render_hkl.c 7.35 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
/*
 * render_hkl.c
 *
 * Draw pretty renderings of reflection lists
 *
 * (c) 2006-2010 Thomas White <taw@physics.org>
 *
 * 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 <getopt.h>
Thomas White's avatar
Thomas White committed
23
24
#include <cairo.h>
#include <cairo-pdf.h>
25
26
27

#include "utils.h"
#include "reflections.h"
28
#include "povray.h"
29
#include "symmetry.h"
30
31


32
33
34
35
static void show_help(const char *s)
{
	printf("Syntax: %s [options] <file.hkl>\n\n", s);
	printf(
36
"Render intensity lists in various ways.\n"
37
"\n"
38
39
40
41
42
43
44
"  -h, --help            Display this help message.\n"
"      --povray          Render a 3D animation using POV-ray.\n"
"      --zone-axis       Render a 2D zone axis pattern.\n"
"      --boost=<val>     Squash colour scale by <val>.\n"
"  -j <n>                Run <n> instances of POV-ray in parallel.\n"
"  -p, --pdb=<file>      PDB file from which to get the unit cell.\n"
"  -y, --symmetry=<sym>  Expand reflections according to point group <sym>.\n"
45
);
46
47
48
}


49
static void render_za(UnitCell *cell, double *ref, unsigned int *c,
50
                      double boost, const char *sym)
51
{
Thomas White's avatar
Thomas White committed
52
53
	cairo_surface_t *surface;
	cairo_t *dctx;
54
55
	double max_u, max_v, max_res, max_intensity;
	double scale_u, scale_v, scale;
Thomas White's avatar
Thomas White committed
56
	double sep_u, sep_v, max_r;
57
58
	double u, v;
	signed int max_h, max_k;
Thomas White's avatar
Thomas White committed
59
	double as, bs, theta;
60
61
62
	double asx, asy, asz;
	double bsx, bsy, bsz;
	double csx, csy, csz;
Thomas White's avatar
Thomas White committed
63
64
	signed int h, k;
	float wh, ht;
65

Thomas White's avatar
Thomas White committed
66
67
	wh = 1024;
	ht = 1024;
68

Thomas White's avatar
Thomas White committed
69
	surface = cairo_pdf_surface_create("za.pdf", wh, ht);
70

Thomas White's avatar
Thomas White committed
71
72
73
74
75
	if ( cairo_surface_status(surface) != CAIRO_STATUS_SUCCESS ) {
		fprintf(stderr, "Couldn't create Cairo surface\n");
		cairo_surface_destroy(surface);
		return;
	}
76

Thomas White's avatar
Thomas White committed
77
	dctx = cairo_create(surface);
78

Thomas White's avatar
Thomas White committed
79
80
81
82
	/* Black background */
	cairo_rectangle(dctx, 0.0, 0.0, wh, ht);
	cairo_set_source_rgb(dctx, 0.0, 0.0, 0.0);
	cairo_fill(dctx);
83

Thomas White's avatar
Thomas White committed
84
	max_u = 0.0;  max_v = 0.0;  max_intensity = 0.0;
85
	max_res = 0.0;  max_h = 0;  max_k = 0;
Thomas White's avatar
Thomas White committed
86
87

	/* Work out reciprocal lattice spacings and angles for this cut */
88
	if ( cell_get_reciprocal(cell, &asx, &asy, &asz,
Thomas White's avatar
Thomas White committed
89
	                          &bsx, &bsy, &bsz,
90
91
92
93
	                          &csx, &csy, &csz) ) {
		ERROR("Couldn't get reciprocal parameters\n");
		return;
	}
Thomas White's avatar
Thomas White committed
94
95
96
97
98
99
100
101
102
103
	theta = angle_between(asx, asy, asz, bsx, bsy, bsz);
	as = modulus(asx, asy, asz) / 1e9;
	bs = modulus(bsx, bsy, bsz) / 1e9;
	STATUS("theta=%f\n", rad2deg(theta));

	for ( h=-INDMAX; h<INDMAX; h++ ) {
	for ( k=-INDMAX; k<INDMAX; k++ ) {

		double u, v, intensity, res;
		int ct;
104
		int nequiv, p;
Thomas White's avatar
Thomas White committed
105
106
107
108
109
110
111

		ct = lookup_count(c, h, k, 0);
		if ( ct < 1 ) continue;

		intensity = lookup_intensity(ref, h, k, 0) / (float)ct;

		if ( intensity != 0 ) {
112
113
114
115
116
117
118
119
120
121
122
123
124
125

			nequiv = num_equivs(h, k, 0, sym);
			for ( p=0; p<nequiv; p++ ) {

				signed int he, ke, le;
				get_equiv(h, k, 0, &he, &ke, &le, sym, p);

				u =  (double)he*as*sin(theta);
				v =  (double)he*as*cos(theta) + ke*bs;
				if ( fabs(u) > fabs(max_u) ) max_u = fabs(u);
				if ( fabs(v) > fabs(max_v) ) max_v = fabs(v);
				if ( fabs(intensity) > fabs(max_intensity) ) {
					max_intensity = fabs(intensity);
				}
126
127
				if ( fabs(he) > max_h ) max_h = fabs(he);
				if ( fabs(ke) > max_k ) max_k = fabs(ke);
128
129
130
131
				res = resolution(cell, he, ke, 0);
				if ( res > max_res ) max_res = res;

			}
132
133
134
		}

	}
Thomas White's avatar
Thomas White committed
135
	}
136

Thomas White's avatar
Thomas White committed
137
	max_res /= 1e9;
138
139
	printf("Maximum resolution is 1/d = %5.3f nm^-1, d = %5.3f nm\n",
	       max_res*2.0, 1.0/(max_res*2.0));
Thomas White's avatar
Thomas White committed
140
141
142
143

	if ( max_intensity <= 0.0 ) {
		max_r = 4.0;
		goto out;
144
145
	}

Thomas White's avatar
Thomas White committed
146
	/* Choose whichever scaling factor gives the smallest value */
147
148
149
	scale_u = ((double)(wh/2.0)-50.0) / max_u;
	scale_v = ((double)(ht/2.0)-50.0) / max_v;
	scale = (scale_u < scale_v) ? scale_u : scale_v;
150

Thomas White's avatar
Thomas White committed
151
152
	sep_u = as * scale * cos(theta);
	sep_v = bs * scale;
153
154
	max_r = (sep_u < sep_v) ? sep_u : sep_v;
	max_r -= 1.0;  /* Add a tiny separation between circles */
Thomas White's avatar
Thomas White committed
155
156
157
158
159
160

	for ( h=-INDMAX; h<INDMAX; h++ ) {
	for ( k=-INDMAX; k<INDMAX; k++ ) {

		double u, v, intensity, val;
		int ct;
161
		int nequiv, p;
Thomas White's avatar
Thomas White committed
162
163
164
165
166

		ct = lookup_count(c, h, k, 0);
		if ( ct < 1 ) continue;

		intensity = lookup_intensity(ref, h, k, 0) / (float)ct;
167
		val = boost*intensity/max_intensity;
Thomas White's avatar
Thomas White committed
168

169
170
171
172
173
174
175
176
		nequiv = num_equivs(h, k, 0, sym);
		for ( p=0; p<nequiv; p++ ) {

			signed int he, ke, le;
			get_equiv(h, k, 0, &he, &ke, &le, sym, p);

			u = (double)he*as*sin(theta);
			v = (double)he*as*cos(theta) + ke*bs;
Thomas White's avatar
Thomas White committed
177

178
179
			cairo_arc(dctx, ((double)wh/2)+u*scale,
					((double)ht/2)+v*scale, max_r,
180
					0, 2*M_PI);
Thomas White's avatar
Thomas White committed
181

182
183
184
185
			cairo_set_source_rgb(dctx, val, val, val);
			cairo_fill(dctx);

		}
Thomas White's avatar
Thomas White committed
186
187

	}
188
189
	}

Thomas White's avatar
Thomas White committed
190
191
192
193
194
195
196
out:
	/* Centre marker */
	cairo_arc(dctx, (double)wh/2,
			(double)ht/2, max_r, 0, 2*M_PI);
	cairo_set_source_rgb(dctx, 1.0, 0.0, 0.0);
	cairo_fill(dctx);

197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
	/* Draw indexing lines */
	cairo_set_line_width(dctx, 4.0);
	cairo_move_to(dctx, (double)wh/2, (double)ht/2);
	u = (double)max_h*as*sin(theta);
	v = (double)max_h*as*cos(theta) + 0*bs;
	cairo_line_to(dctx, ((double)wh/2)+u*scale,
	                    ((double)ht/2)+v*scale);
	cairo_set_source_rgb(dctx, 0.0, 1.0, 0.0);
	cairo_stroke(dctx);

	cairo_move_to(dctx,((double)wh/2)+u*scale-40.0,
	                   ((double)ht/2)+v*scale+40.0);
	                   cairo_set_font_size(dctx, 40.0);
	cairo_show_text(dctx, "h");
	cairo_fill(dctx);

	cairo_move_to(dctx, (double)wh/2, (double)ht/2);
	u = 0.0;
	v = (double)max_k*bs;
	cairo_line_to(dctx, ((double)wh/2)+u*scale,
	                    ((double)ht/2)+v*scale);
	cairo_set_source_rgb(dctx, 0.0, 1.0, 0.0);
	cairo_stroke(dctx);

	cairo_move_to(dctx,((double)wh/2)+u*scale-40.0,
	                   ((double)ht/2)+v*scale-40.0);
	                   cairo_set_font_size(dctx, 40.0);
	cairo_show_text(dctx, "k");
	cairo_fill(dctx);

Thomas White's avatar
Thomas White committed
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
	cairo_surface_finish(surface);
	cairo_destroy(dctx);
}


int main(int argc, char *argv[])
{
	int c;
	UnitCell *cell;
	char *infile;
	double *ref;
	unsigned int *cts;
	int config_povray = 0;
	int config_zoneaxis = 0;
	unsigned int nproc = 1;
242
	char *pdb = NULL;
243
	int r = 0;
244
	double boost = 1.0;
245
	char *sym = NULL;
Thomas White's avatar
Thomas White committed
246
247
248
249
250
251

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"povray",             0, &config_povray,      1},
		{"zone-axis",          0, &config_zoneaxis,    1},
252
		{"pdb",                1, NULL,               'p'},
253
		{"boost",              1, NULL,               'b'},
254
		{"symmetry",           1, NULL,               'y'},
Thomas White's avatar
Thomas White committed
255
256
257
258
		{0, 0, NULL, 0}
	};

	/* Short options */
259
	while ((c = getopt_long(argc, argv, "hj:p:", longopts, NULL)) != -1) {
Thomas White's avatar
Thomas White committed
260
261

		switch (c) {
Thomas White's avatar
Thomas White committed
262
		case 'h' :
Thomas White's avatar
Thomas White committed
263
264
265
			show_help(argv[0]);
			return 0;

Thomas White's avatar
Thomas White committed
266
		case 'j' :
Thomas White's avatar
Thomas White committed
267
268
269
			nproc = atoi(optarg);
			break;

270
271
272
273
		case 'p' :
			pdb = strdup(optarg);
			break;

274
275
276
277
		case 'b' :
			boost = atof(optarg);
			break;

278
279
280
281
		case 'y' :
			sym = strdup(optarg);
			break;

Thomas White's avatar
Thomas White committed
282
		case 0 :
Thomas White's avatar
Thomas White committed
283
284
			break;

Thomas White's avatar
Thomas White committed
285
		default :
Thomas White's avatar
Thomas White committed
286
287
288
289
290
			return 1;
		}

	}

291
292
293
294
	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

295
296
297
298
	if ( sym == NULL ) {
		sym = strdup("1");
	}

Thomas White's avatar
Thomas White committed
299
300
	infile = argv[optind];

301
	cell = load_cell_from_pdb(pdb);
302
303
304
305
	if ( cell == NULL ) {
		ERROR("Couldn't load unit cell from %s\n", pdb);
		return 1;
	}
Thomas White's avatar
Thomas White committed
306
307
308
309
310
311
312
313
	cts = new_list_count();
	ref = read_reflections(infile, cts, NULL);
	if ( ref == NULL ) {
		ERROR("Couldn't open file '%s'\n", infile);
		return 1;
	}

	if ( config_povray ) {
314
		r = povray_render_animation(cell, ref, cts, nproc);
Thomas White's avatar
Thomas White committed
315
	} else if ( config_zoneaxis ) {
316
		render_za(cell, ref, cts, boost, sym);
Thomas White's avatar
Thomas White committed
317
318
319
320
	} else {
		ERROR("Try again with either --povray or --zone-axis.\n");
	}

321
	free(pdb);
322
	free(sym);
323

324
	return r;
325
}