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
|
/*
* process_image.c
*
* The processing pipeline for one image
*
* Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2013 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 <hdf5.h>
#include <gsl/gsl_errno.h>
#include "utils.h"
#include "hdf5-file.h"
#include "index.h"
#include "peaks.h"
#include "detector.h"
#include "filters.h"
#include "thread-pool.h"
#include "beam-parameters.h"
#include "geometry.h"
#include "stream.h"
#include "reflist-utils.h"
#include "process_image.h"
#include "integration.h"
void process_image(const struct index_args *iargs, struct pattern_args *pargs,
Stream *st, int cookie)
{
float *data_for_measurement;
size_t data_size;
int check;
struct hdfile *hdfile;
struct image image;
int i;
char filename[1024];
/* Prefix to jump out of temporary folder */
if ( pargs->filename[0] != '/' ) {
snprintf(filename, 1023, "../../%s", pargs->filename);
} else {
snprintf(filename, 1023, "%s", pargs->filename);
}
image.features = NULL;
image.data = NULL;
image.flags = NULL;
image.copyme = iargs->copyme;
image.id = cookie;
image.filename = pargs->filename; /* Relative to top level */
image.beam = iargs->beam;
image.det = iargs->det;
image.crystals = NULL;
image.n_crystals = 0;
hdfile = hdfile_open(filename); /* Relative to temporary folder */
if ( hdfile == NULL ) return;
if ( iargs->element != NULL ) {
int r;
r = hdfile_set_image(hdfile, iargs->element);
if ( r ) {
ERROR("Couldn't select path '%s'\n", iargs->element);
hdfile_close(hdfile);
return;
}
} else {
int r;
r = hdfile_set_first_image(hdfile, "/");
if ( r ) {
ERROR("Couldn't select first path\n");
hdfile_close(hdfile);
return;
}
}
check = hdf5_read(hdfile, &image, 1);
if ( check ) {
hdfile_close(hdfile);
return;
}
/* Take snapshot of image after CM subtraction but before applying
* horrible noise filters to it */
data_size = image.width * image.height * sizeof(float);
data_for_measurement = malloc(data_size);
memcpy(data_for_measurement, image.data, data_size);
if ( iargs->median_filter > 0 ) {
filter_median(&image, iargs->median_filter);
}
if ( iargs->noisefilter ) {
filter_noise(&image);
}
switch ( iargs->peaks ) {
case PEAK_HDF5:
/* Get peaks from HDF5 */
if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) {
ERROR("Failed to get peaks from HDF5 file.\n");
}
if ( !iargs->no_revalidate ) {
validate_peaks(&image, iargs->min_snr,
iargs->ir_inn, iargs->ir_mid,
iargs->ir_out, iargs->use_saturated);
}
break;
case PEAK_ZAEF:
search_peaks(&image, iargs->threshold,
iargs->min_gradient, iargs->min_snr,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
iargs->use_saturated);
break;
}
/* Get rid of noise-filtered version at this point
* - it was strictly for the purposes of peak detection. */
free(image.data);
image.data = data_for_measurement;
/* Index the pattern */
index_pattern(&image, iargs->indm, iargs->ipriv);
pargs->n_crystals = image.n_crystals;
/* Default beam parameters */
image.div = image.beam->divergence;
image.bw = image.beam->bandwidth;
/* Integrate each crystal's diffraction spots */
for ( i=0; i<image.n_crystals; i++ ) {
/* Set default crystal parameter(s) */
crystal_set_profile_radius(image.crystals[i],
image.beam->profile_radius);
crystal_set_mosaicity(image.crystals[i], 2e-3); /* radians */
crystal_set_image(image.crystals[i], &image);
}
/* Integrate all the crystals at once - need all the crystals so that
* overlaps can be detected. */
integrate_all(&image, iargs->int_meth,
iargs->ir_inn, iargs->ir_mid, iargs->ir_out);
write_chunk(st, &image, hdfile,
iargs->stream_peaks, iargs->stream_refls);
for ( i=0; i<image.n_crystals; i++ ) {
cell_free(crystal_get_cell(image.crystals[i]));
reflist_free(crystal_get_reflections(image.crystals[i]));
crystal_free(image.crystals[i]);
}
for ( i=0; i<image.det->n_panels; i++ ) {
free(image.dp[i]);
free(image.bad[i]);
}
free(image.data);
if ( image.flags != NULL ) free(image.flags);
image_feature_list_free(image.features);
hdfile_close(hdfile);
}
|
