check_hkl.c 7.42 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
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
/*
 * check_hkl.c
 *
 * Characterise 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>

#include "utils.h"
#include "sfac.h"
#include "reflections.h"
#include "statistics.h"
#include "symmetry.h"


/* Number of bins for plot of resolution shells */
#define NBINS (10)


static void show_help(const char *s)
{
	printf("Syntax: %s [options] <file.hkl>\n\n", s);
	printf(
"Characterise an intensity list.\n"
"\n"
"  -h, --help                 Display this help message.\n"
"  -y, --symmetry=<sym>       The symmetry of both the input files.\n"
"  -p, --pdb=<filename>       PDB file to use (default: molecule.pdb).\n"
"      --rmin=<res>           Fix lower resolution limit for --shells (m^-1).\n"
"      --rmax=<res>           Fix upper resolution limit for --shells (m^-1).\n"
"\n");
}


Thomas White's avatar
Thomas White committed
50
static void plot_shells(const double *ref, ReflItemList *items, UnitCell *cell,
51
52
53
54
55
56
57
58
59
60
61
62
63
                        const char *sym, unsigned int *counts,
                        const double *sigma, double rmin_fix, double rmax_fix)
{
	double num[NBINS];
	int cts[NBINS];
	int possible[NBINS];
	unsigned int *counted;
	unsigned int measurements[NBINS];
	unsigned int measured[NBINS];
	double total_vol, vol_per_shell;
	double rmins[NBINS];
	double rmaxs[NBINS];
	double snr[NBINS];
Thomas White's avatar
Thomas White committed
64
65
	double mean[NBINS];
	double var[NBINS];
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
	double rmin, rmax;
	signed int h, k, l;
	int i;
	FILE *fh;
	double snr_total = 0;
	int nmeas = 0;
	int nmeastot = 0;
	int nout = 0;

	if ( cell == NULL ) {
		ERROR("Need the unit cell to plot resolution shells.\n");
		return;
	}

	fh = fopen("shells.dat", "w");
	if ( fh == NULL ) {
		ERROR("Couldn't open 'shells.dat'\n");
		return;
	}

	for ( i=0; i<NBINS; i++ ) {
		num[i] = 0.0;
		cts[i] = 0;
		possible[i] = 0;
		measured[i] = 0;
		measurements[i] = 0;
		snr[i] = 0;
Thomas White's avatar
Thomas White committed
93
94
		var[i] = 0;
		mean[i] = 0;
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
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
144
145
146
147
148
149
150
151
	}

	rmin = +INFINITY;
	rmax = 0.0;
	for ( i=0; i<num_items(items); i++ ) {

		struct refl_item *it;
		signed int h, k, l;
		double d;

		it = get_item(items, i);
		h = it->h;  k = it->k;  l = it->l;

		d = resolution(cell, h, k, l) * 2.0;
		if ( d > rmax ) rmax = d;
		if ( d < rmin ) rmin = d;

	}

	STATUS("1/d goes from %f to %f nm^-1\n", rmin/1e9, rmax/1e9);

	/* Widen the range just a little bit */
	rmin -= 0.001e9;
	rmax += 0.001e9;

	/* Fixed resolution shells if needed */
	if ( rmin_fix > 0.0 ) rmin = rmin_fix;
	if ( rmax_fix > 0.0 ) rmax = rmax_fix;

	total_vol = pow(rmax, 3.0) - pow(rmin, 3.0);
	vol_per_shell = total_vol / NBINS;
	rmins[0] = rmin;
	for ( i=1; i<NBINS; i++ ) {

		double r;

		r = vol_per_shell + pow(rmins[i-1], 3.0);
		r = pow(r, 1.0/3.0);

		/* Shells of constant volume */
		rmaxs[i-1] = r;
		rmins[i] = r;

		/* Shells of constant thickness */
		//rmins[i] = rmins[i-1] + (rmax-rmin)/NBINS;
		//rmaxs[i-1] = rmins[i-1] + (rmax-rmin)/NBINS;

		STATUS("Shell %i: %f to %f\n", i-1,
		       rmins[i-1]/1e9, rmaxs[i-1]/1e9);

	}
	rmaxs[NBINS-1] = rmax;
	STATUS("Shell %i: %f to %f\n", NBINS-1,
	       rmins[NBINS-1]/1e9, rmaxs[NBINS-1]/1e9);

	/* Count the number of reflections possible in each shell */
	counted = new_list_count();
Thomas White's avatar
Thomas White committed
152
153
154
	for ( h=-150; h<=+150; h++ ) {
	for ( k=-150; k<=+150; k++ ) {
	for ( l=-150; l<=+150; l++ ) {
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170

		double d;
		signed int hs, ks, ls;
		int bin;

		d = resolution(cell, h, k, l) * 2.0;

		bin = -1;
		for ( i=0; i<NBINS; i++ ) {
			if ( (d>rmins[i]) && (d<=rmaxs[i]) ) {
				bin = i;
				break;
			}
		}
		if ( bin == -1 ) continue;

Thomas White's avatar
Thomas White committed
171
172
173
174
		get_asymm(h, k, l, &hs, &ks, &ls, sym);
		if ( lookup_count(counted, hs, ks, ls) ) continue;
		set_count(counted, hs, ks, ls, 1);

175
176
177
178
179
180
181
		possible[bin]++;

	}
	}
	}
	free(counted);

Thomas White's avatar
Thomas White committed
182
	/* Characterise the data set */
183
184
185
186
187
188
189
190
191
192
193
194
195
196
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
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
	for ( i=0; i<num_items(items); i++ ) {

		struct refl_item *it;
		signed int h, k, l;
		double d;
		int bin;
		int j;

		it = get_item(items, i);
		h = it->h;  k = it->k;  l = it->l;

		d = resolution(cell, h, k, l) * 2.0;

		bin = -1;
		for ( j=0; j<NBINS; j++ ) {
			if ( (d>rmins[j]) && (d<=rmaxs[j]) ) {
				bin = j;
				break;
			}
		}
		if ( bin == -1 ) {
			nout++;
			continue;
		}

		measured[bin]++;
		measurements[bin] += lookup_count(counts, h, k, l);
		snr[bin] += (lookup_intensity(ref1, h, k, l) /
		                              lookup_intensity(sigma, h, k, l));
		snr_total += (lookup_intensity(ref1, h, k, l) /
		                              lookup_intensity(sigma, h, k, l));
		nmeas++;
		nmeastot += lookup_count(counts, h, k, l);

	}
	STATUS("overall <snr> = %f\n", snr_total/(double)nmeas);
	STATUS("%i measurements in total.\n", nmeastot);
	STATUS("%i reflections in total.\n", nmeas);

	if ( nout ) {
		STATUS("Warning; %i reflections outside resolution range.\n",
		       nout);
	}

	for ( i=0; i<NBINS; i++ ) {

		double r, cen;
		cen = rmins[i] + (rmaxs[i] - rmins[i])/2.0;
		r = (num[i]/den)*((double)ctot/cts[i]);
		fprintf(fh, "%f %i %i %5.2f %i %f %f\n", cen*1.0e-9, measured[i],
		        possible[i], 100.0*(float)measured[i]/possible[i],
		        measurements[i], (float)measurements[i]/measured[i],
		        (snr[i]/(double)measured[i]));

	}

	fclose(fh);
}


int main(int argc, char *argv[])
{
	int c;
	double *ref;
	UnitCell *cell;
	char *file = NULL;
	char *sym = NULL;
	int i;
	ReflItemList *items;
	ReflItemList *good_items;
	char *pdb = NULL;
	double *esd;
	int rej = 0;
	unsigned int *cts;
	float rmin_fix = -1.0;
	float rmax_fix = -1.0;

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"symmetry",           1, NULL,               'y'},
		{"pdb",                1, NULL,               'p'},
		{"rmin",               1, NULL,               2},
		{"rmax",               1, NULL,               3},
		{0, 0, NULL, 0}
	};

	/* Short options */
	while ((c = getopt_long(argc, argv, "hy:p:", longopts, NULL)) != -1) {

		switch (c) {
		case 'h' :
			show_help(argv[0]);
			return 0;

		case 'y' :
			sym = strdup(optarg);
			break;

		case 'p' :
			pdb = strdup(optarg);
			break;

		case 0 :
			break;

		case 2 :
			if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
				ERROR("Invalid value for --rmin\n");
				return 1;
			}
			break;

		case 3 :
			if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
				ERROR("Invalid value for --rmax\n");
				return 1;
			}
			break;

		default :
			return 1;
		}

	}

	if ( argc != (optind+1) ) {
		ERROR("Please provide exactly one HKL files to check.\n");
		return 1;
	}

	if ( sym == NULL ) {
		sym = strdup("1");
	}

	file = strdup(argv[optind++]);

	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}
	cell = load_cell_from_pdb(pdb);
	free(pdb);

	ref = new_list_intensity();
	esd = new_list_sigma();
	cts = new_list_count();
	items = read_reflections(file, ref, NULL, cts, esd);
	if ( items == NULL ) {
		ERROR("Couldn't open file '%s'\n", file);
		return 1;
	}

	/* Reject reflections */
	good_items = new_items();
	for ( i=0; i<num_items(items); i++ ) {

		struct refl_item *it;
		signed int h, k, l;
		double val, sig;
		int ig = 0;
		double d;

		it = get_item(items, i);
		h = it->h;  k = it->k;  l = it->l;

		val = lookup_intensity(ref, h, k, l);
		sig = lookup_sigma(esd, h, k, l);

		if ( val < 3.0 * sig ) {
			rej++;
			ig = 1;
		}

		d = 0.5/resolution(cell, h, k, l);
		if ( d > 55.0e-10 ) ig = 1;
		//if ( d < 15.0e-10 ) ig = 1;

		//if ( ig ) continue;

		add_item(good_items, h, k, l);

	}

	plot_shells(ref, items, cell, sym, cts, esd, rmin_fix, rmax_fix);

	return 0;
}