aboutsummaryrefslogtreecommitdiff
path: root/src/scaling.c
blob: f007b757911ee740e72a351e46569466b948ebe2 (plain)
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
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
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
94
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
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
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
/*
 * scaling.c
 *
 * Scaling
 *
 * Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 *
 * Authors:
 *   2010-2020 Thomas White <taw@physics.org>
 *
 * This file is part of CrystFEL.
 *
 * CrystFEL is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * CrystFEL is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

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


#include <stdlib.h>
#include <assert.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_eigen.h>
#include <gsl/gsl_fit.h>
#include <gsl/gsl_statistics_double.h>

#include "merge.h"
#include "post-refinement.h"
#include "symmetry.h"
#include "cell.h"
#include "cell-utils.h"
#include "scaling.h"
#include "reflist-utils.h"


struct scale_args
{
	RefList *full;
	Crystal *crystal;
	int flags;
};


struct scale_queue_args
{
	int n_started;
	int n_done;
	Crystal **crystals;
	int n_crystals;
	struct scale_args task_defaults;
};


static void scale_crystal(void *task, int id)
{
	struct scale_args *pargs = task;
	scale_one_crystal(pargs->crystal, pargs->full, pargs->flags);
}


static void *get_crystal(void *vqargs)
{
	struct scale_args *task;
	struct scale_queue_args *qargs = vqargs;

	task = malloc(sizeof(struct scale_args));
	memcpy(task, &qargs->task_defaults, sizeof(struct scale_args));

	task->crystal = qargs->crystals[qargs->n_started];

	qargs->n_started++;

	return task;
}


static void done_crystal(void *vqargs, void *task)
{
	struct scale_queue_args *qa = vqargs;
	qa->n_done++;
	progress_bar(qa->n_done, qa->n_crystals, "Scaling");
	free(task);
}


static double total_log_r(Crystal **crystals, int n_crystals, RefList *full,
                          int *ninc)
{
	int i;
	double total = 0.0;
	int n = 0;

	for ( i=0; i<n_crystals; i++ ) {
		double r;
		if ( crystal_get_user_flag(crystals[i]) ) continue;
		r = log_residual(crystals[i], full, 0, NULL, NULL);
		if ( isnan(r) ) continue;
		total += r;
		n++;
	}

	if ( ninc != NULL ) *ninc = n;
	return total;
}


/* Perform iterative scaling, all the way to convergence */
void scale_all(Crystal **crystals, int n_crystals, int nthreads, int scaleflags)
{
	struct scale_args task_defaults;
	struct scale_queue_args qargs;
	double old_res, new_res;
	int niter = 0;

	task_defaults.crystal = NULL;
	task_defaults.flags = scaleflags;
	task_defaults.full = NULL;  /* (not used) */

	qargs.task_defaults = task_defaults;
	qargs.n_crystals = n_crystals;
	qargs.crystals = crystals;

	/* Don't have threads which are doing nothing */
	if ( n_crystals < nthreads ) nthreads = n_crystals;

	new_res = INFINITY;
	do {
		RefList *full;
		int ninc;
		double bef_res;

		full = merge_intensities(crystals, n_crystals, nthreads,
		                         2, INFINITY, 0, 1);
		old_res = new_res;
		bef_res = total_log_r(crystals, n_crystals, full, NULL);

		qargs.task_defaults.full = full;
		qargs.n_started = 0;
		qargs.n_done = 0;
		run_threads(nthreads, scale_crystal, get_crystal, done_crystal,
		            &qargs, n_crystals, 0, 0, 0);

		new_res = total_log_r(crystals, n_crystals, full, &ninc);
		STATUS("Log residual went from %e to %e, %i crystals\n",
		       bef_res, new_res, ninc);

		int i;
		double meanB = 0.0;
		for ( i=0; i<n_crystals; i++ ) {
			meanB += crystal_get_Bfac(crystals[i]);
		}
		meanB /= n_crystals;
		STATUS("Mean B = %e\n", meanB);

		free_contribs(full);
		reflist_free(full);
		niter++;

	} while ( (fabs(new_res-old_res) >= 0.01*old_res) && (niter < 10) );

	if ( niter == 10 ) {
		ERROR("Too many iterations - giving up!\n");
	}
}


/* Calculates G and B, by which cr's reflections should be multiplied to fit reference */
int scale_one_crystal(Crystal *cr, const RefList *listR, int flags)
{
	const Reflection *reflS;
	RefListIterator *iter;
	int max_n = 256;
	int n = 0;
	double *x;
	double *y;
	double *w;
	int r;
	double cov00, cov01, cov11, chisq;
	int n_esdS = 0;
	int n_ihS = 0;
	int n_ihR = 0;
	int n_nanS = 0;
	int n_nanR = 0;
	int n_infS = 0;
	int n_infR = 0;
	int n_part = 0;
	int n_nom = 0;
	int n_red = 0;
	RefList *listS = crystal_get_reflections(cr);
	UnitCell *cell = crystal_get_cell(cr);
	double G, B;

	assert(cell != NULL);
	assert(listR != NULL);
	assert(listS != NULL);

	x = malloc(max_n*sizeof(double));
	w = malloc(max_n*sizeof(double));
	y = malloc(max_n*sizeof(double));
	if ( (x==NULL) || (y==NULL) || (w==NULL) ) {
		ERROR("Failed to allocate memory for scaling.\n");
		return 1;
	}

	int nb = 0;
	for ( reflS = first_refl_const(listS, &iter);
	      reflS != NULL;
	      reflS = next_refl_const(reflS, iter) )
	{
		signed int h, k, l;
		const Reflection *reflR;
		double IhR, IhS, esdS, pS, LS;
		double s;

		nb++;

		get_indices(reflS, &h, &k, &l);
		reflR = find_refl(listR, h, k, l);
		if ( reflR == NULL ) {
			n_nom++;
			continue;
		}

		s = resolution(cell, h, k, l);

		IhR = get_intensity(reflR);
		IhS = get_intensity(reflS);
		esdS = get_esd_intensity(reflS);
		pS = get_partiality(reflS);
		LS = get_lorentz(reflS);

		/* Problem cases in approximate descending order of severity */
		if ( isnan(IhR) ) { n_nanR++; continue; }
		if ( isinf(IhR) ) { n_infR++; continue; }
		if ( isnan(IhS) ) { n_nanS++; continue; }
		if ( isinf(IhS) ) { n_infS++; continue; }
		if ( pS < 0.3 ) { n_part++; continue; }
		if ( IhS <= 0.0 ) { n_ihS++; continue; }
		if ( IhS <= 3.0*esdS ) { n_esdS++; continue; }
		if ( IhR <= 0.0 ) { n_ihR++; continue; }
		if ( get_redundancy(reflR) < 2 ) { n_red++; continue; }

		if ( n == max_n ) {
			max_n *= 2;
			x = srealloc(x, max_n*sizeof(double));
			y = srealloc(y, max_n*sizeof(double));
			w = srealloc(w, max_n*sizeof(double));
			if ( (x==NULL) || (y==NULL) || (w==NULL) ) {
				free(x);
				free(y);
				free(w);
				ERROR("Failed to allocate memory for scaling.\n");
				return 1;
			}

		}

		x[n] = s*s;
		y[n] = log(LS) + log(IhS) -log(pS) - log(IhR);
		w[n] = pS;
		n++;

	}

	if ( n < 2 ) {
		if ( flags & SCALE_VERBOSE_ERRORS ) {
			ERROR("Not enough reflections for scaling (had %i, but %i remain)\n", nb, n);
			if ( n_esdS ) ERROR("%i subject reflection esd\n", n_esdS);
			if ( n_ihR ) ERROR("%i reference reflection intensity\n", n_ihR);
			if ( n_red ) ERROR("%i reference reflection redundancy\n", n_red);
			if ( n_ihS ) ERROR("%i subject reflection intensity\n", n_ihS);
			if ( n_nanR ) ERROR("%i reference reflection nan\n", n_nanR);
			if ( n_nanS ) ERROR("%i subject reflection nan\n", n_nanS);
			if ( n_infR ) ERROR("%i reference reflection inf\n", n_infR);
			if ( n_infS ) ERROR("%i subject reflection inf\n", n_infS);
			if ( n_part ) ERROR("%i subject reflection partiality\n", n_part);
			if ( n_nom ) ERROR("%i no match in reference list\n", n_nom);
		}
		free(x);
		free(y);
		free(w);
		return 1;
	}

	if ( flags & SCALE_NO_B ) {
		G = gsl_stats_wmean(w, 1, y, 1, n);
		B = 0.0;
		r = 0;
	} else {
		r = gsl_fit_wlinear(x, 1, w, 1, y, 1, n, &G, &B, &cov00, &cov01, &cov11, &chisq);
	}

	if ( r ) {
		ERROR("Scaling failed.\n");
		free(x);
		free(y);
		free(w);
		return 1;
	}

	if ( isnan(G) ) {

		if ( flags & SCALE_VERBOSE_ERRORS ) {
			ERROR("Scaling gave NaN (%i pairs)\n", n);
			if ( n < 10 ) {
				int i;
				for ( i=0; i<n; i++ ) {
					STATUS("%3i %e %e %e\n", i, x[i], y[i], w[i]);
				}
			}
		}

		free(x);
		free(y);
		free(w);
		return 1;
	}

	crystal_set_osf(cr, exp(G));
	crystal_set_Bfac(cr, -B);

	free(x);
	free(y);
	free(w);

	return 0;
}