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Diffstat (limited to 'libcrystfel/src/taketwo.c')
| -rw-r--r-- | libcrystfel/src/taketwo.c | 1624 |
1 files changed, 1624 insertions, 0 deletions
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c new file mode 100644 index 00000000..605ced7f --- /dev/null +++ b/libcrystfel/src/taketwo.c @@ -0,0 +1,1624 @@ +/* + * taketwo.c + * + * 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. + * + * Authors: + * 2016 Helen Ginn <helen@strubi.ox.ac.uk> + * 2016 Thomas White <taw@physics.org> + * + * This file is part of CrystFEL. + * + * CrystFEL is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * CrystFEL is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. + * + */ + +#include <gsl/gsl_matrix.h> +#include <gsl/gsl_blas.h> +#include <float.h> +#include <math.h> +#include <assert.h> +#include <time.h> + +#include "cell-utils.h" +#include "index.h" +#include "taketwo.h" +#include "peaks.h" +#include "symmetry.h" + +/** + * spotvec + * @obsvec: an observed vector between two spots + * @matches: array of matching theoretical vectors from unit cell + * @match_num: number of matches + * @distance: length of obsvec (do I need this?) + * @her_rlp: pointer to first rlp position for difference vec + * @his_rlp: pointer to second rlp position for difference vec + * + * Structure representing 3D vector between two potential Bragg peaks + * in reciprocal space, and an array of potential matching theoretical + * vectors from unit cell/centering considerations. + **/ +struct SpotVec +{ + struct rvec obsvec; + struct rvec *matches; + int match_num; + struct rvec *asym_matches; + int asym_match_num; + double distance; + struct rvec *her_rlp; + struct rvec *his_rlp; +}; + + +struct taketwo_private +{ + IndexingMethod indm; + float *ltl; + UnitCell *cell; +}; + +// These rotation symmetry operators +struct TakeTwoCell +{ + UnitCell *cell; + gsl_matrix **rotSymOps; + unsigned int numOps; + struct SpotVec **obs_vecs; // Pointer to an array + int obs_vec_count; + gsl_matrix *twiz1Tmp; + gsl_matrix *twiz2Tmp; + gsl_vector *vec1Tmp; + gsl_vector *vec2Tmp; +}; + + +/* Maximum distance between two rlp sizes to consider info for indexing */ +#define MAX_RECIP_DISTANCE (0.15*1e10) + +/* Tolerance for two lengths in reciprocal space to be considered the same */ +#define RECIP_TOLERANCE (0.0010*1e10) + +/* Threshold for network members to consider a potential solution */ +#define NETWORK_MEMBER_THRESHOLD (20) + +/* Maximum network members (obviously a solution so should stop) */ +#define MAX_NETWORK_MEMBERS (NETWORK_MEMBER_THRESHOLD + 3) + +/* Maximum dead ends for a single branch extension during indexing */ +#define MAX_DEAD_ENDS (10) + +/* Maximum observed vectors before TakeTwo gives up and deals with + * what is already there. */ +#define MAX_OBS_VECTORS 100000 + +/* Tolerance for two angles to be considered the same */ +#define ANGLE_TOLERANCE (deg2rad(0.6)) + +/* Tolerance for rot_mats_are_similar */ +#define TRACE_TOLERANCE (deg2rad(3.0)) + +/** TODO: + * + * - May need to be capable of playing with the tolerances/#defined stuff. + * - Multiple lattices + */ + + +/* ------------------------------------------------------------------------ + * apologetic function + * ------------------------------------------------------------------------*/ + +void apologise() +{ + printf("Error - could not allocate memory for indexing.\n"); +} + +/* ------------------------------------------------------------------------ + * functions concerning aspects of rvec which are very likely to be + * incorporated somewhere else in CrystFEL and therefore may need to be + * deleted and references connected to a pre-existing function. (Lowest level) + * ------------------------------------------------------------------------*/ + +static struct rvec new_rvec(double new_u, double new_v, double new_w) +{ + struct rvec new_rvector; + new_rvector.u = new_u; + new_rvector.v = new_v; + new_rvector.w = new_w; + + return new_rvector; +} + + +static struct rvec diff_vec(struct rvec from, struct rvec to) +{ + struct rvec diff = new_rvec(to.u - from.u, + to.v - from.v, + to.w - from.w); + + return diff; +} + +static double sq_length(struct rvec vec) +{ + double sqlength = (vec.u * vec.u + vec.v * vec.v + vec.w * vec.w); + + return sqlength; +} + + +static double rvec_length(struct rvec vec) +{ + return sqrt(sq_length(vec)); +} + + +static void normalise_rvec(struct rvec *vec) +{ + double length = rvec_length(*vec); + vec->u /= length; + vec->v /= length; + vec->w /= length; +} + + +static double rvec_cosine(struct rvec v1, struct rvec v2) +{ + double dot_prod = v1.u * v2.u + v1.v * v2.v + v1.w * v2.w; + double v1_length = rvec_length(v1); + double v2_length = rvec_length(v2); + + double cos_theta = dot_prod / (v1_length * v2_length); + + return cos_theta; +} + + +static double rvec_angle(struct rvec v1, struct rvec v2) +{ + double cos_theta = rvec_cosine(v1, v2); + double angle = acos(cos_theta); + + return angle; +} + + +static struct rvec rvec_cross(struct rvec a, struct rvec b) +{ + struct rvec c; + + c.u = a.v*b.w - a.w*b.v; + c.v = -(a.u*b.w - a.w*b.u); + c.w = a.u*b.v - a.v*b.u; + + return c; +} + +/* +static void show_rvec(struct rvec r2) +{ + struct rvec r = r2; + normalise_rvec(&r); + STATUS("[ %.3f %.3f %.3f ]\n", r.u, r.v, r.w); +} +*/ + + +/* ------------------------------------------------------------------------ + * functions called under the core functions, still specialised (Level 3) + * ------------------------------------------------------------------------*/ + +static void rotation_around_axis(struct rvec c, double th, + gsl_matrix *res) +{ + double omc = 1.0 - cos(th); + double s = sin(th); + gsl_matrix_set(res, 0, 0, cos(th) + c.u*c.u*omc); + gsl_matrix_set(res, 0, 1, c.u*c.v*omc - c.w*s); + gsl_matrix_set(res, 0, 2, c.u*c.w*omc + c.v*s); + gsl_matrix_set(res, 1, 0, c.u*c.v*omc + c.w*s); + gsl_matrix_set(res, 1, 1, cos(th) + c.v*c.v*omc); + gsl_matrix_set(res, 1, 2, c.v*c.w*omc - c.u*s); + gsl_matrix_set(res, 2, 0, c.w*c.u*omc - c.v*s); + gsl_matrix_set(res, 2, 1, c.w*c.v*omc + c.u*s); + gsl_matrix_set(res, 2, 2, cos(th) + c.w*c.w*omc); +} + + +/* Rotate vector (vec1) around axis (axis) by angle theta. Find value of + * theta for which the angle between (vec1) and (vec2) is minimised. */ +static void closest_rot_mat(struct rvec vec1, struct rvec vec2, + struct rvec axis, gsl_matrix *twizzle) +{ + /* Let's have unit vectors */ + normalise_rvec(&vec1); + normalise_rvec(&vec2); + normalise_rvec(&axis); + + /* Redeclaring these to try and maintain readability and + * check-ability against the maths I wrote down */ + double a = vec2.u; double b = vec2.v; double c = vec2.w; + double p = vec1.u; double q = vec1.v; double r = vec1.w; + double x = axis.u; double y = axis.v; double z = axis.w; + + /* Components in handwritten maths online when I upload it */ + double A = a*(p*x*x - p + x*y*q + x*z*r) + + b*(p*x*y + q*y*y - q + r*y*z) + + c*(p*x*z + q*y*z + r*z*z - r); + + double B = a*(y*r - z*q) + b*(p*z - r*x) + c*(q*x - p*y); + + double tan_theta = - B / A; + double theta = atan(tan_theta); + + /* Now we have two possible solutions, theta or theta+pi + * and we need to work out which one. This could potentially be + * simplified - do we really need so many cos/sins? maybe check + * the 2nd derivative instead? */ + double cc = cos(theta); + double C = 1 - cc; + double s = sin(theta); + double occ = -cc; + double oC = 1 - occ; + double os = -s; + + double pPrime = (x*x*C+cc)*p + (x*y*C-z*s)*q + (x*z*C+y*s)*r; + double qPrime = (y*x*C+z*s)*p + (y*y*C+cc)*q + (y*z*C-x*s)*r; + double rPrime = (z*x*C-y*s)*p + (z*y*C+x*s)*q + (z*z*C+cc)*r; + + double pDbPrime = (x*x*oC+occ)*p + (x*y*oC-z*os)*q + (x*z*oC+y*os)*r; + double qDbPrime = (y*x*oC+z*os)*p + (y*y*oC+occ)*q + (y*z*oC-x*os)*r; + double rDbPrime = (z*x*oC-y*os)*p + (z*y*oC+x*os)*q + (z*z*oC+occ)*r; + + double cosAlpha = pPrime * a + qPrime * b + rPrime * c; + double cosAlphaOther = pDbPrime * a + qDbPrime * b + rDbPrime * c; + + int addPi = (cosAlphaOther > cosAlpha); + double bestAngle = theta + addPi * M_PI; + + /* Don't return an identity matrix which has been rotated by + * theta around "axis", but do assign it to twizzle. */ + rotation_around_axis(axis, bestAngle, twizzle); +} + + +static double matrix_trace(gsl_matrix *a) +{ + int i; + double tr = 0.0; + + assert(a->size1 == a->size2); + for ( i=0; i<a->size1; i++ ) { + tr += gsl_matrix_get(a, i, i); + } + return tr; +} + +static char *add_ua(const char *inp, char ua) +{ + char *pg = malloc(64); + if ( pg == NULL ) return NULL; + snprintf(pg, 63, "%s_ua%c", inp, ua); + return pg; +} + + +static char *get_chiral_holohedry(UnitCell *cell) +{ + LatticeType lattice = cell_get_lattice_type(cell); + char *pg = malloc(64); + char *pgout = 0; + + if ( pg == NULL ) return NULL; + + switch (lattice) + { + case L_TRICLINIC: + pg = "1"; + break; + + case L_MONOCLINIC: + pg = "2"; + break; + + case L_ORTHORHOMBIC: + pg = "222"; + break; + + case L_TETRAGONAL: + pg = "422"; + break; + + case L_RHOMBOHEDRAL: + pg = "3_R"; + break; + + case L_HEXAGONAL: + if ( cell_get_centering(cell) == 'H' ) { + pg = "3_H"; + } else { + pg = "622"; + } + break; + + case L_CUBIC: + pg = "432"; + break; + + default: + pg = "error"; + break; + } + + switch (lattice) + { + case L_TRICLINIC: + case L_ORTHORHOMBIC: + case L_RHOMBOHEDRAL: + case L_CUBIC: + pgout = strdup(pg); + break; + + case L_MONOCLINIC: + case L_TETRAGONAL: + case L_HEXAGONAL: + pgout = add_ua(pg, cell_get_unique_axis(cell)); + break; + + default: + break; + } + + return pgout; +} + + +static SymOpList *sym_ops_for_cell(UnitCell *cell) +{ + SymOpList *rawList; + + 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) +{ + double tr; + + gsl_matrix_memcpy(sub, rot1); + gsl_matrix_sub(sub, rot2); /* sub = rot1 - rot2 */ + + gsl_blas_dgemm(CblasNoTrans, CblasTrans, 1.0, sub, sub, 0.0, mul); + + tr = matrix_trace(mul); + if (score != NULL) *score = tr; + + double max = sqrt(4.0*(1.0-cos(TRACE_TOLERANCE))); + + return (tr < max); +} + +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)) { + gsl_matrix_free(testRot); + gsl_matrix_free(sub); + gsl_matrix_free(mul); + return 1; + } + + gsl_matrix_free(testRot); + } + + gsl_matrix_free(sub); + gsl_matrix_free(mul); + + return 0; +} + +static void rotation_between_vectors(struct rvec a, struct rvec b, + gsl_matrix *twizzle) +{ + double th = rvec_angle(a, b); + struct rvec c = rvec_cross(a, b); + normalise_rvec(&c); + rotation_around_axis(c, th, twizzle); +} + + +static void rvec_to_gsl(gsl_vector *newVec, struct rvec v) +{ + gsl_vector_set(newVec, 0, v.u); + gsl_vector_set(newVec, 1, v.v); + gsl_vector_set(newVec, 2, v.w); +} + + +struct rvec gsl_to_rvec(gsl_vector *a) +{ + struct rvec v; + v.u = gsl_vector_get(a, 0); + v.v = gsl_vector_get(a, 1); + v.w = gsl_vector_get(a, 2); + return v; +} + + +/* Code me in gsl_matrix language to copy the contents of the function + * in cppxfel (IndexingSolution::createSolution). This function is quite + * intensive on the number crunching side so simple angle checks are used + * to 'pre-scan' vectors beforehand. */ +static gsl_matrix *generate_rot_mat(struct rvec obs1, struct rvec obs2, + struct rvec cell1, struct rvec cell2, + struct TakeTwoCell *cell) +{ + gsl_matrix *fullMat; + rvec_to_gsl(cell->vec1Tmp, cell2); + +// gsl_vector *cell2v = rvec_to_gsl(cell2); +// gsl_vector *cell2vr = gsl_vector_calloc(3); + + normalise_rvec(&obs1); + normalise_rvec(&obs2); + normalise_rvec(&cell1); + normalise_rvec(&cell2); + + /* Rotate reciprocal space so that the first simulated vector lines up + * with the observed vector. */ + rotation_between_vectors(cell1, obs1, cell->twiz1Tmp); + + normalise_rvec(&obs1); + + /* Multiply cell2 by rotateSpotDiffMatrix --> cell2vr */ + gsl_blas_dgemv(CblasNoTrans, 1.0, cell->twiz1Tmp, cell->vec1Tmp, + 0.0, cell->vec2Tmp); + + /* Now we twirl around the firstAxisUnit until the rotated simulated + * vector matches the second observed vector as closely as possible. */ + + closest_rot_mat(gsl_to_rvec(cell->vec2Tmp), obs2, obs1, cell->twiz2Tmp); + + /* We want to apply the first matrix and then the second matrix, + * so we multiply these. */ + fullMat = gsl_matrix_calloc(3, 3); + gsl_blas_dgemm(CblasTrans, CblasTrans, 1.0, + cell->twiz1Tmp, cell->twiz2Tmp, 0.0, fullMat); + gsl_matrix_transpose(fullMat); + + return fullMat; +} + + +static int obs_vecs_share_spot(struct SpotVec *her_obs, struct SpotVec *his_obs) +{ + if ( (her_obs->her_rlp == his_obs->her_rlp) || + (her_obs->her_rlp == his_obs->his_rlp) || + (her_obs->his_rlp == his_obs->her_rlp) || + (her_obs->his_rlp == his_obs->his_rlp) ) { + return 1; + } + + return 0; +} + + +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++ ) { + struct SpotVec *his_obs = &obs_vecs[members[i]]; + + int shares = obs_vecs_share_spot(her_obs, his_obs); + + if ( shares ) return 1; + } + + return 0; +} + + +static int obs_vecs_match_angles(struct SpotVec *her_obs, + struct SpotVec *his_obs, + int **her_match_idxs, int **his_match_idxs, + int *match_count) +{ + int i, j; + *match_count = 0; + + double min_angle = deg2rad(2.5); + double max_angle = deg2rad(187.5); + + /* calculate angle between observed vectors */ + double obs_angle = rvec_angle(her_obs->obsvec, his_obs->obsvec); + + /* calculate angle between all potential theoretical vectors */ + + for ( i=0; i<her_obs->match_num; i++ ) { + for ( j=0; j<his_obs->match_num; j++ ) { + + struct rvec *her_match = &her_obs->matches[i]; + struct rvec *his_match = &his_obs->matches[j]; + + double theory_angle = rvec_angle(*her_match, + *his_match); + + /* is this angle a match? */ + + double angle_diff = fabs(theory_angle - obs_angle); + + if ( angle_diff < ANGLE_TOLERANCE ) { + // 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 || + theory_angle > max_angle) { + continue; + } + + // 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); + + 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) + { + /* Reallocate the array to fit in another match */ + int *temp_hers; + int *temp_his; + temp_hers = realloc(*her_match_idxs, new_size); + temp_his = realloc(*his_match_idxs, new_size); + + if ( temp_hers == NULL || temp_his == NULL ) { + apologise(); + } + + (*her_match_idxs) = temp_hers; + (*his_match_idxs) = temp_his; + + (*her_match_idxs)[*match_count] = i; + (*his_match_idxs)[*match_count] = j; + } + + (*match_count)++; + } + } + } + + return (*match_count > 0); +} + +/* ------------------------------------------------------------------------ + * core functions regarding the meat of the TakeTwo algorithm (Level 2) + * ------------------------------------------------------------------------*/ + +static signed int finish_solution(gsl_matrix *rot, struct SpotVec *obs_vecs, + int *obs_members, int *match_members, + int member_num, struct TakeTwoCell *cell) +{ + 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); + + int i, j, count; + + count = 0; + for ( i=0; i<1; i++ ) { + for ( j=0; j<member_num; j++ ) { + if (i == j) continue; + struct SpotVec i_vec = obs_vecs[obs_members[i]]; + struct SpotVec j_vec = obs_vecs[obs_members[j]]; + + struct rvec i_obsvec = i_vec.obsvec; + struct rvec j_obsvec = j_vec.obsvec; + struct rvec i_cellvec = i_vec.matches[match_members[i]]; + struct rvec j_cellvec = j_vec.matches[match_members[j]]; + + rotations[count] = generate_rot_mat(i_obsvec, j_obsvec, + i_cellvec, j_cellvec, + cell); + + count++; + } + } + + double min_score = FLT_MAX; + int min_rot_index = 0; + + for (i=0; i<count; i++) { + double current_score = 0; + for (j=0; j<count; j++) { + double addition; + rot_mats_are_similar(rotations[i], rotations[j], + sub, mul, + &addition); + + current_score += addition; + } + + if (current_score < min_score) { + min_score = current_score; + min_rot_index = i; + } + } + + gsl_matrix_memcpy(rot, rotations[min_rot_index]); + + for (i=0; i<count; i++) { + gsl_matrix_free(rotations[i]); + } + + free(rotations); + gsl_matrix_free(sub); + gsl_matrix_free(mul); + + return 1; +} + +static int weed_duplicate_matches(struct SpotVec *her_obs, + struct SpotVec *his_obs, + int **her_match_idxs, int **his_match_idxs, + int *match_count, struct TakeTwoCell *cell) +{ + int num_occupied = 0; + gsl_matrix **old_mats = calloc(*match_count, sizeof(gsl_matrix *)); + + if (old_mats == NULL) + { + apologise(); + return 0; + } + + 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]; + struct rvec j_cellvec = his_obs->matches[his_match]; + + gsl_matrix *mat = generate_rot_mat(i_obsvec, j_obsvec, + 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)) + { + // we have found a duplicate, so flag as bad. + (*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]); + } + } + + free(old_mats); + + return 1; +} + +static signed int find_next_index(gsl_matrix *rot, int *obs_members, + int *match_members, int start, int member_num, + int *match_found, struct TakeTwoCell *cell) +{ + struct SpotVec *obs_vecs = *(cell->obs_vecs); + 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 */ + int shared = obs_shares_spot_w_array(obs_vecs, i, 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]]; + + struct rvec me_obs = me->obsvec; + struct rvec you_obs = you->obsvec; + + int one_is_okay = 0; + + for ( k=0; k<me->match_num; k++ ) { + + gsl_matrix *test_rot; + + struct rvec me_cell = me->matches[k]; + + test_rot = generate_rot_mat(me_obs, + you_obs, me_cell, you_cell, + cell); + + double trace = 0; + int ok = rot_mats_are_similar(rot, test_rot, + sub, mul, &trace); + + gsl_matrix_free(test_rot); + + if (ok) { + one_is_okay = 1; + + if (matched >= 0 && k == matched) { + *match_found = k; + } else if (matched < 0) { + matched = k; + } else { + one_is_okay = 0; + break; + } + } + } + + if (!one_is_okay) { + all_ok = 0; + break; + } + } + + + if (all_ok) { + + for ( j=0; j<member_num; j++ ) { + // STATUS("%i ", obs_members[j]); + } + //STATUS("%i\n", i); + + return i; + } + } + + /* give up. */ + + return -1; +} + + +static int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2, + int match_idx1, int match_idx2, int *max_members, + struct TakeTwoCell *cell) +{ + struct SpotVec *obs_vecs = *(cell->obs_vecs); + int obs_vec_count = cell->obs_vec_count; + + /* indices of members of the self-consistent network of vectors */ + int obs_members[MAX_NETWORK_MEMBERS]; + int match_members[MAX_NETWORK_MEMBERS]; + + /* initialise the ones we know already */ + obs_members[0] = obs_idx1; + obs_members[1] = obs_idx2; + match_members[0] = match_idx1; + match_members[1] = match_idx2; + int member_num = 2; + *max_members = 2; + + /* counter for dead ends which must not exceed MAX_DEAD_ENDS + * before it is reset in an additional branch */ + int dead_ends = 0; + + /* we start from 0 */ + int start = 0; + + while ( 1 ) { + + if (start > obs_vec_count) { + return 0; + } + + int match_found = -1; + + signed int next_index = find_next_index(rot, obs_members, + match_members, + start, member_num, + &match_found, cell); + + if ( member_num < 2 ) { + return 0; + } + + if ( next_index < 0 ) { + /* If there have been too many dead ends, give up + * on indexing altogether. + **/ + if ( dead_ends > MAX_DEAD_ENDS ) { + break; + } + + /* We have not had too many dead ends. Try removing + the last member and continue. */ + start = obs_members[member_num - 1] + 1; + member_num--; + dead_ends++; + + continue; + } + + /* we have elongated membership - so reset dead_ends counter */ + // dead_ends = 0; + + obs_members[member_num] = next_index; + match_members[member_num] = match_found; + + member_num++; + + 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; + } + + finish_solution(rot, obs_vecs, obs_members, + match_members, member_num, cell); + + return ( member_num > NETWORK_MEMBER_THRESHOLD ); +} + + +static int start_seed(int i, int j, int i_match, int j_match, + gsl_matrix **rotation, int *max_members, + struct TakeTwoCell *cell) +{ + 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], + obs_vecs[j].matches[j_match], + cell); + + /* Try to expand this rotation matrix to a larger network */ + + int success = grow_network(rot_mat, i, j, i_match, j_match, max_members, + cell); + + /* return this matrix and if it was immediately successful */ + *rotation = rot_mat; + + return success; +} + +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; + +// unsigned long start_time = time(NULL); + + /* loop round pairs of vectors to try and find a suitable + * seed to start building a self-consistent network of vectors + */ + int i, j; + + for ( i=0; i<obs_vec_count; i++ ) { + for ( j=0; j<i; j++ ) { + + /** Check to see if there is a shared spot - opportunity + * for optimisation by generating a look-up table + * by spot instead of by vector. + */ + int shared = obs_vecs_share_spot(&obs_vecs[i], &obs_vecs[j]); + + if ( !shared ) continue; + + /* cell vector index matches stored in i, j and total number + * stored in int matches. + */ + int *i_idx = 0; + int *j_idx = 0; + int matches; + + // double dist1Pc = 100 * obs_vecs[i].distance / MAX_RECIP_DISTANCE; +// double dist2Pc = 100 * obs_vecs[j].distance / MAX_RECIP_DISTANCE; + + /* 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); + if ( matches == 0 ) { + free(i_idx); + free(j_idx); + continue; + } + + /* Weed out the duplicate seeds (from symmetric + * reflection pairs) + */ + + weed_duplicate_matches(&obs_vecs[i], &obs_vecs[j], + &i_idx, &j_idx, &matches, cell); + + /* We have seeds! Pass each of them through the seed-starter */ + /* If a seed has the highest achieved membership, make note...*/ + int k; + for ( k=0; k<matches; k++ ) { + if (i_idx[k] < 0 || j_idx[k] < 0) { + continue; + } + + int max_members = 0; + + int success = start_seed(i, j, + i_idx[k], j_idx[k], + rotation, &max_members, + cell); + + if (success) { + free(i_idx); free(j_idx); + gsl_matrix_free(best_rotation); + return success; + } else { + if (max_members > max_max_members) { + max_max_members = max_members; + gsl_matrix_free(best_rotation); + best_rotation = *rotation; + *rotation = NULL; + } else { + gsl_matrix_free(*rotation); + *rotation = NULL; + } + } + } + + free(i_idx); + free(j_idx); + } + } /* yes this } is meant to be here */ + + *rotation = best_rotation; + return (best_rotation != NULL); +} + +static void set_gsl_matrix(gsl_matrix *mat, double asx, double asy, double asz, + double bsx, double bsy, double bsz, + double csx, double csy, double csz) +{ + gsl_matrix_set(mat, 0, 0, asx); + gsl_matrix_set(mat, 0, 1, asy); + gsl_matrix_set(mat, 0, 2, asz); + gsl_matrix_set(mat, 1, 0, bsx); + gsl_matrix_set(mat, 1, 1, bsy); + gsl_matrix_set(mat, 1, 2, bsz); + gsl_matrix_set(mat, 2, 0, csx); + gsl_matrix_set(mat, 2, 1, csy); + gsl_matrix_set(mat, 2, 2, csz); +} + +static int generate_rotation_sym_ops(struct TakeTwoCell *ttCell) +{ + SymOpList *rawList = sym_ops_for_cell(ttCell->cell); + + /* 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; + + gsl_matrix *recip = gsl_matrix_alloc(3, 3); + gsl_matrix *cart = gsl_matrix_alloc(3, 3); + cell_get_reciprocal(ttCell->cell, &asx, &asy, &asz, &bsx, &bsy, + &bsz, &csx, &csy, &csz); + + set_gsl_matrix(recip, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz); + + 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 */ + + 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; +} + + +struct sortme +{ + struct rvec v; + double dist; +}; + +static int sort_func(const void *av, const void *bv) +{ + struct sortme *a = (struct sortme *)av; + struct sortme *b = (struct sortme *)bv; + return a->dist > b->dist; +} + + +static int match_obs_to_cell_vecs(struct rvec *cell_vecs, int cell_vec_count, + struct SpotVec *obs_vecs, int obs_vec_count, + int is_asymmetric) +{ + int i, j; + + for ( i=0; i<obs_vec_count; i++ ) { + + 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]); + double obs_length = obs_vecs[i].distance; + + /* check if this matches the observed length */ + double dist_diff = fabs(cell_length - obs_length); + + if ( dist_diff > RECIP_TOLERANCE ) continue; + + /* we have a match, add to array! */ + + size_t new_size = (count+1)*sizeof(struct sortme); + for_sort = realloc(for_sort, new_size); + + if ( for_sort == NULL ) return 0; + + for_sort[count].v = cell_vecs[j]; + for_sort[count].dist = dist_diff; + 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); + } + + /* Sort in order to get most agreeable matches first */ + qsort(for_sort, count, sizeof(struct sortme), sort_func); + *match_array = malloc(count*sizeof(struct rvec)); + *match_count = count; + for ( j=0; j<count; j++ ) { + (*match_array)[j] = for_sort[j].v; + + } + free(for_sort); + } + + return 1; +} + +static int compare_spot_vecs(const void *av, const void *bv) +{ + struct SpotVec *a = (struct SpotVec *)av; + struct SpotVec *b = (struct SpotVec *)bv; + return a->distance > b->distance; +} + +static int gen_observed_vecs(struct rvec *rlps, int rlp_count, + struct SpotVec **obs_vecs, int *obs_vec_count) +{ + int i, j; + int count = 0; + + /* maximum distance squared for comparisons */ + double max_sq_length = pow(MAX_RECIP_DISTANCE, 2); + + for ( i=0; i<rlp_count-1 && count < MAX_OBS_VECTORS; i++ ) { + for ( j=i+1; j<rlp_count; j++ ) { + + + /* calculate difference vector between rlps */ + struct rvec diff = diff_vec(rlps[i], rlps[j]); + + /* are these two far from each other? */ + double sqlength = sq_length(diff); + + if ( sqlength > max_sq_length ) continue; + + count++; + + struct SpotVec *temp_obs_vecs; + temp_obs_vecs = realloc(*obs_vecs, + count*sizeof(struct SpotVec)); + + if ( temp_obs_vecs == NULL ) { + return 0; + } else { + *obs_vecs = temp_obs_vecs; + + /* initialise all SpotVec struct members */ + + struct SpotVec spot_vec; + spot_vec.obsvec = diff; + spot_vec.distance = sqrt(sqlength); + spot_vec.matches = NULL; + spot_vec.match_num = 0; + spot_vec.her_rlp = &rlps[i]; + spot_vec.his_rlp = &rlps[j]; + + (*obs_vecs)[count - 1] = spot_vec; + } + } + } + + /* Sort such that the shortest and least error-prone distances + are searched first. + */ + qsort(*obs_vecs, count, sizeof(struct SpotVec), compare_spot_vecs); + + *obs_vec_count = count; + + return 1; +} + + +static int gen_theoretical_vecs(UnitCell *cell, struct rvec **cell_vecs, + struct rvec **asym_vecs, int *vec_count, + int *asym_vec_count) +{ + double a, b, c, alpha, beta, gamma; + int h_max, k_max, l_max; + double asx, asy, asz; + double bsx, bsy, bsz; + double csx, csy, csz; + + cell_get_reciprocal(cell, &asx, &asy, &asz, + &bsx, &bsy, &bsz, + &csx, &csy, &csz); + + SymOpList *rawList = sym_ops_for_cell(cell); + + cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma); + + /* find maximum Miller (h, k, l) indices for a given resolution */ + h_max = MAX_RECIP_DISTANCE * a; + k_max = MAX_RECIP_DISTANCE * b; + l_max = MAX_RECIP_DISTANCE * c; + + int h, k, l; + int _h, _k, _l; + int count = 0; + int asym_count = 0; + + for ( h=-h_max; h<=+h_max; h++ ) { + for ( k=-k_max; k<=+k_max; k++ ) { + for ( l=-l_max; l<=+l_max; l++ ) { + + struct rvec cell_vec; + + /* Exclude systematic absences from centering concerns */ + if ( forbidden_reflection(cell, h, k, l) ) continue; + + 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; + + /* add this to our array - which may require expanding */ + count++; + + struct rvec *temp_cell_vecs; + temp_cell_vecs = realloc(*cell_vecs, count*sizeof(struct rvec)); + struct rvec *temp_asym_vecs = NULL; + + if (asymmetric) { + temp_asym_vecs = realloc(*asym_vecs, + count*sizeof(struct rvec)); + } + + if ( temp_cell_vecs == NULL ) { + return 0; + } else if (asymmetric && temp_asym_vecs == NULL) { + return 0; + } 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; + } + } + } + } + + *vec_count = count; + *asym_vec_count = asym_count; + + free_symoplist(rawList); + + + return 1; +} + + +/* ------------------------------------------------------------------------ + * cleanup functions - called from run_taketwo(). + * ------------------------------------------------------------------------*/ + +static void cleanup_taketwo_obs_vecs(struct SpotVec *obs_vecs, + int obs_vec_count) +{ + int i; + for ( i=0; i<obs_vec_count; i++ ) { + free(obs_vecs[i].matches); + free(obs_vecs[i].asym_matches); + } + + free(obs_vecs); +} + +static void cleanup_taketwo_cell(struct TakeTwoCell *ttCell) +{ + int i; + for ( i=0; i<ttCell->numOps; i++ ) { + gsl_matrix_free(ttCell->rotSymOps[i]); + } + + free(ttCell->vec1Tmp); + free(ttCell->vec2Tmp); + free(ttCell->twiz1Tmp); + free(ttCell->twiz2Tmp); + free(ttCell->rotSymOps); +} + + +/* ------------------------------------------------------------------------ + * external functions - top level functions (Level 1) + * ------------------------------------------------------------------------*/ + +/** + * @cell: target unit cell + * @rlps: spot positions on detector back-projected into recripocal + * space depending on detector geometry etc. + * @rlp_count: number of rlps in rlps array. + * @rot: pointer to be given an assignment (hopefully) if indexing is + * successful. + **/ +static UnitCell *run_taketwo(UnitCell *cell, struct rvec *rlps, int rlp_count) +{ + int cell_vec_count = 0; + int asym_vec_count = 0; + struct rvec *cell_vecs = NULL; + struct rvec *asym_vecs = NULL; + UnitCell *result; + int obs_vec_count = 0; + struct SpotVec *obs_vecs = NULL; + int success = 0; + gsl_matrix *solution = NULL; + + struct TakeTwoCell ttCell; + ttCell.cell = cell; + ttCell.rotSymOps = 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; + + success = generate_rotation_sym_ops(&ttCell); + + success = gen_theoretical_vecs(cell, &cell_vecs, &asym_vecs, + &cell_vec_count, &asym_vec_count); + if ( !success ) return NULL; + + success = gen_observed_vecs(rlps, rlp_count, &obs_vecs, &obs_vec_count); + if ( !success ) return NULL; + + ttCell.obs_vecs = &obs_vecs; + ttCell.obs_vec_count = obs_vec_count; + + success = match_obs_to_cell_vecs(asym_vecs, asym_vec_count, + obs_vecs, obs_vec_count, 1); + + success = match_obs_to_cell_vecs(cell_vecs, cell_vec_count, + obs_vecs, obs_vec_count, 0); + + free(cell_vecs); + free(asym_vecs); + + if ( !success ) return NULL; + + find_seed(&solution, &ttCell); + + if ( solution == NULL ) { + cleanup_taketwo_obs_vecs(obs_vecs, obs_vec_count); + return NULL; + } + + result = transform_cell_gsl(cell, solution); + gsl_matrix_free(solution); + cleanup_taketwo_obs_vecs(obs_vecs, obs_vec_count); + cleanup_taketwo_cell(&ttCell); + + return result; +} + + +/* CrystFEL interface hooks */ + +int taketwo_index(struct image *image, void *priv) +{ + Crystal *cr; + 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; + + cell = run_taketwo(tp->cell, rlps, n_rlps); + free(rlps); + if ( cell == NULL ) return 0; + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + + crystal_set_cell(cr, cell); + + if ( tp->indm & INDEXING_CHECK_PEAKS ) { + if ( !peak_sanity_check(image, &cr, 1) ) { + cell_free(cell); + crystal_free(cr); + // STATUS("Rubbish!!\n"); + + return 0; + } else { + // STATUS("That's good!\n"); + } + } + + image_add_crystal(image, cr); + + return 1; +} + + +void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell, + struct detector *det, float *ltl) +{ + struct taketwo_private *tp; + + /* Flags that TakeTwo knows about */ + *indm &= INDEXING_METHOD_MASK | INDEXING_CHECK_PEAKS + | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS + | INDEXING_CONTROL_FLAGS; + + if ( !( (*indm & INDEXING_USE_LATTICE_TYPE) + && (*indm & INDEXING_USE_CELL_PARAMETERS)) ) + { + ERROR("TakeTwo indexing requires cell and lattice type " + "information.\n"); + return NULL; + } + + if ( cell == NULL ) { + ERROR("TakeTwo indexing requires a unit cell.\n"); + return NULL; + } + + STATUS("*******************************************************************\n"); + STATUS("***** Welcome to TakeTwo *****\n"); + STATUS("*******************************************************************\n"); + STATUS(" If you use these indexing results, please keep a roof\n"); + STATUS(" over the author's head by citing this paper.\n\n"); + + STATUS("o o o o o o o o o o o o\n"); + STATUS(" o o o o o o o o o o o \n"); + STATUS("o o\n"); + STATUS(" o The citation is: o \n"); + STATUS("o Ginn et al., Acta Cryst. (2016). D72, 956-965 o\n"); + STATUS(" o Thank you! o \n"); + STATUS("o o\n"); + STATUS(" o o o o o o o o o o o \n"); + STATUS("o o o o o o o o o o o o\n"); + + + STATUS("\n"); + + tp = malloc(sizeof(struct taketwo_private)); + if ( tp == NULL ) return NULL; + + tp->ltl = ltl; + tp->cell = cell; + tp->indm = *indm; + + return tp; +} + + +void taketwo_cleanup(IndexingPrivate *pp) +{ + struct taketwo_private *tp = (struct taketwo_private *)pp; + free(tp); +} + |