diff options
Diffstat (limited to 'libcrystfel/src/index.h')
| -rw-r--r-- | libcrystfel/src/index.h | 100 |
1 files changed, 68 insertions, 32 deletions
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h index 4a724645..31ee4339 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -3,13 +3,13 @@ * * Perform indexing (somehow) * - * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, - * a research centre of the Helmholtz Association. + * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * Copyright © 2012 Lorenzo Galli * * Authors: - * 2010-2012 Thomas White <taw@physics.org> + * 2010-2013 Thomas White <taw@physics.org> * 2010 Richard Kirian * 2012 Lorenzo Galli * @@ -38,10 +38,25 @@ #endif -#include "cell.h" -#include "image.h" -#include "detector.h" +#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \ + | INDEXING_CHECK_CELL_COMBINATIONS) + +#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS \ + | INDEXING_CHECK_CELL_COMBINATIONS \ + | INDEXING_USE_LATTICE_TYPE) + +#define INDEXING_DEFAULTS_REAX (INDEXING_REAX | INDEXING_USE_LATTICE_TYPE \ + | INDEXING_USE_CELL_PARAMETERS \ + | INDEXING_CHECK_PEAKS) +#define INDEXING_DEFAULTS_GRAINSPOTTER (INDEXING_GRAINSPOTTER \ + | INDEXING_USE_LATTICE_TYPE \ + | INDEXING_USE_CELL_PARAMETERS \ + | INDEXING_CHECK_PEAKS) + +#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \ + | INDEXING_USE_CELL_PARAMETERS \ + | INDEXING_CHECK_PEAKS) /** * IndexingMethod: @@ -49,24 +64,45 @@ * @INDEXING_DIRAX: Invoke DirAx * @INDEXING_MOSFLM: Invoke MOSFLM * @INDEXING_REAX: DPS algorithm using known cell parameters + * @INDEXING_GRAINSPOTTER: Invoke GrainSpotter + * @INDEXING_XDS: Invokve XDS + * @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell + * axes for agreement with given cell. + * @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given + * cell, and permute them if necessary. + * @INDEXING_CHECK_PEAKS: Check that the peaks can be explained by the indexing + * result. + * @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 + * indexingprocess. * * An enumeration of all the available indexing methods. **/ typedef enum { - INDEXING_NONE, - INDEXING_DIRAX, - INDEXING_MOSFLM, - INDEXING_REAX, -} IndexingMethod; + INDEXING_NONE = 0, -/* Cell reduction methods */ -enum { - CELLR_NONE, - CELLR_REDUCE, - CELLR_COMPARE, - CELLR_COMPARE_AB, -}; + /* The core indexing methods themselves */ + INDEXING_DIRAX = 1, + INDEXING_MOSFLM = 2, + INDEXING_REAX = 3, + INDEXING_GRAINSPOTTER = 4, + INDEXING_XDS = 5, + + /* 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; + +/* This defines the bits in "IndexingMethod" which are used to represent the + * core of the indexing method */ +#define INDEXING_METHOD_MASK (0xff) /** @@ -75,24 +111,24 @@ enum { * This is an opaque data structure containing information needed by the * indexing method. **/ -typedef struct _indexingprivate IndexingPrivate; +typedef void *IndexingPrivate; -extern IndexingPrivate *indexing_private(IndexingMethod indm); - -extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell, - const char *filename, - struct detector *det, - double nominal_photon_energy); +extern IndexingMethod *build_indexer_list(const char *str); +extern char *indexer_str(IndexingMethod indm); -extern void map_all_peaks(struct image *image); +#include "beam-parameters.h" +#include "detector.h" +#include "cell.h" +#include "image.h" -extern void index_pattern(struct image *image, UnitCell *cell, - IndexingMethod *indm, int cellr, int verbose, - IndexingPrivate **priv, int config_insane, - const float *ltl); +extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell, + const char *filename, + struct detector *det, + struct beam_params *beam, float *ltl); -extern void cleanup_indexing(IndexingPrivate **priv); +extern void index_pattern(struct image *image, + IndexingMethod *indms, IndexingPrivate **iprivs); -extern IndexingMethod *build_indexer_list(const char *str, int *need_cell); +extern void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs); #endif /* INDEX_H */ |