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
|
/*
* stream.h
*
* Stream tools
*
* Copyright © 2013-2018 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2018 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
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
struct image;
struct hdfile;
struct event;
struct imagefile;
#include "cell.h"
#define GEOM_START_MARKER "----- Begin geometry file -----"
#define GEOM_END_MARKER "----- End geometry file -----"
#define CELL_START_MARKER "----- Begin unit cell -----"
#define CELL_END_MARKER "----- End unit cell -----"
#define CHUNK_START_MARKER "----- Begin chunk -----"
#define CHUNK_END_MARKER "----- End chunk -----"
#define PEAK_LIST_START_MARKER "Peaks from peak search"
#define PEAK_LIST_END_MARKER "End of peak list"
#define CRYSTAL_START_MARKER "--- Begin crystal"
#define CRYSTAL_END_MARKER "--- End crystal"
#define REFLECTION_START_MARKER "Reflections measured after indexing"
/* REFLECTION_END_MARKER is over in reflist-utils.h because it is also
* used to terminate a standalone list of reflections */
typedef struct _stream Stream;
/**
* StreamReadFlags:
* @STREAM_READ_UNITCELL: Read the unit cell
* @STREAM_READ_REFLECTIONS: Read the integrated reflections
* @STREAM_READ_PEAKS: Read the peak search results
* @STREAM_READ_CRYSTALS: Read the general information about crystals
*
* A bitfield of things that can be read from a stream. Use this (and
* read_chunk_2()) to read the stream faster if you don't need the entire
* contents of the stream.
*
* Using either or both of @STREAM_READ_REFLECTIONS and @STREAM_READ_UNITCELL
* implies @STREAM_READ_CRYSTALS.
**/
typedef enum {
STREAM_READ_UNITCELL = 1,
STREAM_READ_REFLECTIONS = 2,
STREAM_READ_PEAKS = 4,
STREAM_READ_CRYSTALS = 8,
} StreamReadFlags;
struct stuff_from_stream
{
char **fields;
int n_fields;
};
#ifdef __cplusplus
extern "C" {
#endif
extern Stream *open_stream_for_read(const char *filename);
extern Stream *open_stream_for_write(const char *filename);
extern Stream *open_stream_for_write_2(const char *filename,
const char* geom_filename, int argc,
char *argv[]);
extern Stream *open_stream_for_write_3(const char *filename,
const char* geom_filename, UnitCell *cell,
int argc, char *argv[]);
extern Stream *open_stream_fd_for_write(int fd);
extern int get_stream_fd(Stream *st);
extern void close_stream(Stream *st);
extern int read_chunk(Stream *st, struct image *image);
extern int read_chunk_2(Stream *st, struct image *image,
StreamReadFlags srf);
extern int stream_has_old_indexers(Stream *st);
extern int write_chunk(Stream *st, struct image *image, struct imagefile *imfile,
int include_peaks, int include_reflections,
struct event *ev);
extern int write_chunk_2(Stream *st, struct image *image,
struct imagefile *imfile,
int include_peaks, int include_reflections,
struct event *ev);
extern void write_command(Stream *st, int argc, char *argv[]);
extern void write_geometry_file(Stream *st, const char *geom_filename);
extern int rewind_stream(Stream *st);
extern int is_stream(const char *filename);
extern char *stream_audit_info(Stream *st);
#ifdef __cplusplus
}
#endif
#endif /* STREAM_H */
|
