diff options
| -rw-r--r-- | libcrystfel/src/integration.c | 36 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.c | 12 | ||||
| -rw-r--r-- | src/process_hkl.c | 14 |
3 files changed, 30 insertions, 32 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c index cad0a75c..d2c06db7 100644 --- a/libcrystfel/src/integration.c +++ b/libcrystfel/src/integration.c @@ -1342,17 +1342,16 @@ static void setup_profile_boxes(struct intcontext *ic, RefList *list) void integrate_prof2d(IntegrationMethod meth, - Crystal *cr, struct image *image, IntDiag int_diag, + Crystal *cr, RefList *list, + struct image *image, IntDiag int_diag, signed int idh, signed int idk, signed int idl, double ir_inn, double ir_mid, double ir_out, pthread_mutex_t *term_lock, int **masks) { - RefList *list; UnitCell *cell; struct intcontext *ic; int i; - list = crystal_get_reflections(cr); cell = crystal_get_cell(cr); ic = intcontext_new(image, cell, meth, @@ -1593,12 +1592,12 @@ static double estimate_resolution(Crystal *cr, struct image *image) static void integrate_rings(IntegrationMethod meth, - Crystal *cr, struct image *image, IntDiag int_diag, + Crystal *cr, RefList *list, + struct image *image, IntDiag int_diag, signed int idh, signed int idk, signed int idl, double ir_inn, double ir_mid, double ir_out, pthread_mutex_t *term_lock, int **masks) { - RefList *list; Reflection *refl; RefListIterator *iter; UnitCell *cell; @@ -1606,7 +1605,6 @@ static void integrate_rings(IntegrationMethod meth, int n_rej = 0; int n_refl = 0; - list = crystal_get_reflections(cr); cell = crystal_get_cell(cr); ic = intcontext_new(image, cell, meth, @@ -1653,23 +1651,21 @@ void integrate_all_5(struct image *image, IntegrationMethod meth, /* Predict all reflections */ for ( i=0; i<image->n_crystals; i++ ) { - RefList *list; double res; - double saved_R = crystal_get_profile_radius(image->crystals[i]); + double saved_R = crystal_get_profile_radius(image->crystals[i].cr); if ( overpredict ) { - crystal_set_profile_radius(image->crystals[i], + crystal_set_profile_radius(image->crystals[i].cr, saved_R * 5); } - res = estimate_resolution(image->crystals[i], image); - crystal_set_resolution_limit(image->crystals[i], res); + res = estimate_resolution(image->crystals[i].cr, image); + crystal_set_resolution_limit(image->crystals[i].cr, res); - list = predict_to_res(image->crystals[i], image, res+push_res); - crystal_set_reflections(image->crystals[i], list); + image->crystals[i].refls = predict_to_res(image->crystals[i].cr, image, res+push_res); if ( overpredict ) { - crystal_set_profile_radius(image->crystals[i], saved_R); + crystal_set_profile_radius(image->crystals[i].cr, saved_R); } } @@ -1681,22 +1677,26 @@ void integrate_all_5(struct image *image, IntegrationMethod meth, for ( i=0; i<image->n_crystals; i++ ) { - Crystal *cr = image->crystals[i]; - switch ( meth & INTEGRATION_METHOD_MASK ) { case INTEGRATION_NONE : break; case INTEGRATION_RINGS : - integrate_rings(meth, cr, image, + integrate_rings(meth, + image->crystals[i].cr, + image->crystals[i].refls, + image, int_diag, idh, idk, idl, ir_inn, ir_mid, ir_out, term_lock, masks); break; case INTEGRATION_PROF2D : - integrate_prof2d(meth, cr, image, + integrate_prof2d(meth, + image->crystals[i].cr, + image->crystals[i].refls, + image, int_diag, idh, idk, idl, ir_inn, ir_mid, ir_out, term_lock, masks); diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index d56f6d03..63dd6966 100644 --- a/libcrystfel/src/peaks.c +++ b/libcrystfel/src/peaks.c @@ -62,15 +62,15 @@ /** \file peaks.h */ -static void add_crystal_to_mask(struct image *image, - struct detgeom_panel *p, int pn, - double ir_inn, int *mask, Crystal *cr) +static void add_reflections_to_mask(struct image *image, + struct detgeom_panel *p, int pn, + double ir_inn, int *mask, RefList *list) { Reflection *refl; RefListIterator *iter; /* Loop over all reflections */ - for ( refl = first_refl(crystal_get_reflections(cr), &iter); + for ( refl = first_refl(list, &iter); refl != NULL; refl = next_refl(refl, iter) ) { @@ -121,8 +121,8 @@ int *make_BgMask(struct image *image, struct detgeom_panel *p, if ( image->crystals == NULL ) return mask; for ( i=0; i<image->n_crystals; i++ ) { - add_crystal_to_mask(image, p, pn, ir_inn, - mask, image->crystals[i]); + add_reflections_to_mask(image, p, pn, ir_inn, + mask, image->crystals[i].refls); } return mask; diff --git a/src/process_hkl.c b/src/process_hkl.c index be1c95d4..31e4b1fc 100644 --- a/src/process_hkl.c +++ b/src/process_hkl.c @@ -271,7 +271,7 @@ static void apply_kpred(double k, RefList *list) static int merge_crystal(RefList *model, struct image *image, Crystal *cr, - RefList *reference, const SymOpList *sym, + RefList *new_refl, RefList *reference, const SymOpList *sym, double **hist_vals, signed int hist_h, signed int hist_k, signed int hist_l, int *hist_n, struct polarisation p, double min_snr, double max_adu, @@ -280,11 +280,8 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr, { Reflection *refl; RefListIterator *iter; - RefList *new_refl; double scale; - new_refl = crystal_get_reflections(cr); - /* First, correct for polarisation */ apply_kpred(1.0/image->lambda, new_refl); polarisation_correction(new_refl, crystal_get_cell(cr), p); @@ -309,7 +306,7 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr, scale = 1.0; } - for ( refl = first_refl(crystal_get_reflections(cr), &iter); + for ( refl = first_refl(new_refl, &iter); refl != NULL; refl = next_refl(refl, iter) ) { @@ -431,7 +428,8 @@ static int merge_stream(Stream *st, for ( i=0; i<image->n_crystals; i++ ) { - Crystal *cr = image->crystals[i]; + Crystal *cr = image->crystals[i].cr; + RefList *refls = image->crystals[i].refls; n_crystals_seen++; if ( (n_crystals_seen > start_after) @@ -440,8 +438,8 @@ static int merge_stream(Stream *st, { int r; n_crystals++; - r = merge_crystal(model, image, cr, reference, - sym, hist_vals, + r = merge_crystal(model, image, cr, refls, + reference, sym, hist_vals, hist_h, hist_k, hist_l, hist_i, p, min_snr, max_adu, push_res, |