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/*
* main.c
*
* (c) 2006-2009 Thomas White <thomas.white@desy.de>
*
* pattern_sim - Simulate diffraction patterns from small crystals
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include "image.h"
#include "diffraction.h"
#include "cell.h"
#include "utils.h"
#include "hdf5-file.h"
#include "detector.h"
/* Crystal size in metres */
#define CRYSTAL_SIZE (500.0e-9)
static void show_help(const char *s)
{
printf("Syntax: %s\n\n", s);
printf("Simulate diffraction patterns from small crystals\n");
printf(" probed with femosecond pulses from a free electron laser\n\n");
printf(" -h, --help Display this help message\n");
printf(" --simulation-details Show details of the simulation\n");
}
static void show_details(const char *s)
{
printf("%s: Simulation Details\n\n", s);
printf("Simulates diffraction patterns from small crystals\n");
printf("probed with femtosecond pulses from a free electron laser\n\n");
}
int main(int argc, char *argv[])
{
int c, done;
struct image image;
char filename[1024];
int number = 1;
int config_simdetails = 0;
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"simulation-details", 0, &config_simdetails, 1},
{0, 0, NULL, 0}
};
while ((c = getopt_long(argc, argv, "h", longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
show_help(argv[0]);
return 0;
}
case 0 : {
break;
}
default : {
return 1;
}
}
}
if ( config_simdetails ) {
show_details(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 = NULL;
/* Splurge a few useful numbers */
printf("Wavelength is %f nm\n", image.lambda/1.0e-9);
again:
/* Read quaternion from stdin */
done = 0;
do {
int r;
float w, x, y, z;
char line[1024];
char *rval;
printf("Please input quaternion: w x y z\n");
rval = fgets(line, 1023, stdin);
if ( rval == NULL ) return 0;
chomp(line);
r = sscanf(line, "%f %f %f %f", &w, &x, &y, &z);
if ( r == 4 ) {
printf("Rotation is: %f %f %f %f (modulus=%f)\n",
w, x, y, z, sqrtf(w*w + x*x + y*y + z*z));
image.orientation.w = w;
image.orientation.x = x;
image.orientation.y = y;
image.orientation.z = z;
done = 1;
} else {
fprintf(stderr, "Invalid rotation '%s'\n", line);
}
} while ( !done );
/* Ensure no residual information */
image.qvecs = NULL;
image.sfacs = NULL;
image.data = NULL;
image.twotheta = NULL;
image.hdr = NULL;
get_diffraction(&image);
record_image(&image);
snprintf(filename, 1023, "results/sim-%i.h5", number);
number++;
/* Write the output file */
hdf5_write(filename, image.data, image.width, image.height);
/* Clean up */
free(image.data);
free(image.qvecs);
free(image.hdr);
free(image.sfacs);
free(image.twotheta);
/* Do it all again */
goto again;
}
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