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-rw-r--r--src/predict-refine.c166
-rw-r--r--src/predict-refine.h1
-rw-r--r--src/process_image.c127
3 files changed, 117 insertions, 177 deletions
diff --git a/src/predict-refine.c b/src/predict-refine.c
index a2a4ce53..52496198 100644
--- a/src/predict-refine.c
+++ b/src/predict-refine.c
@@ -55,28 +55,77 @@ struct reflpeak {
* (we assume this never changes) */
};
-static int pair_peaks(ImageFeatureList *flist, UnitCell *cell, RefList *reflist,
- struct reflpeak *rps, struct detector *det)
+
+static void twod_mapping(double fs, double ss, double *px, double *py,
+ struct panel *p)
+{
+ double xs, ys;
+
+ xs = fs*p->fsx + ss*p->ssx;
+ ys = fs*p->fsy + ss*p->ssy;
+
+ *px = (xs + p->cnx) / p->res;
+ *py = (ys + p->cny) / p->res;
+}
+
+
+static double r_dev(struct reflpeak *rp)
+{
+ /* Excitation error term */
+ double rlow, rhigh, p;
+ get_partial(rp->refl, &rlow, &rhigh, &p);
+ return (rlow+rhigh)/2.0;
+}
+
+
+static double x_dev(struct reflpeak *rp, struct detector *det)
+{
+ /* Peak position term */
+ double xpk, ypk, xh, yh;
+ double fsh, ssh;
+ twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
+ get_detector_pos(rp->refl, &fsh, &ssh);
+ twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
+ return xh-xpk;
+}
+
+
+static double y_dev(struct reflpeak *rp, struct detector *det)
+{
+ /* Peak position term */
+ double xpk, ypk, xh, yh;
+ double fsh, ssh;
+ twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
+ get_detector_pos(rp->refl, &fsh, &ssh);
+ twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
+ return yh-ypk;
+}
+
+
+/* Associate a Reflection with each peak in "image" which is close to Bragg.
+ * Reflections will be added to "reflist", which can be NULL if this is not
+ * needed. "rps" must be an array of sufficient size for all the peaks */
+static int pair_peaks(struct image *image, Crystal *cr,
+ RefList *reflist, struct reflpeak *rps)
{
int i;
const double min_dist = 0.05;
int n_acc = 0;
- int n_notintegrated = 0;
- for ( i=0; i<image_feature_count(flist); i++ ) {
+ for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
double h, k, l, hd, kd, ld;
/* Assume all image "features" are genuine peaks */
- f = image_get_feature(flist, i);
+ f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
- cell_get_cartesian(cell,
+ cell_get_cartesian(crystal_get_cell(cr),
&ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
/* Decimal and fractional Miller indices of nearest
@@ -94,17 +143,28 @@ static int pair_peaks(ImageFeatureList *flist, UnitCell *cell, RefList *reflist,
&& (fabs(l - ld) < min_dist) )
{
Reflection *refl;
+ struct panel *p;
- /* Dig out the reflection */
- refl = find_refl(reflist, h, k, l);
+ refl = reflection_new(h, k, l);
if ( refl == NULL ) {
- n_notintegrated++;
- continue;
+ ERROR("Failed to create reflection\n");
+ return 0;
}
+ if ( reflist != NULL ) add_refl_to_list(refl, reflist);
+ set_symmetric_indices(refl, h, k, l);
+
+ /* It doesn't matter if the actual predicted location
+ * doesn't fall on this panel. We're only interested
+ * in how far away it is from the peak location.
+ * The predicted position and excitation errors will be
+ * filled in by update_partialities(). */
+ p = find_panel(image->det, f->fs, f->ss);
+ set_panel(refl, p);
+
rps[n_acc].refl = refl;
rps[n_acc].peak = f;
- rps[n_acc].panel = find_panel(det, f->fs, f->ss);
+ rps[n_acc].panel = p;
n_acc++;
}
@@ -114,19 +174,48 @@ static int pair_peaks(ImageFeatureList *flist, UnitCell *cell, RefList *reflist,
}
-static void twod_mapping(double fs, double ss, double *px, double *py,
- struct panel *p)
+static int cmpd2(const void *av, const void *bv)
{
- double xs, ys;
+ struct reflpeak *a, *b;
- xs = fs*p->fsx + ss*p->ssx;
- ys = fs*p->fsy + ss*p->ssy;
+ a = (struct reflpeak *)av;
+ b = (struct reflpeak *)bv;
- *px = (xs + p->cnx) / p->res;
- *py = (ys + p->cny) / p->res;
+ if ( fabs(r_dev(a)) < fabs(r_dev(b)) ) return -1;
+ return 1;
}
+void refine_radius(Crystal *cr, struct image *image)
+{
+ int n, n_acc;
+ struct reflpeak *rps;
+ RefList *reflist;
+
+ /* Maximum possible size */
+ rps = malloc(image_feature_count(image->features)
+ * sizeof(struct reflpeak));
+ if ( rps == NULL ) return;
+
+ reflist = reflist_new();
+ n_acc = pair_peaks(image, cr, reflist, rps);
+ if ( n_acc < 3 ) {
+ ERROR("Too few paired peaks (%i) to determine radius\n", n_acc);
+ free(rps);
+ return;
+ }
+ crystal_set_reflections(cr, reflist);
+ update_partialities(cr, PMODEL_SCSPHERE);
+ crystal_set_reflections(cr, NULL);
+
+ qsort(rps, n_acc, sizeof(struct reflpeak), cmpd2);
+ n = (n_acc-1) - n_acc/50;
+ if ( n < 2 ) n = 2; /* n_acc is always >= 2 */
+ crystal_set_profile_radius(cr, fabs(r_dev(&rps[n])));
+
+ reflist_free(reflist);
+ free(rps);
+}
/* Returns d(xh-xpk)/dP + d(yh-ypk)/dP, where P = any parameter */
@@ -239,39 +328,6 @@ static double y_gradient(int param, struct reflpeak *rp, struct detector *det,
}
-static double r_dev(struct reflpeak *rp)
-{
- /* Excitation error term */
- double rlow, rhigh, p;
- get_partial(rp->refl, &rlow, &rhigh, &p);
- return (rlow+rhigh)/2.0;
-}
-
-
-static double x_dev(struct reflpeak *rp, struct detector *det)
-{
- /* Peak position term */
- double xpk, ypk, xh, yh;
- double fsh, ssh;
- twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
- get_detector_pos(rp->refl, &fsh, &ssh);
- twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
- return xh-xpk;
-}
-
-
-static double y_dev(struct reflpeak *rp, struct detector *det)
-{
- /* Peak position term */
- double xpk, ypk, xh, yh;
- double fsh, ssh;
- twod_mapping(rp->peak->fs, rp->peak->ss, &xpk, &ypk, rp->panel);
- get_detector_pos(rp->refl, &fsh, &ssh);
- twod_mapping(fsh, ssh, &xh, &yh, rp->panel);
- return yh-ypk;
-}
-
-
static int iterate(struct reflpeak *rps, int n, UnitCell *cell,
struct image *image)
{
@@ -459,18 +515,20 @@ int refine_prediction(struct image *image, Crystal *cr)
int i;
struct reflpeak *rps;
double max_I;
+ RefList *reflist;
rps = malloc(image_feature_count(image->features)
* sizeof(struct reflpeak));
if ( rps == NULL ) return 1;
- n = pair_peaks(image->features, crystal_get_cell(cr),
- crystal_get_reflections(cr), rps, image->det);
+ reflist = reflist_new();
+ n = pair_peaks(image, cr, reflist, rps);
if ( n < 10 ) {
ERROR("Too few paired peaks to refine orientation.\n");
free(rps);
return 1;
}
+ crystal_set_reflections(cr, reflist);
/* Normalise the intensities to max 1 */
max_I = -INFINITY;
@@ -493,6 +551,8 @@ int refine_prediction(struct image *image, Crystal *cr)
update_partialities(cr, PMODEL_SCSPHERE);
}
+ crystal_set_reflections(cr, NULL);
+ reflist_free(reflist);
free(rps);
return 0;
}
diff --git a/src/predict-refine.h b/src/predict-refine.h
index 9742f9e2..c763d2ca 100644
--- a/src/predict-refine.h
+++ b/src/predict-refine.h
@@ -39,6 +39,7 @@
struct image;
extern int refine_prediction(struct image *image, Crystal *cr);
+extern void refine_radius(Crystal *cr, struct image *image);
#endif /* PREDICT_REFINE_H */
diff --git a/src/process_image.c b/src/process_image.c
index f40b8cff..cea685f8 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -53,118 +53,6 @@
#include "predict-refine.h"
-static int cmpd2(const void *av, const void *bv)
-{
- double a, b;
-
- a = *(double *)av;
- b = *(double *)bv;
-
- if ( fabs(a) < fabs(b) ) return -1;
- return 1;
-}
-
-
-static double *excitation_errors(UnitCell *cell, ImageFeatureList *flist,
- RefList *reflist, int *pnacc)
-{
- int i;
- const double min_dist = 0.05;
- double *acc;
- int n_acc = 0;
- int n_notintegrated = 0;
- int max_acc = 1024;
-
- acc = malloc(max_acc*sizeof(double));
- if ( acc == NULL ) {
- ERROR("Allocation failed when refining radius!\n");
- return NULL;
- }
-
- for ( i=0; i<image_feature_count(flist); i++ ) {
-
- struct imagefeature *f;
- double h, k, l, hd, kd, ld;
-
- /* Assume all image "features" are genuine peaks */
- f = image_get_feature(flist, i);
- if ( f == NULL ) continue;
-
- double ax, ay, az;
- double bx, by, bz;
- double cx, cy, cz;
-
- cell_get_cartesian(cell,
- &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
-
- /* Decimal and fractional Miller indices of nearest
- * reciprocal lattice point */
- hd = f->rx * ax + f->ry * ay + f->rz * az;
- kd = f->rx * bx + f->ry * by + f->rz * bz;
- ld = f->rx * cx + f->ry * cy + f->rz * cz;
- h = lrint(hd);
- k = lrint(kd);
- l = lrint(ld);
-
- /* Check distance */
- if ( (fabs(h - hd) < min_dist)
- && (fabs(k - kd) < min_dist)
- && (fabs(l - ld) < min_dist) )
- {
- double rlow, rhigh, p;
- Reflection *refl;
-
- /* Dig out the reflection */
- refl = find_refl(reflist, h, k, l);
- if ( refl == NULL ) {
- n_notintegrated++;
- continue;
- }
-
- get_partial(refl, &rlow, &rhigh, &p);
- acc[n_acc++] = fabs(rlow+rhigh)/2.0;
- if ( n_acc == max_acc ) {
- max_acc += 1024;
- acc = realloc(acc, max_acc*sizeof(double));
- if ( acc == NULL ) {
- ERROR("Allocation failed during"
- " estimate_resolution!\n");
- return NULL;
- }
- }
- }
-
- }
-
- if ( n_acc < 3 ) {
- STATUS("WARNING: Too few peaks to estimate profile radius.\n");
- return NULL;
- }
-
- *pnacc = n_acc;
- return acc;
-}
-
-
-static void refine_radius(Crystal *cr, ImageFeatureList *flist)
-{
- int n = 0;
- int n_acc;
- double *acc;
-
- acc = excitation_errors(crystal_get_cell(cr), flist,
- crystal_get_reflections(cr), &n_acc);
- if ( acc == NULL ) return;
-
- qsort(acc, n_acc, sizeof(double), cmpd2);
- n = n_acc/50;
- if ( n < 2 ) n = 2; /* n_acc is always >= 2 */
- crystal_set_profile_radius(cr, acc[(n_acc-1)-n]);
-
- free(acc);
-}
-
-
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
Stream *st, int cookie, const char *tmpdir, int results_pipe,
int serial)
@@ -311,15 +199,9 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
}
}
- /* Preliminary integration, needed for refinement */
- integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE,
- iargs->push_res,
- iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
- INTDIAG_NONE, 0, 0, 0, results_pipe);
-
/* Measure R before refinement */
for ( i=0; i<image.n_crystals; i++ ) {
- refine_radius(image.crystals[i], image.features);
+ refine_radius(image.crystals[i], &image);
}
/* Integrate all the crystals at once - need all the crystals so that
@@ -341,7 +223,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
/* Reset the profile radius and estimate again with
* better geometry */
crystal_set_profile_radius(image.crystals[i], 0.02e9);
- refine_radius(image.crystals[i], image.features);
+ refine_radius(image.crystals[i], &image);
new_R = crystal_get_profile_radius(image.crystals[i]);
@@ -360,10 +242,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
}
- /* The final, definitive, integration */
- for ( i=0; i<image.n_crystals; i++ ) {
- reflist_free(crystal_get_reflections(image.crystals[i]));
- }
+ /* Integrate! */
integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE,
iargs->push_res,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 21:25:33 +0000