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
|
/*
* post-refinement.c
*
* Post refinement
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <gsl/gsl_poly.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"
/* Return the gradient of parameter 'k' given the current status of 'image'. */
double gradient(struct image *image, int k,
struct cpeak spot, double I_partial)
{
double ds;
double nom, den;
ds = 2.0 * resolution(image->indexed_cell, spot.h, spot.k, spot.l);
switch ( k ) {
case REF_SCALE :
return I_partial;
case REF_DIV :
nom = sqrt(2.0) * ds * sin(image->div);
den = sqrt(1.0 - cos(image->div));
return nom/den;
}
ERROR("No gradient defined for parameter %i\n", k);
abort();
}
/* Apply the given shift to the 'k'th parameter of 'image'. */
void apply_shift(struct image *image, int k, double shift)
{
switch ( k ) {
case REF_SCALE :
image->osf += shift;
break;
case REF_DIV :
STATUS("Shifting div by %e\n", shift);
image->div += shift;
break;
default :
ERROR("No shift defined for parameter %i\n", k);
abort();
}
}
double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
const char *sym, double *i_full, FILE *graph)
{
int h;
double delta_I = 0.0;
for ( h=0; h<n; h++ ) {
signed int hind, kind, lind;
signed int ha, ka, la;
double I_full;
float I_partial;
float xc, yc;
hind = spots[h].h;
kind = spots[h].k;
lind = spots[h].l;
/* Don't attempt to use spots with very small
* partialities, since it won't be accurate. */
if ( spots[h].p < 0.1 ) continue;
/* Actual measurement of this reflection from this
* pattern? */
/* FIXME: Coordinates aren't whole numbers */
if ( integrate_peak(image, spots[h].x, spots[h].y,
&xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
continue;
}
I_partial *= image->osf;
get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
I_full = lookup_intensity(i_full, ha, ka, la);
delta_I += fabs(I_partial - spots[h].p * I_full);
if ( graph != NULL ) {
fprintf(graph, "%3i %3i %3i %5.2f (at %5.2f,%5.2f)"
" %5.2f %5.2f\n",
hind, kind, lind, I_partial/spots[h].p, xc, yc,
spots[h].p, I_partial / I_full);
}
}
return delta_I / (double)n;
}
/* Perform one cycle of post refinement on 'image' against 'i_full' */
double pr_iterate(struct image *image, double *i_full, const char *sym,
struct cpeak **pspots, int *n)
{
gsl_matrix *M;
gsl_vector *v;
gsl_vector *shifts;
int h, param;
struct cpeak *spots = *pspots;
M = gsl_matrix_calloc(NUM_PARAMS, NUM_PARAMS);
v = gsl_vector_calloc(NUM_PARAMS);
/* Construct the equations, one per reflection in this image */
for ( h=0; h<*n; h++ ) {
signed int hind, kind, lind;
signed int ha, ka, la;
double I_full, delta_I;
float I_partial;
float xc, yc;
int k;
hind = spots[h].h;
kind = spots[h].k;
lind = spots[h].l;
/* Don't attempt to use spots with very small
* partialities, since it won't be accurate. */
if ( spots[h].p < 0.1 ) continue;
/* Actual measurement of this reflection from this
* pattern? */
/* FIXME: Coordinates aren't whole numbers */
if ( integrate_peak(image, spots[h].x, spots[h].y,
&xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
continue;
}
I_partial *= image->osf;
get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
I_full = lookup_intensity(i_full, ha, ka, la);
delta_I = I_partial - spots[h].p * I_full;
for ( k=0; k<NUM_PARAMS; k++ ) {
int g;
double v_c;
for ( g=0; g<NUM_PARAMS; g++ ) {
double M_curr, M_c;
M_curr = gsl_matrix_get(M, g, k);
M_c = gradient(image, g, spots[h], I_partial)
* gradient(image, k, spots[h], I_partial);
M_c *= pow(I_full, 2.0);
gsl_matrix_set(M, g, k, M_curr + M_c);
}
v_c = delta_I * I_full * gradient(image, k, spots[h],
I_partial);
gsl_vector_set(v, k, v_c);
}
}
shifts = gsl_vector_alloc(NUM_PARAMS);
gsl_linalg_HH_solve(M, v, shifts);
for ( param=0; param<NUM_PARAMS; param++ ) {
double shift = gsl_vector_get(shifts, param);
apply_shift(image, param, shift);
}
gsl_matrix_free(M);
gsl_vector_free(v);
gsl_vector_free(shifts);
free(spots);
spots = find_intersections(image, image->indexed_cell, n, 0);
*pspots = spots;
return mean_partial_dev(image, spots, *n, sym, i_full, NULL);
}
|
