diff options
Diffstat (limited to 'libcrystfel/src/peaks.c')
| -rw-r--r-- | libcrystfel/src/peaks.c | 45 |
1 files changed, 31 insertions, 14 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; } |