diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/indexamajig.c | 13 | ||||
| -rw-r--r-- | src/peaks.c | 17 | ||||
| -rw-r--r-- | src/peaks.h | 2 | ||||
| -rw-r--r-- | src/sum_stack.c | 17 |
4 files changed, 37 insertions, 12 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 79bf69e6..26ea158d 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -68,6 +68,7 @@ struct static_index_args int config_bgsub; float threshold; float min_gradient; + float min_snr; struct detector *det; IndexingMethod *indm; IndexingPrivate **ipriv; @@ -182,6 +183,8 @@ static void show_help(const char *s) " --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\n" " --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n" " Default: 100,000.\n" +" --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n" +" Default: 5.\n" " -e, --image=<element> Use this image from the HDF5 file.\n" " Example: /data/data0.\n" " Default: The first one found.\n" @@ -310,7 +313,8 @@ static void process_image(void *pp, int cookie) break; case PEAK_ZAEF : search_peaks(&image, pargs->static_args.threshold, - pargs->static_args.min_gradient); + pargs->static_args.min_gradient, + pargs->static_args.min_snr); break; } @@ -506,6 +510,7 @@ int main(int argc, char *argv[]) int config_basename = 0; float threshold = 800.0; float min_gradient = 100000.0; + float min_snr = 5; struct detector *det; char *geometry = NULL; IndexingMethod *indm; @@ -563,6 +568,7 @@ int main(int argc, char *argv[]) {"sat-corr", 0, &config_satcorr, 1}, /* Compat */ {"threshold", 1, NULL, 't'}, {"min-gradient", 1, NULL, 4}, + {"min-snr", 1, NULL, 11}, {"no-check-prefix", 0, &config_checkprefix, 0}, {"no-closer-peak", 0, &config_closer, 0}, {"insane", 0, &config_insane, 1}, @@ -641,6 +647,10 @@ int main(int argc, char *argv[]) min_gradient = strtof(optarg, NULL); break; + case 11 : + min_snr = strtof(optarg, NULL); + break; + case 'e' : element = strdup(optarg); break; @@ -899,6 +909,7 @@ int main(int argc, char *argv[]) qargs.static_args.cellr = cellr; qargs.static_args.threshold = threshold; qargs.static_args.min_gradient = min_gradient; + qargs.static_args.min_snr = min_snr; qargs.static_args.det = det; qargs.static_args.indm = indm; qargs.static_args.ipriv = ipriv; diff --git a/src/peaks.c b/src/peaks.c index fd1b0983..92556ea6 100644 --- a/src/peaks.c +++ b/src/peaks.c @@ -281,7 +281,8 @@ int integrate_peak(struct image *image, int cfs, int css, static void search_peaks_in_panel(struct image *image, float threshold, - float min_gradient, struct panel *p) + float min_gradient, float min_snr, + struct panel *p) { int fs, ss, stride; float *data; @@ -297,6 +298,7 @@ static void search_peaks_in_panel(struct image *image, float threshold, int nrej_pro = 0; int nrej_fra = 0; int nrej_bad = 0; + int nrej_snr = 0; int nacc = 0; int ncull; const int pws = p->peak_sep/2; @@ -404,8 +406,8 @@ static void search_peaks_in_panel(struct image *image, float threshold, continue; } - if (intensity/sigma < 5) { - //printf("SNR: %g\n",intensity/sigma); + if (intensity/sigma < min_snr) { + nrej_snr++; continue; } @@ -434,12 +436,13 @@ static void search_peaks_in_panel(struct image *image, float threshold, } // STATUS("%i accepted, %i box, %i proximity, %i outside panel, " -// "%i in bad regions, %i badrow culled.\n", -// nacc, nrej_dis, nrej_pro, nrej_fra, nrej_bad, ncull); +// "%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); } -void search_peaks(struct image *image, float threshold, float min_gradient) +void search_peaks(struct image *image, float threshold, float min_gradient, + float min_snr) { int i; @@ -453,7 +456,7 @@ void search_peaks(struct image *image, float threshold, float min_gradient) struct panel *p = &image->det->panels[i]; if ( p->no_index ) continue; - search_peaks_in_panel(image, threshold, min_gradient, p); + search_peaks_in_panel(image, threshold, min_gradient, min_snr, p); } } diff --git a/src/peaks.h b/src/peaks.h index 07c257e6..7b66b9ac 100644 --- a/src/peaks.h +++ b/src/peaks.h @@ -22,7 +22,7 @@ #include "reflist.h" extern void search_peaks(struct image *image, float threshold, - float min_gradient); + float min_gradient, float min_snr); extern void integrate_reflections(struct image *image, int polar, int use_closer, int bgsub); diff --git a/src/sum_stack.c b/src/sum_stack.c index 2e5b138e..a6e7599a 100644 --- a/src/sum_stack.c +++ b/src/sum_stack.c @@ -49,6 +49,7 @@ struct sum_args SumMethod sum_method; double threshold; double min_gradient; + double min_snr; char *element; }; @@ -64,6 +65,7 @@ struct queue_args SumMethod sum_method; double threshold; double min_gradient; + double min_snr; char *element; char *use_this_one_instead; @@ -100,6 +102,8 @@ static void show_help(const char *s) " method. Default: 400 adu\n" " --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n" " Default: 100,000.\n" +" --min-snr=<n> Minimum signal-to-noise ration for peaks.\n" +" Default: 5.\n" " -e, --image=<element> Use this image from the HDF5 file.\n" " Example: /data/data0.\n" " Default: The first one found.\n" @@ -116,14 +120,14 @@ static void show_help(const char *s) static void sum_peaks(struct image *image, double *sum, double threshold, - double min_gradient) + double min_gradient, double min_snr) { int i; int w = image->width; int h = image->height; const int lim = INTEGRATION_RADIUS * INTEGRATION_RADIUS; - search_peaks(image, threshold, min_gradient); + search_peaks(image, threshold, min_gradient, min_snr); for ( i=0; i<image_feature_count(image->features); i++ ) { @@ -231,7 +235,7 @@ static void add_image(void *args, int cookie) case SUM_PEAKS : sum_peaks(&image, pargs->sum, pargs->threshold, - pargs->min_gradient); + pargs->min_gradient, pargs->min_snr); break; } @@ -261,6 +265,7 @@ static void *get_image(void *qp) pargs->sum_method = qargs->sum_method; pargs->threshold = qargs->threshold; pargs->min_gradient = qargs->min_gradient; + pargs->min_snr = qargs->min_snr; pargs->config_cmfilter = qargs->config_cmfilter; pargs->config_noisefilter = qargs->config_noisefilter; pargs->sum = qargs->sum; @@ -312,6 +317,7 @@ int main(int argc, char *argv[]) char *intermediate = NULL; double threshold = 400.0; float min_gradient = 100000.0; + float min_snr = 5; SumMethod sum; int nthreads = 1; struct queue_args qargs; @@ -337,6 +343,7 @@ int main(int argc, char *argv[]) {"intermediate", 1, NULL, 'p'}, {"threshold", 1, NULL, 't'}, {"min-gradient", 1, NULL, 4}, + {"min-snr", 1, NULL, 11}, {"basename", 0, &config_basename, 1}, {"image", 1, NULL, 'e'}, {0, 0, NULL, 0} @@ -387,6 +394,10 @@ int main(int argc, char *argv[]) min_gradient = strtof(optarg, NULL); break; + case 11 : + min_snr = strtof(optarg, NULL); + break; + case 0 : break; |