diff options
| -rw-r--r-- | src/index.c | 7 | ||||
| -rw-r--r-- | src/indexamajig.c | 12 | ||||
| -rw-r--r-- | src/peaks.c | 63 | ||||
| -rw-r--r-- | src/peaks.h | 3 |
4 files changed, 30 insertions, 55 deletions
diff --git a/src/index.c b/src/index.c index 862f5145..ced8bbb8 100644 --- a/src/index.c +++ b/src/index.c @@ -30,6 +30,7 @@ #include "index.h" #include "index-priv.h" #include "reax.h" +#include "geometry.h" /* Base class constructor for unspecialised indexing private data */ @@ -204,8 +205,12 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm, if ( new_cell == NULL ) continue; /* Sanity check */ + image->reflections = find_intersections(image, + new_cell); if ( !config_insane && - !peak_sanity_check(image, new_cell, 0, 0.1) ) { + !peak_sanity_check(image->reflections, + image->features) ) + { cell_free(new_cell); continue; } diff --git a/src/indexamajig.c b/src/indexamajig.c index 384195ac..d27ff4d4 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -314,20 +314,16 @@ static void process_image(void *pp, int cookie) image.data = data_for_measurement; /* Calculate orientation matrix (by magic) */ + image.div = beam->divergence; + image.bw = beam->bandwidth; + image.profile_radius = 0.0001e9; index_pattern(&image, cell, indm, pargs->static_args.cellr, config_verbose, pargs->static_args.ipriv, pargs->static_args.config_insane); - if ( image.indexed_cell != NULL ) pargs->indexable = 1; - - /* Measure intensities */ if ( image.indexed_cell != NULL ) { - image.div = beam->divergence; - image.bw = beam->bandwidth; - image.profile_radius = 0.0001e9; - image.reflections = find_intersections(&image, - image.indexed_cell); + pargs->indexable = 1; if ( image.reflections != NULL ) { integrate_reflections(&image, config_polar, diff --git a/src/peaks.c b/src/peaks.c index 67b8d9c4..1c3564d1 100644 --- a/src/peaks.c +++ b/src/peaks.c @@ -31,6 +31,7 @@ #include "detector.h" #include "filters.h" #include "diffraction.h" +#include "reflist-utils.h" /* How close a peak must be to an indexed position to be considered "close" @@ -449,62 +450,36 @@ void search_peaks(struct image *image, float threshold, float min_gradient) } -int peak_sanity_check(struct image *image, UnitCell *cell, - int circular_domain, double domain_r) +int peak_sanity_check(RefList *rlist, ImageFeatureList *flist) { int i; int n_feat = 0; int n_sane = 0; - double ax, ay, az; - double bx, by, bz; - double cx, cy, cz; - double aslen, bslen, cslen; - /* "Borrow" direction values to get reciprocal lengths */ - cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); - aslen = modulus(ax, ay, az); - bslen = modulus(bx, by, bz); - cslen = modulus(cx, cy, cz); - - cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); - - fesetround(1); /* Round towards nearest */ - for ( i=0; i<image_feature_count(image->features); i++ ) { + for ( i=0; i<image_feature_count(flist); i++ ) { double dist; - struct rvec q; struct imagefeature *f; - double hd, kd, ld; - signed int h, k, l; - double dh, dk, dl; + Reflection *refl; + RefListIterator *iter; - f = image_get_feature(image->features, i); + f = image_get_feature(flist, i); if ( f == NULL ) continue; n_feat++; - /* Get closest hkl */ - q = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda); - - hd = q.u * ax + q.v * ay + q.w * az; - kd = q.u * bx + q.v * by + q.w * bz; - ld = q.u * cx + q.v * cy + q.w * cz; - - h = lrint(hd); k = lrint(kd); l = lrint(ld); - - dh = hd - h; dk = kd - k; dl = ld - l; - - if ( circular_domain ) { - - /* Circular integration domain */ - dist = sqrt(pow(dh*aslen, 2.0) + pow(dk*bslen, 2.0) - + pow(dl*cslen, 2.0)); - if ( dist <= domain_r ) n_sane++; - - } else { - - /* "Crystallographic" integration domain */ - dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0)); - if ( dist <= domain_r ) n_sane++; + /* Find closest predicted peak */ + + for ( refl = first_refl(rlist, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) + { + double fs, ss; + get_detector_pos(refl, &fs, &ss); + dist = sqrt(pow(fs-f->fs, 2.0) + pow(ss-f->ss, 2.0)); + if ( dist < PEAK_CLOSE ) { + n_sane++; + continue; + } } } diff --git a/src/peaks.h b/src/peaks.h index 3d21bbde..07c257e6 100644 --- a/src/peaks.h +++ b/src/peaks.h @@ -27,8 +27,7 @@ extern void search_peaks(struct image *image, float threshold, extern void integrate_reflections(struct image *image, int polar, int use_closer, int bgsub); -extern int peak_sanity_check(struct image *image, UnitCell *cell, - int circular_domain, double domain_r); +extern int peak_sanity_check(RefList *rlist, ImageFeatureList *flist); /* Exported so it can be poked by integration_check */ extern int integrate_peak(struct image *image, int cfs, int css, |