diff options
Diffstat (limited to 'libcrystfel/src')
| -rw-r--r-- | libcrystfel/src/image.h | 2 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.c | 19 | ||||
| -rw-r--r-- | libcrystfel/src/stream.c | 8 |
3 files changed, 24 insertions, 5 deletions
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index ac011d14..afa9e4a7 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -104,6 +104,7 @@ typedef struct _imagefeaturelist ImageFeatureList; * int height; * * RefList *reflections; + * long long unsigned int n_saturated; * * ImageFeatureList *features; * }; @@ -169,6 +170,7 @@ struct image { /* Integrated (or about-to-be-integrated) reflections */ RefList *reflections; + long long int n_saturated; /* Number of overloads */ /* Detected peaks */ ImageFeatureList *features; diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index 4ae4bb30..f5fa6c70 100644 --- a/libcrystfel/src/peaks.c +++ b/libcrystfel/src/peaks.c @@ -216,7 +216,7 @@ static int integrate_peak(struct image *image, int cfs, int css, double *pfs, double *pss, double *intensity, double *sigma, double ir_inn, double ir_mid, double ir_out, - int use_max_adu, int *bgPkMask) + int use_max_adu, int *bgPkMask, int *saturated) { signed int dfs, dss; double lim_sq, out_lim_sq, mid_lim_sq; @@ -292,7 +292,10 @@ static int integrate_peak(struct image *image, int cfs, int css, val = image->data[idx]; /* Veto peak if it contains saturation in bg region */ - if ( use_max_adu && (val > p->max_adu) ) return 1; + if ( use_max_adu && (val > p->max_adu) ) { + if ( saturated != NULL ) *saturated = 1; + return 1; + } bg_tot += val; bg_tot_sq += pow(val, 2.0); @@ -347,7 +350,10 @@ static int integrate_peak(struct image *image, int cfs, int css, val = image->data[idx] - bg_mean; /* Veto peak if it contains saturation */ - if ( use_max_adu && (image->data[idx] > p->max_adu) ) return 1; + if ( use_max_adu && (val > p->max_adu) ) { + if ( saturated != NULL ) *saturated = 1; + return 1; + } pk_counts++; pk_total += val; @@ -481,7 +487,7 @@ 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); + ir_inn, ir_mid, ir_out, 0, NULL, NULL); if ( r ) { /* Bad region - don't detect peak */ @@ -730,6 +736,7 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub, signed int h, k, l; struct panel *p; int pnum, j, found; + int saturated; refl = il[i].refl; @@ -781,7 +788,9 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub, r = integrate_peak(image, pfs, pss, &fs, &ss, &intensity, &sigma, ir_inn, ir_mid, ir_out, - 1, bgMasks[pnum]); + 1, bgMasks[pnum], &saturated); + + if ( saturated ) image->n_saturated++; /* I/sigma(I) cutoff */ if ( intensity/sigma < min_snr ) r = 1; diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c index 6627e7ea..b8ff9238 100644 --- a/libcrystfel/src/stream.c +++ b/libcrystfel/src/stream.c @@ -261,6 +261,9 @@ void write_chunk(FILE *ofh, struct image *i, struct hdfile *hdfile, int f) i->diffracting_resolution/1e9, 1e9 / i->diffracting_resolution); + fprintf(ofh, "num_saturated_reflections" + " = %lli\n", i->n_saturated); + } if ( i->det != NULL ) { @@ -343,6 +346,7 @@ int read_chunk(FILE *fh, struct image *image) image->features = NULL; image->reflections = NULL; image->indexed_cell = NULL; + image->n_saturated = 0; do { @@ -417,6 +421,10 @@ int read_chunk(FILE *fh, struct image *image) have_ev = 1; } + if ( strncmp(line, "num_saturated_reflections = ", 28) == 0 ) { + image->n_saturated = atoi(line+28); + } + if ( strcmp(line, PEAK_LIST_START_MARKER) == 0 ) { if ( read_peaks(fh, image) ) { ERROR("Failed while reading peaks\n"); |