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
|
/*
* get_hkl.c
*
* Small program to write out a list of h,k,l,I values given a structure
*
* (c) 2006-2009 Thomas White <thomas.white@desy.de>
*
* 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"
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Write idealised intensity lists.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -t, --template=<filename> Only include reflections mentioned in file.\n"
" --poisson Simulate Poisson samples.\n"
" -o --output=<filename> Output filename (default: stdout).\n");
}
static double *template_reflections(double *ref, const char *filename)
{
char *rval;
double *out;
FILE *fh;
fh = fopen(filename, "r");
if ( fh == NULL ) {
return NULL;
}
out = new_list_intensity();
do {
char line[1024];
double val;
int r;
signed int h, k, l;
rval = fgets(line, 1023, fh);
r = sscanf(line, "%i %i %i", &h, &k, &l);
if ( r != 3 ) continue;
val = lookup_intensity(ref, h, k, l);
set_intensity(out, h, k, l, val);
} while ( rval != NULL );
fclose(fh);
return out;
}
/* Apply Poisson noise to all reflections */
static void noisify_reflections(double *ref)
{
signed int h, k, l;
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double val;
int c;
val = lookup_intensity(ref, h, k, l);
c = poisson_noise(val);
set_intensity(ref, h, k, l, c);
}
}
progress_bar(h+INDMAX, 2*INDMAX, "Simulating noise");
}
}
int main(int argc, char *argv[])
{
int c;
double *ref;
struct molecule *mol;
char *template = NULL;
int config_noisify = 0;
char *output = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"template", 1, NULL, 't'},
{"poisson", 0, &config_noisify, 1},
{"output", 1, NULL, 'o'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "ht:o:", longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
show_help(argv[0]);
return 0;
}
case 't' : {
template = strdup(optarg);
break;
}
case 'o' : {
output = strdup(optarg);
break;
}
case 0 : {
break;
}
default : {
return 1;
}
}
}
mol = load_molecule();
get_reflections_cached(mol, eV_to_J(2.0e3));
ref = ideal_intensities(mol->reflections);
if ( template != NULL ) {
double *tref;
tref = template_reflections(ref, template);
if ( tref == NULL ) {
ERROR("Couldn't read template file!\n");
return 1;
}
free(ref);
ref = tref;
}
if ( config_noisify ) noisify_reflections(ref);
write_reflections(output, NULL, ref, 1, mol->cell);
return 0;
}
|