diff options
| -rw-r--r-- | libcrystfel/src/peaks.c | 14 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.h | 3 | ||||
| -rw-r--r-- | src/im-sandbox.c | 3 | ||||
| -rw-r--r-- | src/im-sandbox.h | 1 | ||||
| -rw-r--r-- | src/indexamajig.c | 5 |
5 files changed, 18 insertions, 8 deletions
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index bf6a92f0..f13c7245 100644 --- a/libcrystfel/src/peaks.c +++ b/libcrystfel/src/peaks.c @@ -293,10 +293,9 @@ static int integrate_peak(struct image *image, int cfs, int css, val = image->data[idx]; - /* Veto peak if it contains saturation in bg region */ + /* Check if peak contains saturation in bg region */ if ( use_max_adu && (val > p->max_adu) ) { if ( saturated != NULL ) *saturated = 1; - return 1; } bg_tot += val; @@ -353,10 +352,9 @@ static int integrate_peak(struct image *image, int cfs, int css, val = image->data[idx] - bg_mean; - /* Veto peak if it contains saturation */ + /* Check if peak contains saturation */ if ( use_max_adu && (val > p->max_adu) ) { if ( saturated != NULL ) *saturated = 1; - return 1; } pk_counts++; @@ -697,7 +695,8 @@ static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell, /* Integrate the list of predicted reflections in "image" */ void integrate_reflections(struct image *image, int use_closer, int bgsub, double min_snr, - double ir_inn, double ir_mid, double ir_out) + double ir_inn, double ir_mid, double ir_out, + int integrate_saturated) { struct integr_ind *il; int n, i; @@ -794,7 +793,10 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub, &intensity, &sigma, ir_inn, ir_mid, ir_out, 1, bgMasks[pnum], &saturated); - if ( saturated ) image->n_saturated++; + if ( saturated ) { + image->n_saturated++; + if ( !integrate_saturated ) r = 1; + } /* I/sigma(I) cutoff */ if ( intensity/sigma < min_snr ) r = 1; diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h index 39fdf54c..ec76fd3b 100644 --- a/libcrystfel/src/peaks.h +++ b/libcrystfel/src/peaks.h @@ -43,7 +43,8 @@ extern void search_peaks(struct image *image, float threshold, extern void integrate_reflections(struct image *image, int use_closer, int bgsub, double min_snr, - double ir_inn, double ir_mid, double ir_out); + double ir_inn, double ir_mid, double ir_out, + int integrate_saturated); extern double peak_lattice_agreement(struct image *image, UnitCell *cell, double *pst); diff --git a/src/im-sandbox.c b/src/im-sandbox.c index 70839f21..80bb78e0 100644 --- a/src/im-sandbox.c +++ b/src/im-sandbox.c @@ -328,7 +328,8 @@ static void process_image(const struct index_args *iargs, iargs->min_int_snr, iargs->ir_inn, iargs->ir_mid, - iargs->ir_out); + iargs->ir_out, + iargs->integrate_saturated); } } else { image.reflections = NULL; diff --git a/src/im-sandbox.h b/src/im-sandbox.h index 8ad9fd90..9f23f88b 100644 --- a/src/im-sandbox.h +++ b/src/im-sandbox.h @@ -66,6 +66,7 @@ struct index_args double ir_mid; double ir_out; struct copy_hdf5_field *copyme; + int integrate_saturated; }; diff --git a/src/indexamajig.c b/src/indexamajig.c index f628eb29..2e5c8904 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -161,6 +161,8 @@ static void show_help(const char *s) " least 10%% of the located peaks.\n" " --no-bg-sub Don't subtract local background estimates from\n" " integrated intensities.\n" +" --integrate-saturated During the final integration stage, don't reject\n" +" peaks which contain pixels above max_adu.\n" ); } @@ -242,6 +244,7 @@ int main(int argc, char *argv[]) float ir_inn = 4.0; float ir_mid = 5.0; float ir_out = 7.0; + int integrate_saturated = 0; copyme = new_copy_hdf5_field_list(); if ( copyme == NULL ) { @@ -288,6 +291,7 @@ int main(int argc, char *argv[]) {"min-integration-snr",1, NULL, 12}, {"tolerance", 1, NULL, 13}, {"int-radius", 1, NULL, 14}, + {"integrate-saturated",0, &integrate_saturated,1}, {0, 0, NULL, 0} }; @@ -634,6 +638,7 @@ int main(int argc, char *argv[]) iargs.ir_inn = ir_inn; iargs.ir_mid = ir_mid; iargs.ir_out = ir_out; + iargs.integrate_saturated = integrate_saturated; create_sandbox(&iargs, n_proc, prefix, config_basename, fh, use_this_one_instead, ofh); |