stream.h File Reference

Macros
#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"

Typedefs
typedef struct _stream	Stream
typedef struct _streamindex	StreamIndex

Enumerations
enum	StreamFlags {   STREAM_REFLECTIONS = 2 ,   STREAM_PEAKS = 4 ,   STREAM_DATA_DETGEOM = 8 }

Functions
Stream *	stream_open_for_read (const char *filename)
Stream *	stream_open_for_write (const char *filename, const DataTemplate *dtempl)
Stream *	stream_open_fd_for_write (int fd, const DataTemplate *dtempl)
void	stream_close (Stream *st)
void	stream_write_data_template (Stream *st, const DataTemplate *dtempl)
void	stream_write_geometry_file (Stream *st, const char *geom_filename)
void	stream_write_target_cell (Stream *st, UnitCell *cell)
void	stream_write_commandline_args (Stream *st, int argc, char *argv[])
void	stream_write_indexing_methods (Stream *st, const char *indm_str)
int	stream_has_old_indexers (Stream *st)
char *	stream_audit_info (Stream *st)
char *	stream_geometry_file (Stream *st)
int	stream_get_fd (Stream *st)
int	stream_rewind (Stream *st)
StreamIndex *	stream_make_index (const char *filename)
int	stream_select_chunk (Stream *st, StreamIndex *index, const char *filename, const char *ev)
void	stream_index_free (StreamIndex *index)
struct image *	stream_read_chunk (Stream *st, StreamFlags srf)
int	stream_write_chunk (Stream *st, const struct image *image, StreamFlags srf)

Detailed Description

Stream functions (for indexing results)

Typedef Documentation

Stream

typedef struct _stream Stream

An opaque structure representing a stream being read or written

Enumeration Type Documentation

StreamFlags

enum StreamFlags

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.

Enumerator
STREAM_REFLECTIONS	Read the integrated reflections
STREAM_PEAKS	Read the peak search results
STREAM_DATA_DETGEOM	Reconstruct the detgeom structure, and create (blank) data/mask arrays. (NB this is (currently) a slow operation)

Function Documentation

stream_close()

void stream_close

(

Stream *

st

)

Parameters

st

A Stream

Closes the stream

stream_open_fd_for_write()

Stream * stream_open_fd_for_write	(	int	fd,
		const DataTemplate *	dtempl
	)

Parameters

fd	File descriptor (e.g. from open()) to use for stream data.

Creates a new Stream from fd, so that stream data can be written to fd using stream_write_chunk.

In contrast to stream_open_for_write, this function does not write any of the usual headers. This function is mostly for use when multiple substreams need to be multiplexed into a single master stream. The master would be opened using stream_open_for_write, and the substreams using this function.

Returns

A Stream, or NULL on failure.

stream_open_for_write()

Stream * stream_open_for_write	(	const char *	filename,
		const DataTemplate *	dtempl
	)

Parameters

filename	Filename of new stream
dtempl	A DataTemplate

Creates a new stream with name filename. If filename already exists, it will be overwritten.

The CrystFEL version number will be written, but you should call stream_write_geometry_file, stream_write_target_cell, stream_write_commandline_args and stream_write_Indexing_methods to write extended audit information.

Returns

A Stream, or NULL on failure.

stream_read_chunk()

struct image * stream_read_chunk	(	Stream *	st,
		StreamFlags	srf
	)

Read the next chunk from a stream and return an image structure

stream_rewind()

int stream_rewind

(

Stream *

st

)

Parameters

st

A Stream

Attempts to set the file pointer for st to the start of the stream, so that later calls to stream_read_chunk will repeat the sequence of chunks from the start.

Programs must not assume that this operation always succeeds!

Returns

Non-zero if the stream could not be rewound.

stream_write_chunk()

int stream_write_chunk	(	Stream *	st,
		const struct image *	i,
		StreamFlags	srf
	)

Parameters

st	A Stream
i	An image structure
srf	A StreamFlags enum saying what to write

Writes a new chunk to st.

Returns

non-zero on error.

stream_write_commandline_args()

void stream_write_commandline_args	(	Stream *	st,
		int	argc,
		char *	argv[]
	)

Parameters

st	A Stream
argc	number of arguments
argv	command-line arguments

Writes the command line to st. argc and argv should be exactly as were given to main(). This should usually be called immediately after stream_open_for_write.

stream_write_data_template()

void stream_write_data_template	(	Stream *	st,
		const DataTemplate *	dtempl
	)

Parameters

st	A Stream
geom_filename	geomtry file name

Writes the content of the geometry file to st. This (or stream_write_geometry_file) should usually be called immediately after write_command.

stream_write_geometry_file()

void stream_write_geometry_file	(	Stream *	st,
		const char *	geom_filename
	)

Parameters

st	A Stream
geom_filename	geomtry file name

Writes the content of the geometry file to st. This (or stream_write_data_template) should usually be called immediately after write_command.