diff options
Diffstat (limited to 'src/reflections.c')
| -rw-r--r-- | src/reflections.c | 230 |
1 files changed, 0 insertions, 230 deletions
diff --git a/src/reflections.c b/src/reflections.c deleted file mode 100644 index 4743aeee..00000000 --- a/src/reflections.c +++ /dev/null @@ -1,230 +0,0 @@ -/* - * reflections.c - * - * Utilities for handling reflections - * - * (c) 2006-2010 Thomas White <taw@physics.org> - * - * Part of CrystFEL - crystallography with a FEL - * - */ - - -#include <stdlib.h> -#include <math.h> -#include <stdio.h> -#include <complex.h> -#include <string.h> - -#include "utils.h" -#include "cell.h" -#include "reflections.h" -#include "beam-parameters.h" - - -double *poisson_esds(double *intensities, ReflItemList *items, - double adu_per_photon) -{ - int i; - double *esds = new_list_sigma(); - - for ( i=0; i<num_items(items); i++ ) { - - struct refl_item *it; - signed int h, k, l; - double intensity, sigma; - - it = get_item(items, i); - h = it->h; k = it->k; l = it->l; - - intensity = lookup_intensity(intensities, h, k, l); - - if ( intensity > 0.0 ) { - sigma = adu_per_photon * sqrt(intensity/adu_per_photon); - } else { - sigma = 0.0; - } - - set_sigma(esds, h, k, l, sigma); - - } - - return esds; -} - - -void write_reflections(const char *filename, ReflItemList *items, - double *intensities, double *esds, double *phases, - unsigned int *counts, UnitCell *cell) -{ - FILE *fh; - int i; - - if ( filename == NULL ) { - fh = stdout; - } else { - fh = fopen(filename, "w"); - } - - if ( fh == NULL ) { - ERROR("Couldn't open output file '%s'.\n", filename); - return; - } - - /* Write spacings and angle if zone axis pattern */ - fprintf(fh, " h k l I phase sigma(I) " - " 1/d(nm^-1) counts\n"); - - for ( i=0; i<num_items(items); i++ ) { - - struct refl_item *it; - signed int h, k, l; - - it = get_item(items, i); - h = it->h; k = it->k; l = it->l; - - int N; - double intensity, s, sigma; - char ph[32]; - - if ( counts != NULL ) { - N = lookup_count(counts, h, k, l); - } else { - N = 1; - } - - intensity = lookup_intensity(intensities, h, k, l); - - if ( phases != NULL ) { - double p; - p = lookup_phase(phases, h, k, l); - snprintf(ph, 31, "%8.6f", p); - } else { - strncpy(ph, " -", 31); - } - - if ( cell != NULL ) { - s = 2.0*resolution(cell, h, k, l); - } else { - s = 0.0; - } - - if ( esds != NULL ) { - sigma = lookup_sigma(esds, h, k, l); - } else { - sigma = 0.0; - } - - /* h, k, l, I, sigma(I), s */ - fprintf(fh, "%3i %3i %3i %10.2f %s %10.2f %10.2f %7i\n", - h, k, l, intensity, ph, sigma, s/1.0e9, N); - - } - fclose(fh); -} - - -/* Read reflections from file. Returns the list of reflections successfully - * read in. "intensities", "phases" and "counts" are lists which will be - * populated with the values read from the file. Existing values in either list - * will be overwritten if the reflection is read from the file, but other values - * will be left intact. - * - * "intensities", "phases" or "counts" can be NULL, if you don't need them. - */ -ReflItemList *read_reflections(const char *filename, - double *intensities, double *phases, - unsigned int *counts, double *esds) -{ - FILE *fh; - char *rval; - ReflItemList *items; - - fh = fopen(filename, "r"); - if ( fh == NULL ) { - ERROR("Failed to open input file '%s'\n", filename); - return NULL; - } - - items = new_items(); - - do { - - char line[1024]; - signed int h, k, l; - float intensity, ph, res, sigma; - char phs[1024]; - int r; - int cts; - - rval = fgets(line, 1023, fh); - if ( rval == NULL ) continue; - r = sscanf(line, "%i %i %i %f %s %f %f %i", - &h, &k, &l, &intensity, phs, &sigma, &res, &cts); - if ( r >= 8 ) { - /* Woohoo */ - } else if ( r >= 7 ) { - /* No "counts", that's fine.. */ - cts = 1; - } else if ( r >= 6 ) { - /* No resolution. Didn't want it anyway. */ - res = 0.0; - } else if ( r >= 5 ) { - /* No sigma. It's OK today, but one - * day I'll get you... */ - sigma = 0.0; - } else if ( r >= 4 ) { - /* No phase. Better not need it.. */ - if ( phases != NULL ) { - ERROR("Need phases and none were specified!\n"); - abort(); - } - } else { - /* You lose. */ - continue; - } - - add_item(items, h, k, l); - - if ( intensities != NULL ) { - set_intensity(intensities, h, k, l, intensity); - } - if ( phases != NULL ) { - ph = atof(phs); - set_phase(phases, h, k, l, ph); - } - if ( counts != NULL ) { - set_count(counts, h, k, l, cts); - } - if ( esds != NULL ) { - set_sigma(esds, h, k, l, sigma); - } - - } while ( rval != NULL ); - - fclose(fh); - - return items; -} - - -double *ideal_intensities(double complex *sfac) -{ - double *ref; - signed int h, k, l; - - ref = new_list_intensity(); - - /* Generate ideal reflections from complex structure factors */ - for ( h=-INDMAX; h<=INDMAX; h++ ) { - for ( k=-INDMAX; k<=INDMAX; k++ ) { - for ( l=-INDMAX; l<=INDMAX; l++ ) { - double complex F = lookup_sfac(sfac, h, k, l); - double intensity = pow(cabs(F), 2.0); - set_intensity(ref, h, k, l, intensity); - } - } - } - - return ref; -} |