diff options
| -rw-r--r-- | src/indexamajig.c | 11 | ||||
| -rw-r--r-- | src/pattern_sim.c | 2 | ||||
| -rw-r--r-- | src/peaks.c | 15 | ||||
| -rw-r--r-- | src/peaks.h | 9 |
4 files changed, 25 insertions, 12 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index b7ec6345..eef9a381 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -65,6 +65,7 @@ struct static_index_args int config_satcorr; int config_closer; int config_insane; + int config_bgsub; float threshold; float min_gradient; struct detector *det; @@ -179,6 +180,8 @@ static void show_help(const char *s) " --unpolarized Don't correct for the polarisation of the X-rays.\n" " --no-sat-corr Don't correct values of saturated peaks using a\n" " table included in the HDF5 file.\n" +" --bg-sub Subtract local background estimates from\n" +" integrated intensities.\n" " --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" @@ -333,7 +336,8 @@ static void process_image(void *pp, int cookie) 0, 0.1); integrate_reflections(&image, config_polar, - pargs->static_args.config_closer); + pargs->static_args.config_closer, + pargs->static_args.config_bgsub); /* OR */ @@ -505,6 +509,7 @@ int main(int argc, char *argv[]) int config_checkprefix = 1; int config_closer = 1; int config_insane = 0; + int config_bgsub = 0; int config_basename = 0; float threshold = 800.0; float min_gradient = 100000.0; @@ -565,7 +570,8 @@ int main(int argc, char *argv[]) {"record", 1, NULL, 5}, {"cpus", 1, NULL, 6}, {"cpugroup", 1, NULL, 7}, - {"cpuoffset", 1, NULL, 8}, + {"cpuoffset", 1, NULL, 8}, + {"bg-sub", 1, &config_bgsub, 0}, {0, 0, NULL, 0} }; @@ -872,6 +878,7 @@ int main(int argc, char *argv[]) qargs.static_args.config_satcorr = config_satcorr; qargs.static_args.config_closer = config_closer; qargs.static_args.config_insane = config_insane; + qargs.static_args.config_bgsub = config_bgsub; qargs.static_args.cellr = cellr; qargs.static_args.threshold = threshold; qargs.static_args.min_gradient = min_gradient; diff --git a/src/pattern_sim.c b/src/pattern_sim.c index ba760e32..f1fbce7e 100644 --- a/src/pattern_sim.c +++ b/src/pattern_sim.c @@ -558,7 +558,7 @@ int main(int argc, char *argv[]) image.reflections = find_projected_peaks(&image, image.indexed_cell, 0, 0.1); - integrate_reflections(&image, 0, 0); + integrate_reflections(&image, 0, 0, 0); /* OR */ diff --git a/src/peaks.c b/src/peaks.c index b838b810..4b87ba08 100644 --- a/src/peaks.c +++ b/src/peaks.c @@ -144,7 +144,7 @@ static int cull_peaks(struct image *image) int integrate_peak(struct image *image, int cfs, int css, double *pfs, double *pss, double *intensity, double *pbg, double *pmax, double *sigma, - int do_polar, int centroid) + int do_polar, int centroid, int bgsub) { signed int fs, ss; double lim, out_lim; @@ -246,11 +246,14 @@ int integrate_peak(struct image *image, int cfs, int css, if ( centroid && (total != 0) ) { *pfs = (double)fsct / total; *pss = (double)ssct / total; - *intensity = total - pixel_counts*noise_mean; } else { *pfs = (double)cfs; *pss = (double)css; + } + if ( bgsub ) { *intensity = total - pixel_counts*noise_mean; + } else { + *intensity = total; } if ( in_bad_region(image->det, *pfs, *pss) ) return 1; @@ -380,7 +383,7 @@ static void search_peaks_in_panel(struct image *image, float threshold, * intensity of this peak is only an estimate at this stage. */ r = integrate_peak(image, mask_fs, mask_ss, &f_fs, &f_ss, &intensity, - NULL, NULL, NULL, 0, 1); + NULL, NULL, NULL, 0, 1, 0); if ( r ) { /* Bad region - don't detect peak */ nrej_bad++; @@ -592,7 +595,8 @@ int peak_sanity_check(struct image *image, UnitCell *cell, /* Integrate the list of predicted reflections in "image" */ -void integrate_reflections(struct image *image, int polar, int use_closer) +void integrate_reflections(struct image *image, int polar, int use_closer, + int bgsub) { Reflection *refl; RefListIterator *iter; @@ -635,7 +639,8 @@ void integrate_reflections(struct image *image, int polar, int use_closer) } r = integrate_peak(image, pfs, pss, &fs, &ss, - &intensity, &bg, &max, &sigma, polar, 0); + &intensity, &bg, &max, &sigma, polar, 0, + bgsub); /* Record intensity and set redundancy to 1 on success */ if ( r == 0 ) { diff --git a/src/peaks.h b/src/peaks.h index 2faa2b5e..ec473fd1 100644 --- a/src/peaks.h +++ b/src/peaks.h @@ -25,7 +25,7 @@ extern void search_peaks(struct image *image, float threshold, float min_gradient); extern void integrate_reflections(struct image *image, - int polar, int use_closer); + int polar, int use_closer, int bgsub); extern int peak_sanity_check(struct image *image, UnitCell *cell, int circular_domain, double domain_r); @@ -33,9 +33,10 @@ extern int peak_sanity_check(struct image *image, UnitCell *cell, extern RefList *find_projected_peaks(struct image *image, UnitCell *cell, int circular_domain, double domain_r); -extern int integrate_peak(struct image *image, int xp, int yp, - double *xc, double *yc, double *intensity, +/* Exported so it can be poked by integration_check */ +extern int integrate_peak(struct image *image, int cfs, int css, + double *pfs, double *pss, double *intensity, double *pbg, double *pmax, double *sigma, - int do_polar, int centroid); + int do_polar, int centroid, int bgsub); #endif /* PEAKS_H */ |