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/*
* integr_sim.c
*
* Test integration of intensities
*
* (c) 2006-2009 Thomas White <thomas.white@desy.de>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include "cell.h"
#include "image.h"
#include "utils.h"
#include "statistics.h"
#include "sfac.h"
static void main_show_help(const char *s)
{
printf("Syntax: %s\n\n", s);
printf("Test relrod integration\n\n");
printf(" -h Display this help message\n");
}
static void write_RvsQ(const char *name, double *ref, double *trueref,
unsigned int *counts, double scale, UnitCell *cell)
{
FILE *fh;
double smax, sbracket;
signed int h, k, l;
fh = fopen(name, "w");
smax = 0.0;
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double s = resolution(cell, h, k, l);
if ( (lookup_count(counts, h, k, l) > 0) && (s > smax) ) {
smax = s;
}
}
}
}
for ( sbracket=0.0; sbracket<smax; sbracket+=smax/10.0 ) {
double top = 0.0;
double bot = 0.0;
int n = 0;
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double s;
int c;
c = lookup_count(counts, h, k, l);
s = resolution(cell, h, k, l);
if ((s>=sbracket) && (s<sbracket+smax/10.0) && (c>0)) {
double obs, calc, obsi;
obs = lookup_intensity(ref, h, k, l);
calc = lookup_intensity(trueref, h, k, l);
obsi = obs / (double)c;
top += fabs(obsi/scale - calc);
bot += obsi/scale;
n++;
}
}
}
}
fprintf(fh, "%8.5f %8.5f %i\n", sbracket+smax/20.0, top/bot, n);
}
fclose(fh);
}
int main(int argc, char *argv[])
{
int c;
int i;
struct image image;
double *ref, *trueref;
unsigned int *counts;
size_t ref_size;
signed int h, k, l;
double R, scale;
FILE *fh;
while ((c = getopt(argc, argv, "h")) != -1) {
switch ( c ) {
case 'h' : {
main_show_help(argv[0]);
return 0;
}
}
}
/* Define image parameters */
image.width = 1024;
image.height = 1024;
image.fmode = FORMULATION_CLEN;
image.x_centre = 512.5;
image.y_centre = 512.5;
image.camera_len = 0.05; /* 5 cm (front CCD can move from 5cm-20cm) */
image.resolution = 13333.3; /* 75 micron pixel size */
image.xray_energy = eV_to_J(2.0e3); /* 2 keV energy */
image.lambda = ph_en_to_lambda(image.xray_energy); /* Wavelength */
image.molecule = load_molecule();
/* Prepare array for integrated intensities */
ref = new_list_intensity();
/* Array for sample counts */
counts = new_list_count();
/* Calculate true intensities */
get_reflections_cached(image.molecule, image.xray_energy);
/* Complex structure factors now in image.molecule->reflections */
for ( i=1; i<=10e3; i++ ) {
#if 0
image.orientation = random_quaternion();
/* Calculate reflections using large smax
* (rather than the actual value) */
//get_reflections(&image, cell, 1.0e9);
nrefl = image_feature_count(image.rflist);
for ( j=0; j<nrefl; j++ ) {
struct imagefeature *f;
double t, s, intensity, F;
f = image_get_feature(image.rflist, j);
t = 100.0e-9; /* Thickness 100 nm */
s = f->s; /* Get excitation error */
F = structure_factor(f->h, f->k, f->l);
/* Calculate intensity from this reflection */
intensity = pow( F * SINC(M_PI*t*s), 2.0);
if ( intensity < 0.1 ) continue;
if ( (f->h == 2) && (f->k == 2) && (f->l == 2) ) {
fprintf(fh1, "%f %f\n", s, intensity);
}
if ( (f->h == 15) && (f->k == 15) && (f->l == 15) ) {
fprintf(fh2, "%f %f\n", s, intensity);
}
integrate_reflection(ref, f->h, f->k, f->l, intensity);
add_count(counts, f->h, f->k, f->l, 1);
}
#endif
if ( i % 1000 == 0 ) {
int j;
double mean_counts;
int ctot = 0;
int nmeas = 0;
double ff;
char name[64];
for ( j=0; j<ref_size; j++ ) {
ctot += counts[j];
if ( counts[j] > 0 ) nmeas++;
}
mean_counts = (double)ctot/nmeas;
ff = lookup_intensity(ref, 2, 2, 2)
/ lookup_count(counts, 2, 2, 2);
R = stat_r2(ref, trueref, counts, ref_size, &scale);
printf("%8i: R=%5.2f%% (sf=%7.4f)"
" mean meas/refl=%5.2f,"
" %i reflections measured. %f\n",
i, R*100.0, scale, mean_counts, nmeas,
ff);
/* Record graph of R against q for this N */
snprintf(name, 63, "R_vs_q-%i.dat", i);
write_RvsQ(name, ref, trueref, counts,
scale, image.molecule->cell);
}
}
fh = fopen("reflections.dat", "w");
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
int N;
N = lookup_count(counts, h, k, l);
if ( N == 0 ) continue;
double F = lookup_intensity(ref, h, k, l) / N;
fprintf(fh, "%3i %3i %3i %f\n", h, k, l, F);
}
}
}
fclose(fh);
return 0;
}
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