From 667c06f12ca19986acfc00b0bc3adc2ca7f58f58 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 9 Nov 2011 14:45:58 +0100 Subject: partialator: Use all reflections (not just the ones found the first time around) --- doc/reference/CrystFEL-sections.txt | 3 ++ src/geometry.c | 29 +++++++++--------- src/geometry.h | 3 +- src/partialator.c | 11 +------ src/post-refinement.c | 2 +- src/reflist.c | 59 +++++++++++++++++++++++++++++++++++-- src/reflist.h | 3 ++ 7 files changed, 80 insertions(+), 30 deletions(-) diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt index 060ecf97..1d5b4016 100644 --- a/doc/reference/CrystFEL-sections.txt +++ b/doc/reference/CrystFEL-sections.txt @@ -6,8 +6,11 @@ RefListIterator reflist_new reflist_free +reflection_new +reflection_free add_refl +add_refl_to_list first_refl next_refl diff --git a/src/geometry.c b/src/geometry.c index bb946120..485abba3 100644 --- a/src/geometry.c +++ b/src/geometry.c @@ -122,7 +122,7 @@ static double partiality(double r1, double r2, double r) } -static Reflection *check_reflection(struct image *image, RefList *reflections, +static Reflection *check_reflection(struct image *image, signed int h, signed int k, signed int l, double asx, double asy, double asz, double bsx, double bsy, double bsz, @@ -216,7 +216,7 @@ static Reflection *check_reflection(struct image *image, RefList *reflections, if ( p == -1 ) return NULL; /* Add peak to list */ - refl = add_refl(reflections, h, k, l); + refl = reflection_new(h, k, l); set_detector_pos(refl, 0.0, xda, yda); set_partial(refl, rlow, rhigh, part, clamp_low, clamp_high); set_symmetric_indices(refl, h, k, l); @@ -274,8 +274,16 @@ RefList *find_intersections(struct image *image, UnitCell *cell) for ( h=-hmax; h<=hmax; h++ ) { for ( k=-kmax; k<=kmax; k++ ) { for ( l=-lmax; l<=lmax; l++ ) { - check_reflection(image, reflections, h, k, l, - asx,asy,asz,bsx,bsy,bsz,csx,csy,csz); + + Reflection *refl; + + refl = check_reflection(image, h, k, l, + asx,asy,asz,bsx,bsy,bsz,csx,csy,csz); + + if ( refl != NULL ) { + refl = add_refl_to_list(refl, reflections); + } + } } } @@ -285,8 +293,7 @@ RefList *find_intersections(struct image *image, UnitCell *cell) /* Calculate partialities and apply them to the image's reflections */ -void update_partialities(struct image *image, - int *n_expected, int *n_found, int *n_notfound) +void update_partialities(struct image *image) { Reflection *refl; RefListIterator *iter; @@ -295,10 +302,6 @@ void update_partialities(struct image *image, double bsx, bsy, bsz; double csx, csy, csz; - if ( n_expected != NULL ) *n_expected = 0; - if ( n_found != NULL) *n_found = 0; - if ( n_notfound != NULL) *n_notfound = 0; - cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz, &bsx, &bsy, &bsz, &csx, &csy, &csz); @@ -314,19 +317,15 @@ void update_partialities(struct image *image, signed int h, k, l; int clamp1, clamp2; - if ( n_expected != NULL ) (*n_expected)++; - get_symmetric_indices(refl, &h, &k, &l); - vals = check_reflection(image, predicted, h, k, l, + vals = check_reflection(image, h, k, l, asx,asy,asz,bsx,bsy,bsz,csx,csy,csz); if ( vals == NULL ) { - if ( n_notfound != NULL) (*n_notfound)++; set_redundancy(refl, 0); continue; } - if ( n_found != NULL) (*n_found)++; set_redundancy(refl, 1); /* Transfer partiality stuff */ diff --git a/src/geometry.h b/src/geometry.h index 486f1a60..ddf04b80 100644 --- a/src/geometry.h +++ b/src/geometry.h @@ -21,7 +21,6 @@ extern RefList *find_intersections(struct image *image, UnitCell *cell); -extern void update_partialities(struct image *image, - int *n_expected, int *n_found, int *n_notfound); +extern void update_partialities(struct image *image); #endif /* GEOMETRY_H */ diff --git a/src/partialator.c b/src/partialator.c index 6b4719eb..4edf7bf4 100644 --- a/src/partialator.c +++ b/src/partialator.c @@ -269,9 +269,6 @@ int main(int argc, char *argv[]) int n_iter = 10; struct beam_params *beam = NULL; RefList *full; - int n_found = 0; - int n_expected = 0; - int n_notfound = 0; int n_usable_patterns = 0; int nobs; char *reference_file = NULL; @@ -435,7 +432,6 @@ int main(int argc, char *argv[]) RefList *as; struct image *cur; - int nn_expected, nn_found, nn_notfound; cur = &images[n_usable_patterns]; @@ -474,10 +470,7 @@ int main(int argc, char *argv[]) reflist_free(cur->reflections); cur->reflections = as; - update_partialities(cur, &nn_expected, &nn_found, &nn_notfound); - n_expected += nn_expected; - n_found += nn_found; - n_notfound += nn_notfound; + update_partialities(cur); nobs += select_scalable_reflections(cur->reflections, reference); @@ -487,8 +480,6 @@ int main(int argc, char *argv[]) } fclose(fh); - STATUS("Found %5.2f%% of the expected peaks (missed %i of %i).\n", - 100.0 * (double)n_found / n_expected, n_notfound, n_expected); /* Make initial estimates */ STATUS("Performing initial scaling.\n"); diff --git a/src/post-refinement.c b/src/post-refinement.c index 97957840..0f541ace 100644 --- a/src/post-refinement.c +++ b/src/post-refinement.c @@ -526,7 +526,7 @@ void pr_refine(struct image *image, const RefList *full) max_shift = pr_iterate(image, full); - update_partialities(image, NULL, NULL, NULL); + update_partialities(image); if ( verbose ) { dev = guide_dev(image, full); diff --git a/src/reflist.c b/src/reflist.c index 33a8d60e..18856c67 100644 --- a/src/reflist.c +++ b/src/reflist.c @@ -162,6 +162,34 @@ RefList *reflist_new() } +/** + * reflection_new: + * @h: The h index of the new reflection + * @k: The k index of the new reflection + * @l: The l index of the new reflection + * + * Creates a new individual reflection. You'll probably want to use + * add_refl_to_list() at some later point. + */ +Reflection *reflection_new(signed int h, signed int k, signed int l) +{ + return new_node(SERIAL(h, k, l)); +} + + +/** + * reflection_free: + * @refl: The reflection to free. + * + * Destroys an individual reflection. + */ +void reflection_free(Reflection *refl) +{ + pthread_mutex_destroy(&refl->lock); + free(refl); +} + + static void recursive_free(Reflection *refl) { if ( refl->child[0] != NULL ) recursive_free(refl->child[0]); @@ -169,8 +197,7 @@ static void recursive_free(Reflection *refl) while ( refl != NULL ) { Reflection *next = refl->next; - pthread_mutex_destroy(&refl->lock); - free(refl); + reflection_free(refl); refl = next; } } @@ -806,6 +833,34 @@ Reflection *add_refl(RefList *list, signed int h, signed int k, signed int l) } +/** + * add_refl_to_list + * @refl: A %Reflection + * @list: A %RefList + * + * Adds a reflection to @list. The reflection that actually gets added will be + * a newly created one, and all the data will be copied across. The original + * reflection will be destroyed and the new reflection returned. + * + * Returns: The newly created reflection, or NULL on failure. + * + **/ +Reflection *add_refl_to_list(Reflection *refl, RefList *list) +{ + signed int h, k, l; + Reflection *r_added; + + get_indices(refl, &h, &k, &l); + r_added = add_refl(list, h, k, l); + if ( r_added == NULL ) return NULL; + + copy_data(r_added, refl); + reflection_free(refl); + + return r_added; +} + + /********************************* Iteration **********************************/ struct _reflistiterator { diff --git a/src/reflist.h b/src/reflist.h index 6d64498a..955db69b 100644 --- a/src/reflist.h +++ b/src/reflist.h @@ -50,6 +50,8 @@ typedef struct _reflistiterator RefListIterator; /* Creation/deletion */ extern RefList *reflist_new(void); extern void reflist_free(RefList *list); +extern Reflection *reflection_new(signed int h, signed int k, signed int l); +extern void reflection_free(Reflection *refl); /* Search */ extern Reflection *find_refl(const RefList *list, signed int h, signed int k, signed int l); @@ -95,6 +97,7 @@ extern void set_symmetric_indices(Reflection *refl, /* Insertion */ extern Reflection *add_refl(RefList *list, signed int h, signed int k, signed int l); +extern Reflection *add_refl_to_list(Reflection *refl, RefList *list); /* Iteration */ extern Reflection *first_refl(RefList *list, RefListIterator **piter); -- cgit v1.2.3