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-rw-r--r--src/post-refinement.c64
1 files changed, 36 insertions, 28 deletions
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);
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-30 13:18:36 +0000