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CrystFEL Reference Manual | ![]() |
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Top | Description |
enum IndexingMethod; typedef IndexingPrivate; #define INDEXING_DEFAULTS_DIRAX #define INDEXING_DEFAULTS_GRAINSPOTTER #define INDEXING_DEFAULTS_MOSFLM #define INDEXING_DEFAULTS_REAX #define INDEXING_DEFAULTS_XDS #define INDEXING_METHOD_MASK IndexingMethod * build_indexer_list (const char *str
); void cleanup_indexing (IndexingMethod *indms
,IndexingPrivate **privs
); IndexingPrivate ** prepare_indexing (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
); void index_pattern (struct image *image
,IndexingMethod *indms
,IndexingPrivate **iprivs
); char * indexer_str (IndexingMethod indm
); IndexingPrivate * dirax_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
); int run_dirax (struct image *image
,IndexingPrivate *ipriv
); void dirax_cleanup (IndexingPrivate *pp
); IndexingPrivate * mosflm_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
); int run_mosflm (struct image *image
,IndexingPrivate *ipriv
); void mosflm_cleanup (IndexingPrivate *pp
); IndexingPrivate * xds_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
); int run_xds (struct image *image
,IndexingPrivate *ipriv
); void xds_cleanup (IndexingPrivate *pp
); IndexingPrivate * reax_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
); int reax_index (IndexingPrivate *pp
,struct image *image
); void reax_cleanup (IndexingPrivate *pp
); IndexingPrivate * grainspotter_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
); int grainspotter_index (struct image *image
,IndexingPrivate *p
); void grainspotter_cleanup (IndexingPrivate *pp
);
typedef enum { INDEXING_NONE = 0, /* The core indexing methods themselves */ INDEXING_DIRAX = 1, INDEXING_MOSFLM = 2, INDEXING_REAX = 3, INDEXING_GRAINSPOTTER = 4, INDEXING_XDS = 5, INDEXING_SIMULATION = 6, /* Bits at the top of the IndexingMethod are flags which modify the * behaviour of the indexer. */ INDEXING_CHECK_CELL_COMBINATIONS = 256, INDEXING_CHECK_CELL_AXES = 512, INDEXING_CHECK_PEAKS = 1024, INDEXING_USE_LATTICE_TYPE = 2048, INDEXING_USE_CELL_PARAMETERS = 4096, } 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.
No indexing to be performed | |
Invoke DirAx | |
Invoke MOSFLM | |
DPS algorithm using known cell parameters | |
Invoke GrainSpotter | |
Invoke XDS | |
Dummy value | |
Check linear combinations of unit cell axes for agreement with given cell. | |
Check unit cell axes for agreement with given cell, and permute them if necessary. | |
Check that the peaks can be explained by the indexing result. | |
Use lattice type and centering information to guide the indexing process. | |
Use the unit cell parameters to guide the indexingprocess. |
typedef void *IndexingPrivate;
This is an opaque data structure containing information needed by the indexing method.
IndexingPrivate ** prepare_indexing (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
);
void index_pattern (struct image *image
,IndexingMethod *indms
,IndexingPrivate **iprivs
);
IndexingPrivate * dirax_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
);
IndexingPrivate * mosflm_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
);
IndexingPrivate * xds_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
);
IndexingPrivate * reax_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
);
IndexingPrivate * grainspotter_prepare (IndexingMethod *indm
,UnitCell *cell
,struct detector *det
,struct beam_params *beam
,float *ltl
);