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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"
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");
printf(" --near-bragg Output h,k,l,I near Bragg conditions\n");
printf(" -r, --random-orientation Use a randomly generated orientation\n");
printf(" (a new orientation will be used for each image)\n");
printf(" -n, --number=<N> Generate N images. Default 1\n");
}
static void show_details()
{
printf("This program simulates diffraction patterns from small crystals illuminated\n");
printf("with femtosecond X-ray pulses from a free electron laser.\n\n");
printf("Scattering Factors\n");
printf("------------------\n");
printf("Scattering factors\n");
}
static struct quaternion read_quaternion()
{
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 invalid_quaternion();
chomp(line);
r = sscanf(line, "%f %f %f %f", &w, &x, &y, &z);
if ( r == 4 ) {
struct quaternion quat;
quat.w = w;
quat.x = x;
quat.y = y;
quat.z = z;
return quat;
} else {
fprintf(stderr, "Invalid rotation '%s'\n", line);
}
} while ( 1 );
}
int main(int argc, char *argv[])
{
int c;
struct image image;
char filename[1024];
int config_simdetails = 0;
int config_nearbragg = 0;
int config_randomquat = 0;
int number = 1; /* Index for the current image */
int n_images = 1; /* Generate one image by default */
int done = 0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"simulation-details", 0, &config_simdetails, 1},
{"near-bragg", 0, &config_nearbragg, 1},
{"random-orientation", 0, NULL, 'r'},
{"number", 1, NULL, 'n'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hrn:", longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
show_help(argv[0]);
return 0;
}
case 'r' : {
config_randomquat = 1;
break;
}
case 'n' : {
n_images = atoi(optarg);
break;
}
case 0 : {
break;
}
default : {
return 1;
}
}
}
if ( config_simdetails ) {
show_details();
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);
do {
/* Read quaternion from stdin */
if ( config_randomquat ) {
image.orientation = random_quaternion();
} else {
image.orientation = read_quaternion();
}
if ( quaternion_valid(image.orientation) ) {
fprintf(stderr, "Orientation modulus is not zero!\n");
return 1;
}
/* 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);
if ( n_images && (number >= n_images) ) done = 1;
} while ( !done );
}
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