static void write_stream_reflections(FILE *fh, RefList *list)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I sigma(I) peak background"
" fs/px ss/px\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, bg, pk;
double fs, ss;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
pk = get_peak(refl);
bg = get_mean_bg(refl);
/* Reflections with redundancy = 0 are not written */
if ( get_redundancy(refl) == 0 ) continue;
fprintf(fh,
"%4i %4i %4i %10.2f %10.2f %10.2f %10.2f %6.1f %6.1f\n",
h, k, l, intensity, esd_i, pk, bg, fs, ss);
}
}
static int write_stream_reflections_2_2(FILE *fh, RefList *list,
struct image *image)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I sigma(I) "
"peak background fs/px ss/px\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, bg, pk;
double fs, ss;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
pk = get_peak(refl);
bg = get_mean_bg(refl);
/* Reflections with redundancy = 0 are not written */
if ( get_redundancy(refl) == 0 ) continue;
if ( image->det != NULL ) {
struct panel *p;
double write_fs, write_ss;
p = find_orig_panel(image->det, fs, ss);
if ( p == NULL ) {
ERROR("Panel not found\n");
return 1;
}
/* Convert coordinates to match arrangement of panels in HDF5
* file */
write_fs = fs - p->min_fs + p->orig_min_fs;
write_ss = ss - p->min_ss + p->orig_min_ss;
fprintf(fh, "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f"
" %6.1f %6.1f\n",
h, k, l, intensity, esd_i, pk, bg, write_fs,
write_ss);
} else {
fprintf(fh, "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f"
" %6.1f %6.1f\n",
h, k, l, intensity, esd_i, pk, bg, fs, ss);
}
}
return 0;
}
static int write_stream_reflections_2_3(FILE *fh, RefList *list,
struct image *image)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I sigma(I) "
"peak background fs/px ss/px panel\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, pk, bg;
double fs, ss;
double write_fs, write_ss;
struct panel *p = NULL;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
pk = get_peak(refl);
bg = get_mean_bg(refl);
/* Reflections with redundancy = 0 are not written */
if ( get_redundancy(refl) == 0 ) continue;
p = find_panel(image->det,fs,ss);
if ( p == NULL ) {
ERROR("Panel not found\n");
return 1;
}
write_fs = fs-p->min_fs+p->orig_min_fs;
write_ss = ss-p->min_ss+p->orig_min_ss;
fprintf(fh,
"%4i %4i %4i %10.2f %10.2f %10.2f %10.2f "
"%6.1f %6.1f %s\n",
h, k, l, intensity, esd_i, pk, bg,
write_fs, write_ss, p->name);
}
return 0;
}
static double guide_dev(Crystal *cr, const RefList *full)
{
double dev = 0.0;
/* For each reflection */
Reflection *refl;
RefListIterator *iter;
for ( refl = first_refl(crystal_get_reflections(cr), &iter);
refl != NULL;
refl = next_refl(refl, iter) ) {
double G, p;
signed int h, k, l;
Reflection *full_version;
double I_full, I_partial;
if ( (get_intensity(refl) < 3.0*get_esd_intensity(refl))
|| (get_partiality(refl) < MIN_PART_REFINE) ) continue;
get_indices(refl, &h, &k, &l);
assert((h!=0) || (k!=0) || (l!=0));
full_version = find_refl(full, h, k, l);
if ( full_version == NULL ) continue;
/* Some reflections may have recently become scalable, but
* scale_intensities() might not yet have been called, so the
* full version may not have been calculated yet. */
G = crystal_get_osf(cr);
p = get_partiality(refl);
I_partial = get_intensity(refl);
I_full = get_intensity(full_version);
//STATUS("%3i %3i %3i %5.2f %5.2f %5.2f %5.2f %5.2f\n",
// h, k, l, G, p, I_partial, I_full,
// I_partial - p*G*I_full);
dev += pow(I_partial - p*G*I_full, 2.0);
}
return dev;
}
static void write_stream_reflections_2_1(FILE *fh, RefList *list)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I phase sigma(I) "
" counts fs/px ss/px\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, ph;
int red;
double fs, ss;
char phs[16];
int have_phase;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
red = get_redundancy(refl);
ph = get_phase(refl, &have_phase);
/* Reflections with redundancy = 0 are not written */
if ( red == 0 ) continue;
if ( have_phase ) {
snprintf(phs, 16, "%8.2f", rad2deg(ph));
} else {
strncpy(phs, " -", 15);
}
fprintf(fh,
"%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f\n",
h, k, l, intensity, phs, esd_i, red, fs, ss);
}
}
static int write_stream_reflections_2_1(FILE *fh, RefList *list,
struct image *image)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I phase sigma(I) "
" counts fs/px ss/px\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, ph;
int red;
double fs, ss;
char phs[16];
int have_phase;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
red = get_redundancy(refl);
ph = get_phase(refl, &have_phase);
/* Reflections with redundancy = 0 are not written */
if ( red == 0 ) continue;
if ( have_phase ) {
snprintf(phs, 16, "%8.2f", rad2deg(ph));
} else {
strncpy(phs, " -", 15);
}
if ( image->det != NULL ) {
struct panel *p;
double write_fs, write_ss;
p = find_orig_panel(image->det, fs, ss);
if ( p == NULL ) {
ERROR("Panel not found\n");
return 1;
}
/* Convert coordinates to match arrangement of panels
* in HDF5 file */
write_fs = fs - p->min_fs + p->orig_min_fs;
write_ss = ss - p->min_ss + p->orig_min_ss;
fprintf(fh, "%3i %3i %3i %10.2f %s %10.2f %7i "
"%6.1f %6.1f\n",
h, k, l, intensity, phs, esd_i, red,
write_fs, write_ss);
} else {
fprintf(fh, "%3i %3i %3i %10.2f %s %10.2f %7i "
"%6.1f %6.1f\n",
h, k, l, intensity, phs, esd_i, red,
fs, ss);
}
}
return 0;
}
/* Perform one cycle of post refinement on 'image' against 'full' */
static double pr_iterate(Crystal *cr, const RefList *full,
PartialityModel pmodel, int *n_filtered)
{
gsl_matrix *M;
gsl_vector *v;
gsl_vector *shifts;
int param;
Reflection *refl;
RefListIterator *iter;
RefList *reflections;
double max_shift;
int nref = 0;
const int verbose = 0;
int num_params = 0;
enum gparam rv[32];
*n_filtered = 0;
/* If partiality model is anything other than "unity", refine all the
* geometrical parameters */
if ( pmodel != PMODEL_UNITY ) {
rv[num_params++] = GPARAM_ASX;
rv[num_params++] = GPARAM_ASY;
rv[num_params++] = GPARAM_ASZ;
rv[num_params++] = GPARAM_BSX;
rv[num_params++] = GPARAM_BSY;
rv[num_params++] = GPARAM_BSZ;
rv[num_params++] = GPARAM_CSX;
rv[num_params++] = GPARAM_CSY;
rv[num_params++] = GPARAM_CSZ;
}
STATUS("Refining %i parameters.\n", num_params);
reflections = crystal_get_reflections(cr);
M = gsl_matrix_calloc(num_params, num_params);
v = gsl_vector_calloc(num_params);
/* Construct the equations, one per reflection in this image */
for ( refl = first_refl(reflections, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int ha, ka, la;
double I_full, delta_I;
double w;
double I_partial;
int k;
double p, l;
Reflection *match;
double gradients[num_params];
/* Find the full version */
get_indices(refl, &ha, &ka, &la);
match = find_refl(full, ha, ka, la);
if ( match == NULL ) continue;
if ( (get_intensity(refl) < 3.0*get_esd_intensity(refl))
|| (get_partiality(refl) < MIN_PART_REFINE)
|| (get_redundancy(match) < 2) ) continue;
I_full = get_intensity(match);
/* Actual measurement of this reflection from this pattern? */
I_partial = get_intensity(refl) / crystal_get_osf(cr);
p = get_partiality(refl);
l = get_lorentz(refl);
/* Calculate the weight for this reflection */
w = pow(get_esd_intensity(refl), 2.0);
w += l * p * I_full * pow(get_esd_intensity(match), 2.0);
w = pow(w, -1.0);
/* Calculate all gradients for this reflection */
for ( k=0; k<num_params; k++ ) {
gradients[k] = p_gradient(cr, rv[k], refl, pmodel) * l;
}
for ( k=0; k<num_params; k++ ) {
int g;
double v_c, v_curr;
for ( g=0; g<num_params; g++ ) {
double M_c, M_curr;
/* Matrix is symmetric */
if ( g > k ) continue;
M_c = gradients[g] * gradients[k];
M_c *= w * pow(I_full, 2.0);
M_curr = gsl_matrix_get(M, k, g);
gsl_matrix_set(M, k, g, M_curr + M_c);
gsl_matrix_set(M, g, k, M_curr + M_c);
}
delta_I = I_partial - (l * p * I_full);
v_c = w * delta_I * I_full * gradients[k];
v_curr = gsl_vector_get(v, k);
gsl_vector_set(v, k, v_curr + v_c);
}
nref++;
}
if ( verbose ) {
STATUS("The original equation:\n");
show_matrix_eqn(M, v);
}
//STATUS("%i reflections went into the equations.\n", nref);
if ( nref == 0 ) {
crystal_set_user_flag(cr, 2);
gsl_matrix_free(M);
gsl_vector_free(v);
return 0.0;
}
max_shift = 0.0;
shifts = solve_svd(v, M, n_filtered, verbose);
if ( shifts != NULL ) {
for ( param=0; param<num_params; param++ ) {
double shift = gsl_vector_get(shifts, param);
apply_shift(cr, rv[param], shift);
//STATUS("Shift %i: %e\n", param, shift);
if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
}
} else {
crystal_set_user_flag(cr, 3);
}
gsl_matrix_free(M);
gsl_vector_free(v);
gsl_vector_free(shifts);
return max_shift;
}
