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authorThomas White <taw@physics.org>2013-10-09 15:56:59 +0200
committerThomas White <taw@physics.org>2013-10-09 15:56:59 +0200
commit36e817b4002703148e29aa0289195113ed4848e1 (patch)
treec34a73104bfb182559f5e94b5a82ead0645eb372 /libcrystfel
parent0b2555c9a3656b082ef31d19194d36f13cbe80c3 (diff)
Remove old resolution estimation code
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/integration.c220
1 files changed, 10 insertions, 210 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 1f2bf25b..c366f30c 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1316,16 +1316,23 @@ static void refine_rigid_groups(struct intcontext *ic)
}
-static void measure_all_intensities(IntegrationMethod meth, RefList *list,
- struct image *image, UnitCell *cell,
- double ir_inn, double ir_mid, double ir_out)
+static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
+ struct image *image,
+ double ir_inn, double ir_mid, double ir_out)
{
+ RefList *list;
+ UnitCell *cell;
Reflection *refl;
RefListIterator *iter;
struct intcontext ic;
int i;
int n_saturated = 0;
+ cell = crystal_get_cell(cr);
+
+ /* Create initial list of reflections with nominal parameters */
+ list = find_intersections(image, cr);
+
ic.halfw = ir_out;
ic.image = image;
ic.k = 1.0/image->lambda;
@@ -1471,215 +1478,8 @@ static void measure_all_intensities(IntegrationMethod meth, RefList *list,
free_intcontext(&ic);
image->num_saturated_peaks = n_saturated;
-}
-
-
-static void UNUSED estimate_mosaicity(IntegrationMethod meth, Crystal *cr,
- struct image *image,
- double ir_inn, double ir_mid, double ir_out)
-{
- int msteps = 50;
- int i;
- const double mest = crystal_get_mosaicity(cr);
- const double mmax = 2.0 * mest;
- RefList *list;
-
- STATUS("Initial estimate: m = %f\n", mest);
- crystal_set_mosaicity(cr, mmax);
- list = find_intersections(image, cr);
crystal_set_reflections(cr, list);
- measure_all_intensities(meth, list, image, crystal_get_cell(cr),
- ir_inn, ir_mid, ir_out);
-
- for ( i=1; i<=msteps; i++ ) {
-
- /* "m" varies from just over zero up to 2x the given estimate */
- Reflection *refl;
- RefListIterator *iter;
- const double m = mmax*((double)i/msteps);
- int n_gained = 0;
- int n_lost = 0;
- double i_gained = 0.0;
- double i_lost = 0.0;
-
- crystal_set_mosaicity(cr, m);
- update_partialities(cr, PMODEL_SPHERE);
-
- for ( refl = first_refl(list, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) )
- {
- if ( get_redundancy(refl) == 0 ) {
- if ( get_temp1(refl) > 0.0 ) {
- i_lost += get_intensity(refl);
- n_lost++;
- }
- set_temp1(refl, -1.0);
- } else if ( get_temp1(refl) < 0.0 ) {
- i_gained += get_intensity(refl);
- n_gained++;
- set_temp1(refl, 1.0);
- }
- }
-
- if ( i > 1 ) {
- STATUS("%.2e %10.2f %4i %10.2f %4i %10.2f\n", m,
- i_gained, n_gained, i_lost, n_lost,
- i_gained - i_lost);
- }
-
- }
-}
-
-
-struct integr_ind
-{
- double res;
- Reflection *refl;
-};
-
-
-static int compare_resolution(const void *av, const void *bv)
-{
- const struct integr_ind *a = av;
- const struct integr_ind *b = bv;
-
- return a->res > b->res;
-}
-
-
-static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
- int *np)
-{
- struct integr_ind *il;
- Reflection *refl;
- RefListIterator *iter;
- int i, n;
-
- *np = 0; /* For now */
-
- n = num_reflections(list);
- if ( n == 0 ) return NULL;
-
- il = calloc(n, sizeof(struct integr_ind));
- if ( il == NULL ) return NULL;
-
- i = 0;
- for ( refl = first_refl(list, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) )
- {
- signed int h, k, l;
- double res;
-
- if ( get_redundancy(refl) == 0 ) continue;
-
- get_indices(refl, &h, &k, &l);
- res = resolution(cell, h, k, l);
-
- il[i].res = res;
- il[i].refl = refl;
-
- i++;
- }
-
- qsort(il, i, sizeof(struct integr_ind), compare_resolution);
-
- *np = i;
- return il;
-}
-
-
-static void UNUSED estimate_resolution(RefList *reflections, Crystal *cr,
- struct image *image)
-{
- struct integr_ind *il;
- int n, i;
- int score = 1000; /* FIXME */
- int cutoff = 0;
- double limit = 0.0;
-
- if ( num_reflections(reflections) == 0 ) return;
-
- il = sort_reflections(reflections, crystal_get_cell(cr), &n);
- if ( il == NULL ) {
- ERROR("Couldn't sort reflections\n");
- return;
- }
-
- for ( i=0; i<n; i++ ) {
-
- double intensity, sigma, snr;
- Reflection *refl;
-
- refl = il[i].refl;
- intensity = get_intensity(refl);
- sigma = get_esd_intensity(refl);
-
- /* I/sigma(I) cutoff
- * Rejects reflections below --min-integration-snr, or if the
- * SNR is clearly silly. Silly indicates that the intensity
- * was zero. */
- snr = fabs(intensity)/sigma;
-
- /* Record intensity and set redundancy to 1 on success */
- if ( cutoff ) {
- set_redundancy(refl, 0);
- }
-
- if ( snr > 3.0 ) {
- score++;
- } else {
- score--;
- }
-
- //STATUS("%5.2f A, %5.2f, %i\n", 1e10/il[i].res, snr, score);
- if ( score == 0 ) {
- limit = il[i].res;
- cutoff = 1;
- }
-
- }
-
- crystal_set_resolution_limit(cr, limit);
-
- free(il);
-}
-
-
-static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
- struct image *image,
- double ir_inn, double ir_mid, double ir_out)
-{
- RefList *reflections;
- UnitCell *cell;
-
- cell = crystal_get_cell(cr);
-
- /* Create initial list of reflections with nominal parameters */
- reflections = find_intersections(image, cr);
- measure_all_intensities(meth, reflections, image, cell,
- ir_inn, ir_mid, ir_out);
-
- /* Find resolution limit of pattern using this list */
- //estimate_resolution(reflections, cr, image);
-
- //reflist_free(reflections);
-
- STATUS("Initial resolution estimate = %.2f nm^-1 or %.2f A\n",
- crystal_get_resolution_limit(cr)/1e9,
- 1e9 / crystal_get_resolution_limit(cr));
-
- /* Estimate the mosaicity of the crystal using this resolution limit */
- //estimate_mosaicity(cr, image);
-
- /* Create new list of reflections with refined mosaicity */
- //reflections = find_intersections(image, cr);
- //measure_all_intensities(reflections, image, ir_inn, ir_mid, ir_out);
- crystal_set_reflections(cr, reflections);
-
- //estimate_resolution(reflections, cr, image);
}