aboutsummaryrefslogtreecommitdiff
path: root/src/process_image.h
blob: 8174f73da6433120bc2483d81e3de5e6a0715748 (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
/*
 * process_image.h
 *
 * The processing pipeline for one image
 *
 * Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 *
 * Authors:
 *   2010-2020 Thomas White <taw@physics.org>
 *   2014-2017 Valerio Mariani <valerio.mariani@desy.de>
 *   2017-2018 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de>
 *
 * 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/>.
 *
 */

#ifndef PROCESS_IMAGE_H
#define PROCESS_IMAGE_H

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

struct index_args;

#ifdef HAVE_MSGPACK
#include <msgpack.h>
#endif

#include "integration.h"
#include "im-sandbox.h"
#include "time-accounts.h"
#include "peaks.h"


/* Information about the indexing process which is common to all patterns */
struct index_args
{
	UnitCell *cell;
	int cmfilter;
	int noisefilter;
	int median_filter;
	float threshold;
	float min_sq_gradient;
	float min_snr;
	int check_hdf5_snr;
	DataTemplate *dtempl;
	IndexingPrivate *ipriv;
	enum peak_search_method peaks;
	float tols[6];
	int half_pixel_shift;
	float pk_inn;
	float pk_mid;
	float pk_out;
	float ir_inn;
	float ir_mid;
	float ir_out;
	int min_res;
	int max_res;
	int max_n_peaks;
	int min_pix_count;
	int max_pix_count;
	int local_bg_radius;
	int min_peaks;
	float min_snr_biggest_pix;
	float min_snr_peak_pix;
	float min_sig;
	float min_peak_over_neighbour;
	int integrate_saturated;
	int use_saturated;
	int no_revalidate;
	int stream_flags;
	int stream_nonhits;
	IntegrationMethod int_meth;
	IntDiag int_diag;
	signed int int_diag_h;
	signed int int_diag_k;
	signed int int_diag_l;
	float push_res;
	float highres;
	float fix_profile_r;
	float fix_divergence;
	int overpredict;
	signed int wait_for_file; /* -1 means wait forever */
	int no_image_data;
	int no_mask_data;
	float wavelength_estimate;
};


/* Information about the indexing process for one pattern */
struct pattern_args
{
	/* "Input" */
	char *filename;
	char *event;
#ifdef HAVE_MSGPACK
	msgpack_object *msgpack_obj;
#else
	void *msgpack_obj;
#endif
};


extern void process_image(const struct index_args *iargs,
                          struct pattern_args *pargs, Stream *st,
                          int cookie, const char *tmpdir, int serial,
                          struct sb_shm *sb_shared, TimeAccounts *taccs,
                          char *last_task);


#endif	/* PROCESS_IMAGE_H */