index(struct image *image, IndexingPrivate *ipriv) UnitCell *cell; struct rvec *rlps; int n_rlps = 0; + int i; struct taketwo_private *tp = (struct taketwo_private *)ipriv; + 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); + if ( pk == NULL ) continue; + rlps[n_rlps].u = pk->rx; + rlps[n_rlps].v = pk->ry; + rlps[n_rlps].w = pk->rz; + n_rlps++; + } + rlps[n_rlps].u = 0.0; + rlps[n_rlps].v = 0.0; + rlps[n_rlps++].w = 0.0; + +/* FILE *fh = fopen("../../spots.csv", "r"); rlps = malloc(500*sizeof(struct rvec)); while ( (fh != NULL) && !feof(fh) ) { @@ -1122,7 +1131,8 @@ int taketwo_index(struct image *image, IndexingPrivate *ipriv) rlps[n_rlps].u = 0.0; rlps[n_rlps].v = 0.0; rlps[n_rlps++].w = 0.0; - if ( fh != NULL ) fclose(fh); + + if ( fh != NULL ) fclose(fh);*/ cell = run_taketwo(tp->cell, rlps, n_rlps); if ( cell == NULL ) return 0; |