pattern_sim.c 2.57 KB
Newer Older
1
2
3
4
5
/*
 * main.c
 *
 * (c) 2006-2009 Thomas White <thomas.white@desy.de>
 *
6
 * pattern_sim - Simulate diffraction patterns from small crystals
7
8
9
10
11
12
13
14
15
16
17
18
19
20
 *
 */


#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>

21
#include "image.h"
Thomas White's avatar
Thomas White committed
22
#include "diffraction.h"
23
#include "cell.h"
24
25
#include "utils.h"
#include "hdf5-file.h"
Thomas White's avatar
Thomas White committed
26
#include "detector.h"
27
28
29
30


/* Crystal size in metres */
#define CRYSTAL_SIZE (500.0e-9)
31

32
33
34
35

static void main_show_help(const char *s)
{
	printf("Syntax: %s <file1.h5> <file2.h5> [...]\n\n", s);
Thomas White's avatar
Thomas White committed
36
	printf("Simulate diffraction patterns\n\n");
37
38
39
40
41
42
	printf("  -h              Display this help message\n");
}


int main(int argc, char *argv[])
{
43
	int c, done;
44
	struct image image;
45
46
	char filename[1024];
	int number = 1;
47
48
49
50
51
52
53
54
55
56
57
58
59
60

	while ((c = getopt(argc, argv, "h")) != -1) {

		switch ( c ) {

			case 'h' : {
				main_show_help(argv[0]);
				return 0;
			}

		}

	}

Thomas White's avatar
Thomas White committed
61
	/* Define image parameters */
Thomas White's avatar
Thomas White committed
62
63
	image.width = 1024;
	image.height = 1024;
Thomas White's avatar
Thomas White committed
64
	image.fmode = FORMULATION_CLEN;
Thomas White's avatar
Thomas White committed
65
66
	image.x_centre = 512.5;
	image.y_centre = 512.5;
Thomas White's avatar
Thomas White committed
67
	image.camera_len = 0.05;  /* 5 cm (front CCD can move from 5cm-20cm) */
Thomas White's avatar
Thomas White committed
68
	image.resolution = 13333.3; /* 75 micron pixel size */
Thomas White's avatar
Thomas White committed
69
70
71
72
73
74
75
	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);

76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
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 );

Thomas White's avatar
Thomas White committed
111
	/* Ensure no residual information */
Thomas White's avatar
Thomas White committed
112
113
114
	image.qvecs = NULL;
	image.sfacs = NULL;
	image.data = NULL;
Thomas White's avatar
Thomas White committed
115
	image.twotheta = NULL;
Thomas White's avatar
Thomas White committed
116
	image.hdr = NULL;
Thomas White's avatar
Thomas White committed
117

118
	get_diffraction(&image);
Thomas White's avatar
Thomas White committed
119
	record_image(&image);
Thomas White's avatar
Thomas White committed
120

121
122
	snprintf(filename, 1023, "results/sim-%i.h5", number);
	number++;
123

124
125
	/* Write the output file */
	hdf5_write(filename, image.data, image.width, image.height);
Thomas White's avatar
Thomas White committed
126
127
128
129
130
131
132
133
134

	/* Clean up */
	free(image.data);
	free(image.qvecs);
	free(image.hdr);
	free(image.sfacs);
	free(image.twotheta);

	/* Do it all again */
135
	goto again;
136
}