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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"
#include "parameters.tmp"
void write_reflections(const char *filename, ReflItemList *items,
double *intensities, 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 ( intensity > 0.0 ) {
sigma = DETECTOR_GAIN * sqrt(intensity/DETECTOR_GAIN);
} 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);
}
STATUS("Warning: Errors have been estimated from Poisson distribution"
" assuming %5.2f ADU per photon.\n", DETECTOR_GAIN);
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;
}
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