diff options
Diffstat (limited to 'src/check_hkl.c')
| -rw-r--r-- | src/check_hkl.c | 92 |
1 files changed, 46 insertions, 46 deletions
diff --git a/src/check_hkl.c b/src/check_hkl.c index fb6d02d5..903188a1 100644 --- a/src/check_hkl.c +++ b/src/check_hkl.c @@ -22,9 +22,10 @@ #include <getopt.h> #include "utils.h" -#include "reflections.h" #include "statistics.h" #include "symmetry.h" +#include "reflist.h" +#include "reflist-utils.h" /* Number of bins for plot of resolution shells */ @@ -46,9 +47,8 @@ static void show_help(const char *s) } -static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, - const char *sym, unsigned int *counts, - const double *sigma, double rmin_fix, double rmax_fix) +static void plot_shells(RefList *list, UnitCell *cell, const char *sym, + double rmin_fix, double rmax_fix) { double num[NBINS]; int cts[NBINS]; @@ -70,6 +70,8 @@ static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, int nmeas = 0; int nmeastot = 0; int nout = 0; + Reflection *refl; + RefListIterator *iter; if ( cell == NULL ) { ERROR("Need the unit cell to plot resolution shells.\n"); @@ -93,16 +95,17 @@ static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, mean[i] = 0; } - rmin = +INFINITY; - rmax = 0.0; - for ( i=0; i<num_items(items); i++ ) { + /* Iterate over all common reflections and calculate min and max + * resolution */ + rmin = +INFINITY; rmax = 0.0; + for ( refl = first_refl(list, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) { - struct refl_item *it; signed int h, k, l; double d; - it = get_item(items, i); - h = it->h; k = it->k; l = it->l; + get_indices(refl, &h, &k, &l); d = resolution(cell, h, k, l) * 2.0; if ( d > rmax ) rmax = d; @@ -179,16 +182,16 @@ static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, free(counted); /* Calculate means */ - for ( i=0; i<num_items(items); i++ ) { + for ( refl = first_refl(list, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) { - struct refl_item *it; signed int h, k, l; double d; int bin; int j; - it = get_item(items, i); - h = it->h; k = it->k; l = it->l; + get_indices(refl, &h, &k, &l); d = resolution(cell, h, k, l) * 2.0; @@ -205,7 +208,7 @@ static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, } measured[bin]++; - mean[bin] += lookup_intensity(ref, h, k, l); + mean[bin] += get_intensity(refl); } @@ -214,21 +217,21 @@ static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, } /* Characterise the data set */ - for ( i=0; i<num_items(items); i++ ) { + for ( refl = first_refl(list, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) { - struct refl_item *it; signed int h, k, l; double d; int bin; int j; double val, esd; - it = get_item(items, i); - h = it->h; k = it->k; l = it->l; + get_indices(refl, &h, &k, &l); d = resolution(cell, h, k, l) * 2.0; - val = lookup_intensity(ref, h, k, l); - esd = lookup_sigma(sigma, h, k, l); + val = get_intensity(refl); + esd = get_esd_intensity(refl); bin = -1; for ( j=0; j<NBINS; j++ ) { @@ -245,11 +248,11 @@ static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, if ( !isfinite(val/esd) ) continue; /* measured[bin] was done earlier */ - measurements[bin] += lookup_count(counts, h, k, l); + measurements[bin] += get_redundancy(refl); snr[bin] += val / esd; snr_total += val / esd; nmeas++; - nmeastot += lookup_count(counts, h, k, l); + nmeastot += get_redundancy(refl); var[bin] += pow(val-mean[bin], 2.0); @@ -289,17 +292,15 @@ static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell, int main(int argc, char *argv[]) { int c; - double *ref; UnitCell *cell; char *file = NULL; char *sym = NULL; - int i; - ReflItemList *items; - ReflItemList *good_items; + RefList *raw_list; + RefList *list; + Reflection *refl; + RefListIterator *iter; char *pdb = NULL; - double *esd; int rej = 0; - unsigned int *cts; float rmin_fix = -1.0; float rmax_fix = -1.0; @@ -369,37 +370,35 @@ int main(int argc, char *argv[]) cell = load_cell_from_pdb(pdb); free(pdb); - ref = new_list_intensity(); - esd = new_list_sigma(); - cts = new_list_count(); - items = read_reflections(file, ref, NULL, cts, esd); - if ( items == NULL ) { - ERROR("Couldn't open file '%s'\n", file); + raw_list = read_reflections(file); + if ( raw_list == NULL ) { + ERROR("Couldn't read file '%s'\n", file); return 1; } /* Check that the intensities have the correct symmetry */ - if ( check_symmetry(items, sym) ) { + if ( check_list_symmetry(raw_list, sym) ) { ERROR("The input reflection list does not appear to" " have symmetry %s\n", sym); return 1; } - /* Reject reflections */ - good_items = new_items(); - for ( i=0; i<num_items(items); i++ ) { + /* Reject some reflections */ + list = reflist_new(); + for ( refl = first_refl(list, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) { - struct refl_item *it; signed int h, k, l; double val, sig; int ig = 0; double d; + Reflection *new; - it = get_item(items, i); - h = it->h; k = it->k; l = it->l; + get_indices(refl, &h, &k, &l); - val = lookup_intensity(ref, h, k, l); - sig = lookup_sigma(esd, h, k, l); + val = get_intensity(refl); + sig = get_esd_intensity(refl); if ( val < 3.0 * sig ) { rej++; @@ -412,11 +411,12 @@ int main(int argc, char *argv[]) //if ( ig ) continue; - add_item(good_items, h, k, l); + new = add_refl(list, h, k, l); + copy_data(new, refl); } - plot_shells(ref, items, cell, sym, cts, esd, rmin_fix, rmax_fix); + plot_shells(list, cell, sym, rmin_fix, rmax_fix); return 0; } |