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-rw-r--r--libcrystfel/src/crystal.c42
-rw-r--r--libcrystfel/src/crystal.h2
-rw-r--r--libcrystfel/src/geometry.c3
-rw-r--r--libcrystfel/src/geometry.h2
-rw-r--r--src/hrs-scaling.c77
-rw-r--r--src/partialator.c3
-rw-r--r--src/post-refinement.c64
-rw-r--r--src/post-refinement.h2
-rw-r--r--src/scaling-report.c70
9 files changed, 163 insertions, 102 deletions
diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index 8ba955f6..6ff251e0 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -49,6 +49,9 @@
struct _crystal
{
+ /* The image containing the crystal */
+ struct image *image;
+
/* Information about the crystal */
UnitCell *cell;
double m; /* Mosaicity in radians */
@@ -60,6 +63,9 @@ struct _crystal
/* Integrated (or about-to-be-integrated) reflections */
RefList *reflections;
long long int n_saturated; /* Number of overloads */
+
+ /* User flag, e.g. for "this is a bad crystal". */
+ int user_flag;
};
@@ -139,6 +145,24 @@ long long int crystal_get_num_saturated_reflections(Crystal *cryst)
}
+struct image *crystal_get_image(Crystal *cryst)
+{
+ return cryst->image;
+}
+
+
+double crystal_get_osf(Crystal *cryst)
+{
+ return cryst->osf;
+}
+
+
+int crystal_get_user_flag(Crystal *cryst)
+{
+ return cryst->user_flag;
+}
+
+
/********************************** Setters ***********************************/
@@ -172,3 +196,21 @@ void crystal_set_num_saturated_reflections(Crystal *cryst, long long int n)
{
cryst->n_saturated = n;
}
+
+
+void crystal_set_image(Crystal *cryst, struct image *image)
+{
+ cryst->image = image;
+}
+
+
+void crystal_set_osf(Crystal *cryst, double osf)
+{
+ cryst->osf = osf;
+}
+
+
+void crystal_set_user_flag(Crystal *cryst, int user_flag)
+{
+ cryst->user_flag = user_flag;
+}
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
index f418f23a..f7c49a81 100644
--- a/libcrystfel/src/crystal.h
+++ b/libcrystfel/src/crystal.h
@@ -57,6 +57,7 @@ extern double crystal_get_resolution_limit(Crystal *cryst);
extern long long int crystal_get_num_saturated_reflections(Crystal *cryst);
extern int crystal_get_user_flag(Crystal *cryst);
extern double crystal_get_osf(Crystal *cryst);
+extern struct image *crystal_get_image(Crystal *cryst);
extern void crystal_set_cell(Crystal *cryst, UnitCell *cell);
extern void crystal_set_profile_radius(Crystal *cryst, double r);
@@ -66,5 +67,6 @@ extern void crystal_set_num_saturated_reflections(Crystal *cryst,
long long int n);
extern void crystal_set_user_flag(Crystal *cryst, int flag);
extern void crystal_set_osf(Crystal *cryst, double osf);
+extern void crystal_set_image(Crystal *cryst, struct image *image);
#endif /* CRYSTAL_H */
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 9c494e2c..704baa51 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -346,7 +346,7 @@ RefList *select_intersections(struct image *image, Crystal *cryst)
/* Calculate partialities and apply them to the image's reflections */
-void update_partialities(struct image *image, Crystal *cryst)
+void update_partialities(Crystal *cryst)
{
Reflection *refl;
RefListIterator *iter;
@@ -354,6 +354,7 @@ void update_partialities(struct image *image, Crystal *cryst)
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
+ struct image *image = crystal_get_image(cryst);
cell_get_reciprocal(crystal_get_cell(cryst), &asx, &asy, &asz,
&bsx, &bsy, &bsz, &csx, &csy, &csz);
diff --git a/libcrystfel/src/geometry.h b/libcrystfel/src/geometry.h
index 9d8fa475..aecdc28a 100644
--- a/libcrystfel/src/geometry.h
+++ b/libcrystfel/src/geometry.h
@@ -46,7 +46,7 @@ extern "C" {
extern RefList *find_intersections(struct image *image, Crystal *cryst);
extern RefList *select_intersections(struct image *image, Crystal *cryst);
-extern void update_partialities(struct image *image, Crystal *cryst);
+extern void update_partialities(Crystal *cryst);
#ifdef __cplusplus
}
diff --git a/src/hrs-scaling.c b/src/hrs-scaling.c
index f86ae0bb..0498a532 100644
--- a/src/hrs-scaling.c
+++ b/src/hrs-scaling.c
@@ -57,7 +57,7 @@
struct scale_queue_args
{
RefList *reference;
- struct image *images;
+ Crystal **crystals;
int n_started;
double max_shift;
};
@@ -65,7 +65,7 @@ struct scale_queue_args
struct scale_worker_args
{
- struct image *image;
+ Crystal *crystal;
double shift;
RefList *reference;
};
@@ -79,7 +79,7 @@ static void *create_scale_job(void *vqargs)
wargs = malloc(sizeof(struct scale_worker_args));
wargs->reference = qargs->reference;
- wargs->image = &qargs->images[qargs->n_started++];
+ wargs->crystal = qargs->crystals[qargs->n_started++];
return wargs;
}
@@ -88,20 +88,21 @@ static void *create_scale_job(void *vqargs)
static void run_scale_job(void *vwargs, int cookie)
{
struct scale_worker_args *wargs = vwargs;
- struct image *image = wargs->image;
+ Crystal *cr = wargs->crystal;
RefList *reference = wargs->reference;
Reflection *refl;
RefListIterator *iter;
double num = 0.0;
double den = 0.0;
double corr;
+ const double osf = crystal_get_osf(cr);
- if ( image->pr_dud ) {
+ if ( crystal_get_user_flag(cr) ) {
wargs->shift = 0.0;
return;
}
- for ( refl = first_refl(image->reflections, &iter);
+ for ( refl = first_refl(crystal_get_reflections(cr), &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
@@ -128,8 +129,8 @@ static void run_scale_job(void *vwargs, int cookie)
Ihl = get_intensity(refl) / get_partiality(refl);
esd = get_esd_intensity(refl) / get_partiality(refl);
- num += Ih * (Ihl/image->osf) / pow(esd/image->osf, 2.0);
- den += pow(Ih, 2.0)/pow(esd/image->osf, 2.0);
+ num += Ih * (Ihl/osf) / pow(esd/osf, 2.0);
+ den += pow(Ih, 2.0)/pow(esd/osf, 2.0);
}
@@ -138,7 +139,7 @@ static void run_scale_job(void *vwargs, int cookie)
corr = num / den;
if ( !isnan(corr) && !isinf(corr) ) {
- image->osf *= corr;
+ crystal_set_osf(cr, osf*corr);
}
wargs->shift = fabs(corr-1.0);
@@ -155,7 +156,7 @@ static void finalise_scale_job(void *vqargs, void *vwargs)
}
-static double iterate_scale(struct image *images, int n, RefList *reference,
+static double iterate_scale(Crystal **crystals, int n, RefList *reference,
int n_threads)
{
struct scale_queue_args qargs;
@@ -164,7 +165,7 @@ static double iterate_scale(struct image *images, int n, RefList *reference,
qargs.reference = reference;
qargs.n_started = 0;
- qargs.images = images;
+ qargs.crystals = crystals;
qargs.max_shift = 0.0;
run_threads(n_threads, run_scale_job, create_scale_job,
@@ -178,14 +179,14 @@ struct merge_queue_args
{
RefList *full;
pthread_mutex_t full_lock;
- struct image *images;
+ Crystal **crystals;
int n_started;
};
struct merge_worker_args
{
- struct image *image;
+ Crystal *crystal;
RefList *full;
pthread_mutex_t *full_lock;
};
@@ -200,7 +201,7 @@ static void *create_merge_job(void *vqargs)
wargs->full = qargs->full;
wargs->full_lock = &qargs->full_lock;
- wargs->image = &qargs->images[qargs->n_started++];
+ wargs->crystal = qargs->crystals[qargs->n_started++];
return wargs;
}
@@ -209,17 +210,17 @@ static void *create_merge_job(void *vqargs)
static void run_merge_job(void *vwargs, int cookie)
{
struct merge_worker_args *wargs = vwargs;
- struct image *image = wargs->image;
+ Crystal *cr = wargs->crystal;
RefList *full = wargs->full;
Reflection *refl;
RefListIterator *iter;
double G;
- if ( image->pr_dud ) return;
+ if ( crystal_get_user_flag(cr)) return;
- G = image->osf;
+ G = crystal_get_osf(cr);
- for ( refl = first_refl(image->reflections, &iter);
+ for ( refl = first_refl(crystal_get_reflections(cr), &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
@@ -272,7 +273,7 @@ static void finalise_merge_job(void *vqargs, void *vwargs)
}
-static RefList *lsq_intensities(struct image *images, int n, int n_threads)
+static RefList *lsq_intensities(Crystal **crystals, int n, int n_threads)
{
RefList *full;
struct merge_queue_args qargs;
@@ -283,7 +284,7 @@ static RefList *lsq_intensities(struct image *images, int n, int n_threads)
qargs.full = full;
qargs.n_started = 0;
- qargs.images = images;
+ qargs.crystals = crystals;
pthread_mutex_init(&qargs.full_lock, NULL);
run_threads(n_threads, run_merge_job, create_merge_job,
@@ -308,14 +309,14 @@ static RefList *lsq_intensities(struct image *images, int n, int n_threads)
struct esd_queue_args
{
RefList *full;
- struct image *images;
+ Crystal **crystals;
int n_started;
};
struct esd_worker_args
{
- struct image *image;
+ Crystal *crystal;
RefList *full;
};
@@ -328,7 +329,7 @@ static void *create_esd_job(void *vqargs)
wargs = malloc(sizeof(struct esd_worker_args));
wargs->full = qargs->full;
- wargs->image = &qargs->images[qargs->n_started++];
+ wargs->crystal = qargs->crystals[qargs->n_started++];
return wargs;
}
@@ -337,17 +338,17 @@ static void *create_esd_job(void *vqargs)
static void run_esd_job(void *vwargs, int cookie)
{
struct esd_worker_args *wargs = vwargs;
- struct image *image = wargs->image;
+ Crystal *cr = wargs->crystal;
RefList *full = wargs->full;
Reflection *refl;
RefListIterator *iter;
double G;
- if ( image->pr_dud ) return;
+ if ( crystal_get_user_flag(cr) ) return;
- G = image->osf;
+ G = crystal_get_osf(cr);
- for ( refl = first_refl(image->reflections, &iter);
+ for ( refl = first_refl(crystal_get_reflections(cr), &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
@@ -383,7 +384,7 @@ static void finalise_esd_job(void *vqargs, void *vwargs)
}
-static void calculate_esds(struct image *images, int n, RefList *full,
+static void calculate_esds(Crystal **crystals, int n, RefList *full,
int n_threads, int min_red)
{
struct esd_queue_args qargs;
@@ -392,7 +393,7 @@ static void calculate_esds(struct image *images, int n, RefList *full,
qargs.full = full;
qargs.n_started = 0;
- qargs.images = images;
+ qargs.crystals = crystals;
for ( refl = first_refl(full, &iter);
refl != NULL;
@@ -423,7 +424,7 @@ static void calculate_esds(struct image *images, int n, RefList *full,
/* Scale the stack of images */
-RefList *scale_intensities(struct image *images, int n, RefList *gref,
+RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
int n_threads, int noscale)
{
int i;
@@ -431,17 +432,17 @@ RefList *scale_intensities(struct image *images, int n, RefList *gref,
RefList *full = NULL;
const int min_redundancy = 3;
- for ( i=0; i<n; i++ ) images[i].osf = 1.0;
+ for ( i=0; i<n; i++ ) crystal_set_osf(crystals[i], 1.0);
if ( noscale ) {
- full = lsq_intensities(images, n, n_threads);
- calculate_esds(images, n, full, n_threads, min_redundancy);
+ full = lsq_intensities(crystals, n, n_threads);
+ calculate_esds(crystals, n, full, n_threads, min_redundancy);
return full;
}
/* No reference -> create an initial list to refine against */
if ( gref == NULL ) {
- full = lsq_intensities(images, n, n_threads);
+ full = lsq_intensities(crystals, n, n_threads);
}
/* Iterate */
@@ -457,14 +458,14 @@ RefList *scale_intensities(struct image *images, int n, RefList *gref,
reference = full;
}
- max_corr = iterate_scale(images, n, reference, n_threads);
+ max_corr = iterate_scale(crystals, n, reference, n_threads);
//STATUS("Scaling iteration %2i: max correction = %5.2f\n",
// i+1, max_corr);
/* No reference -> generate list for next iteration */
if ( gref == NULL ) {
reflist_free(full);
- full = lsq_intensities(images, n, n_threads);
+ full = lsq_intensities(crystals, n, n_threads);
}
//show_scale_factors(images, n);
@@ -474,10 +475,10 @@ RefList *scale_intensities(struct image *images, int n, RefList *gref,
} while ( (max_corr > 0.01) && (i < MAX_CYCLES) );
if ( gref != NULL ) {
- full = lsq_intensities(images, n, n_threads);
+ full = lsq_intensities(crystals, n, n_threads);
} /* else we already did it */
- calculate_esds(images, n, full, n_threads, min_redundancy);
+ calculate_esds(crystals, n, full, n_threads, min_redundancy);
return full;
}
diff --git a/src/partialator.c b/src/partialator.c
index 35e25320..30f9bfe4 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -506,6 +506,7 @@ int main(int argc, char *argv[])
crystals = crystals_new;
crystals[n_crystals] = crystal_new();
cr = crystals[n_crystals];
+ crystal_set_image(cr, cur);
/* Fill in initial estimates of stuff */
crystal_set_osf(cr, 1.0);
@@ -516,7 +517,7 @@ int main(int argc, char *argv[])
as = asymmetric_indices(crystal_get_reflections(cr),
sym);
crystal_set_reflections(cr, as);
- update_partialities(cur, cr);
+ update_partialities(cr);
nobs += select_scalable_reflections(as, reference);
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 7410d931..31558ec7 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -3,11 +3,11 @@
*
* Post refinement
*
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- * a research centre of the Helmholtz Association.
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2012 Thomas White <taw@physics.org>
+ * 2010-2013 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -88,7 +88,7 @@ static double partiality_rgradient(double r, double profile_radius)
/* Return the gradient of parameter 'k' given the current status of 'image'. */
-double gradient(struct image *image, int k, Reflection *refl, double r)
+double gradient(Crystal *cr, int k, Reflection *refl, double r)
{
double ds, azix, aziy;
double ttlow, tthigh, tt;
@@ -103,17 +103,18 @@ double gradient(struct image *image, int k, Reflection *refl, double r)
int clamp_low, clamp_high;
double klow, khigh;
double gr;
+ struct image *image = crystal_get_image(cr);
get_symmetric_indices(refl, &hs, &ks, &ls);
- cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz);
+ cell_get_reciprocal(crystal_get_cell(cr), &asx, &asy, &asz,
+ &bsx, &bsy, &bsz,
+ &csx, &csy, &csz);
xl = hs*asx + ks*bsx + ls*csx;
yl = hs*asy + ks*bsy + ls*csy;
zl = hs*asz + ks*bsz + ls*csz;
- ds = 2.0 * resolution(image->indexed_cell, hs, ks, ls);
+ ds = 2.0 * resolution(crystal_get_cell(cr), hs, ks, ls);
get_partial(refl, &r1, &r2, &p, &clamp_low, &clamp_high);
klow = 1.0/(image->lambda - image->lambda*image->bw/2.0);
@@ -237,8 +238,11 @@ static void apply_cell_shift(UnitCell *cell, int k, double shift)
/* Apply the given shift to the 'k'th parameter of 'image'. */
-static void apply_shift(struct image *image, int k, double shift)
+static void apply_shift(Crystal *cr, int k, double shift)
{
+ double t;
+ struct image *image = crystal_get_image(cr);
+
switch ( k ) {
case REF_DIV :
@@ -251,7 +255,9 @@ static void apply_shift(struct image *image, int k, double shift)
break;
case REF_R :
- image->profile_radius += shift;
+ t = crystal_get_profile_radius(cr);
+ t += shift;
+ crystal_set_profile_radius(cr, t);
break;
case REF_ASX :
@@ -263,7 +269,7 @@ static void apply_shift(struct image *image, int k, double shift)
case REF_CSX :
case REF_CSY :
case REF_CSZ :
- apply_cell_shift(image->indexed_cell, k, shift);
+ apply_cell_shift(crystal_get_cell(cr), k, shift);
break;
default :
@@ -357,7 +363,7 @@ static gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M)
/* Perform one cycle of post refinement on 'image' against 'full' */
-static double pr_iterate(struct image *image, const RefList *full)
+static double pr_iterate(Crystal *cr, const RefList *full)
{
gsl_matrix *M;
gsl_vector *v;
@@ -369,7 +375,7 @@ static double pr_iterate(struct image *image, const RefList *full)
double max_shift;
int nref = 0;
- reflections = image->reflections;
+ reflections = crystal_get_reflections(cr);
M = gsl_matrix_calloc(NUM_PARAMS, NUM_PARAMS);
v = gsl_vector_calloc(NUM_PARAMS);
@@ -387,6 +393,7 @@ static double pr_iterate(struct image *image, const RefList *full)
double p;
Reflection *match;
double gradients[NUM_PARAMS];
+ const double osf = crystal_get_osf(cr);
if ( !get_refinable(refl) ) continue;
@@ -398,7 +405,7 @@ static double pr_iterate(struct image *image, const RefList *full)
" is it marked as refinable?\n", ha, ka, la);
continue;
}
- I_full = image->osf * get_intensity(match);
+ I_full = osf * get_intensity(match);
/* Actual measurement of this reflection from this pattern? */
I_partial = get_intensity(refl);
@@ -412,7 +419,8 @@ static double pr_iterate(struct image *image, const RefList *full)
/* Calculate all gradients for this reflection */
for ( k=0; k<NUM_PARAMS; k++ ) {
double gr;
- gr = gradient(image, k, refl, image->profile_radius);
+ gr = gradient(cr, k, refl,
+ crystal_get_profile_radius(cr));
gradients[k] = gr;
}
@@ -429,7 +437,7 @@ static double pr_iterate(struct image *image, const RefList *full)
if ( g > k ) continue;
M_c = gradients[g] * gradients[k];
- M_c *= w * pow(image->osf * I_full, 2.0);
+ M_c *= w * pow(osf * I_full, 2.0);
M_curr = gsl_matrix_get(M, k, g);
gsl_matrix_set(M, k, g, M_curr + M_c);
@@ -450,7 +458,7 @@ static double pr_iterate(struct image *image, const RefList *full)
//STATUS("%i reflections went into the equations.\n", nref);
if ( nref == 0 ) {
- image->pr_dud = 1;
+ crystal_set_user_flag(cr, 1);
gsl_matrix_free(M);
gsl_vector_free(v);
return 0.0;
@@ -462,7 +470,7 @@ static double pr_iterate(struct image *image, const RefList *full)
for ( param=0; param<NUM_PARAMS; param++ ) {
double shift = gsl_vector_get(shifts, param);
- apply_shift(image, param, shift);
+ apply_shift(cr, param, shift);
//STATUS("Shift %i: %e\n", param, shift);
if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
}
@@ -480,7 +488,7 @@ static double pr_iterate(struct image *image, const RefList *full)
}
-static double guide_dev(struct image *image, const RefList *full)
+static double guide_dev(Crystal *cr, const RefList *full)
{
double dev = 0.0;
@@ -488,7 +496,7 @@ static double guide_dev(struct image *image, const RefList *full)
Reflection *refl;
RefListIterator *iter;
- for ( refl = first_refl(image->reflections, &iter);
+ for ( refl = first_refl(crystal_get_reflections(cr), &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
@@ -508,7 +516,7 @@ static double guide_dev(struct image *image, const RefList *full)
* scale_intensities() might not yet have been called, so the
* full version may not have been calculated yet. */
- G = image->osf;
+ G = crystal_get_osf(cr);
p = get_partiality(refl);
I_partial = get_intensity(refl);
I_full = get_intensity(full_version);
@@ -524,21 +532,21 @@ static double guide_dev(struct image *image, const RefList *full)
}
-void pr_refine(struct image *image, const RefList *full)
+void pr_refine(Crystal *cr, const RefList *full)
{
double max_shift, dev;
int i;
const int verbose = 0;
if ( verbose ) {
- dev = guide_dev(image, full);
+ dev = guide_dev(cr, full);
STATUS("\n"); /* Deal with progress bar */
STATUS("Before iteration: dev = %10.5e\n",
dev);
}
i = 0;
- image->pr_dud = 0;
+ crystal_set_user_flag(cr, 0);
do {
double asx, asy, asz;
@@ -546,15 +554,15 @@ void pr_refine(struct image *image, const RefList *full)
double csx, csy, csz;
double dev;
- cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
+ cell_get_reciprocal(crystal_get_cell(cr), &asx, &asy, &asz,
&bsx, &bsy, &bsz, &csx, &csy, &csz);
- max_shift = pr_iterate(image, full);
+ max_shift = pr_iterate(cr, full);
- update_partialities(image);
+ update_partialities(cr);
if ( verbose ) {
- dev = guide_dev(image, full);
+ dev = guide_dev(cr, full);
STATUS("PR Iteration %2i: max shift = %10.2f"
" dev = %10.5e\n", i+1, max_shift, dev);
}
diff --git a/src/post-refinement.h b/src/post-refinement.h
index 637c0bb0..52e70b2b 100644
--- a/src/post-refinement.h
+++ b/src/post-refinement.h
@@ -62,7 +62,7 @@ enum {
extern void pr_refine(Crystal *cr, const RefList *full);
/* Exported so it can be poked by tests/pr_gradient_check */
-extern double gradient(struct image *image, int k, Reflection *refl, double r);
+extern double gradient(Crystal *cr, int k, Reflection *refl, double r);
#endif /* POST_REFINEMENT_H */
diff --git a/src/scaling-report.c b/src/scaling-report.c
index ba425b96..3de82517 100644
--- a/src/scaling-report.c
+++ b/src/scaling-report.c
@@ -183,7 +183,7 @@ static void plot_point(cairo_t *cr, double g_width, double g_height,
}
-static void partiality_graph(cairo_t *cr, const struct image *images, int n,
+static void partiality_graph(cairo_t *cr, Crystal **crystals, int n,
RefList *full)
{
const double g_width = 200.0;
@@ -219,7 +219,7 @@ static void partiality_graph(cairo_t *cr, const struct image *images, int n,
num_nondud = 0;
for ( i=0; i<n; i++ ) {
- if ( images[i].pr_dud ) continue;
+ if ( crystal_get_user_flag(crystals[i]) ) continue;
num_nondud++;
}
@@ -229,10 +229,13 @@ static void partiality_graph(cairo_t *cr, const struct image *images, int n,
Reflection *refl;
RefListIterator *iter;
+ Crystal *cryst;
- if ( images[i].pr_dud ) continue;
+ cryst = crystals[i];
- for ( refl = first_refl(images[i].reflections, &iter);
+ if ( crystal_get_user_flag(cryst) ) continue;
+
+ for ( refl = first_refl(crystal_get_reflections(cryst), &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
@@ -249,7 +252,7 @@ static void partiality_graph(cairo_t *cr, const struct image *images, int n,
if ( get_redundancy(f) < 2 ) continue;
Ipart = get_intensity(refl);
- Ifull = images[i].osf * get_intensity(f);
+ Ifull = crystal_get_osf(cryst) * get_intensity(f);
//if ( Ifull < 10 ) continue; /* FIXME: Ugh */
@@ -267,7 +270,7 @@ static void partiality_graph(cairo_t *cr, const struct image *images, int n,
double esd_pobs, esd_Ip, esd_If;
esd_Ip = get_esd_intensity(refl);
esd_If = get_esd_intensity(f);
- esd_If *= images[i].osf;
+ esd_If *= crystal_get_osf(cryst);
esd_pobs = pow(esd_Ip/Ipart, 2.0);
esd_pobs += pow(esd_If/Ifull, 2.0);
esd_pobs = sqrt(esd_pobs);
@@ -313,8 +316,8 @@ static void partiality_graph(cairo_t *cr, const struct image *images, int n,
}
-static void partiality_histogram(cairo_t *cr, const struct image *images,
- int n, RefList *full, int calc, int backwards)
+static void partiality_histogram(cairo_t *cr, Crystal **crystals, int n,
+ RefList *full, int calc, int backwards)
{
int f_max;
int i, b;
@@ -344,10 +347,11 @@ static void partiality_histogram(cairo_t *cr, const struct image *images,
Reflection *refl;
RefListIterator *iter;
+ Crystal *cryst = crystals[i];
- if ( images[i].pr_dud ) continue;
+ if ( crystal_get_user_flag(cryst) ) continue;
- for ( refl = first_refl(images[i].reflections, &iter);
+ for ( refl = first_refl(crystal_get_reflections(cryst), &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
@@ -364,7 +368,7 @@ static void partiality_histogram(cairo_t *cr, const struct image *images,
Ipart = get_intensity(refl);
Ifull = get_intensity(f);
- pobs = Ipart/(images[i].osf*Ifull);
+ pobs = Ipart/(crystal_get_osf(cryst)*Ifull);
pcalc = get_partiality(refl);
if ( calc ) {
@@ -426,8 +430,8 @@ static void partiality_histogram(cairo_t *cr, const struct image *images,
}
-static void scale_factor_histogram(cairo_t *cr, const struct image *images,
- int n, const char *title)
+static void scale_factor_histogram(cairo_t *cr, Crystal **crystals, int n,
+ const char *title)
{
int f_max;
int i, b;
@@ -451,8 +455,8 @@ static void scale_factor_histogram(cairo_t *cr, const struct image *images,
osf_max = 0.0;
for ( i=0; i<n; i++ ) {
- double osf = images[i].osf;
- if ( images[i].pr_dud ) continue;
+ double osf = crystal_get_osf(crystals[i]);
+ if ( crystal_get_user_flag(crystals[i]) ) continue;
if ( osf > osf_max ) osf_max = osf;
}
osf_max = ceil(osf_max+osf_max/10000.0);
@@ -473,9 +477,9 @@ static void scale_factor_histogram(cairo_t *cr, const struct image *images,
for ( i=0; i<n; i++ ) {
- double osf = images[i].osf;
+ double osf = crystal_get_osf(crystals[i]);
- if ( images[i].pr_dud ) continue;
+ if ( crystal_get_user_flag(crystals[i]) ) continue;
for ( b=0; b<nbins; b++ ) {
if ( (osf >= osf_low[b])
@@ -544,8 +548,8 @@ static void scale_factor_histogram(cairo_t *cr, const struct image *images,
}
-static void intensity_histogram(cairo_t *cr, const struct image *images,
- int n, RefList *full,
+static void intensity_histogram(cairo_t *cr, Crystal **crystals, int n,
+ RefList *full,
signed int h, signed int k, signed int l)
{
int f_max;
@@ -582,12 +586,13 @@ static void intensity_histogram(cairo_t *cr, const struct image *images,
for ( i=0; i<n; i++ ) {
double osf;
+ Crystal *cryst = crystals[i];
- if ( images[i].pr_dud ) continue;
+ if ( crystal_get_user_flag(cryst) ) continue;
- osf = images[i].osf;
+ osf = crystal_get_osf(cryst);
- for ( f = find_refl(images[i].reflections, h, k, l);
+ for ( f = find_refl(crystal_get_reflections(cryst), h, k, l);
f != NULL;
f = next_found_refl(f) )
{
@@ -616,12 +621,13 @@ static void intensity_histogram(cairo_t *cr, const struct image *images,
for ( i=0; i<n; i++ ) {
double osf;
+ Crystal *cryst = crystals[i];
- if ( images[i].pr_dud ) continue;
+ if ( crystal_get_user_flag(cryst) ) continue;
- osf = images[i].osf;
+ osf = crystal_get_osf(cryst);
- for ( f = find_refl(images[i].reflections, h, k, l);
+ for ( f = find_refl(crystal_get_reflections(cryst), h, k, l);
f != NULL;
f = next_found_refl(f) )
{
@@ -771,7 +777,7 @@ static void find_most_sampled_reflections(RefList *list, int n, signed int *h,
-SRContext *sr_titlepage(struct image *images, int n,
+SRContext *sr_titlepage(Crystal **crystals, int n,
const char *filename, const char *stream_filename,
const char *cmdline)
{
@@ -805,7 +811,7 @@ SRContext *sr_titlepage(struct image *images, int n,
}
-void sr_iteration(SRContext *sr, int iteration, struct image *images, int n,
+void sr_iteration(SRContext *sr, int iteration, Crystal **crystals, int n,
RefList *full)
{
int i;
@@ -822,7 +828,7 @@ void sr_iteration(SRContext *sr, int iteration, struct image *images, int n,
cairo_save(sr->cr);
cairo_translate(sr->cr, 480.0, 350.0);
- scale_factor_histogram(sr->cr, images, n,
+ scale_factor_histogram(sr->cr, crystals, n,
"Distribution of overall scale factors");
cairo_restore(sr->cr);
@@ -830,7 +836,7 @@ void sr_iteration(SRContext *sr, int iteration, struct image *images, int n,
cairo_save(sr->cr);
cairo_translate(sr->cr, 70.0, 330.0);
- partiality_graph(sr->cr, images, n, full);
+ partiality_graph(sr->cr, crystals, n, full);
cairo_save(sr->cr);
cairo_move_to(sr->cr, 0.0, 0.0);
@@ -841,7 +847,7 @@ void sr_iteration(SRContext *sr, int iteration, struct image *images, int n,
cairo_stroke(sr->cr);
cairo_set_dash(sr->cr, NULL, 0, 0.0);
cairo_translate(sr->cr, 0.0, -150.0);
- partiality_histogram(sr->cr, images, n, full, 1, 0);
+ partiality_histogram(sr->cr, crystals, n, full, 1, 0);
cairo_restore(sr->cr);
cairo_save(sr->cr);
@@ -854,7 +860,7 @@ void sr_iteration(SRContext *sr, int iteration, struct image *images, int n,
cairo_set_dash(sr->cr, NULL, 0, 0.0);
cairo_translate(sr->cr, 230.0, 200.0);
cairo_rotate(sr->cr, -M_PI_2);
- partiality_histogram(sr->cr, images, n, full, 0, 1);
+ partiality_histogram(sr->cr, crystals, n, full, 0, 1);
cairo_restore(sr->cr);
cairo_restore(sr->cr);
@@ -873,7 +879,7 @@ void sr_iteration(SRContext *sr, int iteration, struct image *images, int n,
cairo_save(sr->cr);
cairo_translate(sr->cr, 400.0+140.0*x, 60.0+80.0*y);
- intensity_histogram(sr->cr, images, n, full,
+ intensity_histogram(sr->cr, crystals, n, full,
sr->ms_h[i], sr->ms_k[i], sr->ms_l[i]);
cairo_restore(sr->cr);