aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/stream.h
blob: 7bb1b6abead5358666d3ead4bbcf6c0b42ea0592 (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
127
/*
 * stream.h
 *
 * Stream tools
 *
 * Copyright © 2013-2020 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 *
 * Authors:
 *   2010-2020 Thomas White <taw@physics.org>
 *   2014      Valerio Mariani
 *   2011      Andrew Aquila
 *
 * 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 STREAM_H
#define STREAM_H

/**
 * \file stream.h
 * Stream functions (for indexing results)
 */

struct image;

#include "datatemplate.h"
#include "cell.h"

#define STREAM_GEOM_START_MARKER "----- Begin geometry file -----"
#define STREAM_GEOM_END_MARKER "----- End geometry file -----"
#define STREAM_CELL_START_MARKER "----- Begin unit cell -----"
#define STREAM_CELL_END_MARKER "----- End unit cell -----"
#define STREAM_CHUNK_START_MARKER "----- Begin chunk -----"
#define STREAM_CHUNK_END_MARKER "----- End chunk -----"
#define STREAM_PEAK_LIST_START_MARKER "Peaks from peak search"
#define STREAM_PEAK_LIST_END_MARKER "End of peak list"
#define STREAM_CRYSTAL_START_MARKER "--- Begin crystal"
#define STREAM_CRYSTAL_END_MARKER "--- End crystal"
#define STREAM_REFLECTION_START_MARKER "Reflections measured after indexing"
#define STREAM_REFLECTION_END_MARKER "End of reflections"

/**
 * An opaque structure representing a stream being read or written
 */
typedef struct _stream Stream;

/**
 * A bitfield of things that can be read from or written to a stream.
 * Use this together with stream_{read,write}_chunk to read/write the
 * stream faster if you don't need all the information.
 *
 * General information about crystals (including unit cell parameters)
 * is always read and written.
 **/
typedef enum {

	/** Read the integrated reflections */
	STREAM_REFLECTIONS = 2,

	/** Read the peak search results */
	STREAM_PEAKS = 4,

	/** Read the image data */
	STREAM_IMAGE_DATA = 16,

} StreamFlags;

#ifdef __cplusplus
extern "C" {
#endif

/* Opening/closing streams */
extern Stream *stream_open_for_read(const char *filename);
extern Stream *stream_open_for_write(const char *filename,
                                     const DataTemplate *dtempl);
extern Stream *stream_open_fd_for_write(int fd,
                                        const DataTemplate *dtempl);
extern void stream_close(Stream *st);

/* Writing things to stream header */
extern void stream_write_geometry_file(Stream *st,
                                       const char *geom_filename);
extern void stream_write_target_cell(Stream *st,
                                     const UnitCell *cell);
extern void stream_write_commandline_args(Stream *st,
                                          int argc, char *argv[]);
extern void stream_write_indexing_methods(Stream *st,
                                          const char *indm_str);

/* Metadata */
extern int stream_has_old_indexers(Stream *st);
extern char *stream_audit_info(Stream *st);
extern char *stream_geometry_file(Stream *st);

/* Low-level stuff used for indexamajig sandbox */
extern int stream_get_fd(Stream *st);
extern int stream_rewind(Stream *st);

/* Random access */
extern int stream_scan_chunks(Stream *st);
extern int stream_select_chunk(Stream *st, int chunk_number);

/* Read/write chunks */
extern struct image *stream_read_chunk(Stream *st, StreamFlags srf);
extern int stream_write_chunk(Stream *st, const struct image *image,
                              StreamFlags srf);

#ifdef __cplusplus
}
#endif

#endif	/* STREAM_H */