aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorHelen Ginn <helen@strubi.ox.ac.uk>2018-04-29 18:56:28 +0200
committerThomas White <taw@physics.org>2018-05-02 09:46:15 +0200
commit67fb3922a3b0535f8dea5a46a90f5b3e4226fca1 (patch)
treee2619437d06597ed7a61d5d6197d69ecd151c02c
parent6885e4c27b0cf3eff6f7910542b328ce060e2191 (diff)
Mass movement of functions to higher up
-rw-r--r--libcrystfel/src/taketwo.c370
1 files changed, 191 insertions, 179 deletions
diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c
index 7d0c33f2..d4e71705 100644
--- a/libcrystfel/src/taketwo.c
+++ b/libcrystfel/src/taketwo.c
@@ -1094,10 +1094,198 @@ static signed int find_next_index(gsl_matrix *rot, int *obs_members,
return -1;
}
+/**
+ * Reward target function for refining solution to all vectors in a
+ * given image. Sum of exponentials of the negative distances, which
+ * means that the reward decays as the distance from the nearest
+ * theoretical vector reduces. */
+static double obs_to_sol_score(struct TakeTwoCell *ttCell)
+{
+ double total = 0;
+ int count = 0;
+ int i;
+ gsl_matrix *solution = ttCell->solution;
+ gsl_matrix *full_rot = gsl_matrix_alloc(3, 3);
+ rotate_gsl_by_angles(solution, ttCell->x_ang, ttCell->y_ang,
+ ttCell->z_ang, full_rot);
+
+ for (i = 0; i < ttCell->obs_vec_count; i++)
+ {
+ struct rvec *obs = &ttCell->obs_vecs[i].obsvec;
+ rvec_to_gsl(ttCell->vec1Tmp, *obs);
+
+ /* Rotate all the observed vectors by the modified soln */
+ /* ttCell->vec2Tmp = 1.0 * full_rot * ttCell->vec1Tmp */
+ gsl_blas_dgemv(CblasTrans, 1.0, full_rot, ttCell->vec1Tmp,
+ 0.0, ttCell->vec2Tmp);
+ struct rvec rotated = gsl_to_rvec(ttCell->vec2Tmp);
+
+ int j = ttCell->obs_vecs[i].assignment;
+
+ if (j < 0) continue;
+
+ struct rvec *match = &ttCell->obs_vecs[i].matches[j].vec;
+ struct rvec diff = diff_vec(rotated, *match);
+
+ double length = rvec_length(diff);
+
+ double addition = exp(-(1 / RECIP_TOLERANCE) * length);
+ total += addition;
+ count++;
+ }
+
+ total /= (double)-count;
+
+ gsl_matrix_free(full_rot);
+
+ return total;
+}
+
+/**
+ * Matches every observed vector in the image to its closest theoretical
+ * neighbour after applying the rotation matrix, in preparation for
+ * refining the rotation matrix to match these. */
+static void match_all_obs_to_sol(struct TakeTwoCell *ttCell)
+{
+ int i, j;
+ double total = 0;
+ int count = 0;
+ gsl_matrix *solution = ttCell->solution;
+
+ for (i = 0; i < ttCell->obs_vec_count; i++)
+ {
+ struct rvec *obs = &ttCell->obs_vecs[i].obsvec;
+ rvec_to_gsl(ttCell->vec1Tmp, *obs);
+
+ /* ttCell->vec2Tmp = 1.0 * solution * ttCell->vec1Tmp */
+ gsl_blas_dgemv(CblasTrans, 1.0, solution, ttCell->vec1Tmp,
+ 0.0, ttCell->vec2Tmp);
+ struct rvec rotated = gsl_to_rvec(ttCell->vec2Tmp);
+
+ double smallest = FLT_MAX;
+ int assigned = -1;
+
+ for (j = 0; j < ttCell->obs_vecs[i].match_num; j++)
+ {
+ struct rvec *match = &ttCell->obs_vecs[i].matches[j].vec;
+ struct rvec diff = diff_vec(rotated, *match);
+
+ double length = rvec_length(diff);
+ if (length < smallest)
+ {
+ smallest = length;
+ assigned = j;
+ }
+ }
+
+ ttCell->obs_vecs[i].assignment = assigned;
+
+ if (smallest != FLT_MAX)
+ {
+ double addition = exp(-(1 / RECIP_TOLERANCE) * smallest);
+ total += addition;
+ count++;
+
+ }
+ }
+
+ total /= (double)count;
+}
+
+/**
+ * Refines a matrix against all of the observed vectors against their
+ * closest theoretical neighbour, by perturbing the matrix along the principle
+ * axes until it maximises a reward function consisting of the sum of
+ * the distances of individual observed vectors to their closest
+ * theoretical neighbour. Reward function means that noise and alternative
+ * lattices do not dominate the equation!
+ **/
+static void refine_solution(struct TakeTwoCell *ttCell)
+{
+ match_all_obs_to_sol(ttCell);
+
+ int i, j, k;
+ const int total = 3 * 3 * 3;
+ const int middle = (total - 1) / 2;
+
+ struct rvec steps[total];
+ double start = obs_to_sol_score(ttCell);
+ const int max_tries = 100;
+
+ int count = 0;
+ double size = ANGLE_STEP_SIZE;
+
+ /* First we create our combinations of steps */
+ for (i = -1; i <= 1; i++) {
+ for (j = -1; j <= 1; j++) {
+ for (k = -1; k <= 1; k++) {
+ struct rvec vec = new_rvec(i, j, k);
+ steps[count] = vec;
+ count++;
+ }
+ }
+ }
+
+ struct rvec current = new_rvec(ttCell->x_ang, ttCell->y_ang,
+ ttCell->z_ang);
+
+ double best = start;
+ count = 0;
+
+ while (size > ANGLE_CONVERGE_SIZE && count < max_tries)
+ {
+ struct rvec sized[total];
+
+ int best_num = middle;
+ for (i = 0; i < total; i++)
+ {
+ struct rvec sized_step = steps[i];
+ sized_step.u *= size;
+ sized_step.v *= size;
+ sized_step.w *= size;
+
+ struct rvec new_angles = rvec_add_rvec(current,
+ sized_step);
+
+ sized[i] = new_angles;
+
+ ttCell->x_ang = sized[i].u;
+ ttCell->y_ang = sized[i].v;
+ ttCell->z_ang = sized[i].w;
+
+ double score = obs_to_sol_score(ttCell);
+
+ if (score < best)
+ {
+ best = score;
+ best_num = i;
+ }
+ }
+
+ if (best_num == middle)
+ {
+ size /= 2;
+ }
+
+ current = sized[best_num];
+ count++;
+ }
+
+ ttCell->x_ang = 0;
+ ttCell->y_ang = 0;
+ ttCell->z_ang = 0;
+
+ gsl_matrix *tmp = gsl_matrix_alloc(3, 3);
+ rotate_gsl_by_angles(ttCell->solution, current.u,
+ current.v, current.w, tmp);
+ gsl_matrix_free(ttCell->solution);
+ ttCell->solution = tmp;
+}
+
-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)
+static unsigned int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2,
+ int match_idx1, int match_idx2,
+ struct TakeTwoCell *cell)
{
struct SpotVec *obs_vecs = cell->obs_vecs;
@@ -1505,182 +1693,6 @@ static int sort_theory_distances(const void *av, const void *bv)
return a->dist > b->dist;
}
-static double obs_to_sol_score(struct TakeTwoCell *ttCell)
-{
- double total = 0;
- int count = 0;
- int i;
- gsl_matrix *solution = ttCell->solution;
- gsl_matrix *full_rot = gsl_matrix_alloc(3, 3);
- rotate_gsl_by_angles(solution, ttCell->x_ang, ttCell->y_ang,
- ttCell->z_ang, full_rot);
-
- for (i = 0; i < ttCell->obs_vec_count; i++)
- {
- struct rvec *obs = &ttCell->obs_vecs[i].obsvec;
- rvec_to_gsl(ttCell->vec1Tmp, *obs);
-
- /* Rotate all the observed vectors by the modified soln */
- /* ttCell->vec2Tmp = 1.0 * full_rot * ttCell->vec1Tmp */
- gsl_blas_dgemv(CblasTrans, 1.0, full_rot, ttCell->vec1Tmp,
- 0.0, ttCell->vec2Tmp);
- struct rvec rotated = gsl_to_rvec(ttCell->vec2Tmp);
-
- int j = ttCell->obs_vecs[i].assignment;
-
- if (j < 0) continue;
-
- struct rvec *match = &ttCell->obs_vecs[i].matches[j].vec;
- struct rvec diff = diff_vec(rotated, *match);
-
- double length = rvec_length(diff);
-
- double addition = exp(-(1 / RECIP_TOLERANCE) * length);
- total += addition;
- count++;
- }
-
- total /= (double)-count;
-
- gsl_matrix_free(full_rot);
-
- return total;
-}
-
-/* At the moment this is just going to do a step search of 3x3x3 until
- * the angles are sufficiently tiny */
-static void refine_solution(struct TakeTwoCell *ttCell)
-{
- int i, j, k;
- const int total = 3 * 3 * 3;
- const int middle = (total - 1) / 2;
-
- struct rvec steps[total];
- double start = obs_to_sol_score(ttCell);
- const int max_tries = 100;
-
- int count = 0;
- double size = ANGLE_STEP_SIZE;
-
- /* First we create our combinations of steps */
- for (i = -1; i <= 1; i++) {
- for (j = -1; j <= 1; j++) {
- for (k = -1; k <= 1; k++) {
- struct rvec vec = new_rvec(i, j, k);
- steps[count] = vec;
- count++;
- }
- }
- }
-
- struct rvec current = new_rvec(ttCell->x_ang, ttCell->y_ang,
- ttCell->z_ang);
-
- double best = start;
- count = 0;
-
- while (size > ANGLE_CONVERGE_SIZE && count < max_tries)
- {
- struct rvec sized[total];
-
- int best_num = middle;
- for (i = 0; i < total; i++)
- {
- struct rvec sized_step = steps[i];
- sized_step.u *= size;
- sized_step.v *= size;
- sized_step.w *= size;
-
- struct rvec new_angles = rvec_add_rvec(current,
- sized_step);
-
- sized[i] = new_angles;
-
- ttCell->x_ang = sized[i].u;
- ttCell->y_ang = sized[i].v;
- ttCell->z_ang = sized[i].w;
-
- double score = obs_to_sol_score(ttCell);
-
- if (score < best)
- {
- best = score;
- best_num = i;
- }
- }
-
- if (best_num == middle)
- {
- size /= 2;
- }
-
- current = sized[best_num];
- count++;
- }
-
- ttCell->x_ang = current.u;
- ttCell->y_ang = current.v;
- ttCell->z_ang = current.w;
-
- double end = obs_to_sol_score(ttCell);
-
- ttCell->x_ang = 0;
- ttCell->y_ang = 0;
- ttCell->z_ang = 0;
-
- gsl_matrix *tmp = gsl_matrix_alloc(3, 3);
- rotate_gsl_by_angles(ttCell->solution, current.u,
- current.v, current.w, tmp);
- gsl_matrix_free(ttCell->solution);
- ttCell->solution = tmp;
-}
-
-static void match_all_obs_to_sol(struct TakeTwoCell *ttCell)
-{
- int i, j;
- double total = 0;
- int count = 0;
- gsl_matrix *solution = ttCell->solution;
-
- for (i = 0; i < ttCell->obs_vec_count; i++)
- {
- struct rvec *obs = &ttCell->obs_vecs[i].obsvec;
- rvec_to_gsl(ttCell->vec1Tmp, *obs);
-
- /* ttCell->vec2Tmp = 1.0 * solution * ttCell->vec1Tmp */
- gsl_blas_dgemv(CblasTrans, 1.0, solution, ttCell->vec1Tmp,
- 0.0, ttCell->vec2Tmp);
- struct rvec rotated = gsl_to_rvec(ttCell->vec2Tmp);
-
- double smallest = FLT_MAX;
- int assigned = -1;
-
- for (j = 0; j < ttCell->obs_vecs[i].match_num; j++)
- {
- struct rvec *match = &ttCell->obs_vecs[i].matches[j].vec;
- struct rvec diff = diff_vec(rotated, *match);
-
- double length = rvec_length(diff);
- if (length < smallest)
- {
- smallest = length;
- assigned = j;
- }
- }
-
- ttCell->obs_vecs[i].assignment = assigned;
-
- if (smallest != FLT_MAX)
- {
- double addition = exp(-(1 / RECIP_TOLERANCE) * smallest);
- total += addition;
- count++;
-
- }
- }
-
- total /= (double)count;
-}
static int match_obs_to_cell_vecs(struct TheoryVec *cell_vecs, int cell_vec_count,
struct TakeTwoCell *cell)