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
|
/*
* indexamajig.c
*
* Find hits, index patterns, output hkl+intensity etc.
*
* (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 <hdf5.h>
#include "utils.h"
#include "hdf5-file.h"
#include "index.h"
#include "intensities.h"
#include "peaks.h"
#include "diffraction.h"
#include "detector.h"
#include "sfac.h"
#include "filters.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Process and index FEL diffraction images.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify file containing list of images to process.\n"
" '-' means stdin, which is the default.\n"
" --indexing=<method> Use 'method' for indexing. Choose from:\n"
" none : no indexing\n"
" dirax : invoke DirAx\n"
" --write-drx Write 'xfel.drx' for visualisation of reciprocal\n"
" space. Implied by any indexing method other than"
" 'none'.\n"
" --dump-peaks Write the results of the peak search to stdout.\n"
" --near-bragg Output a list of reflection intensities to stdout.\n"
" --simulate Simulate the diffraction pattern using the indexed\n"
" unit cell.\n"
" --clean-image Perform common-mode noise subtraction and\n"
" background removal on images before proceeding.\n"
" --no-match Don't attempt to match the indexed cell to the\n"
" model, just proceed with the one generated by the\n"
" auto-indexing procedure.\n"
"\n");
}
int main(int argc, char *argv[])
{
int c;
char *filename = NULL;
FILE *fh;
char *rval;
int n_images;
int n_hits;
int config_noindex = 0;
int config_dumpfound = 0;
int config_nearbragg = 0;
int config_writedrx = 0;
int config_simulate = 0;
int config_clean = 0;
int config_nomatch = 0;
IndexingMethod indm;
char *indm_str = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"no-index", 0, &config_noindex, 1},
{"dump-peaks", 0, &config_dumpfound, 1},
{"near-bragg", 0, &config_nearbragg, 1},
{"write-drx", 0, &config_writedrx, 1},
{"indexing", 1, NULL, 'z'},
{"simulate", 0, &config_simulate, 1},
{"clean-image", 0, &config_clean, 1},
{"no-match", 0, &config_nomatch, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:w", longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
show_help(argv[0]);
return 0;
}
case 'i' : {
filename = strdup(optarg);
break;
}
case 'z' : {
indm_str = strdup(optarg);
break;
}
case 0 : {
break;
}
default : {
return 1;
}
}
}
if ( filename == NULL ) {
filename = strdup("-");
}
if ( strcmp(filename, "-") == 0 ) {
fh = stdin;
} else {
fh = fopen(filename, "r");
}
free(filename);
if ( fh == NULL ) {
ERROR("Failed to open input file\n");
return 1;
}
if ( indm_str == NULL ) {
STATUS("You didn't specify an indexing method, so I won't"
" try to index anything. If that isn't what you\n"
" wanted, re-run with --indexing=<method>.\n");
indm = INDEXING_NONE;
} else if ( strcmp(indm_str, "none") == 0 ) {
indm = INDEXING_NONE;
} else if ( strcmp(indm_str, "dirax") == 0) {
indm = INDEXING_DIRAX;
} else {
ERROR("Unrecognised indexing method '%s'\n", indm_str);
return 1;
}
n_images = 0;
n_hits = 0;
do {
char line[1024];
struct hdfile *hdfile;
struct image image;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
image.features = NULL;
image.molecule = load_molecule();
image.data = NULL;
image.indexed_cell = NULL;
/* Set up detector configuration */
image.det.n_panels = 2;
image.det.panels = malloc(2*sizeof(struct panel));
/* Upper panel */
image.det.panels[0].min_x = 0;
image.det.panels[0].max_x = 1023;
image.det.panels[0].min_y = 512;
image.det.panels[0].max_y = 1023;
image.det.panels[0].cx = 491.9;
image.det.panels[0].cy = 440.7;
image.det.panels[0].clen = 67.0e-3;
image.det.panels[0].res = 13333.3; /* 75 micron pixel size */
/* Lower panel */
image.det.panels[1].min_x = 0;
image.det.panels[1].max_x = 1023;
image.det.panels[1].min_y = 0;
image.det.panels[1].max_y = 511;
image.det.panels[1].cx = 492.0;
image.det.panels[1].cy = 779.7;
image.det.panels[1].clen = 75.0e-3;
image.det.panels[1].res = 13333.3; /* 75 micron pixel size */
STATUS("Processing '%s'\n", line);
n_images++;
hdfile = hdfile_open(line);
if ( hdfile == NULL ) {
continue;
} else if ( hdfile_set_first_image(hdfile, "/") ) {
ERROR("Couldn't select path\n");
continue;
}
hdf5_read(hdfile, &image);
if ( config_clean ) {
clean_image(&image);
}
/* Perform 'fine' peak search */
search_peaks(&image);
if ( image_feature_count(image.features) > 5 ) {
if ( config_dumpfound ) dump_peaks(&image);
/* Not indexing nor writing xfel.drx?
* Then there's nothing left to do. */
if ( (!config_writedrx) && (indm == INDEXING_NONE) ) {
goto done;
}
/* Calculate orientation matrix (by magic) */
if ( config_writedrx || (indm != INDEXING_NONE) ) {
index_pattern(&image, indm, config_nomatch);
}
/* No cell at this point? Then we're done. */
if ( image.indexed_cell == NULL ) goto done;
n_hits++;
/* Simulation or intensity measurements both require
* Ewald sphere vectors */
if ( config_nearbragg || config_simulate ) {
/* Simulate a diffraction pattern */
image.sfacs = NULL;
image.twotheta = NULL;
image.hdr = NULL;
/* View head-on (unit cell is tilted) */
image.orientation.w = 1.0;
image.orientation.x = 0.0;
image.orientation.y = 0.0;
image.orientation.z = 0.0;
}
/* Measure intensities if requested */
if ( config_nearbragg ) {
output_intensities(&image, image.indexed_cell);
}
/* Simulate pattern if requested */
if ( config_simulate ) {
image.data = NULL;
get_diffraction(&image, 8, 8, 8, 0);
if ( image.molecule == NULL ) {
ERROR("Couldn't open molecule.pdb\n");
return 1;
}
record_image(&image, 0, 0, 0);
hdf5_write("simulated.h5", image.data,
image.width, image.height,
H5T_NATIVE_INT16);
}
}
done:
free(image.data);
image_feature_list_free(image.features);
hdfile_close(hdfile);
H5close();
} while ( rval != NULL );
fclose(fh);
STATUS("There were %i images.\n", n_images);
STATUS("%i hits were found.\n", n_hits);
return 0;
}
|
