index.h File Reference

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

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_FFBIDX = 12 ,   INDEXING_SMALLCELL = 13 ,   INDEXING_ERROR = 255 }
enum	IndexingFlags {   INDEXING_RETRY = 1 ,   INDEXING_MULTI = 2 ,   INDEXING_REFINE = 4 ,   INDEXING_CHECK_PEAKS = 32 ,   INDEXING_CHECK_CELL = 64 }

Functions
const 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)
void	default_method_options (struct taketwo_options **ttopts, struct xgandalf_options **xgandalf_opts, struct ffbidx_options **ffbidx_opts, struct pinkindexer_options **pinkIndexer_opts, struct felix_options **felix_opts, struct fromfile_options **fromfile_opts, struct smallcell_options **smallcell_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 ffbidx_options *ffbidx_opts, struct pinkindexer_options *pinkIndexer_opts, struct felix_options *felix_opts, struct fromfile_options *fromfile_opts, struct smallcell_options *smallcell_opts, struct asdf_options *asdf_opts)
void	print_indexing_info (IndexingPrivate *ipriv)
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	index_pattern_5 (struct image *image, IndexingPrivate *ipriv, 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	ffbidx_argp
struct argp	fromfile_argp
struct argp	smallcell_argp
struct argp	asdf_argp

Detailed Description

The indexing subsystem

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_FFBIDX	Use PSI Fast Indexer (via optional library)
INDEXING_SMALLCELL	Use Smallcell
INDEXING_ERROR	Special value for unrecognised indexing engine