aboutsummaryrefslogtreecommitdiff
path: root/src/post-refinement.c
blob: c3432af122505e66deeb6ac6ee45b93e0026018c (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
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
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
/*
 * post-refinement.c
 *
 * Post refinement
 *
 * (c) 2006-2011 Thomas White <taw@physics.org>
 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */

#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 "image.h"
#include "post-refinement.h"
#include "peaks.h"
#include "symmetry.h"
#include "geometry.h"
#include "cell.h"


/* Maximum number of iterations of NLSq to do for each image per macrocycle. */
#define MAX_CYCLES (10)


/* Refineable parameters */
enum {
	REF_ASX,
	REF_BSX,
	REF_CSX,
	NUM_PARAMS,
	REF_ASY,
	REF_BSY,
	REF_CSY,
	REF_ASZ,
	REF_BSZ,
	REF_CSZ,
	REF_DIV,
	REF_R,
};


/* Returns dp/dr at "r" */
static double partiality_gradient(double r, double profile_radius)
{
	double q, dpdq, dqdr;

	/* Calculate degree of penetration */
	q = (r + profile_radius)/(2.0*profile_radius);
	//STATUS("q=%f\n", q);

	/* dp/dq */
	dpdq = 6.0*(q-pow(q, 2.0));

	/* dq/dr */
	dqdr = 1.0 / (2.0*profile_radius);

	return dpdq * dqdr;
}


/* Returns dp/drad at "r" */
static double partiality_rgradient(double r, double profile_radius)
{
	double q, dpdq, dqdrad;

	/* Calculate degree of penetration */
	q = (r + profile_radius)/(2.0*profile_radius);

	/* dp/dq */
	dpdq = 6.0*(q-pow(q, 2.0));

	/* dq/drad */
	dqdrad = 0.5 * (1.0 - r * pow(profile_radius, -2.0));

	return dpdq * dqdrad;
}


/* Return the gradient of parameter 'k' given the current status of 'image'. */
static double gradient(struct image *image, int k, Reflection *refl, double r)
{
	double ds, tt, azi;
	double nom, den;
	double g;
	double asx, asy, asz;
	double bsx, bsy, bsz;
	double csx, csy, csz;
	double xl, yl, zl;
	signed int hs, ks, ls;
	double r1, r2, p;
	int clamp_low, clamp_high;

	get_symmetric_indices(refl, &hs, &ks, &ls);

	cell_get_reciprocal(image->indexed_cell, &asx, &asy, &asz,
	                                         &bsx, &bsy, &bsz,
	                                         &csx, &csy, &csz);
	xl = hs*asx + ks*bsx + ls*csx;
	yl = hs*asy + ks*bsy + ls*csy;
	zl = hs*asz + ks*bsz + ls*csz;
	//STATUS("%3i %3i %3i\n", hs, ks, ls);

	ds = 2.0 * resolution(image->indexed_cell, hs, ks, ls);
	tt = angle_between(0.0, 0.0, 1.0, xl, yl, zl+1.0/image->lambda);
	azi = angle_between(1.0, 0.0, 0.0, xl, yl, 0.0);
	//STATUS("d*=%.2e, 2theta=%.2f deg, azi=%.2f deg\n",
	//       ds, rad2deg(tt), rad2deg(azi));

	get_partial(refl, &r1, &r2, &p, &clamp_low, &clamp_high);

	/* Calculate the gradient of partiality wrt excitation error. */
	g = 0.0;
	if ( clamp_low == 0 ) {
		g += partiality_gradient(r1, r);
	}
	if ( clamp_high == 0 ) {
		g -= partiality_gradient(r2, r);
	}
	//STATUS("clamp status low=%i high=%i\n", clamp_low, clamp_high);
	//STATUS("excitation errors %e %e\n", r1, r2);
	//STATUS("dp/dr = %e\n", g);

	/* For many gradients, just multiply the above number by the gradient
	 * of excitation error wrt whatever. */
	switch ( k ) {

	case REF_DIV :
		nom = sqrt(2.0) * ds * sin(image->div/2.0);
		den = sqrt(1.0 - cos(image->div/2.0));
		return (nom/den) * g;

	case REF_R :
		g = 0.0;
		if ( clamp_low == 0 ) {
			g += partiality_rgradient(r1, r);
		}
		if ( clamp_high == 0 ) {
			g += partiality_rgradient(r2, r);
		}
		return g;

	/* Cell parameters and orientation */
	case REF_ASX :
		return -hs * sin(tt) * cos(azi) * g;
	case REF_BSX :
		return -ks * sin(tt) * cos(azi) * g;
	case REF_CSX :
		return -ls * sin(tt) * cos(azi) * g;
	case REF_ASY :
		return hs * sin(tt) * sin(azi) * g;
	case REF_BSY :
		return ks * sin(tt) * sin(azi) * g;
	case REF_CSY :
		return ls * sin(tt) * sin(azi) * g;
	case REF_ASZ :
		return hs * cos(tt) * g;
	case REF_BSZ :
		return ks * cos(tt) * g;
	case REF_CSZ :
		return ls * cos(tt) * g;

	}

	ERROR("No gradient defined for parameter %i\n", k);
	abort();
}


static void apply_cell_shift(UnitCell *cell, int k, double shift)
{
	double asx, asy, asz;
	double bsx, bsy, bsz;
	double csx, csy, csz;

	cell_get_reciprocal(cell, &asx, &asy, &asz,
	                          &bsx, &bsy, &bsz,
	                          &csx, &csy, &csz);

	//STATUS("Shifting by %e\n", shift);

	switch ( k )
	{
		case REF_ASX :  asx += shift;  break;
		case REF_ASY :  asy += shift;  break;
		case REF_ASZ :  asz += shift;  break;
		case REF_BSX :  bsx += shift;  break;
		case REF_BSY :  bsy += shift;  break;
		case REF_BSZ :  bsz += shift;  break;
		case REF_CSX :  csx += shift;  break;
		case REF_CSY :  csy += shift;  break;
		case REF_CSZ :  csz += shift;  break;
	}

	cell_set_reciprocal(cell, asx, asy, asz,
	                          bsx, bsy, bsz,
	                          csx, csy, csz);

	if ( k == REF_CSZ ) {
		double a, b, c, al, be, ga;
		cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
		STATUS("New cell: %5.2f %5.2f %5.2f nm %5.2f %5.2f %5.2f deg\n",
		       a/1.0e-9, b/1.0e-9, c/1.0e-9,
		       rad2deg(al), rad2deg(be), rad2deg(ga));
	}
}


/* Apply the given shift to the 'k'th parameter of 'image'. */
static void apply_shift(struct image *image, int k, double shift)
{
	switch ( k ) {

	case REF_DIV :
		image->div += shift;
		break;

	case REF_R :
		image->profile_radius += shift;
		break;

	case REF_ASX :
	case REF_ASY :
	case REF_ASZ :
	case REF_BSX :
	case REF_BSY :
	case REF_BSZ :
	case REF_CSX :
	case REF_CSY :
	case REF_CSZ :
		apply_cell_shift(image->indexed_cell, k, shift);
		break;

	default :
		ERROR("No shift defined for parameter %i\n", k);
		abort();

	}
}


/* Perform one cycle of post refinement on 'image' against 'full' */
static double pr_iterate(struct image *image, const RefList *full,
                         const char *sym)
{
	gsl_matrix *M;
	gsl_vector *v;
	gsl_vector *shifts;
	int param;
	Reflection *refl;
	RefListIterator *iter;
	RefList *reflections;
	double max_shift;

	reflections = image->reflections;

	M = gsl_matrix_calloc(NUM_PARAMS, NUM_PARAMS);
	v = gsl_vector_calloc(NUM_PARAMS);

	/* Construct the equations, one per reflection in this image */
	for ( refl = first_refl(reflections, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {

		signed int ha, ka, la;
		double I_full, delta_I;
		double I_partial;
		int k;
		double p;
		Reflection *match;
		double gradients[NUM_PARAMS];

		if ( !get_scalable(refl) ) continue;

		/* Find the full version */
		get_indices(refl, &ha, &ka, &la);
		match = find_refl(full, ha, ka, la);
		if ( match == NULL ) continue;
		/* Some reflections may have recently become scalable, but
		 * scale_intensities() might not yet have been called, so the
		 * full version may not have been calculated yet. */
		I_full = get_intensity(match);

		/* Actual measurement of this reflection from this pattern? */
		I_partial = get_intensity(refl);
		p = get_partiality(refl);
		delta_I = I_partial - (p * image->osf * I_full);

		/* Calculate all gradients for this reflection */
		for ( k=0; k<NUM_PARAMS; k++ ) {
			double gr;
			gr = gradient(image, k, refl, image->profile_radius);
			gradients[k] = gr;
		}

		for ( k=0; k<NUM_PARAMS; k++ ) {

			int g;
			double v_c, v_curr;
			double gr;

			for ( g=0; g<NUM_PARAMS; g++ ) {

				double M_c, M_curr;

				M_c = gradients[g] * gradients[k];
				M_c *= pow(image->osf * I_full, 2.0);

				M_curr = gsl_matrix_get(M, g, k);
				gsl_matrix_set(M, g, k, M_curr + M_c);

			}

			gr = gradients[k];
			v_c = delta_I * image->osf * I_full * gr;
			v_curr = gsl_vector_get(v, k);
			gsl_vector_set(v, k, v_curr + v_c);

		}

	}
	//STATUS("total gradient = %e\n",  gsl_matrix_get(M, 0, 0));
	//show_matrix_eqn(M, v, NUM_PARAMS);

	shifts = gsl_vector_alloc(NUM_PARAMS);
	max_shift = 0.0;
	if ( gsl_linalg_HH_solve(M, v, shifts) ) {
		ERROR("Couldn't solve normal equations!\n");
	} else {

		for ( param=0; param<NUM_PARAMS; param++ ) {
			double shift = gsl_vector_get(shifts, param);
			apply_shift(image, param, shift);
			if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
		}

	}

	gsl_matrix_free(M);
	gsl_vector_free(v);
	gsl_vector_free(shifts);

	return max_shift;
}


static void check_scalable(RefList *check)
{
	Reflection *refl;
	RefListIterator *iter;

	STATUS("------ Scalability check ------\n");
	for ( refl = first_refl(check, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{

		signed int h, k, l;
		if ( get_scalable(refl) ) continue;

		get_indices(refl, &h, &k, &l);
		STATUS("%3i %3i %3i is not scalable.\n", h, k, l);

	}
	STATUS("------ End of scalability check ------\n");
}


static double mean_partial_dev(struct image *image,
                               const RefList *full, const char *sym)
{
	double dev = 0.0;

	/* For each reflection */
	Reflection *refl;
	RefListIterator *iter;

	for ( refl = first_refl(image->reflections, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {

		double G, p;
		signed int h, k, l;
		Reflection *full_version;
		double I_full, I_partial;

		if ( !get_scalable(refl) ) continue;

		get_indices(refl, &h, &k, &l);
		assert ((h!=0) || (k!=0) || (l!=0));

		if ( !get_scalable(refl) ) continue;

		full_version = find_refl(full, h, k, l);
		if ( full_version == NULL ) continue;
		/* Some reflections may have recently become scalable, but
		 * scale_intensities() might not yet have been called, so the
		 * full version may not have been calculated yet. */

		G = image->osf;
		p = get_partiality(refl);
		I_partial = get_intensity(refl);
		I_full = get_intensity(full_version);
		//STATUS("%3i %3i %3i  %5.2f  %5.2f  %5.2f  %5.2f  %5.2f\n",
		//       h, k, l, G, p, I_partial, I_full,
		//       I_partial - p*G*I_full);

		dev += pow(I_partial - p*G*I_full, 2.0);

	}

	return dev;
}


static void plot_curve(struct image *image, const RefList *full,
                       const char *sym)
{
	double ax, ay, az;
	double bx, by, bz;
	double cx, cy, cz;
	UnitCell *cell = image->indexed_cell;
	double shval, origval;
	int i;

	cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
	STATUS("Starting ax* = %e\n", ax);
	shval = 0.01*ax;
	origval = ax;

	for ( i=-10; i<=10; i++ ) {

		double dev;

		cell_get_reciprocal(cell, &ax, &ay, &az, &bx,
		                         &by, &bz, &cx, &cy, &cz);
		ax = origval + (double)i*shval;
		cell_set_reciprocal(cell, ax, ay, az, bx, by, bz, cx, cy, cz);

		update_partialities(image, sym, NULL, NULL, NULL, NULL);

		dev = mean_partial_dev(image, full, sym);
		STATUS("%i %e %e\n", i, ax, dev);

	}
}


void pr_refine(struct image *image, const RefList *full, const char *sym)
{
	double max_shift, dev;
	int i;
	double ax, ay, az;
	double bx, by, bz;
	double cx, cy, cz;

	cell_get_reciprocal(image->indexed_cell, &ax, &ay, &az,
	                    &bx, &by, &bz, &cx, &cy, &cz);
	STATUS("At start of post refinement, ax*=%e\n", ax);

	dev = mean_partial_dev(image, full, sym);
	//STATUS("PR starting dev = %5.2f\n", dev);

	/* FIXME: This is for debugging */
	//plot_curve(image, full, sym);
	//return;

	i = 0;
	do {

		double dev;

		max_shift = pr_iterate(image, full, sym);

		update_partialities(image, sym, NULL, NULL, NULL, NULL);

		dev = mean_partial_dev(image, full, sym);
		STATUS("PR Iteration %2i: max shift = %5.2f dev = %5.2f\n",
		       i, max_shift, dev);

		i++;

	} while ( (max_shift > 0.01) && (i < MAX_CYCLES) );

	cell_get_reciprocal(image->indexed_cell, &ax, &ay, &az,
	                    &bx, &by, &bz, &cx, &cy, &cz);
	STATUS("At end of post refinement, ax*=%e\n", ax);
}