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authorThomas White <taw@physics.org>2012-11-28 17:41:46 +0100
committerThomas White <taw@physics.org>2012-11-29 12:01:34 +0100
commitfcba20a4c51793701c5946cca8fc264aa2e72450 (patch)
treefb87187f6b6686c7b2d2506f4d819376b7b0f250 /libcrystfel
parentf322397ceee6a12518c193fafd73487b7b19b875 (diff)
indexamajig: Add --use-saturated
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/peaks.c45
-rw-r--r--libcrystfel/src/peaks.h6
2 files changed, 35 insertions, 16 deletions
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 7ab194c7..6bf956e2 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -385,7 +385,8 @@ static int integrate_peak(struct image *image, int cfs, int css,
static void search_peaks_in_panel(struct image *image, float threshold,
float min_gradient, float min_snr,
struct panel *p,
- double ir_inn, double ir_mid, double ir_out)
+ double ir_inn, double ir_mid, double ir_out,
+ int use_saturated)
{
int fs, ss, stride;
float *data;
@@ -400,6 +401,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
int nrej_fra = 0;
int nrej_bad = 0;
int nrej_snr = 0;
+ int nrej_sat = 0;
int nacc = 0;
int ncull;
@@ -417,6 +419,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
double max;
unsigned int did_something;
int r;
+ int saturated;
/* Overall threshold */
if ( data[fs+stride*ss] < threshold ) continue;
@@ -489,7 +492,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
/* Centroid peak and get better coordinates. */
r = integrate_peak(image, mask_fs, mask_ss,
&f_fs, &f_ss, &intensity, &sigma,
- ir_inn, ir_mid, ir_out, 0, NULL, NULL);
+ ir_inn, ir_mid, ir_out, 0, NULL, &saturated);
if ( r ) {
/* Bad region - don't detect peak */
@@ -516,6 +519,11 @@ static void search_peaks_in_panel(struct image *image, float threshold,
continue;
}
+ if ( saturated && !use_saturated ) {
+ nrej_sat++;
+ continue;
+ }
+
/* Add using "better" coordinates */
image_add_feature(image->features, f_fs, f_ss, image, intensity,
NULL);
@@ -533,10 +541,11 @@ static void search_peaks_in_panel(struct image *image, float threshold,
ncull = 0;
}
-// STATUS("%i accepted, %i box, %i proximity, %i outside panel, "
-// "%i in bad regions, %i with SNR < %g, %i badrow culled.\n",
-// nacc, nrej_dis, nrej_pro, nrej_fra, nrej_bad,
-// nrej_snr, min_snr, ncull);
+ //STATUS("%i accepted, %i box, %i proximity, %i outside panel, "
+ // "%i in bad regions, %i with SNR < %g, %i badrow culled, "
+ // "%i saturated.\n",
+ // nacc, nrej_dis, nrej_pro, nrej_fra, nrej_bad,
+ // nrej_snr, min_snr, ncull, nrej_sat);
if ( ncull != 0 ) {
STATUS("WARNING: %i peaks were badrow culled. This feature"
@@ -547,7 +556,8 @@ static void search_peaks_in_panel(struct image *image, float threshold,
void search_peaks(struct image *image, float threshold, float min_gradient,
- float min_snr, double ir_inn, double ir_mid, double ir_out)
+ float min_snr, double ir_inn, double ir_mid, double ir_out,
+ int use_saturated)
{
int i;
@@ -562,7 +572,8 @@ void search_peaks(struct image *image, float threshold, float min_gradient,
if ( p->no_index ) continue;
search_peaks_in_panel(image, threshold, min_gradient,
- min_snr, p, ir_inn, ir_mid, ir_out);
+ min_snr, p, ir_inn, ir_mid, ir_out,
+ use_saturated);
}
}
@@ -838,11 +849,11 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
void validate_peaks(struct image *image, double min_snr,
- int ir_inn, int ir_mid, int ir_out)
+ int ir_inn, int ir_mid, int ir_out, int use_saturated)
{
int i, n;
ImageFeatureList *flist;
- int n_wtf, n_int, n_dft, n_snr, n_prx;
+ int n_wtf, n_int, n_dft, n_snr, n_prx, n_sat;
flist = image_feature_list_new();
if ( flist == NULL ) return;
@@ -850,7 +861,7 @@ void validate_peaks(struct image *image, double min_snr,
n = image_feature_count(image->features);
/* Loop over peaks, putting each one through the integrator */
- n_wtf = 0; n_int = 0; n_dft = 0; n_snr = 0; n_prx = 0;
+ n_wtf = 0; n_int = 0; n_dft = 0; n_snr = 0; n_prx = 0; n_sat = 0;
for ( i=0; i<n; i++ ) {
struct imagefeature *f;
@@ -860,6 +871,7 @@ void validate_peaks(struct image *image, double min_snr,
double f_fs, f_ss;
double intensity, sigma;
struct panel *p;
+ int saturated;
f = image_get_feature(image->features, i);
if ( f == NULL ) {
@@ -875,7 +887,7 @@ void validate_peaks(struct image *image, double min_snr,
r = integrate_peak(image, f->fs, f->ss,
&f_fs, &f_ss, &intensity, &sigma,
- ir_inn, ir_mid, ir_out, 0, NULL, NULL);
+ ir_inn, ir_mid, ir_out, 0, NULL, &saturated);
if ( r ) {
n_int++;
continue;
@@ -901,15 +913,20 @@ void validate_peaks(struct image *image, double min_snr,
continue;
}
+ if ( saturated && !use_saturated ) {
+ n_sat++;
+ continue;
+ }
+
/* Add using "better" coordinates */
image_add_feature(flist, f_fs, f_ss, image, intensity, NULL);
}
//STATUS("HDF5: %i peaks, validated: %i. WTF: %i, integration: %i,"
- // " drifted: %i, SNR: %i, proximity: %i\n",
+ // " drifted: %i, SNR: %i, proximity: %i, saturated: %i\n",
// n, image_feature_count(flist),
- // n_wtf, n_int, n_dft, n_snr, n_prx);
+ // n_wtf, n_int, n_dft, n_snr, n_prx, n_sat);
image_feature_list_free(image->features);
image->features = flist;
}
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index ec76fd3b..3fae13fb 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -39,7 +39,8 @@
extern void search_peaks(struct image *image, float threshold,
float min_gradient, float min_snr,
- double ir_inn, double ir_mid, double ir_out);
+ double ir_inn, double ir_mid, double ir_out,
+ int use_saturated);
extern void integrate_reflections(struct image *image,
int use_closer, int bgsub, double min_snr,
@@ -55,6 +56,7 @@ extern void estimate_resolution(RefList *list, UnitCell *cell,
double *min, double *max);
extern void validate_peaks(struct image *image, double min_snr,
- int ir_inn, int ir_mid, int ir_out);
+ int ir_inn, int ir_mid, int ir_out,
+ int use_saturated);
#endif /* PEAKS_H */