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/*
* 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"
void write_reflections(const char *filename, unsigned int *counts,
double *ref, int zone_axis, UnitCell *cell,
unsigned int min_counts)
{
FILE *fh;
signed int h, k, l;
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 */
if ( zone_axis ) {
double a, b, c, alpha, beta, gamma;
cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma);
fprintf(fh, "a %5.3f nm\n", a*1e9);
fprintf(fh, "b %5.3f nm\n", b*1e9);
fprintf(fh, "angle %5.3f deg\n", rad2deg(gamma));
fprintf(fh, "scale 10\n");
} else {
fprintf(fh, " h k l I sigma(I) 1/d / nm^-1\n");
}
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
int N;
double intensity, s;
if ( counts ) {
N = lookup_count(counts, h, k, l);
if ( N < min_counts ) continue;
} else {
N = 1;
}
if ( zone_axis && (l != 0) ) continue;
intensity = lookup_intensity(ref, h, k, l) / N;
if ( cell != NULL ) {
s = 2.0*resolution(cell, h, k, l);
} else {
s = 0.0;
}
/* h, k, l, I, sigma(I), s */
fprintf(fh, "%3i %3i %3i %f %f %f\n", h, k, l, intensity,
0.0, s/1.0e9);
}
}
}
fclose(fh);
}
double *read_reflections(const char *filename, unsigned int *counts)
{
double *ref;
FILE *fh;
char *rval;
fh = fopen(filename, "r");
if ( fh == NULL ) {
ERROR("Failed to open input file\n");
return NULL;
}
ref = new_list_intensity();
do {
char line[1024];
signed int h, k, l;
float intensity;
int r;
rval = fgets(line, 1023, fh);
r = sscanf(line, "%i %i %i %f", &h, &k, &l, &intensity);
if ( r != 4 ) continue;
set_intensity(ref, h, k, l, intensity);
if ( counts != NULL ) set_count(counts, h, k, l, 1);
} while ( rval != NULL );
fclose(fh);
return ref;
}
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;
}
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