diff options
| -rw-r--r-- | libcrystfel/src/crystal.h | 9 | ||||
| -rw-r--r-- | libcrystfel/src/geometry.c | 43 |
2 files changed, 34 insertions, 18 deletions
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h index 4f53eead..466116a4 100644 --- a/libcrystfel/src/crystal.h +++ b/libcrystfel/src/crystal.h @@ -33,6 +33,11 @@ #include <config.h> #endif + +#include "cell.h" +#include "reflist.h" + + /** * Crystal: * @@ -45,4 +50,8 @@ typedef struct _crystal Crystal; extern Crystal *crystal_new(void); extern void crystal_free(Crystal *cryst); +extern UnitCell *crystal_get_cell(Crystal *cryst); +extern double crystal_get_profile_radius(Crystal *cryst); +extern RefList *crystal_get_reflections(Crystal *cryst); + #endif /* CRYSTAL_H */ diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c index 79a438ec..02629421 100644 --- a/libcrystfel/src/geometry.c +++ b/libcrystfel/src/geometry.c @@ -118,7 +118,7 @@ static double partiality(double rlow, double rhigh, double r) } -static Reflection *check_reflection(struct image *image, +static Reflection *check_reflection(struct image *image, Crystal *cryst, signed int h, signed int k, signed int l, double xl, double yl, double zl) { @@ -132,6 +132,9 @@ static Reflection *check_reflection(struct image *image, double klow, khigh; /* Wavenumber */ Reflection *refl; double cet, cez; + double pr; + + pr = crystal_get_profile_radius(cryst); /* "low" gives the largest Ewald sphere (wavelength short => k large) * "high" gives the smallest Ewald sphere (wavelength long => k small) @@ -153,8 +156,8 @@ static Reflection *check_reflection(struct image *image, rlow = klow - distance(cet, cez, tl, zl); /* Loss of precision */ if ( (signbit(rlow) == signbit(rhigh)) - && (fabs(rlow) > image->profile_radius) - && (fabs(rhigh) > image->profile_radius) ) return NULL; + && (fabs(rlow) > pr) + && (fabs(rhigh) > pr) ) return NULL; /* If the "lower" Ewald sphere is a long way away, use the * position at which the Ewald sphere would just touch the @@ -165,26 +168,26 @@ static Reflection *check_reflection(struct image *image, * et al. (1979). */ clamp_low = 0; clamp_high = 0; - if ( rlow < -image->profile_radius ) { - rlow = -image->profile_radius; + if ( rlow < -pr ) { + rlow = -pr; clamp_low = -1; } - if ( rlow > +image->profile_radius ) { - rlow = +image->profile_radius; + if ( rlow > +pr ) { + rlow = +pr; clamp_low = +1; } - if ( rhigh < -image->profile_radius ) { - rhigh = -image->profile_radius; + if ( rhigh < -pr ) { + rhigh = -pr; clamp_high = -1; } - if ( rhigh > +image->profile_radius ) { - rhigh = +image->profile_radius; + if ( rhigh > +pr ) { + rhigh = +pr; clamp_high = +1; } assert(clamp_low >= clamp_high); /* Calculate partiality */ - part = partiality(rlow, rhigh, image->profile_radius); + part = partiality(rlow, rhigh, pr); /* Locate peak on detector. */ p = locate_peak(xl, yl, zl, 1.0/image->lambda, image->det, &xda, &yda); @@ -206,7 +209,7 @@ static Reflection *check_reflection(struct image *image, } -RefList *find_intersections(struct image *image, UnitCell *cell) +RefList *find_intersections(struct image *image, Crystal *cryst) { double ax, ay, az; double bx, by, bz; @@ -218,6 +221,10 @@ RefList *find_intersections(struct image *image, UnitCell *cell) int hmax, kmax, lmax; double mres; signed int h, k, l; + UnitCell *cell; + + cell = crystal_get_cell(cryst); + if ( cell == NULL ) return NULL; reflections = reflist_new(); @@ -263,7 +270,7 @@ RefList *find_intersections(struct image *image, UnitCell *cell) yl = h*asy + k*bsy + l*csy; zl = h*asz + k*bsz + l*csz; - refl = check_reflection(image, h, k, l, xl, yl, zl); + refl = check_reflection(image, cryst, h, k, l, xl, yl, zl); if ( refl != NULL ) { add_refl_to_list(refl, reflections); @@ -337,7 +344,7 @@ RefList *select_intersections(struct image *image, UnitCell *cell) /* Calculate partialities and apply them to the image's reflections */ -void update_partialities(struct image *image) +void update_partialities(struct image *image, Crystal *cryst) { Reflection *refl; RefListIterator *iter; @@ -346,13 +353,13 @@ void update_partialities(struct image *image) double bsx, bsy, bsz; double csx, csy, csz; - cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz, + cell_get_reciprocal(crystal_get_cell(cryst), &asx, &asy, &asz, &bsx, &bsy, &bsz, &csx, &csy, &csz); /* Scratch list to give check_reflection() something to add to */ predicted = reflist_new(); - for ( refl = first_refl(image->reflections, &iter); + for ( refl = first_refl(crystal_get_reflections(cryst), &iter); refl != NULL; refl = next_refl(refl, iter) ) { @@ -369,7 +376,7 @@ void update_partialities(struct image *image) yl = h*asy + k*bsy + l*csy; zl = h*asz + k*bsz + l*csz; - vals = check_reflection(image, h, k, l, xl, yl, zl); + vals = check_reflection(image, cryst, h, k, l, xl, yl, zl); if ( vals == NULL ) { set_redundancy(refl, 0); |