index.h File Reference

Data Structures
struct	asdf_options
struct	pinkindexer_options
struct	xgandalf_options
struct	taketwo_options
struct	fromfile_options
struct	felix_options

Macros
#define	INDEXING_DEFAULTS_DIRAX   (INDEXING_DIRAX)
#define	INDEXING_DEFAULTS_ASDF   (INDEXING_ASDF | INDEXING_USE_CELL_PARAMETERS)
#define	INDEXING_DEFAULTS_MOSFLM
#define	INDEXING_DEFAULTS_FELIX
#define	INDEXING_DEFAULTS_TAKETWO
#define	INDEXING_DEFAULTS_XDS
#define	INDEXING_DEFAULTS_XGANDALF   (INDEXING_XGANDALF | INDEXING_USE_CELL_PARAMETERS)
#define	INDEXING_DEFAULTS_PINKINDEXER   (INDEXING_PINKINDEXER | INDEXING_USE_CELL_PARAMETERS)
#define	INDEXING_METHOD_MASK   (0xff)

Typedefs
typedef struct _indexingprivate	IndexingPrivate

Enumerations
enum	IndexingMethod {   INDEXING_NONE = 0 ,   INDEXING_DIRAX = 1 ,   INDEXING_MOSFLM = 2 ,   INDEXING_FELIX = 4 ,   INDEXING_XDS = 5 ,   INDEXING_SIMULATION = 6 ,   INDEXING_FILE = 7 ,   INDEXING_ASDF = 8 ,   INDEXING_TAKETWO = 9 ,   INDEXING_XGANDALF = 10 ,   INDEXING_PINKINDEXER = 11 ,   INDEXING_ERROR = 255 ,   INDEXING_USE_LATTICE_TYPE = 2048 ,   INDEXING_USE_CELL_PARAMETERS = 4096 }
enum	IndexingFlags {   INDEXING_RETRY = 1 ,   INDEXING_MULTI = 2 ,   INDEXING_REFINE = 4 ,   INDEXING_CHECK_PEAKS = 32 ,   INDEXING_CHECK_CELL = 64 }

Functions
char *	indexer_str (IndexingMethod indm)
IndexingMethod	get_indm_from_string (const char *method)
IndexingMethod	get_indm_from_string_2 (const char *method, int *err)
IndexingMethod *	parse_indexing_methods (const char *method_list, int *pn)
char *	base_indexer_str (IndexingMethod indm)
void	default_method_options (struct taketwo_options **ttopts, struct xgandalf_options **xgandalf_opts, struct pinkindexer_options **pinkIndexer_opts, struct felix_options **felix_opts, struct fromfile_options **fromfile_opts, struct asdf_options **asdf_opts)
IndexingPrivate *	setup_indexing (const char *methods, UnitCell *cell, float *ltl, IndexingFlags flags, double wavelength_estimate, double clen_estimate, int n_threads, struct taketwo_options *ttopts, struct xgandalf_options *xgandalf_opts, struct pinkindexer_options *pinkIndexer_opts, struct felix_options *felix_opts, struct fromfile_options *fromfile_opts, struct asdf_options *asdf_opts)
const IndexingMethod *	indexing_methods (IndexingPrivate *p, int *n)
char *	detect_indexing_methods (UnitCell *cell)
void	index_pattern (struct image *image, IndexingPrivate *ipriv)
void	index_pattern_2 (struct image *image, IndexingPrivate *ipriv, int *ping)
void	index_pattern_3 (struct image *image, IndexingPrivate *ipriv, int *ping, char *last_task)
void	index_pattern_4 (struct image *image, IndexingPrivate *ipriv, int *ping, char *last_task, Mille *mille, int max_mille_level)
void	cleanup_indexing (IndexingPrivate *ipriv)

Variables
struct argp	felix_argp
struct argp	pinkIndexer_argp
struct argp	taketwo_argp
struct argp	xgandalf_argp
struct argp	fromfile_argp
struct argp	asdf_argp

Detailed Description

The indexing subsystem

Macro Definition Documentation

INDEXING_DEFAULTS_FELIX

#define INDEXING_DEFAULTS_FELIX

Value:

                                     (INDEXING_FELIX | INDEXING_USE_LATTICE_TYPE \
                                     | INDEXING_USE_CELL_PARAMETERS)

INDEXING_DEFAULTS_MOSFLM

#define INDEXING_DEFAULTS_MOSFLM

Value:

                                  (INDEXING_MOSFLM | INDEXING_USE_LATTICE_TYPE  \
                                  | INDEXING_USE_CELL_PARAMETERS)

INDEXING_DEFAULTS_TAKETWO

#define INDEXING_DEFAULTS_TAKETWO

Value:

                                   (INDEXING_TAKETWO \
                                   | INDEXING_USE_CELL_PARAMETERS \
                                   | INDEXING_USE_LATTICE_TYPE)

INDEXING_DEFAULTS_XDS

#define INDEXING_DEFAULTS_XDS

Value:

                                     (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
                                     | INDEXING_USE_CELL_PARAMETERS)

INDEXING_METHOD_MASK

#define INDEXING_METHOD_MASK   (0xff)

This defines the bits in "IndexingMethod" which are used to represent the core of the indexing method

Typedef Documentation

IndexingPrivate

typedef struct _indexingprivate IndexingPrivate

This is an opaque data structure containing information needed by the indexing system.

Enumeration Type Documentation

IndexingFlags

enum IndexingFlags

Flags affecting how the indexing system processes the results from the indexing engine

Enumerator
INDEXING_RETRY	Retry indexing if it doesn't work
INDEXING_MULTI	Attempt to index remaining peaks to find more lattices
INDEXING_REFINE	Refine the indexing solution
INDEXING_CHECK_PEAKS	Check that the peaks agree with the indexing solution
INDEXING_CHECK_CELL	Check that the unit cell agrees with the target cell

IndexingMethod

enum IndexingMethod

An enumeration of all the available indexing methods.

Enumerator
INDEXING_NONE	No indexing to be performed
INDEXING_DIRAX	Invoke DirAx program
INDEXING_MOSFLM	Invoke MOSFLM program
INDEXING_FELIX	Invoke Felix program
INDEXING_XDS	Invoke XDS program (NB not nXDS)
INDEXING_SIMULATION	Dummy value for simulated data
INDEXING_FILE	Results injector for debugging
INDEXING_ASDF	Use built-in ASDF algorithm
INDEXING_TAKETWO	Use built-in TakeTwo algorithm
INDEXING_XGANDALF	Use XGANDALF (via optional library)
INDEXING_PINKINDEXER	Use PinkIndexer (via optional library)
INDEXING_ERROR	Special value for unrecognised indexing engine
INDEXING_USE_LATTICE_TYPE	Use lattice type and centering information
INDEXING_USE_CELL_PARAMETERS	Use the cell parameters themselves