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-rw-r--r--src/geometry.c29
-rw-r--r--src/hrs-scaling.c15
-rw-r--r--src/partial_sim.c13
-rw-r--r--src/partialator.c41
-rw-r--r--src/post-refinement.c79
5 files changed, 126 insertions, 51 deletions
diff --git a/src/geometry.c b/src/geometry.c
index b3d4c8ee..db261e6b 100644
--- a/src/geometry.c
+++ b/src/geometry.c
@@ -292,6 +292,34 @@ double integrate_all(struct image *image, RefList *reflections)
}
+/* Decide which reflections can be scaled */
+static int select_scalable_reflections(RefList *list)
+{
+ int n_scalable = 0;
+
+ Reflection *refl;
+ RefListIterator *iter;
+
+ for ( refl = first_refl(list, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+
+ int scalable = 1;
+ double v;
+
+ if ( get_partiality(refl) < 0.1 ) scalable = 0;
+ v = fabs(get_intensity(refl));
+ if ( v < 0.1 ) scalable = 0;
+
+ set_scalable(refl, scalable);
+ if ( scalable ) n_scalable++;
+
+ }
+
+ return n_scalable;
+}
+
+
/* Calculate partialities and apply them to the image's raw_reflections */
void update_partialities(struct image *image, const char *sym,
int *n_expected, int *n_found, int *n_notfound)
@@ -355,6 +383,7 @@ void update_partialities_and_asymm(struct image *image, const char *sym,
* to get the list used for scaling and post refinement */
image->reflections = asymmetric_indices(image->raw_reflections,
sym, obs);
+ select_scalable_reflections(image->reflections);
/* Need these lists to work fast */
optimise_reflist(image->reflections);
diff --git a/src/hrs-scaling.c b/src/hrs-scaling.c
index 4b9b932d..cb0f8cde 100644
--- a/src/hrs-scaling.c
+++ b/src/hrs-scaling.c
@@ -338,12 +338,11 @@ static RefList *lsq_intensities(struct image *images, int n,
for ( refl = find_refl(images[m].reflections,
it->h, it->k, it->l);
refl != NULL;
- refl = next_found_refl(refl) ) {
+ refl = next_found_refl(refl) )
+ {
double p;
- if ( !get_scalable(refl) ) continue;
-
p = get_partiality(refl);
num += get_intensity(refl) * p * G;
@@ -353,8 +352,14 @@ static RefList *lsq_intensities(struct image *images, int n,
}
- new = add_refl(full, it->h, it->k, it->l);
- set_int(new, num/den);
+ if ( !isnan(num/den) ) {
+ new = add_refl(full, it->h, it->k, it->l);
+ set_int(new, num/den);
+ } else {
+ ERROR("Couldn't calculate LSQ full intensity for"
+ "%3i %3i %3i\n", it->h, it->k, it->l);
+ /* Doom is probably impending */
+ }
}
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 824b1b5d..a9abb55b 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -39,10 +39,11 @@ static void mess_up_cell(UnitCell *cell)
double cx, cy, cz;
cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
- ax += 0.01 * ax;
+ ax += 0.005*ax;
cell_set_cartesian(cell, ax, ay, az, bx, by, bz, cx, cy, cz);
}
+
/* For each reflection in "partial", fill in what the intensity would be
* according to "full" */
static void calculate_partials(RefList *partial, double osf,
@@ -112,6 +113,7 @@ int main(int argc, char *argv[])
struct quaternion orientation;
struct image image;
FILE *ofh;
+ UnitCell *new;
/* Long options */
const struct option longopts[] = {
@@ -252,12 +254,17 @@ int main(int argc, char *argv[])
reflist_free(image.reflections);
/* Alter the cell by a tiny amount */
- mess_up_cell(image.indexed_cell);
image.filename = "(simulated 2)";
+ new = rotate_cell(cell, deg2rad(0.001), deg2rad(0.0), 0.0);
+ cell_free(image.indexed_cell);
+ image.indexed_cell = new;
- /* Write another chunk */
+ /* Calculate new partials */
image.reflections = find_intersections(&image, image.indexed_cell, 0);
calculate_partials(image.reflections, 0.5, full, sym);
+
+ /* Give a slightly incorrect cell in the stream */
+ //mess_up_cell(image.indexed_cell);
write_chunk(ofh, &image, STREAM_INTEGRATED);
reflist_free(image.reflections);
diff --git a/src/partialator.c b/src/partialator.c
index 54022e9e..9f931496 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -136,43 +136,12 @@ static void refine_all(struct image *images, int n_total_patterns,
qargs.task_defaults = task_defaults;
qargs.n = 0;
qargs.n_done = 0;
- qargs.n_total_patterns = n_total_patterns;
- qargs.images = images;
+ /* FIXME: Not refining the first image, for now */
+ qargs.n_total_patterns = n_total_patterns-1;
+ qargs.images = images+1;
run_threads(nthreads, refine_image, get_image, done_image,
- &qargs, n_total_patterns, 0, 0, 0);
-}
-
-
-/* Decide which reflections can be scaled */
-static void select_scalable_reflections(struct image *images, int n)
-{
- int m;
- int n_scalable = 0;
-
- for ( m=0; m<n; m++ ) {
-
- Reflection *refl;
- RefListIterator *iter;
-
- for ( refl = first_refl(images[m].reflections, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) ) {
-
- int scalable = 1;
- double v;
-
- if ( get_partiality(refl) < 0.1 ) scalable = 0;
- v = fabs(get_intensity(refl));
- if ( v < 0.1 ) scalable = 0;
-
- set_scalable(refl, scalable);
- if ( scalable ) n_scalable++;
-
- }
-
- }
- STATUS("%i reflections selected as scalable.\n", n_scalable);
+ &qargs, n_total_patterns-1, 0, 0, 0);
}
@@ -369,7 +338,6 @@ int main(int argc, char *argv[])
/* Make initial estimates */
STATUS("Performing initial scaling.\n");
- select_scalable_reflections(images, n_total_patterns);
full = scale_intensities(images, n_usable_patterns, sym, obs, cref);
/* Iterate */
@@ -401,7 +369,6 @@ int main(int argc, char *argv[])
/* Re-estimate all the full intensities */
reflist_free(full);
- select_scalable_reflections(images, n_usable_patterns);
full = scale_intensities(images, n_usable_patterns,
sym, obs, cref);
diff --git a/src/post-refinement.c b/src/post-refinement.c
index d5f9d3f8..7d851c17 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -29,15 +29,13 @@
/* Maximum number of iterations of NLSq to do for each image per macrocycle. */
-#define MAX_CYCLES (100)
+#define MAX_CYCLES (10)
/* Refineable parameters */
enum {
- REF_SCALE,
- REF_DIV,
- REF_R,
REF_ASX,
+ NUM_PARAMS,
REF_BSX,
REF_CSX,
REF_ASY,
@@ -46,7 +44,9 @@ enum {
REF_ASZ,
REF_BSZ,
REF_CSZ,
- NUM_PARAMS
+ REF_SCALE,
+ REF_DIV,
+ REF_R,
};
@@ -321,7 +321,7 @@ static double pr_iterate(struct image *image, const RefList *full,
}
}
- show_matrix_eqn(M, v, NUM_PARAMS);
+ //show_matrix_eqn(M, v, NUM_PARAMS);
shifts = gsl_vector_alloc(NUM_PARAMS);
gsl_linalg_HH_solve(M, v, shifts);
@@ -341,10 +341,77 @@ static double pr_iterate(struct image *image, const RefList *full,
}
+static double mean_partial_dev(struct image *image,
+ const RefList *full, const char *sym)
+{
+ double dev = 0.0;
+
+ /* For each reflection */
+ Reflection *refl;
+ RefListIterator *iter;
+
+ for ( refl = first_refl(image->reflections, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+
+ double G, p;
+ signed int h, k, l;
+ Reflection *full_version;
+ double I_full, I_partial;
+
+ if ( !get_scalable(refl) ) continue;
+
+ get_indices(refl, &h, &k, &l);
+ G = image->osf;
+
+ full_version = find_refl(full, h, k, l);
+ assert(full_version != NULL);
+
+ p = get_partiality(refl);
+ I_partial = get_intensity(refl);
+ I_full = get_intensity(full_version);
+ //STATUS("%3i %3i %3i %5.2f %5.2f %5.2f %5.2f\n",
+ // h, k, l, G, p, I_partial, I_full);
+
+ dev += pow(I_partial - p*G*I_full, 2.0);
+
+ }
+
+ return dev;
+}
+
+
void pr_refine(struct image *image, const RefList *full, const char *sym)
{
double max_shift;
int i;
+ double ax, ay, az;
+ double bx, by, bz;
+ double cx, cy, cz;
+ UnitCell *cell = image->indexed_cell;
+ double shval, origval;
+
+ cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+ shval = 0.001*ax;
+ origval = ax;
+
+ for ( i=-10; i<=10; i++ ) {
+
+ double dev;
+
+ cell_get_cartesian(cell, &ax, &ay, &az, &bx,
+ &by, &bz, &cx, &cy, &cz);
+ ax = origval + (double)i*shval;
+ cell_set_cartesian(cell, ax, ay, az, bx, by, bz, cx, cy, cz);
+
+ update_partialities_and_asymm(image, sym,
+ NULL, NULL, NULL, NULL);
+
+ dev = mean_partial_dev(image, full, sym);
+ STATUS("%i %e %e\n", i, ax, dev);
+
+ }
+ return;
i = 0;
do {
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-10 08:52:59 +0000