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authorThomas White <taw@physics.org>2017-07-24 11:41:40 +0200
committerThomas White <taw@physics.org>2017-07-24 11:41:40 +0200
commit86d1ad63431c33019f1c6214588eddc83be7be70 (patch)
tree6ce8dba53fe5a57aca1aa8e390813c16352edb4d
parent1585396d6bbe3375d21b2906251ee6762a6fcca4 (diff)
Formatting/copyright dates
-rw-r--r--libcrystfel/src/taketwo.c172
1 files changed, 86 insertions, 86 deletions
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
index ecd2c447..7d934ceb 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/taketwo.c
@@ -3,13 +3,13 @@
*
* Rewrite of TakeTwo algorithm (Acta D72 (8) 956-965) for CrystFEL
*
- * Copyright © 2016 Helen Ginn
- * Copyright © 2016 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2016-2017 Helen Ginn
+ * Copyright © 2016-2017 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
*
* Authors:
- * 2016 Helen Ginn <helen@strubi.ox.ac.uk>
- * 2016 Thomas White <taw@physics.org>
+ * 2016-2017 Helen Ginn <helen@strubi.ox.ac.uk>
+ * 2016-2017 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -382,7 +382,7 @@ static char *get_chiral_holohedry(UnitCell *cell)
default:
break;
}
-
+
return pgout;
}
@@ -394,13 +394,13 @@ static SymOpList *sym_ops_for_cell(UnitCell *cell)
char *pg = get_chiral_holohedry(cell);
rawList = get_pointgroup(pg);
free(pg);
-
+
return rawList;
}
static int rot_mats_are_similar(gsl_matrix *rot1, gsl_matrix *rot2,
- gsl_matrix *sub, gsl_matrix *mul,
- double *score, struct TakeTwoCell *cell)
+ gsl_matrix *sub, gsl_matrix *mul,
+ double *score, struct TakeTwoCell *cell)
{
double tr;
@@ -419,30 +419,30 @@ static int symm_rot_mats_are_similar(gsl_matrix *rot1, gsl_matrix *rot2,
struct TakeTwoCell *cell)
{
int i;
-
+
gsl_matrix *sub = gsl_matrix_calloc(3, 3);
gsl_matrix *mul = gsl_matrix_calloc(3, 3);
for (i = 0; i < cell->numOps; i++) {
gsl_matrix *testRot = gsl_matrix_alloc(3, 3);
gsl_matrix *symOp = cell->rotSymOps[i];
-
+
gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, rot1, symOp,
0.0, testRot);
-
+
if (rot_mats_are_similar(testRot, rot2, sub, mul, NULL, cell)) {
gsl_matrix_free(testRot);
gsl_matrix_free(sub);
gsl_matrix_free(mul);
return 1;
}
-
- gsl_matrix_free(testRot);
+
+ gsl_matrix_free(testRot);
}
-
+
gsl_matrix_free(sub);
gsl_matrix_free(mul);
-
+
return 0;
}
@@ -536,7 +536,7 @@ static int obs_shares_spot_w_array(struct SpotVec *obs_vecs, int test_idx,
int *members, int num)
{
int i;
-
+
struct SpotVec *her_obs = &obs_vecs[test_idx];
for ( i=0; i<num; i++ ) {
@@ -581,11 +581,11 @@ static int obs_vecs_match_angles(struct SpotVec *her_obs,
double angle_diff = fabs(theory_angle - obs_angle);
if ( angle_diff < cell->options->angle_tol ) {
- // in the case of a brief check only
+ // in the case of a brief check only
if (!her_match_idxs || !his_match_idxs) {
return 1;
}
-
+
/* If the angles are too close to 0
or 180, one axis ill-determined */
if (theory_angle < min_angle ||
@@ -594,11 +594,11 @@ static int obs_vecs_match_angles(struct SpotVec *her_obs,
}
// check the third vector
-
+
struct rvec theory_diff = diff_vec(*his_match, *her_match);
struct rvec obs_diff = diff_vec(his_obs->obsvec,
her_obs->obsvec);
-
+
theory_angle = rvec_angle(*her_match,
theory_diff);
obs_angle = rvec_angle(her_obs->obsvec, obs_diff);
@@ -606,15 +606,15 @@ static int obs_vecs_match_angles(struct SpotVec *her_obs,
if (fabs(obs_angle - theory_angle) > ANGLE_TOLERANCE) {
continue;
}
-
+
theory_angle = rvec_angle(*his_match,
theory_diff);
obs_angle = rvec_angle(his_obs->obsvec, obs_diff);
-
+
if (fabs(obs_angle - theory_angle) > ANGLE_TOLERANCE) {
continue;
}
-
+
size_t new_size = (*match_count + 1) *
sizeof(int);
if (her_match_idxs && his_match_idxs)
@@ -654,7 +654,7 @@ 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);
@@ -720,7 +720,7 @@ static int weed_duplicate_matches(struct SpotVec *her_obs,
{
int num_occupied = 0;
gsl_matrix **old_mats = calloc(*match_count, sizeof(gsl_matrix *));
-
+
if (old_mats == NULL)
{
apologise();
@@ -729,11 +729,11 @@ static int weed_duplicate_matches(struct SpotVec *her_obs,
signed int i, j;
int duplicates = 0;
-
+
for (i = *match_count - 1; i >= 0; i--) {
int her_match = (*her_match_idxs)[i];
int his_match = (*his_match_idxs)[i];
-
+
struct rvec i_obsvec = her_obs->obsvec;
struct rvec j_obsvec = his_obs->obsvec;
struct rvec i_cellvec = her_obs->matches[her_match];
@@ -743,7 +743,7 @@ static int weed_duplicate_matches(struct SpotVec *her_obs,
i_cellvec, j_cellvec, cell);
int found = 0;
-
+
for (j = 0; j < num_occupied; j++) {
if (old_mats[j] && mat &&
symm_rot_mats_are_similar(old_mats[j], mat, cell))
@@ -752,21 +752,21 @@ static int weed_duplicate_matches(struct SpotVec *her_obs,
(*her_match_idxs)[i] = -1;
(*his_match_idxs)[i] = -1;
found = 1;
-
+
duplicates++;
gsl_matrix_free(mat);
break;
}
}
-
+
if (!found) {
// we have not found a duplicate, add to list.
old_mats[num_occupied] = mat;
num_occupied++;
}
}
-
+
for (i = 0; i < num_occupied; i++) {
if (old_mats[i]) {
gsl_matrix_free(old_mats[i]);
@@ -774,7 +774,7 @@ static int weed_duplicate_matches(struct SpotVec *her_obs,
}
free(old_mats);
-
+
return 1;
}
@@ -786,9 +786,9 @@ static signed int find_next_index(gsl_matrix *rot, int *obs_members,
int obs_vec_count = cell->obs_vec_count;
gsl_matrix *sub = gsl_matrix_calloc(3, 3);
gsl_matrix *mul = gsl_matrix_calloc(3, 3);
-
+
int i, j, k;
-
+
for ( i=start; i<obs_vec_count; i++ ) {
/* first we check for a shared spot - harshest condition */
@@ -796,23 +796,23 @@ static signed int find_next_index(gsl_matrix *rot, int *obs_members,
member_num);
if ( !shared ) continue;
-
+
int skip = 0;
for ( j=0; j<member_num && skip == 0; j++ ) {
if (i == obs_members[j]) {
skip = 1;
}
}
-
+
if (skip) {
continue;
}
int all_ok = 1;
int matched = -1;
-
+
for ( j=0; j<member_num && all_ok; j++ ) {
-
+
struct SpotVec *me = &obs_vecs[i];
struct SpotVec *you = &obs_vecs[obs_members[j]];
struct rvec you_cell = you->matches[match_members[j]];
@@ -823,24 +823,24 @@ static signed int find_next_index(gsl_matrix *rot, int *obs_members,
int one_is_okay = 0;
for ( k=0; k<me->match_num; k++ ) {
-
+
gsl_matrix *test_rot;
-
- struct rvec me_cell = me->matches[k];
+
+ struct rvec me_cell = me->matches[k];
test_rot = generate_rot_mat(me_obs,
you_obs, me_cell, you_cell,
- cell);
+ cell);
double trace = 0;
int ok = rot_mats_are_similar(rot, test_rot,
sub, mul, &trace, cell);
-
+
gsl_matrix_free(test_rot);
if (ok) {
one_is_okay = 1;
-
+
if (matched >= 0 && k == matched) {
*match_found = k;
} else if (matched < 0) {
@@ -848,10 +848,10 @@ static signed int find_next_index(gsl_matrix *rot, int *obs_members,
} else {
one_is_okay = 0;
break;
- }
+ }
}
}
-
+
if (!one_is_okay) {
all_ok = 0;
break;
@@ -860,12 +860,12 @@ static signed int find_next_index(gsl_matrix *rot, int *obs_members,
if (all_ok) {
-
+
for ( j=0; j<member_num; j++ ) {
// STATUS("%i ", obs_members[j]);
}
//STATUS("%i\n", i);
-
+
return i;
}
}
@@ -943,7 +943,7 @@ static int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
match_members[member_num] = match_found;
member_num++;
-
+
if (member_num > *max_members) {
*max_members = member_num;
}
@@ -954,7 +954,7 @@ static int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
finish_solution(rot, obs_vecs, obs_members,
match_members, member_num, cell);
-
+
return ( member_num > cell->options->member_thresh );
}
@@ -966,7 +966,7 @@ static int start_seed(int i, int j, int i_match, int j_match,
struct SpotVec *obs_vecs = *(cell->obs_vecs);
gsl_matrix *rot_mat;
-
+
rot_mat = generate_rot_mat(obs_vecs[i].obsvec,
obs_vecs[j].obsvec,
obs_vecs[i].matches[i_match],
@@ -988,7 +988,7 @@ static int find_seed(gsl_matrix **rotation, struct TakeTwoCell *cell)
{
struct SpotVec *obs_vecs = *(cell->obs_vecs);
int obs_vec_count = cell->obs_vec_count;
-
+
/* META: Maximum achieved maximum network membership */
int max_max_members = 0;
gsl_matrix *best_rotation = NULL;
@@ -1017,7 +1017,7 @@ static int find_seed(gsl_matrix **rotation, struct TakeTwoCell *cell)
int *i_idx = 0;
int *j_idx = 0;
int matches;
-
+
/* Check to see if any angles match from the cell vectors */
obs_vecs_match_angles(&obs_vecs[i], &obs_vecs[j],
&i_idx, &j_idx, &matches, cell);
@@ -1097,7 +1097,7 @@ static int generate_rotation_sym_ops(struct TakeTwoCell *ttCell)
/* Now we must convert these into rotation matrices rather than hkl
* transformations (affects triclinic, monoclinic, rhombohedral and
* hexagonal space groups only) */
-
+
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
@@ -1111,59 +1111,59 @@ static int generate_rotation_sym_ops(struct TakeTwoCell *ttCell)
cell_get_cartesian(ttCell->cell, &asx, &asy, &asz, &bsx, &bsy,
&bsz, &csx, &csy, &csz);
-
+
set_gsl_matrix(cart, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
int i, j, k;
int numOps = num_equivs(rawList, NULL);
-
+
ttCell->rotSymOps = malloc(numOps * sizeof(gsl_matrix *));
ttCell->numOps = numOps;
-
+
if (ttCell->rotSymOps == NULL) {
apologise();
return 0;
}
-
+
for (i = 0; i < numOps; i++)
{
gsl_matrix *symOp = gsl_matrix_alloc(3, 3);
IntegerMatrix *op = get_symop(rawList, NULL, i);
-
+
for (j = 0; j < 3; j++) {
for (k = 0; k < 3; k++) {
gsl_matrix_set(symOp, j, k, intmat_get(op, j, k));
}
}
-
+
gsl_matrix *first = gsl_matrix_calloc(3, 3);
gsl_matrix *second = gsl_matrix_calloc(3, 3);
-
+
/* Each equivalence is of the form:
- cartesian * symOp * reciprocal.
- First multiplication: symOp * reciprocal */
-
+ cartesian * symOp * reciprocal.
+ First multiplication: symOp * reciprocal */
+
gsl_blas_dgemm(CblasNoTrans, CblasNoTrans,
1.0, symOp, recip,
0.0, first);
-
+
/* Second multiplication: cartesian * first */
-
+
gsl_blas_dgemm(CblasNoTrans, CblasNoTrans,
1.0, cart, first,
0.0, second);
-
+
ttCell->rotSymOps[i] = second;
-
+
gsl_matrix_free(symOp);
gsl_matrix_free(first);
}
gsl_matrix_free(cart);
gsl_matrix_free(recip);
-
+
free_symoplist(rawList);
-
+
return 1;
}
@@ -1192,7 +1192,7 @@ static int match_obs_to_cell_vecs(struct rvec *cell_vecs, int cell_vec_count,
int count = 0;
struct sortme *for_sort = NULL;
-
+
for ( j=0; j<cell_vec_count; j++ ) {
/* get distance for unit cell vector */
double cell_length = rvec_length(cell_vecs[j]);
@@ -1217,16 +1217,16 @@ static int match_obs_to_cell_vecs(struct rvec *cell_vecs, int cell_vec_count,
}
/* Pointers to relevant things */
-
+
struct rvec **match_array;
int *match_count;
-
+
if (!is_asymmetric) {
match_array = &(obs_vecs[i].matches);
match_count = &(obs_vecs[i].match_num);
} else {
match_array = &(obs_vecs[i].asym_matches);
- match_count = &(obs_vecs[i].asym_match_num);
+ match_count = &(obs_vecs[i].asym_match_num);
}
/* Sort in order to get most agreeable matches first */
@@ -1235,7 +1235,7 @@ static int match_obs_to_cell_vecs(struct rvec *cell_vecs, int cell_vec_count,
*match_count = count;
for ( j=0; j<count; j++ ) {
(*match_array)[j] = for_sort[j].v;
-
+
}
free(for_sort);
}
@@ -1347,12 +1347,12 @@ static int gen_theoretical_vecs(UnitCell *cell, struct rvec **cell_vecs,
int asymmetric = 0;
get_asymm(rawList, h, k, l, &_h, &_k, &_l);
-
+
if (h == _h && k == _k && l == _l) {
asymmetric = 1;
asym_count++;
}
-
+
cell_vec.u = h*asx + k*bsx + l*csx;
cell_vec.v = h*asy + k*bsy + l*csy;
cell_vec.w = h*asz + k*bsz + l*csz;
@@ -1376,11 +1376,11 @@ static int gen_theoretical_vecs(UnitCell *cell, struct rvec **cell_vecs,
} else {
*cell_vecs = temp_cell_vecs;
(*cell_vecs)[count - 1] = cell_vec;
-
+
if (!asymmetric) {
continue;
}
-
+
*asym_vecs = temp_asym_vecs;
(*asym_vecs)[asym_count - 1] = cell_vec;
}
@@ -1390,7 +1390,7 @@ static int gen_theoretical_vecs(UnitCell *cell, struct rvec **cell_vecs,
*vec_count = count;
*asym_vec_count = asym_count;
-
+
free_symoplist(rawList);
@@ -1401,7 +1401,7 @@ static int gen_theoretical_vecs(UnitCell *cell, struct rvec **cell_vecs,
/* ------------------------------------------------------------------------
* cleanup functions - called from run_taketwo().
* ------------------------------------------------------------------------*/
-
+
static void cleanup_taketwo_obs_vecs(struct SpotVec *obs_vecs,
int obs_vec_count)
{
@@ -1453,7 +1453,7 @@ static UnitCell *run_taketwo(UnitCell *cell, struct taketwo_options *opts,
struct SpotVec *obs_vecs = NULL;
int success = 0;
gsl_matrix *solution = NULL;
-
+
struct TakeTwoCell ttCell;
ttCell.cell = cell;
ttCell.options = opts;
@@ -1498,7 +1498,7 @@ static UnitCell *run_taketwo(UnitCell *cell, struct taketwo_options *opts,
gsl_matrix_free(solution);
cleanup_taketwo_obs_vecs(obs_vecs, obs_vec_count);
cleanup_taketwo_cell(&ttCell);
-
+
return result;
}
@@ -1523,7 +1523,7 @@ int taketwo_index(struct image *image, struct taketwo_options *opts, void *priv)
if (opts->len_tol < 0) {
opts->len_tol = RECIP_TOLERANCE;
}
-
+
if (opts->angle_tol < 0) {
opts->angle_tol = ANGLE_TOLERANCE;
}
@@ -1531,7 +1531,7 @@ int taketwo_index(struct image *image, struct taketwo_options *opts, void *priv)
if (opts->trace_tol < 0) {
opts->trace_tol = TRACE_TOLERANCE;
}
-
+
opts->trace_tol = sqrt(4.0*(1.0-cos(opts->trace_tol)));
rlps = malloc((image_feature_count(image->features)+1)*sizeof(struct rvec));