indexing

indexing

Functions

char * detect_indexing_methods ()
IndexingPrivate * setup_indexing ()
void cleanup_indexing ()
IndexingMethod get_indm_from_string ()
IndexingMethod get_indm_from_string_2 ()
void index_pattern ()
void index_pattern_2 ()
char * indexer_str ()
const char * dirax_probe ()
void * dirax_prepare ()
int run_dirax ()
void dirax_cleanup ()
const char * mosflm_probe ()
void * mosflm_prepare ()
int run_mosflm ()
void mosflm_cleanup ()
const char * xds_probe ()
void * xds_prepare ()
int run_xds ()
void xds_cleanup ()
const char * asdf_probe ()
void * asdf_prepare ()
int run_asdf ()
void asdf_cleanup ()
const char * felix_probe ()
void * felix_prepare ()
int felix_index ()
void felix_cleanup ()
const char * taketwo_probe ()
void * taketwo_prepare ()
int taketwo_index ()
void taketwo_cleanup ()

Types and Values

Description

Functions

detect_indexing_methods ()

char *
detect_indexing_methods (UnitCell *cell);

setup_indexing ()

IndexingPrivate *
setup_indexing (const char *methods,
                UnitCell *cell,
                struct detector *det,
                float *ltl,
                IndexingFlags flags,
                struct taketwo_options *ttopts,
                struct felix_options *felix_opts);

cleanup_indexing ()

void
cleanup_indexing (IndexingPrivate *ipriv);

get_indm_from_string ()

IndexingMethod
get_indm_from_string (const char *method);

get_indm_from_string_2 ()

IndexingMethod
get_indm_from_string_2 (const char *method,
                        int *err);

index_pattern ()

void
index_pattern (struct image *image,
               IndexingPrivate *ipriv);

index_pattern_2 ()

void
index_pattern_2 (struct image *image,
                 IndexingPrivate *ipriv,
                 int *ping);

indexer_str ()

char *
indexer_str (IndexingMethod indm);

dirax_probe ()

const char *
dirax_probe (UnitCell *cell);

dirax_prepare ()

void *
dirax_prepare (IndexingMethod *indm,
               UnitCell *cell);

run_dirax ()

int
run_dirax (struct image *image,
           void *ipriv);

dirax_cleanup ()

void
dirax_cleanup (void *pp);

mosflm_probe ()

const char *
mosflm_probe (UnitCell *cell);

mosflm_prepare ()

void *
mosflm_prepare (IndexingMethod *indm,
                UnitCell *cell);

run_mosflm ()

int
run_mosflm (struct image *image,
            void *ipriv);

mosflm_cleanup ()

void
mosflm_cleanup (void *pp);

xds_probe ()

const char *
xds_probe (UnitCell *cell);

xds_prepare ()

void *
xds_prepare (IndexingMethod *indm,
             UnitCell *cell);

run_xds ()

int
run_xds (struct image *image,
         void *ipriv);

xds_cleanup ()

void
xds_cleanup (void *pp);

asdf_probe ()

const char *
asdf_probe (UnitCell *cell);

asdf_prepare ()

void *
asdf_prepare (IndexingMethod *indm,
              UnitCell *cell);

run_asdf ()

int
run_asdf (struct image *image,
          void *ipriv);

asdf_cleanup ()

void
asdf_cleanup (void *pp);

felix_probe ()

const char *
felix_probe (UnitCell *cell);

felix_prepare ()

void *
felix_prepare (IndexingMethod *indm,
               UnitCell *cell,
               struct felix_options *opts);

felix_index ()

int
felix_index (struct image *image,
             IndexingPrivate *p);

felix_cleanup ()

void
felix_cleanup (IndexingPrivate *pp);

taketwo_probe ()

const char *
taketwo_probe (UnitCell *cell);

taketwo_prepare ()

void *
taketwo_prepare (IndexingMethod *indm,
                 UnitCell *cell);

taketwo_index ()

int
taketwo_index (struct image *image,
               const struct taketwo_options *opts,
               void *priv);

taketwo_cleanup ()

void
taketwo_cleanup (IndexingPrivate *pp);

Types and Values

enum IndexingMethod

An enumeration of all the available indexing methods. The dummy value INDEXING_SIMULATION is used by partial_sim to indicate that no indexing was performed, and that the indexing results are just from simulation.

Members

INDEXING_NONE

No indexing to be performed

 

INDEXING_DIRAX

Invoke DirAx

 

INDEXING_MOSFLM

Invoke MOSFLM

 

INDEXING_FELIX

Invoke Felix

 

INDEXING_XDS

Invoke XDS

 

INDEXING_SIMULATION

Dummy value

 

INDEXING_DEBUG

Results injector for debugging

 

INDEXING_ASDF

Use in-built "asdf" indexer

 

INDEXING_TAKETWO

Use in-built "taketwo" indexer

 

INDEXING_ERROR

Special value for unrecognised indexing engine name

 

INDEXING_USE_LATTICE_TYPE

Use lattice type and centering information to guide the indexing process.

 

INDEXING_USE_CELL_PARAMETERS

Use the unit cell parameters to guide the indexing process.

 

IndexingPrivate

typedef struct _indexingprivate IndexingPrivate;

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


enum IndexingFlags

Members

INDEXING_RETRY

   

INDEXING_MULTI

   

INDEXING_REFINE

   

INDEXING_CHECK_CELL_COMBINATIONS

   

INDEXING_CHECK_CELL_AXES

   

INDEXING_CHECK_PEAKS

   

INDEXING_DEFAULTS_DIRAX

#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX)

INDEXING_DEFAULTS_MOSFLM

#define             INDEXING_DEFAULTS_MOSFLM

INDEXING_DEFAULTS_XDS

#define             INDEXING_DEFAULTS_XDS

INDEXING_DEFAULTS_ASDF

#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_USE_CELL_PARAMETERS)

INDEXING_DEFAULTS_FELIX

#define             INDEXING_DEFAULTS_FELIX

INDEXING_DEFAULTS_TAKETWO

#define             INDEXING_DEFAULTS_TAKETWO

INDEXING_METHOD_MASK

#define INDEXING_METHOD_MASK (0xff)

struct felix_options

struct felix_options {
	double ttmin;  /* radians */
	double ttmax;  /* radians */
	int min_visits;
	double min_completeness;
	double max_uniqueness;
	int n_voxels;
	double fraction_max_visits;
	double sigma;
	double domega;
	double max_internal_angle;
};

struct taketwo_options

struct taketwo_options {
	int member_thresh;
	double len_tol;
	double angle_tol;
	double trace_tol;
};