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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, double *phases, 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",
(0.5/resolution(cell, 1, 0, 0))*1e9);
fprintf(fh, "b %5.3f nm\n",
(0.5/resolution(cell, 0, 1, 0))*1e9);
fprintf(fh, "angle %5.3f deg\n", rad2deg(alpha));
fprintf(fh, "scale 10\n");
} else {
fprintf(fh, " h k l I phase sigma(I) "
" 1/d(nm^-1) counts\n");
}
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
int N;
double intensity, s;
char ph[32];
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_phase(ref, h, k, l) / N;
if ( phases != NULL ) {
double p;
p = lookup_intensity(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;
}
/* 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, 0.0, s/1.0e9, N);
}
}
}
fclose(fh);
}
double *read_reflections(const char *filename, unsigned int *counts,
double *phases)
{
double *ref;
FILE *fh;
char *rval;
fh = fopen(filename, "r");
if ( fh == NULL ) {
ERROR("Failed to open input file '%s'\n", filename);
return NULL;
}
ref = new_list_intensity();
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);
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;
}
set_intensity(ref, 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);
/* In this case, the intensity must be multiplied up
* because other parts of the program will try to
* divide it down. */
set_intensity(ref, h, k, l, intensity*(double)cts);
}
} 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;
}
void divide_down(double *intensities, unsigned int *counts)
{
int i;
for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
if ( counts[i] > 0 ) {
intensities[i] /= (double)counts[i];
counts[i] = 1;
}
}
}
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