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-rw-r--r--libcrystfel/src/integration.c109
-rw-r--r--libcrystfel/src/integration.h7
2 files changed, 59 insertions, 57 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 5decd69a..9c5c8825 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -673,7 +673,7 @@ static void calculate_reference_profiles(struct intcontext *ic)
}
-static int check_box(struct intcontext *ic, struct peak_box *bx)
+static int check_box(struct intcontext *ic, struct peak_box *bx, int *sat)
{
int p, q;
int n_pk = 0;
@@ -719,6 +719,11 @@ static int check_box(struct intcontext *ic, struct peak_box *bx)
bx->bm[p+ic->w*q] = BM_IG;
}
+ if ( (bx->bm[p+ic->w*q] != BM_IG)
+ && (boxi(ic, bx, p, q) > bx->p->max_adu) ) {
+ *sat = 1;
+ }
+
/* Ignore if this pixel is closer to the next reciprocal lattice
* point */
dv = get_q_for_panel(bx->p, fs, ss, NULL, ic->k);
@@ -910,13 +915,14 @@ static int suitable_reference(struct intcontext *ic, struct peak_box *bx)
}
-static void measure_all_intensities(RefList *list, struct image *image,
- UnitCell *cell)
+static void measure_all_intensities(IntegrationMethod meth, RefList *list,
+ struct image *image, UnitCell *cell)
{
Reflection *refl;
RefListIterator *iter;
struct intcontext ic;
int i;
+ int n_saturated = 0;
ic.halfw = 4;
ic.image = image;
@@ -940,6 +946,7 @@ static void measure_all_intensities(RefList *list, struct image *image,
int fid_fs, fid_ss; /* Center coordinates, rounded,
* in overall data block */
int cfs, css; /* Corner coordinates */
+ int saturated;
set_redundancy(refl, 0);
@@ -967,11 +974,19 @@ static void measure_all_intensities(RefList *list, struct image *image,
/* Which reference profile? */
bx->rp = 0;//bx->pn;
- if ( check_box(&ic, bx) ) {
+ if ( check_box(&ic, bx, &saturated) ) {
delete_box(&ic, bx);
continue;
}
+ if ( saturated ) {
+ n_saturated++;
+ if ( !(meth & INTEGRATION_SATURATED) ) {
+ delete_box(&ic, bx);
+ continue;
+ }
+ }
+
get_indices(refl, &h, &k, &l);
if ( (h==-24) && (k==6) && (l==-12) ) {
bx->verbose = 1;
@@ -1034,10 +1049,13 @@ static void measure_all_intensities(RefList *list, struct image *image,
set_redundancy(bx->refl, 1);
}
}
+
+ image->num_saturated_peaks = n_saturated;
}
-static void estimate_mosaicity(Crystal *cr, struct image *image)
+static void estimate_mosaicity(IntegrationMethod meth, Crystal *cr,
+ struct image *image)
{
int msteps = 50;
int i;
@@ -1050,7 +1068,7 @@ static void estimate_mosaicity(Crystal *cr, struct image *image)
crystal_set_mosaicity(cr, mmax);
list = find_intersections(image, cr);
crystal_set_reflections(cr, list);
- measure_all_intensities(list, image, crystal_get_cell(cr));
+ measure_all_intensities(meth, list, image, crystal_get_cell(cr));
for ( i=1; i<=msteps; i++ ) {
@@ -1208,10 +1226,9 @@ static void estimate_resolution(RefList *reflections, Crystal *cr,
}
-static void integrate_prof2d(Crystal *cr, struct image *image, int use_closer,
- double min_snr,
- double ir_inn, double ir_mid, double ir_out,
- int integrate_saturated)
+static void integrate_prof2d(IntegrationMethod meth, Crystal *cr,
+ struct image *image, double min_snr,
+ double ir_inn, double ir_mid, double ir_out)
{
RefList *reflections;
UnitCell *cell;
@@ -1220,7 +1237,7 @@ static void integrate_prof2d(Crystal *cr, struct image *image, int use_closer,
/* Create initial list of reflections with nominal parameters */
reflections = find_intersections(image, cr);
- measure_all_intensities(reflections, image, cell);
+ measure_all_intensities(meth, reflections, image, cell);
/* Find resolution limit of pattern using this list */
//estimate_resolution(reflections, cr, image);
@@ -1244,7 +1261,7 @@ static void integrate_prof2d(Crystal *cr, struct image *image, int use_closer,
static void integrate_box(struct intcontext *ic, struct peak_box *bx,
- double *intensity, double *sigma, int *saturated)
+ double *intensity, double *sigma)
{
double pk_total;
int pk_counts;
@@ -1257,8 +1274,6 @@ static void integrate_box(struct intcontext *ic, struct peak_box *bx,
double aduph;
int p, q;
- if ( saturated != NULL ) *saturated = 0;
-
aduph = bx->p->adu_per_eV * ph_lambda_to_eV(ic->image->lambda);
/* Measure the background */
@@ -1271,10 +1286,6 @@ static void integrate_box(struct intcontext *ic, struct peak_box *bx,
double bi = boxi(ic, bx, p, q);
if ( bx->bm[p + ic->w*q] != BM_BG ) continue;
- if ( (saturated != NULL) && (bi > bx->p->max_adu) ) {
- *saturated = 1;
- }
-
bg_tot += bi;
bg_tot_sq += pow(bi, 2.0);
bg_counts++;
@@ -1296,10 +1307,6 @@ static void integrate_box(struct intcontext *ic, struct peak_box *bx,
double bi = boxi(ic, bx, p, q);
if ( bx->bm[p + ic->w*q] != BM_PK ) continue;
- if ( (saturated != NULL) && (bi > bx->p->max_adu) ) {
- *saturated = 1;
- }
-
pk_counts++;
pk_total += (bi - bg_mean);
fsct += (bi-bg_mean)*p;
@@ -1319,9 +1326,9 @@ static void integrate_box(struct intcontext *ic, struct peak_box *bx,
}
-static void integrate_rings(Crystal *cr, struct image *image, double min_snr,
- double ir_inn, double ir_mid, double ir_out,
- int integrate_saturated)
+static void integrate_rings(IntegrationMethod meth, Crystal *cr,
+ struct image *image, double min_snr,
+ double ir_inn, double ir_mid, double ir_out)
{
RefList *list;
Reflection *refl;
@@ -1367,7 +1374,6 @@ static void integrate_rings(Crystal *cr, struct image *image, double min_snr,
double sigma, snr;
int saturated;
double one_over_d;
- int r;
set_redundancy(refl, 0);
@@ -1392,43 +1398,39 @@ static void integrate_rings(Crystal *cr, struct image *image, double min_snr,
bx->p = p;
bx->pn = pn;
- if ( check_box(&ic, bx) ) {
+ if ( check_box(&ic, bx, &saturated) ) {
delete_box(&ic, bx);
continue;
}
+ if ( saturated ) {
+ n_saturated++;
+ if ( !(meth & INTEGRATION_SATURATED) ) {
+ delete_box(&ic, bx);
+ continue;
+ }
+ }
+
get_indices(refl, &h, &k, &l);
-// if ( (h==-1) && (k==14) && (l==13) ) {
-// bx->verbose = 1;
-// }
+ if ( (h==0) && (k==13) && (l==13) ) {
+ bx->verbose = 1;
+ }
if ( bx->verbose ) show_peak_box(&ic, bx);
- integrate_box(&ic, bx, &intensity, &sigma, &saturated);
-
- r = 0;
- if ( saturated ) {
- n_saturated++;
- if ( !integrate_saturated ) r = 1;
- }
+ integrate_box(&ic, bx, &intensity, &sigma);
/* 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;
- if ( !r && (isnan(snr) || (snr < min_snr)) ) {
- r = 1;
- }
+ if ( (isnan(snr) || (snr < min_snr)) ) continue;
/* Record intensity and set redundancy to 1 on success */
- if ( !r ) {
- set_intensity(refl, intensity);
- set_esd_intensity(refl, sigma);
- set_redundancy(refl, 1);
- } else {
- set_redundancy(refl, 0);
- }
+ set_intensity(refl, intensity);
+ set_esd_intensity(refl, sigma);
+ set_redundancy(refl, 1);
one_over_d = resolution(cell, h, k, l);
if ( one_over_d > limit ) limit = one_over_d;
@@ -1456,15 +1458,13 @@ void integrate_all(struct image *image, IntegrationMethod meth,
return;
case INTEGRATION_RINGS :
- integrate_rings(image->crystals[i], image, min_snr,
- ir_inn, ir_mid, ir_out,
- integrate_saturated);
+ integrate_rings(meth, image->crystals[i], image,
+ min_snr, ir_inn, ir_mid, ir_out);
return;
case INTEGRATION_PROF2D :
- integrate_prof2d(image->crystals[i], image, use_closer,
- min_snr, ir_inn, ir_mid, ir_out,
- integrate_saturated);
+ integrate_prof2d(meth, image->crystals[i], image,
+ min_snr, ir_inn, ir_mid, ir_out);
return;
default :
@@ -1497,6 +1497,9 @@ IntegrationMethod integration_method(const char *str, int *err)
} else if ( strcmp(methods[i], "none") == 0) {
return INTEGRATION_NONE;
+ } else if ( strcmp(methods[i], "sat") == 0) {
+ meth |= INTEGRATION_SATURATED;
+
} else {
ERROR("Bad integration method: '%s'\n", str);
if ( err != NULL ) *err = 1;
diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h
index 36f1d5bd..fe939e21 100644
--- a/libcrystfel/src/integration.h
+++ b/libcrystfel/src/integration.h
@@ -33,8 +33,8 @@
#include <config.h>
#endif
-#define INTEGRATION_DEFAULTS_RINGS (INTEGRATION_RINGS | INTEGRATION_SATURATED)
-#define INTEGRATION_DEFAULTS_PROF2D (INTEGRATION_PROF2D | INTEGRATION_SATURATED)
+#define INTEGRATION_DEFAULTS_RINGS (INTEGRATION_RINGS)
+#define INTEGRATION_DEFAULTS_PROF2D (INTEGRATION_PROF2D)
/**
* IntegrationMethod:
@@ -56,8 +56,7 @@ typedef enum {
/* Bits at the top of the IntegrationMethod are flags which modify the
* behaviour of the integration. */
- INTEGRATION_SATURATED = 256,
- INTEGRATION_CLOSER = 512,
+ INTEGRATION_SATURATED = 256
} IntegrationMethod;
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-29 09:17:51 +0000