pattern_sim.c 9.61 KB
Newer Older
1
2
3
/*
 * main.c
 *
Thomas White's avatar
Thomas White committed
4
 * (c) 2006-2010 Thomas White <taw@physics.org>
5
 *
Thomas White's avatar
Thomas White committed
6
 * Part of CrystFEL - crystallography with a FEL
7
8
9
10
11
12
13
14
15
16
17
18
19
 *
 */


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

#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
Thomas White's avatar
Thomas White committed
20
#include <getopt.h>
21

22
#include "image.h"
Thomas White's avatar
Thomas White committed
23
#include "diffraction.h"
24
#include "diffraction-gpu.h"
25
#include "cell.h"
26
27
#include "utils.h"
#include "hdf5-file.h"
Thomas White's avatar
Thomas White committed
28
#include "detector.h"
Thomas White's avatar
Thomas White committed
29
#include "intensities.h"
Thomas White's avatar
Thomas White committed
30
#include "sfac.h"
31
32


Thomas White's avatar
Thomas White committed
33
static void show_help(const char *s)
34
{
35
	printf("Syntax: %s [options]\n\n", s);
Thomas White's avatar
Thomas White committed
36
	printf(
Thomas White's avatar
Thomas White committed
37
"Simulate diffraction patterns from small crystals probed with femtosecond\n"
Thomas White's avatar
Thomas White committed
38
39
"pulses of X-rays from a free electron laser.\n"
"\n"
40
41
" -h, --help                Display this help message.\n"
"     --simulation-details  Show technical details of the simulation.\n"
42
"     --gpu                 Use the GPU to speed up the calculation.\n"
43
44
"\n"
"     --near-bragg          Output h,k,l,I near Bragg conditions.\n"
45
"     --powder              Output a powder pattern as results/powder.h5.\n"
46
47
" -n, --number=<N>          Generate N images.  Default 1.\n"
"     --no-images           Do not output any HDF5 files.\n"
Thomas White's avatar
Thomas White committed
48
" -r, --random-orientation  Use a randomly generated orientation\n"
49
"                            (a new orientation will be used for each image).\n"
Thomas White's avatar
Thomas White committed
50
51
52
53
54
"\n"
"By default, the simulation aims to be as accurate as possible.  For greater\n"
"speed, or for testing, you can choose to disable certain things using the\n"
"following options.\n"
"\n"
55
"     --no-water            Do not simulate water background.\n"
Thomas White's avatar
Thomas White committed
56
"     --no-noise            Do not calculate Poisson noise.\n"
Thomas White's avatar
Thomas White committed
57
58
59
"     --no-bloom            Do not calculate CCD bloom (intensities which are\n"
"                            above the recordable range will be clamped to\n"
"                            the maximum allowable value).\n"
60
);
Thomas White's avatar
Thomas White committed
61
62
63
}


64
static void show_details()
Thomas White's avatar
Thomas White committed
65
{
Thomas White's avatar
Thomas White committed
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
	printf(
"This program simulates diffraction patterns from small crystals illuminated\n"
"with femtosecond X-ray pulses from a free electron laser.\n"
"\n"
"The lattice transform from the specified number of unit cells is calculated\n"
"using the closed-form solution for a truncated lattice:\n"
"\n"
"F(q) =  sin(pi*na*q.a)/sin(pi*q.a)\n"
"      * sin(pi*nb*q.b)/sin(pi*q.b)\n"
"      * sin(pi*nc*q.c)/sin(pi*q.c)\n"
"\n"
"na = number of unit cells in 'a' direction (likewise nb, nc)\n"
" q = reciprocal vector (1/d convention, not 2pi/d)\n"
"\n"
"This value is multiplied by the complex structure factor at the nearest\n"
"Bragg position, i.e. the gradient of the shape transform across each\n"
"appearance of the shape transform is not included, for speed of calculation.\n"
"\n"
"Complex structure factors are calculated using a combination of the Henke\n"
"and Waasmeier-Kirfel scattering factors. The Henke factors are complex\n"
"and energy dependence, whereas the Waas-Kirf values are real-valued and\n"
"|q|-dependent.  The difference between the Waas-Kirf value at the\n"
"appropriate |q| and the same value at |q|=0 is subtracted from the Henke\n"
"value.  The Henke values are linearly interpolated from the provided tables\n"
"(note that the interpolation should really be exponential).\n"
"\n"
"The modulus of the structure factor is taken and squared.  Intensity from\n"
"water is then added according to the first term of equation 5 from\n"
Thomas White's avatar
Thomas White committed
94
"Phys Chem Chem Phys 2003 (5) 1981--1991.\n"
Thomas White's avatar
Thomas White committed
95
96
97
98
99
100
101
102
103
104
"\n"
"Expected intensities at the CCD are then calculated using:\n"
"\n"
"I(q) = I0 * r^2 * |F(q)|^2 * S\n"
"\n"
"I0 = number of photons per unit area in the incident beam\n"
" r = Thomson radius\n"
" S = solid angle of corresponding pixel\n"
"\n"
"Poisson counts are generated from the expected intensities using Knuth's\n"
Thomas White's avatar
Thomas White committed
105
106
107
"algorithm.  When the intensity is sufficiently high that Knuth's algorithm\n"
"would result in machine precision problems, a normal distribution with\n"
"standard deviation sqrt(I) is used instead.\n"
Thomas White's avatar
Thomas White committed
108
109
110
111
112
113
"\n"
"Bloom of the CCD is included.  Any excess intensity in a particular pixel\n"
"is divided between the neighbouring pixels.  Diagonal neighbours receive\n"
"half the contribution of adjacent pixels.  This process is repeated for\n"
"every pixel until all pixels are below the saturation value.  Note that this\n"
"process is slow for very saturated images.\n");
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
}


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 {
144
			ERROR("Invalid rotation '%s'\n", line);
145
146
147
		}

	} while ( 1 );
148
149
150
151
152
}


int main(int argc, char *argv[])
{
153
	int c;
154
	struct image image;
155
	long long int *powder;
Thomas White's avatar
Thomas White committed
156
	int config_simdetails = 0;
157
158
	int config_nearbragg = 0;
	int config_randomquat = 0;
159
	int config_noimages = 0;
160
	int config_nowater = 0;
Thomas White's avatar
Thomas White committed
161
	int config_nonoise = 0;
Thomas White's avatar
Thomas White committed
162
	int config_nobloom = 0;
163
	int config_nosfac = 0;
164
	int config_gpu = 0;
165
	int config_powder = 0;
Thomas White's avatar
Thomas White committed
166
167
168
	int ndone = 0;    /* Number of simulations done (images or not) */
	int number = 1;   /* Number used for filename of image */
	int n_images = 1; /* Generate one image by default */
169
	int done = 0;
Thomas White's avatar
Thomas White committed
170

171
	/* Long options */
Thomas White's avatar
Thomas White committed
172
	const struct option longopts[] = {
173
174
		{"help",               0, NULL,               'h'},
		{"simulation-details", 0, &config_simdetails,  1},
175
		{"gpu",                0, &config_gpu,         1},
176
177
178
		{"near-bragg",         0, &config_nearbragg,   1},
		{"random-orientation", 0, NULL,               'r'},
		{"number",             1, NULL,               'n'},
Thomas White's avatar
Thomas White committed
179
		{"no-images",          0, &config_noimages,    1},
180
		{"no-water",           0, &config_nowater,     1},
Thomas White's avatar
Thomas White committed
181
		{"no-noise",           0, &config_nonoise,     1},
Thomas White's avatar
Thomas White committed
182
		{"no-bloom",           0, &config_nobloom,     1},
183
184
		{"no-sfac",            0, &config_nosfac,      1},
		{"powder",             0, &config_powder,      1},
185
		{0, 0, NULL, 0}
Thomas White's avatar
Thomas White committed
186
	};
187

188
189
	/* Short options */
	while ((c = getopt_long(argc, argv, "hrn:", longopts, NULL)) != -1) {
190

Thomas White's avatar
Thomas White committed
191
192
193
194
195
		switch (c) {
		case 'h' : {
			show_help(argv[0]);
			return 0;
		}
196

197
198
199
200
201
202
203
204
205
206
		case 'r' : {
			config_randomquat = 1;
			break;
		}

		case 'n' : {
			n_images = atoi(optarg);
			break;
		}

Thomas White's avatar
Thomas White committed
207
208
209
		case 0 : {
			break;
		}
210

Thomas White's avatar
Thomas White committed
211
212
213
		default : {
			return 1;
		}
214
215
216
217
		}

	}

Thomas White's avatar
Thomas White committed
218
	if ( config_simdetails ) {
219
		show_details();
Thomas White's avatar
Thomas White committed
220
221
222
		return 0;
	}

Thomas White's avatar
Thomas White committed
223
	/* Define image parameters */
Thomas White's avatar
Thomas White committed
224
225
	image.width = 1024;
	image.height = 1024;
226
	image.lambda = ph_en_to_lambda(eV_to_J(2.0e3));  /* Wavelength */
227
	image.molecule = load_molecule();
Thomas White's avatar
Thomas White committed
228

229
230
231
232
233
234
235
236
237
238
	/* Set up detector configuration */
	image.det.n_panels = 2;
	image.det.panels = malloc(2*sizeof(struct panel));
	/* Upper panel */
	image.det.panels[0].min_x = 0;
	image.det.panels[0].max_x = 1023;
	image.det.panels[0].min_y = 512;
	image.det.panels[0].max_y = 1023;
	image.det.panels[0].cx = 491.9;
	image.det.panels[0].cy = 440.7;
Thomas White's avatar
Thomas White committed
239
240
	image.det.panels[0].clen = 67.0e-3;
	image.det.panels[0].res = 13333.3;  /* 75 micron pixel size */
241
242
243
244
245
246
247
	/* Lower panel */
	image.det.panels[1].min_x = 0;
	image.det.panels[1].max_x = 1023;
	image.det.panels[1].min_y = 0;
	image.det.panels[1].max_y = 511;
	image.det.panels[1].cx = 492.0;
	image.det.panels[1].cy = 779.7;
Thomas White's avatar
Thomas White committed
248
249
	image.det.panels[1].clen = 75.0e-3;
	image.det.panels[1].res = 13333.3;  /* 75 micron pixel size */
250

251
252
	powder = calloc(image.width*image.height, sizeof(*powder));

Thomas White's avatar
Thomas White committed
253
	/* Splurge a few useful numbers */
254
	STATUS("Wavelength is %f nm\n", image.lambda/1.0e-9);
Thomas White's avatar
Thomas White committed
255

256
257
	do {

Thomas White's avatar
Thomas White committed
258
		int na, nb, nc;
259
		double a, b, c, d;
Thomas White's avatar
Thomas White committed
260

261
262
263
		na = 8*random()/RAND_MAX + 4;
		nb = 8*random()/RAND_MAX + 4;
		nc = 16*random()/RAND_MAX + 30;
Thomas White's avatar
Thomas White committed
264

265
266
267
		/* Read quaternion from stdin */
		if ( config_randomquat ) {
			image.orientation = random_quaternion();
268
		} else {
269
			image.orientation = read_quaternion();
270
271
		}

Thomas White's avatar
Thomas White committed
272
273
274
275
		STATUS("Orientation is %5.3f %5.3f %5.3f %5.3f\n",
		       image.orientation.w, image.orientation.x,
		       image.orientation.y, image.orientation.z);

Thomas White's avatar
D'oh    
Thomas White committed
276
		if ( !quaternion_valid(image.orientation) ) {
277
			ERROR("Orientation modulus is not zero!\n");
278
279
280
281
282
283
284
285
			return 1;
		}

		/* Ensure no residual information */
		image.sfacs = NULL;
		image.data = NULL;
		image.twotheta = NULL;
		image.hdr = NULL;
286

287
288
289
290
		cell_get_parameters(image.molecule->cell, &a, &b, &c, &d, &d, &d);
		STATUS("Particle size = %i x %i x %i (=%5.2f x %5.2f x %5.2f nm)\n",
	               na, nb, nc, na*a/1.0e-9, nb*b/1.0e-9, nc*c/1.0e-9);

291
292
293
294
295
		if ( config_gpu ) {
			get_diffraction_gpu(&image, na, nb, nc, config_nosfac);
		} else {
			get_diffraction(&image, na, nb, nc, config_nosfac);
		}
Thomas White's avatar
Thomas White committed
296
297
298
299
		if ( image.molecule == NULL ) {
			ERROR("Couldn't open molecule.pdb\n");
			return 1;
		}
300
301
302
303
304
		if ( image.sfacs == NULL ) {
			ERROR("Diffraction calculation failed.\n");
			goto skip;
		}

Thomas White's avatar
Thomas White committed
305
306
		record_image(&image, !config_nowater, !config_nonoise,
		             !config_nobloom);
Thomas White's avatar
Thomas White committed
307

Thomas White's avatar
Thomas White committed
308
		if ( config_nearbragg ) {
309
			output_intensities(&image, image.molecule->cell);
Thomas White's avatar
Thomas White committed
310
311
		}

312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
		if ( config_powder ) {

			int x, y, w;

			w = image.width;

			for ( x=0; x<image.width; x++ ) {
			for ( y=0; y<image.height; y++ ) {
				powder[x+w*y] += image.data[x+w*y];
			}
			}

			if ( !(ndone % 10) ) {
				hdf5_write("results/integr-bw.h5", powder,
				           image.width, image.height,
				           H5T_NATIVE_LLONG);
			}
		}

331
332
333
334
335
336
		if ( !config_noimages ) {

			char filename[1024];

			snprintf(filename, 1023, "results/sim-%i.h5", number);
			number++;
Thomas White's avatar
Thomas White committed
337

338
339
			/* Write the output file */
			hdf5_write(filename, image.data,
340
			           image.width, image.height, H5T_NATIVE_INT16);
341
342

		}
343

344
345
346
347
348
		/* Clean up */
		free(image.data);
		free(image.hdr);
		free(image.sfacs);
		free(image.twotheta);
Thomas White's avatar
Thomas White committed
349

350
skip:
Thomas White's avatar
Thomas White committed
351
		ndone++;
352

353
		if ( n_images && (ndone >= n_images) ) done = 1;
Thomas White's avatar
Thomas White committed
354

355
	} while ( !done );
356
357

	return 0;
358
}