diff options
| -rw-r--r-- | libcrystfel/src/peaks.c | 5 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.h | 3 | ||||
| -rw-r--r-- | src/indexamajig.c | 12 |
3 files changed, 17 insertions, 3 deletions
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index 0d72e514..34e0b8ca 100644 --- a/libcrystfel/src/peaks.c +++ b/libcrystfel/src/peaks.c @@ -564,7 +564,7 @@ int peak_sanity_check(struct image *image) /* Integrate the list of predicted reflections in "image" */ void integrate_reflections(struct image *image, int polar, int use_closer, - int bgsub) + int bgsub, double min_snr) { Reflection *refl; RefListIterator *iter; @@ -606,6 +606,9 @@ void integrate_reflections(struct image *image, int polar, int use_closer, &intensity, &bg, &max, &sigma, polar, 0, bgsub); + /* I/sigma(I) cutoff */ + if ( intensity/sigma < min_snr ) r = 0; + /* Record intensity and set redundancy to 1 on success */ if ( r == 0 ) { set_int(refl, intensity); diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h index 88dab26d..d52c75e4 100644 --- a/libcrystfel/src/peaks.h +++ b/libcrystfel/src/peaks.h @@ -25,7 +25,8 @@ extern void search_peaks(struct image *image, float threshold, float min_gradient, float min_snr); extern void integrate_reflections(struct image *image, - int polar, int use_closer, int bgsub); + int polar, int use_closer, int bgsub, + double min_snr); extern int peak_sanity_check(struct image * image); diff --git a/src/indexamajig.c b/src/indexamajig.c index 361d0514..293ebe58 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -69,6 +69,7 @@ struct static_index_args float threshold; float min_gradient; float min_snr; + double min_int_snr; struct detector *det; IndexingMethod *indm; IndexingPrivate **ipriv; @@ -185,6 +186,8 @@ static void show_help(const char *s) " Default: 100,000.\n" " --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n" " Default: 5.\n" +" --min-integration-snr=<n> Minimum signal-to-noise ratio for peaks\n" +" during integration. Default: -infinity.\n" " -e, --image=<element> Use this image from the HDF5 file.\n" " Example: /data/data0.\n" " Default: The first one found.\n" @@ -363,7 +366,8 @@ static void process_image(void *pp, int cookie) integrate_reflections(&image, config_polar, pargs->static_args.config_closer, - pargs->static_args.config_bgsub); + pargs->static_args.config_bgsub, + pargs->static_args.min_int_snr); estimate_resolution(image.reflections, image.indexed_cell, &min, &max); @@ -544,6 +548,7 @@ int main(int argc, char *argv[]) float threshold = 800.0; float min_gradient = 100000.0; float min_snr = 5.0; + double min_int_snr = -INFINITY; struct detector *det; char *geometry = NULL; IndexingMethod *indm; @@ -602,6 +607,7 @@ int main(int argc, char *argv[]) {"threshold", 1, NULL, 't'}, {"min-gradient", 1, NULL, 4}, {"min-snr", 1, NULL, 11}, + {"min-integration-snr",1, NULL, 12}, {"no-check-prefix", 0, &config_checkprefix, 0}, {"no-closer-peak", 0, &config_closer, 0}, {"insane", 0, &config_insane, 1}, @@ -684,6 +690,10 @@ int main(int argc, char *argv[]) min_snr = strtof(optarg, NULL); break; + case 12 : + min_int_snr = strtof(optarg, NULL); + break; + case 'e' : element = strdup(optarg); break; |